diff --git a/.gitignore b/.gitignore index 46e82730f3..b6098e8c05 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ /nipype/build /nipype/nipype.egg-info /doc/_build +/doc/preproc /doc/users/examples /doc/api/generated *.pyc @@ -17,3 +18,6 @@ .DS_Store nipype/testing/data/von-ray_errmap.nii.gz nipype/testing/data/von_errmap.nii.gz +crash*.pklz +.coverage +htmlcov/ diff --git a/.travis.yml b/.travis.yml index 744efcf545..29f009a7cf 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,16 +3,17 @@ cache: language: python python: - 2.7 +- 3.4 env: - INSTALL_DEB_DEPENDECIES=true - INSTALL_DEB_DEPENDECIES=false before_install: - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh - -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh + -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi - chmod +x miniconda.sh - "./miniconda.sh -b" -- export PATH=/home/travis/miniconda/bin:$PATH +- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi - if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); @@ -27,15 +28,16 @@ install: - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION - source activate testenv - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi -- conda install --yes numpy scipy nose traits networkx dateutil -- pip install nibabel +- conda install --yes numpy scipy nose networkx dateutil +- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi - pip install python-coveralls - pip install nose-cov +- pip install -r requirements.txt # finish remaining requirements - pip install https://github.com/RDFLib/rdflib/archive/master.zip - pip install https://github.com/trungdong/prov/archive/rdf.zip - python setup.py install script: -- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO +- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=INFO after_success: - coveralls --config_file .coveragerc deploy: diff --git a/THANKS.rst b/THANKS.rst index 26c93dcf1d..252512d2c0 100644 --- a/THANKS.rst +++ b/THANKS.rst @@ -10,9 +10,11 @@ Contributors to Nipype include but are not limited to: * Aimi Watanabe * Alexander Schaefer * Alexandre Gramfort + * Alexandre Savio * Anisha Keshavan * Ariel Rokem * Ben Acland + * Ben Cipollini * Basile Pinsard * Brendan Moloney * Brian Cheung diff --git a/build_docs.py b/build_docs.py index 937ed269cc..474bf868d2 100644 --- a/build_docs.py +++ b/build_docs.py @@ -8,6 +8,8 @@ python setup.py build_sphinx """ +from __future__ import print_function + # Standard library imports import sys import os @@ -43,7 +45,7 @@ def run(self): install.run() # Horrible trick to reload nipype with our temporary instal - for key in sys.modules.keys(): + for key in list(sys.modules.keys()): if key.startswith('nipype'): sys.modules.pop(key, None) sys.path.append(os.path.abspath(self.temp_install_dir)) @@ -131,7 +133,7 @@ def run(self): def zip_docs(self): if not os.path.exists(DOC_BUILD_DIR): - raise OSError, 'Doc directory does not exist.' + raise OSError('Doc directory does not exist.') target_file = os.path.join('doc', 'documentation.zip') # ZIP_DEFLATED actually compresses the archive. However, there # will be a RuntimeError if zlib is not installed, so we check @@ -170,17 +172,17 @@ def run(self): clean.run(self) api_path = os.path.join('doc', 'api', 'generated') if os.path.exists(api_path): - print "Removing %s" % api_path + print("Removing %s" % api_path) shutil.rmtree(api_path) interface_path = os.path.join('doc', 'interfaces', 'generated') if os.path.exists(interface_path): - print "Removing %s" % interface_path + print("Removing %s" % interface_path) shutil.rmtree(interface_path) if os.path.exists(DOC_BUILD_DIR): - print "Removing %s" % DOC_BUILD_DIR + print("Removing %s" % DOC_BUILD_DIR) shutil.rmtree(DOC_BUILD_DIR) if os.path.exists(DOC_DOCTREES_DIR): - print "Removing %s" % DOC_DOCTREES_DIR + print("Removing %s" % DOC_DOCTREES_DIR) shutil.rmtree(DOC_DOCTREES_DIR) diff --git a/doc/devel/matlab_interface_devel.rst b/doc/devel/matlab_interface_devel.rst index c64622b390..4e6ff6f598 100644 --- a/doc/devel/matlab_interface_devel.rst +++ b/doc/devel/matlab_interface_devel.rst @@ -93,7 +93,7 @@ By subclassing **MatlabCommand** for your main class, and **MatlabInputSpec** fo >>> hello = HelloWorld() >>> hello.inputs.name = 'hello_world' >>> out = hello.run() - >>> print out.outputs.matlab_output + >>> print(out.outputs.matlab_output) """ input_spec = HelloWorldInputSpec output_spec = HelloWorldOutputSpec diff --git a/doc/sphinxext/autosummary_generate.py b/doc/sphinxext/autosummary_generate.py index d0ab331b79..7fd1e94459 100755 --- a/doc/sphinxext/autosummary_generate.py +++ b/doc/sphinxext/autosummary_generate.py @@ -16,6 +16,8 @@ ./ext/autosummary_generate.py -o source/generated source/*.rst """ + +from __future__ import print_function import glob, re, inspect, os, optparse, pydoc from autosummary import import_by_name @@ -44,7 +46,7 @@ def main(): # read names = {} - for name, loc in get_documented(args).items(): + for name, loc in list(get_documented(args).items()): for (filename, sec_title, keyword, toctree) in loc: if toctree is not None: path = os.path.join(os.path.dirname(filename), toctree) @@ -60,8 +62,8 @@ def main(): try: obj, name = import_by_name(name) - except ImportError, e: - print "Failed to import '%s': %s" % (name, e) + except ImportError as e: + print("Failed to import '%s': %s" % (name, e)) continue fn = os.path.join(path, '%s.rst' % name) @@ -129,8 +131,8 @@ def get_documented_in_docstring(name, module=None, filename=None): return get_documented_in_lines(lines, module=name, filename=filename) except AttributeError: pass - except ImportError, e: - print "Failed to import '%s': %s" % (name, e) + except ImportError as e: + print("Failed to import '%s': %s" % (name, e)) return {} def get_documented_in_lines(lines, module=None, filename=None): diff --git a/doc/sphinxext/numpy_ext/docscrape.py b/doc/sphinxext/numpy_ext/docscrape.py index bbd3fcaccc..ba35086cb6 100644 --- a/doc/sphinxext/numpy_ext/docscrape.py +++ b/doc/sphinxext/numpy_ext/docscrape.py @@ -2,13 +2,20 @@ """ +from __future__ import print_function +from future import standard_library +standard_library.install_aliases() +from builtins import object + import inspect import textwrap import re import pydoc -from StringIO import StringIO from warnings import warn +from nipype.external.six import StringIO + + class Reader(object): """A line-based string reader. @@ -113,7 +120,7 @@ def __getitem__(self,key): return self._parsed_data[key] def __setitem__(self,key,val): - if not self._parsed_data.has_key(key): + if key not in self._parsed_data: warn("Unknown section %s" % key) else: self._parsed_data[key] = val @@ -370,7 +377,7 @@ def _str_index(self): idx = self['index'] out = [] out += ['.. index:: %s' % idx.get('default','')] - for section, references in idx.iteritems(): + for section, references in list(idx.items()): if section == 'default': continue out += [' :%s: %s' % (section, ', '.join(references))] @@ -428,7 +435,7 @@ def __init__(self, func, role='func', doc=None, config={}): argspec = inspect.formatargspec(*argspec) argspec = argspec.replace('*','\*') signature = '%s%s' % (func_name, argspec) - except TypeError, e: + except TypeError as e: signature = '%s()' % func_name self['Signature'] = signature @@ -450,8 +457,8 @@ def __str__(self): 'meth': 'method'} if self._role: - if not roles.has_key(self._role): - print "Warning: invalid role %s" % self._role + if self._role not in roles: + print("Warning: invalid role %s" % self._role) out += '.. %s:: %s\n \n\n' % (roles.get(self._role,''), func_name) diff --git a/doc/sphinxext/numpy_ext/docscrape_sphinx.py b/doc/sphinxext/numpy_ext/docscrape_sphinx.py index 0f38188477..9d76da3b27 100644 --- a/doc/sphinxext/numpy_ext/docscrape_sphinx.py +++ b/doc/sphinxext/numpy_ext/docscrape_sphinx.py @@ -1,7 +1,10 @@ +from __future__ import absolute_import import re, inspect, textwrap, pydoc import sphinx -from docscrape import NumpyDocString, FunctionDoc, ClassDoc -from nipype.external import six +from .docscrape import NumpyDocString, FunctionDoc, ClassDoc +from nipype.external.six import string_types + + class SphinxDocString(NumpyDocString): def __init__(self, docstring, config={}): @@ -128,7 +131,7 @@ def _str_index(self): return out out += ['.. index:: %s' % idx.get('default','')] - for section, references in idx.iteritems(): + for section, references in list(idx.items()): if section == 'default': continue elif section == 'refguide': @@ -141,7 +144,7 @@ def _str_references(self): out = [] if self['References']: out += self._str_header('References') - if isinstance(self['References'], six.string_types): + if isinstance(self['References'], string_types): self['References'] = [self['References']] out.extend(self['References']) out += [''] diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index 41950dda45..f55c4d4c1c 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -16,13 +16,16 @@ """ +from __future__ import absolute_import +from builtins import object + import sphinx if sphinx.__version__ < '1.0.1': raise RuntimeError("Sphinx 1.0.1 or newer is required") import os, re, pydoc -from docscrape_sphinx import get_doc_object, SphinxDocString +from .docscrape_sphinx import get_doc_object, SphinxDocString from sphinx.util.compat import Directive import inspect @@ -39,7 +42,7 @@ def mangle_docstrings(app, what, name, obj, options, lines, lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n") else: doc = get_doc_object(obj, what, u"\n".join(lines), config=cfg) - lines[:] = unicode(doc).split(u"\n") + lines[:] = str(doc).split(u"\n") if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \ obj.__name__: @@ -120,7 +123,7 @@ def __init__(self, *a, **kw): self.wrap_mangling_directives() def wrap_mangling_directives(self): - for name, objtype in self.directive_mangling_map.items(): + for name, objtype in list(self.directive_mangling_map.items()): self.directives[name] = wrap_mangling_directive( self.directives[name], objtype) diff --git a/examples/dmri_camino_dti.py b/examples/dmri_camino_dti.py index f3a23d5d9a..3c3e358dcc 100755 --- a/examples/dmri_camino_dti.py +++ b/examples/dmri_camino_dti.py @@ -91,7 +91,7 @@ def get_affine(volume): """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_connectivity.py b/examples/dmri_connectivity.py index 3f76c11c58..c4ef738153 100755 --- a/examples/dmri_connectivity.py +++ b/examples/dmri_connectivity.py @@ -146,7 +146,7 @@ def select_aparc_annot(list_of_files): """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_connectivity_advanced.py b/examples/dmri_connectivity_advanced.py index c20d70c0fa..edad0d13ec 100755 --- a/examples/dmri_connectivity_advanced.py +++ b/examples/dmri_connectivity_advanced.py @@ -66,7 +66,7 @@ try: package_check('cmp') -except Exception, e: +except Exception as e: warnings.warn('cmp not installed') else: import cmp @@ -114,7 +114,7 @@ """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_dtk_dti.py b/examples/dmri_dtk_dti.py index f1d9690fd9..ee755d0e12 100755 --- a/examples/dmri_dtk_dti.py +++ b/examples/dmri_dtk_dti.py @@ -98,7 +98,7 @@ """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_dtk_odf.py b/examples/dmri_dtk_odf.py index c84b9806a8..3ca87df9bc 100755 --- a/examples/dmri_dtk_odf.py +++ b/examples/dmri_dtk_odf.py @@ -98,7 +98,7 @@ """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_fsl_dti.py b/examples/dmri_fsl_dti.py index b9093d6c05..a9b2db60dd 100755 --- a/examples/dmri_fsl_dti.py +++ b/examples/dmri_fsl_dti.py @@ -107,7 +107,7 @@ """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_group_connectivity_camino.py b/examples/dmri_group_connectivity_camino.py index 1fb1c4148a..dac4ab90c4 100644 --- a/examples/dmri_group_connectivity_camino.py +++ b/examples/dmri_group_connectivity_camino.py @@ -126,7 +126,7 @@ title = '' for idx, group_id in enumerate(group_list.keys()): title += group_id - if not idx == len(group_list.keys()) - 1: + if not idx == len(list(group_list.keys())) - 1: title += '-' info = dict(dwi=[['subject_id', 'dti']], diff --git a/examples/dmri_group_connectivity_mrtrix.py b/examples/dmri_group_connectivity_mrtrix.py index bb64356d9f..10f535c042 100644 --- a/examples/dmri_group_connectivity_mrtrix.py +++ b/examples/dmri_group_connectivity_mrtrix.py @@ -131,7 +131,7 @@ title = '' for idx, group_id in enumerate(group_list.keys()): title += group_id - if not idx == len(group_list.keys()) - 1: + if not idx == len(list(group_list.keys())) - 1: title += '-' info = dict(dwi=[['subject_id', 'dti']], diff --git a/examples/dmri_mrtrix_dti.py b/examples/dmri_mrtrix_dti.py index cb72abe1ec..a0f44d1d69 100755 --- a/examples/dmri_mrtrix_dti.py +++ b/examples/dmri_mrtrix_dti.py @@ -57,7 +57,7 @@ """ datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/dmri_preprocessing.py b/examples/dmri_preprocessing.py index 373ae64994..bbf6da096f 100644 --- a/examples/dmri_preprocessing.py +++ b/examples/dmri_preprocessing.py @@ -81,7 +81,7 @@ """ datasource = pe.Node(nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), name='datasource') + outfields=list(info.keys())), name='datasource') datasource.inputs.template = "%s/%s" diff --git a/examples/fmri_ants_openfmri.py b/examples/fmri_ants_openfmri.py index a4ea61c1c1..2acc96bc0c 100755 --- a/examples/fmri_ants_openfmri.py +++ b/examples/fmri_ants_openfmri.py @@ -12,10 +12,12 @@ python fmri_ants_openfmri.py --datasetdir ds107 """ +from __future__ import division +from builtins import range + from nipype import config config.enable_provenance() -from nipype.external import six from glob import glob import os @@ -23,9 +25,8 @@ import nipype.pipeline.engine as pe import nipype.algorithms.modelgen as model import nipype.algorithms.rapidart as ra -import nipype.interfaces.fsl as fsl -import nipype.interfaces.ants as ants from nipype.algorithms.misc import TSNR +from nipype.external.six import string_types from nipype.interfaces.c3 import C3dAffineTool import nipype.interfaces.io as nio import nipype.interfaces.utility as niu @@ -37,9 +38,9 @@ from nipype import Workflow, Node, MapNode from nipype.interfaces import (fsl, Function, ants, freesurfer) -from nipype.interfaces.utility import Rename, Merge, IdentityInterface +from nipype.interfaces.utility import Merge, IdentityInterface from nipype.utils.filemanip import filename_to_list -from nipype.interfaces.io import DataSink, FreeSurferSource +from nipype.interfaces.io import FreeSurferSource import nipype.interfaces.freesurfer as fs version = 0 @@ -78,7 +79,7 @@ def median(in_files): average = data else: average = average + data - median_img = nb.Nifti1Image(average/float(idx + 1), + median_img = nb.Nifti1Image(average / float(idx + 1), img.get_affine(), img.get_header()) filename = os.path.join(os.getcwd(), 'median.nii.gz') median_img.to_filename(filename) @@ -573,7 +574,7 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id): import json with open(json_info, 'rt') as fp: data = json.load(fp) - TR = data['global']['const']['RepetitionTime']/1000. + TR = data['global']['const']['RepetitionTime'] / 1000. else: task_scan_key = os.path.join(base_dir, subject_id, 'BOLD', 'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]), @@ -713,7 +714,7 @@ def analyze_openfmri_dataset(data_dir, subject=None, model_id=None, ]) def get_highpass(TR, hpcutoff): - return hpcutoff / (2 * TR) + return hpcutoff / (2. * TR) gethighpass = pe.Node(niu.Function(input_names=['TR', 'hpcutoff'], output_names=['highpass'], function=get_highpass), @@ -766,14 +767,14 @@ def get_contrasts(contrast_file, task_id, conds): modelspec.inputs.input_units = 'secs' def check_behav_list(behav, run_id, conds): - from nipype.external import six import numpy as np num_conds = len(conds) - if isinstance(behav, six.string_types): + if isinstance(behav, string_types): behav = [behav] behav_array = np.array(behav).flatten() num_elements = behav_array.shape[0] - return behav_array.reshape(num_elements/num_conds, num_conds).tolist() + return behav_array.reshape(int(num_elements / num_conds), + num_conds).tolist() reshape_behav = pe.Node(niu.Function(input_names=['behav', 'run_id', 'conds'], output_names=['behav'], @@ -836,8 +837,10 @@ def sort_copes(copes, varcopes, contrasts): n_runs = len(copes) all_copes = np.array(copes).flatten() all_varcopes = np.array(varcopes).flatten() - outcopes = all_copes.reshape(len(all_copes)/num_copes, num_copes).T.tolist() - outvarcopes = all_varcopes.reshape(len(all_varcopes)/num_copes, num_copes).T.tolist() + outcopes = all_copes.reshape(int(len(all_copes) / num_copes), + num_copes).T.tolist() + outvarcopes = all_varcopes.reshape(int(len(all_varcopes) / num_copes), + num_copes).T.tolist() return outcopes, outvarcopes, n_runs cope_sorter = pe.Node(niu.Function(input_names=['copes', 'varcopes', diff --git a/examples/fmri_freesurfer_smooth.py b/examples/fmri_freesurfer_smooth.py index e34a15dbc9..0bb5cd7601 100755 --- a/examples/fmri_freesurfer_smooth.py +++ b/examples/fmri_freesurfer_smooth.py @@ -39,6 +39,9 @@ """ +from __future__ import print_function +from builtins import range + import os # system functions import nipype.algorithms.modelgen as model # model generation @@ -446,11 +449,11 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n"%str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), @@ -574,7 +577,7 @@ def getsubs(subject_id): l2inputnode = pe.Node(interface=util.IdentityInterface(fields=['contrasts', 'hemi']), name='inputnode') -l2inputnode.iterables = [('contrasts', range(1,len(contrasts)+1)), +l2inputnode.iterables = [('contrasts', list(range(1,len(contrasts)+1))), ('hemi', ['lh','rh'])] """ @@ -607,7 +610,7 @@ def ordersubjects(files, subj_list): if '/%s/'%s in f: outlist.append(f) continue - print outlist + print(outlist) return outlist l2flow.connect(l2source,('con', ordersubjects, subject_list), mergenode, 'in1') diff --git a/examples/fmri_fsl.py b/examples/fmri_fsl.py index 964249e95a..b4a1225db1 100755 --- a/examples/fmri_fsl.py +++ b/examples/fmri_fsl.py @@ -15,6 +15,10 @@ First tell python where to find the appropriate functions. """ +from __future__ import print_function +from __future__ import division +from builtins import range + import os # system functions import nipype.interfaces.io as nio # Data i/o @@ -104,7 +108,7 @@ def getmiddlevolume(func): if isinstance(func, list): funcfile = func[0] _,_,_,timepoints = load(funcfile).get_shape() - return (timepoints/2)-1 + return int(timepoints / 2) - 1 preproc.connect(inputnode, ('func', getmiddlevolume), extract_ref, 't_min') @@ -286,7 +290,7 @@ def getusans(x): """ def getinormscale(medianvals): - return ['-mul %.10f'%(10000./val) for val in medianvals] + return ['-mul %.10f' % (10000. / val) for val in medianvals] preproc.connect(medianval, ('out_stat', getinormscale), intnorm, 'op_string') """ @@ -551,9 +555,9 @@ def num_copes(files): smoothnode.iterables = ('fwhm', [5.,10.]) hpcutoff = 120 -TR = 3. +TR = 3. # ensure float firstlevel.inputs.preproc.highpass.suffix = '_hpf' -firstlevel.inputs.preproc.highpass.op_string = '-bptf %d -1'%(hpcutoff/TR) +firstlevel.inputs.preproc.highpass.op_string = '-bptf %d -1' % (hpcutoff / TR) """ @@ -568,11 +572,11 @@ def num_copes(files): def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), diff --git a/examples/fmri_fsl_feeds.py b/examples/fmri_fsl_feeds.py index 88c1a4bab5..c065146bb2 100755 --- a/examples/fmri_fsl_feeds.py +++ b/examples/fmri_fsl_feeds.py @@ -13,6 +13,9 @@ """ +from __future__ import division +from builtins import range + import os # system functions import nipype.interfaces.io as nio # Data i/o @@ -36,7 +39,6 @@ fsl.FSLCommand.set_default_output_type('NIFTI_GZ') - """ Experiment specific components ------------------------------ @@ -69,7 +71,7 @@ preproc = create_featreg_preproc(whichvol='first') TR = 3. preproc.inputs.inputspec.fwhm = 5 -preproc.inputs.inputspec.highpass = 100/TR +preproc.inputs.inputspec.highpass = 100. / TR modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec") @@ -77,13 +79,13 @@ modelspec.inputs.time_repetition = TR modelspec.inputs.high_pass_filter_cutoff = 100 modelspec.inputs.subject_info = [Bunch(conditions=['Visual','Auditory'], - onsets=[range(0,int(180*TR),60),range(0,int(180*TR),90)], - durations=[[30], [45]], - amplitudes=None, - tmod=None, - pmod=None, - regressor_names=None, - regressors=None)] + onsets=[list(range(0,int(180*TR),60)),list(range(0,int(180*TR),90))], + durations=[[30], [45]], + amplitudes=None, + tmod=None, + pmod=None, + regressor_names=None, + regressors=None)] modelfit = create_modelfit_workflow(f_contrasts=True) modelfit.inputs.inputspec.interscan_interval = TR @@ -141,4 +143,3 @@ if __name__ == '__main__': l1pipeline.run() - diff --git a/examples/fmri_fsl_reuse.py b/examples/fmri_fsl_reuse.py index 0918a5394c..8d0ea99e34 100755 --- a/examples/fmri_fsl_reuse.py +++ b/examples/fmri_fsl_reuse.py @@ -15,6 +15,10 @@ First tell python where to find the appropriate functions. """ +from __future__ import print_function +from __future__ import division +from builtins import range + import os # system functions import nipype.interfaces.io as nio # Data i/o @@ -25,8 +29,8 @@ import nipype.algorithms.rapidart as ra # artifact detection from nipype.workflows.fmri.fsl import (create_featreg_preproc, - create_modelfit_workflow, - create_fixed_effects_flow) + create_modelfit_workflow, + create_fixed_effects_flow) """ @@ -181,7 +185,7 @@ def num_copes(files): hpcutoff = 120. TR = 3. -inputnode.inputs.highpass = hpcutoff/(2*TR) +inputnode.inputs.highpass = hpcutoff / (2. * TR) """ Setup a function that returns subject-specific information about the @@ -195,11 +199,11 @@ def num_copes(files): def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n"%str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), diff --git a/examples/fmri_nipy_glm.py b/examples/fmri_nipy_glm.py index b4cfc51595..b1416634cc 100755 --- a/examples/fmri_nipy_glm.py +++ b/examples/fmri_nipy_glm.py @@ -16,6 +16,9 @@ """ +from __future__ import print_function +from builtins import range + from nipype.interfaces.nipy.model import FitGLM, EstimateContrast from nipype.interfaces.nipy.preprocess import ComputeMask @@ -156,11 +159,11 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n"%str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), diff --git a/examples/fmri_openfmri.py b/examples/fmri_openfmri.py index 3375caeb87..70f9c25bc9 100755 --- a/examples/fmri_openfmri.py +++ b/examples/fmri_openfmri.py @@ -12,9 +12,8 @@ python fmri_openfmri.py --datasetdir ds107 """ -from nipype import config -#config.enable_provenance() -from nipype.external import six +from __future__ import division +from builtins import range from glob import glob import os @@ -25,6 +24,7 @@ import nipype.interfaces.fsl as fsl import nipype.interfaces.io as nio import nipype.interfaces.utility as niu +from nipype.external.six import string_types from nipype.workflows.fmri.fsl import (create_featreg_preproc, create_modelfit_workflow, create_fixed_effects_flow, @@ -38,6 +38,7 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id): Parameters ---------- + subject_id : string Subject identifier (e.g., sub001) base_dir : string @@ -49,6 +50,7 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id): Returns ------- + run_ids : list of ints Run numbers conds : list of str @@ -62,6 +64,7 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id): condition_info = [] cond_file = os.path.join(base_dir, 'models', 'model%03d' % model_id, 'condition_key.txt') + with open(cond_file, 'rt') as fp: for line in fp: info = line.strip().split() @@ -82,7 +85,7 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id): subject_id, 'BOLD', 'task%03d_run*' % (idx + 1))) - run_ids.insert(idx, range(1, len(files) + 1)) + run_ids.insert(idx, list(range(1, len(files) + 1))) TR = np.genfromtxt(os.path.join(base_dir, 'scan_key.txt'))[1] return run_ids[task_id - 1], conds[task_id - 1], TR @@ -186,7 +189,7 @@ def analyze_openfmri_dataset(data_dir, subject=None, model_id=None, ]) def get_highpass(TR, hpcutoff): - return hpcutoff / (2 * TR) + return hpcutoff / (2. * TR) gethighpass = pe.Node(niu.Function(input_names=['TR', 'hpcutoff'], output_names=['highpass'], function=get_highpass), @@ -237,9 +240,8 @@ def get_contrasts(contrast_file, task_id, conds): modelspec.inputs.input_units = 'secs' def check_behav_list(behav): - from nipype.external import six out_behav = [] - if isinstance(behav, six.string_types): + if isinstance(behav, string_types): behav = [behav] for val in behav: if not isinstance(val, list): diff --git a/examples/fmri_spm.py b/examples/fmri_spm.py index 818aa9df17..16538cc124 100755 --- a/examples/fmri_spm.py +++ b/examples/fmri_spm.py @@ -15,6 +15,9 @@ Import necessary modules from nipype.""" +from __future__ import print_function +from builtins import range + import os # system functions from nipype import config @@ -180,11 +183,11 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n"%str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), @@ -347,7 +350,7 @@ def getstripdir(subject_id): """ # collect all the con images for each contrast. -contrast_ids = range(1,len(contrasts)+1) +contrast_ids = list(range(1,len(contrasts)+1)) l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source") # we use .*i* to capture both .img (SPM8) and .nii (SPM12) l2source.inputs.template=os.path.abspath('spm_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*') diff --git a/examples/fmri_spm_auditory.py b/examples/fmri_spm_auditory.py index 666b8bfcdb..f75b3cc43a 100755 --- a/examples/fmri_spm_auditory.py +++ b/examples/fmri_spm_auditory.py @@ -17,6 +17,8 @@ Import necessary modules from nipype.""" +from builtins import range + import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.spm as spm # spm import nipype.interfaces.fsl as fsl # fsl @@ -237,7 +239,7 @@ def makelist(item): # Specify the subject directories subject_list = ['M00223'] # Map field names to individual subject runs. -info = dict(func=[['f', 'subject_id', 'f', 'subject_id', range(16,100)]], +info = dict(func=[['f', 'subject_id', 'f', 'subject_id', list(range(16,100))]], struct=[['s', 'subject_id', 's', 'subject_id', 2]]) infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']), name="infosource") @@ -282,7 +284,7 @@ def makelist(item): from nipype.interfaces.base import Bunch subjectinfo = [Bunch(conditions=['Task'], - onsets=[range(6,84,12)], + onsets=[list(range(6,84,12))], durations=[[6]])] """Setup the contrast structure that needs to be evaluated. This is a diff --git a/examples/fmri_spm_dartel.py b/examples/fmri_spm_dartel.py index 39cf8378b3..7bd25ff5a7 100755 --- a/examples/fmri_spm_dartel.py +++ b/examples/fmri_spm_dartel.py @@ -15,6 +15,9 @@ Import necessary modules from nipype.""" +from __future__ import print_function +from builtins import range + import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.spm as spm # spm import nipype.workflows.fmri.spm as spm_wf # spm @@ -323,11 +326,11 @@ def pickFieldFlow(dartel_flow_fields, subject_id): def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n"%str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), @@ -479,7 +482,7 @@ def getstripdir(subject_id): """ # collect all the con images for each contrast. -contrast_ids = range(1,len(contrasts)+1) +contrast_ids = list(range(1,len(contrasts)+1)) l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source") # we use .*i* to capture both .img (SPM8) and .nii (SPM12) l2source.inputs.template=os.path.abspath('spm_dartel_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*') diff --git a/examples/fmri_spm_face.py b/examples/fmri_spm_face.py index ec22dfe2da..ffdd745bc2 100755 --- a/examples/fmri_spm_face.py +++ b/examples/fmri_spm_face.py @@ -17,6 +17,9 @@ Import necessary modules from nipype.""" +from __future__ import division +from builtins import range + import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.spm as spm # spm import nipype.interfaces.matlab as mlab # how to run matlab @@ -324,9 +327,9 @@ def makelist(item): slice_timingref = l1pipeline.inputs.preproc.slice_timing slice_timingref.num_slices = num_slices slice_timingref.time_repetition = TR -slice_timingref.time_acquisition = TR - TR/float(num_slices) -slice_timingref.slice_order = range(num_slices,0,-1) -slice_timingref.ref_slice = int(num_slices/2) +slice_timingref.time_acquisition = TR - TR / float(num_slices) +slice_timingref.slice_order = list(range(num_slices,0,-1)) +slice_timingref.ref_slice = int(num_slices / 2) l1pipeline.inputs.preproc.smooth.fwhm = [8, 8, 8] diff --git a/examples/fmri_spm_nested.py b/examples/fmri_spm_nested.py index be60d6a9c3..738a97aded 100755 --- a/examples/fmri_spm_nested.py +++ b/examples/fmri_spm_nested.py @@ -15,6 +15,9 @@ Import necessary modules from nipype.""" +from __future__ import print_function +from builtins import range + import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.spm as spm # spm import nipype.interfaces.matlab as mlab # how to run matlab @@ -286,11 +289,11 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print "Subject ID: %s\n"%str(subject_id) + print("Subject ID: %s\n"%str(subject_id)) output = [] names = ['Task-Odd','Task-Even'] for r in range(4): - onsets = [range(15,240,60),range(45,240,60)] + onsets = [list(range(15,240,60)),list(range(45,240,60))] output.insert(r, Bunch(conditions=names, onsets=deepcopy(onsets), @@ -433,7 +436,7 @@ def getstripdir(subject_id): """ # collect all the con images for each contrast. -contrast_ids = range(1,len(contrasts)+1) +contrast_ids = list(range(1,len(contrasts)+1)) l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source") # we use .*i* to capture both .img (SPM8) and .nii (SPM12) l2source.inputs.template=os.path.abspath('spm_tutorial2/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*') diff --git a/examples/frontiers_paper/smoothing_comparison.py b/examples/frontiers_paper/smoothing_comparison.py index 6c9379faa0..46b4b8bc5e 100644 --- a/examples/frontiers_paper/smoothing_comparison.py +++ b/examples/frontiers_paper/smoothing_comparison.py @@ -6,6 +6,7 @@ =========================== """ +from builtins import range import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.spm as spm # spm @@ -91,8 +92,8 @@ 'inlist') def chooseindex(roi): - return {'isotropic_voxel':range(0,4), 'anisotropic_voxel':range(4,8), - 'isotropic_surface':range(8,12)}[roi] + return {'isotropic_voxel':list(range(0,4)), 'anisotropic_voxel':list(range(4,8)), + 'isotropic_surface':list(range(8,12))}[roi] preprocessing.connect(iter_smoothing_method, ("smoothing_method", chooseindex), select_smoothed_files, 'index') @@ -108,8 +109,8 @@ def chooseindex(roi): specify_model.inputs.time_repetition = 3. specify_model.inputs.high_pass_filter_cutoff = 120 specify_model.inputs.subject_info = [Bunch(conditions=['Task-Odd','Task-Even'], - onsets=[range(15,240,60), - range(45,240,60)], + onsets=[list(range(15,240,60)), + list(range(45,240,60))], durations=[[15], [15]])]*4 level1design = pe.Node(interface=spm.Level1Design(), name= "level1design") diff --git a/examples/frontiers_paper/workflow_from_scratch.py b/examples/frontiers_paper/workflow_from_scratch.py index 70d5462819..9560737651 100644 --- a/examples/frontiers_paper/workflow_from_scratch.py +++ b/examples/frontiers_paper/workflow_from_scratch.py @@ -7,6 +7,8 @@ """ +from builtins import range + import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.spm as spm # spm import nipype.pipeline.engine as pe # pypeline engine @@ -65,8 +67,8 @@ specify_model.inputs.time_repetition = 3. specify_model.inputs.high_pass_filter_cutoff = 120 specify_model.inputs.subject_info = [Bunch(conditions=['Task-Odd','Task-Even'], - onsets=[range(15,240,60), - range(45,240,60)], + onsets=[list(range(15,240,60)), + list(range(45,240,60))], durations=[[15], [15]])]*4 level1design = pe.Node(interface=spm.Level1Design(), name= "level1design") diff --git a/examples/rsfmri_vol_surface_preprocessing.py b/examples/rsfmri_vol_surface_preprocessing.py index 06fd9e5154..408bfd582a 100644 --- a/examples/rsfmri_vol_surface_preprocessing.py +++ b/examples/rsfmri_vol_surface_preprocessing.py @@ -43,6 +43,8 @@ - `MNI template `_ """ +from __future__ import division +from builtins import range import os @@ -96,7 +98,7 @@ def get_info(dicom_files): meta = default_extractor(read_file(filename_to_list(dicom_files)[0], stop_before_pixels=True, force=True)) - return (meta['RepetitionTime']/1000., meta['CsaImage.MosaicRefAcqTimes'], + return (meta['RepetitionTime'] / 1000., meta['CsaImage.MosaicRefAcqTimes'], meta['SpacingBetweenSlices']) @@ -123,7 +125,7 @@ def median(in_files): average = data else: average = average + data - median_img = nb.Nifti1Image(average/float(idx + 1), + median_img = nb.Nifti1Image(average / float(idx + 1), img.get_affine(), img.get_header()) filename = os.path.join(os.getcwd(), 'median.nii.gz') median_img.to_filename(filename) @@ -150,7 +152,7 @@ def bandpass_filter(files, lowpass_freq, highpass_freq, fs): img = nb.load(filename) timepoints = img.shape[-1] F = np.zeros((timepoints)) - lowidx = timepoints/2 + 1 + lowidx = int(timepoints / 2) + 1 if lowpass_freq > 0: lowidx = np.round(lowpass_freq / fs * timepoints) highidx = 0 @@ -275,7 +277,7 @@ def extract_noise_components(realigned_file, mask_file, num_components=5, stdX[stdX == 0] = 1. stdX[np.isnan(stdX)] = 1. stdX[np.isinf(stdX)] = 1. - X = (X - np.mean(X, axis=0))/stdX + X = (X - np.mean(X, axis=0)) / stdX u, _, _ = svd(X, full_matrices=False) if components is None: components = u[:, :num_components] @@ -597,7 +599,7 @@ def create_workflow(files, iterfield=['in_file', 'run'], name='rename') name_unique.inputs.keep_ext = True - name_unique.inputs.run = range(1, len(files) + 1) + name_unique.inputs.run = list(range(1, len(files) + 1)) name_unique.inputs.in_file = files realign = Node(interface=spm.Realign(), name="realign") @@ -607,9 +609,9 @@ def create_workflow(files, slice_timing = Node(interface=spm.SliceTiming(), name="slice_timing") slice_timing.inputs.num_slices = num_slices slice_timing.inputs.time_repetition = TR - slice_timing.inputs.time_acquisition = TR - TR/float(num_slices) + slice_timing.inputs.time_acquisition = TR - TR / float(num_slices) slice_timing.inputs.slice_order = (np.argsort(slice_times) + 1).tolist() - slice_timing.inputs.ref_slice = int(num_slices/2) + slice_timing.inputs.ref_slice = int(num_slices / 2) # Comute TSNR on realigned data regressing polynomials upto order 2 tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr') @@ -742,7 +744,7 @@ def merge_files(in1, in2): function=bandpass_filter, imports=imports), name='bandpass_unsmooth') - bandpass.inputs.fs = 1./TR + bandpass.inputs.fs = 1. / TR bandpass.inputs.highpass_freq = highpass_freq bandpass.inputs.lowpass_freq = lowpass_freq wf.connect(filter2, 'out_res', bandpass, 'files') @@ -800,9 +802,9 @@ def merge_files(in1, in2): iterfield=['in_file', 'summary_file', 'avgwf_txt_file'], name='aparc_ts') - sampleaparc.inputs.segment_id = ([8] + range(10, 14) + [17, 18, 26, 47] + - range(49, 55) + [58] + range(1001, 1036) + - range(2001, 2036)) + sampleaparc.inputs.segment_id = ([8] + list(range(10, 14)) + [17, 18, 26, 47] + + list(range(49, 55)) + [58] + list(range(1001, 1036)) + + list(range(2001, 2036))) wf.connect(registration, 'outputspec.aparc', sampleaparc, 'segmentation_file') @@ -871,8 +873,8 @@ def get_names(files, suffix): imports=imports), iterfield=['timeseries_file'], name='getsubcortts') - ts2txt.inputs.indices = [8] + range(10, 14) + [17, 18, 26, 47] +\ - range(49, 55) + [58] + ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\ + list(range(49, 55)) + [58] ts2txt.inputs.label_file = \ os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_' '2mm_v2.nii.gz')) @@ -948,7 +950,7 @@ def create_resting_workflow(args, name=None): slice_times = args.slice_times if args.dicom_file: TR, slice_times, slice_thickness = get_info(args.dicom_file) - slice_times = (np.array(slice_times)/1000.).tolist() + slice_times = (np.array(slice_times) / 1000.).tolist() if name is None: name = 'resting_' + args.subject_id kwargs = dict(files=[os.path.abspath(filename) for filename in args.files], diff --git a/examples/rsfmri_vol_surface_preprocessing_nipy.py b/examples/rsfmri_vol_surface_preprocessing_nipy.py index 8a61c3c202..9055a98866 100644 --- a/examples/rsfmri_vol_surface_preprocessing_nipy.py +++ b/examples/rsfmri_vol_surface_preprocessing_nipy.py @@ -44,6 +44,9 @@ """ +from __future__ import division +from builtins import range + import os from nipype.interfaces.base import CommandLine @@ -91,7 +94,7 @@ def get_info(dicom_files): meta = default_extractor(read_file(filename_to_list(dicom_files)[0], stop_before_pixels=True, force=True)) - return (meta['RepetitionTime']/1000., meta['CsaImage.MosaicRefAcqTimes'], + return (meta['RepetitionTime'] / 1000., meta['CsaImage.MosaicRefAcqTimes'], meta['SpacingBetweenSlices']) @@ -116,7 +119,7 @@ def median(in_files): average = data else: average = average + data - median_img = nb.Nifti1Image(average/float(idx + 1), + median_img = nb.Nifti1Image(average / float(idx + 1), img.get_affine(), img.get_header()) filename = os.path.join(os.getcwd(), 'median.nii.gz') median_img.to_filename(filename) @@ -140,7 +143,7 @@ def bandpass_filter(files, lowpass_freq, highpass_freq, fs): img = nb.load(filename) timepoints = img.shape[-1] F = np.zeros((timepoints)) - lowidx = timepoints/2 + 1 + lowidx = int(timepoints / 2) + 1 if lowpass_freq > 0: lowidx = np.round(float(lowpass_freq) / fs * timepoints) highidx = 0 @@ -257,7 +260,7 @@ def extract_noise_components(realigned_file, mask_file, num_components=5, stdX[stdX == 0] = 1. stdX[np.isnan(stdX)] = 1. stdX[np.isinf(stdX)] = 1. - X = (X - np.mean(X, axis=0))/stdX + X = (X - np.mean(X, axis=0)) / stdX u, _, _ = sp.linalg.svd(X, full_matrices=False) if components is None: components = u[:, :num_components] @@ -584,7 +587,7 @@ def create_workflow(files, iterfield=['in_file', 'run'], name='rename') name_unique.inputs.keep_ext = True - name_unique.inputs.run = range(1, len(files) + 1) + name_unique.inputs.run = list(range(1, len(files) + 1)) name_unique.inputs.in_file = files realign = Node(nipy.SpaceTimeRealigner(), name="spacetime_realign") @@ -732,7 +735,7 @@ def merge_files(in1, in2): function=bandpass_filter, imports=imports), name='bandpass_unsmooth') - bandpass.inputs.fs = 1./TR + bandpass.inputs.fs = 1. / TR bandpass.inputs.highpass_freq = highpass_freq bandpass.inputs.lowpass_freq = lowpass_freq wf.connect(filter2, 'out_res', bandpass, 'files') @@ -791,9 +794,9 @@ def merge_files(in1, in2): iterfield=['in_file', 'summary_file', 'avgwf_txt_file'], name='aparc_ts') - sampleaparc.inputs.segment_id = ([8] + range(10, 14) + [17, 18, 26, 47] + - range(49, 55) + [58] + range(1001, 1036) + - range(2001, 2036)) + sampleaparc.inputs.segment_id = ([8] + list(range(10, 14)) + [17, 18, 26, 47] + + list(range(49, 55)) + [58] + list(range(1001, 1036)) + + list(range(2001, 2036))) wf.connect(registration, 'outputspec.aparc', sampleaparc, 'segmentation_file') @@ -863,8 +866,8 @@ def get_names(files, suffix): imports=imports), iterfield=['timeseries_file'], name='getsubcortts') - ts2txt.inputs.indices = [8] + range(10, 14) + [17, 18, 26, 47] +\ - range(49, 55) + [58] + ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\ + list(range(49, 55)) + [58] ts2txt.inputs.label_file = \ os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_' '2mm_v2.nii.gz')) @@ -958,7 +961,7 @@ def create_resting_workflow(args, name=None): slice_times = args.slice_times if args.dicom_file: TR, slice_times, slice_thickness = get_info(args.dicom_file) - slice_times = (np.array(slice_times)/1000.).tolist() + slice_times = (np.array(slice_times) / 1000.).tolist() if name is None: name = 'resting_' + args.subject_id diff --git a/examples/smri_ants_build_template.py b/examples/smri_ants_build_template.py index ee0149b2db..65797b3943 100644 --- a/examples/smri_ants_build_template.py +++ b/examples/smri_ants_build_template.py @@ -12,6 +12,10 @@ 1. Tell python where to find the appropriate functions. """ +from __future__ import print_function +from future import standard_library +standard_library.install_aliases() + import os import nipype.interfaces.utility as util import nipype.interfaces.ants as ants @@ -24,13 +28,13 @@ 2. Download T1 volumes into home directory """ -import urllib2 +import urllib.request, urllib.error, urllib.parse homeDir=os.getenv("HOME") requestedPath=os.path.join(homeDir,'nipypeTestPath') mydatadir=os.path.realpath(requestedPath) if not os.path.exists(mydatadir): os.makedirs(mydatadir) -print mydatadir +print(mydatadir) MyFileURLs=[ ('http://slicer.kitware.com/midas3/download?bitstream=13121','01_T1_half.nii.gz'), @@ -44,7 +48,7 @@ myURL=tt[0] localFilename=os.path.join(mydatadir,tt[1]) if not os.path.exists(localFilename): - remotefile = urllib2.urlopen(myURL) + remotefile = urllib.request.urlopen(myURL) localFile = open(localFilename, 'wb') localFile.write(remotefile.read()) diff --git a/examples/smri_ants_registration.py b/examples/smri_ants_registration.py index 3db3e28972..c1c3044977 100644 --- a/examples/smri_ants_registration.py +++ b/examples/smri_ants_registration.py @@ -12,8 +12,12 @@ 1. Tell python where to find the appropriate functions. """ +from __future__ import print_function +from future import standard_library +standard_library.install_aliases() + import os -import urllib2 +import urllib.request, urllib.error, urllib.parse from nipype.interfaces.ants import Registration """ @@ -25,7 +29,7 @@ mydatadir=os.path.realpath(requestedPath) if not os.path.exists(mydatadir): os.makedirs(mydatadir) -print mydatadir +print(mydatadir) MyFileURLs=[ ('http://slicer.kitware.com/midas3/download?bitstream=13121','01_T1_half.nii.gz'), @@ -35,7 +39,7 @@ myURL=tt[0] localFilename=os.path.join(mydatadir,tt[1]) if not os.path.exists(localFilename): - remotefile = urllib2.urlopen(myURL) + remotefile = urllib.request.urlopen(myURL) localFile = open(localFilename, 'wb') localFile.write(remotefile.read()) @@ -81,7 +85,7 @@ reg.inputs.use_histogram_matching = [False] * 3 + [True] reg.inputs.initial_moving_transform_com = True -print reg.cmdline +print(reg.cmdline) """ diff --git a/examples/smri_antsregistration_build_template.py b/examples/smri_antsregistration_build_template.py index d22ee95c38..2b1f8b6130 100644 --- a/examples/smri_antsregistration_build_template.py +++ b/examples/smri_antsregistration_build_template.py @@ -12,6 +12,10 @@ 1. Tell python where to find the appropriate functions. """ +from __future__ import print_function +from future import standard_library +standard_library.install_aliases() + import os import nipype.interfaces.utility as util import nipype.interfaces.ants as ants @@ -24,13 +28,13 @@ 2. Download T1 volumes into home directory """ -import urllib2 +import urllib.request, urllib.error, urllib.parse homeDir=os.getenv("HOME") requestedPath=os.path.join(homeDir,'nipypeTestPath') mydatadir=os.path.realpath(requestedPath) if not os.path.exists(mydatadir): os.makedirs(mydatadir) -print mydatadir +print(mydatadir) MyFileURLs=[ ('http://slicer.kitware.com/midas3/download?bitstream=13121','01_T1_half.nii.gz'), @@ -44,7 +48,7 @@ myURL=tt[0] localFilename=os.path.join(mydatadir,tt[1]) if not os.path.exists(localFilename): - remotefile = urllib2.urlopen(myURL) + remotefile = urllib.request.urlopen(myURL) localFile = open(localFilename, 'wb') localFile.write(remotefile.read()) diff --git a/examples/test_spm.py b/examples/test_spm.py index 273066d49d..e524b63a28 100644 --- a/examples/test_spm.py +++ b/examples/test_spm.py @@ -1,3 +1,5 @@ +from __future__ import division +from builtins import range import nipype.pipeline.engine as pe from nipype.interfaces import spm from nipype.interfaces import fsl @@ -12,8 +14,8 @@ stc = pe.Node(interface=spm.SliceTiming(), name='stc') stc.inputs.num_slices = 21 stc.inputs.time_repetition = 1.0 -stc.inputs.time_acquisition = 2. - 2./32 -stc.inputs.slice_order = range(21,0,-1) +stc.inputs.time_acquisition = 2. - 2. / 32 +stc.inputs.slice_order = list(range(21,0,-1)) stc.inputs.ref_slice = 10 realign_estimate = pe.Node(interface=spm.Realign(), name='realign_estimate') @@ -47,8 +49,8 @@ stc = pe.Node(interface=spm.SliceTiming(), name='stc') stc.inputs.num_slices = 21 stc.inputs.time_repetition = 1.0 -stc.inputs.time_acquisition = 2. - 2./32 -stc.inputs.slice_order = range(21,0,-1) +stc.inputs.time_acquisition = 2. - 2. / 32 +stc.inputs.slice_order = list(range(21,0,-1)) stc.inputs.ref_slice = 10 realign_estimate = pe.Node(interface=spm.Realign(), name='realign_estimate') diff --git a/examples/workshop_dartmouth_2010.py b/examples/workshop_dartmouth_2010.py index b7d0809d24..6a035c4924 100644 --- a/examples/workshop_dartmouth_2010.py +++ b/examples/workshop_dartmouth_2010.py @@ -96,9 +96,11 @@ Having interfaces allows us to use third party software (like FSL BET) as function. Look how simple it is. """ +from __future__ import print_function + import nipype.interfaces.fsl as fsl result = fsl.BET(in_file='data/s1/struct.nii').run() -print result +print(result) """ Running a single program is not much of a breakthrough. Lets run motion correction followed by smoothing @@ -231,20 +233,20 @@ datasource1.inputs.template = 'data/s1/f3.nii' datasource1.inputs.sort_filelist = True results = datasource1.run() -print results.outputs +print(results.outputs) datasource2 = nio.DataGrabber() datasource2.inputs.template = 'data/s*/f*.nii' datasource2.inputs.sort_filelist = True results = datasource2.run() -print results.outputs +print(results.outputs) datasource3 = nio.DataGrabber(infields=['run']) datasource3.inputs.template = 'data/s1/f%d.nii' datasource3.inputs.sort_filelist = True datasource3.inputs.run = [3, 7] results = datasource3.run() -print results.outputs +print(results.outputs) datasource4 = nio.DataGrabber(infields=['subject_id', 'run']) datasource4.inputs.template = 'data/%s/f%d.nii' @@ -252,7 +254,7 @@ datasource4.inputs.run = [3, 7] datasource4.inputs.subject_id = ['s1', 's3'] results = datasource4.run() -print results.outputs +print(results.outputs) """ Iterables diff --git a/nipype/__init__.py b/nipype/__init__.py index a5183e022c..bfe2ab0563 100644 --- a/nipype/__init__.py +++ b/nipype/__init__.py @@ -1,14 +1,16 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import absolute_import + import os -from info import (LONG_DESCRIPTION as __doc__, +from .info import (LONG_DESCRIPTION as __doc__, URL as __url__, STATUS as __status__, __version__) -from utils.config import NipypeConfig +from .utils.config import NipypeConfig config = NipypeConfig() -from utils.logger import Logging +from .utils.logger import Logging logging = Logging(config) from distutils.version import LooseVersion @@ -31,7 +33,7 @@ def test(self, label='fast', verbose=1, extra_argv=['--exe'], This will run the test suite and stop at the first failing example >>> from nipype import test - >>> test(extra_argv=['--exe', '-sx']) #doctest: +SKIP + >>> test(extra_argv=['--exe', '-sx']) # doctest: +SKIP """ return super(_NoseTester, self).test(label=label, verbose=verbose, @@ -60,7 +62,7 @@ def _test_local_install(): _test_local_install() # Set up package information function -from pkg_info import get_pkg_info as _get_pkg_info +from .pkg_info import get_pkg_info as _get_pkg_info get_info = lambda: _get_pkg_info(os.path.dirname(__file__)) # Cleanup namespace @@ -74,6 +76,6 @@ def _test_local_install(): pass -from pipeline import Node, MapNode, JoinNode, Workflow -from interfaces import (DataGrabber, DataSink, SelectFiles, +from .pipeline import Node, MapNode, JoinNode, Workflow +from .interfaces import (DataGrabber, DataSink, SelectFiles, IdentityInterface, Rename, Function, Select, Merge) diff --git a/nipype/algorithms/icc.py b/nipype/algorithms/icc.py index 3e291c0dc3..d2a018cd37 100644 --- a/nipype/algorithms/icc.py +++ b/nipype/algorithms/icc.py @@ -1,3 +1,5 @@ +from __future__ import division +from builtins import range from numpy import ones, kron, mean, eye, hstack, dot, tile from scipy.linalg import pinv from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \ @@ -122,7 +124,7 @@ def ICC_rep_anova(Y): # ICC(3,1) = (mean square subjeT - mean square error) / (mean square subjeT + (k-1)*-mean square error) ICC = (MSR - MSE) / (MSR + dfc * MSE) - e_var = MSE #variance of error - r_var = (MSR - MSE)/nb_conditions #variance between subjects + e_var = MSE # variance of error + r_var = (MSR - MSE) / nb_conditions # variance between subjects return ICC, r_var, e_var, session_effect_F, dfc, dfe diff --git a/nipype/algorithms/mesh.py b/nipype/algorithms/mesh.py index 6e67b85a26..e8bd62585d 100644 --- a/nipype/algorithms/mesh.py +++ b/nipype/algorithms/mesh.py @@ -10,18 +10,19 @@ >>> os.chdir(datadir) ''' +from __future__ import division +from builtins import zip +import os.path as op +from warnings import warn import numpy as np from numpy import linalg as nla -import os.path as op -from ..external import six from .. import logging - +from ..external.six import string_types from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File, BaseInterfaceInputSpec) -from warnings import warn iflogger = logging.getLogger('interface') @@ -201,7 +202,7 @@ class ComputeMeshWarp(BaseInterface): >>> dist = m.ComputeMeshWarp() >>> dist.inputs.surface1 = 'surf1.vtk' >>> dist.inputs.surface2 = 'surf2.vtk' - >>> res = dist.run() # doctest: +SKIP + >>> res = dist.run() # doctest: +SKIP """ @@ -342,7 +343,7 @@ class MeshWarpMaths(BaseInterface): >>> mmath.inputs.in_surf = 'surf1.vtk' >>> mmath.inputs.operator = 'surf2.vtk' >>> mmath.inputs.operation = 'mul' - >>> res = mmath.run() # doctest: +SKIP + >>> res = mmath.run() # doctest: +SKIP """ @@ -375,7 +376,7 @@ def _run_interface(self, runtime): operator = self.inputs.operator opfield = np.ones_like(points1) - if isinstance(operator, six.string_types): + if isinstance(operator, string_types): r2 = tvtk.PolyDataReader(file_name=self.inputs.surface2) vtk2 = r2.output r2.update() diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index b26e63639a..9d7d8dc66f 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -11,29 +11,25 @@ >>> os.chdir(datadir) ''' +from __future__ import division +from builtins import zip +from builtins import range import os import os.path as op import nibabel as nb import numpy as np -from math import floor, ceil -from scipy.ndimage.morphology import grey_dilation from scipy.ndimage.morphology import binary_erosion from scipy.spatial.distance import cdist, euclidean, dice, jaccard from scipy.ndimage.measurements import center_of_mass, label -from scipy.special import legendre -import scipy.io as sio -import itertools -import scipy.stats as stats from .. import logging from ..utils.misc import package_check from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File, - InputMultiPath, OutputMultiPath, + InputMultiPath, BaseInterfaceInputSpec, isdefined) -from ..utils.filemanip import fname_presuffix, split_filename iflogger = logging.getLogger('interface') @@ -288,7 +284,7 @@ def _run_interface(self, runtime): if self.inputs.vol_units == 'mm': voxvol = nii1.get_header().get_zooms() - for i in xrange(nii1.get_data().ndim-1): + for i in range(nii1.get_data().ndim-1): scale = scale * voxvol[i] data1 = nii1.get_data() @@ -339,8 +335,8 @@ def _run_interface(self, runtime): self._labels = labels self._ove_rois = results - self._vol_rois = ((np.array(volumes1) - np.array(volumes2)) / - np.array(volumes1)) + self._vol_rois = (np.array(volumes1) + - np.array(volumes2)) / np.array(volumes1) self._dice = round(np.sum(weights*results['dice']), 5) self._jaccard = round(np.sum(weights*results['jaccard']), 5) @@ -434,21 +430,22 @@ def _run_interface(self, runtime): for ref_comp, tst_comp, diff_comp in zip( img_ref, img_tst, diff_im ): num = np.minimum( ref_comp, tst_comp ) ddr = np.maximum( ref_comp, tst_comp ) - diff_comp[ddr>0]+= 1.0-(num[ddr>0]/ddr[ddr>0]) - self._jaccards.append( np.sum( num ) / np.sum( ddr ) ) - volumes.append( np.sum( ref_comp ) ) + diff_comp[ddr>0] += 1.0 - (num[ddr>0] / ddr[ddr>0]) + self._jaccards.append(np.sum(num) / np.sum(ddr)) + volumes.append(np.sum(ref_comp)) - self._dices = 2.0*np.array(self._jaccards) / (np.array(self._jaccards) +1.0 ) + self._dices = 2.0 * (np.array(self._jaccards) / + (np.array(self._jaccards) + 1.0)) if self.inputs.weighting != "none": weights = 1.0 / np.array(volumes) if self.inputs.weighting == "squared_vol": - weights = weights**2 + weights = weights ** 2 - weights = weights / np.sum( weights ) + weights = weights / np.sum(weights) - setattr( self, '_jaccard', np.sum( weights * self._jaccards ) ) - setattr( self, '_dice', np.sum( weights * self._dices ) ) + setattr(self, '_jaccard', np.sum( weights * self._jaccards ) ) + setattr(self, '_dice', np.sum( weights * self._dices ) ) diff = np.zeros( diff_im[0].shape ) @@ -630,7 +627,7 @@ class Similarity(BaseInterface): def __init__(self, **inputs): try: package_check('nipy') - except Exception, e: + except Exception as e: self._have_nipy = False super(Similarity,self).__init__(**inputs) diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py index 8704860f39..2394818434 100644 --- a/nipype/algorithms/misc.py +++ b/nipype/algorithms/misc.py @@ -10,6 +10,11 @@ >>> os.chdir(datadir) ''' +from __future__ import print_function +from __future__ import absolute_import +from __future__ import division +from builtins import zip +from builtins import range import os import os.path as op @@ -18,9 +23,6 @@ import numpy as np from math import floor, ceil from scipy.ndimage.morphology import grey_dilation -from scipy.ndimage.morphology import binary_erosion -from scipy.spatial.distance import cdist, euclidean, dice, jaccard -from scipy.ndimage.measurements import center_of_mass, label from scipy.special import legendre import scipy.io as sio import itertools @@ -30,7 +32,7 @@ import warnings -import metrics as nam +from . import metrics as nam from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File, InputMultiPath, OutputMultiPath, BaseInterfaceInputSpec, isdefined, @@ -98,9 +100,9 @@ def _get_brodmann_area(self): for lab in labels: newdata[origdata == lab] = 1 if self.inputs.hemi == 'right': - newdata[floor(float(origdata.shape[0]) / 2):, :, :] = 0 + newdata[int(floor(float(origdata.shape[0]) / 2)):, :, :] = 0 elif self.inputs.hemi == 'left': - newdata[:ceil(float(origdata.shape[0]) / 2), :, :] = 0 + newdata[:int(ceil(float(origdata.shape[0]) / 2)), :, :] = 0 if self.inputs.dilation_size != 0: newdata = grey_dilation( @@ -439,7 +441,7 @@ def _run_interface(self, runtime): # name and a .csv extension. saved_variables = list() - for key in in_dict.keys(): + for key in list(in_dict.keys()): if not key.startswith('__'): if isinstance(in_dict[key][0], np.ndarray): saved_variables.append(key) @@ -473,7 +475,7 @@ def _list_outputs(self): outputs = self.output_spec().get() in_dict = sio.loadmat(op.abspath(self.inputs.in_file)) saved_variables = list() - for key in in_dict.keys(): + for key in list(in_dict.keys()): if not key.startswith('__'): if isinstance(in_dict[key][0], np.ndarray): saved_variables.append(key) @@ -495,10 +497,10 @@ def merge_csvs(in_list): for idx, in_file in enumerate(in_list): try: in_array = np.loadtxt(in_file, delimiter=',') - except ValueError, ex: + except ValueError as ex: try: in_array = np.loadtxt(in_file, delimiter=',', skiprows=1) - except ValueError, ex: + except ValueError as ex: first = open(in_file, 'r') header_line = first.readline() header_list = header_line.split(',') @@ -506,11 +508,11 @@ def merge_csvs(in_list): try: in_array = np.loadtxt( in_file, delimiter=',', skiprows=1, - usecols=range(1, n_cols) + usecols=list(range(1, n_cols)) ) - except ValueError, ex: + except ValueError as ex: in_array = np.loadtxt( - in_file, delimiter=',', skiprows=1, usecols=range(1, n_cols-1)) + in_file, delimiter=',', skiprows=1, usecols=list(range(1, n_cols-1))) if idx == 0: out_array = in_array else: @@ -523,7 +525,7 @@ def merge_csvs(in_list): def remove_identical_paths(in_files): import os.path as op - from nipype.utils.filemanip import split_filename + from ..utils.filemanip import split_filename if len(in_files) > 1: out_names = list() commonprefix = op.commonprefix(in_files) @@ -865,7 +867,7 @@ def _run_interface(self, runtime): ' thread-safe in multi-processor execution')) input_dict = {} - for key, val in self.inputs._outputs.items(): + for key, val in list(self.inputs._outputs.items()): # expand lists to several columns if key == 'trait_added' and val in self.inputs.copyable_trait_names(): continue @@ -970,7 +972,7 @@ def calc_moments(timeseries_file, moment): m2 = stats.moment(timeseries, 2, axis=0) m3 = stats.moment(timeseries, moment, axis=0) zero = (m2 == 0) - return np.where(zero, 0, m3 / m2**(moment/2.0)) + return np.where(zero, 0, m3 / m2 ** (moment / 2.0)) class AddNoiseInputSpec(TraitedSpec): @@ -1045,7 +1047,7 @@ def gen_noise(self, image, mask=None, snr_db=10.0, dist='normal', bg_dist='norma added gaussian noise (rayleigh for background in mask) """ from math import sqrt - snr = sqrt(np.power(10.0, snr_db/10.0)) + snr = sqrt(np.power(10.0, snr_db / 10.0)) if mask is None: mask = np.ones_like(image) @@ -1060,7 +1062,7 @@ def gen_noise(self, image, mask=None, snr_db=10.0, dist='normal', bg_dist='norma if dist == 'normal': signal = signal - signal.mean() - sigma_n = sqrt(signal.var()/snr) + sigma_n = sqrt(signal.var() / snr) noise = np.random.normal(size=image.shape, scale=sigma_n) if (np.any(mask == 0)) and (bg_dist == 'rayleigh'): @@ -1070,11 +1072,11 @@ def gen_noise(self, image, mask=None, snr_db=10.0, dist='normal', bg_dist='norma im_noise = image + noise elif dist == 'rician': - sigma_n = signal.mean()/snr + sigma_n = signal.mean() / snr n_1 = np.random.normal(size=image.shape, scale=sigma_n) n_2 = np.random.normal(size=image.shape, scale=sigma_n) - stde_1 = n_1/sqrt(2.0) - stde_2 = n_2/sqrt(2.0) + stde_1 = n_1 / sqrt(2.0) + stde_2 = n_2 / sqrt(2.0) im_noise = np.sqrt((image + stde_1)**2 + (stde_2)**2) else: raise NotImplementedError(('Only normal and rician distributions ' @@ -1180,7 +1182,7 @@ def _run_interface(self, runtime): def _list_outputs(self): outputs = self.output_spec().get() - for k, v in self._outnames.iteritems(): + for k, v in self._outnames.items(): outputs[k] = v return outputs @@ -1207,9 +1209,9 @@ class MergeROIs(BaseInterface): >>> from nipype.algorithms import misc >>> rois = misc.MergeROIs() - >>> rois.inputs.in_files = ['roi%02d.nii' % i for i in xrange(1, 6)] + >>> rois.inputs.in_files = ['roi%02d.nii' % i for i in range(1, 6)] >>> rois.inputs.in_reference = 'mask.nii' - >>> rois.inputs.in_index = ['roi%02d_idx.npz' % i for i in xrange(1, 6)] + >>> rois.inputs.in_index = ['roi%02d_idx.npz' % i for i in range(1, 6)] >>> rois.run() # doctest: +SKIP """ @@ -1317,7 +1319,7 @@ def split_rois(in_file, mask=None, roishape=None): mask = mask.reshape(-1).astype(np.uint8) nzels = np.nonzero(mask) els = np.sum(mask) - nrois = int(ceil(els/roisize)) + nrois = int(ceil(els / float(roisize))) data = im.get_data().reshape((mask.size, -1)) data = np.squeeze(data.take(nzels, axis=0)) @@ -1331,7 +1333,7 @@ def split_rois(in_file, mask=None, roishape=None): out_mask = [] out_idxs = [] - for i in xrange(nrois): + for i in range(nrois): first = i * roisize last = (i+1) * roisize fill = 0 @@ -1428,7 +1430,7 @@ def merge_rois(in_files, in_idxs, in_ref, else: hdr.set_data_shape(rsh[:3]) nii = [] - for d in xrange(ndirs): + for d in range(ndirs): fname = op.abspath('vol%06d.nii' % d) nb.Nifti1Image(np.zeros(rsh[:3]), aff, hdr).to_filename(fname) nii.append(fname) diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index bfa53874fa..8ef80c4976 100644 --- a/nipype/algorithms/modelgen.py +++ b/nipype/algorithms/modelgen.py @@ -18,6 +18,9 @@ """ +from __future__ import division +from builtins import range + from copy import deepcopy import os @@ -25,12 +28,12 @@ import numpy as np from scipy.special import gammaln -from nipype.interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath, - traits, File, Bunch, BaseInterfaceInputSpec, - isdefined) -from nipype.utils.filemanip import filename_to_list +from ..external.six import string_types +from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath, + traits, File, Bunch, BaseInterfaceInputSpec, + isdefined) +from ..utils.filemanip import filename_to_list from .. import config, logging -from nipype.external import six iflogger = logging.getLogger('interface') @@ -77,7 +80,7 @@ def spm_hrf(RT, P=None, fMRI_T=16): hrf = gamma.pdf(u, p[0]/p[2], scale=dt/p[2]) - gamma.pdf(u, p[1]/p[3], scale=dt/p[3])/p[4] - >>> print spm_hrf(2) + >>> print(spm_hrf(2)) [ 0.00000000e+00 8.65660810e-02 3.74888236e-01 3.84923382e-01 2.16117316e-01 7.68695653e-02 1.62017720e-03 -3.06078117e-02 -3.73060781e-02 -3.08373716e-02 -2.05161334e-02 -1.16441637e-02 @@ -138,7 +141,7 @@ def scale_timings(timelist, input_units, output_units, time_repetition): if (input_units == 'scans') and (output_units == 'secs'): _scalefactor = time_repetition if (input_units == 'secs') and (output_units == 'scans'): - _scalefactor = 1./time_repetition + _scalefactor = 1. / time_repetition timelist = [np.max([0., _scalefactor * t]) for t in timelist] return timelist @@ -452,7 +455,7 @@ def _concatenate_info(self, infolist): for i, f in enumerate(self.inputs.functional_runs): if isinstance(f, list): numscans = len(f) - elif isinstance(f, six.string_types): + elif isinstance(f, string_types): img = load(f) numscans = img.get_shape()[3] else: @@ -697,9 +700,9 @@ def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans): timeline2 = np.zeros((npts)) reg = [] regderiv = [] - for i, trial in enumerate(np.arange(nscans)/nvol): + for i, trial in enumerate(np.arange(nscans) / nvol): scanstart = int((SCANONSET + trial * TR + (i % nvol) * TA) / dt) - scanidx = scanstart+np.arange(int(TA/dt)) + scanidx = scanstart+np.arange(int(TA / dt)) timeline2[scanidx] = np.max(timeline) reg.insert(i, np.mean(timeline[scanidx]) * reg_scale) if isdefined(self.inputs.use_temporal_deriv) and \ @@ -756,7 +759,7 @@ def _cond_to_regress(self, info, nscans): nvol = self.inputs.volumes_in_cluster if nvol > 1: for i in range(nvol-1): - treg = np.zeros((nscans/nvol, nvol)) + treg = np.zeros((nscans / nvol, nvol)) treg[:, i] = 1 reg.insert(len(reg), treg.ravel().tolist()) regnames.insert(len(regnames), 'T1effect_%d' % i) diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py index f304136d35..b565a23d1a 100644 --- a/nipype/algorithms/rapidart.py +++ b/nipype/algorithms/rapidart.py @@ -18,22 +18,23 @@ >>> os.chdir(datadir) """ +from __future__ import division +from builtins import range + import os from copy import deepcopy -from warnings import warn from nibabel import load, funcs, Nifti1Image import numpy as np from scipy import signal import scipy.io as sio -from nipype.external import six +from ..external.six import string_types from ..interfaces.base import (BaseInterface, traits, InputMultiPath, OutputMultiPath, TraitedSpec, File, BaseInterfaceInputSpec, isdefined) from ..utils.filemanip import filename_to_list, save_json, split_filename from ..utils.misc import find_indices - from .. import logging, config iflogger = logging.getLogger('interface') @@ -111,7 +112,7 @@ def _calc_norm(mc, use_differences, source, brain_pts=None): n_pts = all_pts.size - all_pts.shape[1] newpos = np.zeros((mc.shape[0], n_pts)) if brain_pts is not None: - displacement = np.zeros((mc.shape[0], n_pts / 3)) + displacement = np.zeros((mc.shape[0], int(n_pts / 3))) for i in range(mc.shape[0]): affine = _get_affine_matrix(mc[i, :], source) newpos[i, :] = np.dot(affine, @@ -260,7 +261,7 @@ class ArtifactDetect(BaseInterface): >>> ad.inputs.norm_threshold = 1 >>> ad.inputs.use_differences = [True, False] >>> ad.inputs.zintensity_threshold = 3 - >>> ad.run() # doctest: +SKIP + >>> ad.run() # doctest: +SKIP """ input_spec = ArtifactDetectInputSpec @@ -280,7 +281,7 @@ def _get_output_filenames(self, motionfile, output_dir): output_dir: string output directory in which the files will be generated """ - if isinstance(motionfile, six.string_types): + if isinstance(motionfile, string_types): infile = motionfile elif isinstance(motionfile, list): infile = motionfile[0] @@ -351,7 +352,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None): cwd = os.getcwd() # read in functional image - if isinstance(imgfile, six.string_types): + if isinstance(imgfile, string_types): nim = load(imgfile) elif isinstance(imgfile, list): if len(imgfile) == 1: @@ -392,7 +393,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None): mask_tmp = vol > \ (_nanmean(vol) / self.inputs.global_threshold) mask[:, :, :, t0] = mask_tmp - g[t0] = np.nansum(vol * mask_tmp)/np.nansum(mask_tmp) + g[t0] = np.nansum(vol * mask_tmp) / np.nansum(mask_tmp) elif masktype == 'file': # uses a mask image to determine intensity maskimg = load(self.inputs.mask_file) mask = maskimg.get_data() @@ -642,7 +643,7 @@ def _get_spm_submatrix(self, spmmat, sessidx, rows=None): U = spmmat['SPM'][0][0].Sess[0][sessidx].U[0] if rows is None: rows = spmmat['SPM'][0][0].Sess[0][sessidx].row[0] - 1 - cols = spmmat['SPM'][0][0].Sess[0][sessidx].col[0][range(len(U))] - 1 + cols = spmmat['SPM'][0][0].Sess[0][sessidx].col[0][list(range(len(U)))] - 1 outmatrix = designmatrix.take(rows.tolist(), axis=0).take(cols.tolist(), axis=1) return outmatrix diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index aca82e442f..14b6dfb452 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import AddCSVColumn +from ...testing import assert_equal +from ..misc import AddCSVColumn def test_AddCSVColumn_inputs(): input_map = dict(extra_column_heading=dict(), @@ -12,8 +12,8 @@ def test_AddCSVColumn_inputs(): ) inputs = AddCSVColumn.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AddCSVColumn_outputs(): @@ -21,7 +21,7 @@ def test_AddCSVColumn_outputs(): ) outputs = AddCSVColumn.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index 09b2c58adb..766665a816 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import AddCSVRow +from ...testing import assert_equal +from ..misc import AddCSVRow def test_AddCSVRow_inputs(): input_map = dict(_outputs=dict(usedefault=True, @@ -13,8 +13,8 @@ def test_AddCSVRow_inputs(): ) inputs = AddCSVRow.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AddCSVRow_outputs(): @@ -22,7 +22,7 @@ def test_AddCSVRow_outputs(): ) outputs = AddCSVRow.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py index 86994fe3d2..747bf51a21 100644 --- a/nipype/algorithms/tests/test_auto_AddNoise.py +++ b/nipype/algorithms/tests/test_auto_AddNoise.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import AddNoise +from ...testing import assert_equal +from ..misc import AddNoise def test_AddNoise_inputs(): input_map = dict(bg_dist=dict(mandatory=True, @@ -18,8 +18,8 @@ def test_AddNoise_inputs(): ) inputs = AddNoise.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AddNoise_outputs(): @@ -27,7 +27,7 @@ def test_AddNoise_outputs(): ) outputs = AddNoise.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 598bb0752b..4e1c5a1641 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.rapidart import ArtifactDetect +from ...testing import assert_equal +from ..rapidart import ArtifactDetect def test_ArtifactDetect_inputs(): input_map = dict(bound_by_brainmask=dict(usedefault=True, @@ -46,8 +46,8 @@ def test_ArtifactDetect_inputs(): ) inputs = ArtifactDetect.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ArtifactDetect_outputs(): @@ -61,7 +61,7 @@ def test_ArtifactDetect_outputs(): ) outputs = ArtifactDetect.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index f27766ea00..f779679928 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import CalculateNormalizedMoments +from ...testing import assert_equal +from ..misc import CalculateNormalizedMoments def test_CalculateNormalizedMoments_inputs(): input_map = dict(moment=dict(mandatory=True, @@ -10,8 +10,8 @@ def test_CalculateNormalizedMoments_inputs(): ) inputs = CalculateNormalizedMoments.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CalculateNormalizedMoments_outputs(): @@ -19,7 +19,7 @@ def test_CalculateNormalizedMoments_outputs(): ) outputs = CalculateNormalizedMoments.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 6318daa344..b1727ca477 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.mesh import ComputeMeshWarp +from ...testing import assert_equal +from ..mesh import ComputeMeshWarp def test_ComputeMeshWarp_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -21,8 +21,8 @@ def test_ComputeMeshWarp_inputs(): ) inputs = ComputeMeshWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeMeshWarp_outputs(): @@ -32,7 +32,7 @@ def test_ComputeMeshWarp_outputs(): ) outputs = ComputeMeshWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index ead44c873e..62c0926bb9 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import CreateNifti +from ...testing import assert_equal +from ..misc import CreateNifti def test_CreateNifti_inputs(): input_map = dict(affine=dict(), @@ -14,8 +14,8 @@ def test_CreateNifti_inputs(): ) inputs = CreateNifti.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CreateNifti_outputs(): @@ -23,7 +23,7 @@ def test_CreateNifti_outputs(): ) outputs = CreateNifti.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index dd6f682de2..9ae3e7f9b0 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import Distance +from ...testing import assert_equal +from ..misc import Distance def test_Distance_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -16,8 +16,8 @@ def test_Distance_inputs(): ) inputs = Distance.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Distance_outputs(): @@ -28,7 +28,7 @@ def test_Distance_outputs(): ) outputs = Distance.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index f9be02dc31..b303866349 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import FuzzyOverlap +from ...testing import assert_equal +from ..misc import FuzzyOverlap def test_FuzzyOverlap_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -17,8 +17,8 @@ def test_FuzzyOverlap_inputs(): ) inputs = FuzzyOverlap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FuzzyOverlap_outputs(): @@ -30,7 +30,7 @@ def test_FuzzyOverlap_outputs(): ) outputs = FuzzyOverlap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index eb665716a5..ad48e0b405 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import Gunzip +from ...testing import assert_equal +from ..misc import Gunzip def test_Gunzip_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -11,8 +11,8 @@ def test_Gunzip_inputs(): ) inputs = Gunzip.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Gunzip_outputs(): @@ -20,7 +20,7 @@ def test_Gunzip_outputs(): ) outputs = Gunzip.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index cedefe009f..292e8ae7a8 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.icc import ICC +from ...testing import assert_equal +from ..icc import ICC def test_ICC_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -13,8 +13,8 @@ def test_ICC_inputs(): ) inputs = ICC.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ICC_outputs(): @@ -24,7 +24,7 @@ def test_ICC_outputs(): ) outputs = ICC.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index bdf47a21b3..41f91baebd 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import Matlab2CSV +from ...testing import assert_equal +from ..misc import Matlab2CSV def test_Matlab2CSV_inputs(): input_map = dict(in_file=dict(mandatory=True, @@ -10,8 +10,8 @@ def test_Matlab2CSV_inputs(): ) inputs = Matlab2CSV.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Matlab2CSV_outputs(): @@ -19,7 +19,7 @@ def test_Matlab2CSV_outputs(): ) outputs = Matlab2CSV.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index fcdbd535d0..d63189e1ab 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import MergeCSVFiles +from ...testing import assert_equal +from ..misc import MergeCSVFiles def test_MergeCSVFiles_inputs(): input_map = dict(column_headings=dict(), @@ -16,8 +16,8 @@ def test_MergeCSVFiles_inputs(): ) inputs = MergeCSVFiles.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MergeCSVFiles_outputs(): @@ -25,7 +25,7 @@ def test_MergeCSVFiles_outputs(): ) outputs = MergeCSVFiles.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_MergeROIs.py b/nipype/algorithms/tests/test_auto_MergeROIs.py index 78206e3c24..6fc41742f8 100644 --- a/nipype/algorithms/tests/test_auto_MergeROIs.py +++ b/nipype/algorithms/tests/test_auto_MergeROIs.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import MergeROIs +from ...testing import assert_equal +from ..misc import MergeROIs def test_MergeROIs_inputs(): input_map = dict(in_files=dict(), @@ -9,8 +9,8 @@ def test_MergeROIs_inputs(): ) inputs = MergeROIs.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MergeROIs_outputs(): @@ -18,7 +18,7 @@ def test_MergeROIs_outputs(): ) outputs = MergeROIs.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index f953ed6b41..21a34fb9b8 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.mesh import MeshWarpMaths +from ...testing import assert_equal +from ..mesh import MeshWarpMaths def test_MeshWarpMaths_inputs(): input_map = dict(float_trait=dict(), @@ -20,8 +20,8 @@ def test_MeshWarpMaths_inputs(): ) inputs = MeshWarpMaths.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MeshWarpMaths_outputs(): @@ -30,7 +30,7 @@ def test_MeshWarpMaths_outputs(): ) outputs = MeshWarpMaths.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index 3186757ad8..7817620e1b 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import ModifyAffine +from ...testing import assert_equal +from ..misc import ModifyAffine def test_ModifyAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -13,8 +13,8 @@ def test_ModifyAffine_inputs(): ) inputs = ModifyAffine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ModifyAffine_outputs(): @@ -22,7 +22,7 @@ def test_ModifyAffine_outputs(): ) outputs = ModifyAffine.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py index 97645d68ee..49a7035037 100644 --- a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py +++ b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import NormalizeProbabilityMapSet +from ...testing import assert_equal +from ..misc import NormalizeProbabilityMapSet def test_NormalizeProbabilityMapSet_inputs(): input_map = dict(in_files=dict(), @@ -8,8 +8,8 @@ def test_NormalizeProbabilityMapSet_inputs(): ) inputs = NormalizeProbabilityMapSet.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NormalizeProbabilityMapSet_outputs(): @@ -17,7 +17,7 @@ def test_NormalizeProbabilityMapSet_outputs(): ) outputs = NormalizeProbabilityMapSet.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 44bcf4b2ec..fa8f582fd4 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.mesh import P2PDistance +from ...testing import assert_equal +from ..mesh import P2PDistance def test_P2PDistance_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -21,8 +21,8 @@ def test_P2PDistance_inputs(): ) inputs = P2PDistance.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_P2PDistance_outputs(): @@ -32,7 +32,7 @@ def test_P2PDistance_outputs(): ) outputs = P2PDistance.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index e4ad2e46be..a60645a368 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import PickAtlas +from ...testing import assert_equal +from ..misc import PickAtlas def test_PickAtlas_inputs(): input_map = dict(atlas=dict(mandatory=True, @@ -18,8 +18,8 @@ def test_PickAtlas_inputs(): ) inputs = PickAtlas.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PickAtlas_outputs(): @@ -27,7 +27,7 @@ def test_PickAtlas_outputs(): ) outputs = PickAtlas.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index c5f87f33d8..a69dcb5f1b 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.metrics import Similarity +from ...testing import assert_equal +from ..metrics import Similarity def test_Similarity_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -17,8 +17,8 @@ def test_Similarity_inputs(): ) inputs = Similarity.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Similarity_outputs(): @@ -26,7 +26,7 @@ def test_Similarity_outputs(): ) outputs = Similarity.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index 7a0c50ff10..f0840a6fd9 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import SimpleThreshold +from ...testing import assert_equal +from ..misc import SimpleThreshold def test_SimpleThreshold_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -13,8 +13,8 @@ def test_SimpleThreshold_inputs(): ) inputs = SimpleThreshold.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SimpleThreshold_outputs(): @@ -22,7 +22,7 @@ def test_SimpleThreshold_outputs(): ) outputs = SimpleThreshold.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index 9544ae4cc4..ca3ccc69d3 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.modelgen import SpecifyModel +from ...testing import assert_equal +from ..modelgen import SpecifyModel def test_SpecifyModel_inputs(): input_map = dict(event_files=dict(mandatory=True, @@ -28,8 +28,8 @@ def test_SpecifyModel_inputs(): ) inputs = SpecifyModel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SpecifyModel_outputs(): @@ -37,7 +37,7 @@ def test_SpecifyModel_outputs(): ) outputs = SpecifyModel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index 3715c1d208..e0c300b621 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.modelgen import SpecifySPMModel +from ...testing import assert_equal +from ..modelgen import SpecifySPMModel def test_SpecifySPMModel_inputs(): input_map = dict(concatenate_runs=dict(usedefault=True, @@ -32,8 +32,8 @@ def test_SpecifySPMModel_inputs(): ) inputs = SpecifySPMModel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SpecifySPMModel_outputs(): @@ -41,7 +41,7 @@ def test_SpecifySPMModel_outputs(): ) outputs = SpecifySPMModel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index cd3a266561..b8601014e1 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.modelgen import SpecifySparseModel +from ...testing import assert_equal +from ..modelgen import SpecifySparseModel def test_SpecifySparseModel_inputs(): input_map = dict(event_files=dict(mandatory=True, @@ -42,8 +42,8 @@ def test_SpecifySparseModel_inputs(): ) inputs = SpecifySparseModel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SpecifySparseModel_outputs(): @@ -53,7 +53,7 @@ def test_SpecifySparseModel_outputs(): ) outputs = SpecifySparseModel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_SplitROIs.py b/nipype/algorithms/tests/test_auto_SplitROIs.py index fa905d96fc..553f937a1c 100644 --- a/nipype/algorithms/tests/test_auto_SplitROIs.py +++ b/nipype/algorithms/tests/test_auto_SplitROIs.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import SplitROIs +from ...testing import assert_equal +from ..misc import SplitROIs def test_SplitROIs_inputs(): input_map = dict(in_file=dict(mandatory=True, @@ -10,8 +10,8 @@ def test_SplitROIs_inputs(): ) inputs = SplitROIs.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SplitROIs_outputs(): @@ -21,7 +21,7 @@ def test_SplitROIs_outputs(): ) outputs = SplitROIs.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index ad51cfdd2a..3f7f9ed11b 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.rapidart import StimulusCorrelation +from ...testing import assert_equal +from ..rapidart import StimulusCorrelation def test_StimulusCorrelation_inputs(): input_map = dict(concatenated_design=dict(mandatory=True, @@ -17,8 +17,8 @@ def test_StimulusCorrelation_inputs(): ) inputs = StimulusCorrelation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_StimulusCorrelation_outputs(): @@ -26,7 +26,7 @@ def test_StimulusCorrelation_outputs(): ) outputs = StimulusCorrelation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_TSNR.py b/nipype/algorithms/tests/test_auto_TSNR.py index e3a7fc13cd..1ea1bc6192 100644 --- a/nipype/algorithms/tests/test_auto_TSNR.py +++ b/nipype/algorithms/tests/test_auto_TSNR.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.algorithms.misc import TSNR +from ...testing import assert_equal +from ..misc import TSNR def test_TSNR_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -12,8 +12,8 @@ def test_TSNR_inputs(): ) inputs = TSNR.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TSNR_outputs(): @@ -24,7 +24,7 @@ def test_TSNR_outputs(): ) outputs = TSNR.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py new file mode 100644 index 0000000000..918a8eeb96 --- /dev/null +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -0,0 +1,36 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from ...testing import assert_equal +from ..mesh import WarpPoints + +def test_WarpPoints_inputs(): + input_map = dict(ignore_exception=dict(nohash=True, + usedefault=True, + ), + interp=dict(mandatory=True, + usedefault=True, + ), + out_points=dict(keep_extension=True, + name_source='points', + name_template='%s_warped', + output_name='out_points', + ), + points=dict(mandatory=True, + ), + warp=dict(mandatory=True, + ), + ) + inputs = WarpPoints.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(inputs.traits()[key], metakey), value + +def test_WarpPoints_outputs(): + output_map = dict(out_points=dict(), + ) + outputs = WarpPoints.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_icc_anova.py b/nipype/algorithms/tests/test_icc_anova.py index aac0758555..21b6db7eca 100644 --- a/nipype/algorithms/tests/test_icc_anova.py +++ b/nipype/algorithms/tests/test_icc_anova.py @@ -1,3 +1,4 @@ +from __future__ import division import numpy as np from nipype.testing import assert_equal from nipype.algorithms.icc import ICC_rep_anova @@ -18,4 +19,4 @@ def test_ICC_rep_anova(): yield assert_equal, round(icc, 2), 0.71 yield assert_equal, dfc, 3 yield assert_equal, dfe, 15 - yield assert_equal, r_var/(r_var + e_var), icc + yield assert_equal, r_var / (r_var + e_var), icc diff --git a/nipype/algorithms/tests/test_modelgen.py b/nipype/algorithms/tests/test_modelgen.py index 6dcca51f5f..4ebd7bd030 100644 --- a/nipype/algorithms/tests/test_modelgen.py +++ b/nipype/algorithms/tests/test_modelgen.py @@ -1,5 +1,7 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import division + from copy import deepcopy import os from shutil import rmtree @@ -85,7 +87,7 @@ def test_modelgen_spm_concat(): yield assert_equal, s.inputs.output_units, 'scans' s.inputs.subject_info = deepcopy(info) res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0])/6 + yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0]) / 6 # Test case for no concatenation with seconds as output units s.inputs.concatenate_runs = False s.inputs.subject_info = deepcopy(info) diff --git a/nipype/algorithms/tests/test_moments.py b/nipype/algorithms/tests/test_moments.py index 26f24207b1..b4d2c88993 100644 --- a/nipype/algorithms/tests/test_moments.py +++ b/nipype/algorithms/tests/test_moments.py @@ -126,7 +126,7 @@ def test_skew(): -0.5057854071 -2.415896554 -9.663571931 -5.714041661 -6.037933426 8.673756933 10.03557773 8.629816199 3.622185659 0.4716627142 -10.92515308 -3.705286841 -2.776089545 2.271920902 9.251504922 5.744980887 """ - with tempfile.NamedTemporaryFile(delete=True) as f: + with tempfile.NamedTemporaryFile(mode='w', delete=True) as f: f.write(data) f.flush() skewness = calc_moments(f.name, 3) diff --git a/nipype/algorithms/tests/test_normalize_tpms.py b/nipype/algorithms/tests/test_normalize_tpms.py index 1484874751..f74c8f4257 100644 --- a/nipype/algorithms/tests/test_normalize_tpms.py +++ b/nipype/algorithms/tests/test_normalize_tpms.py @@ -2,6 +2,7 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from builtins import range import os from shutil import rmtree from tempfile import mkdtemp diff --git a/nipype/algorithms/tests/test_rapidart.py b/nipype/algorithms/tests/test_rapidart.py index dfed3b6b90..1ba6414e29 100644 --- a/nipype/algorithms/tests/test_rapidart.py +++ b/nipype/algorithms/tests/test_rapidart.py @@ -1,5 +1,7 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import division + import numpy as np from ...testing import (assert_equal, assert_false, assert_true, @@ -76,7 +78,7 @@ def test_sc_populate_inputs(): intensity_values=None, spm_mat_file=None, concatenated_design=None) - yield assert_equal, sc.inputs.__dict__.keys(), inputs.__dict__.keys() + yield assert_equal, set(sc.inputs.__dict__.keys()), set(inputs.__dict__.keys()) def test_sc_output_filenames(): diff --git a/nipype/caching/__init__.py b/nipype/caching/__init__.py index 9c8b0d4d55..b6815e9724 100644 --- a/nipype/caching/__init__.py +++ b/nipype/caching/__init__.py @@ -1,2 +1,2 @@ -from nipype.caching.memory import Memory +from .memory import Memory diff --git a/nipype/caching/memory.py b/nipype/caching/memory.py index abb2cca6ba..4da6980a73 100644 --- a/nipype/caching/memory.py +++ b/nipype/caching/memory.py @@ -9,6 +9,9 @@ >>> os.chdir(datadir) """ +from __future__ import print_function +from builtins import object + import os import hashlib import pickle @@ -16,9 +19,9 @@ import shutil import glob -from nipype.interfaces.base import BaseInterface -from nipype.pipeline.engine import Node -from nipype.pipeline.utils import modify_paths +from ..interfaces.base import BaseInterface +from ..pipeline.engine import Node +from ..pipeline.utils import modify_paths ################################################################################ # PipeFunc object: callable interface to nipype.interface objects @@ -130,7 +133,7 @@ def rm_all_but(base_dir, dirs_to_keep, warn=False): dir_name = os.path.join(base_dir, dir_name) if os.path.exists(dir_name): if warn: - print 'removing directory: %s' % dir_name + print('removing directory: %s' % dir_name) shutil.rmtree(dir_name) @@ -288,7 +291,7 @@ def _clear_all_but(self, runs, warn=True): input. """ rm_all_but(self.base_dir, set(runs.keys()), warn=warn) - for dir_name, job_names in runs.iteritems(): + for dir_name, job_names in runs.items(): rm_all_but(os.path.join(self.base_dir, dir_name), job_names, warn=warn) diff --git a/nipype/external/cloghandler.py b/nipype/external/cloghandler.py index 9929db40d7..ec8eaab64d 100644 --- a/nipype/external/cloghandler.py +++ b/nipype/external/cloghandler.py @@ -43,6 +43,8 @@ """ +from builtins import range + __version__ = "$Id: cloghandler.py 6175 2009-11-02 18:40:35Z lowell $" __author__ = "Lowell Alleman" diff --git a/nipype/external/portalocker.py b/nipype/external/portalocker.py index 199d1b490e..25860c30e1 100644 --- a/nipype/external/portalocker.py +++ b/nipype/external/portalocker.py @@ -48,6 +48,8 @@ Version: $Id: portalocker.py 5474 2008-05-16 20:53:50Z lowell $ ''' +from __future__ import print_function +from __future__ import absolute_import __all__ = [ @@ -80,14 +82,14 @@ class LockException(Exception): LOCK_SH = fcntl.LOCK_SH LOCK_NB = fcntl.LOCK_NB else: - raise RuntimeError, 'PortaLocker only defined for nt and posix platforms' + raise RuntimeError('PortaLocker only defined for nt and posix platforms') if os.name == 'nt': def lock(file, flags): hfile = win32file._get_osfhandle(file.fileno()) try: win32file.LockFileEx(hfile, flags, 0, -0x10000, __overlapped) - except pywintypes.error, exc_value: + except pywintypes.error as exc_value: # error: (33, 'LockFileEx', 'The process cannot access the file because another process has locked a portion of the file.') if exc_value[0] == 33: raise LockException(LockException.LOCK_FAILED, exc_value[2]) @@ -99,7 +101,7 @@ def unlock(file): hfile = win32file._get_osfhandle(file.fileno()) try: win32file.UnlockFileEx(hfile, 0, -0x10000, __overlapped) - except pywintypes.error, exc_value: + except pywintypes.error as exc_value: if exc_value[0] == 158: # error: (158, 'UnlockFileEx', 'The segment is already unlocked.') # To match the 'posix' implementation, silently ignore this error @@ -112,7 +114,7 @@ def unlock(file): def lock(file, flags): try: fcntl.flock(file.fileno(), flags) - except IOError, exc_value: + except IOError as exc_value: # The exception code varies on different systems so we'll catch # every IO error raise LockException(*exc_value) @@ -125,7 +127,7 @@ def unlock(file): if __name__ == '__main__': from time import time, strftime, localtime import sys - import portalocker + from . import portalocker log = open('log.txt', 'a+') portalocker.lock(log, portalocker.LOCK_EX) @@ -133,7 +135,7 @@ def unlock(file): timestamp = strftime('%m/%d/%Y %H:%M:%S\n', localtime(time())) log.write( timestamp ) - print 'Wrote lines. Hit enter to release lock.' + print('Wrote lines. Hit enter to release lock.') dummy = sys.stdin.readline() log.close() diff --git a/nipype/external/provcopy.py b/nipype/external/provcopy.py index 59686f3b9b..cddf96c64f 100644 --- a/nipype/external/provcopy.py +++ b/nipype/external/provcopy.py @@ -9,15 +9,16 @@ @author: Trung Dong Huynh @copyright: University of Southampton 2013 ''' +from __future__ import absolute_import +from builtins import zip +from builtins import object import logging import datetime import json -import re import dateutil.parser import collections from collections import defaultdict -import six try: from rdflib.term import URIRef, BNode @@ -35,6 +36,8 @@ from ordereddict import OrderedDict logger = logging.getLogger(__name__) +from ..external.six import string_types + # # PROV record constants - PROV-DM LC # C1. Entities/Activities PROV_REC_ENTITY = 1 @@ -177,7 +180,7 @@ # Converting an attribute to the normal form for comparison purposes -_normalise_attributes = lambda attr: (unicode(attr[0]), unicode(attr[1])) +_normalise_attributes = lambda attr: (str(attr[0]), str(attr[1])) # Datatypes @@ -188,7 +191,7 @@ def _parse_xsd_dateTime(s): def _ensure_datetime(time): - if isinstance(time, six.string_types): + if isinstance(time, string_types): return _parse_xsd_dateTime(time) else: return time @@ -212,14 +215,14 @@ def parse_datatype(value, datatype): return DATATYPE_PARSERS[datatype](value) else: # No parser found for the given data type - raise Exception(u'No parser found for the data type <%s>' % unicode(datatype)) + raise Exception(u'No parser found for the data type <%s>' % str(datatype)) # Mappings for XSD datatypes to Python standard types XSD_DATATYPE_PARSERS = { - u"xsd:string": unicode, + u"xsd:string": str, u"xsd:double": float, - u"xsd:long": long, + u"xsd:long": int, u"xsd:int": int, u"xsd:boolean": bool, u"xsd:dateTime": parse_xsd_dateTime, @@ -228,27 +231,27 @@ def parse_datatype(value, datatype): def parse_xsd_types(value, datatype): # if the datatype is a QName, convert it to a Unicode string - datatype = unicode(datatype) + datatype = str(datatype) return XSD_DATATYPE_PARSERS[datatype](value) if datatype in XSD_DATATYPE_PARSERS else None def _ensure_multiline_string_triple_quoted(s): - format_str = u'"""%s"""' if isinstance(s, six.string_types) and '\n' in s else u'"%s"' + format_str = u'"""%s"""' if isinstance(s, string_types) and '\n' in s else u'"%s"' return format_str % s def encoding_PROV_N_value(value): - if isinstance(value, six.string_types): + if isinstance(value, string_types): return _ensure_multiline_string_triple_quoted(value) elif isinstance(value, datetime.datetime): return value.isoformat() elif isinstance(value, float): return u'"%f" %%%% xsd:float' % value else: - return unicode(value) + return str(value) -class AnonymousIDGenerator(): +class AnonymousIDGenerator(object): def __init__(self): self._cache = {} self._count = 0 @@ -277,7 +280,7 @@ def __unicode__(self): return self.provn_representation() def __str__(self): - return unicode(self).encode('utf-8') + return str(self).encode('utf-8') def __eq__(self, other): return self._value == other._value and self._datatype == other._datatype and self._langtag == other._langtag if isinstance(other, Literal) else False @@ -300,20 +303,20 @@ def has_no_langtag(self): def provn_representation(self): if self._langtag: # a language tag can only go with prov:InternationalizedString - return u'%s@%s' % (_ensure_multiline_string_triple_quoted(self._value), unicode(self._langtag)) + return u'%s@%s' % (_ensure_multiline_string_triple_quoted(self._value), str(self._langtag)) else: - return u'%s %%%% %s' % (_ensure_multiline_string_triple_quoted(self._value), unicode(self._datatype)) + return u'%s %%%% %s' % (_ensure_multiline_string_triple_quoted(self._value), str(self._datatype)) def json_representation(self): if self._langtag: # a language tag can only go with prov:InternationalizedString - return {'$': unicode(self._value), 'lang': self._langtag} + return {'$': str(self._value), 'lang': self._langtag} else: if isinstance(self._datatype, QName): - return {'$': unicode(self._value), 'type': unicode(self._datatype)} + return {'$': str(self._value), 'type': str(self._datatype)} else: # Assuming it is a valid identifier - return {'$': unicode(self._value), 'type': self._datatype.get_uri()} + return {'$': str(self._value), 'type': self._datatype.get_uri()} def rdf_representation(self): @@ -325,7 +328,7 @@ def rdf_representation(self): class Identifier(object): def __init__(self, uri): - self._uri = unicode(uri) # Ensure this is a unicode string + self._uri = str(uri) # Ensure this is a unicode string def get_uri(self): return self._uri @@ -334,7 +337,7 @@ def __unicode__(self): return self._uri def __str__(self): - return unicode(self).encode('utf-8') + return str(self).encode('utf-8') def __eq__(self, other): return self.get_uri() == other.get_uri() if isinstance(other, Identifier) else False @@ -370,7 +373,7 @@ def __unicode__(self): return self._str def __str__(self): - return unicode(self).encode('utf-8') + return str(self).encode('utf-8') def provn_representation(self): return u"'%s'" % self._str @@ -392,11 +395,11 @@ def get_uri(self): return self._uri def contains(self, identifier): - uri = identifier if isinstance(identifier, (str, unicode)) else (identifier.get_uri() if isinstance(identifier, Identifier) else None) + uri = identifier if isinstance(identifier, (str, string_types)) else (identifier.get_uri() if isinstance(identifier, Identifier) else None) return uri.startswith(self._uri) if uri else False def qname(self, identifier): - uri = identifier if isinstance(identifier, (str, unicode)) else (identifier.get_uri() if isinstance(identifier, Identifier) else None) + uri = identifier if isinstance(identifier, (str, string_types)) else (identifier.get_uri() if isinstance(identifier, Identifier) else None) if uri and uri.startswith(self._uri): return QName(self, uri[len(self._uri):]) else: @@ -441,7 +444,7 @@ def __init__(self, record_type, attribute, attribute_types): self.record_type = record_type self.attribute = attribute self.attribute_types = attribute_types - self.args += (PROV_N_MAP[record_type], unicode(attribute), attribute_types) + self.args += (PROV_N_MAP[record_type], str(attribute), attribute_types) def __str__(self): return 'Invalid attribute value: %s. %s expected' % (self.attribute, self.attribute_types) @@ -537,8 +540,8 @@ def _auto_literal_conversion(self, literal): if isinstance(literal, URIRef): return literal - if isinstance(literal, six.string_types): - return unicode(literal) + if isinstance(literal, string_types): + return str(literal) if isinstance(literal, Literal) and literal.has_no_langtag(): # try convert generic Literal object to Python standard type if possible @@ -553,7 +556,7 @@ def _auto_literal_conversion(self, literal): def parse_extra_attributes(self, extra_attributes): if isinstance(extra_attributes, dict): # Converting the dictionary into a list of tuples (i.e. attribute-value pairs) - extra_attributes = extra_attributes.items() + extra_attributes = list(extra_attributes.items()) attr_set = set((self._bundle.valid_identifier(attribute), self._auto_literal_conversion(value)) for attribute, value in extra_attributes) @@ -572,7 +575,7 @@ def add_attributes(self, attributes, extra_attributes): if self._attributes is None: self._attributes = attributes else: - self._attributes.update(dict((k, v) for k, v in attributes.iteritems() if v is not None)) + self._attributes.update(dict((k, v) for k, v in attributes.items() if v is not None)) self.add_extra_attributes(extra_attributes) def get_attributes(self): @@ -620,7 +623,7 @@ def _parse_attribute(self, attribute, attribute_types): attribute_types = (attribute_types,) # attempt to find an existing record having the same identifier - if any(map(lambda x: issubclass(x, ProvRecord), attribute_types)): + if any([issubclass(x, ProvRecord) for x in attribute_types]): record = self._parse_record(attribute, attribute_types) if record: return record @@ -679,7 +682,7 @@ def __eq__(self, other): if self._attributes and other._attributes: if len(self._attributes) != len(other._attributes): return False - for attr, value_a in self._attributes.items(): + for attr, value_a in list(self._attributes.items()): value_b = other._attributes[attr] if isinstance(value_a, ProvRecord) and value_a._identifier: if not (value_a._identifier == value_b._identifier): @@ -687,12 +690,12 @@ def __eq__(self, other): elif not (value_a == value_b): return False elif other._attributes and not self._attributes: - other_attrs = [(key, value) for key, value in other._attributes.items() if value is not None] + other_attrs = [(key, value) for key, value in list(other._attributes.items()) if value is not None] if other_attrs: # the other's attributes set is not empty. return False elif self._attributes and not other._attributes: - my_attrs = [(key, value) for key, value in self._attributes.items() if value is not None] + my_attrs = [(key, value) for key, value in list(self._attributes.items()) if value is not None] if my_attrs: # my attributes set is not empty. return False @@ -713,23 +716,23 @@ def __unicode__(self): return self.get_provn() def __str__(self): - return unicode(self).encode('utf-8') + return str(self).encode('utf-8') def get_provn(self, _indent_level=0): items = [] if self._identifier: - items.append(unicode(self._identifier)) + items.append(str(self._identifier)) if self._attributes: - for (attr, value) in self._attributes.items(): + for (attr, value) in list(self._attributes.items()): if value is None: items.append(u'-') else: if isinstance(value, ProvRecord): record_id = value.get_identifier() - items.append(unicode(record_id)) + items.append(str(record_id)) else: # Assuming this is a datetime or QName value - items.append(value.isoformat() if isinstance(value, datetime.datetime) else unicode(value)) + items.append(value.isoformat() if isinstance(value, datetime.datetime) else str(value)) if self._extra_attributes: extra = [] @@ -739,7 +742,7 @@ def get_provn(self, _indent_level=0): provn_represenation = value.provn_representation() except: provn_represenation = encoding_PROV_N_value(value) - extra.append(u'%s=%s' % (unicode(attr), provn_represenation)) + extra.append(u'%s=%s' % (str(attr), provn_represenation)) if extra: items.append(u'[%s]' % u', '.join(extra)) prov_n = u'%s(%s)' % (PROV_N_MAP[self.get_type()], u', '.join(items)) @@ -752,7 +755,7 @@ def rdf(self, graph=None, subj=None): # this method need a subject as relations may not have identifiers return graph if self._attributes: - for (attr, value) in self._attributes.items(): + for (attr, value) in list(self._attributes.items()): if value is None: continue pred = attr2rdf(attr) @@ -767,7 +770,7 @@ def rdf(self, graph=None, subj=None): try: # try if there is a RDF representation defined obj = value.rdf_representation() - except Exception, e: + except Exception as e: obj = RDFLiteral(value) if attr == PROV['location']: pred = PROV['atLocation'].rdf_representation() @@ -1283,13 +1286,13 @@ def __init__(self, namespaces={}, default_namespaces={PROV.get_prefix(): PROV, X self.add_namespaces(namespaces) def get_namespace(self, uri): - for namespace in self.values(): + for namespace in list(self.values()): if uri == namespace._uri: return namespace return None def get_registered_namespaces(self): - return self._namespaces.values() + return list(self._namespaces.values()) def set_default_namespace(self, uri): self._default = Namespace('', uri) @@ -1299,7 +1302,7 @@ def get_default_namespace(self): return self._default def add_namespace(self, namespace): - if namespace in self.values(): + if namespace in list(self.values()): # no need to do anything return if namespace in self._rename_map: @@ -1320,7 +1323,7 @@ def add_namespace(self, namespace): def add_namespaces(self, namespaces): if namespaces: - for prefix, uri in namespaces.items(): + for prefix, uri in list(namespaces.items()): ns = Namespace(prefix, uri) self.add_namespace(ns) @@ -1345,7 +1348,7 @@ def get_valid_identifier(self, identifier): else: # return the original identifier return identifier - elif isinstance(identifier, (str, unicode)): + elif isinstance(identifier, (str, string_types)): if identifier.startswith('_:'): return None elif ':' in identifier: @@ -1357,7 +1360,7 @@ def get_valid_identifier(self, identifier): else: # treat as a URI (with the first part as its scheme) # check if the URI can be compacted - for namespace in self.values(): + for namespace in list(self.values()): if identifier.startswith(namespace.get_uri()): # create a QName with the namespace return namespace[identifier.replace(namespace.get_uri(), '')] @@ -1383,7 +1386,7 @@ def _get_unused_prefix(self, original_prefix): return original_prefix count = 1 while True: - new_prefix = '_'.join((original_prefix, unicode(count))) + new_prefix = '_'.join((original_prefix, str(count))) if new_prefix in self: count += 1 else: @@ -1428,7 +1431,7 @@ def get_records(self, class_or_type_or_tuple=None): # Only returning asserted records results = [rec for rec in self._records if rec.is_asserted()] if class_or_type_or_tuple: - return filter(lambda rec: isinstance(rec, class_or_type_or_tuple), results) + return [rec for rec in results if isinstance(rec, class_or_type_or_tuple)] else: return results @@ -1520,7 +1523,7 @@ def _encode_JSON_container(self): rec_type = record.get_type() rec_label = PROV_N_MAP[rec_type] - identifier = unicode(real_or_anon_id(record)) + identifier = str(real_or_anon_id(record)) if rec_type == PROV_REC_BUNDLE: # encoding the sub-bundle @@ -1528,16 +1531,16 @@ def _encode_JSON_container(self): else: record_json = {} if record._attributes: - for (attr, value) in record._attributes.items(): + for (attr, value) in list(record._attributes.items()): if isinstance(value, ProvRecord): attr_record_id = real_or_anon_id(value) - record_json[PROV_ID_ATTRIBUTES_MAP[attr]] = unicode(attr_record_id) + record_json[PROV_ID_ATTRIBUTES_MAP[attr]] = str(attr_record_id) elif value is not None: # Assuming this is a datetime value - record_json[PROV_ID_ATTRIBUTES_MAP[attr]] = value.isoformat() if isinstance(value, datetime.datetime) else unicode(value) + record_json[PROV_ID_ATTRIBUTES_MAP[attr]] = value.isoformat() if isinstance(value, datetime.datetime) else str(value) if record._extra_attributes: for (attr, value) in record._extra_attributes: - attr_id = unicode(attr) + attr_id = str(attr) value_json = self._encode_json_representation(value) if attr_id in record_json: # Multi-value attribute @@ -1558,7 +1561,7 @@ def _encode_JSON_container(self): def _decode_JSON_container(self, jc): if u'prefix' in jc: prefixes = jc[u'prefix'] - for prefix, uri in prefixes.items(): + for prefix, uri in list(prefixes.items()): if prefix != 'default': self.add_namespace(Namespace(prefix, uri)) else: @@ -1569,7 +1572,7 @@ def _decode_JSON_container(self, jc): key=lambda tuple_rec: tuple_rec[0]) record_map = {} - _parse_attr_value = lambda value: record_map[value] if (isinstance(value, six.string_types) and value in record_map) else self._decode_json_representation(value) + _parse_attr_value = lambda value: record_map[value] if (isinstance(value, string_types) and value in record_map) else self._decode_json_representation(value) # Create all the records before setting their attributes for (record_type, identifier, content) in records: if record_type == PROV_REC_BUNDLE: @@ -1593,7 +1596,7 @@ def _decode_JSON_container(self, jc): extra_attributes = [] # Splitting PROV attributes and the others membership_extra_members = None # this is for the multiple-entity membership hack to come - for attr, value in element.items(): + for attr, value in list(element.items()): if attr in PROV_ATTRIBUTES_ID_MAP: attr_id = PROV_ATTRIBUTES_ID_MAP[attr] if isinstance(value, list): @@ -1675,7 +1678,7 @@ def rdf(self, graph=None): uri = self.get_identifier().rdf_representation() graph = Graph(graph.store, uri) - for prefix, namespace in self._namespaces.items(): + for prefix, namespace in list(self._namespaces.items()): graph.bind(prefix, namespace.get_uri()) for record in self._records: @@ -1748,11 +1751,11 @@ def __eq__(self, other): continue else: logger.debug("Equality (ProvBundle): Unequal PROV records:") - logger.debug("%s", unicode(record_a)) - logger.debug("%s", unicode(record_b)) + logger.debug("%s", str(record_a)) + logger.debug("%s", str(record_b)) return False else: - logger.debug("Equality (ProvBundle): Could not find a record with this identifier: %s", unicode(record_a._identifier)) + logger.debug("Equality (ProvBundle): Could not find a record with this identifier: %s", str(record_a._identifier)) return False else: # Manually look for the record @@ -1763,7 +1766,7 @@ def __eq__(self, other): found = True break if not found: - logger.debug("Equality (ProvBundle): Could not find this record: %s", unicode(record_a)) + logger.debug("Equality (ProvBundle): Could not find this record: %s", str(record_a)) return False return True @@ -1780,7 +1783,7 @@ def _add_record(self, record): if not merge_target._asserted and record._asserted: if record.__class__ in merge_target.get_allowed_types(): - for attribute_id, attribute in merge_target._infered_for._attributes.iteritems(): + for attribute_id, attribute in merge_target._infered_for._attributes.items(): if attribute == merge_target: merge_target._infered_for._attributes[attribute_id] = record self._records.remove(merge_target) diff --git a/nipype/external/six.py b/nipype/external/six.py index 21b0e8032f..ffa3fe166a 100644 --- a/nipype/external/six.py +++ b/nipype/external/six.py @@ -1,6 +1,6 @@ """Utilities for writing code that runs on Python 2 and 3""" -# Copyright (c) 2010-2014 Benjamin Peterson +# Copyright (c) 2010-2015 Benjamin Peterson # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -23,12 +23,13 @@ from __future__ import absolute_import import functools +import itertools import operator import sys import types __author__ = "Benjamin Peterson " -__version__ = "1.8.0" +__version__ = "1.9.0" # Useful for very coarse version differentiation. @@ -88,8 +89,12 @@ def __init__(self, name): def __get__(self, obj, tp): result = self._resolve() setattr(obj, self.name, result) # Invokes __set__. - # This is a bit ugly, but it avoids running this again. - delattr(obj.__class__, self.name) + try: + # This is a bit ugly, but it avoids running this again by + # removing this descriptor. + delattr(obj.__class__, self.name) + except AttributeError: + pass return result @@ -554,6 +559,12 @@ def iteritems(d, **kw): def iterlists(d, **kw): return iter(d.lists(**kw)) + + viewkeys = operator.methodcaller("keys") + + viewvalues = operator.methodcaller("values") + + viewitems = operator.methodcaller("items") else: def iterkeys(d, **kw): return iter(d.iterkeys(**kw)) @@ -567,6 +578,12 @@ def iteritems(d, **kw): def iterlists(d, **kw): return iter(d.iterlists(**kw)) + viewkeys = operator.methodcaller("viewkeys") + + viewvalues = operator.methodcaller("viewvalues") + + viewitems = operator.methodcaller("viewitems") + _add_doc(iterkeys, "Return an iterator over the keys of a dictionary.") _add_doc(itervalues, "Return an iterator over the values of a dictionary.") _add_doc(iteritems, @@ -593,6 +610,9 @@ def int2byte(i): import io StringIO = io.StringIO BytesIO = io.BytesIO + _assertCountEqual = "assertCountEqual" + _assertRaisesRegex = "assertRaisesRegex" + _assertRegex = "assertRegex" else: def b(s): return s @@ -605,14 +625,28 @@ def byte2int(bs): return ord(bs[0]) def indexbytes(buf, i): return ord(buf[i]) - def iterbytes(buf): - return (ord(byte) for byte in buf) + iterbytes = functools.partial(itertools.imap, ord) import StringIO StringIO = BytesIO = StringIO.StringIO + _assertCountEqual = "assertItemsEqual" + _assertRaisesRegex = "assertRaisesRegexp" + _assertRegex = "assertRegexpMatches" _add_doc(b, """Byte literal""") _add_doc(u, """Text literal""") +def assertCountEqual(self, *args, **kwargs): + return getattr(self, _assertCountEqual)(*args, **kwargs) + + +def assertRaisesRegex(self, *args, **kwargs): + return getattr(self, _assertRaisesRegex)(*args, **kwargs) + + +def assertRegex(self, *args, **kwargs): + return getattr(self, _assertRegex)(*args, **kwargs) + + if PY3: exec_ = getattr(moves.builtins, "exec") @@ -643,6 +677,21 @@ def exec_(_code_, _globs_=None, _locs_=None): """) +if sys.version_info[:2] == (3, 2): + exec_("""def raise_from(value, from_value): + if from_value is None: + raise value + raise value from from_value +""") +elif sys.version_info[:2] > (3, 2): + exec_("""def raise_from(value, from_value): + raise value from from_value +""") +else: + def raise_from(value, from_value): + raise value + + print_ = getattr(moves.builtins, "print", None) if print_ is None: def print_(*args, **kwargs): @@ -697,6 +746,14 @@ def write(data): write(sep) write(arg) write(end) +if sys.version_info[:2] < (3, 3): + _print = print_ + def print_(*args, **kwargs): + fp = kwargs.get("file", sys.stdout) + flush = kwargs.pop("flush", False) + _print(*args, **kwargs) + if flush and fp is not None: + fp.flush() _add_doc(reraise, """Reraise an exception.""") @@ -704,7 +761,7 @@ def write(data): def wraps(wrapped, assigned=functools.WRAPPER_ASSIGNMENTS, updated=functools.WRAPPER_UPDATES): def wrapper(f): - f = functools.wraps(wrapped)(f) + f = functools.wraps(wrapped, assigned, updated)(f) f.__wrapped__ = wrapped return f return wrapper @@ -737,6 +794,25 @@ def wrapper(cls): return metaclass(cls.__name__, cls.__bases__, orig_vars) return wrapper + +def python_2_unicode_compatible(klass): + """ + A decorator that defines __unicode__ and __str__ methods under Python 2. + Under Python 3 it does nothing. + + To support Python 2 and 3 with a single code base, define a __str__ method + returning text and apply this decorator to the class. + """ + if PY2: + if '__str__' not in klass.__dict__: + raise ValueError("@python_2_unicode_compatible cannot be applied " + "to %s because it doesn't define __str__()." % + klass.__name__) + klass.__unicode__ = klass.__str__ + klass.__str__ = lambda self: self.__unicode__().encode('utf-8') + return klass + + # Complete the moves implementation. # This code is at the end of this module to speed up module loading. # Turn this module into a package. diff --git a/nipype/fixes/numpy/testing/noseclasses.py b/nipype/fixes/numpy/testing/noseclasses.py index 0a1bd711f4..a7b4c6bad0 100644 --- a/nipype/fixes/numpy/testing/noseclasses.py +++ b/nipype/fixes/numpy/testing/noseclasses.py @@ -1,3 +1,5 @@ +from __future__ import absolute_import +from builtins import object # These classes implement a doctest runner plugin for nose, a "known failure" # error class, and a customized TestProgram for NumPy. @@ -14,7 +16,7 @@ from nose.plugins.base import Plugin from nose.util import src import numpy -from nosetester import get_package_name +from .nosetester import get_package_name import inspect # Some of the classes in this module begin with 'Numpy' to clearly distinguish @@ -35,7 +37,7 @@ def _from_module(self, module, object): return True elif inspect.isfunction(object): #print '_fm C2' # dbg - return module.__dict__ is object.func_globals + return module.__dict__ is object.__globals__ elif inspect.isbuiltin(object): #print '_fm C2-1' # dbg return module.__name__ == object.__module__ @@ -48,7 +50,7 @@ def _from_module(self, module, object): # to make by extension code writers, having this safety in place # isn't such a bad idea #print '_fm C3-1' # dbg - return module.__name__ == object.im_class.__module__ + return module.__name__ == object.__self__.__class__.__module__ elif inspect.getmodule(object) is not None: #print '_fm C4' # dbg #print 'C4 mod',module,'obj',object # dbg @@ -81,7 +83,7 @@ def _find(self, tests, obj, name, module, source_lines, globs, seen): # Look for tests in a module's contained objects. if ismodule(obj) and self._recurse: - for valname, val in obj.__dict__.items(): + for valname, val in list(obj.__dict__.items()): valname1 = '%s.%s' % (name, valname) if ( (isroutine(val) or isclass(val)) and self._from_module(module, val) ): @@ -93,14 +95,14 @@ def _find(self, tests, obj, name, module, source_lines, globs, seen): # Look for tests in a class's contained objects. if isclass(obj) and self._recurse: #print 'RECURSE into class:',obj # dbg - for valname, val in obj.__dict__.items(): + for valname, val in list(obj.__dict__.items()): #valname1 = '%s.%s' % (name, valname) # dbg #print 'N',name,'VN:',valname,'val:',str(val)[:77] # dbg # Special handling for staticmethod/classmethod. if isinstance(val, staticmethod): val = getattr(obj, valname) if isinstance(val, classmethod): - val = getattr(obj, valname).im_func + val = getattr(obj, valname).__func__ # Recurse to methods, properties, and nested classes. if ((isfunction(val) or isclass(val) or diff --git a/nipype/fixes/numpy/testing/nosetester.py b/nipype/fixes/numpy/testing/nosetester.py index 735a5be749..7ea071f03c 100644 --- a/nipype/fixes/numpy/testing/nosetester.py +++ b/nipype/fixes/numpy/testing/nosetester.py @@ -4,9 +4,16 @@ This module implements ``test()`` and ``bench()`` functions for NumPy modules. """ + +from __future__ import print_function +from __future__ import absolute_import +from builtins import object + import os import sys -from nipype.external import six + +from ....external.six import string_types + def get_package_name(filepath): """ @@ -167,7 +174,7 @@ def _test_argv(self, label, verbose, extra_argv): ''' argv = [__file__, self.package_path, '-s'] if label and label != 'full': - if not isinstance(label, six.string_types): + if not isinstance(label, string_types): raise TypeError('Selection label should be a string') if label == 'fast': label = 'not slow' @@ -181,19 +188,19 @@ def _show_system_info(self): nose = import_nose() import numpy - print "NumPy version %s" % numpy.__version__ + print("NumPy version %s" % numpy.__version__) npdir = os.path.dirname(numpy.__file__) - print "NumPy is installed in %s" % npdir + print("NumPy is installed in %s" % npdir) if 'scipy' in self.package_name: import scipy - print "SciPy version %s" % scipy.__version__ + print("SciPy version %s" % scipy.__version__) spdir = os.path.dirname(scipy.__file__) - print "SciPy is installed in %s" % spdir + print("SciPy is installed in %s" % spdir) pyversion = sys.version.replace('\n','') - print "Python version %s" % pyversion - print "nose version %d.%d.%d" % nose.__versioninfo__ + print("Python version %s" % pyversion) + print("nose version %d.%d.%d" % nose.__versioninfo__) def _get_custom_doctester(self): """ Return instantiated plugin for doctests @@ -202,7 +209,7 @@ def _get_custom_doctester(self): A return value of None means use the nose builtin doctest plugin """ - from noseclasses import NumpyDoctest + from .noseclasses import NumpyDoctest return NumpyDoctest() def prepare_test_args(self, label='fast', verbose=1, extra_argv=None, @@ -231,7 +238,7 @@ def prepare_test_args(self, label='fast', verbose=1, extra_argv=None, '--cover-tests', '--cover-inclusive', '--cover-erase'] # construct list of plugins import nose.plugins.builtin - from noseclasses import KnownFailure, Unplugger + from .noseclasses import KnownFailure, Unplugger plugins = [KnownFailure()] plugins += [p() for p in nose.plugins.builtin.plugins] # add doctesting if required @@ -310,13 +317,13 @@ def test(self, label='fast', verbose=1, extra_argv=None, doctests=False, # cap verbosity at 3 because nose becomes *very* verbose beyond that verbose = min(verbose, 3) - import utils + from . import utils utils.verbose = verbose if doctests: - print "Running unit tests and doctests for %s" % self.package_name + print("Running unit tests and doctests for %s" % self.package_name) else: - print "Running unit tests for %s" % self.package_name + print("Running unit tests for %s" % self.package_name) self._show_system_info() @@ -326,7 +333,7 @@ def test(self, label='fast', verbose=1, extra_argv=None, doctests=False, argv, plugins = self.prepare_test_args(label, verbose, extra_argv, doctests, coverage) - from noseclasses import NumpyTestProgram + from .noseclasses import NumpyTestProgram t = NumpyTestProgram(argv=argv, exit=False, plugins=plugins) return t.result @@ -386,7 +393,7 @@ def bench(self, label='fast', verbose=1, extra_argv=None): """ - print "Running benchmarks for %s" % self.package_name + print("Running benchmarks for %s" % self.package_name) self._show_system_info() argv = self._test_argv(label, verbose, extra_argv) @@ -396,7 +403,7 @@ def bench(self, label='fast', verbose=1, extra_argv=None): nose = import_nose() # get plugin to disable doctests - from noseclasses import Unplugger + from .noseclasses import Unplugger add_plugins = [Unplugger('doctest')] return nose.run(argv=argv, addplugins=add_plugins) diff --git a/nipype/info.py b/nipype/info.py index 78f654a7cd..24f2b3500d 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -12,6 +12,7 @@ _version_micro = 0 _version_extra = '-dev' # Remove -dev for release + def get_nipype_gitversion(): """Nipype version as reported by the last commit in git @@ -38,7 +39,7 @@ def get_nipype_gitversion(): except Exception: pass else: - ver = o.strip().split('-')[-1] + ver = o.decode().strip().split('-')[-1] return ver if '-dev' in _version_extra: @@ -107,6 +108,8 @@ def get_nipype_gitversion(): TRAITS_MIN_VERSION = '4.3' DATEUTIL_MIN_VERSION = '1.5' NOSE_MIN_VERSION = '1.2' +FUTURE_MIN_VERSION = '0.15.2' +SIMPLEJSON_MIN_VERSION = '3.8.0' NAME = 'nipype' MAINTAINER = "nipype developers" @@ -126,18 +129,13 @@ def get_nipype_gitversion(): ISRELEASE = _version_extra == '' VERSION = __version__ PROVIDES = ['nipype'] -REQUIRES = ["nibabel (>=%s)" % NIBABEL_MIN_VERSION, - "networkx (>=%s)" % NETWORKX_MIN_VERSION, - "numpy (>=%s)" % NUMPY_MIN_VERSION, - "python-dateutil (>=%s)" % DATEUTIL_MIN_VERSION, - "scipy (>=%s)" % SCIPY_MIN_VERSION, - "traits (>=%s)" % TRAITS_MIN_VERSION, - "nose (>=%s)" % NOSE_MIN_VERSION] REQUIRES = ["nibabel>=%s" % NIBABEL_MIN_VERSION, "networkx>=%s" % NETWORKX_MIN_VERSION, "numpy>=%s" % NUMPY_MIN_VERSION, "python-dateutil>=%s" % DATEUTIL_MIN_VERSION, "scipy>=%s" % SCIPY_MIN_VERSION, "traits>=%s" % TRAITS_MIN_VERSION, - "nose>=%s" % NOSE_MIN_VERSION] + "nose>=%s" % NOSE_MIN_VERSION, + "future>=%s" % FUTURE_MIN_VERSION, + "simplejson>=%s" % SIMPLEJSON_MIN_VERSION] STATUS = 'stable' diff --git a/nipype/interfaces/__init__.py b/nipype/interfaces/__init__.py index 861ebcd739..c9ff7936ba 100644 --- a/nipype/interfaces/__init__.py +++ b/nipype/interfaces/__init__.py @@ -5,7 +5,9 @@ Requires Packages to be installed """ + +from __future__ import absolute_import __docformat__ = 'restructuredtext' -from io import DataGrabber, DataSink, SelectFiles -from utility import IdentityInterface, Rename, Function, Select, Merge +from .io import DataGrabber, DataSink, SelectFiles +from .utility import IdentityInterface, Rename, Function, Select, Merge diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index bd2eeed948..c702c8cc78 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -2,6 +2,8 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Provide interface to AFNI commands.""" +from builtins import object + import os import warnings @@ -11,7 +13,6 @@ CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec) warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class Info(object): @@ -93,7 +94,7 @@ def standard_image(img_name): class AFNICommandInputSpec(CommandLineInputSpec): - outputtype = traits.Enum('AFNI', Info.ftypes.keys(), + outputtype = traits.Enum('AFNI', list(Info.ftypes.keys()), desc='AFNI output filetype') out_file = File(name_template="%s_afni", desc='output image file name', argstr='-prefix %s', @@ -151,7 +152,7 @@ def _overload_extension(self, value, name=None): def _list_outputs(self): outputs = super(AFNICommand, self)._list_outputs() metadata = dict(name_source=lambda t: t is not None) - out_names = self.inputs.traits(**metadata).keys() + out_names = list(self.inputs.traits(**metadata).keys()) if out_names: for name in out_names: if outputs[name]: diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index ea7256ac77..40a6f40bc4 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -13,17 +13,14 @@ import os import re +from .base import AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec +from ..base import CommandLineInputSpec, CommandLine, OutputMultiPath from ..base import (Directory, TraitedSpec, traits, isdefined, File, InputMultiPath, Undefined) from ...utils.filemanip import (load_json, save_json, split_filename) -from nipype.utils.filemanip import fname_presuffix -from .base import AFNICommand, AFNICommandInputSpec,\ - AFNICommandOutputSpec -from nipype.interfaces.base import CommandLineInputSpec, CommandLine,\ - OutputMultiPath +from ...utils.filemanip import fname_presuffix warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class To3DInputSpec(AFNICommandInputSpec): @@ -1852,7 +1849,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None): m = re.search(pattern, line) if m: d = m.groupdict() - for k in d.keys(): + for k in list(d.keys()): d[k] = int(d[k]) outputs.set(**d) outputs.set(out_file=self._gen_filename('out_file')) diff --git a/nipype/interfaces/afni/svm.py b/nipype/interfaces/afni/svm.py index 58f2d8172c..492ebc10a9 100644 --- a/nipype/interfaces/afni/svm.py +++ b/nipype/interfaces/afni/svm.py @@ -23,7 +23,6 @@ OutputMultiPath warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class SVMTrainInputSpec(AFNICommandInputSpec): #training options diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index bce966ab42..14769735dd 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.base import AFNICommand +from ....testing import assert_equal +from ..base import AFNICommand def test_AFNICommand_inputs(): input_map = dict(args=dict(argstr='%s', @@ -21,7 +21,7 @@ def test_AFNICommand_inputs(): ) inputs = AFNICommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 348bc43c5f..96334c4a20 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import AFNItoNIFTI +from ....testing import assert_equal +from ..preprocess import AFNItoNIFTI def test_AFNItoNIFTI_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_AFNItoNIFTI_inputs(): ) inputs = AFNItoNIFTI.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AFNItoNIFTI_outputs(): @@ -35,7 +35,7 @@ def test_AFNItoNIFTI_outputs(): ) outputs = AFNItoNIFTI.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 1c5d408bd5..6f30731692 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Allineate +from ....testing import assert_equal +from ..preprocess import Allineate def test_Allineate_inputs(): input_map = dict(args=dict(argstr='%s', @@ -106,8 +106,8 @@ def test_Allineate_inputs(): ) inputs = Allineate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Allineate_outputs(): @@ -116,7 +116,7 @@ def test_Allineate_outputs(): ) outputs = Allineate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index c3b2cc0305..312ab7ef90 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import AutoTcorrelate +from ....testing import assert_equal +from ..preprocess import AutoTcorrelate def test_AutoTcorrelate_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_AutoTcorrelate_inputs(): ) inputs = AutoTcorrelate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AutoTcorrelate_outputs(): @@ -47,7 +47,7 @@ def test_AutoTcorrelate_outputs(): ) outputs = AutoTcorrelate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index 8898b192bf..184956660c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Autobox +from ....testing import assert_equal +from ..preprocess import Autobox def test_Autobox_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_Autobox_inputs(): ) inputs = Autobox.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Autobox_outputs(): @@ -43,7 +43,7 @@ def test_Autobox_outputs(): ) outputs = Autobox.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index 35197800cf..514559fad6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Automask +from ....testing import assert_equal +from ..preprocess import Automask def test_Automask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_Automask_inputs(): ) inputs = Automask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Automask_outputs(): @@ -46,7 +46,7 @@ def test_Automask_outputs(): ) outputs = Automask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index ccc03c0d7c..bf4e819284 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Bandpass +from ....testing import assert_equal +from ..preprocess import Bandpass def test_Bandpass_inputs(): input_map = dict(args=dict(argstr='%s', @@ -61,8 +61,8 @@ def test_Bandpass_inputs(): ) inputs = Bandpass.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Bandpass_outputs(): @@ -70,7 +70,7 @@ def test_Bandpass_outputs(): ) outputs = Bandpass.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index 8ade0fc3f8..a911469623 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import BlurInMask +from ....testing import assert_equal +from ..preprocess import BlurInMask def test_BlurInMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_BlurInMask_inputs(): ) inputs = BlurInMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BlurInMask_outputs(): @@ -52,7 +52,7 @@ def test_BlurInMask_outputs(): ) outputs = BlurInMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index aba21056fe..6c423a2232 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import BrickStat +from ....testing import assert_equal +from ..preprocess import BrickStat def test_BrickStat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_BrickStat_inputs(): ) inputs = BrickStat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BrickStat_outputs(): @@ -40,7 +40,7 @@ def test_BrickStat_outputs(): ) outputs = BrickStat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index 00423715c4..b33fc3de88 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Calc +from ....testing import assert_equal +from ..preprocess import Calc def test_Calc_inputs(): input_map = dict(args=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_Calc_inputs(): ) inputs = Calc.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Calc_outputs(): @@ -51,7 +51,7 @@ def test_Calc_outputs(): ) outputs = Calc.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index b9d7741d63..c82385085e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Copy +from ....testing import assert_equal +from ..preprocess import Copy def test_Copy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_Copy_inputs(): ) inputs = Copy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Copy_outputs(): @@ -36,7 +36,7 @@ def test_Copy_outputs(): ) outputs = Copy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index f5ed23389e..51590348de 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Despike +from ....testing import assert_equal +from ..preprocess import Despike def test_Despike_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_Despike_inputs(): ) inputs = Despike.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Despike_outputs(): @@ -35,7 +35,7 @@ def test_Despike_outputs(): ) outputs = Despike.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 07385f8a8d..b066a58b88 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Detrend +from ....testing import assert_equal +from ..preprocess import Detrend def test_Detrend_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_Detrend_inputs(): ) inputs = Detrend.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Detrend_outputs(): @@ -35,7 +35,7 @@ def test_Detrend_outputs(): ) outputs = Detrend.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 6a9235994b..3f9ad93ec5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Eval +from ....testing import assert_equal +from ..preprocess import Eval def test_Eval_inputs(): input_map = dict(args=dict(argstr='%s', @@ -44,8 +44,8 @@ def test_Eval_inputs(): ) inputs = Eval.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Eval_outputs(): @@ -53,7 +53,7 @@ def test_Eval_outputs(): ) outputs = Eval.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index 19ba24c620..a926568c3a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Fim +from ....testing import assert_equal +from ..preprocess import Fim def test_Fim_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_Fim_inputs(): ) inputs = Fim.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Fim_outputs(): @@ -45,7 +45,7 @@ def test_Fim_outputs(): ) outputs = Fim.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 7d80605dcf..0ae0aec8bf 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Fourier +from ....testing import assert_equal +from ..preprocess import Fourier def test_Fourier_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_Fourier_inputs(): ) inputs = Fourier.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Fourier_outputs(): @@ -43,7 +43,7 @@ def test_Fourier_outputs(): ) outputs = Fourier.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index 2114c6a072..d85d2ad213 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Maskave +from ....testing import assert_equal +from ..preprocess import Maskave def test_Maskave_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_Maskave_inputs(): ) inputs = Maskave.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Maskave_outputs(): @@ -43,7 +43,7 @@ def test_Maskave_outputs(): ) outputs = Maskave.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 15a42ad2a9..567f9d50d8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Means +from ....testing import assert_equal +from ..preprocess import Means def test_Means_inputs(): input_map = dict(args=dict(argstr='%s', @@ -44,8 +44,8 @@ def test_Means_inputs(): ) inputs = Means.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Means_outputs(): @@ -53,7 +53,7 @@ def test_Means_outputs(): ) outputs = Means.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index ae870c13eb..2513765f4f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Merge +from ....testing import assert_equal +from ..preprocess import Merge def test_Merge_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_Merge_inputs(): ) inputs = Merge.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Merge_outputs(): @@ -40,7 +40,7 @@ def test_Merge_outputs(): ) outputs = Merge.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 11562fc00a..5a72acb63b 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import ROIStats +from ....testing import assert_equal +from ..preprocess import ROIStats def test_ROIStats_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_ROIStats_inputs(): ) inputs = ROIStats.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ROIStats_outputs(): @@ -40,7 +40,7 @@ def test_ROIStats_outputs(): ) outputs = ROIStats.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index 3480ec2588..abd12546b4 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Refit +from ....testing import assert_equal +from ..preprocess import Refit def test_Refit_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_Refit_inputs(): ) inputs = Refit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Refit_outputs(): @@ -46,7 +46,7 @@ def test_Refit_outputs(): ) outputs = Refit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 314e5a5134..be5534f3de 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Resample +from ....testing import assert_equal +from ..preprocess import Resample def test_Resample_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_Resample_inputs(): ) inputs = Resample.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Resample_outputs(): @@ -43,7 +43,7 @@ def test_Resample_outputs(): ) outputs = Resample.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 76f3bf5c3d..5c9729e83b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Retroicor +from ....testing import assert_equal +from ..preprocess import Retroicor def test_Retroicor_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_Retroicor_inputs(): ) inputs = Retroicor.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Retroicor_outputs(): @@ -55,7 +55,7 @@ def test_Retroicor_outputs(): ) outputs = Retroicor.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 2a600ab1a2..86cc47f6d7 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.svm import SVMTest +from ....testing import assert_equal +from ..svm import SVMTest def test_SVMTest_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_SVMTest_inputs(): ) inputs = SVMTest.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SVMTest_outputs(): @@ -47,7 +47,7 @@ def test_SVMTest_outputs(): ) outputs = SVMTest.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index b50cae8bf6..9006b45fb5 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.svm import SVMTrain +from ....testing import assert_equal +from ..svm import SVMTrain def test_SVMTrain_inputs(): input_map = dict(alphas=dict(argstr='-alpha %s', @@ -57,8 +57,8 @@ def test_SVMTrain_inputs(): ) inputs = SVMTrain.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SVMTrain_outputs(): @@ -68,7 +68,7 @@ def test_SVMTrain_outputs(): ) outputs = SVMTrain.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index 2958d9a2b3..2bcdb7a6b5 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import SkullStrip +from ....testing import assert_equal +from ..preprocess import SkullStrip def test_SkullStrip_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_SkullStrip_inputs(): ) inputs = SkullStrip.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SkullStrip_outputs(): @@ -35,7 +35,7 @@ def test_SkullStrip_outputs(): ) outputs = SkullStrip.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 3eac3044be..47aac8af8a 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import TCat +from ....testing import assert_equal +from ..preprocess import TCat def test_TCat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_TCat_inputs(): ) inputs = TCat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TCat_outputs(): @@ -38,7 +38,7 @@ def test_TCat_outputs(): ) outputs = TCat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index 7b83fe1780..6de2ba4f07 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import TCorr1D +from ....testing import assert_equal +from ..preprocess import TCorr1D def test_TCorr1D_inputs(): input_map = dict(args=dict(argstr='%s', @@ -47,8 +47,8 @@ def test_TCorr1D_inputs(): ) inputs = TCorr1D.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TCorr1D_outputs(): @@ -56,7 +56,7 @@ def test_TCorr1D_outputs(): ) outputs = TCorr1D.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 4566f4456e..d2185e3641 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import TCorrMap +from ....testing import assert_equal +from ..preprocess import TCorrMap def test_TCorrMap_inputs(): input_map = dict(absolute_threshold=dict(argstr='-Thresh %f %s', @@ -102,8 +102,8 @@ def test_TCorrMap_inputs(): ) inputs = TCorrMap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TCorrMap_outputs(): @@ -123,7 +123,7 @@ def test_TCorrMap_outputs(): ) outputs = TCorrMap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index 5de2f44ce3..f0b9000213 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import TCorrelate +from ....testing import assert_equal +from ..preprocess import TCorrelate def test_TCorrelate_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_TCorrelate_inputs(): ) inputs = TCorrelate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TCorrelate_outputs(): @@ -46,7 +46,7 @@ def test_TCorrelate_outputs(): ) outputs = TCorrelate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index aefad226bb..b7252feef8 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import TShift +from ....testing import assert_equal +from ..preprocess import TShift def test_TShift_inputs(): input_map = dict(args=dict(argstr='%s', @@ -44,8 +44,8 @@ def test_TShift_inputs(): ) inputs = TShift.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TShift_outputs(): @@ -53,7 +53,7 @@ def test_TShift_outputs(): ) outputs = TShift.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index dc15259fad..8a82a42cc6 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import TStat +from ....testing import assert_equal +from ..preprocess import TStat def test_TStat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_TStat_inputs(): ) inputs = TStat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TStat_outputs(): @@ -39,7 +39,7 @@ def test_TStat_outputs(): ) outputs = TStat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 44f97fd607..7e47b9c9e4 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import To3D +from ....testing import assert_equal +from ..preprocess import To3D def test_To3D_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_To3D_inputs(): ) inputs = To3D.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_To3D_outputs(): @@ -44,7 +44,7 @@ def test_To3D_outputs(): ) outputs = To3D.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index eb30e06286..784715dc32 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Volreg +from ....testing import assert_equal +from ..preprocess import Volreg def test_Volreg_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_Volreg_inputs(): ) inputs = Volreg.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Volreg_outputs(): @@ -66,7 +66,7 @@ def test_Volreg_outputs(): ) outputs = Volreg.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index 1e4e1f99f7..4d7ba9ec22 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import Warp +from ....testing import assert_equal +from ..preprocess import Warp def test_Warp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_Warp_inputs(): ) inputs = Warp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Warp_outputs(): @@ -51,7 +51,7 @@ def test_Warp_outputs(): ) outputs = Warp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index f755ddaeb9..998bfe3d97 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.afni.preprocess import ZCutUp +from ....testing import assert_equal +from ..preprocess import ZCutUp def test_ZCutUp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_ZCutUp_inputs(): ) inputs = ZCutUp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ZCutUp_outputs(): @@ -37,7 +37,7 @@ def test_ZCutUp_outputs(): ) outputs = ZCutUp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/legacy.py b/nipype/interfaces/ants/legacy.py index 13b01d0d88..84cedf5f20 100644 --- a/nipype/interfaces/ants/legacy.py +++ b/nipype/interfaces/ants/legacy.py @@ -10,14 +10,18 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) >>> os.chdir(datadir) """ -# Local imports -from ..base import (TraitedSpec, File, traits, InputMultiPath, - isdefined) -from ...utils.filemanip import split_filename -from .base import ANTSCommand, ANTSCommandInputSpec + +from builtins import range + import os from glob import glob -from nipype.interfaces.base import OutputMultiPath + + +from .base import ANTSCommand, ANTSCommandInputSpec +from ..base import (TraitedSpec, File, traits, InputMultiPath, + isdefined, OutputMultiPath) +from ...utils.filemanip import split_filename + class antsIntroductionInputSpec(ANTSCommandInputSpec): dimension = traits.Enum(3, 2, argstr='-d %d', usedefault=True, diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index 2e1c23377c..28a4bb5df3 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -7,6 +7,8 @@ >>> os.chdir(datadir) """ +from builtins import range + from ..base import (TraitedSpec, File, traits, InputMultiPath) from .base import ANTSCommand, ANTSCommandInputSpec import os @@ -379,7 +381,7 @@ class Registration(ANTSCommand): """ Examples -------- - >>> import copy + >>> import copy, pprint >>> from nipype.interfaces.ants import Registration >>> reg = Registration() >>> reg.inputs.fixed_image = 'fixed1.nii' @@ -412,7 +414,7 @@ class Registration(ANTSCommand): >>> reg1.inputs.winsorize_lower_quantile = 0.025 >>> reg1.cmdline 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.025, 1.0 ] --write-composite-transform 1' - >>> reg1.run() #doctest: +SKIP + >>> reg1.run() # doctest: +SKIP >>> reg2 = copy.deepcopy(reg) >>> reg2.inputs.winsorize_upper_quantile = 0.975 @@ -442,16 +444,33 @@ class Registration(ANTSCommand): >>> reg4.inputs.initialize_transforms_per_stage = True >>> reg4.inputs.collapse_output_transforms = True >>> outputs = reg4._list_outputs() - >>> print outputs #doctest: +ELLIPSIS - {'reverse_invert_flags': [], 'inverse_composite_transform': '.../nipype/testing/data/output_InverseComposite.h5', 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz', 'inverse_warped_image': , 'forward_invert_flags': [], 'reverse_transforms': [], 'save_state': , 'composite_transform': '.../nipype/testing/data/output_Composite.h5', 'forward_transforms': []} + >>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE + {'composite_transform': '.../nipype/testing/data/output_Composite.h5', + 'forward_invert_flags': [], + 'forward_transforms': [], + 'inverse_composite_transform': '.../nipype/testing/data/output_InverseComposite.h5', + 'inverse_warped_image': , + 'reverse_invert_flags': [], + 'reverse_transforms': [], + 'save_state': , + 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz'} >>> # Test collapse transforms flag >>> reg4b = copy.deepcopy(reg4) >>> reg4b.inputs.write_composite_transform = False >>> outputs = reg4b._list_outputs() - >>> print outputs #doctest: +ELLIPSIS - {'reverse_invert_flags': [True, False], 'inverse_composite_transform': , 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz', 'inverse_warped_image': , 'forward_invert_flags': [False, False], 'reverse_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', '.../nipype/testing/data/output_1InverseWarp.nii.gz'], 'save_state': , 'composite_transform': , 'forward_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', '.../nipype/testing/data/output_1Warp.nii.gz']} - >>> reg4b.aggregate_outputs() #doctest: +SKIP + >>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE + {'composite_transform': , + 'forward_invert_flags': [False, False], + 'forward_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', + '.../nipype/testing/data/output_1Warp.nii.gz'], + 'inverse_composite_transform': , + 'inverse_warped_image': , + 'reverse_invert_flags': [True, False], + 'reverse_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', '.../nipype/testing/data/output_1InverseWarp.nii.gz'], + 'save_state': , + 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz'} + >>> reg4b.aggregate_outputs() # doctest: +SKIP >>> # Test multiple metrics per stage >>> reg5 = copy.deepcopy(reg) @@ -519,8 +538,8 @@ def _formatMetric(self, index): # Otherwise, make a singleton list of the metric specification # from the non-list inputs. if isinstance(name_input, list): - items = stage_inputs.items() - indexes = range(0, len(name_input)) + items = list(stage_inputs.items()) + indexes = list(range(0, len(name_input))) specs = list() for i in indexes: temp = dict([(k, v[i]) for k, v in items]) @@ -550,9 +569,9 @@ def _formatMetricArgument(self, **kwargs): kwargs['radius_or_bins']) # The optional sampling strategy. - if kwargs.has_key('sampling_strategy'): + if 'sampling_strategy' in kwargs: sampling_strategy = kwargs['sampling_strategy'] - elif kwargs.has_key('sampling_percentage'): + elif 'sampling_percentage' in kwargs: # The sampling percentage is specified but not the # sampling strategy. Use the default strategy. sampling_strategy = Registration.DEF_SAMPLING_STRATEGY @@ -561,7 +580,7 @@ def _formatMetricArgument(self, **kwargs): # Format the optional sampling arguments. if sampling_strategy: retval += ', %s' % sampling_strategy - if kwargs.has_key('sampling_percentage'): + if 'sampling_percentage' in kwargs: retval += ', %g' % kwargs['sampling_percentage'] retval += ' ]' @@ -711,7 +730,7 @@ def _outputFileNames(self, prefix, count, transform, inverse=False): 'Translation': 'Translation.mat', 'BSpline': 'BSpline.txt', 'Initial': 'DerivedInitialMovingTranslation.mat'} - if transform in self.lowDimensionalTransformMap.keys(): + if transform in list(self.lowDimensionalTransformMap.keys()): suffix = self.lowDimensionalTransformMap[transform] inverse_mode = inverse else: diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py index 37c360c27a..df3469bd34 100644 --- a/nipype/interfaces/ants/resampling.py +++ b/nipype/interfaces/ants/resampling.py @@ -6,13 +6,14 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) >>> os.chdir(datadir) """ + +from builtins import range import os from .base import ANTSCommand, ANTSCommandInputSpec from ..base import (TraitedSpec, File, traits, - isdefined) + isdefined, InputMultiPath) from ...utils.filemanip import split_filename -from nipype.interfaces.base import InputMultiPath class WarpTimeSeriesImageMultiTransformInputSpec(ANTSCommandInputSpec): diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 3d6b34aec0..655741fd0e 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/nipype/interfaces/ants/segmentation.py @@ -8,6 +8,8 @@ """ +from builtins import range + from ..base import (TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined) from ...utils.filemanip import split_filename @@ -309,6 +311,7 @@ class N4BiasFieldCorrection(ANTSCommand): >>> n4_4 = N4BiasFieldCorrection() >>> n4_4.inputs.input_image = 'structural.nii' >>> n4_4.inputs.save_bias = True + >>> n4_4.inputs.dimension = 3 >>> n4_4.cmdline 'N4BiasFieldCorrection -d 3 --input-image structural.nii \ --output [ structural_corrected.nii, structural_bias.nii ]' diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 59598d8854..955170b803 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.registration import ANTS +from ....testing import assert_equal +from ..registration import ANTS def test_ANTS_inputs(): input_map = dict(affine_gradient_descent_option=dict(argstr='%s', @@ -75,8 +75,8 @@ def test_ANTS_inputs(): ) inputs = ANTS.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ANTS_outputs(): @@ -88,7 +88,7 @@ def test_ANTS_outputs(): ) outputs = ANTS.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index 6ece89808a..8db8ffd534 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.base import ANTSCommand +from ....testing import assert_equal +from ..base import ANTSCommand def test_ANTSCommand_inputs(): input_map = dict(args=dict(argstr='%s', @@ -19,7 +19,7 @@ def test_ANTSCommand_inputs(): ) inputs = ANTSCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index 4594e3f767..a20be833ea 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.resampling import ApplyTransforms +from ....testing import assert_equal +from ..resampling import ApplyTransforms def test_ApplyTransforms_inputs(): input_map = dict(args=dict(argstr='%s', @@ -47,8 +47,8 @@ def test_ApplyTransforms_inputs(): ) inputs = ApplyTransforms.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyTransforms_outputs(): @@ -56,7 +56,7 @@ def test_ApplyTransforms_outputs(): ) outputs = ApplyTransforms.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index f1d45e1803..42011a59e2 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.resampling import ApplyTransformsToPoints +from ....testing import assert_equal +from ..resampling import ApplyTransformsToPoints def test_ApplyTransformsToPoints_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_ApplyTransformsToPoints_inputs(): ) inputs = ApplyTransformsToPoints.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyTransformsToPoints_outputs(): @@ -42,7 +42,7 @@ def test_ApplyTransformsToPoints_outputs(): ) outputs = ApplyTransformsToPoints.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 0565865ff4..b4672972b1 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.segmentation import Atropos +from ....testing import assert_equal +from ..segmentation import Atropos def test_Atropos_inputs(): input_map = dict(args=dict(argstr='%s', @@ -63,8 +63,8 @@ def test_Atropos_inputs(): ) inputs = Atropos.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Atropos_outputs(): @@ -73,7 +73,7 @@ def test_Atropos_outputs(): ) outputs = Atropos.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 1648fcc13e..df53cfe25e 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.utils import AverageAffineTransform +from ....testing import assert_equal +from ..utils import AverageAffineTransform def test_AverageAffineTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_AverageAffineTransform_inputs(): ) inputs = AverageAffineTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AverageAffineTransform_outputs(): @@ -41,7 +41,7 @@ def test_AverageAffineTransform_outputs(): ) outputs = AverageAffineTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 3284f6f1bb..370b4967dc 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.utils import AverageImages +from ....testing import assert_equal +from ..utils import AverageImages def test_AverageImages_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_AverageImages_inputs(): ) inputs = AverageImages.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AverageImages_outputs(): @@ -45,7 +45,7 @@ def test_AverageImages_outputs(): ) outputs = AverageImages.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index 80cfb8f335..82638eb74a 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.visualization import ConvertScalarImageToRGB +from ....testing import assert_equal +from ..visualization import ConvertScalarImageToRGB def test_ConvertScalarImageToRGB_inputs(): input_map = dict(args=dict(argstr='%s', @@ -61,8 +61,8 @@ def test_ConvertScalarImageToRGB_inputs(): ) inputs = ConvertScalarImageToRGB.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ConvertScalarImageToRGB_outputs(): @@ -70,7 +70,7 @@ def test_ConvertScalarImageToRGB_outputs(): ) outputs = ConvertScalarImageToRGB.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index f629473b10..079043e4b3 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.visualization import CreateTiledMosaic +from ....testing import assert_equal +from ..visualization import CreateTiledMosaic def test_CreateTiledMosaic_inputs(): input_map = dict(alpha_value=dict(argstr='-a %.2f', @@ -44,8 +44,8 @@ def test_CreateTiledMosaic_inputs(): ) inputs = CreateTiledMosaic.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CreateTiledMosaic_outputs(): @@ -53,7 +53,7 @@ def test_CreateTiledMosaic_outputs(): ) outputs = CreateTiledMosaic.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index 2abefa78dc..6005f18db4 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.legacy import GenWarpFields +from ....testing import assert_equal +from ..legacy import GenWarpFields def test_GenWarpFields_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_GenWarpFields_inputs(): ) inputs = GenWarpFields.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenWarpFields_outputs(): @@ -63,7 +63,7 @@ def test_GenWarpFields_outputs(): ) outputs = GenWarpFields.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py b/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py index b84a90e0f4..dbba4dd31f 100644 --- a/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py +++ b/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.utils import JacobianDeterminant +from ....testing import assert_equal +from ..utils import JacobianDeterminant def test_JacobianDeterminant_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_JacobianDeterminant_inputs(): ) inputs = JacobianDeterminant.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JacobianDeterminant_outputs(): @@ -55,7 +55,7 @@ def test_JacobianDeterminant_outputs(): ) outputs = JacobianDeterminant.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index aec5b468aa..c354c3eefc 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.segmentation import JointFusion +from ....testing import assert_equal +from ..segmentation import JointFusion def test_JointFusion_inputs(): input_map = dict(alpha=dict(requires=['method'], @@ -66,8 +66,8 @@ def test_JointFusion_inputs(): ) inputs = JointFusion.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JointFusion_outputs(): @@ -75,7 +75,7 @@ def test_JointFusion_outputs(): ) outputs = JointFusion.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index c1cb5ef611..fbfce8e0e6 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.segmentation import LaplacianThickness +from ....testing import assert_equal +from ..segmentation import LaplacianThickness def test_LaplacianThickness_inputs(): input_map = dict(args=dict(argstr='%s', @@ -49,8 +49,8 @@ def test_LaplacianThickness_inputs(): ) inputs = LaplacianThickness.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_LaplacianThickness_outputs(): @@ -58,7 +58,7 @@ def test_LaplacianThickness_outputs(): ) outputs = LaplacianThickness.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 117b72987e..951a277deb 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.utils import MultiplyImages +from ....testing import assert_equal +from ..utils import MultiplyImages def test_MultiplyImages_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_MultiplyImages_inputs(): ) inputs = MultiplyImages.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MultiplyImages_outputs(): @@ -45,7 +45,7 @@ def test_MultiplyImages_outputs(): ) outputs = MultiplyImages.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 5ff634fbc4..4c7ba99e02 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.segmentation import N4BiasFieldCorrection +from ....testing import assert_equal +from ..segmentation import N4BiasFieldCorrection def test_N4BiasFieldCorrection_inputs(): input_map = dict(args=dict(argstr='%s', @@ -49,8 +49,8 @@ def test_N4BiasFieldCorrection_inputs(): ) inputs = N4BiasFieldCorrection.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_N4BiasFieldCorrection_outputs(): @@ -59,7 +59,7 @@ def test_N4BiasFieldCorrection_outputs(): ) outputs = N4BiasFieldCorrection.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 1e27e2ea2c..6c3006e14f 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.registration import Registration +from ....testing import assert_equal +from ..registration import Registration def test_Registration_inputs(): input_map = dict(args=dict(argstr='%s', @@ -114,8 +114,8 @@ def test_Registration_inputs(): ) inputs = Registration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Registration_outputs(): @@ -131,7 +131,7 @@ def test_Registration_outputs(): ) outputs = Registration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index a5ccc93a39..0c04deea33 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.resampling import WarpImageMultiTransform +from ....testing import assert_equal +from ..resampling import WarpImageMultiTransform def test_WarpImageMultiTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_WarpImageMultiTransform_inputs(): ) inputs = WarpImageMultiTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_WarpImageMultiTransform_outputs(): @@ -63,7 +63,7 @@ def test_WarpImageMultiTransform_outputs(): ) outputs = WarpImageMultiTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index 25cef11e99..7b741cd5c0 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.resampling import WarpTimeSeriesImageMultiTransform +from ....testing import assert_equal +from ..resampling import WarpTimeSeriesImageMultiTransform def test_WarpTimeSeriesImageMultiTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -47,8 +47,8 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): ) inputs = WarpTimeSeriesImageMultiTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_WarpTimeSeriesImageMultiTransform_outputs(): @@ -56,7 +56,7 @@ def test_WarpTimeSeriesImageMultiTransform_outputs(): ) outputs = WarpTimeSeriesImageMultiTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py index 6b85d78027..d51d52e011 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.segmentation import antsCorticalThickness +from ....testing import assert_equal +from ..segmentation import antsCorticalThickness def test_antsCorticalThickness_inputs(): input_map = dict(anatomical_image=dict(argstr='-a %s', @@ -69,8 +69,8 @@ def test_antsCorticalThickness_inputs(): ) inputs = antsCorticalThickness.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_antsCorticalThickness_outputs(): @@ -89,7 +89,7 @@ def test_antsCorticalThickness_outputs(): ) outputs = antsCorticalThickness.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index d1a486bedd..dcd08203b6 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.legacy import antsIntroduction +from ....testing import assert_equal +from ..legacy import antsIntroduction def test_antsIntroduction_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_antsIntroduction_inputs(): ) inputs = antsIntroduction.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_antsIntroduction_outputs(): @@ -63,7 +63,7 @@ def test_antsIntroduction_outputs(): ) outputs = antsIntroduction.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 495f8202fa..c75c9ca133 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.ants.legacy import buildtemplateparallel +from ....testing import assert_equal +from ..legacy import buildtemplateparallel def test_buildtemplateparallel_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_buildtemplateparallel_inputs(): ) inputs = buildtemplateparallel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_buildtemplateparallel_outputs(): @@ -65,7 +65,7 @@ def test_buildtemplateparallel_outputs(): ) outputs = buildtemplateparallel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/ants/tests/test_spec_JointFusion.py b/nipype/interfaces/ants/tests/test_spec_JointFusion.py index ad6b1b3d56..1eaf601edd 100644 --- a/nipype/interfaces/ants/tests/test_spec_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_spec_JointFusion.py @@ -1,3 +1,5 @@ +from __future__ import division +from builtins import range from nipype.testing import assert_equal, assert_raises, example_data from nipype.interfaces.base import InputMultiPath from traits.trait_errors import TraitError diff --git a/nipype/interfaces/ants/utils.py b/nipype/interfaces/ants/utils.py index f739c0031b..bf29473f70 100644 --- a/nipype/interfaces/ants/utils.py +++ b/nipype/interfaces/ants/utils.py @@ -10,9 +10,8 @@ from .base import ANTSCommand, ANTSCommandInputSpec from ..base import (TraitedSpec, File, traits, - isdefined) + isdefined, InputMultiPath) from ...utils.filemanip import split_filename -from nipype.interfaces.base import InputMultiPath class AverageAffineTransformInputSpec(ANTSCommandInputSpec): diff --git a/nipype/interfaces/ants/visualization.py b/nipype/interfaces/ants/visualization.py index 458f15eae4..5e83e13cc7 100644 --- a/nipype/interfaces/ants/visualization.py +++ b/nipype/interfaces/ants/visualization.py @@ -5,15 +5,15 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) >>> os.chdir(datadir) """ - -from ..base import (TraitedSpec, File, traits) -from .base import ANTSCommand, ANTSCommandInputSpec -from nipype.utils.filemanip import split_filename -from nipype.interfaces.base import InputMultiPath -from nipype.interfaces.traits_extension import isdefined import numpy as np import os +from .base import ANTSCommand, ANTSCommandInputSpec +from ..base import (TraitedSpec, File, traits, InputMultiPath) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename + + class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec): dimension=traits.Enum(3, 2, argstr= '%d', usedefault=True, desc='image dimension (2 or 3)', mandatory=True, diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index ac6b7b8af4..7d43901908 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -8,7 +8,14 @@ Requires Packages to be installed """ -from ConfigParser import NoOptionError +from __future__ import print_function +from __future__ import division +from future import standard_library +standard_library.install_aliases() +from builtins import range +from builtins import object + +from configparser import NoOptionError from copy import deepcopy import datetime import errno @@ -20,11 +27,11 @@ import select import subprocess import sys +import random, time, fnmatch from textwrap import wrap from datetime import datetime as dt from dateutil.parser import parse as parseutc from warnings import warn -from nipype.external import six from .traits_extension import (traits, Undefined, TraitDictObject, @@ -38,7 +45,7 @@ from ..utils.provenance import write_provenance from .. import config, logging, LooseVersion from .. import __version__ -import random, time, fnmatch +from ..external.six import string_types nipype_version = LooseVersion(__version__) @@ -141,12 +148,12 @@ def update(self, *args, **kwargs): def items(self): """iterates over bunch attributes as key, value pairs""" - return self.__dict__.items() + return list(self.__dict__.items()) def iteritems(self): """iterates over bunch attributes as key, value pairs""" warn('iteritems is deprecated, use items instead') - return self.items() + return list(self.items()) def get(self, *args): '''Support dictionary get() functionality @@ -196,13 +203,12 @@ def _hash_infile(self, adict, key): for afile in stuff: if os.path.isfile(afile): md5obj = md5() - fp = file(afile, 'rb') - while True: - data = fp.read(8192) - if not data: - break - md5obj.update(data) - fp.close() + with open(afile, 'rb') as fp: + while True: + data = fp.read(8192) + if not data: + break + md5obj.update(data) md5hex = md5obj.hexdigest() else: md5hex = None @@ -231,7 +237,7 @@ def _get_bunch_hash(self): """ infile_list = [] - for key, val in self.items(): + for key, val in list(self.items()): if is_container(val): # XXX - SG this probably doesn't catch numpy arrays # containing embedded file names either. @@ -259,7 +265,7 @@ def _get_bunch_hash(self): # representation so we get a predictable order of the # dictionary. sorted_dict = str(sorted(dict_nofilename.items())) - return (dict_withhash, md5(sorted_dict).hexdigest()) + return dict_withhash, md5(sorted_dict.encode()).hexdigest() def __pretty__(self, p, cycle): '''Support for the pretty module @@ -415,7 +421,7 @@ def _requires_warn(self, obj, name, old, new): if not msg: msg = 'Input %s requires inputs: %s' \ % (name, ', '.join(trait_spec.requires)) - if msg: + if msg: # only one requires warning at a time. warn(msg) def _deprecated_warn(self, obj, name, old, new): @@ -439,10 +445,11 @@ def _deprecated_warn(self, obj, name, old, new): if LooseVersion(str(trait_spec.deprecated)) < nipype_version: raise TraitError(msg) else: + if trait_spec.new_name: + msg += 'Unsetting old value %s; setting new value %s.' % ( + name, trait_spec.new_name) warn(msg) if trait_spec.new_name: - warn('Unsetting %s and setting %s.' % (name, - trait_spec.new_name)) self.trait_set(trait_change_notify=False, **{'%s' % name: Undefined, '%s' % trait_spec.new_name: new}) @@ -496,7 +503,7 @@ def _clean_container(self, object, undefinedval=None, skipundefined=False): """ if isinstance(object, TraitDictObject) or isinstance(object, dict): out = {} - for key, val in object.items(): + for key, val in list(object.items()): if isdefined(val): out[key] = self._clean_container(val, undefinedval) else: @@ -561,7 +568,7 @@ def get_hashval(self, hash_method=None): dict_withhash.append((name, self._get_sorteddict(val, True, hash_method=hash_method, hash_files=hash_files))) - return dict_withhash, md5(str(dict_nofilename)).hexdigest() + return dict_withhash, md5(str(dict_nofilename).encode()).hexdigest() def _get_sorteddict(self, object, dictwithhash=False, hash_method=None, hash_files=True): @@ -584,7 +591,7 @@ def _get_sorteddict(self, object, dictwithhash=False, hash_method=None, out = tuple(out) else: if isdefined(object): - if (hash_files and isinstance(object, six.string_types) and + if (hash_files and isinstance(object, string_types) and os.path.isfile(object)): if hash_method is None: hash_method = config.get('execution', 'hash_method') @@ -829,7 +836,7 @@ def _inputs_help(cls): helpstr = ['Inputs::'] inputs = cls.input_spec() - if len(inputs.traits(transient=None).items()) == 0: + if len(list(inputs.traits(transient=None).items())) == 0: helpstr += ['', '\tNone'] return helpstr @@ -914,7 +921,7 @@ def _check_xor(self, spec, name, value): def _check_mandatory_inputs(self): """ Raises an exception if a mandatory input is Undefined """ - for name, spec in self.inputs.traits(mandatory=True).items(): + for name, spec in list(self.inputs.traits(mandatory=True).items()): value = getattr(self.inputs, name) self._check_xor(spec, name, value) if not isdefined(value) and spec.xor is None: @@ -924,8 +931,8 @@ def _check_mandatory_inputs(self): raise ValueError(msg) if isdefined(value): self._check_requires(spec, name, value) - for name, spec in self.inputs.traits(mandatory=None, - transient=None).items(): + for name, spec in list(self.inputs.traits(mandatory=None, + transient=None).items()): self._check_requires(spec, name, getattr(self.inputs, name)) def _check_version_requirements(self, trait_object, raise_exception=True): @@ -935,11 +942,9 @@ def _check_version_requirements(self, trait_object, raise_exception=True): # check minimum version check = dict(min_ver=lambda t: t is not None) names = trait_object.trait_names(**check) - - if names: + + if names and self.version: version = LooseVersion(str(self.version)) - if not version: - return for name in names: min_ver = LooseVersion(str(trait_object.traits()[name].min_ver)) if min_ver > version: @@ -1019,7 +1024,7 @@ def run(self, **inputs): self._check_version_requirements(self.inputs) interface = self.__class__ # initialize provenance tracking - env = deepcopy(os.environ.data) + env = deepcopy(dict(os.environ)) runtime = Bunch(cwd=os.getcwd(), returncode=None, duration=None, @@ -1034,8 +1039,8 @@ def run(self, **inputs): outputs = self.aggregate_outputs(runtime) runtime.endTime = dt.isoformat(dt.utcnow()) timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = timediff.days * 86400 + timediff.seconds + \ - timediff.microseconds/100000. + runtime.duration = (timediff.days * 86400 + timediff.seconds + + timediff.microseconds / 100000.) results = InterfaceResult(interface, runtime, inputs=self.inputs.get_traitsfree(), outputs=outputs) @@ -1043,11 +1048,11 @@ def run(self, **inputs): if str2bool(config.get('execution', 'write_provenance')): prov_record = write_provenance(results) results.provenance = prov_record - except Exception, e: + except Exception as e: runtime.endTime = dt.isoformat(dt.utcnow()) timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = timediff.days * 86400 + timediff.seconds + \ - timediff.microseconds/100000. + runtime.duration = (timediff.days * 86400 + timediff.seconds + + timediff.microseconds / 100000.) if len(e.args) == 0: e.args = ("") @@ -1059,7 +1064,7 @@ def run(self, **inputs): else: inputs_str = '' - if len(e.args) == 1 and isinstance(e.args[0], six.string_types): + if len(e.args) == 1 and isinstance(e.args[0], string_types): e.args = (e.args[0] + " ".join([message, inputs_str]),) else: e.args += (message, ) @@ -1073,7 +1078,7 @@ def run(self, **inputs): inputs = None try: inputs = self.inputs.get_traitsfree() - except Exception, e: + except Exception as e: pass results = InterfaceResult(interface, runtime, inputs=inputs) prov_record = None @@ -1109,7 +1114,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None): if outputs: _unavailable_outputs = \ self._check_version_requirements(self._outputs()) - for key, val in predicted_outputs.items(): + for key, val in list(predicted_outputs.items()): if needed_outputs and key not in needed_outputs: continue if key in _unavailable_outputs: @@ -1120,7 +1125,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None): try: setattr(outputs, key, val) _ = getattr(outputs, key) - except TraitError, error: + except TraitError as error: if hasattr(error, 'info') and \ error.info.startswith("an existing"): msg = ("File/Directory '%s' not found for %s output " @@ -1165,7 +1170,7 @@ def read(self, drain=0): def _read(self, drain): "Read from the file descriptor" fd = self.fileno() - buf = os.read(fd, 4096) + buf = os.read(fd, 4096).decode() if not buf and not self._buf: return None if '\n' not in buf: @@ -1207,7 +1212,7 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False): if output == 'file': errfile = os.path.join(runtime.cwd, 'stderr.nipype') outfile = os.path.join(runtime.cwd, 'stdout.nipype') - stderr = open(errfile, 'wt') + stderr = open(errfile, 'wt') # t=='text'===default stdout = open(outfile, 'wt') proc = subprocess.Popen(cmdline, @@ -1232,7 +1237,7 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False): def _process(drain=0): try: res = select.select(streams, [], [], timeout) - except select.error, e: + except select.error as e: iflogger.info(str(e)) if e[0] == errno.EINTR: return @@ -1258,8 +1263,8 @@ def _process(drain=0): result['merged'] = [r[1] for r in temp] if output == 'allatonce': stdout, stderr = proc.communicate() - result['stdout'] = stdout.split('\n') - result['stderr'] = stderr.split('\n') + result['stdout'] = str(stdout).split('\n') + result['stderr'] = str(stderr).split('\n') result['merged'] = '' if output == 'file': ret_code = proc.wait() @@ -1337,16 +1342,18 @@ class must be instantiated with a command argument Examples -------- - + >>> import pprint >>> from nipype.interfaces.base import CommandLine >>> cli = CommandLine(command='ls', environ={'DISPLAY': ':1'}) >>> cli.inputs.args = '-al' >>> cli.cmdline 'ls -al' - >>> cli.inputs.trait_get() # doctest: +NORMALIZE_WHITESPACE - {'ignore_exception': False, 'terminal_output': 'stream', - 'environ': {'DISPLAY': ':1'}, 'args': '-al'} + >>> pprint.pprint(cli.inputs.trait_get()) # doctest: +NORMALIZE_WHITESPACE + {'args': '-al', + 'environ': {'DISPLAY': ':1'}, + 'ignore_exception': False, + 'terminal_output': 'stream'} >>> cli.inputs.get_hashval() ([('args', '-al')], '11c37f97649cd61627f4afe5136af8c0') @@ -1441,7 +1448,7 @@ def _get_environ(self): def version_from_command(self, flag='-v'): cmdname = self.cmd.split()[0] if _exists_in_path(cmdname): - env = deepcopy(os.environ.data) + env = dict(os.environ) out_environ = self._get_environ() env.update(out_environ) proc = subprocess.Popen(' '.join((cmdname, flag)), @@ -1479,7 +1486,7 @@ def _run_interface(self, runtime, correct_return_codes=[0]): exist_val, cmd_path = _exists_in_path(executable_name, runtime.environ) if not exist_val: - raise IOError("%s could not be found on host %s" % + raise IOError("command '%s' could not be found on host %s" % (self.cmd.split()[0], runtime.hostname)) setattr(runtime, 'command_path', cmd_path) setattr(runtime, 'dependencies', get_dependencies(executable_name, @@ -1559,7 +1566,7 @@ def _filename_from_source(self, name, chain=None): iflogger.warn('Only one name_source per trait is allowed') ns = ns[0] - if not isinstance(ns, six.string_types): + if not isinstance(ns, string_types): raise ValueError(('name_source of \'%s\' trait sould be an ' 'input trait name') % name) @@ -1601,7 +1608,7 @@ def _list_outputs(self): traits = self.inputs.traits(**metadata) if traits: outputs = self.output_spec().get() - for name, trait_spec in traits.iteritems(): + for name, trait_spec in traits.items(): out_name = name if trait_spec.output_name is not None: out_name = trait_spec.output_name @@ -1640,7 +1647,7 @@ def _parse_inputs(self, skip=None): continue pos = spec.position if pos is not None: - if pos >= 0: + if int(pos) >= 0: initial_args[pos] = arg else: final_args[pos] = arg @@ -1721,7 +1728,7 @@ def _list_outputs(self): return self._outputs_from_inputs(outputs) def _outputs_from_inputs(self, outputs): - for name in outputs.keys(): + for name in list(outputs.keys()): corresponding_input = getattr(self.inputs, name) if isdefined(corresponding_input): if (isinstance(corresponding_input, bool) and @@ -1737,7 +1744,7 @@ def _outputs_from_inputs(self, outputs): return outputs def _format_arg(self, name, spec, value): - if name in self._outputs_filenames.keys(): + if name in list(self._outputs_filenames.keys()): if isinstance(value, bool): if value: value = os.path.abspath(self._outputs_filenames[name]) diff --git a/nipype/interfaces/c3.py b/nipype/interfaces/c3.py index 89fee0e61a..6ceb736fc1 100644 --- a/nipype/interfaces/c3.py +++ b/nipype/interfaces/c3.py @@ -6,8 +6,9 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data')) >>> os.chdir(datadir) """ -from nipype.interfaces.base import (CommandLineInputSpec, traits, TraitedSpec, - File, SEMLikeCommandLine) + +from .base import (CommandLineInputSpec, traits, TraitedSpec, + File, SEMLikeCommandLine) class C3dAffineToolInputSpec(CommandLineInputSpec): diff --git a/nipype/interfaces/camino/calib.py b/nipype/interfaces/camino/calib.py index ba4062e1dd..41f410faf6 100644 --- a/nipype/interfaces/camino/calib.py +++ b/nipype/interfaces/camino/calib.py @@ -8,10 +8,11 @@ """ import os -from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, traits, - TraitedSpec, File, StdOutCommandLine, - StdOutCommandLineInputSpec, isdefined) -from nipype.utils.filemanip import split_filename +from ..base import (CommandLineInputSpec, CommandLine, traits, + TraitedSpec, File, StdOutCommandLine, + StdOutCommandLineInputSpec, isdefined) +from ...utils.filemanip import split_filename + class SFPICOCalibDataInputSpec(StdOutCommandLineInputSpec): snr = traits.Float(argstr='-snr %f', units='NA', diff --git a/nipype/interfaces/camino/connectivity.py b/nipype/interfaces/camino/connectivity.py index 10483fef6d..1196717269 100644 --- a/nipype/interfaces/camino/connectivity.py +++ b/nipype/interfaces/camino/connectivity.py @@ -6,11 +6,13 @@ >>> os.chdir(datadir) """ -from nipype.interfaces.base import (traits, TraitedSpec, File, - CommandLine, CommandLineInputSpec, isdefined) -from nipype.utils.filemanip import split_filename import os +from ..base import (traits, TraitedSpec, File, + CommandLine, CommandLineInputSpec, isdefined) +from ...utils.filemanip import split_filename + + class ConmatInputSpec(CommandLineInputSpec): in_file = File(exists=True, argstr='-inputfile %s', mandatory=True, desc='Streamlines as generated by the Track interface') diff --git a/nipype/interfaces/camino/convert.py b/nipype/interfaces/camino/convert.py index af5d42c444..1014bd8f27 100644 --- a/nipype/interfaces/camino/convert.py +++ b/nipype/interfaces/camino/convert.py @@ -9,11 +9,12 @@ import os import glob -from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, traits, - TraitedSpec, File, StdOutCommandLine, - OutputMultiPath, StdOutCommandLineInputSpec, - isdefined) -from nipype.utils.filemanip import split_filename +from ..base import (CommandLineInputSpec, CommandLine, traits, + TraitedSpec, File, StdOutCommandLine, + OutputMultiPath, StdOutCommandLineInputSpec, + isdefined) +from ...utils.filemanip import split_filename + class Image2VoxelInputSpec(StdOutCommandLineInputSpec): in_file = File(exists=True, argstr='-4dimage %s', diff --git a/nipype/interfaces/camino/dti.py b/nipype/interfaces/camino/dti.py index 3851061b16..abd737d6fb 100644 --- a/nipype/interfaces/camino/dti.py +++ b/nipype/interfaces/camino/dti.py @@ -6,13 +6,15 @@ >>> os.chdir(datadir) """ -from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, traits, - TraitedSpec, File, Directory, StdOutCommandLine, - StdOutCommandLineInputSpec, isdefined, - InputMultiPath) -from nipype.utils.filemanip import split_filename import os +from ..base import (CommandLineInputSpec, CommandLine, traits, + TraitedSpec, File, Directory, StdOutCommandLine, + StdOutCommandLineInputSpec, isdefined, + InputMultiPath) +from ...utils.filemanip import split_filename + + class DTIFitInputSpec(StdOutCommandLineInputSpec): in_file = File(exists=True, argstr='%s', mandatory=True, position=1, desc='voxel-order data filename') diff --git a/nipype/interfaces/camino/odf.py b/nipype/interfaces/camino/odf.py index dd097deb40..e10e076775 100644 --- a/nipype/interfaces/camino/odf.py +++ b/nipype/interfaces/camino/odf.py @@ -8,10 +8,11 @@ """ import os -from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, traits, - TraitedSpec, File, StdOutCommandLine, - StdOutCommandLineInputSpec, isdefined) -from nipype.utils.filemanip import split_filename +from ..base import (CommandLineInputSpec, CommandLine, traits, + TraitedSpec, File, StdOutCommandLine, + StdOutCommandLineInputSpec, isdefined) +from ...utils.filemanip import split_filename + class QBallMXInputSpec(StdOutCommandLineInputSpec): basistype = traits.Enum('rbf', 'sh', argstr='-basistype %s', diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index a94dcdfab5..bfe53e3624 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import AnalyzeHeader +from ....testing import assert_equal +from ..convert import AnalyzeHeader def test_AnalyzeHeader_inputs(): input_map = dict(args=dict(argstr='%s', @@ -81,8 +81,8 @@ def test_AnalyzeHeader_inputs(): ) inputs = AnalyzeHeader.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AnalyzeHeader_outputs(): @@ -90,7 +90,7 @@ def test_AnalyzeHeader_outputs(): ) outputs = AnalyzeHeader.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index a552db83bc..37a744a05c 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import ComputeEigensystem +from ....testing import assert_equal +from ..dti import ComputeEigensystem def test_ComputeEigensystem_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_ComputeEigensystem_inputs(): ) inputs = ComputeEigensystem.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeEigensystem_outputs(): @@ -43,7 +43,7 @@ def test_ComputeEigensystem_outputs(): ) outputs = ComputeEigensystem.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 917d49099a..3727068e2b 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import ComputeFractionalAnisotropy +from ....testing import assert_equal +from ..dti import ComputeFractionalAnisotropy def test_ComputeFractionalAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_ComputeFractionalAnisotropy_inputs(): ) inputs = ComputeFractionalAnisotropy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeFractionalAnisotropy_outputs(): @@ -42,7 +42,7 @@ def test_ComputeFractionalAnisotropy_outputs(): ) outputs = ComputeFractionalAnisotropy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 05a3f91087..690f014b99 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import ComputeMeanDiffusivity +from ....testing import assert_equal +from ..dti import ComputeMeanDiffusivity def test_ComputeMeanDiffusivity_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_ComputeMeanDiffusivity_inputs(): ) inputs = ComputeMeanDiffusivity.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeMeanDiffusivity_outputs(): @@ -42,7 +42,7 @@ def test_ComputeMeanDiffusivity_outputs(): ) outputs = ComputeMeanDiffusivity.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 89f8884388..58a1479d24 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import ComputeTensorTrace +from ....testing import assert_equal +from ..dti import ComputeTensorTrace def test_ComputeTensorTrace_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_ComputeTensorTrace_inputs(): ) inputs = ComputeTensorTrace.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeTensorTrace_outputs(): @@ -42,7 +42,7 @@ def test_ComputeTensorTrace_outputs(): ) outputs = ComputeTensorTrace.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index 6e70688e50..5839e02b76 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.connectivity import Conmat +from ....testing import assert_equal +from ..connectivity import Conmat def test_Conmat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -39,8 +39,8 @@ def test_Conmat_inputs(): ) inputs = Conmat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Conmat_outputs(): @@ -49,7 +49,7 @@ def test_Conmat_outputs(): ) outputs = Conmat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index 88ecc27612..754201435f 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import DT2NIfTI +from ....testing import assert_equal +from ..convert import DT2NIfTI def test_DT2NIfTI_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_DT2NIfTI_inputs(): ) inputs = DT2NIfTI.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DT2NIfTI_outputs(): @@ -39,7 +39,7 @@ def test_DT2NIfTI_outputs(): ) outputs = DT2NIfTI.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index edd6c38cf4..4d4bb35174 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import DTIFit +from ....testing import assert_equal +from ..dti import DTIFit def test_DTIFit_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_DTIFit_inputs(): ) inputs = DTIFit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTIFit_outputs(): @@ -42,7 +42,7 @@ def test_DTIFit_outputs(): ) outputs = DTIFit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 0e08bd24c9..2774a6acab 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import DTLUTGen +from ....testing import assert_equal +from ..dti import DTLUTGen def test_DTLUTGen_inputs(): input_map = dict(acg=dict(argstr='-acg', @@ -53,8 +53,8 @@ def test_DTLUTGen_inputs(): ) inputs = DTLUTGen.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTLUTGen_outputs(): @@ -62,7 +62,7 @@ def test_DTLUTGen_outputs(): ) outputs = DTLUTGen.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index bc2b2f886a..45d1029dec 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import DTMetric +from ....testing import assert_equal +from ..dti import DTMetric def test_DTMetric_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_DTMetric_inputs(): ) inputs = DTMetric.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTMetric_outputs(): @@ -42,7 +42,7 @@ def test_DTMetric_outputs(): ) outputs = DTMetric.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index 8e902ce251..81d7e3861e 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import FSL2Scheme +from ....testing import assert_equal +from ..convert import FSL2Scheme def test_FSL2Scheme_inputs(): input_map = dict(args=dict(argstr='%s', @@ -47,8 +47,8 @@ def test_FSL2Scheme_inputs(): ) inputs = FSL2Scheme.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FSL2Scheme_outputs(): @@ -56,7 +56,7 @@ def test_FSL2Scheme_outputs(): ) outputs = FSL2Scheme.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 50067e9244..ab862918ef 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import Image2Voxel +from ....testing import assert_equal +from ..convert import Image2Voxel def test_Image2Voxel_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_Image2Voxel_inputs(): ) inputs = Image2Voxel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Image2Voxel_outputs(): @@ -37,7 +37,7 @@ def test_Image2Voxel_outputs(): ) outputs = Image2Voxel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 2e1b85954a..4c719e5fc2 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.utils import ImageStats +from ....testing import assert_equal +from ..utils import ImageStats def test_ImageStats_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_ImageStats_inputs(): ) inputs = ImageStats.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageStats_outputs(): @@ -39,7 +39,7 @@ def test_ImageStats_outputs(): ) outputs = ImageStats.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 948c9e1614..29835c88dd 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.odf import LinRecon +from ....testing import assert_equal +from ..odf import LinRecon def test_LinRecon_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_LinRecon_inputs(): ) inputs = LinRecon.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_LinRecon_outputs(): @@ -47,7 +47,7 @@ def test_LinRecon_outputs(): ) outputs = LinRecon.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 8f30b0fc61..41f2468492 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.odf import MESD +from ....testing import assert_equal +from ..odf import MESD def test_MESD_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_MESD_inputs(): ) inputs = MESD.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MESD_outputs(): @@ -55,7 +55,7 @@ def test_MESD_outputs(): ) outputs = MESD.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index c1f212813e..201df1069d 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import ModelFit +from ....testing import assert_equal +from ..dti import ModelFit def test_ModelFit_inputs(): input_map = dict(args=dict(argstr='%s', @@ -53,8 +53,8 @@ def test_ModelFit_inputs(): ) inputs = ModelFit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ModelFit_outputs(): @@ -62,7 +62,7 @@ def test_ModelFit_outputs(): ) outputs = ModelFit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index b2c5d7ca16..70ca86a7e9 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import NIfTIDT2Camino +from ....testing import assert_equal +from ..convert import NIfTIDT2Camino def test_NIfTIDT2Camino_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_NIfTIDT2Camino_inputs(): ) inputs = NIfTIDT2Camino.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NIfTIDT2Camino_outputs(): @@ -45,7 +45,7 @@ def test_NIfTIDT2Camino_outputs(): ) outputs = NIfTIDT2Camino.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index f9d93bc93c..2a1bfb2dc2 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import PicoPDFs +from ....testing import assert_equal +from ..dti import PicoPDFs def test_PicoPDFs_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_PicoPDFs_inputs(): ) inputs = PicoPDFs.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PicoPDFs_outputs(): @@ -52,7 +52,7 @@ def test_PicoPDFs_outputs(): ) outputs = PicoPDFs.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 6b895c6226..9cc7627408 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import ProcStreamlines +from ....testing import assert_equal +from ..convert import ProcStreamlines def test_ProcStreamlines_inputs(): input_map = dict(allowmultitargets=dict(argstr='-allowmultitargets', @@ -101,8 +101,8 @@ def test_ProcStreamlines_inputs(): ) inputs = ProcStreamlines.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ProcStreamlines_outputs(): @@ -111,7 +111,7 @@ def test_ProcStreamlines_outputs(): ) outputs = ProcStreamlines.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index 6af68410e5..c6ed4ce435 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.odf import QBallMX +from ....testing import assert_equal +from ..odf import QBallMX def test_QBallMX_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_QBallMX_inputs(): ) inputs = QBallMX.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_QBallMX_outputs(): @@ -47,7 +47,7 @@ def test_QBallMX_outputs(): ) outputs = QBallMX.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index 5ff195e678..5bef04c474 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.calib import SFLUTGen +from ....testing import assert_equal +from ..calib import SFLUTGen def test_SFLUTGen_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_SFLUTGen_inputs(): ) inputs = SFLUTGen.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SFLUTGen_outputs(): @@ -53,7 +53,7 @@ def test_SFLUTGen_outputs(): ) outputs = SFLUTGen.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index 9de595c05b..6988c53f4c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.calib import SFPICOCalibData +from ....testing import assert_equal +from ..calib import SFPICOCalibData def test_SFPICOCalibData_inputs(): input_map = dict(args=dict(argstr='%s', @@ -61,8 +61,8 @@ def test_SFPICOCalibData_inputs(): ) inputs = SFPICOCalibData.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SFPICOCalibData_outputs(): @@ -71,7 +71,7 @@ def test_SFPICOCalibData_outputs(): ) outputs = SFPICOCalibData.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index c1f950d145..4f767b3b54 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.odf import SFPeaks +from ....testing import assert_equal +from ..odf import SFPeaks def test_SFPeaks_inputs(): input_map = dict(args=dict(argstr='%s', @@ -57,8 +57,8 @@ def test_SFPeaks_inputs(): ) inputs = SFPeaks.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SFPeaks_outputs(): @@ -66,7 +66,7 @@ def test_SFPeaks_outputs(): ) outputs = SFPeaks.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 99f0194b2c..58482b0795 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import Shredder +from ....testing import assert_equal +from ..convert import Shredder def test_Shredder_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_Shredder_inputs(): ) inputs = Shredder.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Shredder_outputs(): @@ -45,7 +45,7 @@ def test_Shredder_outputs(): ) outputs = Shredder.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index 40e2877097..e3b14aa85e 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import Track +from ....testing import assert_equal +from ..dti import Track def test_Track_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -69,8 +69,8 @@ def test_Track_inputs(): ) inputs = Track.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Track_outputs(): @@ -78,7 +78,7 @@ def test_Track_outputs(): ) outputs = Track.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 4aa35e7c4b..57d7a3e098 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackBallStick +from ....testing import assert_equal +from ..dti import TrackBallStick def test_TrackBallStick_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -69,8 +69,8 @@ def test_TrackBallStick_inputs(): ) inputs = TrackBallStick.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackBallStick_outputs(): @@ -78,7 +78,7 @@ def test_TrackBallStick_outputs(): ) outputs = TrackBallStick.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index a7a67ab149..40a5418c35 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackBayesDirac +from ....testing import assert_equal +from ..dti import TrackBayesDirac def test_TrackBayesDirac_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -89,8 +89,8 @@ def test_TrackBayesDirac_inputs(): ) inputs = TrackBayesDirac.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackBayesDirac_outputs(): @@ -98,7 +98,7 @@ def test_TrackBayesDirac_outputs(): ) outputs = TrackBayesDirac.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 025360885f..0e44d68310 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackBedpostxDeter +from ....testing import assert_equal +from ..dti import TrackBedpostxDeter def test_TrackBedpostxDeter_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -75,8 +75,8 @@ def test_TrackBedpostxDeter_inputs(): ) inputs = TrackBedpostxDeter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackBedpostxDeter_outputs(): @@ -84,7 +84,7 @@ def test_TrackBedpostxDeter_outputs(): ) outputs = TrackBedpostxDeter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index aecdea7a1c..2fe581ec1e 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackBedpostxProba +from ....testing import assert_equal +from ..dti import TrackBedpostxProba def test_TrackBedpostxProba_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -78,8 +78,8 @@ def test_TrackBedpostxProba_inputs(): ) inputs = TrackBedpostxProba.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackBedpostxProba_outputs(): @@ -87,7 +87,7 @@ def test_TrackBedpostxProba_outputs(): ) outputs = TrackBedpostxProba.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index bffe3aa376..aa0af20159 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackBootstrap +from ....testing import assert_equal +from ..dti import TrackBootstrap def test_TrackBootstrap_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -82,8 +82,8 @@ def test_TrackBootstrap_inputs(): ) inputs = TrackBootstrap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackBootstrap_outputs(): @@ -91,7 +91,7 @@ def test_TrackBootstrap_outputs(): ) outputs = TrackBootstrap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 46a21f97ad..4b04104ec6 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackDT +from ....testing import assert_equal +from ..dti import TrackDT def test_TrackDT_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -69,8 +69,8 @@ def test_TrackDT_inputs(): ) inputs = TrackDT.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackDT_outputs(): @@ -78,7 +78,7 @@ def test_TrackDT_outputs(): ) outputs = TrackDT.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 11ef8d7c23..374e04bb36 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.dti import TrackPICo +from ....testing import assert_equal +from ..dti import TrackPICo def test_TrackPICo_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', @@ -74,8 +74,8 @@ def test_TrackPICo_inputs(): ) inputs = TrackPICo.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackPICo_outputs(): @@ -83,7 +83,7 @@ def test_TrackPICo_outputs(): ) outputs = TrackPICo.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index 7e6af4ba19..e129b51363 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import TractShredder +from ....testing import assert_equal +from ..convert import TractShredder def test_TractShredder_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_TractShredder_inputs(): ) inputs = TractShredder.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TractShredder_outputs(): @@ -45,7 +45,7 @@ def test_TractShredder_outputs(): ) outputs = TractShredder.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index c33db8ef2f..6ebcae1985 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino.convert import VtkStreamlines +from ....testing import assert_equal +from ..convert import VtkStreamlines def test_VtkStreamlines_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_VtkStreamlines_inputs(): ) inputs = VtkStreamlines.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VtkStreamlines_outputs(): @@ -55,7 +55,7 @@ def test_VtkStreamlines_outputs(): ) outputs = VtkStreamlines.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino/utils.py b/nipype/interfaces/camino/utils.py index 3b6903280b..33497f2bdc 100644 --- a/nipype/interfaces/camino/utils.py +++ b/nipype/interfaces/camino/utils.py @@ -6,12 +6,14 @@ >>> os.chdir(datadir) """ -from nipype.interfaces.base import (traits, TraitedSpec, File, - CommandLine, CommandLineInputSpec, isdefined, - InputMultiPath) -from nipype.utils.filemanip import split_filename import os +from ..base import (traits, TraitedSpec, File, + CommandLine, CommandLineInputSpec, isdefined, + InputMultiPath) +from ...utils.filemanip import split_filename + + class ImageStatsInputSpec(CommandLineInputSpec): in_files = InputMultiPath(File(exists=True), argstr='-images %s', mandatory=True, position=-1, desc=('List of images to process. They must ' diff --git a/nipype/interfaces/camino2trackvis/convert.py b/nipype/interfaces/camino2trackvis/convert.py index 0b9b40588b..bb95f5f8d0 100644 --- a/nipype/interfaces/camino2trackvis/convert.py +++ b/nipype/interfaces/camino2trackvis/convert.py @@ -1,4 +1,6 @@ """ +Provides interfaces to various commands provided by Camino-Trackvis + Change directory to provide relative paths for doctests >>> import os >>> filepath = os.path.dirname( os.path.realpath( __file__ ) ) @@ -6,12 +8,11 @@ >>> os.chdir(datadir) """ - -from nipype.interfaces.base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File -from nipype.utils.filemanip import split_filename import os -"""Provides interfaces to various commands provided by Camino-Trackvis """ +from ..base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File +from ...utils.filemanip import split_filename + class Camino2TrackvisInputSpec(CommandLineInputSpec): in_file = File(exists=True, argstr='-i %s', mandatory=True, position=1, diff --git a/nipype/interfaces/camino2trackvis/tests/__init__.py b/nipype/interfaces/camino2trackvis/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index af61b989ab..8a0e0590cf 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino2trackvis.convert import Camino2Trackvis +from ....testing import assert_equal +from ..convert import Camino2Trackvis def test_Camino2Trackvis_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_Camino2Trackvis_inputs(): ) inputs = Camino2Trackvis.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Camino2Trackvis_outputs(): @@ -54,7 +54,7 @@ def test_Camino2Trackvis_outputs(): ) outputs = Camino2Trackvis.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 9fc4b3289b..7ebf190c39 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.camino2trackvis.convert import Trackvis2Camino +from ....testing import assert_equal +from ..convert import Trackvis2Camino def test_Trackvis2Camino_inputs(): input_map = dict(append_file=dict(argstr='-a %s', @@ -27,8 +27,8 @@ def test_Trackvis2Camino_inputs(): ) inputs = Trackvis2Camino.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Trackvis2Camino_outputs(): @@ -36,7 +36,7 @@ def test_Trackvis2Camino_outputs(): ) outputs = Trackvis2Camino.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py index 46303c69f6..2e1b1e0501 100644 --- a/nipype/interfaces/cmtk/cmtk.py +++ b/nipype/interfaces/cmtk/cmtk.py @@ -1,773 +1,778 @@ -# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: -""" - Change directory to provide relative paths for doctests - >>> import os - >>> filepath = os.path.dirname( os.path.realpath( __file__ ) ) - >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) - >>> os.chdir(datadir) - -""" - -from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec, traits, - File, TraitedSpec, InputMultiPath, Directory, - OutputMultiPath, isdefined) -from nipype.utils.filemanip import split_filename -import pickle -import scipy.io as sio -import os, os.path as op -import numpy as np -import nibabel as nb -import networkx as nx -import sys - -from ... import logging -iflogger = logging.getLogger('interface') - -def length(xyz, along=False): - """ - Euclidean length of track line - - Parameters - ---------- - xyz : array-like shape (N,3) - array representing x,y,z of N points in a track - along : bool, optional - If True, return array giving cumulative length along track, - otherwise (default) return scalar giving total length. - - Returns - ------- - L : scalar or array shape (N-1,) - scalar in case of `along` == False, giving total length, array if - `along` == True, giving cumulative lengths. - - Examples - -------- - >>> xyz = np.array([[1,1,1],[2,3,4],[0,0,0]]) - >>> expected_lens = np.sqrt([1+2**2+3**2, 2**2+3**2+4**2]) - >>> length(xyz) == expected_lens.sum() - True - >>> len_along = length(xyz, along=True) - >>> np.allclose(len_along, expected_lens.cumsum()) - True - >>> length([]) - 0 - >>> length([[1, 2, 3]]) - 0 - >>> length([], along=True) - array([0]) - """ - xyz = np.asarray(xyz) - if xyz.shape[0] < 2: - if along: - return np.array([0]) - return 0 - dists = np.sqrt((np.diff(xyz, axis=0) ** 2).sum(axis=1)) - if along: - return np.cumsum(dists) - return np.sum(dists) - -def get_rois_crossed(pointsmm, roiData, voxelSize): - n_points = len(pointsmm) - rois_crossed = [] - for j in xrange(0, n_points): - # store point - x = int(pointsmm[j, 0] / float(voxelSize[0])) - y = int(pointsmm[j, 1] / float(voxelSize[1])) - z = int(pointsmm[j, 2] / float(voxelSize[2])) - if not roiData[x, y, z] == 0: - rois_crossed.append(roiData[x, y, z]) - rois_crossed = dict.fromkeys(rois_crossed).keys() #Removed duplicates from the list - return rois_crossed - -def get_connectivity_matrix(n_rois, list_of_roi_crossed_lists): - connectivity_matrix = np.zeros((n_rois, n_rois), dtype=np.uint) - for rois_crossed in list_of_roi_crossed_lists: - for idx_i, roi_i in enumerate(rois_crossed): - for idx_j, roi_j in enumerate(rois_crossed): - if idx_i > idx_j: - if not roi_i == roi_j: - connectivity_matrix[roi_i - 1, roi_j - 1] += 1 - connectivity_matrix = connectivity_matrix + connectivity_matrix.T - return connectivity_matrix - -def create_allpoints_cmat(streamlines, roiData, voxelSize, n_rois): - """ Create the intersection arrays for each fiber - """ - n_fib = len(streamlines) - pc = -1 - # Computation for each fiber - final_fiber_ids = [] - list_of_roi_crossed_lists = [] - for i, fiber in enumerate(streamlines): - pcN = int(round(float(100 * i) / n_fib)) - if pcN > pc and pcN % 1 == 0: - pc = pcN - print '%4.0f%%' % (pc) - rois_crossed = get_rois_crossed(fiber[0], roiData, voxelSize) - if len(rois_crossed) > 0: - list_of_roi_crossed_lists.append(list(rois_crossed)) - final_fiber_ids.append(i) - - connectivity_matrix = get_connectivity_matrix(n_rois, list_of_roi_crossed_lists) - dis = n_fib - len(final_fiber_ids) - iflogger.info("Found %i (%f percent out of %i fibers) fibers that start or terminate in a voxel which is not labeled. (orphans)" % (dis, dis * 100.0 / n_fib, n_fib)) - iflogger.info("Valid fibers: %i (%f percent)" % (n_fib - dis, 100 - dis * 100.0 / n_fib)) - iflogger.info('Returning the intersecting point connectivity matrix') - return connectivity_matrix, final_fiber_ids - -def create_endpoints_array(fib, voxelSize): - """ Create the endpoints arrays for each fiber - Parameters - ---------- - fib: the fibers data - voxelSize: 3-tuple containing the voxel size of the ROI image - Returns - ------- - (endpoints: matrix of size [#fibers, 2, 3] containing for each fiber the - index of its first and last point in the voxelSize volume - endpointsmm) : endpoints in milimeter coordinates - """ - - # Init - n = len(fib) - endpoints = np.zeros((n, 2, 3)) - endpointsmm = np.zeros((n, 2, 3)) - pc = -1 - - # Computation for each fiber - for i, fi in enumerate(fib): - f = fi[0] - - # store startpoint - endpoints[i, 0, :] = f[0, :] - # store endpoint - endpoints[i, 1, :] = f[-1, :] - - # store startpoint - endpointsmm[i, 0, :] = f[0, :] - # store endpoint - endpointsmm[i, 1, :] = f[-1, :] - - # Translate from mm to index - endpoints[i, 0, 0] = int(endpoints[i, 0, 0] / float(voxelSize[0])) - endpoints[i, 0, 1] = int(endpoints[i, 0, 1] / float(voxelSize[1])) - endpoints[i, 0, 2] = int(endpoints[i, 0, 2] / float(voxelSize[2])) - endpoints[i, 1, 0] = int(endpoints[i, 1, 0] / float(voxelSize[0])) - endpoints[i, 1, 1] = int(endpoints[i, 1, 1] / float(voxelSize[1])) - endpoints[i, 1, 2] = int(endpoints[i, 1, 2] / float(voxelSize[2])) - - # Return the matrices - iflogger.info('Returning the endpoint matrix') - return (endpoints, endpointsmm) - -def cmat(track_file, roi_file, resolution_network_file, matrix_name, matrix_mat_name, endpoint_name, intersections=False): - """ Create the connection matrix for each resolution using fibers and ROIs. """ - - stats = {} - iflogger.info('Running cmat function') - # Identify the endpoints of each fiber - en_fname = op.abspath(endpoint_name + '_endpoints.npy') - en_fnamemm = op.abspath(endpoint_name + '_endpointsmm.npy') - - iflogger.info('Reading Trackvis file {trk}'.format(trk=track_file)) - fib, hdr = nb.trackvis.read(track_file, False) - stats['orig_n_fib'] = len(fib) - - roi = nb.load(roi_file) - roiData = roi.get_data() - roiVoxelSize = roi.get_header().get_zooms() - (endpoints, endpointsmm) = create_endpoints_array(fib, roiVoxelSize) - - # Output endpoint arrays - iflogger.info('Saving endpoint array: {array}'.format(array=en_fname)) - np.save(en_fname, endpoints) - iflogger.info('Saving endpoint array in mm: {array}'.format(array=en_fnamemm)) - np.save(en_fnamemm, endpointsmm) - - n = len(fib) - iflogger.info('Number of fibers {num}'.format(num=n)) - - # Create empty fiber label array - fiberlabels = np.zeros((n, 2)) - final_fiberlabels = [] - final_fibers_idx = [] - - # Add node information from specified parcellation scheme - path, name, ext = split_filename(resolution_network_file) - if ext == '.pck': - gp = nx.read_gpickle(resolution_network_file) - elif ext == '.graphml': - gp = nx.read_graphml(resolution_network_file) - - nROIs = len(gp.nodes()) - - # add node information from parcellation - if gp.node[gp.nodes()[0]].has_key('dn_position'): - G = gp.copy() - else: - G = nx.Graph() - for u, d in gp.nodes_iter(data=True): - G.add_node(int(u), d) - # compute a position for the node based on the mean position of the - # ROI in voxel coordinates (segmentation volume ) - xyz = tuple(np.mean(np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])) , axis=1)) - G.node[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]]) - - if intersections: - iflogger.info("Filtering tractography from intersections") - intersection_matrix, final_fiber_ids = create_allpoints_cmat(fib, roiData, roiVoxelSize, nROIs) - finalfibers_fname = op.abspath(endpoint_name + '_intersections_streamline_final.trk') - stats['intersections_n_fib'] = save_fibers(hdr, fib, finalfibers_fname, final_fiber_ids) - intersection_matrix = np.matrix(intersection_matrix) - I = G.copy() - H = nx.from_numpy_matrix(np.matrix(intersection_matrix)) - H = nx.relabel_nodes(H, lambda x: x + 1) #relabel nodes so they start at 1 - I.add_weighted_edges_from(((u, v, d['weight']) for u, v, d in H.edges(data=True))) - - dis = 0 - for i in xrange(endpoints.shape[0]): - - # ROI start => ROI end - try: - startROI = int(roiData[endpoints[i, 0, 0], endpoints[i, 0, 1], endpoints[i, 0, 2]]) - endROI = int(roiData[endpoints[i, 1, 0], endpoints[i, 1, 1], endpoints[i, 1, 2]]) - except IndexError: - iflogger.error(("AN INDEXERROR EXCEPTION OCCURED FOR FIBER %s. PLEASE CHECK ENDPOINT GENERATION" % i)) - break - - # Filter - if startROI == 0 or endROI == 0: - dis += 1 - fiberlabels[i, 0] = -1 - continue - - if startROI > nROIs or endROI > nROIs: - iflogger.error("Start or endpoint of fiber terminate in a voxel which is labeled higher") - iflogger.error("than is expected by the parcellation node information.") - iflogger.error("Start ROI: %i, End ROI: %i" % (startROI, endROI)) - iflogger.error("This needs bugfixing!") - continue - - # Update fiber label - # switch the rois in order to enforce startROI < endROI - if endROI < startROI: - tmp = startROI - startROI = endROI - endROI = tmp - - fiberlabels[i, 0] = startROI - fiberlabels[i, 1] = endROI - - final_fiberlabels.append([ startROI, endROI ]) - final_fibers_idx.append(i) - - # Add edge to graph - if G.has_edge(startROI, endROI) and G.edge[startROI][endROI].has_key('fiblist'): - G.edge[startROI][endROI]['fiblist'].append(i) - else: - G.add_edge(startROI, endROI, fiblist=[i]) - - # create a final fiber length array - finalfiberlength = [] - if intersections: - final_fibers_indices = final_fiber_ids - else: - final_fibers_indices = final_fibers_idx - - for idx in final_fibers_indices: - # compute length of fiber - finalfiberlength.append(length(fib[idx][0])) - - # convert to array - final_fiberlength_array = np.array(finalfiberlength) - - # make final fiber labels as array - final_fiberlabels_array = np.array(final_fiberlabels, dtype=int) - - iflogger.info("Found %i (%f percent out of %i fibers) fibers that start or terminate in a voxel which is not labeled. (orphans)" % (dis, dis * 100.0 / n, n)) - iflogger.info("Valid fibers: %i (%f percent)" % (n - dis, 100 - dis * 100.0 / n)) - - numfib = nx.Graph() - numfib.add_nodes_from(G) - fibmean = numfib.copy() - fibmedian = numfib.copy() - fibdev = numfib.copy() - for u, v, d in G.edges_iter(data=True): - G.remove_edge(u, v) - di = {} - if d.has_key('fiblist'): - di['number_of_fibers'] = len(d['fiblist']) - idx = np.where((final_fiberlabels_array[:, 0] == int(u)) & (final_fiberlabels_array[:, 1] == int(v)))[0] - di['fiber_length_mean'] = float(np.mean(final_fiberlength_array[idx])) - di['fiber_length_median'] = float(np.median(final_fiberlength_array[idx])) - di['fiber_length_std'] = float(np.std(final_fiberlength_array[idx])) - else: - di['number_of_fibers'] = 0 - di['fiber_length_mean'] = 0 - di['fiber_length_median'] = 0 - di['fiber_length_std'] = 0 - if not u == v: #Fix for self loop problem - G.add_edge(u, v, di) - if d.has_key('fiblist'): - numfib.add_edge(u, v, weight=di['number_of_fibers']) - fibmean.add_edge(u, v, weight=di['fiber_length_mean']) - fibmedian.add_edge(u, v, weight=di['fiber_length_median']) - fibdev.add_edge(u, v, weight=di['fiber_length_std']) - - iflogger.info('Writing network as {ntwk}'.format(ntwk=matrix_name)) - nx.write_gpickle(G, op.abspath(matrix_name)) - - numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) - numfib_dict = {'number_of_fibers': numfib_mlab} - fibmean_mlab = nx.to_numpy_matrix(fibmean, dtype=np.float64) - fibmean_dict = {'mean_fiber_length':fibmean_mlab} - fibmedian_mlab = nx.to_numpy_matrix(fibmedian, dtype=np.float64) - fibmedian_dict = {'median_fiber_length':fibmedian_mlab} - fibdev_mlab = nx.to_numpy_matrix(fibdev, dtype=np.float64) - fibdev_dict = {'fiber_length_std':fibdev_mlab} - - if intersections: - path, name, ext = split_filename(matrix_name) - intersection_matrix_name = op.abspath(name + '_intersections') + ext - iflogger.info('Writing intersection network as {ntwk}'.format(ntwk=intersection_matrix_name)) - nx.write_gpickle(I, intersection_matrix_name) - - path, name, ext = split_filename(matrix_mat_name) - if not ext == '.mat': - ext = '.mat' - matrix_mat_name = matrix_mat_name + ext - - iflogger.info('Writing matlab matrix as {mat}'.format(mat=matrix_mat_name)) - sio.savemat(matrix_mat_name, numfib_dict) - - if intersections: - intersect_dict = {'intersections': intersection_matrix} - intersection_matrix_mat_name = op.abspath(name + '_intersections') + ext - iflogger.info('Writing intersection matrix as {mat}'.format(mat=intersection_matrix_mat_name)) - sio.savemat(intersection_matrix_mat_name, intersect_dict) - - mean_fiber_length_matrix_name = op.abspath(name + '_mean_fiber_length') + ext - iflogger.info('Writing matlab mean fiber length matrix as {mat}'.format(mat=mean_fiber_length_matrix_name)) - sio.savemat(mean_fiber_length_matrix_name, fibmean_dict) - - median_fiber_length_matrix_name = op.abspath(name + '_median_fiber_length') + ext - iflogger.info('Writing matlab median fiber length matrix as {mat}'.format(mat=median_fiber_length_matrix_name)) - sio.savemat(median_fiber_length_matrix_name, fibmedian_dict) - - fiber_length_std_matrix_name = op.abspath(name + '_fiber_length_std') + ext - iflogger.info('Writing matlab fiber length deviation matrix as {mat}'.format(mat=fiber_length_std_matrix_name)) - sio.savemat(fiber_length_std_matrix_name, fibdev_dict) - - fiberlengths_fname = op.abspath(endpoint_name + '_final_fiberslength.npy') - iflogger.info("Storing final fiber length array as %s" % fiberlengths_fname) - np.save(fiberlengths_fname, final_fiberlength_array) - - fiberlabels_fname = op.abspath(endpoint_name + '_filtered_fiberslabel.npy') - iflogger.info("Storing all fiber labels (with orphans) as %s" % fiberlabels_fname) - np.save(fiberlabels_fname, np.array(fiberlabels, dtype=np.int32),) - - fiberlabels_noorphans_fname = op.abspath(endpoint_name + '_final_fiberslabels.npy') - iflogger.info("Storing final fiber labels (no orphans) as %s" % fiberlabels_noorphans_fname) - np.save(fiberlabels_noorphans_fname, final_fiberlabels_array) - - iflogger.info("Filtering tractography - keeping only no orphan fibers") - finalfibers_fname = op.abspath(endpoint_name + '_streamline_final.trk') - stats['endpoint_n_fib'] = save_fibers(hdr, fib, finalfibers_fname, final_fibers_idx) - stats['endpoints_percent'] = float(stats['endpoint_n_fib'])/float(stats['orig_n_fib'])*100 - stats['intersections_percent'] = float(stats['intersections_n_fib'])/float(stats['orig_n_fib'])*100 - - out_stats_file = op.abspath(endpoint_name + '_statistics.mat') - iflogger.info("Saving matrix creation statistics as %s" % out_stats_file) - sio.savemat(out_stats_file, stats) - -def save_fibers(oldhdr, oldfib, fname, indices): - """ Stores a new trackvis file fname using only given indices """ - hdrnew = oldhdr.copy() - outstreams = [] - for i in indices: - outstreams.append(oldfib[i]) - n_fib_out = len(outstreams) - hdrnew['n_count'] = n_fib_out - iflogger.info("Writing final non-orphan fibers as %s" % fname) - nb.trackvis.write(fname, outstreams, hdrnew) - return n_fib_out - -class CreateMatrixInputSpec(TraitedSpec): - roi_file = File(exists=True, mandatory=True, desc='Freesurfer aparc+aseg file') - tract_file = File(exists=True, mandatory=True, desc='Trackvis tract file') - resolution_network_file = File(exists=True, mandatory=True, desc='Parcellation files from Connectome Mapping Toolkit') - count_region_intersections = traits.Bool(False, usedefault=True, desc='Counts all of the fiber-region traversals in the connectivity matrix (requires significantly more computational time)') - out_matrix_file = File(genfile=True, desc='NetworkX graph describing the connectivity') - out_matrix_mat_file = File('cmatrix.mat', usedefault=True, desc='Matlab matrix describing the connectivity') - out_mean_fiber_length_matrix_mat_file = File(genfile=True, desc='Matlab matrix describing the mean fiber lengths between each node.') - out_median_fiber_length_matrix_mat_file = File(genfile=True, desc='Matlab matrix describing the mean fiber lengths between each node.') - out_fiber_length_std_matrix_mat_file = File(genfile=True, desc='Matlab matrix describing the deviation in fiber lengths connecting each node.') - out_intersection_matrix_mat_file = File(genfile=True, desc='Matlab connectivity matrix if all region/fiber intersections are counted.') - out_endpoint_array_name = File(genfile=True, desc='Name for the generated endpoint arrays') - -class CreateMatrixOutputSpec(TraitedSpec): - matrix_file = File(desc='NetworkX graph describing the connectivity', exists=True) - intersection_matrix_file = File(desc='NetworkX graph describing the connectivity', exists=True) - matrix_files = OutputMultiPath(File(desc='All of the gpickled network files output by this interface', exists=True)) - matlab_matrix_files = OutputMultiPath(File(desc='All of the MATLAB .mat files output by this interface', exists=True)) - matrix_mat_file = File(desc='Matlab matrix describing the connectivity', exists=True) - intersection_matrix_mat_file = File(desc='Matlab matrix describing the mean fiber lengths between each node.', exists=True) - mean_fiber_length_matrix_mat_file = File(desc='Matlab matrix describing the mean fiber lengths between each node.', exists=True) - median_fiber_length_matrix_mat_file = File(desc='Matlab matrix describing the median fiber lengths between each node.', exists=True) - fiber_length_std_matrix_mat_file = File(desc='Matlab matrix describing the deviation in fiber lengths connecting each node.', exists=True) - endpoint_file = File(desc='Saved Numpy array with the endpoints of each fiber', exists=True) - endpoint_file_mm = File(desc='Saved Numpy array with the endpoints of each fiber (in millimeters)', exists=True) - fiber_length_file = File(desc='Saved Numpy array with the lengths of each fiber', exists=True) - fiber_label_file = File(desc='Saved Numpy array with the labels for each fiber', exists=True) - fiber_labels_noorphans = File(desc='Saved Numpy array with the labels for each non-orphan fiber', exists=True) - filtered_tractography = File(desc='TrackVis file containing only those fibers originate in one and terminate in another region', exists=True) - filtered_tractography_by_intersections = File(desc='TrackVis file containing all fibers which connect two regions', exists=True) - filtered_tractographies = OutputMultiPath(File(desc='TrackVis file containing only those fibers originate in one and terminate in another region', exists=True)) - stats_file = File(desc='Saved Matlab .mat file with the number of fibers saved at each stage', exists=True) - -class CreateMatrix(BaseInterface): - """ - Performs connectivity mapping and outputs the result as a NetworkX graph and a Matlab matrix - - Example - ------- - - >>> import nipype.interfaces.cmtk as cmtk - >>> conmap = cmtk.CreateMatrix() - >>> conmap.roi_file = 'fsLUT_aparc+aseg.nii' - >>> conmap.tract_file = 'fibers.trk' - >>> conmap.run() # doctest: +SKIP - """ - - input_spec = CreateMatrixInputSpec - output_spec = CreateMatrixOutputSpec - - def _run_interface(self, runtime): - if isdefined(self.inputs.out_matrix_file): - path, name, _ = split_filename(self.inputs.out_matrix_file) - matrix_file = op.abspath(name + '.pck') - else: - matrix_file = self._gen_outfilename('.pck') - - matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file) - path, name, ext = split_filename(matrix_mat_file) - if not ext == '.mat': - ext = '.mat' - matrix_mat_file = matrix_mat_file + ext - - if isdefined(self.inputs.out_mean_fiber_length_matrix_mat_file): - mean_fiber_length_matrix_mat_file = op.abspath(self.inputs.out_mean_fiber_length_matrix_mat_file) - else: - mean_fiber_length_matrix_name = op.abspath(self._gen_outfilename('_mean_fiber_length.mat')) - - if isdefined(self.inputs.out_median_fiber_length_matrix_mat_file): - median_fiber_length_matrix_mat_file = op.abspath(self.inputs.out_median_fiber_length_matrix_mat_file) - else: - median_fiber_length_matrix_name = op.abspath(self._gen_outfilename('_median_fiber_length.mat')) - - if isdefined(self.inputs.out_fiber_length_std_matrix_mat_file): - fiber_length_std_matrix_mat_file = op.abspath(self.inputs.out_fiber_length_std_matrix_mat_file) - else: - fiber_length_std_matrix_name = op.abspath(self._gen_outfilename('_fiber_length_std.mat')) - - if not isdefined(self.inputs.out_endpoint_array_name): - _, endpoint_name , _ = split_filename(self.inputs.tract_file) - endpoint_name = op.abspath(endpoint_name) - else: - endpoint_name = op.abspath(self.inputs.out_endpoint_array_name) - - cmat(self.inputs.tract_file, self.inputs.roi_file, self.inputs.resolution_network_file, - matrix_file, matrix_mat_file, endpoint_name, self.inputs.count_region_intersections) - return runtime - - def _list_outputs(self): - outputs = self.output_spec().get() - if isdefined(self.inputs.out_matrix_file): - path, name, _ = split_filename(self.inputs.out_matrix_file) - out_matrix_file = op.abspath(name + '.pck') - out_intersection_matrix_file = op.abspath(name + '_intersections.pck') - else: - out_matrix_file = op.abspath(self._gen_outfilename('.pck')) - out_intersection_matrix_file = op.abspath(self._gen_outfilename('_intersections.pck')) - - outputs['matrix_file'] = out_matrix_file - outputs['intersection_matrix_file'] = out_intersection_matrix_file - - matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file) - path, name, ext = split_filename(matrix_mat_file) - if not ext == '.mat': - ext = '.mat' - matrix_mat_file = matrix_mat_file + ext - - outputs['matrix_mat_file'] = matrix_mat_file - if isdefined(self.inputs.out_mean_fiber_length_matrix_mat_file): - outputs['mean_fiber_length_matrix_mat_file'] = op.abspath(self.inputs.out_mean_fiber_length_matrix_mat_file) - else: - outputs['mean_fiber_length_matrix_mat_file'] = op.abspath(self._gen_outfilename('_mean_fiber_length.mat')) - - if isdefined(self.inputs.out_median_fiber_length_matrix_mat_file): - outputs['median_fiber_length_matrix_mat_file'] = op.abspath(self.inputs.out_median_fiber_length_matrix_mat_file) - else: - outputs['median_fiber_length_matrix_mat_file'] = op.abspath(self._gen_outfilename('_median_fiber_length.mat')) - - if isdefined(self.inputs.out_fiber_length_std_matrix_mat_file): - outputs['fiber_length_std_matrix_mat_file'] = op.abspath(self.inputs.out_fiber_length_std_matrix_mat_file) - else: - outputs['fiber_length_std_matrix_mat_file'] = op.abspath(self._gen_outfilename('_fiber_length_std.mat')) - - if isdefined(self.inputs.out_intersection_matrix_mat_file): - outputs['intersection_matrix_mat_file'] = op.abspath(self.inputs.out_intersection_matrix_mat_file) - else: - outputs['intersection_matrix_mat_file'] = op.abspath(self._gen_outfilename('_intersections.mat')) - - if isdefined(self.inputs.out_endpoint_array_name): - endpoint_name = self.inputs.out_endpoint_array_name - outputs['endpoint_file'] = op.abspath(self.inputs.out_endpoint_array_name + '_endpoints.npy') - outputs['endpoint_file_mm'] = op.abspath(self.inputs.out_endpoint_array_name + '_endpointsmm.npy') - outputs['fiber_length_file'] = op.abspath(self.inputs.out_endpoint_array_name + '_final_fiberslength.npy') - outputs['fiber_label_file'] = op.abspath(self.inputs.out_endpoint_array_name + '_filtered_fiberslabel.npy') - outputs['fiber_labels_noorphans'] = op.abspath(self.inputs.out_endpoint_array_name + '_final_fiberslabels.npy') - else: - _, endpoint_name , _ = split_filename(self.inputs.tract_file) - outputs['endpoint_file'] = op.abspath(endpoint_name + '_endpoints.npy') - outputs['endpoint_file_mm'] = op.abspath(endpoint_name + '_endpointsmm.npy') - outputs['fiber_length_file'] = op.abspath(endpoint_name + '_final_fiberslength.npy') - outputs['fiber_label_file'] = op.abspath(endpoint_name + '_filtered_fiberslabel.npy') - outputs['fiber_labels_noorphans'] = op.abspath(endpoint_name + '_final_fiberslabels.npy') - - if self.inputs.count_region_intersections: - outputs['matrix_files'] = [out_matrix_file, out_intersection_matrix_file] - outputs['matlab_matrix_files'] = [outputs['matrix_mat_file'], - outputs['mean_fiber_length_matrix_mat_file'], outputs['median_fiber_length_matrix_mat_file'], - outputs['fiber_length_std_matrix_mat_file'], outputs['intersection_matrix_mat_file']] - else: - outputs['matrix_files'] = [out_matrix_file] - outputs['matlab_matrix_files'] = [outputs['matrix_mat_file'], - outputs['mean_fiber_length_matrix_mat_file'], outputs['median_fiber_length_matrix_mat_file'], - outputs['fiber_length_std_matrix_mat_file']] - - outputs['filtered_tractography'] = op.abspath(endpoint_name + '_streamline_final.trk') - outputs['filtered_tractography_by_intersections'] = op.abspath(endpoint_name + '_intersections_streamline_final.trk') - outputs['filtered_tractographies'] = [outputs['filtered_tractography'], outputs['filtered_tractography_by_intersections']] - outputs['stats_file'] = op.abspath(endpoint_name + '_statistics.mat') - return outputs - - def _gen_outfilename(self, ext): - if ext.endswith("mat") and isdefined(self.inputs.out_matrix_mat_file): - _, name , _ = split_filename(self.inputs.out_matrix_mat_file) - elif isdefined(self.inputs.out_matrix_file): - _, name , _ = split_filename(self.inputs.out_matrix_file) - else: - _, name , _ = split_filename(self.inputs.tract_file) - return name + ext - -class ROIGenInputSpec(BaseInterfaceInputSpec): - aparc_aseg_file = File(exists=True, mandatory=True, desc='Freesurfer aparc+aseg file') - LUT_file = File(exists=True, xor=['use_freesurfer_LUT'], desc='Custom lookup table (cf. FreeSurferColorLUT.txt)') - use_freesurfer_LUT = traits.Bool(xor=['LUT_file'], desc='Boolean value; Set to True to use default Freesurfer LUT, False for custom LUT') - freesurfer_dir = Directory(requires=['use_freesurfer_LUT'], desc='Freesurfer main directory') - out_roi_file = File(genfile=True, desc='Region of Interest file for connectivity mapping') - out_dict_file = File(genfile=True, desc='Label dictionary saved in Pickle format') - -class ROIGenOutputSpec(TraitedSpec): - roi_file = File(desc='Region of Interest file for connectivity mapping') - dict_file = File(desc='Label dictionary saved in Pickle format') - -class ROIGen(BaseInterface): - """ - Generates a ROI file for connectivity mapping and a dictionary file containing relevant node information - - Example - ------- - - >>> import nipype.interfaces.cmtk as cmtk - >>> rg = cmtk.ROIGen() - >>> rg.inputs.aparc_aseg_file = 'aparc+aseg.nii' - >>> rg.inputs.use_freesurfer_LUT = True - >>> rg.inputs.freesurfer_dir = '/usr/local/freesurfer' - >>> rg.run() # doctest: +SKIP - - The label dictionary is written to disk using Pickle. Resulting data can be loaded using: - - >>> file = open("FreeSurferColorLUT_adapted_aparc+aseg_out.pck", "r") - >>> file = open("fsLUT_aparc+aseg.pck", "r") - >>> labelDict = pickle.load(file) # doctest: +SKIP - >>> print labelDict # doctest: +SKIP - """ - - input_spec = ROIGenInputSpec - output_spec = ROIGenOutputSpec - - def _run_interface(self, runtime): - aparc_aseg_file = self.inputs.aparc_aseg_file - aparcpath, aparcname, aparcext = split_filename(aparc_aseg_file) - iflogger.info('Using Aparc+Aseg file: {name}'.format(name=aparcname + aparcext)) - niiAPARCimg = nb.load(aparc_aseg_file) - niiAPARCdata = niiAPARCimg.get_data() - niiDataLabels = np.unique(niiAPARCdata) - numDataLabels = np.size(niiDataLabels) - iflogger.info('Number of labels in image: {n}'.format(n=numDataLabels)) - - write_dict = True - if self.inputs.use_freesurfer_LUT: - self.LUT_file = self.inputs.freesurfer_dir + '/FreeSurferColorLUT.txt' - iflogger.info('Using Freesurfer LUT: {name}'.format(name=self.LUT_file)) - prefix = 'fsLUT' - elif not self.inputs.use_freesurfer_LUT and isdefined(self.inputs.LUT_file): - self.LUT_file = op.abspath(self.inputs.LUT_file) - lutpath, lutname, lutext = split_filename(self.LUT_file) - iflogger.info('Using Custom LUT file: {name}'.format(name=lutname + lutext)) - prefix = lutname - else: - prefix = 'hardcoded' - write_dict = False - - if isdefined(self.inputs.out_roi_file): - roi_file = op.abspath(self.inputs.out_roi_file) - else: - roi_file = op.abspath(prefix + '_' + aparcname + '.nii') - - if isdefined(self.inputs.out_dict_file): - dict_file = op.abspath(self.inputs.out_dict_file) - else: - dict_file = op.abspath(prefix + '_' + aparcname + '.pck') - - if write_dict: - iflogger.info('Lookup table: {name}'.format(name=op.abspath(self.LUT_file))) - LUTlabelsRGBA = np.loadtxt(self.LUT_file, skiprows=4, usecols=[0, 1, 2, 3, 4, 5], comments='#', - dtype={'names': ('index', 'label', 'R', 'G', 'B', 'A'), 'formats': ('int', '|S30', 'int', 'int', 'int', 'int')}) - numLUTLabels = np.size(LUTlabelsRGBA) - if numLUTLabels < numDataLabels: - iflogger.error('LUT file provided does not contain all of the regions in the image') - iflogger.error('Removing unmapped regions') - iflogger.info('Number of labels in LUT: {n}'.format(n=numLUTLabels)) - LUTlabelDict = {} - - """ Create dictionary for input LUT table""" - for labels in xrange(0, numLUTLabels): - LUTlabelDict[LUTlabelsRGBA[labels][0]] = [LUTlabelsRGBA[labels][1], LUTlabelsRGBA[labels][2], LUTlabelsRGBA[labels][3], LUTlabelsRGBA[labels][4], LUTlabelsRGBA[labels][5]] - - iflogger.info('Printing LUT label dictionary') - iflogger.info(LUTlabelDict) - - mapDict = {} - MAPPING = [[1, 2012], [2, 2019], [3, 2032], [4, 2014], [5, 2020], [6, 2018], [7, 2027], [8, 2028], [9, 2003], [10, 2024], [11, 2017], [12, 2026], - [13, 2002], [14, 2023], [15, 2010], [16, 2022], [17, 2031], [18, 2029], [19, 2008], [20, 2025], [21, 2005], [22, 2021], [23, 2011], - [24, 2013], [25, 2007], [26, 2016], [27, 2006], [28, 2033], [29, 2009], [30, 2015], [31, 2001], [32, 2030], [33, 2034], [34, 2035], - [35, 49], [36, 50], [37, 51], [38, 52], [39, 58], [40, 53], [41, 54], [42, 1012], [43, 1019], [44, 1032], [45, 1014], [46, 1020], [47, 1018], - [48, 1027], [49, 1028], [50, 1003], [51, 1024], [52, 1017], [53, 1026], [54, 1002], [55, 1023], [56, 1010], [57, 1022], [58, 1031], - [59, 1029], [60, 1008], [61, 1025], [62, 1005], [63, 1021], [64, 1011], [65, 1013], [66, 1007], [67, 1016], [68, 1006], [69, 1033], - [70, 1009], [71, 1015], [72, 1001], [73, 1030], [74, 1034], [75, 1035], [76, 10], [77, 11], [78, 12], [79, 13], [80, 26], [81, 17], - [82, 18], [83, 16]] - - """ Create empty grey matter mask, Populate with only those regions defined in the mapping.""" - niiGM = np.zeros(niiAPARCdata.shape, dtype=np.uint) - for ma in MAPPING: - niiGM[ niiAPARCdata == ma[1]] = ma[0] - mapDict[ma[0]] = ma[1] - iflogger.info('Grey matter mask created') - greyMaskLabels = np.unique(niiGM) - numGMLabels = np.size(greyMaskLabels) - iflogger.info('Number of grey matter labels: {num}'.format(num=numGMLabels)) - - labelDict = {} - GMlabelDict = {} - for label in greyMaskLabels: - try: - mapDict[label] - if write_dict: - GMlabelDict['originalID'] = mapDict[label] - except: - iflogger.info('Label {lbl} not in provided mapping'.format(lbl=label)) - if write_dict: - del GMlabelDict - GMlabelDict = {} - GMlabelDict['labels'] = LUTlabelDict[label][0] - GMlabelDict['colors'] = [LUTlabelDict[label][1], LUTlabelDict[label][2], LUTlabelDict[label][3]] - GMlabelDict['a'] = LUTlabelDict[label][4] - labelDict[label] = GMlabelDict - - roi_image = nb.Nifti1Image(niiGM, niiAPARCimg.get_affine(), niiAPARCimg.get_header()) - iflogger.info('Saving ROI File to {path}'.format(path=roi_file)) - nb.save(roi_image, roi_file) - - if write_dict: - iflogger.info('Saving Dictionary File to {path} in Pickle format'.format(path=dict_file)) - file = open(dict_file, 'w') - pickle.dump(labelDict, file) - file.close() - return runtime - - def _list_outputs(self): - outputs = self._outputs().get() - if isdefined(self.inputs.out_roi_file): - outputs['roi_file'] = op.abspath(self.inputs.out_roi_file) - else: - outputs['roi_file'] = op.abspath(self._gen_outfilename('nii')) - if isdefined(self.inputs.out_dict_file): - outputs['dict_file'] = op.abspath(self.inputs.out_dict_file) - else: - outputs['dict_file'] = op.abspath(self._gen_outfilename('pck')) - return outputs - - def _gen_outfilename(self, ext): - _, name , _ = split_filename(self.inputs.aparc_aseg_file) - if self.inputs.use_freesurfer_LUT: - prefix = 'fsLUT' - elif not self.inputs.use_freesurfer_LUT and isdefined(self.inputs.LUT_file): - lutpath, lutname, lutext = split_filename(self.inputs.LUT_file) - prefix = lutname - else: - prefix = 'hardcoded' - return prefix + '_' + name + '.' + ext - -def create_nodes(roi_file, resolution_network_file, out_filename): - G = nx.Graph() - gp = nx.read_graphml(resolution_network_file) - roi_image = nb.load(roi_file) - roiData = roi_image.get_data() - nROIs = len(gp.nodes()) - for u, d in gp.nodes_iter(data=True): - G.add_node(int(u), d) - xyz = tuple(np.mean(np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])) , axis=1)) - G.node[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]]) - nx.write_gpickle(G, out_filename) - return out_filename - -class CreateNodesInputSpec(BaseInterfaceInputSpec): - roi_file = File(exists=True, mandatory=True, desc='Region of interest file') - resolution_network_file = File(exists=True, mandatory=True, desc='Parcellation file from Connectome Mapping Toolkit') - out_filename = File('nodenetwork.pck', usedefault=True, desc='Output gpickled network with the nodes defined.') - -class CreateNodesOutputSpec(TraitedSpec): - node_network = File(desc='Output gpickled network with the nodes defined.') - -class CreateNodes(BaseInterface): - """ - Generates a NetworkX graph containing nodes at the centroid of each region in the input ROI file. - Node data is added from the resolution network file. - - Example - ------- - - >>> import nipype.interfaces.cmtk as cmtk - >>> mknode = cmtk.CreateNodes() - >>> mknode.inputs.roi_file = 'ROI_scale500.nii.gz' - >>> mknode.run() # doctest: +SKIP - """ - - input_spec = CreateNodesInputSpec - output_spec = CreateNodesOutputSpec - - def _run_interface(self, runtime): - iflogger.info('Creating nodes...') - create_nodes(self.inputs.roi_file, self.inputs.resolution_network_file, self.inputs.out_filename) - iflogger.info('Saving node network to {path}'.format(path=op.abspath(self.inputs.out_filename))) - return runtime - - def _list_outputs(self): - outputs = self._outputs().get() - outputs['node_network'] = op.abspath(self.inputs.out_filename) - return outputs +# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- +# vi: set ft=python sts=4 ts=4 sw=4 et: +""" + Change directory to provide relative paths for doctests + >>> import os + >>> filepath = os.path.dirname( os.path.realpath( __file__ ) ) + >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) + >>> os.chdir(datadir) + +""" + +from __future__ import print_function +from __future__ import division +from builtins import range + +import pickle +import os.path as op + +import numpy as np +import nibabel as nb +import networkx as nx +import scipy.io as sio + +from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, + File, TraitedSpec, InputMultiPath, Directory, + OutputMultiPath, isdefined) +from ...utils.filemanip import split_filename +from ... import logging +iflogger = logging.getLogger('interface') + + +def length(xyz, along=False): + """ + Euclidean length of track line + + Parameters + ---------- + xyz : array-like shape (N,3) + array representing x,y,z of N points in a track + along : bool, optional + If True, return array giving cumulative length along track, + otherwise (default) return scalar giving total length. + + Returns + ------- + L : scalar or array shape (N-1,) + scalar in case of `along` == False, giving total length, array if + `along` == True, giving cumulative lengths. + + Examples + -------- + >>> xyz = np.array([[1,1,1],[2,3,4],[0,0,0]]) + >>> expected_lens = np.sqrt([1+2**2+3**2, 2**2+3**2+4**2]) + >>> length(xyz) == expected_lens.sum() + True + >>> len_along = length(xyz, along=True) + >>> np.allclose(len_along, expected_lens.cumsum()) + True + >>> length([]) + 0 + >>> length([[1, 2, 3]]) + 0 + >>> length([], along=True) + array([0]) + """ + xyz = np.asarray(xyz) + if xyz.shape[0] < 2: + if along: + return np.array([0]) + return 0 + dists = np.sqrt((np.diff(xyz, axis=0) ** 2).sum(axis=1)) + if along: + return np.cumsum(dists) + return np.sum(dists) + +def get_rois_crossed(pointsmm, roiData, voxelSize): + n_points = len(pointsmm) + rois_crossed = [] + for j in range(0, n_points): + # store point + x = int(pointsmm[j, 0] / float(voxelSize[0])) + y = int(pointsmm[j, 1] / float(voxelSize[1])) + z = int(pointsmm[j, 2] / float(voxelSize[2])) + if not roiData[x, y, z] == 0: + rois_crossed.append(roiData[x, y, z]) + rois_crossed = list(dict.fromkeys(rois_crossed).keys()) #Removed duplicates from the list + return rois_crossed + +def get_connectivity_matrix(n_rois, list_of_roi_crossed_lists): + connectivity_matrix = np.zeros((n_rois, n_rois), dtype=np.uint) + for rois_crossed in list_of_roi_crossed_lists: + for idx_i, roi_i in enumerate(rois_crossed): + for idx_j, roi_j in enumerate(rois_crossed): + if idx_i > idx_j: + if not roi_i == roi_j: + connectivity_matrix[roi_i - 1, roi_j - 1] += 1 + connectivity_matrix = connectivity_matrix + connectivity_matrix.T + return connectivity_matrix + +def create_allpoints_cmat(streamlines, roiData, voxelSize, n_rois): + """ Create the intersection arrays for each fiber + """ + n_fib = len(streamlines) + pc = -1 + # Computation for each fiber + final_fiber_ids = [] + list_of_roi_crossed_lists = [] + for i, fiber in enumerate(streamlines): + pcN = int(round(float(100 * i) / n_fib)) + if pcN > pc and pcN % 1 == 0: + pc = pcN + print('%4.0f%%' % (pc)) + rois_crossed = get_rois_crossed(fiber[0], roiData, voxelSize) + if len(rois_crossed) > 0: + list_of_roi_crossed_lists.append(list(rois_crossed)) + final_fiber_ids.append(i) + + connectivity_matrix = get_connectivity_matrix(n_rois, list_of_roi_crossed_lists) + dis = n_fib - len(final_fiber_ids) + iflogger.info("Found %i (%f percent out of %i fibers) fibers that start or terminate in a voxel which is not labeled. (orphans)" % (dis, dis * 100.0 / n_fib, n_fib)) + iflogger.info("Valid fibers: %i (%f percent)" % (n_fib - dis, 100 - dis * 100.0 / n_fib)) + iflogger.info('Returning the intersecting point connectivity matrix') + return connectivity_matrix, final_fiber_ids + +def create_endpoints_array(fib, voxelSize): + """ Create the endpoints arrays for each fiber + Parameters + ---------- + fib: the fibers data + voxelSize: 3-tuple containing the voxel size of the ROI image + Returns + ------- + (endpoints: matrix of size [#fibers, 2, 3] containing for each fiber the + index of its first and last point in the voxelSize volume + endpointsmm) : endpoints in milimeter coordinates + """ + + # Init + n = len(fib) + endpoints = np.zeros((n, 2, 3)) + endpointsmm = np.zeros((n, 2, 3)) + pc = -1 + + # Computation for each fiber + for i, fi in enumerate(fib): + f = fi[0] + + # store startpoint + endpoints[i, 0, :] = f[0, :] + # store endpoint + endpoints[i, 1, :] = f[-1, :] + + # store startpoint + endpointsmm[i, 0, :] = f[0, :] + # store endpoint + endpointsmm[i, 1, :] = f[-1, :] + + # Translate from mm to index + endpoints[i, 0, 0] = int(endpoints[i, 0, 0] / float(voxelSize[0])) + endpoints[i, 0, 1] = int(endpoints[i, 0, 1] / float(voxelSize[1])) + endpoints[i, 0, 2] = int(endpoints[i, 0, 2] / float(voxelSize[2])) + endpoints[i, 1, 0] = int(endpoints[i, 1, 0] / float(voxelSize[0])) + endpoints[i, 1, 1] = int(endpoints[i, 1, 1] / float(voxelSize[1])) + endpoints[i, 1, 2] = int(endpoints[i, 1, 2] / float(voxelSize[2])) + + # Return the matrices + iflogger.info('Returning the endpoint matrix') + return (endpoints, endpointsmm) + +def cmat(track_file, roi_file, resolution_network_file, matrix_name, matrix_mat_name, endpoint_name, intersections=False): + """ Create the connection matrix for each resolution using fibers and ROIs. """ + + stats = {} + iflogger.info('Running cmat function') + # Identify the endpoints of each fiber + en_fname = op.abspath(endpoint_name + '_endpoints.npy') + en_fnamemm = op.abspath(endpoint_name + '_endpointsmm.npy') + + iflogger.info('Reading Trackvis file {trk}'.format(trk=track_file)) + fib, hdr = nb.trackvis.read(track_file, False) + stats['orig_n_fib'] = len(fib) + + roi = nb.load(roi_file) + roiData = roi.get_data() + roiVoxelSize = roi.get_header().get_zooms() + (endpoints, endpointsmm) = create_endpoints_array(fib, roiVoxelSize) + + # Output endpoint arrays + iflogger.info('Saving endpoint array: {array}'.format(array=en_fname)) + np.save(en_fname, endpoints) + iflogger.info('Saving endpoint array in mm: {array}'.format(array=en_fnamemm)) + np.save(en_fnamemm, endpointsmm) + + n = len(fib) + iflogger.info('Number of fibers {num}'.format(num=n)) + + # Create empty fiber label array + fiberlabels = np.zeros((n, 2)) + final_fiberlabels = [] + final_fibers_idx = [] + + # Add node information from specified parcellation scheme + path, name, ext = split_filename(resolution_network_file) + if ext == '.pck': + gp = nx.read_gpickle(resolution_network_file) + elif ext == '.graphml': + gp = nx.read_graphml(resolution_network_file) + + nROIs = len(gp.nodes()) + + # add node information from parcellation + if 'dn_position' in gp.node[gp.nodes()[0]]: + G = gp.copy() + else: + G = nx.Graph() + for u, d in gp.nodes_iter(data=True): + G.add_node(int(u), d) + # compute a position for the node based on the mean position of the + # ROI in voxel coordinates (segmentation volume ) + xyz = tuple(np.mean(np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])) , axis=1)) + G.node[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]]) + + if intersections: + iflogger.info("Filtering tractography from intersections") + intersection_matrix, final_fiber_ids = create_allpoints_cmat(fib, roiData, roiVoxelSize, nROIs) + finalfibers_fname = op.abspath(endpoint_name + '_intersections_streamline_final.trk') + stats['intersections_n_fib'] = save_fibers(hdr, fib, finalfibers_fname, final_fiber_ids) + intersection_matrix = np.matrix(intersection_matrix) + I = G.copy() + H = nx.from_numpy_matrix(np.matrix(intersection_matrix)) + H = nx.relabel_nodes(H, lambda x: x + 1) #relabel nodes so they start at 1 + I.add_weighted_edges_from(((u, v, d['weight']) for u, v, d in H.edges(data=True))) + + dis = 0 + for i in range(endpoints.shape[0]): + + # ROI start => ROI end + try: + startROI = int(roiData[endpoints[i, 0, 0], endpoints[i, 0, 1], endpoints[i, 0, 2]]) + endROI = int(roiData[endpoints[i, 1, 0], endpoints[i, 1, 1], endpoints[i, 1, 2]]) + except IndexError: + iflogger.error(("AN INDEXERROR EXCEPTION OCCURED FOR FIBER %s. PLEASE CHECK ENDPOINT GENERATION" % i)) + break + + # Filter + if startROI == 0 or endROI == 0: + dis += 1 + fiberlabels[i, 0] = -1 + continue + + if startROI > nROIs or endROI > nROIs: + iflogger.error("Start or endpoint of fiber terminate in a voxel which is labeled higher") + iflogger.error("than is expected by the parcellation node information.") + iflogger.error("Start ROI: %i, End ROI: %i" % (startROI, endROI)) + iflogger.error("This needs bugfixing!") + continue + + # Update fiber label + # switch the rois in order to enforce startROI < endROI + if endROI < startROI: + tmp = startROI + startROI = endROI + endROI = tmp + + fiberlabels[i, 0] = startROI + fiberlabels[i, 1] = endROI + + final_fiberlabels.append([ startROI, endROI ]) + final_fibers_idx.append(i) + + # Add edge to graph + if G.has_edge(startROI, endROI) and 'fiblist' in G.edge[startROI][endROI]: + G.edge[startROI][endROI]['fiblist'].append(i) + else: + G.add_edge(startROI, endROI, fiblist=[i]) + + # create a final fiber length array + finalfiberlength = [] + if intersections: + final_fibers_indices = final_fiber_ids + else: + final_fibers_indices = final_fibers_idx + + for idx in final_fibers_indices: + # compute length of fiber + finalfiberlength.append(length(fib[idx][0])) + + # convert to array + final_fiberlength_array = np.array(finalfiberlength) + + # make final fiber labels as array + final_fiberlabels_array = np.array(final_fiberlabels, dtype=int) + + iflogger.info("Found %i (%f percent out of %i fibers) fibers that start or terminate in a voxel which is not labeled. (orphans)" % (dis, dis * 100.0 / n, n)) + iflogger.info("Valid fibers: %i (%f percent)" % (n - dis, 100 - dis * 100.0 / n)) + + numfib = nx.Graph() + numfib.add_nodes_from(G) + fibmean = numfib.copy() + fibmedian = numfib.copy() + fibdev = numfib.copy() + for u, v, d in G.edges_iter(data=True): + G.remove_edge(u, v) + di = {} + if 'fiblist' in d: + di['number_of_fibers'] = len(d['fiblist']) + idx = np.where((final_fiberlabels_array[:, 0] == int(u)) & (final_fiberlabels_array[:, 1] == int(v)))[0] + di['fiber_length_mean'] = float(np.mean(final_fiberlength_array[idx])) + di['fiber_length_median'] = float(np.median(final_fiberlength_array[idx])) + di['fiber_length_std'] = float(np.std(final_fiberlength_array[idx])) + else: + di['number_of_fibers'] = 0 + di['fiber_length_mean'] = 0 + di['fiber_length_median'] = 0 + di['fiber_length_std'] = 0 + if not u == v: #Fix for self loop problem + G.add_edge(u, v, di) + if 'fiblist' in d: + numfib.add_edge(u, v, weight=di['number_of_fibers']) + fibmean.add_edge(u, v, weight=di['fiber_length_mean']) + fibmedian.add_edge(u, v, weight=di['fiber_length_median']) + fibdev.add_edge(u, v, weight=di['fiber_length_std']) + + iflogger.info('Writing network as {ntwk}'.format(ntwk=matrix_name)) + nx.write_gpickle(G, op.abspath(matrix_name)) + + numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) + numfib_dict = {'number_of_fibers': numfib_mlab} + fibmean_mlab = nx.to_numpy_matrix(fibmean, dtype=np.float64) + fibmean_dict = {'mean_fiber_length':fibmean_mlab} + fibmedian_mlab = nx.to_numpy_matrix(fibmedian, dtype=np.float64) + fibmedian_dict = {'median_fiber_length':fibmedian_mlab} + fibdev_mlab = nx.to_numpy_matrix(fibdev, dtype=np.float64) + fibdev_dict = {'fiber_length_std':fibdev_mlab} + + if intersections: + path, name, ext = split_filename(matrix_name) + intersection_matrix_name = op.abspath(name + '_intersections') + ext + iflogger.info('Writing intersection network as {ntwk}'.format(ntwk=intersection_matrix_name)) + nx.write_gpickle(I, intersection_matrix_name) + + path, name, ext = split_filename(matrix_mat_name) + if not ext == '.mat': + ext = '.mat' + matrix_mat_name = matrix_mat_name + ext + + iflogger.info('Writing matlab matrix as {mat}'.format(mat=matrix_mat_name)) + sio.savemat(matrix_mat_name, numfib_dict) + + if intersections: + intersect_dict = {'intersections': intersection_matrix} + intersection_matrix_mat_name = op.abspath(name + '_intersections') + ext + iflogger.info('Writing intersection matrix as {mat}'.format(mat=intersection_matrix_mat_name)) + sio.savemat(intersection_matrix_mat_name, intersect_dict) + + mean_fiber_length_matrix_name = op.abspath(name + '_mean_fiber_length') + ext + iflogger.info('Writing matlab mean fiber length matrix as {mat}'.format(mat=mean_fiber_length_matrix_name)) + sio.savemat(mean_fiber_length_matrix_name, fibmean_dict) + + median_fiber_length_matrix_name = op.abspath(name + '_median_fiber_length') + ext + iflogger.info('Writing matlab median fiber length matrix as {mat}'.format(mat=median_fiber_length_matrix_name)) + sio.savemat(median_fiber_length_matrix_name, fibmedian_dict) + + fiber_length_std_matrix_name = op.abspath(name + '_fiber_length_std') + ext + iflogger.info('Writing matlab fiber length deviation matrix as {mat}'.format(mat=fiber_length_std_matrix_name)) + sio.savemat(fiber_length_std_matrix_name, fibdev_dict) + + fiberlengths_fname = op.abspath(endpoint_name + '_final_fiberslength.npy') + iflogger.info("Storing final fiber length array as %s" % fiberlengths_fname) + np.save(fiberlengths_fname, final_fiberlength_array) + + fiberlabels_fname = op.abspath(endpoint_name + '_filtered_fiberslabel.npy') + iflogger.info("Storing all fiber labels (with orphans) as %s" % fiberlabels_fname) + np.save(fiberlabels_fname, np.array(fiberlabels, dtype=np.int32),) + + fiberlabels_noorphans_fname = op.abspath(endpoint_name + '_final_fiberslabels.npy') + iflogger.info("Storing final fiber labels (no orphans) as %s" % fiberlabels_noorphans_fname) + np.save(fiberlabels_noorphans_fname, final_fiberlabels_array) + + iflogger.info("Filtering tractography - keeping only no orphan fibers") + finalfibers_fname = op.abspath(endpoint_name + '_streamline_final.trk') + stats['endpoint_n_fib'] = save_fibers(hdr, fib, finalfibers_fname, final_fibers_idx) + stats['endpoints_percent'] = float(stats['endpoint_n_fib'])/float(stats['orig_n_fib'])*100 + stats['intersections_percent'] = float(stats['intersections_n_fib'])/float(stats['orig_n_fib'])*100 + + out_stats_file = op.abspath(endpoint_name + '_statistics.mat') + iflogger.info("Saving matrix creation statistics as %s" % out_stats_file) + sio.savemat(out_stats_file, stats) + +def save_fibers(oldhdr, oldfib, fname, indices): + """ Stores a new trackvis file fname using only given indices """ + hdrnew = oldhdr.copy() + outstreams = [] + for i in indices: + outstreams.append(oldfib[i]) + n_fib_out = len(outstreams) + hdrnew['n_count'] = n_fib_out + iflogger.info("Writing final non-orphan fibers as %s" % fname) + nb.trackvis.write(fname, outstreams, hdrnew) + return n_fib_out + +class CreateMatrixInputSpec(TraitedSpec): + roi_file = File(exists=True, mandatory=True, desc='Freesurfer aparc+aseg file') + tract_file = File(exists=True, mandatory=True, desc='Trackvis tract file') + resolution_network_file = File(exists=True, mandatory=True, desc='Parcellation files from Connectome Mapping Toolkit') + count_region_intersections = traits.Bool(False, usedefault=True, desc='Counts all of the fiber-region traversals in the connectivity matrix (requires significantly more computational time)') + out_matrix_file = File(genfile=True, desc='NetworkX graph describing the connectivity') + out_matrix_mat_file = File('cmatrix.mat', usedefault=True, desc='Matlab matrix describing the connectivity') + out_mean_fiber_length_matrix_mat_file = File(genfile=True, desc='Matlab matrix describing the mean fiber lengths between each node.') + out_median_fiber_length_matrix_mat_file = File(genfile=True, desc='Matlab matrix describing the mean fiber lengths between each node.') + out_fiber_length_std_matrix_mat_file = File(genfile=True, desc='Matlab matrix describing the deviation in fiber lengths connecting each node.') + out_intersection_matrix_mat_file = File(genfile=True, desc='Matlab connectivity matrix if all region/fiber intersections are counted.') + out_endpoint_array_name = File(genfile=True, desc='Name for the generated endpoint arrays') + +class CreateMatrixOutputSpec(TraitedSpec): + matrix_file = File(desc='NetworkX graph describing the connectivity', exists=True) + intersection_matrix_file = File(desc='NetworkX graph describing the connectivity', exists=True) + matrix_files = OutputMultiPath(File(desc='All of the gpickled network files output by this interface', exists=True)) + matlab_matrix_files = OutputMultiPath(File(desc='All of the MATLAB .mat files output by this interface', exists=True)) + matrix_mat_file = File(desc='Matlab matrix describing the connectivity', exists=True) + intersection_matrix_mat_file = File(desc='Matlab matrix describing the mean fiber lengths between each node.', exists=True) + mean_fiber_length_matrix_mat_file = File(desc='Matlab matrix describing the mean fiber lengths between each node.', exists=True) + median_fiber_length_matrix_mat_file = File(desc='Matlab matrix describing the median fiber lengths between each node.', exists=True) + fiber_length_std_matrix_mat_file = File(desc='Matlab matrix describing the deviation in fiber lengths connecting each node.', exists=True) + endpoint_file = File(desc='Saved Numpy array with the endpoints of each fiber', exists=True) + endpoint_file_mm = File(desc='Saved Numpy array with the endpoints of each fiber (in millimeters)', exists=True) + fiber_length_file = File(desc='Saved Numpy array with the lengths of each fiber', exists=True) + fiber_label_file = File(desc='Saved Numpy array with the labels for each fiber', exists=True) + fiber_labels_noorphans = File(desc='Saved Numpy array with the labels for each non-orphan fiber', exists=True) + filtered_tractography = File(desc='TrackVis file containing only those fibers originate in one and terminate in another region', exists=True) + filtered_tractography_by_intersections = File(desc='TrackVis file containing all fibers which connect two regions', exists=True) + filtered_tractographies = OutputMultiPath(File(desc='TrackVis file containing only those fibers originate in one and terminate in another region', exists=True)) + stats_file = File(desc='Saved Matlab .mat file with the number of fibers saved at each stage', exists=True) + +class CreateMatrix(BaseInterface): + """ + Performs connectivity mapping and outputs the result as a NetworkX graph and a Matlab matrix + + Example + ------- + + >>> import nipype.interfaces.cmtk as cmtk + >>> conmap = cmtk.CreateMatrix() + >>> conmap.roi_file = 'fsLUT_aparc+aseg.nii' + >>> conmap.tract_file = 'fibers.trk' + >>> conmap.run() # doctest: +SKIP + """ + + input_spec = CreateMatrixInputSpec + output_spec = CreateMatrixOutputSpec + + def _run_interface(self, runtime): + if isdefined(self.inputs.out_matrix_file): + path, name, _ = split_filename(self.inputs.out_matrix_file) + matrix_file = op.abspath(name + '.pck') + else: + matrix_file = self._gen_outfilename('.pck') + + matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file) + path, name, ext = split_filename(matrix_mat_file) + if not ext == '.mat': + ext = '.mat' + matrix_mat_file = matrix_mat_file + ext + + if isdefined(self.inputs.out_mean_fiber_length_matrix_mat_file): + mean_fiber_length_matrix_mat_file = op.abspath(self.inputs.out_mean_fiber_length_matrix_mat_file) + else: + mean_fiber_length_matrix_name = op.abspath(self._gen_outfilename('_mean_fiber_length.mat')) + + if isdefined(self.inputs.out_median_fiber_length_matrix_mat_file): + median_fiber_length_matrix_mat_file = op.abspath(self.inputs.out_median_fiber_length_matrix_mat_file) + else: + median_fiber_length_matrix_name = op.abspath(self._gen_outfilename('_median_fiber_length.mat')) + + if isdefined(self.inputs.out_fiber_length_std_matrix_mat_file): + fiber_length_std_matrix_mat_file = op.abspath(self.inputs.out_fiber_length_std_matrix_mat_file) + else: + fiber_length_std_matrix_name = op.abspath(self._gen_outfilename('_fiber_length_std.mat')) + + if not isdefined(self.inputs.out_endpoint_array_name): + _, endpoint_name , _ = split_filename(self.inputs.tract_file) + endpoint_name = op.abspath(endpoint_name) + else: + endpoint_name = op.abspath(self.inputs.out_endpoint_array_name) + + cmat(self.inputs.tract_file, self.inputs.roi_file, self.inputs.resolution_network_file, + matrix_file, matrix_mat_file, endpoint_name, self.inputs.count_region_intersections) + return runtime + + def _list_outputs(self): + outputs = self.output_spec().get() + if isdefined(self.inputs.out_matrix_file): + path, name, _ = split_filename(self.inputs.out_matrix_file) + out_matrix_file = op.abspath(name + '.pck') + out_intersection_matrix_file = op.abspath(name + '_intersections.pck') + else: + out_matrix_file = op.abspath(self._gen_outfilename('.pck')) + out_intersection_matrix_file = op.abspath(self._gen_outfilename('_intersections.pck')) + + outputs['matrix_file'] = out_matrix_file + outputs['intersection_matrix_file'] = out_intersection_matrix_file + + matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file) + path, name, ext = split_filename(matrix_mat_file) + if not ext == '.mat': + ext = '.mat' + matrix_mat_file = matrix_mat_file + ext + + outputs['matrix_mat_file'] = matrix_mat_file + if isdefined(self.inputs.out_mean_fiber_length_matrix_mat_file): + outputs['mean_fiber_length_matrix_mat_file'] = op.abspath(self.inputs.out_mean_fiber_length_matrix_mat_file) + else: + outputs['mean_fiber_length_matrix_mat_file'] = op.abspath(self._gen_outfilename('_mean_fiber_length.mat')) + + if isdefined(self.inputs.out_median_fiber_length_matrix_mat_file): + outputs['median_fiber_length_matrix_mat_file'] = op.abspath(self.inputs.out_median_fiber_length_matrix_mat_file) + else: + outputs['median_fiber_length_matrix_mat_file'] = op.abspath(self._gen_outfilename('_median_fiber_length.mat')) + + if isdefined(self.inputs.out_fiber_length_std_matrix_mat_file): + outputs['fiber_length_std_matrix_mat_file'] = op.abspath(self.inputs.out_fiber_length_std_matrix_mat_file) + else: + outputs['fiber_length_std_matrix_mat_file'] = op.abspath(self._gen_outfilename('_fiber_length_std.mat')) + + if isdefined(self.inputs.out_intersection_matrix_mat_file): + outputs['intersection_matrix_mat_file'] = op.abspath(self.inputs.out_intersection_matrix_mat_file) + else: + outputs['intersection_matrix_mat_file'] = op.abspath(self._gen_outfilename('_intersections.mat')) + + if isdefined(self.inputs.out_endpoint_array_name): + endpoint_name = self.inputs.out_endpoint_array_name + outputs['endpoint_file'] = op.abspath(self.inputs.out_endpoint_array_name + '_endpoints.npy') + outputs['endpoint_file_mm'] = op.abspath(self.inputs.out_endpoint_array_name + '_endpointsmm.npy') + outputs['fiber_length_file'] = op.abspath(self.inputs.out_endpoint_array_name + '_final_fiberslength.npy') + outputs['fiber_label_file'] = op.abspath(self.inputs.out_endpoint_array_name + '_filtered_fiberslabel.npy') + outputs['fiber_labels_noorphans'] = op.abspath(self.inputs.out_endpoint_array_name + '_final_fiberslabels.npy') + else: + _, endpoint_name , _ = split_filename(self.inputs.tract_file) + outputs['endpoint_file'] = op.abspath(endpoint_name + '_endpoints.npy') + outputs['endpoint_file_mm'] = op.abspath(endpoint_name + '_endpointsmm.npy') + outputs['fiber_length_file'] = op.abspath(endpoint_name + '_final_fiberslength.npy') + outputs['fiber_label_file'] = op.abspath(endpoint_name + '_filtered_fiberslabel.npy') + outputs['fiber_labels_noorphans'] = op.abspath(endpoint_name + '_final_fiberslabels.npy') + + if self.inputs.count_region_intersections: + outputs['matrix_files'] = [out_matrix_file, out_intersection_matrix_file] + outputs['matlab_matrix_files'] = [outputs['matrix_mat_file'], + outputs['mean_fiber_length_matrix_mat_file'], outputs['median_fiber_length_matrix_mat_file'], + outputs['fiber_length_std_matrix_mat_file'], outputs['intersection_matrix_mat_file']] + else: + outputs['matrix_files'] = [out_matrix_file] + outputs['matlab_matrix_files'] = [outputs['matrix_mat_file'], + outputs['mean_fiber_length_matrix_mat_file'], outputs['median_fiber_length_matrix_mat_file'], + outputs['fiber_length_std_matrix_mat_file']] + + outputs['filtered_tractography'] = op.abspath(endpoint_name + '_streamline_final.trk') + outputs['filtered_tractography_by_intersections'] = op.abspath(endpoint_name + '_intersections_streamline_final.trk') + outputs['filtered_tractographies'] = [outputs['filtered_tractography'], outputs['filtered_tractography_by_intersections']] + outputs['stats_file'] = op.abspath(endpoint_name + '_statistics.mat') + return outputs + + def _gen_outfilename(self, ext): + if ext.endswith("mat") and isdefined(self.inputs.out_matrix_mat_file): + _, name , _ = split_filename(self.inputs.out_matrix_mat_file) + elif isdefined(self.inputs.out_matrix_file): + _, name , _ = split_filename(self.inputs.out_matrix_file) + else: + _, name , _ = split_filename(self.inputs.tract_file) + return name + ext + +class ROIGenInputSpec(BaseInterfaceInputSpec): + aparc_aseg_file = File(exists=True, mandatory=True, desc='Freesurfer aparc+aseg file') + LUT_file = File(exists=True, xor=['use_freesurfer_LUT'], desc='Custom lookup table (cf. FreeSurferColorLUT.txt)') + use_freesurfer_LUT = traits.Bool(xor=['LUT_file'], desc='Boolean value; Set to True to use default Freesurfer LUT, False for custom LUT') + freesurfer_dir = Directory(requires=['use_freesurfer_LUT'], desc='Freesurfer main directory') + out_roi_file = File(genfile=True, desc='Region of Interest file for connectivity mapping') + out_dict_file = File(genfile=True, desc='Label dictionary saved in Pickle format') + +class ROIGenOutputSpec(TraitedSpec): + roi_file = File(desc='Region of Interest file for connectivity mapping') + dict_file = File(desc='Label dictionary saved in Pickle format') + +class ROIGen(BaseInterface): + """ + Generates a ROI file for connectivity mapping and a dictionary file containing relevant node information + + Example + ------- + + >>> import nipype.interfaces.cmtk as cmtk + >>> rg = cmtk.ROIGen() + >>> rg.inputs.aparc_aseg_file = 'aparc+aseg.nii' + >>> rg.inputs.use_freesurfer_LUT = True + >>> rg.inputs.freesurfer_dir = '/usr/local/freesurfer' + >>> rg.run() # doctest: +SKIP + + The label dictionary is written to disk using Pickle. Resulting data can be loaded using: + + >>> file = open("FreeSurferColorLUT_adapted_aparc+aseg_out.pck", "r") + >>> file = open("fsLUT_aparc+aseg.pck", "r") + >>> labelDict = pickle.load(file) # doctest: +SKIP + >>> labelDict # doctest: +SKIP + """ + + input_spec = ROIGenInputSpec + output_spec = ROIGenOutputSpec + + def _run_interface(self, runtime): + aparc_aseg_file = self.inputs.aparc_aseg_file + aparcpath, aparcname, aparcext = split_filename(aparc_aseg_file) + iflogger.info('Using Aparc+Aseg file: {name}'.format(name=aparcname + aparcext)) + niiAPARCimg = nb.load(aparc_aseg_file) + niiAPARCdata = niiAPARCimg.get_data() + niiDataLabels = np.unique(niiAPARCdata) + numDataLabels = np.size(niiDataLabels) + iflogger.info('Number of labels in image: {n}'.format(n=numDataLabels)) + + write_dict = True + if self.inputs.use_freesurfer_LUT: + self.LUT_file = self.inputs.freesurfer_dir + '/FreeSurferColorLUT.txt' + iflogger.info('Using Freesurfer LUT: {name}'.format(name=self.LUT_file)) + prefix = 'fsLUT' + elif not self.inputs.use_freesurfer_LUT and isdefined(self.inputs.LUT_file): + self.LUT_file = op.abspath(self.inputs.LUT_file) + lutpath, lutname, lutext = split_filename(self.LUT_file) + iflogger.info('Using Custom LUT file: {name}'.format(name=lutname + lutext)) + prefix = lutname + else: + prefix = 'hardcoded' + write_dict = False + + if isdefined(self.inputs.out_roi_file): + roi_file = op.abspath(self.inputs.out_roi_file) + else: + roi_file = op.abspath(prefix + '_' + aparcname + '.nii') + + if isdefined(self.inputs.out_dict_file): + dict_file = op.abspath(self.inputs.out_dict_file) + else: + dict_file = op.abspath(prefix + '_' + aparcname + '.pck') + + if write_dict: + iflogger.info('Lookup table: {name}'.format(name=op.abspath(self.LUT_file))) + LUTlabelsRGBA = np.loadtxt(self.LUT_file, skiprows=4, usecols=[0, 1, 2, 3, 4, 5], comments='#', + dtype={'names': ('index', 'label', 'R', 'G', 'B', 'A'), 'formats': ('int', '|S30', 'int', 'int', 'int', 'int')}) + numLUTLabels = np.size(LUTlabelsRGBA) + if numLUTLabels < numDataLabels: + iflogger.error('LUT file provided does not contain all of the regions in the image') + iflogger.error('Removing unmapped regions') + iflogger.info('Number of labels in LUT: {n}'.format(n=numLUTLabels)) + LUTlabelDict = {} + + """ Create dictionary for input LUT table""" + for labels in range(0, numLUTLabels): + LUTlabelDict[LUTlabelsRGBA[labels][0]] = [LUTlabelsRGBA[labels][1], LUTlabelsRGBA[labels][2], LUTlabelsRGBA[labels][3], LUTlabelsRGBA[labels][4], LUTlabelsRGBA[labels][5]] + + iflogger.info('Printing LUT label dictionary') + iflogger.info(LUTlabelDict) + + mapDict = {} + MAPPING = [[1, 2012], [2, 2019], [3, 2032], [4, 2014], [5, 2020], [6, 2018], [7, 2027], [8, 2028], [9, 2003], [10, 2024], [11, 2017], [12, 2026], + [13, 2002], [14, 2023], [15, 2010], [16, 2022], [17, 2031], [18, 2029], [19, 2008], [20, 2025], [21, 2005], [22, 2021], [23, 2011], + [24, 2013], [25, 2007], [26, 2016], [27, 2006], [28, 2033], [29, 2009], [30, 2015], [31, 2001], [32, 2030], [33, 2034], [34, 2035], + [35, 49], [36, 50], [37, 51], [38, 52], [39, 58], [40, 53], [41, 54], [42, 1012], [43, 1019], [44, 1032], [45, 1014], [46, 1020], [47, 1018], + [48, 1027], [49, 1028], [50, 1003], [51, 1024], [52, 1017], [53, 1026], [54, 1002], [55, 1023], [56, 1010], [57, 1022], [58, 1031], + [59, 1029], [60, 1008], [61, 1025], [62, 1005], [63, 1021], [64, 1011], [65, 1013], [66, 1007], [67, 1016], [68, 1006], [69, 1033], + [70, 1009], [71, 1015], [72, 1001], [73, 1030], [74, 1034], [75, 1035], [76, 10], [77, 11], [78, 12], [79, 13], [80, 26], [81, 17], + [82, 18], [83, 16]] + + """ Create empty grey matter mask, Populate with only those regions defined in the mapping.""" + niiGM = np.zeros(niiAPARCdata.shape, dtype=np.uint) + for ma in MAPPING: + niiGM[ niiAPARCdata == ma[1]] = ma[0] + mapDict[ma[0]] = ma[1] + iflogger.info('Grey matter mask created') + greyMaskLabels = np.unique(niiGM) + numGMLabels = np.size(greyMaskLabels) + iflogger.info('Number of grey matter labels: {num}'.format(num=numGMLabels)) + + labelDict = {} + GMlabelDict = {} + for label in greyMaskLabels: + try: + mapDict[label] + if write_dict: + GMlabelDict['originalID'] = mapDict[label] + except: + iflogger.info('Label {lbl} not in provided mapping'.format(lbl=label)) + if write_dict: + del GMlabelDict + GMlabelDict = {} + GMlabelDict['labels'] = LUTlabelDict[label][0] + GMlabelDict['colors'] = [LUTlabelDict[label][1], LUTlabelDict[label][2], LUTlabelDict[label][3]] + GMlabelDict['a'] = LUTlabelDict[label][4] + labelDict[label] = GMlabelDict + + roi_image = nb.Nifti1Image(niiGM, niiAPARCimg.get_affine(), niiAPARCimg.get_header()) + iflogger.info('Saving ROI File to {path}'.format(path=roi_file)) + nb.save(roi_image, roi_file) + + if write_dict: + iflogger.info('Saving Dictionary File to {path} in Pickle format'.format(path=dict_file)) + file = open(dict_file, 'w') + pickle.dump(labelDict, file) + file.close() + return runtime + + def _list_outputs(self): + outputs = self._outputs().get() + if isdefined(self.inputs.out_roi_file): + outputs['roi_file'] = op.abspath(self.inputs.out_roi_file) + else: + outputs['roi_file'] = op.abspath(self._gen_outfilename('nii')) + if isdefined(self.inputs.out_dict_file): + outputs['dict_file'] = op.abspath(self.inputs.out_dict_file) + else: + outputs['dict_file'] = op.abspath(self._gen_outfilename('pck')) + return outputs + + def _gen_outfilename(self, ext): + _, name , _ = split_filename(self.inputs.aparc_aseg_file) + if self.inputs.use_freesurfer_LUT: + prefix = 'fsLUT' + elif not self.inputs.use_freesurfer_LUT and isdefined(self.inputs.LUT_file): + lutpath, lutname, lutext = split_filename(self.inputs.LUT_file) + prefix = lutname + else: + prefix = 'hardcoded' + return prefix + '_' + name + '.' + ext + +def create_nodes(roi_file, resolution_network_file, out_filename): + G = nx.Graph() + gp = nx.read_graphml(resolution_network_file) + roi_image = nb.load(roi_file) + roiData = roi_image.get_data() + nROIs = len(gp.nodes()) + for u, d in gp.nodes_iter(data=True): + G.add_node(int(u), d) + xyz = tuple(np.mean(np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])) , axis=1)) + G.node[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]]) + nx.write_gpickle(G, out_filename) + return out_filename + +class CreateNodesInputSpec(BaseInterfaceInputSpec): + roi_file = File(exists=True, mandatory=True, desc='Region of interest file') + resolution_network_file = File(exists=True, mandatory=True, desc='Parcellation file from Connectome Mapping Toolkit') + out_filename = File('nodenetwork.pck', usedefault=True, desc='Output gpickled network with the nodes defined.') + +class CreateNodesOutputSpec(TraitedSpec): + node_network = File(desc='Output gpickled network with the nodes defined.') + +class CreateNodes(BaseInterface): + """ + Generates a NetworkX graph containing nodes at the centroid of each region in the input ROI file. + Node data is added from the resolution network file. + + Example + ------- + + >>> import nipype.interfaces.cmtk as cmtk + >>> mknode = cmtk.CreateNodes() + >>> mknode.inputs.roi_file = 'ROI_scale500.nii.gz' + >>> mknode.run() # doctest: +SKIP + """ + + input_spec = CreateNodesInputSpec + output_spec = CreateNodesOutputSpec + + def _run_interface(self, runtime): + iflogger.info('Creating nodes...') + create_nodes(self.inputs.roi_file, self.inputs.resolution_network_file, self.inputs.out_filename) + iflogger.info('Saving node network to {path}'.format(path=op.abspath(self.inputs.out_filename))) + return runtime + + def _list_outputs(self): + outputs = self._outputs().get() + outputs['node_network'] = op.abspath(self.inputs.out_filename) + return outputs diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py index 12a00e974c..ba980545b4 100644 --- a/nipype/interfaces/cmtk/convert.py +++ b/nipype/interfaces/cmtk/convert.py @@ -21,7 +21,7 @@ have_cfflib = True try: package_check('cfflib') -except Exception, e: +except Exception as e: have_cfflib = False else: import cfflib as cf diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py index b05807ed28..12ff6ee0da 100644 --- a/nipype/interfaces/cmtk/nbs.py +++ b/nipype/interfaces/cmtk/nbs.py @@ -1,21 +1,23 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec, traits, - File, TraitedSpec, InputMultiPath, - OutputMultiPath, isdefined) + import os.path as op +import warnings + import numpy as np import networkx as nx -from nipype.utils.misc import package_check -import warnings +from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, + File, TraitedSpec, InputMultiPath, + OutputMultiPath, isdefined) +from ...utils.misc import package_check from ... import logging iflogger = logging.getLogger('interface') have_cv = True try: package_check('cviewer') -except Exception, e: +except Exception as e: have_cv = False else: import cviewer.libs.pyconto.groupstatistics.nbs as nbs diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py index c003becd72..da9dc6695d 100644 --- a/nipype/interfaces/cmtk/nx.py +++ b/nipype/interfaces/cmtk/nx.py @@ -9,38 +9,41 @@ """ -from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec, traits, - File, TraitedSpec, InputMultiPath, - OutputMultiPath, isdefined) -from nipype.utils.filemanip import split_filename -import os, os.path as op +from __future__ import division +from builtins import range + +import os.path as op +import pickle + import numpy as np import networkx as nx import scipy.io as sio -import pickle -from nipype.utils.misc import package_check -import warnings +from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File, + TraitedSpec, InputMultiPath, OutputMultiPath, isdefined) +from ...utils.filemanip import split_filename +from ...utils.misc import package_check from ... import logging + iflogger = logging.getLogger('interface') have_cmp = True try: package_check('cmp') -except Exception, e: +except Exception as e: have_cmp = False else: import cmp def read_unknown_ntwk(ntwk): - if not isinstance(ntwk, nx.classes.graph.Graph): - path, name, ext = split_filename(ntwk) - if ext == '.pck': - ntwk = nx.read_gpickle(ntwk) - elif ext == '.graphml': - ntwk = nx.read_graphml(ntwk) - return ntwk + if not isinstance(ntwk, nx.classes.graph.Graph): + path, name, ext = split_filename(ntwk) + if ext == '.pck': + ntwk = nx.read_gpickle(ntwk) + elif ext == '.graphml': + ntwk = nx.read_graphml(ntwk) + return ntwk def remove_all_edges(ntwk): @@ -62,22 +65,22 @@ def fix_keys_for_gexf(orig): for node in nodes: newnodedata = {} newnodedata.update(orig.node[node]) - if orig.node[node].has_key('dn_fsname'): - newnodedata['label'] = orig.node[node]['dn_fsname'] + if 'dn_fsname' in orig.node[node]: + newnodedata['label'] = orig.node[node]['dn_fsname'] ntwk.add_node(str(node), newnodedata) - if ntwk.node[str(node)].has_key('dn_position') and newnodedata.has_key('dn_position'): + if 'dn_position' in ntwk.node[str(node)] and 'dn_position' in newnodedata: ntwk.node[str(node)]['dn_position'] = str(newnodedata['dn_position']) for edge in edges: data = {} data = orig.edge[edge[0]][edge[1]] ntwk.add_edge(str(edge[0]), str(edge[1]), data) - if ntwk.edge[str(edge[0])][str(edge[1])].has_key('fiber_length_mean'): + if 'fiber_length_mean' in ntwk.edge[str(edge[0])][str(edge[1])]: ntwk.edge[str(edge[0])][str(edge[1])]['fiber_length_mean'] = str(data['fiber_length_mean']) - if ntwk.edge[str(edge[0])][str(edge[1])].has_key('fiber_length_std'): + if 'fiber_length_std' in ntwk.edge[str(edge[0])][str(edge[1])]: ntwk.edge[str(edge[0])][str(edge[1])]['fiber_length_std'] = str(data['fiber_length_std']) - if ntwk.edge[str(edge[0])][str(edge[1])].has_key('number_of_fibers'): + if 'number_of_fibers' in ntwk.edge[str(edge[0])][str(edge[1])]: ntwk.edge[str(edge[0])][str(edge[1])]['number_of_fibers'] = str(data['number_of_fibers']) - if ntwk.edge[str(edge[0])][str(edge[1])].has_key('value'): + if 'value' in ntwk.edge[str(edge[0])][str(edge[1])]: ntwk.edge[str(edge[0])][str(edge[1])]['value'] = str(data['value']) return ntwk @@ -101,21 +104,27 @@ def average_networks(in_files, ntwk_res_file, group_id): """ import networkx as nx import os.path as op - iflogger.info("Creating average network for group: {grp}".format(grp=group_id)) + iflogger.info(("Creating average network for group: " + "{grp}").format(grp=group_id)) matlab_network_list = [] if len(in_files) == 1: avg_ntwk = read_unknown_ntwk(in_files[0]) else: - count_to_keep_edge = np.round(float(len(in_files)) / 2) - iflogger.info("Number of networks: {L}, an edge must occur in at least {c} to remain in the average network".format(L=len(in_files), c=count_to_keep_edge)) + count_to_keep_edge = np.round(len(in_files) / 2.0) + iflogger.info(("Number of networks: {L}, an edge must occur in at " + "least {c} to remain in the " + "average network").format(L=len(in_files), + c=count_to_keep_edge)) ntwk_res_file = read_unknown_ntwk(ntwk_res_file) - iflogger.info("{n} Nodes found in network resolution file".format(n=ntwk_res_file.number_of_nodes())) + iflogger.info(("{n} Nodes found in network resolution " + "file").format(n=ntwk_res_file.number_of_nodes())) ntwk = remove_all_edges(ntwk_res_file) counting_ntwk = ntwk.copy() # Sums all the relevant variables for index, subject in enumerate(in_files): tmp = nx.read_gpickle(subject) - iflogger.info('File {s} has {n} edges'.format(s=subject, n=tmp.number_of_edges())) + iflogger.info(('File {s} has {n} ' + 'edges').format(s=subject, n=tmp.number_of_edges())) edges = tmp.edges_iter() for edge in edges: data = {} @@ -130,30 +139,32 @@ def average_networks(in_files, ntwk_res_file, group_id): for node in nodes: data = {} data = ntwk.node[node] - if tmp.node[node].has_key('value'): + if 'value' in tmp.node[node]: data['value'] = data['value'] + tmp.node[node]['value'] ntwk.add_node(node, data) # Divides each value by the number of files nodes = ntwk.nodes_iter() edges = ntwk.edges_iter() - iflogger.info('Total network has {n} edges'.format(n=ntwk.number_of_edges())) + iflogger.info(('Total network has {n} ' + 'edges').format(n=ntwk.number_of_edges())) avg_ntwk = nx.Graph() newdata = {} for node in nodes: data = ntwk.node[node] newdata = data - if data.has_key('value'): + if 'value' in data: newdata['value'] = data['value'] / len(in_files) ntwk.node[node]['value'] = newdata avg_ntwk.add_node(node, newdata) edge_dict = {} - edge_dict['count'] = np.zeros((avg_ntwk.number_of_nodes(), avg_ntwk.number_of_nodes())) + edge_dict['count'] = np.zeros((avg_ntwk.number_of_nodes(), + avg_ntwk.number_of_nodes())) for edge in edges: data = ntwk.edge[edge[0]][edge[1]] if ntwk.edge[edge[0]][edge[1]]['count'] >= count_to_keep_edge: - for key in data.keys(): + for key in list(data.keys()): if not key == 'count': data[key] = data[key] / len(in_files) ntwk.edge[edge[0]][edge[1]] = data @@ -165,12 +176,12 @@ def average_networks(in_files, ntwk_res_file, group_id): avg_edges = avg_ntwk.edges_iter() for edge in avg_edges: data = avg_ntwk.edge[edge[0]][edge[1]] - for key in data.keys(): + for key in list(data.keys()): if not key == 'count': edge_dict[key] = np.zeros((avg_ntwk.number_of_nodes(), avg_ntwk.number_of_nodes())) edge_dict[key][edge[0]-1][edge[1]-1] = data[key] - for key in edge_dict.keys(): + for key in list(edge_dict.keys()): tmp = {} network_name = group_id + '_' + key + '_average.mat' matlab_network_list.append(op.abspath(network_name)) @@ -196,23 +207,23 @@ def compute_node_measures(ntwk, calculate_cliques=False): iflogger.info('Computing node measures:') measures = {} iflogger.info('...Computing degree...') - measures['degree'] = np.array(ntwk.degree().values()) + measures['degree'] = np.array(list(ntwk.degree().values())) iflogger.info('...Computing load centrality...') - measures['load_centrality'] = np.array(nx.load_centrality(ntwk).values()) + measures['load_centrality'] = np.array(list(nx.load_centrality(ntwk).values())) iflogger.info('...Computing betweenness centrality...') - measures['betweenness_centrality'] = np.array(nx.betweenness_centrality(ntwk).values()) + measures['betweenness_centrality'] = np.array(list(nx.betweenness_centrality(ntwk).values())) iflogger.info('...Computing degree centrality...') - measures['degree_centrality'] = np.array(nx.degree_centrality(ntwk).values()) + measures['degree_centrality'] = np.array(list(nx.degree_centrality(ntwk).values())) iflogger.info('...Computing closeness centrality...') - measures['closeness_centrality'] = np.array(nx.closeness_centrality(ntwk).values()) + measures['closeness_centrality'] = np.array(list(nx.closeness_centrality(ntwk).values())) # iflogger.info('...Computing eigenvector centrality...') # measures['eigenvector_centrality'] = np.array(nx.eigenvector_centrality(ntwk, max_iter=100000).values()) iflogger.info('...Computing triangles...') - measures['triangles'] = np.array(nx.triangles(ntwk).values()) + measures['triangles'] = np.array(list(nx.triangles(ntwk).values())) iflogger.info('...Computing clustering...') - measures['clustering'] = np.array(nx.clustering(ntwk).values()) + measures['clustering'] = np.array(list(nx.clustering(ntwk).values())) iflogger.info('...Computing k-core number') - measures['core_number'] = np.array(nx.core_number(ntwk).values()) + measures['core_number'] = np.array(list(nx.core_number(ntwk).values())) iflogger.info('...Identifying network isolates...') isolate_list = nx.isolates(ntwk) binarized = np.zeros((ntwk.number_of_nodes(), 1)) @@ -222,9 +233,9 @@ def compute_node_measures(ntwk, calculate_cliques=False): measures['isolates'] = binarized if calculate_cliques: iflogger.info('...Calculating node clique number') - measures['node_clique_number'] = np.array(nx.node_clique_number(ntwk).values()) + measures['node_clique_number'] = np.array(list(nx.node_clique_number(ntwk).values())) iflogger.info('...Computing number of cliques for each node...') - measures['number_of_cliques'] = np.array(nx.number_of_cliques(ntwk).values()) + measures['number_of_cliques'] = np.array(list(nx.number_of_cliques(ntwk).values())) return measures @@ -322,13 +333,13 @@ def add_edge_data(edge_array, ntwk, above=0, below=0): for x, row in enumerate(edge_array): for y in range(0, np.max(np.shape(edge_array[x]))): if not edge_array[x, y] == 0: - data['value'] = edge_array[x, y] - if data['value'] <= below or data['value'] >= above: - if edge_ntwk.has_edge(x + 1, y + 1): - old_edge_dict = edge_ntwk.edge[x + 1][y + 1] - edge_ntwk.remove_edge(x + 1, y + 1) - data.update(old_edge_dict) - edge_ntwk.add_edge(x + 1, y + 1, data) + data['value'] = edge_array[x, y] + if data['value'] <= below or data['value'] >= above: + if edge_ntwk.has_edge(x + 1, y + 1): + old_edge_dict = edge_ntwk.edge[x + 1][y + 1] + edge_ntwk.remove_edge(x + 1, y + 1) + data.update(old_edge_dict) + edge_ntwk.add_edge(x + 1, y + 1, data) return edge_ntwk @@ -399,7 +410,7 @@ def _run_interface(self, runtime): matlab.append(global_out_file) node_measures = compute_node_measures(ntwk, calculate_cliques) - for key in node_measures.keys(): + for key in list(node_measures.keys()): newntwk = add_node_data(node_measures[key], ntwk) out_file = op.abspath(self._gen_outfilename(key, 'pck')) nx.write_gpickle(newntwk, out_file) @@ -413,7 +424,7 @@ def _run_interface(self, runtime): gpickled.extend(nodentwks) edge_measures = compute_edge_measures(ntwk) - for key in edge_measures.keys(): + for key in list(edge_measures.keys()): newntwk = add_edge_data(edge_measures[key], ntwk) out_file = op.abspath(self._gen_outfilename(key, 'pck')) nx.write_gpickle(newntwk, out_file) @@ -427,7 +438,7 @@ def _run_interface(self, runtime): gpickled.extend(edgentwks) ntwk_measures = compute_network_measures(ntwk) - for key in ntwk_measures.keys(): + for key in list(ntwk_measures.keys()): if key == 'k_core': out_file = op.abspath(self._gen_outfilename(self.inputs.out_k_core, 'pck')) if key == 'k_shell': diff --git a/nipype/interfaces/cmtk/parcellation.py b/nipype/interfaces/cmtk/parcellation.py index 07422db5d4..c102e0bb88 100644 --- a/nipype/interfaces/cmtk/parcellation.py +++ b/nipype/interfaces/cmtk/parcellation.py @@ -9,25 +9,27 @@ """ -from nipype.interfaces.base import ( - BaseInterface, BaseInterfaceInputSpec, traits, - File, TraitedSpec, Directory, isdefined) +from builtins import range + import os import os.path as op +import shutil +import warnings + import numpy as np import nibabel as nb import networkx as nx -import shutil -from nipype.utils.misc import package_check -import warnings +from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, + File, TraitedSpec, Directory, isdefined) +from ...utils.misc import package_check from ... import logging iflogger = logging.getLogger('interface') have_cmp = True try: package_check('cmp') -except Exception, e: +except Exception as e: have_cmp = False else: import cmp diff --git a/nipype/interfaces/cmtk/tests/__init__.py b/nipype/interfaces/cmtk/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index 9194faa30c..b150dff97c 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.nx import AverageNetworks +from ....testing import assert_equal +from ..nx import AverageNetworks def test_AverageNetworks_inputs(): input_map = dict(group_id=dict(usedefault=True, @@ -16,8 +16,8 @@ def test_AverageNetworks_inputs(): ) inputs = AverageNetworks.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AverageNetworks_outputs(): @@ -27,7 +27,7 @@ def test_AverageNetworks_outputs(): ) outputs = AverageNetworks.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index e89ac62c60..395c2ee38f 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.convert import CFFConverter +from ....testing import assert_equal +from ..convert import CFFConverter def test_CFFConverter_inputs(): input_map = dict(creator=dict(), @@ -32,8 +32,8 @@ def test_CFFConverter_inputs(): ) inputs = CFFConverter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CFFConverter_outputs(): @@ -41,7 +41,7 @@ def test_CFFConverter_outputs(): ) outputs = CFFConverter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index 4f697009fe..7da385220c 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.cmtk import CreateMatrix +from ....testing import assert_equal +from ..cmtk import CreateMatrix def test_CreateMatrix_inputs(): input_map = dict(count_region_intersections=dict(usedefault=True, @@ -28,8 +28,8 @@ def test_CreateMatrix_inputs(): ) inputs = CreateMatrix.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CreateMatrix_outputs(): @@ -54,7 +54,7 @@ def test_CreateMatrix_outputs(): ) outputs = CreateMatrix.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 98adc0800b..84f3e38ad3 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.cmtk import CreateNodes +from ....testing import assert_equal +from ..cmtk import CreateNodes def test_CreateNodes_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -15,8 +15,8 @@ def test_CreateNodes_inputs(): ) inputs = CreateNodes.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CreateNodes_outputs(): @@ -24,7 +24,7 @@ def test_CreateNodes_outputs(): ) outputs = CreateNodes.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index a00bc45664..a7e7fe169b 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.convert import MergeCNetworks +from ....testing import assert_equal +from ..convert import MergeCNetworks def test_MergeCNetworks_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -13,8 +13,8 @@ def test_MergeCNetworks_inputs(): ) inputs = MergeCNetworks.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MergeCNetworks_outputs(): @@ -22,7 +22,7 @@ def test_MergeCNetworks_outputs(): ) outputs = MergeCNetworks.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index 706386d3e8..3a038ae6c9 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.nbs import NetworkBasedStatistic +from ....testing import assert_equal +from ..nbs import NetworkBasedStatistic def test_NetworkBasedStatistic_inputs(): input_map = dict(edge_key=dict(usedefault=True, @@ -24,8 +24,8 @@ def test_NetworkBasedStatistic_inputs(): ) inputs = NetworkBasedStatistic.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NetworkBasedStatistic_outputs(): @@ -35,7 +35,7 @@ def test_NetworkBasedStatistic_outputs(): ) outputs = NetworkBasedStatistic.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index 19b8b60203..eb596fa650 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.nx import NetworkXMetrics +from ....testing import assert_equal +from ..nx import NetworkXMetrics def test_NetworkXMetrics_inputs(): input_map = dict(compute_clique_related_measures=dict(usedefault=True, @@ -29,8 +29,8 @@ def test_NetworkXMetrics_inputs(): ) inputs = NetworkXMetrics.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NetworkXMetrics_outputs(): @@ -50,7 +50,7 @@ def test_NetworkXMetrics_outputs(): ) outputs = NetworkXMetrics.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index 4d3d1a4cbd..d7cde3f392 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.parcellation import Parcellate +from ....testing import assert_equal +from ..parcellation import Parcellate def test_Parcellate_inputs(): input_map = dict(dilation=dict(usedefault=True, @@ -19,8 +19,8 @@ def test_Parcellate_inputs(): ) inputs = Parcellate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Parcellate_outputs(): @@ -35,7 +35,7 @@ def test_Parcellate_outputs(): ) outputs = Parcellate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index 5651bd99f2..dde9200bd8 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.cmtk.cmtk import ROIGen +from ....testing import assert_equal +from ..cmtk import ROIGen def test_ROIGen_inputs(): input_map = dict(LUT_file=dict(xor=['use_freesurfer_LUT'], @@ -21,8 +21,8 @@ def test_ROIGen_inputs(): ) inputs = ROIGen.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ROIGen_outputs(): @@ -31,7 +31,7 @@ def test_ROIGen_outputs(): ) outputs = ROIGen.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py index 31dc610789..2b093a082b 100644 --- a/nipype/interfaces/dcm2nii.py +++ b/nipype/interfaces/dcm2nii.py @@ -7,14 +7,15 @@ >>> os.chdir(datadir) """ -from nipype.interfaces.base import (CommandLine, CommandLineInputSpec, - InputMultiPath, traits, TraitedSpec, - OutputMultiPath, isdefined, - File, Directory) import os -from copy import deepcopy -from nipype.utils.filemanip import split_filename import re +from copy import deepcopy + +from .base import (CommandLine, CommandLineInputSpec, + InputMultiPath, traits, TraitedSpec, + OutputMultiPath, isdefined, + File, Directory) +from ..utils.filemanip import split_filename class Dcm2niiInputSpec(CommandLineInputSpec): diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py index bd0499be1f..afaf3c1119 100644 --- a/nipype/interfaces/dcmstack.py +++ b/nipype/interfaces/dcmstack.py @@ -9,23 +9,21 @@ """ from __future__ import absolute_import + import os import string import errno from os import path as op from glob import glob -from nipype.interfaces.base import (TraitedSpec, - DynamicTraitedSpec, - InputMultiPath, - File, - Directory, - traits, - BaseInterface, - ) + import nibabel as nb -from nipype.interfaces.traits_extension import isdefined, Undefined import imghdr -from nipype.external import six + +from .base import (TraitedSpec, DynamicTraitedSpec, + InputMultiPath, File, Directory, + traits, BaseInterface) +from .traits_extension import isdefined, Undefined +from ..external.six import string_types have_dcmstack = True try: @@ -131,7 +129,7 @@ class DcmStack(NiftiGeneratorBase): output_spec = DcmStackOutputSpec def _get_filelist(self, trait_input): - if isinstance(trait_input, six.string_types): + if isinstance(trait_input, string_types): if op.isdir(trait_input): return glob(op.join(trait_input, '*.dcm')) else: @@ -184,7 +182,7 @@ def _run_interface(self, runtime): stacks = dcmstack.parse_and_stack(src_paths) self.out_list = [] - for key, stack in stacks.iteritems(): + for key, stack in stacks.items(): nw = NiftiWrapper(stack.to_nifti(embed_meta=True)) const_meta = nw.meta_ext.get_class_dict(('global', 'const')) out_path = self._get_out_path(const_meta) @@ -246,12 +244,12 @@ def _outputs(self): self._make_name_map() outputs = super(LookupMeta, self)._outputs() undefined_traits = {} - for out_name in self._meta_keys.values(): + for out_name in list(self._meta_keys.values()): outputs.add_trait(out_name, traits.Any) undefined_traits[out_name] = Undefined outputs.trait_set(trait_change_notify=False, **undefined_traits) # Not sure why this is needed - for out_name in self._meta_keys.values(): + for out_name in list(self._meta_keys.values()): _ = getattr(outputs, out_name) return outputs @@ -260,7 +258,7 @@ def _run_interface(self, runtime): self._make_name_map() nw = NiftiWrapper.from_filename(self.inputs.in_file) self.result = {} - for meta_key, out_name in self._meta_keys.iteritems(): + for meta_key, out_name in self._meta_keys.items(): self.result[out_name] = nw.meta_ext.get_values(meta_key) return runtime @@ -367,7 +365,7 @@ def _run_interface(self, runtime): ] if self.inputs.sort_order: sort_order = self.inputs.sort_order - if isinstance(sort_order, six.string_types): + if isinstance(sort_order, string_types): sort_order = [sort_order] nws.sort(key=make_key_func(sort_order)) if self.inputs.merge_dim == traits.Undefined: diff --git a/nipype/interfaces/diffusion_toolkit/base.py b/nipype/interfaces/diffusion_toolkit/base.py index 4e6e6b82ad..c330be2f0c 100644 --- a/nipype/interfaces/diffusion_toolkit/base.py +++ b/nipype/interfaces/diffusion_toolkit/base.py @@ -12,6 +12,8 @@ See the docstrings for the individual classes for 'working' examples. """ + +from builtins import object __docformat__ = 'restructuredtext' import re from nipype.interfaces.base import CommandLine diff --git a/nipype/interfaces/diffusion_toolkit/dti.py b/nipype/interfaces/diffusion_toolkit/dti.py index 25aeddb40a..4bdb0d509a 100644 --- a/nipype/interfaces/diffusion_toolkit/dti.py +++ b/nipype/interfaces/diffusion_toolkit/dti.py @@ -9,13 +9,16 @@ >>> os.chdir(datadir) """ -import re -from nipype.utils.filemanip import fname_presuffix, split_filename, copyfile -import os __docformat__ = 'restructuredtext' +from builtins import range + +import os +import re + +from ..base import (TraitedSpec, File, traits, CommandLine, + CommandLineInputSpec, isdefined) +from ...utils.filemanip import fname_presuffix, split_filename, copyfile -from nipype.interfaces.base import (TraitedSpec, File, traits, CommandLine, - CommandLineInputSpec, isdefined) class DTIReconInputSpec(CommandLineInputSpec): DWI = File(desc='Input diffusion volume', argstr='%s',exists=True, mandatory=True,position=1) diff --git a/nipype/interfaces/diffusion_toolkit/odf.py b/nipype/interfaces/diffusion_toolkit/odf.py index 3e0ed0e5a5..a91b6cb071 100644 --- a/nipype/interfaces/diffusion_toolkit/odf.py +++ b/nipype/interfaces/diffusion_toolkit/odf.py @@ -9,13 +9,16 @@ >>> os.chdir(datadir) """ -import re -from nipype.utils.filemanip import fname_presuffix, split_filename, copyfile -import os __docformat__ = 'restructuredtext' +from builtins import range + +import os +import re + +from ..base import (TraitedSpec, File, traits, CommandLine, + CommandLineInputSpec, isdefined) +from ...utils.filemanip import fname_presuffix, split_filename, copyfile -from nipype.interfaces.base import (TraitedSpec, File, traits, CommandLine, - CommandLineInputSpec, isdefined) class HARDIMatInputSpec(CommandLineInputSpec): bvecs = File(exists=True, desc = 'b vectors file', diff --git a/nipype/interfaces/diffusion_toolkit/postproc.py b/nipype/interfaces/diffusion_toolkit/postproc.py index 6e2c92c249..1e36cfa076 100644 --- a/nipype/interfaces/diffusion_toolkit/postproc.py +++ b/nipype/interfaces/diffusion_toolkit/postproc.py @@ -9,11 +9,13 @@ >>> os.chdir(datadir) """ -import os __docformat__ = 'restructuredtext' -from nipype.interfaces.base import (TraitedSpec, File, traits, CommandLine, - InputMultiPath, CommandLineInputSpec) +import os + +from ..base import (TraitedSpec, File, traits, CommandLine, + InputMultiPath, CommandLineInputSpec) + class SplineFilterInputSpec(CommandLineInputSpec): track_file = File(exists=True, desc="file containing tracks to be filtered", position=0, argstr="%s", mandatory=True) diff --git a/nipype/interfaces/diffusion_toolkit/tests/__init__.py b/nipype/interfaces/diffusion_toolkit/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index 5e9bb65eb3..591ead36a9 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.dti import DTIRecon +from ....testing import assert_equal +from ..dti import DTIRecon def test_DTIRecon_inputs(): input_map = dict(DWI=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_DTIRecon_inputs(): ) inputs = DTIRecon.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTIRecon_outputs(): @@ -60,7 +60,7 @@ def test_DTIRecon_outputs(): ) outputs = DTIRecon.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index d79da8b055..47f5b85b75 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.dti import DTITracker +from ....testing import assert_equal +from ..dti import DTITracker def test_DTITracker_inputs(): input_map = dict(angle_threshold=dict(argstr='-at %f', @@ -64,8 +64,8 @@ def test_DTITracker_inputs(): ) inputs = DTITracker.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTITracker_outputs(): @@ -74,7 +74,7 @@ def test_DTITracker_outputs(): ) outputs = DTITracker.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 7d3991612a..449ccc0fb6 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.odf import HARDIMat +from ....testing import assert_equal +from ..odf import HARDIMat def test_HARDIMat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_HARDIMat_inputs(): ) inputs = HARDIMat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_HARDIMat_outputs(): @@ -47,7 +47,7 @@ def test_HARDIMat_outputs(): ) outputs = HARDIMat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index e93812925e..f255fe57b5 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.odf import ODFRecon +from ....testing import assert_equal +from ..odf import ODFRecon def test_ODFRecon_inputs(): input_map = dict(DWI=dict(argstr='%s', @@ -55,8 +55,8 @@ def test_ODFRecon_inputs(): ) inputs = ODFRecon.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ODFRecon_outputs(): @@ -68,7 +68,7 @@ def test_ODFRecon_outputs(): ) outputs = ODFRecon.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 2a2ca5267c..172d3608a9 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.odf import ODFTracker +from ....testing import assert_equal +from ..odf import ODFTracker def test_ODFTracker_inputs(): input_map = dict(ODF=dict(mandatory=True, @@ -74,8 +74,8 @@ def test_ODFTracker_inputs(): ) inputs = ODFTracker.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ODFTracker_outputs(): @@ -83,7 +83,7 @@ def test_ODFTracker_outputs(): ) outputs = ODFTracker.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index f9099ac6ef..e830e4e345 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.postproc import SplineFilter +from ....testing import assert_equal +from ..postproc import SplineFilter def test_SplineFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_SplineFilter_inputs(): ) inputs = SplineFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SplineFilter_outputs(): @@ -37,7 +37,7 @@ def test_SplineFilter_outputs(): ) outputs = SplineFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index a20c47d81a..290f7955b2 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.diffusion_toolkit.postproc import TrackMerge +from ....testing import assert_equal +from ..postproc import TrackMerge def test_TrackMerge_inputs(): input_map = dict(args=dict(argstr='%s', @@ -24,8 +24,8 @@ def test_TrackMerge_inputs(): ) inputs = TrackMerge.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackMerge_outputs(): @@ -33,7 +33,7 @@ def test_TrackMerge_outputs(): ) outputs = TrackMerge.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/preprocess.py b/nipype/interfaces/dipy/preprocess.py index 9a2119a86b..ef7c7451f4 100644 --- a/nipype/interfaces/dipy/preprocess.py +++ b/nipype/interfaces/dipy/preprocess.py @@ -6,22 +6,22 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) >>> os.chdir(datadir) """ - -from nipype.interfaces.base import (traits, TraitedSpec, BaseInterface, - File, isdefined) -from nipype.utils.filemanip import split_filename import os.path as op +import warnings + import nibabel as nb import numpy as np -from nipype.utils.misc import package_check -import warnings + +from ..base import (traits, TraitedSpec, BaseInterface, File, isdefined) +from ...utils.filemanip import split_filename +from ...utils.misc import package_check from ... import logging iflogger = logging.getLogger('interface') have_dipy = True try: package_check('dipy', version='0.6.0') -except Exception, e: +except Exception as e: have_dipy = False else: from dipy.align.aniso2iso import resample diff --git a/nipype/interfaces/dipy/simulate.py b/nipype/interfaces/dipy/simulate.py index be7a553959..569adb1a8c 100644 --- a/nipype/interfaces/dipy/simulate.py +++ b/nipype/interfaces/dipy/simulate.py @@ -6,26 +6,24 @@ >>> os.chdir(datadir) """ -from nipype.interfaces.base import ( - traits, TraitedSpec, BaseInterface, BaseInterfaceInputSpec, File, - InputMultiPath, isdefined) -from nipype.utils.filemanip import split_filename +from __future__ import division +from builtins import range + import os.path as op -import nibabel as nb -import numpy as np -from nipype.utils.misc import package_check -import warnings +from multiprocessing import (Pool, cpu_count) -from multiprocessing import (Process, Pool, cpu_count, pool, - Manager, TimeoutError) +import nibabel as nb +from ..base import (traits, TraitedSpec, BaseInterface, BaseInterfaceInputSpec, + File, InputMultiPath, isdefined) +from ...utils.misc import package_check from ... import logging iflogger = logging.getLogger('interface') have_dipy = True try: package_check('dipy', version='0.8.0') -except Exception, e: +except Exception as e: have_dipy = False else: import numpy as np @@ -328,7 +326,7 @@ def _generate_gradients(ndirs=64, values=[1000, 3000], nb0s=1): bvecs = np.vstack((bvecs, vertices)) bvals = np.hstack((bvals, v * np.ones(vertices.shape[0]))) - for i in xrange(0, nb0s): + for i in range(0, nb0s): bvals = bvals.tolist() bvals.insert(0, 0) diff --git a/nipype/interfaces/dipy/tensors.py b/nipype/interfaces/dipy/tensors.py index 4554b34616..8081f4b1f8 100644 --- a/nipype/interfaces/dipy/tensors.py +++ b/nipype/interfaces/dipy/tensors.py @@ -5,23 +5,22 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) >>> os.chdir(datadir) """ - -from nipype.interfaces.base import ( - TraitedSpec, BaseInterface, File) -from nipype.utils.filemanip import split_filename import os.path as op +import warnings + import nibabel as nb import numpy as np -from nipype.utils.misc import package_check -import warnings +from ..base import (TraitedSpec, BaseInterface, File) +from ...utils.filemanip import split_filename +from ...utils.misc import package_check from ... import logging iflogger = logging.getLogger('interface') have_dipy = True try: package_check('dipy', version='0.6.0') -except Exception, e: +except Exception as e: have_dipy = False else: import dipy.reconst.dti as dti diff --git a/nipype/interfaces/dipy/tests/__init__.py b/nipype/interfaces/dipy/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index 1c94a4bf45..9a979fa262 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dipy.tensors import DTI +from ....testing import assert_equal +from ..tensors import DTI def test_DTI_inputs(): input_map = dict(bvals=dict(mandatory=True, @@ -15,8 +15,8 @@ def test_DTI_inputs(): ) inputs = DTI.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTI_outputs(): @@ -24,7 +24,7 @@ def test_DTI_outputs(): ) outputs = DTI.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/tests/test_auto_Denoise.py b/nipype/interfaces/dipy/tests/test_auto_Denoise.py index 60f284137b..4383e1029b 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Denoise.py +++ b/nipype/interfaces/dipy/tests/test_auto_Denoise.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dipy.preprocess import Denoise +from ....testing import assert_equal +from ..preprocess import Denoise def test_Denoise_inputs(): input_map = dict(block_radius=dict(), @@ -15,8 +15,8 @@ def test_Denoise_inputs(): ) inputs = Denoise.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Denoise_outputs(): @@ -24,7 +24,7 @@ def test_Denoise_outputs(): ) outputs = Denoise.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/tests/test_auto_Resample.py b/nipype/interfaces/dipy/tests/test_auto_Resample.py index 9c3ac97833..9b5636ca80 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Resample.py +++ b/nipype/interfaces/dipy/tests/test_auto_Resample.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dipy.preprocess import Resample +from ....testing import assert_equal +from ..preprocess import Resample def test_Resample_inputs(): input_map = dict(in_file=dict(mandatory=True, @@ -12,8 +12,8 @@ def test_Resample_inputs(): ) inputs = Resample.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Resample_outputs(): @@ -21,7 +21,7 @@ def test_Resample_outputs(): ) outputs = Resample.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index 3be1c504b7..88c3f20bcd 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dipy.simulate import SimulateMultiTensor +from ....testing import assert_equal +from ..simulate import SimulateMultiTensor def test_SimulateMultiTensor_inputs(): input_map = dict(baseline=dict(mandatory=True, @@ -41,8 +41,8 @@ def test_SimulateMultiTensor_inputs(): ) inputs = SimulateMultiTensor.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SimulateMultiTensor_outputs(): @@ -53,7 +53,7 @@ def test_SimulateMultiTensor_outputs(): ) outputs = SimulateMultiTensor.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index c7515f342e..aca8f63751 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dipy.tensors import TensorMode +from ....testing import assert_equal +from ..tensors import TensorMode def test_TensorMode_inputs(): input_map = dict(bvals=dict(mandatory=True, @@ -15,8 +15,8 @@ def test_TensorMode_inputs(): ) inputs = TensorMode.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TensorMode_outputs(): @@ -24,7 +24,7 @@ def test_TensorMode_outputs(): ) outputs = TensorMode.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index b58637b211..c4f926ac8a 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dipy.tracks import TrackDensityMap +from ....testing import assert_equal +from ..tracks import TrackDensityMap def test_TrackDensityMap_inputs(): input_map = dict(data_dims=dict(), @@ -15,8 +15,8 @@ def test_TrackDensityMap_inputs(): ) inputs = TrackDensityMap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TrackDensityMap_outputs(): @@ -24,7 +24,7 @@ def test_TrackDensityMap_outputs(): ) outputs = TrackDensityMap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/dipy/tracks.py b/nipype/interfaces/dipy/tracks.py index fe9751334e..6851da7de2 100644 --- a/nipype/interfaces/dipy/tracks.py +++ b/nipype/interfaces/dipy/tracks.py @@ -6,23 +6,23 @@ >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) >>> os.chdir(datadir) """ -from nipype.interfaces.base import ( - TraitedSpec, BaseInterface, BaseInterfaceInputSpec, - File, isdefined, traits) -from nipype.utils.filemanip import split_filename import os.path as op +import warnings + import nibabel as nb import nibabel.trackvis as nbt -from nipype.utils.misc import package_check -import warnings +from ..base import (TraitedSpec, BaseInterface, BaseInterfaceInputSpec, + File, isdefined, traits) +from ...utils.filemanip import split_filename +from ...utils.misc import package_check from ... import logging iflogger = logging.getLogger('interface') have_dipy = True try: package_check('dipy', version='0.6.0') -except Exception, e: +except Exception as e: have_dipy = False else: from dipy.tracking.utils import density_map diff --git a/nipype/interfaces/dynamic_slicer.py b/nipype/interfaces/dynamic_slicer.py index 7f1aa5a451..95437ae377 100644 --- a/nipype/interfaces/dynamic_slicer.py +++ b/nipype/interfaces/dynamic_slicer.py @@ -111,7 +111,7 @@ def __init__(self, module, **inputs): undefined_traits[name] = Undefined self.inputs.trait_set(trait_change_notify=False, **undefined_traits) - for name in undefined_traits.keys(): + for name in list(undefined_traits.keys()): _ = getattr(self.inputs, name) #self._outputs().trait_set(trait_change_notify=False, **undefined_output_traits) diff --git a/nipype/interfaces/elastix/__init__.py b/nipype/interfaces/elastix/__init__.py index 66819f95db..ab8b968228 100644 --- a/nipype/interfaces/elastix/__init__.py +++ b/nipype/interfaces/elastix/__init__.py @@ -4,5 +4,7 @@ """Top-level namespace for elastix.""" -from registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp -from utils import EditTransform +from __future__ import absolute_import + +from .registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp +from .utils import EditTransform diff --git a/nipype/interfaces/elastix/registration.py b/nipype/interfaces/elastix/registration.py index 6c4c67aaa1..430d1efcfc 100644 --- a/nipype/interfaces/elastix/registration.py +++ b/nipype/interfaces/elastix/registration.py @@ -8,12 +8,14 @@ """ +from __future__ import absolute_import + import os.path as op import re from ..base import (CommandLine, CommandLineInputSpec, isdefined, TraitedSpec, File, traits, InputMultiPath) -from base import ElastixBaseInputSpec +from .base import ElastixBaseInputSpec from ... import logging logger = logging.getLogger('interface') @@ -50,10 +52,10 @@ class Registration(CommandLine): >>> from nipype.interfaces.elastix import Registration >>> reg = Registration() - >>> reg.inputs.fixed_image = 'fixed1.nii' - >>> reg.inputs.moving_image = 'moving1.nii' - >>> reg.inputs.parameters = ['elastix.txt'] - >>> reg.cmdline + >>> reg.inputs.fixed_image = 'fixed1.nii' # doctest: +SKIP + >>> reg.inputs.moving_image = 'moving1.nii' # doctest: +SKIP + >>> reg.inputs.parameters = ['elastix.txt'] # doctest: +SKIP + >>> reg.cmdline # doctest: +SKIP 'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt' @@ -143,9 +145,9 @@ class ApplyWarp(CommandLine): >>> from nipype.interfaces.elastix import ApplyWarp >>> reg = ApplyWarp() - >>> reg.inputs.moving_image = 'moving1.nii' - >>> reg.inputs.transform_file = 'TransformParameters.0.txt' - >>> reg.cmdline + >>> reg.inputs.moving_image = 'moving1.nii' # doctest: +SKIP + >>> reg.inputs.transform_file = 'TransformParameters.0.txt' # doctest: +SKIP + >>> reg.cmdline # doctest: +SKIP 'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt' @@ -183,8 +185,8 @@ class AnalyzeWarp(CommandLine): >>> from nipype.interfaces.elastix import AnalyzeWarp >>> reg = AnalyzeWarp() - >>> reg.inputs.transform_file = 'TransformParameters.0.txt' - >>> reg.cmdline + >>> reg.inputs.transform_file = 'TransformParameters.0.txt' # doctest: +SKIP + >>> reg.cmdline # doctest: +SKIP 'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt' @@ -223,9 +225,9 @@ class PointsWarp(CommandLine): >>> from nipype.interfaces.elastix import PointsWarp >>> reg = PointsWarp() - >>> reg.inputs.points_file = 'surf1.vtk' - >>> reg.inputs.transform_file = 'TransformParameters.0.txt' - >>> reg.cmdline + >>> reg.inputs.points_file = 'surf1.vtk' # doctest: +SKIP + >>> reg.inputs.transform_file = 'TransformParameters.0.txt' # doctest: +SKIP + >>> reg.cmdline # doctest: +SKIP 'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt' diff --git a/nipype/interfaces/elastix/tests/__init__.py b/nipype/interfaces/elastix/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index e80135f760..0f992772cf 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.elastix.registration import AnalyzeWarp +from ....testing import assert_equal +from ..registration import AnalyzeWarp def test_AnalyzeWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_AnalyzeWarp_inputs(): ) inputs = AnalyzeWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AnalyzeWarp_outputs(): @@ -37,7 +37,7 @@ def test_AnalyzeWarp_outputs(): ) outputs = AnalyzeWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index ac7f513750..a367c647e5 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.elastix.registration import ApplyWarp +from ....testing import assert_equal +from ..registration import ApplyWarp def test_ApplyWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_ApplyWarp_inputs(): ) inputs = ApplyWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyWarp_outputs(): @@ -38,7 +38,7 @@ def test_ApplyWarp_outputs(): ) outputs = ApplyWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index d8367dd832..794977331c 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.elastix.utils import EditTransform +from ....testing import assert_equal +from ..utils import EditTransform def test_EditTransform_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -20,8 +20,8 @@ def test_EditTransform_inputs(): ) inputs = EditTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EditTransform_outputs(): @@ -29,7 +29,7 @@ def test_EditTransform_outputs(): ) outputs = EditTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index 288905634f..9084016d2e 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.elastix.registration import PointsWarp +from ....testing import assert_equal +from ..registration import PointsWarp def test_PointsWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_PointsWarp_inputs(): ) inputs = PointsWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PointsWarp_outputs(): @@ -38,7 +38,7 @@ def test_PointsWarp_outputs(): ) outputs = PointsWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 4f7056430f..74450da13b 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.elastix.registration import Registration +from ....testing import assert_equal +from ..registration import Registration def test_Registration_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_Registration_inputs(): ) inputs = Registration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Registration_outputs(): @@ -50,7 +50,7 @@ def test_Registration_outputs(): ) outputs = Registration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/elastix/utils.py b/nipype/interfaces/elastix/utils.py index 09d46adaf9..cd885b5cc2 100644 --- a/nipype/interfaces/elastix/utils.py +++ b/nipype/interfaces/elastix/utils.py @@ -7,15 +7,12 @@ transform files (to configure warpings) """ - import os.path as op import re -from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec, isdefined, - TraitedSpec, File, traits, InputMultiPath) - - -from nipype import logging +from ..base import (BaseInterface, BaseInterfaceInputSpec, isdefined, + TraitedSpec, File, traits, InputMultiPath) +from ... import logging logger = logging.getLogger('interface') @@ -38,6 +35,7 @@ class EditTransformInputSpec(BaseInterfaceInputSpec): desc='set a new image format for resampled images') output_file = File(desc='the filename for the resulting transform file') + class EditTransformOutputSpec(TraitedSpec): output_file = File(exists=True, desc='output transform file') @@ -51,12 +49,11 @@ class EditTransform(BaseInterface): >>> from nipype.interfaces.elastix import EditTransform >>> tfm = EditTransform() - >>> tfm.inputs.transform_file = 'TransformParameters.0.txt' - >>> tfm.inputs.reference_image = 'fixed1.nii' + >>> tfm.inputs.transform_file = 'TransformParameters.0.txt' # doctest: +SKIP + >>> tfm.inputs.reference_image = 'fixed1.nii' # doctest: +SKIP >>> tfm.inputs.output_type = 'unsigned char' >>> tfm.run() # doctest: +SKIP - """ input_spec = EditTransformInputSpec diff --git a/nipype/interfaces/freesurfer/base.py b/nipype/interfaces/freesurfer/base.py index 8bc39dabfa..1b10f9deff 100644 --- a/nipype/interfaces/freesurfer/base.py +++ b/nipype/interfaces/freesurfer/base.py @@ -15,11 +15,14 @@ """ __docformat__ = 'restructuredtext' +from builtins import object + import os -from nipype.utils.filemanip import fname_presuffix -from nipype.interfaces.base import (CommandLine, Directory, - CommandLineInputSpec, isdefined) +from ..base import (CommandLine, Directory, + CommandLineInputSpec, isdefined) +from ...utils.filemanip import fname_presuffix + class Info(object): diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index 8394915488..702978ad3a 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/nipype/interfaces/freesurfer/model.py @@ -14,10 +14,10 @@ import os -from nipype.utils.filemanip import fname_presuffix, split_filename -from nipype.interfaces.freesurfer.base import FSCommand, FSTraitedSpec -from nipype.interfaces.base import (TraitedSpec, File, traits, InputMultiPath, - OutputMultiPath, Directory, isdefined) +from ..freesurfer.base import FSCommand, FSTraitedSpec +from ..base import (TraitedSpec, File, traits, InputMultiPath, + OutputMultiPath, Directory, isdefined) +from ...utils.filemanip import fname_presuffix, split_filename class MRISPreprocInputSpec(FSTraitedSpec): @@ -647,7 +647,7 @@ def _list_outputs(self): src = '_'.join(self.inputs.annot) if isdefined(self.inputs.surf_label): src = '_'.join(self.inputs.surf_label) - for name, suffix in suffices.items(): + for name, suffix in list(suffices.items()): value = getattr(self.inputs, name) if isdefined(value): if isinstance(value, bool): diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index 2ce2dcddbe..7f30a89758 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/nipype/interfaces/freesurfer/preprocess.py @@ -9,28 +9,28 @@ >>> os.chdir(datadir) """ + +from builtins import range __docformat__ = 'restructuredtext' import os import os.path as op from glob import glob -#import itertools -import numpy as np +import numpy as np from nibabel import load -from nipype.utils.filemanip import fname_presuffix -from nipype.interfaces.io import FreeSurferSource - -from nipype.interfaces.freesurfer.base import FSCommand, FSTraitedSpec -from nipype.interfaces.base import (TraitedSpec, File, traits, - Directory, InputMultiPath, - OutputMultiPath, CommandLine, - CommandLineInputSpec, isdefined) - +from ..io import FreeSurferSource +from ..freesurfer.base import FSCommand, FSTraitedSpec +from ..base import (TraitedSpec, File, traits, + Directory, InputMultiPath, + OutputMultiPath, CommandLine, + CommandLineInputSpec, isdefined) +from ...utils.filemanip import fname_presuffix from ... import logging iflogger = logging.getLogger('interface') + class ParseDICOMDirInputSpec(FSTraitedSpec): dicom_dir = Directory(exists=True, argstr='--d %s', mandatory=True, desc='path to siemens dicom directory') @@ -514,7 +514,7 @@ def _get_filelist(self, outdir): if self.inputs.dicom_info: files = [filemap[r] for r in self._get_runs()] else: - files = [filemap[r] for r in filemap.keys()] + files = [filemap[r] for r in list(filemap.keys())] return files @property @@ -1214,7 +1214,7 @@ def _list_outputs(self): half_weights=("src", "_halfweights", True), half_source_xfm=("src", "_robustxfm.lta", False), half_targ_xfm=("trg", "_robustxfm.lta", False)) - for name, sufftup in suffices.items(): + for name, sufftup in list(suffices.items()): value = getattr(self.inputs, name) if isdefined(value): if isinstance(value, bool): diff --git a/nipype/interfaces/freesurfer/tests/__init__.py b/nipype/interfaces/freesurfer/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index e083bd35f7..76d3afa4f1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import ApplyMask +from ....testing import assert_equal +from ..utils import ApplyMask def test_ApplyMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -41,8 +41,8 @@ def test_ApplyMask_inputs(): ) inputs = ApplyMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyMask_outputs(): @@ -50,7 +50,7 @@ def test_ApplyMask_outputs(): ) outputs = ApplyMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index f538d2997b..414eab974f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import ApplyVolTransform +from ....testing import assert_equal +from ..preprocess import ApplyVolTransform def test_ApplyVolTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -73,8 +73,8 @@ def test_ApplyVolTransform_inputs(): ) inputs = ApplyVolTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyVolTransform_outputs(): @@ -82,7 +82,7 @@ def test_ApplyVolTransform_outputs(): ) outputs = ApplyVolTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py index 0a06f56c82..1336d122f2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import BBRegister +from ....testing import assert_equal +from ..preprocess import BBRegister def test_BBRegister_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_BBRegister_inputs(): ) inputs = BBRegister.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BBRegister_outputs(): @@ -66,7 +66,7 @@ def test_BBRegister_outputs(): ) outputs = BBRegister.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index cc889b3c24..a08eed564b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import Binarize +from ....testing import assert_equal +from ..model import Binarize def test_Binarize_inputs(): input_map = dict(abs=dict(argstr='--abs', @@ -75,8 +75,8 @@ def test_Binarize_inputs(): ) inputs = Binarize.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Binarize_outputs(): @@ -85,7 +85,7 @@ def test_Binarize_outputs(): ) outputs = Binarize.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index 485751b832..38b5833527 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import Concatenate +from ....testing import assert_equal +from ..model import Concatenate def test_Concatenate_inputs(): input_map = dict(add_val=dict(argstr='--add %f', @@ -53,8 +53,8 @@ def test_Concatenate_inputs(): ) inputs = Concatenate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Concatenate_outputs(): @@ -62,7 +62,7 @@ def test_Concatenate_outputs(): ) outputs = Concatenate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index 6b75f56a3b..88c63c2abb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import DICOMConvert +from ....testing import assert_equal +from ..preprocess import DICOMConvert def test_DICOMConvert_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,7 +32,7 @@ def test_DICOMConvert_inputs(): ) inputs = DICOMConvert.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index af3b60455d..9a73f060b3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import ExtractMainComponent +from ....testing import assert_equal +from ..utils import ExtractMainComponent def test_ExtractMainComponent_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_ExtractMainComponent_inputs(): ) inputs = ExtractMainComponent.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ExtractMainComponent_outputs(): @@ -34,7 +34,7 @@ def test_ExtractMainComponent_outputs(): ) outputs = ExtractMainComponent.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index 560554aad4..6e44fdbf17 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.base import FSCommand +from ....testing import assert_equal +from ..base import FSCommand def test_FSCommand_inputs(): input_map = dict(args=dict(argstr='%s', @@ -17,7 +17,7 @@ def test_FSCommand_inputs(): ) inputs = FSCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 78a14edd13..947f58ebcf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import FitMSParams +from ....testing import assert_equal +from ..preprocess import FitMSParams def test_FitMSParams_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_FitMSParams_inputs(): ) inputs = FitMSParams.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FitMSParams_outputs(): @@ -40,7 +40,7 @@ def test_FitMSParams_outputs(): ) outputs = FitMSParams.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 3b246b602e..323e425006 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import GLMFit +from ....testing import assert_equal +from ..model import GLMFit def test_GLMFit_inputs(): input_map = dict(allow_ill_cond=dict(argstr='--illcond', @@ -138,8 +138,8 @@ def test_GLMFit_inputs(): ) inputs = GLMFit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GLMFit_outputs(): @@ -163,7 +163,7 @@ def test_GLMFit_outputs(): ) outputs = GLMFit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 61c7a1f568..1e37537505 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import ImageInfo +from ....testing import assert_equal +from ..utils import ImageInfo def test_ImageInfo_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,8 +20,8 @@ def test_ImageInfo_inputs(): ) inputs = ImageInfo.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageInfo_outputs(): @@ -39,7 +39,7 @@ def test_ImageInfo_outputs(): ) outputs = ImageInfo.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index 9d3cc78d39..5e294b9457 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import Label2Vol +from ....testing import assert_equal +from ..model import Label2Vol def test_Label2Vol_inputs(): input_map = dict(annot_file=dict(argstr='--annot %s', @@ -73,8 +73,8 @@ def test_Label2Vol_inputs(): ) inputs = Label2Vol.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Label2Vol_outputs(): @@ -82,7 +82,7 @@ def test_Label2Vol_outputs(): ) outputs = Label2Vol.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 37cac9792d..29ed1ad76c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import MRIConvert +from ....testing import assert_equal +from ..preprocess import MRIConvert def test_MRIConvert_inputs(): input_map = dict(apply_inv_transform=dict(argstr='--apply_inverse_transform %s', @@ -184,8 +184,8 @@ def test_MRIConvert_inputs(): ) inputs = MRIConvert.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRIConvert_outputs(): @@ -193,7 +193,7 @@ def test_MRIConvert_outputs(): ) outputs = MRIConvert.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index aa23924920..d91c90ca53 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import MRIMarchingCubes +from ....testing import assert_equal +from ..utils import MRIMarchingCubes def test_MRIMarchingCubes_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_MRIMarchingCubes_inputs(): ) inputs = MRIMarchingCubes.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRIMarchingCubes_outputs(): @@ -42,7 +42,7 @@ def test_MRIMarchingCubes_outputs(): ) outputs = MRIMarchingCubes.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 8882cc4b13..07dbaf8b1c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import MRIPretess +from ....testing import assert_equal +from ..utils import MRIPretess def test_MRIPretess_inputs(): input_map = dict(args=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_MRIPretess_inputs(): ) inputs = MRIPretess.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRIPretess_outputs(): @@ -49,7 +49,7 @@ def test_MRIPretess_outputs(): ) outputs = MRIPretess.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index 32b3dd3594..97af2b2602 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import MRISPreproc +from ....testing import assert_equal +from ..model import MRISPreproc def test_MRISPreproc_inputs(): input_map = dict(args=dict(argstr='%s', @@ -66,8 +66,8 @@ def test_MRISPreproc_inputs(): ) inputs = MRISPreproc.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRISPreproc_outputs(): @@ -75,7 +75,7 @@ def test_MRISPreproc_outputs(): ) outputs = MRISPreproc.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 3bc63d5413..1b25dbe252 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import MRITessellate +from ....testing import assert_equal +from ..utils import MRITessellate def test_MRITessellate_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_MRITessellate_inputs(): ) inputs = MRITessellate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRITessellate_outputs(): @@ -42,7 +42,7 @@ def test_MRITessellate_outputs(): ) outputs = MRITessellate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 0c8fb5296d..09a3a09dd3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import MRIsConvert +from ....testing import assert_equal +from ..utils import MRIsConvert def test_MRIsConvert_inputs(): input_map = dict(annot_file=dict(argstr='--annot %s', @@ -57,8 +57,8 @@ def test_MRIsConvert_inputs(): ) inputs = MRIsConvert.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRIsConvert_outputs(): @@ -66,7 +66,7 @@ def test_MRIsConvert_outputs(): ) outputs = MRIsConvert.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 25ffbe70bb..6be8c00ea6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import MS_LDA +from ....testing import assert_equal +from ..model import MS_LDA def test_MS_LDA_inputs(): input_map = dict(args=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_MS_LDA_inputs(): ) inputs = MS_LDA.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MS_LDA_outputs(): @@ -52,7 +52,7 @@ def test_MS_LDA_outputs(): ) outputs = MS_LDA.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 4178b478b8..18570afbd7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import MakeAverageSubject +from ....testing import assert_equal +from ..utils import MakeAverageSubject def test_MakeAverageSubject_inputs(): input_map = dict(args=dict(argstr='%s', @@ -24,8 +24,8 @@ def test_MakeAverageSubject_inputs(): ) inputs = MakeAverageSubject.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MakeAverageSubject_outputs(): @@ -33,7 +33,7 @@ def test_MakeAverageSubject_outputs(): ) outputs = MakeAverageSubject.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index fa8edbcc9e..e91215fcec 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import OneSampleTTest +from ....testing import assert_equal +from ..model import OneSampleTTest def test_OneSampleTTest_inputs(): input_map = dict(allow_ill_cond=dict(argstr='--illcond', @@ -138,8 +138,8 @@ def test_OneSampleTTest_inputs(): ) inputs = OneSampleTTest.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_OneSampleTTest_outputs(): @@ -163,7 +163,7 @@ def test_OneSampleTTest_outputs(): ) outputs = OneSampleTTest.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index bf554b148d..ff200ace85 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import ParseDICOMDir +from ....testing import assert_equal +from ..preprocess import ParseDICOMDir def test_ParseDICOMDir_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_ParseDICOMDir_inputs(): ) inputs = ParseDICOMDir.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ParseDICOMDir_outputs(): @@ -36,7 +36,7 @@ def test_ParseDICOMDir_outputs(): ) outputs = ParseDICOMDir.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 365e7f5417..d12305bcb2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import ReconAll +from ....testing import assert_equal +from ..preprocess import ReconAll def test_ReconAll_inputs(): input_map = dict(T1_files=dict(argstr='-i %s...', @@ -38,8 +38,8 @@ def test_ReconAll_inputs(): ) inputs = ReconAll.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ReconAll_outputs(): @@ -124,7 +124,7 @@ def test_ReconAll_outputs(): ) outputs = ReconAll.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 4371e459f3..71c212d0f6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import Resample +from ....testing import assert_equal +from ..preprocess import Resample def test_Resample_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_Resample_inputs(): ) inputs = Resample.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Resample_outputs(): @@ -37,7 +37,7 @@ def test_Resample_outputs(): ) outputs = Resample.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index 02cd6ad1c5..88ad8be0c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import RobustRegister +from ....testing import assert_equal +from ..preprocess import RobustRegister def test_RobustRegister_inputs(): input_map = dict(args=dict(argstr='%s', @@ -82,8 +82,8 @@ def test_RobustRegister_inputs(): ) inputs = RobustRegister.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_RobustRegister_outputs(): @@ -98,7 +98,7 @@ def test_RobustRegister_outputs(): ) outputs = RobustRegister.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index 23b145b323..add9a45d9f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import SampleToSurface +from ....testing import assert_equal +from ..utils import SampleToSurface def test_SampleToSurface_inputs(): input_map = dict(apply_rot=dict(argstr='--rot %.3f %.3f %.3f', @@ -105,8 +105,8 @@ def test_SampleToSurface_inputs(): ) inputs = SampleToSurface.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SampleToSurface_outputs(): @@ -116,7 +116,7 @@ def test_SampleToSurface_outputs(): ) outputs = SampleToSurface.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 200c25c1f1..5c51c8726f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.model import SegStats +from ....testing import assert_equal +from ..model import SegStats def test_SegStats_inputs(): input_map = dict(annot=dict(argstr='--annot %s %s %s', @@ -88,8 +88,8 @@ def test_SegStats_inputs(): ) inputs = SegStats.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SegStats_outputs(): @@ -100,7 +100,7 @@ def test_SegStats_outputs(): ) outputs = SegStats.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 743c483b92..07ea5583db 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import Smooth +from ....testing import assert_equal +from ..preprocess import Smooth def test_Smooth_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_Smooth_inputs(): ) inputs = Smooth.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Smooth_outputs(): @@ -52,7 +52,7 @@ def test_Smooth_outputs(): ) outputs = Smooth.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index bd29c218ed..33c38965ba 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import SmoothTessellation +from ....testing import assert_equal +from ..utils import SmoothTessellation def test_SmoothTessellation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_SmoothTessellation_inputs(): ) inputs = SmoothTessellation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SmoothTessellation_outputs(): @@ -63,7 +63,7 @@ def test_SmoothTessellation_outputs(): ) outputs = SmoothTessellation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 1eac5a32af..65296762f6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import Surface2VolTransform +from ....testing import assert_equal +from ..utils import Surface2VolTransform def test_Surface2VolTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_Surface2VolTransform_inputs(): ) inputs = Surface2VolTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Surface2VolTransform_outputs(): @@ -60,7 +60,7 @@ def test_Surface2VolTransform_outputs(): ) outputs = Surface2VolTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index bb8461bacd..d519f8d413 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import SurfaceSmooth +from ....testing import assert_equal +from ..utils import SurfaceSmooth def test_SurfaceSmooth_inputs(): input_map = dict(args=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_SurfaceSmooth_inputs(): ) inputs = SurfaceSmooth.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SurfaceSmooth_outputs(): @@ -49,7 +49,7 @@ def test_SurfaceSmooth_outputs(): ) outputs = SurfaceSmooth.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 425e265d86..89907da712 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import SurfaceSnapshots +from ....testing import assert_equal +from ..utils import SurfaceSnapshots def test_SurfaceSnapshots_inputs(): input_map = dict(annot_file=dict(argstr='-annotation %s', @@ -94,8 +94,8 @@ def test_SurfaceSnapshots_inputs(): ) inputs = SurfaceSnapshots.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SurfaceSnapshots_outputs(): @@ -103,7 +103,7 @@ def test_SurfaceSnapshots_outputs(): ) outputs = SurfaceSnapshots.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 1b2918dcc4..1567b402c5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import SurfaceTransform +from ....testing import assert_equal +from ..utils import SurfaceTransform def test_SurfaceTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -48,8 +48,8 @@ def test_SurfaceTransform_inputs(): ) inputs = SurfaceTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SurfaceTransform_outputs(): @@ -57,7 +57,7 @@ def test_SurfaceTransform_outputs(): ) outputs = SurfaceTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index 28da077e00..c507b91e7c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import SynthesizeFLASH +from ....testing import assert_equal +from ..preprocess import SynthesizeFLASH def test_SynthesizeFLASH_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_SynthesizeFLASH_inputs(): ) inputs = SynthesizeFLASH.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SynthesizeFLASH_outputs(): @@ -52,7 +52,7 @@ def test_SynthesizeFLASH_outputs(): ) outputs = SynthesizeFLASH.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index c836a600ec..5e03c1fc26 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.utils import Tkregister2 +from ....testing import assert_equal +from ..utils import Tkregister2 def test_Tkregister2_inputs(): input_map = dict(args=dict(argstr='%s', @@ -48,8 +48,8 @@ def test_Tkregister2_inputs(): ) inputs = Tkregister2.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Tkregister2_outputs(): @@ -58,7 +58,7 @@ def test_Tkregister2_outputs(): ) outputs = Tkregister2.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index b95aaae79c..fc9cdca56b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.freesurfer.preprocess import UnpackSDICOMDir +from ....testing import assert_equal +from ..preprocess import UnpackSDICOMDir def test_UnpackSDICOMDir_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,7 +46,7 @@ def test_UnpackSDICOMDir_inputs(): ) inputs = UnpackSDICOMDir.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 716c78e5ee..3879e1e2b4 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -11,12 +11,13 @@ """ __docformat__ = 'restructuredtext' + import os import re -from nipype.utils.filemanip import fname_presuffix, split_filename -from nipype.interfaces.freesurfer.base import FSCommand, FSTraitedSpec -from nipype.interfaces.base import TraitedSpec, File, traits, OutputMultiPath, isdefined, CommandLine, CommandLineInputSpec +from ..freesurfer.base import FSCommand, FSTraitedSpec +from ..base import TraitedSpec, File, traits, OutputMultiPath, isdefined, CommandLine, CommandLineInputSpec +from ...utils.filemanip import fname_presuffix, split_filename filemap = dict(cor='cor', mgh='mgh', mgz='mgz', minc='mnc', afni='brik', brik='brik', bshort='bshort', diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py index 8ce3ca1874..b4fedddc7d 100644 --- a/nipype/interfaces/fsl/base.py +++ b/nipype/interfaces/fsl/base.py @@ -25,6 +25,8 @@ """ +from builtins import object + from glob import glob import os import warnings @@ -35,7 +37,6 @@ File, Directory, InputMultiPath, OutputMultiPath) warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class Info(object): @@ -145,7 +146,7 @@ class FSLCommandInputSpec(CommandLineInputSpec): ------- fsl.ExtractRoi(tmin=42, tsize=1, output_type='NIFTI') """ - output_type = traits.Enum('NIFTI', Info.ftypes.keys(), + output_type = traits.Enum('NIFTI', list(Info.ftypes.keys()), desc='FSL output type') diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index 9648533678..86a53d8efe 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -12,18 +12,19 @@ """ +from builtins import range + import os import shutil import warnings from ... import LooseVersion -from nipype.interfaces.fsl.base import (FSLCommand, FSLCommandInputSpec, Info) -from nipype.interfaces.base import (TraitedSpec, isdefined, File, Directory, - InputMultiPath, OutputMultiPath, traits) -from nipype.utils.filemanip import fname_presuffix, split_filename, copyfile +from ..base import (TraitedSpec, isdefined, File, Directory, + InputMultiPath, OutputMultiPath, traits) +from ..fsl.base import (FSLCommand, FSLCommandInputSpec, Info) +from ...utils.filemanip import fname_presuffix, split_filename, copyfile warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class DTIFitInputSpec(FSLCommandInputSpec): @@ -92,7 +93,7 @@ class DTIFit(FSLCommand): def _list_outputs(self): outputs = self.output_spec().get() - for k in outputs.keys(): + for k in list(outputs.keys()): if k not in ('outputtype', 'environ', 'args'): if k != 'tensor' or (isdefined(self.inputs.save_tensor) and self.inputs.save_tensor): @@ -219,13 +220,13 @@ def _list_outputs(self, out_dir=None): for k in multi_out: outputs[k] = [] - for i in xrange(1, n_fibres + 1): + for i in range(1, n_fibres + 1): outputs['fsamples'].append(self._gen_fname('f%dsamples' % i, cwd=out_dir)) outputs['mean_fsamples'].append(self._gen_fname(('mean_f%d' 'samples') % i, cwd=out_dir)) - for i in xrange(1, n_fibres + 1): + for i in range(1, n_fibres + 1): outputs['dyads'].append(self._gen_fname('dyads%d' % i, cwd=out_dir)) outputs['phsamples'].append(self._gen_fname('ph%dsamples' % i, @@ -370,7 +371,7 @@ def _list_outputs(self): for k in multi_out: outputs[k] = [] - for i in xrange(1, n_fibres + 1): + for i in range(1, n_fibres + 1): outputs['merged_thsamples'].append(self._gen_fname('merged_th%dsamples' % i, cwd=self._out_dir)) outputs['merged_fsamples'].append(self._gen_fname('merged_f%dsamples' % i, @@ -616,7 +617,7 @@ def _list_outputs(self): outputs['xfms_directory'] = os.path.join(bpx_directory + '.bedpostX', 'xfms') - for k in outputs.keys(): + for k in list(outputs.keys()): if k not in ('outputtype', 'environ', 'args', 'bpx_out_directory', 'xfms_directory'): outputs[k] = [] diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index de5bfb68a6..8ce99d21fb 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -13,20 +13,19 @@ """ import os -from glob import glob import warnings +from glob import glob import numpy as np import nibabel as nib -from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec, Info -from nipype.interfaces.base import (traits, TraitedSpec, InputMultiPath, File, - isdefined, Undefined) -from nipype.utils.filemanip import (load_json, save_json, split_filename, - fname_presuffix) +from ..fsl.base import FSLCommand, FSLCommandInputSpec, Info +from ..base import (traits, TraitedSpec, InputMultiPath, File, + isdefined, Undefined) +from ...utils.filemanip import (load_json, save_json, split_filename, + fname_presuffix) warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class PrepareFieldmapInputSpec(FSLCommandInputSpec): @@ -398,7 +397,7 @@ class EddyInputSpec(FSLCommandInputSpec): in_bval = File(exists=True, mandatory=True, argstr='--bvals=%s', desc=('File containing the b-values for all volumes in ' '--imain')) - out_base = traits.Unicode('eddy_corrected', argstr='--out=%s', + out_base = traits.Str('eddy_corrected', argstr='--out=%s', usedefault=True, desc=('basename for output (warped) image')) session = File(exists=True, argstr='--session=%s', diff --git a/nipype/interfaces/fsl/maths.py b/nipype/interfaces/fsl/maths.py index 1660d9612f..b2c0cb6a61 100644 --- a/nipype/interfaces/fsl/maths.py +++ b/nipype/interfaces/fsl/maths.py @@ -3,13 +3,20 @@ """ The maths module provides higher-level interfaces to some of the operations that can be performed with the fslmaths command-line program. + + Change directory to provide relative paths for doctests + >>> import os + >>> filepath = os.path.dirname( os.path.realpath( __file__ ) ) + >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data')) + >>> os.chdir(datadir) """ + +from __future__ import division import os import numpy as np -from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec -from nipype.interfaces.base import (TraitedSpec, File, traits, InputMultiPath, - isdefined) +from ..base import (TraitedSpec, File, traits, InputMultiPath, isdefined) +from ..fsl.base import FSLCommand, FSLCommandInputSpec class MathsInput(FSLCommandInputSpec): @@ -128,12 +135,12 @@ class MaxImage(MathsCommand): Examples -------- - from nipype.interfaces.fsl.maths import MaxImage - maxer = MaxImage() - maxer.inputs.in_file = "functional.nii" - maxer.dimension = "T" - maths.cmdline - fslmaths functional.nii -Tmax functional_max.nii + >>> from nipype.interfaces.fsl.maths import MaxImage + >>> maxer = MaxImage() + >>> maxer.inputs.in_file = "functional.nii" # doctest: +SKIP + >>> maxer.dimension = "T" + >>> maxer.cmdline # doctest: +SKIP + 'fslmaths functional.nii -Tmax functional_max.nii' """ input_spec = MaxImageInput @@ -291,14 +298,14 @@ class MultiImageMaths(MathsCommand): Examples -------- - from nipype.interfaces.fsl import MultiImageMaths - maths = MultiImageMaths() - maths.inputs.in_file = "functional.nii" - maths.inputs.op_string = "-add %s -mul -1 -div %s" - maths.inputs.operand_files = ["functional2.nii", "functional3.nii"] - maths.inputs.out_file = functional4.nii - maths.cmdline - fslmaths functional1.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii + >>> from nipype.interfaces.fsl import MultiImageMaths + >>> maths = MultiImageMaths() + >>> maths.inputs.in_file = "functional.nii" + >>> maths.inputs.op_string = "-add %s -mul -1 -div %s" + >>> maths.inputs.operand_files = ["functional2.nii", "functional3.nii"] + >>> maths.inputs.out_file = "functional4.nii" + >>> maths.cmdline + 'fslmaths functional.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii' """ input_spec = MultiImageMathsInput diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index 7cebdbb629..a000302951 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -11,6 +11,9 @@ >>> os.chdir(datadir) """ +from __future__ import print_function +from builtins import range + import os from glob import glob import warnings @@ -30,7 +33,6 @@ from ...utils.misc import human_order_sorted warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class Level1DesignInputSpec(BaseInterfaceInputSpec): @@ -223,7 +225,7 @@ def _create_ev_files( if con[1] == 'F': ftest_idx.append(j) for c in con[2]: - if c[0] not in con_map.keys(): + if c[0] not in list(con_map.keys()): con_map[c[0]] = [] con_map[c[0]].append(j) else: @@ -250,7 +252,7 @@ def _create_ev_files( element=count, ctype=ctype, val=val) ev_txt += "\n" - if con[0] in con_map.keys(): + if con[0] in list(con_map.keys()): for fconidx in con_map[con[0]]: ev_txt += contrast_ftest_element.substitute( cnum=ftest_idx.index(fconidx) + 1, @@ -292,7 +294,7 @@ def _run_interface(self, runtime): prewhiten = int(self.inputs.model_serial_correlations) usetd = 0 no_bases = False - basis_key = self.inputs.bases.keys()[0] + basis_key = list(self.inputs.bases.keys())[0] if basis_key in ['dgamma', 'gamma']: usetd = int(self.inputs.bases[basis_key]['derivs']) if basis_key == 'none': @@ -344,7 +346,7 @@ def _list_outputs(self): outputs['fsf_files'] = [] outputs['ev_files'] = [] usetd = 0 - basis_key = self.inputs.bases.keys()[0] + basis_key = list(self.inputs.bases.keys())[0] if basis_key in ['dgamma', 'gamma']: usetd = int(self.inputs.bases[basis_key]['derivs']) for runno, runinfo in enumerate(self._format_session_info(self.inputs.session_info)): @@ -404,7 +406,7 @@ def _list_outputs(self): outputs['feat_dir'] = glob(os.path.join(os.getcwd(), '*ica'))[0] else: outputs['feat_dir'] = glob(os.path.join(os.getcwd(), '*feat'))[0] - print 'Outputs from FEATmodel:',outputs + print('Outputs from FEATmodel:',outputs) return outputs @@ -1168,7 +1170,7 @@ def _run_interface(self, runtime): def _list_outputs(self): outputs = self._outputs().get() - for field in outputs.keys(): + for field in list(outputs.keys()): outputs[field] = os.path.join(os.getcwd(), field.replace('_', '.')) return outputs @@ -1315,7 +1317,7 @@ def _run_interface(self, runtime): 'design.grp': grp_txt} # write design files - for key, val in txt.items(): + for key, val in list(txt.items()): if ('fts' in key) and (nfcons == 0): continue filename = key.replace('_', '.') @@ -1328,7 +1330,7 @@ def _run_interface(self, runtime): def _list_outputs(self): outputs = self._outputs().get() nfcons = sum([1 for con in self.inputs.contrasts if con[1] == 'F']) - for field in outputs.keys(): + for field in list(outputs.keys()): if ('fts' in field) and (nfcons == 0): continue outputs[field] = os.path.join(os.getcwd(), @@ -1653,7 +1655,7 @@ class Cluster(FSLCommand): def _list_outputs(self): outputs = self.output_spec().get() - for key, suffix in self.filemap.items(): + for key, suffix in list(self.filemap.items()): outkey = key[4:] inval = getattr(self.inputs, key) if isdefined(inval): @@ -1670,7 +1672,7 @@ def _list_outputs(self): return outputs def _format_arg(self, name, spec, value): - if name in self.filemap.keys(): + if name in list(self.filemap.keys()): if isinstance(value, bool): fname = self._list_outputs()[name[4:]] else: diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py index e1246b457b..6b92acbf8d 100644 --- a/nipype/interfaces/fsl/preprocess.py +++ b/nipype/interfaces/fsl/preprocess.py @@ -11,24 +11,24 @@ >>> os.chdir(datadir) """ +from __future__ import print_function +from __future__ import division +from builtins import range + import os import os.path as op import warnings -import glob import numpy as np - -from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec -from nipype.interfaces.base import (TraitedSpec, File, InputMultiPath, - OutputMultiPath, Undefined, traits, - isdefined, OutputMultiPath) -from nipype.utils.filemanip import split_filename - from nibabel import load +from ..fsl.base import FSLCommand, FSLCommandInputSpec +from ..base import (TraitedSpec, File, InputMultiPath, + OutputMultiPath, Undefined, traits, + isdefined, OutputMultiPath) +from ...utils.filemanip import split_filename warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class BETInputSpec(FSLCommandInputSpec): @@ -892,7 +892,7 @@ class FNIRT(FSLCommand): def _list_outputs(self): outputs = self.output_spec().get() - for key, suffix in self.filemap.items(): + for key, suffix in list(self.filemap.items()): inval = getattr(self.inputs, key) change_ext = True if key in ['warped_file', 'log_file']: @@ -915,7 +915,7 @@ def _list_outputs(self): return outputs def _format_arg(self, name, spec, value): - if name in self.filemap.keys(): + if name in list(self.filemap.keys()): return spec.argstr % self._list_outputs()[name] return super(FNIRT, self)._format_arg(name, spec, value) @@ -938,7 +938,7 @@ def write_config(self, configfile): except IOError: print ('unable to create config_file %s' % (configfile)) - for item in self.inputs.get().items(): + for item in list(self.inputs.get().items()): fid.write('%s\n' % (item)) fid.close() @@ -1120,13 +1120,13 @@ class SUSAN(FSLCommand): >>> from nipype.interfaces import fsl >>> from nipype.testing import example_data - >>> print anatfile #doctest: +SKIP - anatomical.nii #doctest: +SKIP + >>> anatfile # doctest: +SKIP + anatomical.nii # doctest: +SKIP >>> sus = fsl.SUSAN() >>> sus.inputs.in_file = example_data('structural.nii') >>> sus.inputs.brightness_threshold = 2000.0 >>> sus.inputs.fwhm = 8.0 - >>> result = sus.run() #doctest: +SKIP + >>> result = sus.run() # doctest: +SKIP """ _cmd = 'susan' diff --git a/nipype/interfaces/fsl/tests/__init__.py b/nipype/interfaces/fsl/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/fsl/tests/test_FILMGLS.py b/nipype/interfaces/fsl/tests/test_FILMGLS.py index 52118507c3..22caa313fd 100644 --- a/nipype/interfaces/fsl/tests/test_FILMGLS.py +++ b/nipype/interfaces/fsl/tests/test_FILMGLS.py @@ -45,10 +45,10 @@ def test_filmgls(): ) instance = FILMGLS() if isinstance(instance.inputs, FILMGLSInputSpec): - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value else: - for key, metadata in input_map2.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map2.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 2dd9b9d404..a771f914e1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import ApplyMask +from ....testing import assert_equal +from ..maths import ApplyMask def test_ApplyMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -39,8 +39,8 @@ def test_ApplyMask_inputs(): ) inputs = ApplyMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyMask_outputs(): @@ -48,7 +48,7 @@ def test_ApplyMask_outputs(): ) outputs = ApplyMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index b24089cd4c..b6f0d00fcc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import ApplyTOPUP +from ....testing import assert_equal +from ..epi import ApplyTOPUP def test_ApplyTOPUP_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_ApplyTOPUP_inputs(): ) inputs = ApplyTOPUP.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyTOPUP_outputs(): @@ -54,7 +54,7 @@ def test_ApplyTOPUP_outputs(): ) outputs = ApplyTOPUP.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 62c23c7519..8cb17890dd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import ApplyWarp +from ....testing import assert_equal +from ..preprocess import ApplyWarp def test_ApplyWarp_inputs(): input_map = dict(abswarp=dict(argstr='--abs', @@ -54,8 +54,8 @@ def test_ApplyWarp_inputs(): ) inputs = ApplyWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyWarp_outputs(): @@ -63,7 +63,7 @@ def test_ApplyWarp_outputs(): ) outputs = ApplyWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py index 8a0ac469e1..ed830ba059 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import ApplyXfm +from ....testing import assert_equal +from ..preprocess import ApplyXfm def test_ApplyXfm_inputs(): input_map = dict(angle_rep=dict(argstr='-anglerep %s', @@ -146,8 +146,8 @@ def test_ApplyXfm_inputs(): ) inputs = ApplyXfm.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyXfm_outputs(): @@ -157,7 +157,7 @@ def test_ApplyXfm_outputs(): ) outputs = ApplyXfm.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index 0f7aa330cd..5d62437360 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import AvScale +from ....testing import assert_equal +from ..utils import AvScale def test_AvScale_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,8 +20,8 @@ def test_AvScale_inputs(): ) inputs = AvScale.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AvScale_outputs(): @@ -36,7 +36,7 @@ def test_AvScale_outputs(): ) outputs = AvScale.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py index 5eac854d19..677cc8c089 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import BEDPOSTX4 +from ....testing import assert_equal +from ..dti import BEDPOSTX4 def test_BEDPOSTX4_inputs(): input_map = dict(all_ard=dict(argstr='--allard', @@ -80,8 +80,8 @@ def test_BEDPOSTX4_inputs(): ) inputs = BEDPOSTX4.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BEDPOSTX4_outputs(): @@ -97,7 +97,7 @@ def test_BEDPOSTX4_outputs(): ) outputs = BEDPOSTX4.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 2c9287789d..1d7fc047a8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import BEDPOSTX5 +from ....testing import assert_equal +from ..dti import BEDPOSTX5 def test_BEDPOSTX5_inputs(): input_map = dict(all_ard=dict(argstr='--allard', @@ -81,8 +81,8 @@ def test_BEDPOSTX5_inputs(): ) inputs = BEDPOSTX5.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BEDPOSTX5_outputs(): @@ -99,7 +99,7 @@ def test_BEDPOSTX5_outputs(): ) outputs = BEDPOSTX5.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index b5df942520..242f27753a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import BET +from ....testing import assert_equal +from ..preprocess import BET def test_BET_inputs(): input_map = dict(args=dict(argstr='%s', @@ -69,8 +69,8 @@ def test_BET_inputs(): ) inputs = BET.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BET_outputs(): @@ -88,7 +88,7 @@ def test_BET_outputs(): ) outputs = BET.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index 0caf39f057..34db882f71 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import BinaryMaths +from ....testing import assert_equal +from ..maths import BinaryMaths def test_BinaryMaths_inputs(): input_map = dict(args=dict(argstr='%s', @@ -49,8 +49,8 @@ def test_BinaryMaths_inputs(): ) inputs = BinaryMaths.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BinaryMaths_outputs(): @@ -58,7 +58,7 @@ def test_BinaryMaths_outputs(): ) outputs = BinaryMaths.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index c5ca3f3699..5ce774f9de 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import ChangeDataType +from ....testing import assert_equal +from ..maths import ChangeDataType def test_ChangeDataType_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_ChangeDataType_inputs(): ) inputs = ChangeDataType.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ChangeDataType_outputs(): @@ -45,7 +45,7 @@ def test_ChangeDataType_outputs(): ) outputs = ChangeDataType.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index 43cfbd1dcd..f96db2b872 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import Cluster +from ....testing import assert_equal +from ..model import Cluster def test_Cluster_inputs(): input_map = dict(args=dict(argstr='%s', @@ -74,8 +74,8 @@ def test_Cluster_inputs(): ) inputs = Cluster.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Cluster_outputs(): @@ -90,7 +90,7 @@ def test_Cluster_outputs(): ) outputs = Cluster.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index ab452e8880..dc0e3e7edd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Complex +from ....testing import assert_equal +from ..utils import Complex def test_Complex_inputs(): input_map = dict(args=dict(argstr='%s', @@ -90,8 +90,8 @@ def test_Complex_inputs(): ) inputs = Complex.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Complex_outputs(): @@ -103,7 +103,7 @@ def test_Complex_outputs(): ) outputs = Complex.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index cd9e22f7df..4bf7c7a78d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import ContrastMgr +from ....testing import assert_equal +from ..model import ContrastMgr def test_ContrastMgr_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_ContrastMgr_inputs(): ) inputs = ContrastMgr.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ContrastMgr_outputs(): @@ -58,7 +58,7 @@ def test_ContrastMgr_outputs(): ) outputs = ContrastMgr.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index b8da09b37b..d87cc28a93 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import ConvertWarp +from ....testing import assert_equal +from ..utils import ConvertWarp def test_ConvertWarp_inputs(): input_map = dict(abswarp=dict(argstr='--abs', @@ -60,8 +60,8 @@ def test_ConvertWarp_inputs(): ) inputs = ConvertWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ConvertWarp_outputs(): @@ -69,7 +69,7 @@ def test_ConvertWarp_outputs(): ) outputs = ConvertWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index b9bb6ae014..43ca0d63c9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import ConvertXFM +from ....testing import assert_equal +from ..utils import ConvertXFM def test_ConvertXFM_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_ConvertXFM_inputs(): ) inputs = ConvertXFM.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ConvertXFM_outputs(): @@ -52,7 +52,7 @@ def test_ConvertXFM_outputs(): ) outputs = ConvertXFM.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 7274fe483f..9c0a9104fe 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import CopyGeom +from ....testing import assert_equal +from ..utils import CopyGeom def test_CopyGeom_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_CopyGeom_inputs(): ) inputs = CopyGeom.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CopyGeom_outputs(): @@ -41,7 +41,7 @@ def test_CopyGeom_outputs(): ) outputs = CopyGeom.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 6c37ff96dc..53fedc778e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import DTIFit +from ....testing import assert_equal +from ..dti import DTIFit def test_DTIFit_inputs(): input_map = dict(args=dict(argstr='%s', @@ -59,8 +59,8 @@ def test_DTIFit_inputs(): ) inputs = DTIFit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTIFit_outputs(): @@ -78,7 +78,7 @@ def test_DTIFit_outputs(): ) outputs = DTIFit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index b62cf68bbb..93c4ea8faa 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import DilateImage +from ....testing import assert_equal +from ..maths import DilateImage def test_DilateImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_DilateImage_inputs(): ) inputs = DilateImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DilateImage_outputs(): @@ -59,7 +59,7 @@ def test_DilateImage_outputs(): ) outputs = DilateImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index f01268d1f7..1a217d6127 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import DistanceMap +from ....testing import assert_equal +from ..dti import DistanceMap def test_DistanceMap_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_DistanceMap_inputs(): ) inputs = DistanceMap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DistanceMap_outputs(): @@ -41,7 +41,7 @@ def test_DistanceMap_outputs(): ) outputs = DistanceMap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 5afe70ee93..cd92a2d776 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import EPIDeWarp +from ....testing import assert_equal +from ..epi import EPIDeWarp def test_EPIDeWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_EPIDeWarp_inputs(): ) inputs = EPIDeWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EPIDeWarp_outputs(): @@ -66,7 +66,7 @@ def test_EPIDeWarp_outputs(): ) outputs = EPIDeWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 34f9c1ea7d..8b5298cbca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import Eddy +from ....testing import assert_equal +from ..epi import Eddy def test_Eddy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -58,8 +58,8 @@ def test_Eddy_inputs(): ) inputs = Eddy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Eddy_outputs(): @@ -68,7 +68,7 @@ def test_Eddy_outputs(): ) outputs = Eddy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index dcfaa992c5..68fbf8f798 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import EddyCorrect +from ....testing import assert_equal +from ..epi import EddyCorrect def test_EddyCorrect_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_EddyCorrect_inputs(): ) inputs = EddyCorrect.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EddyCorrect_outputs(): @@ -41,7 +41,7 @@ def test_EddyCorrect_outputs(): ) outputs = EddyCorrect.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index 8160f4cd35..9be961c33b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import EpiReg +from ....testing import assert_equal +from ..epi import EpiReg def test_EpiReg_inputs(): input_map = dict(args=dict(argstr='%s', @@ -51,8 +51,8 @@ def test_EpiReg_inputs(): ) inputs = EpiReg.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EpiReg_outputs(): @@ -72,7 +72,7 @@ def test_EpiReg_outputs(): ) outputs = EpiReg.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 5a4d5768df..7c27b20f6d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import ErodeImage +from ....testing import assert_equal +from ..maths import ErodeImage def test_ErodeImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_ErodeImage_inputs(): ) inputs = ErodeImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ErodeImage_outputs(): @@ -59,7 +59,7 @@ def test_ErodeImage_outputs(): ) outputs = ErodeImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index bdcc6fde5b..23708a2df3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import ExtractROI +from ....testing import assert_equal +from ..utils import ExtractROI def test_ExtractROI_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_ExtractROI_inputs(): ) inputs = ExtractROI.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ExtractROI_outputs(): @@ -63,7 +63,7 @@ def test_ExtractROI_outputs(): ) outputs = ExtractROI.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 8a5c4fc334..e50fb80951 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import FAST +from ....testing import assert_equal +from ..preprocess import FAST def test_FAST_inputs(): input_map = dict(args=dict(argstr='%s', @@ -65,8 +65,8 @@ def test_FAST_inputs(): ) inputs = FAST.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FAST_outputs(): @@ -81,7 +81,7 @@ def test_FAST_outputs(): ) outputs = FAST.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 7ef21706a7..66a8e88419 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import FEAT +from ....testing import assert_equal +from ..model import FEAT def test_FEAT_inputs(): input_map = dict(args=dict(argstr='%s', @@ -21,8 +21,8 @@ def test_FEAT_inputs(): ) inputs = FEAT.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FEAT_outputs(): @@ -30,7 +30,7 @@ def test_FEAT_outputs(): ) outputs = FEAT.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index 62ca6e9f2f..0db2b6dd46 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import FEATModel +from ....testing import assert_equal +from ..model import FEATModel def test_FEATModel_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_FEATModel_inputs(): ) inputs = FEATModel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FEATModel_outputs(): @@ -40,7 +40,7 @@ def test_FEATModel_outputs(): ) outputs = FEATModel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index 3320d83eb1..b3b1ebac68 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import FEATRegister +from ....testing import assert_equal +from ..model import FEATRegister def test_FEATRegister_inputs(): input_map = dict(feat_dirs=dict(mandatory=True, @@ -15,8 +15,8 @@ def test_FEATRegister_inputs(): ) inputs = FEATRegister.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FEATRegister_outputs(): @@ -24,7 +24,7 @@ def test_FEATRegister_outputs(): ) outputs = FEATRegister.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index f0e0cff030..ac94aa5873 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import FIRST +from ....testing import assert_equal +from ..preprocess import FIRST def test_FIRST_inputs(): input_map = dict(affine_file=dict(argstr='-a %s', @@ -52,8 +52,8 @@ def test_FIRST_inputs(): ) inputs = FIRST.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FIRST_outputs(): @@ -64,7 +64,7 @@ def test_FIRST_outputs(): ) outputs = FIRST.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index e4dc7c37e1..496b9fc85b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import FLAMEO +from ....testing import assert_equal +from ..model import FLAMEO def test_FLAMEO_inputs(): input_map = dict(args=dict(argstr='%s', @@ -60,8 +60,8 @@ def test_FLAMEO_inputs(): ) inputs = FLAMEO.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FLAMEO_outputs(): @@ -80,7 +80,7 @@ def test_FLAMEO_outputs(): ) outputs = FLAMEO.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index f1abc68dd3..17bf945b48 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import FLIRT +from ....testing import assert_equal +from ..preprocess import FLIRT def test_FLIRT_inputs(): input_map = dict(angle_rep=dict(argstr='-anglerep %s', @@ -145,8 +145,8 @@ def test_FLIRT_inputs(): ) inputs = FLIRT.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FLIRT_outputs(): @@ -156,7 +156,7 @@ def test_FLIRT_outputs(): ) outputs = FLIRT.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 2622ae217c..696d2044a4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import FNIRT +from ....testing import assert_equal +from ..preprocess import FNIRT def test_FNIRT_inputs(): input_map = dict(affine_file=dict(argstr='--aff=%s', @@ -123,8 +123,8 @@ def test_FNIRT_inputs(): ) inputs = FNIRT.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FNIRT_outputs(): @@ -138,7 +138,7 @@ def test_FNIRT_outputs(): ) outputs = FNIRT.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index 58098336cb..07fe34c5f2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.base import FSLCommand +from ....testing import assert_equal +from ..base import FSLCommand def test_FSLCommand_inputs(): input_map = dict(args=dict(argstr='%s', @@ -17,7 +17,7 @@ def test_FSLCommand_inputs(): ) inputs = FSLCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index ed5e01e8d5..b0e9a35d18 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import FSLXCommand +from ....testing import assert_equal +from ..dti import FSLXCommand def test_FSLXCommand_inputs(): input_map = dict(all_ard=dict(argstr='--allard', @@ -78,8 +78,8 @@ def test_FSLXCommand_inputs(): ) inputs = FSLXCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FSLXCommand_outputs(): @@ -94,7 +94,7 @@ def test_FSLXCommand_outputs(): ) outputs = FSLXCommand.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index f08bd21d2c..69f21693a0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import FUGUE +from ....testing import assert_equal +from ..preprocess import FUGUE def test_FUGUE_inputs(): input_map = dict(args=dict(argstr='%s', @@ -89,8 +89,8 @@ def test_FUGUE_inputs(): ) inputs = FUGUE.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FUGUE_outputs(): @@ -101,7 +101,7 @@ def test_FUGUE_outputs(): ) outputs = FUGUE.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 196f67cd2c..913a8feb27 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import FilterRegressor +from ....testing import assert_equal +from ..utils import FilterRegressor def test_FilterRegressor_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_FilterRegressor_inputs(): ) inputs = FilterRegressor.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FilterRegressor_outputs(): @@ -55,7 +55,7 @@ def test_FilterRegressor_outputs(): ) outputs = FilterRegressor.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 4e0c820a59..015928d443 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import FindTheBiggest +from ....testing import assert_equal +from ..dti import FindTheBiggest def test_FindTheBiggest_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_FindTheBiggest_inputs(): ) inputs = FindTheBiggest.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FindTheBiggest_outputs(): @@ -36,7 +36,7 @@ def test_FindTheBiggest_outputs(): ) outputs = FindTheBiggest.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index fb32f698eb..09a15af967 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import GLM +from ....testing import assert_equal +from ..model import GLM def test_GLM_inputs(): input_map = dict(args=dict(argstr='%s', @@ -67,8 +67,8 @@ def test_GLM_inputs(): ) inputs = GLM.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GLM_outputs(): @@ -87,7 +87,7 @@ def test_GLM_outputs(): ) outputs = GLM.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 7f3aefb1dd..671a9a8f7a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import ImageMaths +from ....testing import assert_equal +from ..utils import ImageMaths def test_ImageMaths_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_ImageMaths_inputs(): ) inputs = ImageMaths.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageMaths_outputs(): @@ -45,7 +45,7 @@ def test_ImageMaths_outputs(): ) outputs = ImageMaths.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index f70887653f..e726e775c8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import ImageMeants +from ....testing import assert_equal +from ..utils import ImageMeants def test_ImageMeants_inputs(): input_map = dict(args=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_ImageMeants_inputs(): ) inputs = ImageMeants.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageMeants_outputs(): @@ -51,7 +51,7 @@ def test_ImageMeants_outputs(): ) outputs = ImageMeants.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 6e039a8568..72e4e0b5b3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import ImageStats +from ....testing import assert_equal +from ..utils import ImageStats def test_ImageStats_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_ImageStats_inputs(): ) inputs = ImageStats.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageStats_outputs(): @@ -39,7 +39,7 @@ def test_ImageStats_outputs(): ) outputs = ImageStats.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index b2a6661ee7..c0910b5cb0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import InvWarp +from ....testing import assert_equal +from ..utils import InvWarp def test_InvWarp_inputs(): input_map = dict(absolute=dict(argstr='--abs', @@ -44,8 +44,8 @@ def test_InvWarp_inputs(): ) inputs = InvWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_InvWarp_outputs(): @@ -53,7 +53,7 @@ def test_InvWarp_outputs(): ) outputs = InvWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index b549ef8ae0..89ab3ebeab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import IsotropicSmooth +from ....testing import assert_equal +from ..maths import IsotropicSmooth def test_IsotropicSmooth_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_IsotropicSmooth_inputs(): ) inputs = IsotropicSmooth.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_IsotropicSmooth_outputs(): @@ -54,7 +54,7 @@ def test_IsotropicSmooth_outputs(): ) outputs = IsotropicSmooth.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 7e8f957a68..996410a5ec 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import L2Model +from ....testing import assert_equal +from ..model import L2Model def test_L2Model_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -11,8 +11,8 @@ def test_L2Model_inputs(): ) inputs = L2Model.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_L2Model_outputs(): @@ -22,7 +22,7 @@ def test_L2Model_outputs(): ) outputs = L2Model.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index 3dd68b4041..8b9a245cea 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import Level1Design +from ....testing import assert_equal +from ..model import Level1Design def test_Level1Design_inputs(): input_map = dict(bases=dict(mandatory=True, @@ -18,8 +18,8 @@ def test_Level1Design_inputs(): ) inputs = Level1Design.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Level1Design_outputs(): @@ -28,7 +28,7 @@ def test_Level1Design_outputs(): ) outputs = Level1Design.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index 8c9a97a5a8..1afc30885a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import MCFLIRT +from ....testing import assert_equal +from ..preprocess import MCFLIRT def test_MCFLIRT_inputs(): input_map = dict(args=dict(argstr='%s', @@ -61,8 +61,8 @@ def test_MCFLIRT_inputs(): ) inputs = MCFLIRT.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MCFLIRT_outputs(): @@ -76,7 +76,7 @@ def test_MCFLIRT_outputs(): ) outputs = MCFLIRT.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index 26363abc58..6baf56e764 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import MELODIC +from ....testing import assert_equal +from ..model import MELODIC def test_MELODIC_inputs(): input_map = dict(ICs=dict(argstr='--ICs=%s', @@ -109,8 +109,8 @@ def test_MELODIC_inputs(): ) inputs = MELODIC.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MELODIC_outputs(): @@ -119,7 +119,7 @@ def test_MELODIC_outputs(): ) outputs = MELODIC.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index 8263a9bba8..b1b1c5bdaf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import MakeDyadicVectors +from ....testing import assert_equal +from ..dti import MakeDyadicVectors def test_MakeDyadicVectors_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_MakeDyadicVectors_inputs(): ) inputs = MakeDyadicVectors.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MakeDyadicVectors_outputs(): @@ -46,7 +46,7 @@ def test_MakeDyadicVectors_outputs(): ) outputs = MakeDyadicVectors.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index 9752a7ffb6..c931261962 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import MathsCommand +from ....testing import assert_equal +from ..maths import MathsCommand def test_MathsCommand_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_MathsCommand_inputs(): ) inputs = MathsCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MathsCommand_outputs(): @@ -44,7 +44,7 @@ def test_MathsCommand_outputs(): ) outputs = MathsCommand.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 8a3fbcfaa7..86732a6af2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import MaxImage +from ....testing import assert_equal +from ..maths import MaxImage def test_MaxImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -39,8 +39,8 @@ def test_MaxImage_inputs(): ) inputs = MaxImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MaxImage_outputs(): @@ -48,7 +48,7 @@ def test_MaxImage_outputs(): ) outputs = MaxImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 252fd711c1..fba966582b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import MeanImage +from ....testing import assert_equal +from ..maths import MeanImage def test_MeanImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -39,8 +39,8 @@ def test_MeanImage_inputs(): ) inputs = MeanImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MeanImage_outputs(): @@ -48,7 +48,7 @@ def test_MeanImage_outputs(): ) outputs = MeanImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 56200c1001..9a882c9a18 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Merge +from ....testing import assert_equal +from ..utils import Merge def test_Merge_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_Merge_inputs(): ) inputs = Merge.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Merge_outputs(): @@ -43,7 +43,7 @@ def test_Merge_outputs(): ) outputs = Merge.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index bc2f31a2d0..d0ffbb9d34 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import MotionOutliers +from ....testing import assert_equal +from ..utils import MotionOutliers def test_MotionOutliers_inputs(): input_map = dict(args=dict(argstr='%s', @@ -48,8 +48,8 @@ def test_MotionOutliers_inputs(): ) inputs = MotionOutliers.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MotionOutliers_outputs(): @@ -59,7 +59,7 @@ def test_MotionOutliers_outputs(): ) outputs = MotionOutliers.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 07e23721f2..04a8c10c23 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import MultiImageMaths +from ....testing import assert_equal +from ..maths import MultiImageMaths def test_MultiImageMaths_inputs(): input_map = dict(args=dict(argstr='%s', @@ -41,8 +41,8 @@ def test_MultiImageMaths_inputs(): ) inputs = MultiImageMaths.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MultiImageMaths_outputs(): @@ -50,7 +50,7 @@ def test_MultiImageMaths_outputs(): ) outputs = MultiImageMaths.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 93002e6500..688a5bf29e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import MultipleRegressDesign +from ....testing import assert_equal +from ..model import MultipleRegressDesign def test_MultipleRegressDesign_inputs(): input_map = dict(contrasts=dict(mandatory=True, @@ -14,8 +14,8 @@ def test_MultipleRegressDesign_inputs(): ) inputs = MultipleRegressDesign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MultipleRegressDesign_outputs(): @@ -26,7 +26,7 @@ def test_MultipleRegressDesign_outputs(): ) outputs = MultipleRegressDesign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 164f9d5b82..091657fd1e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Overlay +from ....testing import assert_equal +from ..utils import Overlay def test_Overlay_inputs(): input_map = dict(args=dict(argstr='%s', @@ -71,8 +71,8 @@ def test_Overlay_inputs(): ) inputs = Overlay.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Overlay_outputs(): @@ -80,7 +80,7 @@ def test_Overlay_outputs(): ) outputs = Overlay.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index b78762c27f..08dd904b26 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import PRELUDE +from ....testing import assert_equal +from ..preprocess import PRELUDE def test_PRELUDE_inputs(): input_map = dict(args=dict(argstr='%s', @@ -62,8 +62,8 @@ def test_PRELUDE_inputs(): ) inputs = PRELUDE.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PRELUDE_outputs(): @@ -71,7 +71,7 @@ def test_PRELUDE_outputs(): ) outputs = PRELUDE.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 6a549f2866..583394d138 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import PlotMotionParams +from ....testing import assert_equal +from ..utils import PlotMotionParams def test_PlotMotionParams_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_PlotMotionParams_inputs(): ) inputs = PlotMotionParams.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PlotMotionParams_outputs(): @@ -41,7 +41,7 @@ def test_PlotMotionParams_outputs(): ) outputs = PlotMotionParams.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index c9232d3550..bfb76d8043 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import PlotTimeSeries +from ....testing import assert_equal +from ..utils import PlotTimeSeries def test_PlotTimeSeries_inputs(): input_map = dict(args=dict(argstr='%s', @@ -58,8 +58,8 @@ def test_PlotTimeSeries_inputs(): ) inputs = PlotTimeSeries.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PlotTimeSeries_outputs(): @@ -67,7 +67,7 @@ def test_PlotTimeSeries_outputs(): ) outputs = PlotTimeSeries.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 145967b61c..1f495918ce 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import PowerSpectrum +from ....testing import assert_equal +from ..utils import PowerSpectrum def test_PowerSpectrum_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_PowerSpectrum_inputs(): ) inputs = PowerSpectrum.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PowerSpectrum_outputs(): @@ -35,7 +35,7 @@ def test_PowerSpectrum_outputs(): ) outputs = PowerSpectrum.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index f16ef63fdd..e164bda3ac 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import PrepareFieldmap +from ....testing import assert_equal +from ..epi import PrepareFieldmap def test_PrepareFieldmap_inputs(): input_map = dict(args=dict(argstr='%s', @@ -41,8 +41,8 @@ def test_PrepareFieldmap_inputs(): ) inputs = PrepareFieldmap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PrepareFieldmap_outputs(): @@ -50,7 +50,7 @@ def test_PrepareFieldmap_outputs(): ) outputs = PrepareFieldmap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index 6016186e3c..4793039e07 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import ProbTrackX +from ....testing import assert_equal +from ..dti import ProbTrackX def test_ProbTrackX_inputs(): input_map = dict(args=dict(argstr='%s', @@ -97,8 +97,8 @@ def test_ProbTrackX_inputs(): ) inputs = ProbTrackX.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ProbTrackX_outputs(): @@ -110,7 +110,7 @@ def test_ProbTrackX_outputs(): ) outputs = ProbTrackX.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index 9b5b6e062d..b6946401c3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import ProbTrackX2 +from ....testing import assert_equal +from ..dti import ProbTrackX2 def test_ProbTrackX2_inputs(): input_map = dict(args=dict(argstr='%s', @@ -127,8 +127,8 @@ def test_ProbTrackX2_inputs(): ) inputs = ProbTrackX2.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ProbTrackX2_outputs(): @@ -145,7 +145,7 @@ def test_ProbTrackX2_outputs(): ) outputs = ProbTrackX2.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index 386584b976..f9403de75c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import ProjThresh +from ....testing import assert_equal +from ..dti import ProjThresh def test_ProjThresh_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_ProjThresh_inputs(): ) inputs = ProjThresh.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ProjThresh_outputs(): @@ -34,7 +34,7 @@ def test_ProjThresh_outputs(): ) outputs = ProjThresh.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index e6ca0b733c..97d2ff6352 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import Randomise +from ....testing import assert_equal +from ..model import Randomise def test_Randomise_inputs(): input_map = dict(args=dict(argstr='%s', @@ -77,8 +77,8 @@ def test_Randomise_inputs(): ) inputs = Randomise.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Randomise_outputs(): @@ -91,7 +91,7 @@ def test_Randomise_outputs(): ) outputs = Randomise.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index 206e608d65..b064dd1e51 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Reorient2Std +from ....testing import assert_equal +from ..utils import Reorient2Std def test_Reorient2Std_inputs(): input_map = dict(args=dict(argstr='%s', @@ -24,8 +24,8 @@ def test_Reorient2Std_inputs(): ) inputs = Reorient2Std.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Reorient2Std_outputs(): @@ -33,7 +33,7 @@ def test_Reorient2Std_outputs(): ) outputs = Reorient2Std.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 67c76c41d4..4b75cef50c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import RobustFOV +from ....testing import assert_equal +from ..utils import RobustFOV def test_RobustFOV_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_RobustFOV_inputs(): ) inputs = RobustFOV.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_RobustFOV_outputs(): @@ -35,7 +35,7 @@ def test_RobustFOV_outputs(): ) outputs = RobustFOV.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 1f1f2e44da..071d9c2960 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import SMM +from ....testing import assert_equal +from ..model import SMM def test_SMM_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_SMM_inputs(): ) inputs = SMM.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SMM_outputs(): @@ -41,7 +41,7 @@ def test_SMM_outputs(): ) outputs = SMM.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index 87e50c2b1c..e577e1299c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import SUSAN +from ....testing import assert_equal +from ..preprocess import SUSAN def test_SUSAN_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_SUSAN_inputs(): ) inputs = SUSAN.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SUSAN_outputs(): @@ -55,7 +55,7 @@ def test_SUSAN_outputs(): ) outputs = SUSAN.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index d20d9c2e37..6588a4cfb2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import SigLoss +from ....testing import assert_equal +from ..utils import SigLoss def test_SigLoss_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_SigLoss_inputs(): ) inputs = SigLoss.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SigLoss_outputs(): @@ -38,7 +38,7 @@ def test_SigLoss_outputs(): ) outputs = SigLoss.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index ef6ef2e004..5e4b75cf82 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.preprocess import SliceTimer +from ....testing import assert_equal +from ..preprocess import SliceTimer def test_SliceTimer_inputs(): input_map = dict(args=dict(argstr='%s', @@ -39,8 +39,8 @@ def test_SliceTimer_inputs(): ) inputs = SliceTimer.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SliceTimer_outputs(): @@ -48,7 +48,7 @@ def test_SliceTimer_outputs(): ) outputs = SliceTimer.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index 464373912b..a74470e555 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Slicer +from ....testing import assert_equal +from ..utils import Slicer def test_Slicer_inputs(): input_map = dict(all_axial=dict(argstr='-A', @@ -80,8 +80,8 @@ def test_Slicer_inputs(): ) inputs = Slicer.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Slicer_outputs(): @@ -89,7 +89,7 @@ def test_Slicer_outputs(): ) outputs = Slicer.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index 57fff51552..6738ae4382 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Smooth +from ....testing import assert_equal +from ..utils import Smooth def test_Smooth_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_Smooth_inputs(): ) inputs = Smooth.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Smooth_outputs(): @@ -39,7 +39,7 @@ def test_Smooth_outputs(): ) outputs = Smooth.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index 420ec92962..9e9195bf6b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.model import SmoothEstimate +from ....testing import assert_equal +from ..model import SmoothEstimate def test_SmoothEstimate_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_SmoothEstimate_inputs(): ) inputs = SmoothEstimate.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SmoothEstimate_outputs(): @@ -41,7 +41,7 @@ def test_SmoothEstimate_outputs(): ) outputs = SmoothEstimate.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 37bbb0752a..511072850f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import SpatialFilter +from ....testing import assert_equal +from ..maths import SpatialFilter def test_SpatialFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_SpatialFilter_inputs(): ) inputs = SpatialFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SpatialFilter_outputs(): @@ -59,7 +59,7 @@ def test_SpatialFilter_outputs(): ) outputs = SpatialFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index 9e7c31c4cc..a910fef77e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import Split +from ....testing import assert_equal +from ..utils import Split def test_Split_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_Split_inputs(): ) inputs = Split.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Split_outputs(): @@ -37,7 +37,7 @@ def test_Split_outputs(): ) outputs = Split.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 87b00e4629..65c93c5be6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import SwapDimensions +from ....testing import assert_equal +from ..utils import SwapDimensions def test_SwapDimensions_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_SwapDimensions_inputs(): ) inputs = SwapDimensions.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SwapDimensions_outputs(): @@ -37,7 +37,7 @@ def test_SwapDimensions_outputs(): ) outputs = SwapDimensions.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 6fe136dc8d..2edb5ff1db 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.epi import TOPUP +from ....testing import assert_equal +from ..epi import TOPUP def test_TOPUP_inputs(): input_map = dict(args=dict(argstr='%s', @@ -85,8 +85,8 @@ def test_TOPUP_inputs(): ) inputs = TOPUP.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TOPUP_outputs(): @@ -99,7 +99,7 @@ def test_TOPUP_outputs(): ) outputs = TOPUP.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index afa709bd93..d30e31801f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import TemporalFilter +from ....testing import assert_equal +from ..maths import TemporalFilter def test_TemporalFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_TemporalFilter_inputs(): ) inputs = TemporalFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TemporalFilter_outputs(): @@ -52,7 +52,7 @@ def test_TemporalFilter_outputs(): ) outputs = TemporalFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index 9630b8d77e..f2424ca25c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import Threshold +from ....testing import assert_equal +from ..maths import Threshold def test_Threshold_inputs(): input_map = dict(args=dict(argstr='%s', @@ -44,8 +44,8 @@ def test_Threshold_inputs(): ) inputs = Threshold.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Threshold_outputs(): @@ -53,7 +53,7 @@ def test_Threshold_outputs(): ) outputs = Threshold.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 7433daa602..f6dc2991a6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import TractSkeleton +from ....testing import assert_equal +from ..dti import TractSkeleton def test_TractSkeleton_inputs(): input_map = dict(alt_data_file=dict(argstr='-a %s', @@ -38,8 +38,8 @@ def test_TractSkeleton_inputs(): ) inputs = TractSkeleton.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TractSkeleton_outputs(): @@ -48,7 +48,7 @@ def test_TractSkeleton_outputs(): ) outputs = TractSkeleton.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 1c3817446f..d35f8e4738 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.maths import UnaryMaths +from ....testing import assert_equal +from ..maths import UnaryMaths def test_UnaryMaths_inputs(): input_map = dict(args=dict(argstr='%s', @@ -39,8 +39,8 @@ def test_UnaryMaths_inputs(): ) inputs = UnaryMaths.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_UnaryMaths_outputs(): @@ -48,7 +48,7 @@ def test_UnaryMaths_outputs(): ) outputs = UnaryMaths.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index dbf08a7b44..2e129bef92 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import VecReg +from ....testing import assert_equal +from ..dti import VecReg def test_VecReg_inputs(): input_map = dict(affine_mat=dict(argstr='-t %s', @@ -41,8 +41,8 @@ def test_VecReg_inputs(): ) inputs = VecReg.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VecReg_outputs(): @@ -50,7 +50,7 @@ def test_VecReg_outputs(): ) outputs = VecReg.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 6a99aaf638..553c63665b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import WarpPoints +from ....testing import assert_equal +from ..utils import WarpPoints def test_WarpPoints_inputs(): input_map = dict(args=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_WarpPoints_inputs(): ) inputs = WarpPoints.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_WarpPoints_outputs(): @@ -51,7 +51,7 @@ def test_WarpPoints_outputs(): ) outputs = WarpPoints.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index 888693ba09..f8f7941081 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import WarpPointsToStd +from ....testing import assert_equal +from ..utils import WarpPointsToStd def test_WarpPointsToStd_inputs(): input_map = dict(args=dict(argstr='%s', @@ -44,8 +44,8 @@ def test_WarpPointsToStd_inputs(): ) inputs = WarpPointsToStd.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_WarpPointsToStd_outputs(): @@ -53,7 +53,7 @@ def test_WarpPointsToStd_outputs(): ) outputs = WarpPointsToStd.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index 2047a5a1b0..eea3ada6aa 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.utils import WarpUtils +from ....testing import assert_equal +from ..utils import WarpUtils def test_WarpUtils_inputs(): input_map = dict(args=dict(argstr='%s', @@ -41,8 +41,8 @@ def test_WarpUtils_inputs(): ) inputs = WarpUtils.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_WarpUtils_outputs(): @@ -51,7 +51,7 @@ def test_WarpUtils_outputs(): ) outputs = WarpUtils.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres4.py b/nipype/interfaces/fsl/tests/test_auto_XFibres4.py index a227c5fd0e..a5733fd892 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres4.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres4.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import XFibres4 +from ....testing import assert_equal +from ..dti import XFibres4 def test_XFibres4_inputs(): input_map = dict(all_ard=dict(argstr='--allard', @@ -67,8 +67,8 @@ def test_XFibres4_inputs(): ) inputs = XFibres4.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_XFibres4_outputs(): @@ -82,7 +82,7 @@ def test_XFibres4_outputs(): ) outputs = XFibres4.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 6289732c84..0e2b34d39d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import XFibres5 +from ....testing import assert_equal +from ..dti import XFibres5 def test_XFibres5_inputs(): input_map = dict(all_ard=dict(argstr='--allard', @@ -80,8 +80,8 @@ def test_XFibres5_inputs(): ) inputs = XFibres5.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_XFibres5_outputs(): @@ -96,7 +96,7 @@ def test_XFibres5_outputs(): ) outputs = XFibres5.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/fsl/tests/test_base.py b/nipype/interfaces/fsl/tests/test_base.py index 9e8398f6e0..3aa0f5aae1 100644 --- a/nipype/interfaces/fsl/tests/test_base.py +++ b/nipype/interfaces/fsl/tests/test_base.py @@ -19,7 +19,7 @@ def test_fslversion(): @skipif(no_fsl)#skip if fsl not installed) def test_fsloutputtype(): - types = fsl.Info.ftypes.keys() + types = list(fsl.Info.ftypes.keys()) orig_out_type = fsl.Info.output_type() yield assert_true, orig_out_type in types diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index e610278700..5d114e4d8d 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -207,7 +207,7 @@ def test_randomise2(): 'list_img_voxel_EVs': ('--vxf=6,7,8,9,3', '6,7,8,9,3')} - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): rand4 = fsl.Randomise(input_4D='infile', output_rootname='root', **{name: settings[1]}) yield assert_equal, rand4.cmdline, rand4.cmd + ' -i infile -o root ' \ @@ -292,7 +292,7 @@ def test_Randomise_parallel(): + repr([6, 7, 8, 9, 3]), repr([6, 7, 8, 9, 3]))} - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): rand4 = fsl.Randomise_parallel(input_4D='infile', output_rootname='root', **{name: settings[1]}) @@ -387,7 +387,7 @@ def test_Vec_reg(): 'interpolation': ('--interp=sinc', 'sinc'), 'brainMask': ('-m mask', 'mask')} - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): vrg4 = fsl.VecReg(infile='infile', outfile='outfile', refVolName='MNI152', **{name: settings[1]}) yield assert_equal, vrg4.cmdline, vrg4.cmd + \ diff --git a/nipype/interfaces/fsl/tests/test_maths.py b/nipype/interfaces/fsl/tests/test_maths.py index 045f0ef1d2..299c5157c4 100644 --- a/nipype/interfaces/fsl/tests/test_maths.py +++ b/nipype/interfaces/fsl/tests/test_maths.py @@ -1,5 +1,6 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import division import os from tempfile import mkdtemp @@ -11,17 +12,27 @@ from nipype.testing import (assert_equal, assert_raises, skipif) from nipype.interfaces.base import Undefined import nipype.interfaces.fsl.maths as fsl -from nipype.interfaces.fsl import no_fsl +from nipype.interfaces.fsl import no_fsl, Info +from nipype.interfaces.fsl.base import FSLCommand +def set_output_type(fsl_output_type): + prev_output_type = os.environ.get('FSLOUTPUTTYPE', None) + + if fsl_output_type is not None: + os.environ['FSLOUTPUTTYPE'] = fsl_output_type + elif 'FSLOUTPUTTYPE' in os.environ: + del os.environ['FSLOUTPUTTYPE'] + + FSLCommand.set_default_output_type(Info.output_type()) + + return prev_output_type + def create_files_in_directory(): testdir = os.path.realpath(mkdtemp()) origdir = os.getcwd() os.chdir(testdir) - ftype = os.environ["FSLOUTPUTTYPE"] - os.environ["FSLOUTPUTTYPE"] = "NIFTI" - filelist = ['a.nii','b.nii'] for f in filelist: hdr = nb.Nifti1Header() @@ -30,18 +41,20 @@ def create_files_in_directory(): img = np.random.random(shape) nb.save(nb.Nifti1Image(img,np.eye(4),hdr), os.path.join(testdir,f)) - return filelist, testdir, origdir, ftype -def clean_directory(testdir, origdir, ftype): + out_ext = Info.output_type_to_ext(Info.output_type()) + return filelist, testdir, origdir, out_ext + +def clean_directory(testdir, origdir): if os.path.exists(testdir): rmtree(testdir) os.chdir(origdir) - os.environ["FSLOUTPUTTYPE"] = ftype @skipif(no_fsl) -def test_maths_base(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_maths_base(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get some fslmaths maths = fsl.MathsCommand() @@ -54,21 +67,22 @@ def test_maths_base(): # Set an in file maths.inputs.in_file = "a.nii" + out_file = "a_maths%s" % out_ext # Now test the most basic command line - yield assert_equal, maths.cmdline, "fslmaths a.nii %s"%os.path.join(testdir, "a_maths.nii") + yield assert_equal, maths.cmdline, "fslmaths a.nii %s"%os.path.join(testdir, out_file) # Now test that we can set the various data types dtypes = ["float","char","int","short","double","input"] - int_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, "a_maths.nii") - out_cmdline = "fslmaths a.nii " + os.path.join(testdir, "a_maths.nii") + " -odt %s" - duo_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, "a_maths.nii") + " -odt %s" + int_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, out_file) + out_cmdline = "fslmaths a.nii " + os.path.join(testdir, out_file) + " -odt %s" + duo_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, out_file) + " -odt %s" for dtype in dtypes: - foo = fsl.MathsCommand(in_file="a.nii",internal_datatype=dtype) + foo = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype) yield assert_equal, foo.cmdline, int_cmdline%dtype - bar = fsl.MathsCommand(in_file="a.nii",output_datatype=dtype) - yield assert_equal, bar.cmdline, out_cmdline%dtype - foobar = fsl.MathsCommand(in_file="a.nii",internal_datatype=dtype,output_datatype=dtype) + bar = fsl.MathsCommand(in_file="a.nii", output_datatype=dtype) + yield assert_equal, bar.cmdline, out_cmdline % dtype + foobar = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype, output_datatype=dtype) yield assert_equal, foobar.cmdline, duo_cmdline%(dtype, dtype) # Test that we can ask for an outfile name @@ -76,11 +90,13 @@ def test_maths_base(): yield assert_equal, maths.cmdline, "fslmaths a.nii b.nii" # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_changedt(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_changedt(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get some fslmaths cdt = fsl.ChangeDataType() @@ -106,11 +122,13 @@ def test_changedt(): yield assert_equal, foo.cmdline, cmdline%dtype # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_threshold(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_threshold(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command thresh = fsl.Threshold(in_file="a.nii",out_file="b.nii") @@ -140,12 +158,14 @@ def test_threshold(): yield assert_equal, thresh.cmdline, cmdline%("-uthrP "+val) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_meanimage(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_meanimage(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command meaner = fsl.MeanImage(in_file="a.nii",out_file="b.nii") @@ -164,14 +184,16 @@ def test_meanimage(): # Test the auto naming meaner = fsl.MeanImage(in_file="a.nii") - yield assert_equal, meaner.cmdline, "fslmaths a.nii -Tmean %s"%os.path.join(testdir, "a_mean.nii") + yield assert_equal, meaner.cmdline, "fslmaths a.nii -Tmean %s"%os.path.join(testdir, "a_mean%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_maximage(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_maximage(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command maxer = fsl.MaxImage(in_file="a.nii",out_file="b.nii") @@ -190,14 +212,16 @@ def test_maximage(): # Test the auto naming maxer = fsl.MaxImage(in_file="a.nii") - yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax %s"%os.path.join(testdir, "a_max.nii") + yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax %s"%os.path.join(testdir, "a_max%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_smooth(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_smooth(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command smoother = fsl.IsotropicSmooth(in_file="a.nii",out_file="b.nii") @@ -210,23 +234,25 @@ def test_smooth(): # Test smoothing kernels cmdline = "fslmaths a.nii -s %.5f b.nii" - for val in [0,1.,1,25,0.5,8/3]: + for val in [0, 1., 1, 25, 0.5, 8 / 3.]: smoother = fsl.IsotropicSmooth(in_file="a.nii",out_file="b.nii",sigma=val) yield assert_equal, smoother.cmdline, cmdline%val smoother = fsl.IsotropicSmooth(in_file="a.nii",out_file="b.nii",fwhm=val) - val = float(val)/np.sqrt(8 * np.log(2)) + val = float(val) / np.sqrt(8 * np.log(2)) yield assert_equal, smoother.cmdline, cmdline%val # Test automatic naming smoother = fsl.IsotropicSmooth(in_file="a.nii", sigma=5) - yield assert_equal, smoother.cmdline, "fslmaths a.nii -s %.5f %s"%(5, os.path.join(testdir, "a_smooth.nii")) + yield assert_equal, smoother.cmdline, "fslmaths a.nii -s %.5f %s"%(5, os.path.join(testdir, "a_smooth%s" % out_ext)) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_mask(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_mask(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command masker = fsl.ApplyMask(in_file="a.nii",out_file="c.nii") @@ -243,15 +269,17 @@ def test_mask(): # Test auto name generation masker = fsl.ApplyMask(in_file="a.nii",mask_file="b.nii") - yield assert_equal, masker.cmdline, "fslmaths a.nii -mas b.nii "+os.path.join(testdir, "a_masked.nii") + yield assert_equal, masker.cmdline, "fslmaths a.nii -mas b.nii "+os.path.join(testdir, "a_masked%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_dilation(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_dilation(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command diller = fsl.DilateImage(in_file="a.nii",out_file="b.nii") @@ -285,14 +313,16 @@ def test_dilation(): # Test that we don't need to request an out name dil = fsl.DilateImage(in_file="a.nii", operation="max") - yield assert_equal, dil.cmdline, "fslmaths a.nii -dilF %s"%os.path.join(testdir, "a_dil.nii") + yield assert_equal, dil.cmdline, "fslmaths a.nii -dilF %s"%os.path.join(testdir, "a_dil%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_erosion(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_erosion(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command erode = fsl.ErodeImage(in_file="a.nii",out_file="b.nii") @@ -309,14 +339,16 @@ def test_erosion(): # Test that we don't need to request an out name erode = fsl.ErodeImage(in_file="a.nii") - yield assert_equal, erode.cmdline, "fslmaths a.nii -ero %s"%os.path.join(testdir, "a_ero.nii") + yield assert_equal, erode.cmdline, "fslmaths a.nii -ero %s"%os.path.join(testdir, "a_ero%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_spatial_filter(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_spatial_filter(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command filter = fsl.SpatialFilter(in_file="a.nii",out_file="b.nii") @@ -334,15 +366,17 @@ def test_spatial_filter(): # Test that we don't need to ask for an out name filter = fsl.SpatialFilter(in_file="a.nii", operation="mean") - yield assert_equal, filter.cmdline, "fslmaths a.nii -fmean %s"%os.path.join(testdir, "a_filt.nii") + yield assert_equal, filter.cmdline, "fslmaths a.nii -fmean %s"%os.path.join(testdir, "a_filt%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_unarymaths(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_unarymaths(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command maths = fsl.UnaryMaths(in_file="a.nii",out_file="b.nii") @@ -362,15 +396,17 @@ def test_unarymaths(): # Test that we don't need to ask for an out file for op in ops: maths = fsl.UnaryMaths(in_file="a.nii", operation=op) - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %s"%(op, os.path.join(testdir, "a_%s.nii"%op)) + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %s"%(op, os.path.join(testdir, "a_%s%s"%(op, out_ext))) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_binarymaths(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_binarymaths(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command maths = fsl.BinaryMaths(in_file="a.nii",out_file="c.nii") @@ -394,18 +430,21 @@ def test_binarymaths(): maths.inputs.operand_value = ent yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %.8f c.nii"%(op, ent) + # Test that we don't need to ask for an out file for op in ops: maths = fsl.BinaryMaths(in_file="a.nii", operation=op, operand_file="b.nii") - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii %s"%(op,os.path.join(testdir,"a_maths.nii")) + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii %s"%(op,os.path.join(testdir, "a_maths%s" % out_ext)) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_multimaths(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_multimaths(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command maths = fsl.MultiImageMaths(in_file="a.nii",out_file="c.nii") @@ -428,15 +467,17 @@ def test_multimaths(): # Test that we don't need to ask for an out file maths = fsl.MultiImageMaths(in_file="a.nii", op_string="-add %s -mul 5", operand_files=["b.nii"]) yield assert_equal, maths.cmdline, \ - "fslmaths a.nii -add b.nii -mul 5 %s"%os.path.join(testdir,"a_maths.nii") + "fslmaths a.nii -add b.nii -mul 5 %s"%os.path.join(testdir, "a_maths%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) + clean_directory(testdir, origdir) + set_output_type(prev_type) @skipif(no_fsl) -def test_tempfilt(): - files, testdir, origdir, ftype = create_files_in_directory() +def test_tempfilt(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() # Get the command filt = fsl.TemporalFilter(in_file="a.nii",out_file="b.nii") @@ -457,9 +498,20 @@ def test_tempfilt(): # Test that we don't need to ask for an out file filt = fsl.TemporalFilter(in_file="a.nii", highpass_sigma = 64) yield assert_equal, filt.cmdline, \ - "fslmaths a.nii -bptf 64.000000 -1.000000 %s"%os.path.join(testdir,"a_filt.nii") + "fslmaths a.nii -bptf 64.000000 -1.000000 %s"%os.path.join(testdir,"a_filt%s" % out_ext) # Clean up our mess - clean_directory(testdir, origdir, ftype) - + clean_directory(testdir, origdir) + set_output_type(prev_type) +@skipif(no_fsl) +def test_all_again(): + # Rerun tests with all output file types + all_func = [test_binarymaths, test_changedt, test_dilation, test_erosion, + test_mask, test_maximage, test_meanimage, test_multimaths, + test_smooth, test_tempfilt, test_threshold, test_unarymaths] + + for output_type in Info.ftypes: + for func in all_func: + for test in func(output_type): + yield test diff --git a/nipype/interfaces/fsl/tests/test_model.py b/nipype/interfaces/fsl/tests/test_model.py index 4f2515c258..655c2101e6 100644 --- a/nipype/interfaces/fsl/tests/test_model.py +++ b/nipype/interfaces/fsl/tests/test_model.py @@ -1,5 +1,7 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from builtins import open + import os import tempfile import shutil @@ -21,7 +23,7 @@ def setup_infile(): ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) - file(tmp_infile, 'w') + open(tmp_infile, 'w') os.chdir(tmp_dir) return tmp_infile, tmp_dir @@ -80,9 +82,9 @@ def test_MultipleRegressDesign(): 1 1 """ - yield assert_equal, open(os.path.join(os.getcwd(),'design.con'), 'r').read(), design_con_expected_content - yield assert_equal, open(os.path.join(os.getcwd(),'design.mat'), 'r').read(), design_mat_expected_content - yield assert_equal, open(os.path.join(os.getcwd(),'design.fts'), 'r').read(), design_fts_expected_content - yield assert_equal, open(os.path.join(os.getcwd(),'design.grp'), 'r').read(), design_grp_expected_content + yield assert_equal, open(os.path.join(os.getcwd(), 'design.con'), 'r').read(), design_con_expected_content + yield assert_equal, open(os.path.join(os.getcwd(), 'design.mat'), 'r').read(), design_mat_expected_content + yield assert_equal, open(os.path.join(os.getcwd(), 'design.fts'), 'r').read(), design_fts_expected_content + yield assert_equal, open(os.path.join(os.getcwd(), 'design.grp'), 'r').read(), design_grp_expected_content teardown_infile(tp_dir) diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py index 99b881b8f2..8abf68fa3e 100644 --- a/nipype/interfaces/fsl/tests/test_preprocess.py +++ b/nipype/interfaces/fsl/tests/test_preprocess.py @@ -1,5 +1,7 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from builtins import open + import os import tempfile import shutil @@ -31,7 +33,7 @@ def setup_infile(): ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) - file(tmp_infile, 'w') + open(tmp_infile, 'w') return tmp_infile, tmp_dir @@ -92,7 +94,7 @@ def func(): better = fsl.BET() outfile = fsl_name(better, 'foo_brain') outpath = os.path.join(os.getcwd(), outfile) - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): better = fsl.BET(**{name: settings[1]}) # Add mandatory input better.inputs.in_file = tmp_infile @@ -156,7 +158,7 @@ def test_fast(): } # test each of our arguments - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): faster = fsl.FAST(in_files=tmp_infile, **{name: settings[1]}) yield assert_equal, faster.cmdline, ' '.join([faster.cmd, settings[0], @@ -314,7 +316,7 @@ def test_mcflirt(): 'save_plots': ('-plots', True), } - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): fnt = fsl.MCFLIRT(in_file=infile, **{name: settings[1]}) instr = '-in %s' % (infile) outstr = '-out %s' % (outfile) @@ -406,7 +408,7 @@ def test_fnirt(): 'out_intensitymap_file': ('--intout='), 'log_file': ('--logout=')} - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): fnirt = fsl.FNIRT(in_file=infile, ref_file=reffile, **{name: infile}) @@ -461,7 +463,7 @@ def test_applywarp(): } # in_file, ref_file, field_file mandatory - for name, settings in opt_map.items(): + for name, settings in list(opt_map.items()): awarp = fsl.ApplyWarp(in_file=infile, ref_file=reffile, field_file=reffile, diff --git a/nipype/interfaces/fsl/tests/test_utils.py b/nipype/interfaces/fsl/tests/test_utils.py index 570848ec5d..1e74fc3f7e 100644 --- a/nipype/interfaces/fsl/tests/test_utils.py +++ b/nipype/interfaces/fsl/tests/test_utils.py @@ -11,33 +11,15 @@ from nipype.testing import (assert_equal, assert_not_equal, assert_raises, skipif) import nipype.interfaces.fsl.utils as fsl -from nipype.interfaces.fsl import no_fsl +from nipype.interfaces.fsl import no_fsl, Info - -def create_files_in_directory(): - outdir = mkdtemp() - cwd = os.getcwd() - os.chdir(outdir) - filelist = ['a.nii', 'b.nii'] - for f in filelist: - hdr = nb.Nifti1Header() - shape = (3, 3, 3, 4) - hdr.set_data_shape(shape) - img = np.random.random(shape) - nb.save(nb.Nifti1Image(img, np.eye(4), hdr), - os.path.join(outdir, f)) - return filelist, outdir, cwd - - -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): - rmtree(outdir) - os.chdir(old_wd) +from .test_maths import (set_output_type, create_files_in_directory, + clean_directory) @skipif(no_fsl) def test_fslroi(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() roi = fsl.ExtractROI() @@ -71,7 +53,7 @@ def test_fslroi(): @skipif(no_fsl) def test_fslmerge(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() merger = fsl.Merge() @@ -109,7 +91,7 @@ def test_fslmerge(): # test fslmath @skipif(no_fsl) def test_fslmaths(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() math = fsl.ImageMaths() # make sure command gets called @@ -139,7 +121,7 @@ def test_fslmaths(): @skipif(no_fsl) def test_overlay(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() overlay = fsl.Overlay() # make sure command gets called @@ -173,7 +155,7 @@ def test_overlay(): @skipif(no_fsl) def test_slicer(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() slicer = fsl.Slicer() # make sure command gets called @@ -213,7 +195,7 @@ def create_parfiles(): @skipif(no_fsl) def test_plottimeseries(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() parfiles = create_parfiles() plotter = fsl.PlotTimeSeries() @@ -246,7 +228,7 @@ def test_plottimeseries(): @skipif(no_fsl) def test_plotmotionparams(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() parfiles = create_parfiles() plotter = fsl.PlotMotionParams() @@ -278,7 +260,7 @@ def test_plotmotionparams(): @skipif(no_fsl) def test_convertxfm(): - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir, cwd, _ = create_files_in_directory() cvt = fsl.ConvertXFM() # make sure command gets called @@ -304,8 +286,9 @@ def test_convertxfm(): @skipif(no_fsl) -def test_swapdims(): - files, testdir, origdir = create_files_in_directory() +def test_swapdims(fsl_output_type=None): + prev_type = set_output_type(fsl_output_type) + files, testdir, origdir, out_ext = create_files_in_directory() swap = fsl.SwapDimensions() # Test the underlying command @@ -320,7 +303,7 @@ def test_swapdims(): # Now test a basic command line swap.inputs.in_file = files[0] swap.inputs.new_dims = ("x", "y", "z") - yield assert_equal, swap.cmdline, "fslswapdim a.nii x y z %s" % os.path.realpath(os.path.join(testdir, "a_newdims.nii")) + yield assert_equal, swap.cmdline, "fslswapdim a.nii x y z %s" % os.path.realpath(os.path.join(testdir, "a_newdims%s" % out_ext)) # Test that we can set an output name swap.inputs.out_file = "b.nii" @@ -328,3 +311,4 @@ def test_swapdims(): # Clean up clean_directory(testdir, origdir) + set_output_type(prev_type) diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index d9b09904d9..7324d58b8e 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -15,6 +15,10 @@ >>> os.chdir(datadir) """ +from __future__ import division +from builtins import map +from builtins import range + import os from glob import glob import warnings @@ -29,7 +33,7 @@ fname_presuffix, copyfile) warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) + class CopyGeomInputSpec(FSLCommandInputSpec): in_file = File(exists=True, mandatory=True, argstr="%s", position=0, @@ -290,7 +294,7 @@ class ExtractROI(FSLCommand): def _format_arg(self, name, spec, value): if name == "crop_list": - return " ".join(map(str, sum(map(list, value), []))) + return " ".join(map(str, sum(list(map(list, value)), []))) return super(ExtractROI, self)._format_arg(name, spec, value) def _list_outputs(self): @@ -480,7 +484,7 @@ def _format_arg(self, name, trait_spec, value): n_cols = design.shape[1] except IndexError: n_cols = 1 - return trait_spec.argstr % ",".join(map(str, range(1, n_cols + 1))) + return trait_spec.argstr % ",".join(map(str, list(range(1, n_cols + 1)))) return super(FilterRegressor, self)._format_arg(name, trait_spec, value) def _list_outputs(self): diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 39ae774c21..31eb48ca61 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -17,6 +17,11 @@ >>> os.chdir(datadir) """ + +from builtins import zip +from builtins import filter +from builtins import range + import glob import fnmatch import string @@ -29,11 +34,19 @@ from warnings import warn import sqlite3 -from nipype.utils.misc import human_order_sorted -from nipype.external import six -from ..utils.misc import str2bool +from .base import (TraitedSpec, traits, File, Directory, + BaseInterface, InputMultiPath, isdefined, + OutputMultiPath, DynamicTraitedSpec, + Undefined, BaseInterfaceInputSpec) from .. import config +from ..external.six import string_types +from ..utils.filemanip import (copyfile, list_to_filename, + filename_to_list) +from ..utils.misc import human_order_sorted +from ..utils.misc import str2bool +from .. import logging +iflogger = logging.getLogger('interface') try: import pyxnat @@ -51,16 +64,6 @@ except: pass -from nipype.interfaces.base import (TraitedSpec, traits, File, Directory, - BaseInterface, InputMultiPath, isdefined, - OutputMultiPath, DynamicTraitedSpec, - Undefined, BaseInterfaceInputSpec) -from nipype.utils.filemanip import (copyfile, list_to_filename, - filename_to_list) - -from .. import logging -iflogger = logging.getLogger('interface') - def copytree(src, dst, use_hardlink=False): """Recursively copy a directory tree using @@ -73,7 +76,7 @@ def copytree(src, dst, use_hardlink=False): names = os.listdir(src) try: os.makedirs(dst) - except OSError, why: + except OSError as why: if 'File exists' in why: pass else: @@ -88,11 +91,11 @@ def copytree(src, dst, use_hardlink=False): else: copyfile(srcname, dstname, True, hashmethod='content', use_hardlink=use_hardlink) - except (IOError, os.error), why: + except (IOError, os.error) as why: errors.append((srcname, dstname, str(why))) # catch the Error from the recursive copytree so that we can # continue with other files - except Exception, err: + except Exception as err: errors.extend(err.args[0]) if errors: raise Exception(errors) @@ -216,7 +219,7 @@ class DataSink(IOBase): >>> ds.inputs.structural = 'structural.nii' >>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii']) >>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii']) - >>> ds.run() # doctest: +SKIP + >>> ds.run() # doctest: +SKIP To use DataSink in a MapNode, its inputs have to be defined at the time the interface is created. @@ -227,7 +230,7 @@ class DataSink(IOBase): >>> ds.inputs.structural = 'structural.nii' >>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii']) >>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii']) - >>> ds.run() # doctest: +SKIP + >>> ds.run() # doctest: +SKIP """ input_spec = DataSinkInputSpec @@ -311,14 +314,14 @@ def _list_outputs(self): if not os.path.exists(outdir): try: os.makedirs(outdir) - except OSError, inst: + except OSError as inst: if 'File exists' in inst: pass else: raise(inst) use_hardlink = str2bool(config.get('execution', 'try_hard_link_datasink') ) - for key, files in self.inputs._outputs.items(): + for key, files in list(self.inputs._outputs.items()): if not isdefined(files): continue iflogger.debug("key: %s files: %s" % (key, str(files))) @@ -344,7 +347,7 @@ def _list_outputs(self): if not os.path.exists(path): try: os.makedirs(path) - except OSError, inst: + except OSError as inst: if 'File exists' in inst: pass else: @@ -361,7 +364,7 @@ def _list_outputs(self): if not os.path.exists(path): try: os.makedirs(path) - except OSError, inst: + except OSError as inst: if 'File exists' in inst: pass else: @@ -423,7 +426,7 @@ def __setattr__(self, key, value): class S3DataSink(DataSink): """ Works exactly like DataSink, except the specified files will also be uploaded to Amazon S3 storage in the specified bucket - and location. 'bucket_path' is the s3 analog for + and location. 'bucket_path' is the s3 analog for 'base_directory'. """ @@ -585,7 +588,7 @@ def _list_outputs(self): isdefined(self.inputs.field_template) and \ key in self.inputs.field_template: template = self.inputs.field_template[key] # template override for multiple outfields - if isdefined(self.inputs.bucket_path): + if isdefined(self.inputs.bucket_path): template = os.path.join(self.inputs.bucket_path, template) if not args: filelist = [] @@ -606,7 +609,7 @@ def _list_outputs(self): for argnum, arglist in enumerate(args): maxlen = 1 for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): if (maxlen > 1) and (len(arg) != maxlen): @@ -617,7 +620,7 @@ def _list_outputs(self): for i in range(maxlen): argtuple = [] for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): argtuple.append(arg[i]) @@ -800,7 +803,7 @@ def _add_output_traits(self, base): Using traits.Any instead out OutputMultiPath till add_trait bug is fixed. """ - return add_traits(base, self.inputs.template_args.keys()) + return add_traits(base, list(self.inputs.template_args.keys())) def _list_outputs(self): # infields are mandatory, however I could not figure out how to set 'mandatory' flag dynamically @@ -814,7 +817,7 @@ def _list_outputs(self): raise ValueError(msg) outputs = {} - for key, args in self.inputs.template_args.items(): + for key, args in list(self.inputs.template_args.items()): outputs[key] = [] template = self.inputs.template if hasattr(self.inputs, 'field_template') and \ @@ -842,7 +845,7 @@ def _list_outputs(self): for argnum, arglist in enumerate(args): maxlen = 1 for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): if (maxlen > 1) and (len(arg) != maxlen): @@ -853,7 +856,7 @@ def _list_outputs(self): for i in range(maxlen): argtuple = [] for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): argtuple.append(arg[i]) @@ -916,12 +919,13 @@ class SelectFiles(IOBase): Examples -------- + >>> import pprint >>> from nipype import SelectFiles, Node >>> templates={"T1": "{subject_id}/struct/T1.nii", ... "epi": "{subject_id}/func/f[0, 1].nii"} >>> dg = Node(SelectFiles(templates), "selectfiles") >>> dg.inputs.subject_id = "subj1" - >>> dg.outputs.get() + >>> pprint.pprint(dg.outputs.get()) # doctest: +NORMALIZE_WHITESPACE {'T1': , 'epi': } The same thing with dynamic grabbing of specific files: @@ -956,7 +960,7 @@ def __init__(self, templates, **kwargs): # Infer the infields and outfields from the template infields = [] - for name, template in templates.iteritems(): + for name, template in templates.items(): for _, field_name, _, _ in string.Formatter().parse(template): if field_name is not None and field_name not in infields: infields.append(field_name) @@ -974,12 +978,12 @@ def __init__(self, templates, **kwargs): def _add_output_traits(self, base): """Add the dynamic output fields""" - return add_traits(base, self._templates.keys()) + return add_traits(base, list(self._templates.keys())) def _list_outputs(self): """Find the files and expose them as interface outputs.""" outputs = {} - info = dict([(k, v) for k, v in self.inputs.__dict__.items() + info = dict([(k, v) for k, v in list(self.inputs.__dict__.items()) if k in self._infields]) force_lists = self.inputs.force_lists @@ -994,7 +998,7 @@ def _list_outputs(self): "'templates'.") % (plural, bad_fields, verb) raise ValueError(msg) - for field, template in self._templates.iteritems(): + for field, template in self._templates.items(): # Build the full template path if isdefined(self.inputs.base_directory): @@ -1067,17 +1071,17 @@ class DataFinder(IOBase): >>> df.inputs.root_paths = '.' >>> df.inputs.match_regex = '.+/(?P.+(qT1|ep2d_fid_T1).+)/(?P.+)\.nii.gz' >>> result = df.run() # doctest: +SKIP - >>> print result.outputs.out_paths # doctest: +SKIP + >>> result.outputs.out_paths # doctest: +SKIP ['./027-ep2d_fid_T1_Gd4/acquisition.nii.gz', './018-ep2d_fid_T1_Gd2/acquisition.nii.gz', './016-ep2d_fid_T1_Gd1/acquisition.nii.gz', './013-ep2d_fid_T1_pre/acquisition.nii.gz'] - >>> print result.outputs.series_dir # doctest: +SKIP + >>> result.outputs.series_dir # doctest: +SKIP ['027-ep2d_fid_T1_Gd4', '018-ep2d_fid_T1_Gd2', '016-ep2d_fid_T1_Gd1', '013-ep2d_fid_T1_pre'] - >>> print result.outputs.basename # doctest: +SKIP + >>> result.outputs.basename # doctest: +SKIP ['acquisition', 'acquisition' 'acquisition', @@ -1100,15 +1104,15 @@ def _match_path(self, target_path): match_dict = match.groupdict() if self.result is None: self.result = {'out_paths': []} - for key in match_dict.keys(): + for key in list(match_dict.keys()): self.result[key] = [] self.result['out_paths'].append(target_path) - for key, val in match_dict.iteritems(): + for key, val in match_dict.items(): self.result[key].append(val) def _run_interface(self, runtime): #Prepare some of the inputs - if isinstance(self.inputs.root_paths, six.string_types): + if isinstance(self.inputs.root_paths, string_types): self.inputs.root_paths = [self.inputs.root_paths] self.match_regex = re.compile(self.inputs.match_regex) if self.inputs.max_depth is Undefined: @@ -1154,15 +1158,15 @@ def _run_interface(self, runtime): if (self.inputs.unpack_single and len(self.result['out_paths']) == 1 ): - for key, vals in self.result.iteritems(): + for key, vals in self.result.items(): self.result[key] = vals[0] else: #sort all keys acording to out_paths - for key in self.result.keys(): + for key in list(self.result.keys()): if key == "out_paths": continue - sort_tuples = human_order_sorted(zip(self.result["out_paths"], - self.result[key])) + sort_tuples = human_order_sorted(list(zip(self.result["out_paths"], + self.result[key]))) self.result[key] = [x for (_, x) in sort_tuples] self.result["out_paths"] = human_order_sorted(self.result["out_paths"]) @@ -1312,7 +1316,7 @@ def _list_outputs(self): subject_path = os.path.join(subjects_dir, self.inputs.subject_id) output_traits = self._outputs() outputs = output_traits.get() - for k in outputs.keys(): + for k in list(outputs.keys()): val = self._get_files(subject_path, k, output_traits.traits()[k].loc, output_traits.traits()[k].altkey) @@ -1428,7 +1432,7 @@ def _add_output_traits(self, base): Using traits.Any instead out OutputMultiPath till add_trait bug is fixed. """ - return add_traits(base, self.inputs.query_template_args.keys()) + return add_traits(base, list(self.inputs.query_template_args.keys())) def _list_outputs(self): # infields are mandatory, however I could not figure out @@ -1456,7 +1460,7 @@ def _list_outputs(self): raise ValueError(msg) outputs = {} - for key, args in self.inputs.query_template_args.items(): + for key, args in list(self.inputs.query_template_args.items()): outputs[key] = [] template = self.inputs.query_template if hasattr(self.inputs, 'field_template') and \ @@ -1477,7 +1481,7 @@ def _list_outputs(self): for argnum, arglist in enumerate(args): maxlen = 1 for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): if (maxlen > 1) and (len(arg) != maxlen): @@ -1490,7 +1494,7 @@ def _list_outputs(self): for i in range(maxlen): argtuple = [] for arg in arglist: - if isinstance(arg, six.string_types) and \ + if isinstance(arg, string_types) and \ hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): @@ -1654,7 +1658,7 @@ def _list_outputs(self): uri_template_args['reconstruction_id'] = quote_id(self.inputs.reconstruction_id) # gather outputs and upload them - for key, files in self.inputs._outputs.items(): + for key, files in list(self.inputs._outputs.items()): for name in filename_to_list(files): @@ -1685,7 +1689,7 @@ def push_file(self, xnat, file_name, out_key, uri_template_args): if part.startswith('_') and len(part.split('_')) % 2 ] - keymap = dict(zip(val_list[1::2], val_list[2::2])) + keymap = dict(list(zip(val_list[1::2], val_list[2::2]))) _label = [] for key, val in sorted(keymap.items()): @@ -1732,7 +1736,7 @@ def push_file(self, xnat, file_name, out_key, uri_template_args): ) # unquote values before uploading - for key in uri_template_args.keys(): + for key in list(uri_template_args.keys()): uri_template_args[key] = unquote_id(uri_template_args[key]) # upload file @@ -1965,7 +1969,7 @@ def __init__(self, infields=None, outfields=None, **kwargs): paramiko except NameError: warn( - "The library parmiko needs to be installed" + "The library paramiko needs to be installed" " for this module to run." ) if not outfields: @@ -1994,7 +1998,7 @@ def _list_outputs(self): paramiko except NameError: raise ImportError( - "The library parmiko needs to be installed" + "The library paramiko needs to be installed" " for this module to run." ) @@ -2011,7 +2015,7 @@ def _list_outputs(self): raise ValueError(msg) outputs = {} - for key, args in self.inputs.template_args.items(): + for key, args in list(self.inputs.template_args.items()): outputs[key] = [] template = self.inputs.template if hasattr(self.inputs, 'field_template') and \ @@ -2027,7 +2031,7 @@ def _list_outputs(self): filelist = fnmatch.filter(filelist, template) elif self.inputs.template_expression == 'regexp': regexp = re.compile(template) - filelist = filter(regexp.match, filelist) + filelist = list(filter(regexp.match, filelist)) else: raise ValueError('template_expression value invalid') if len(filelist) == 0: @@ -2047,7 +2051,7 @@ def _list_outputs(self): for argnum, arglist in enumerate(args): maxlen = 1 for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): if (maxlen > 1) and (len(arg) != maxlen): @@ -2058,7 +2062,7 @@ def _list_outputs(self): for i in range(maxlen): argtuple = [] for arg in arglist: - if isinstance(arg, six.string_types) and hasattr(self.inputs, arg): + if isinstance(arg, string_types) and hasattr(self.inputs, arg): arg = getattr(self.inputs, arg) if isinstance(arg, list): argtuple.append(arg[i]) @@ -2080,7 +2084,7 @@ def _list_outputs(self): outfiles = fnmatch.filter(filelist, filledtemplate_base) elif self.inputs.template_expression == 'regexp': regexp = re.compile(filledtemplate_base) - outfiles = filter(regexp.match, filelist) + outfiles = list(filter(regexp.match, filelist)) else: raise ValueError('template_expression value invalid') if len(outfiles) == 0: @@ -2107,7 +2111,7 @@ def _list_outputs(self): elif len(outputs[key]) == 1: outputs[key] = outputs[key][0] - for k, v in outputs.items(): + for k, v in list(outputs.items()): outputs[k] = os.path.join(os.getcwd(), v) return outputs @@ -2146,16 +2150,17 @@ class JSONFileGrabber(IOBase): Example ------- + >>> import pprint >>> from nipype.interfaces.io import JSONFileGrabber >>> jsonSource = JSONFileGrabber() - >>> jsonSource.inputs.defaults = {'param1': u'overrideMe', 'param3': 1.0} + >>> jsonSource.inputs.defaults = {'param1': 'overrideMe', 'param3': 1.0} >>> res = jsonSource.run() - >>> res.outputs.get() - {'param3': 1.0, 'param1': u'overrideMe'} + >>> pprint.pprint(res.outputs.get()) + {'param1': 'overrideMe', 'param3': 1.0} >>> jsonSource.inputs.in_file = 'jsongrabber.txt' >>> res = jsonSource.run() - >>> res.outputs.get() - {'param3': 1.0, 'param2': 4, 'param1': u'exampleStr'} + >>> pprint.pprint(res.outputs.get()) # doctest: +NORMALIZE_WHITESPACE + {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0} """ @@ -2164,23 +2169,23 @@ class JSONFileGrabber(IOBase): _always_run = True def _list_outputs(self): - import json + import simplejson outputs = {} if isdefined(self.inputs.in_file): with open(self.inputs.in_file, 'r') as f: - data = json.load(f) + data = simplejson.load(f) if not isinstance(data, dict): raise RuntimeError('JSON input has no dictionary structure') - for key, value in data.iteritems(): + for key, value in data.items(): outputs[key] = value if isdefined(self.inputs.defaults): defaults = self.inputs.defaults - for key, value in defaults.iteritems(): - if key not in outputs.keys(): + for key, value in defaults.items(): + if key not in list(outputs.keys()): outputs[key] = value return outputs @@ -2266,7 +2271,7 @@ def _process_name(self, name, val): return name, val def _list_outputs(self): - import json + import simplejson import os.path as op if not isdefined(self.inputs.out_file): @@ -2277,14 +2282,14 @@ def _list_outputs(self): out_dict = self.inputs.in_dict # Overwrite in_dict entries automatically - for key, val in self.inputs._outputs.items(): + for key, val in list(self.inputs._outputs.items()): if not isdefined(val) or key == 'trait_added': continue key, val = self._process_name(key, val) out_dict[key] = val with open(out_file, 'w') as f: - json.dump(out_dict, f) + simplejson.dump(out_dict, f) outputs = self.output_spec().get() outputs['out_file'] = out_file return outputs diff --git a/nipype/interfaces/matlab.py b/nipype/interfaces/matlab.py index feb629ae43..8690507ded 100644 --- a/nipype/interfaces/matlab.py +++ b/nipype/interfaces/matlab.py @@ -3,10 +3,11 @@ """ General matlab interface code """ import os -from nipype.interfaces.base import (CommandLineInputSpec, InputMultiPath, isdefined, - CommandLine, traits, File, Directory) +from .base import (CommandLineInputSpec, InputMultiPath, isdefined, + CommandLine, traits, File, Directory) from .. import config + def get_matlab_command(): if 'NIPYPE_NO_MATLAB' in os.environ: return None @@ -20,7 +21,7 @@ def get_matlab_command(): res = CommandLine(command='which', args=matlab_cmd, terminal_output='allatonce').run() matlab_path = res.runtime.stdout.strip() - except Exception, e: + except Exception as e: return None return matlab_cmd @@ -65,9 +66,9 @@ class MatlabCommand(CommandLine): """Interface that runs matlab code >>> import nipype.interfaces.matlab as matlab - >>> mlab = matlab.MatlabCommand() + >>> mlab = matlab.MatlabCommand(mfile=False) # don't write script file >>> mlab.inputs.script = "which('who')" - >>> out = mlab.run() # doctest: +SKIP + >>> out = mlab.run() # doctest: +SKIP """ _cmd = 'matlab' @@ -155,6 +156,7 @@ def _format_arg(self, name, trait_spec, value): return super(MatlabCommand, self)._format_arg(name, trait_spec, value) def _gen_matlab_command(self, argstr, script_lines): + """ Generates commands and, if mfile specified, writes it to disk.""" cwd = os.getcwd() mfile = self.inputs.mfile or self.inputs.uses_mcr paths = [] @@ -178,9 +180,8 @@ def _gen_matlab_command(self, argstr, script_lines): script_lines = '\n'.join(prescript)+script_lines+'\n'.join(postscript) if mfile: - mfile = file(os.path.join(cwd,self.inputs.script_file), 'wt') - mfile.write(script_lines) - mfile.close() + with open(os.path.join(cwd,self.inputs.script_file), 'wt') as mfile: + mfile.write(script_lines) if self.inputs.uses_mcr: script = '%s' % (os.path.join(cwd,self.inputs.script_file)) else: diff --git a/nipype/interfaces/meshfix.py b/nipype/interfaces/meshfix.py index 887fd439c3..b7224740f5 100644 --- a/nipype/interfaces/meshfix.py +++ b/nipype/interfaces/meshfix.py @@ -9,6 +9,7 @@ >>> os.chdir(datadir) """ + from .base import (CommandLine, CommandLineInputSpec, traits, TraitedSpec, isdefined, File) diff --git a/nipype/interfaces/mipav/__init__.py b/nipype/interfaces/mipav/__init__.py index e8b8577830..f7af18ca3c 100644 --- a/nipype/interfaces/mipav/__init__.py +++ b/nipype/interfaces/mipav/__init__.py @@ -1 +1,2 @@ -from developer import JistLaminarVolumetricLayering, JistBrainMgdmSegmentation, JistLaminarProfileGeometry, JistLaminarProfileCalculator, MedicAlgorithmN3, JistLaminarROIAveraging, MedicAlgorithmLesionToads, JistBrainMp2rageSkullStripping, JistCortexSurfaceMeshInflation, RandomVol, MedicAlgorithmImageCalculator, JistBrainMp2rageDuraEstimation, JistLaminarProfileSampling, MedicAlgorithmMipavReorient, MedicAlgorithmSPECTRE2010, JistBrainPartialVolumeFilter, JistIntensityMp2rageMasking, MedicAlgorithmThresholdToBinaryMask +from __future__ import absolute_import +from .developer import JistLaminarVolumetricLayering, JistBrainMgdmSegmentation, JistLaminarProfileGeometry, JistLaminarProfileCalculator, MedicAlgorithmN3, JistLaminarROIAveraging, MedicAlgorithmLesionToads, JistBrainMp2rageSkullStripping, JistCortexSurfaceMeshInflation, RandomVol, MedicAlgorithmImageCalculator, JistBrainMp2rageDuraEstimation, JistLaminarProfileSampling, MedicAlgorithmMipavReorient, MedicAlgorithmSPECTRE2010, JistBrainPartialVolumeFilter, JistIntensityMp2rageMasking, MedicAlgorithmThresholdToBinaryMask diff --git a/nipype/interfaces/mipav/developer.py b/nipype/interfaces/mipav/developer.py index 05d691d7d0..da6aaa6c31 100644 --- a/nipype/interfaces/mipav/developer.py +++ b/nipype/interfaces/mipav/developer.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ..base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class JistLaminarVolumetricLayeringInputSpec(CommandLineInputSpec): inInner = File(desc="Inner Distance Image (GM/WM boundary)", exists=True, argstr="--inInner %s") diff --git a/nipype/interfaces/mipav/generate_classes.py b/nipype/interfaces/mipav/generate_classes.py index 898401db04..9b6c2d719f 100644 --- a/nipype/interfaces/mipav/generate_classes.py +++ b/nipype/interfaces/mipav/generate_classes.py @@ -1,7 +1,7 @@ -from nipype.interfaces.slicer.generate_classes import generate_all_classes - if __name__ == "__main__": + from nipype.interfaces.slicer.generate_classes import generate_all_classes + ## NOTE: For now either the launcher needs to be found on the default path, or ## every tool in the modules list must be found on the default path ## AND calling the module with --xml must be supported and compliant. diff --git a/nipype/interfaces/mipav/tests/__init__.py b/nipype/interfaces/mipav/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index bd31bc125a..c4a08fa091 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistBrainMgdmSegmentation +from ....testing import assert_equal +from ..developer import JistBrainMgdmSegmentation def test_JistBrainMgdmSegmentation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -69,8 +69,8 @@ def test_JistBrainMgdmSegmentation_inputs(): ) inputs = JistBrainMgdmSegmentation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistBrainMgdmSegmentation_outputs(): @@ -81,7 +81,7 @@ def test_JistBrainMgdmSegmentation_outputs(): ) outputs = JistBrainMgdmSegmentation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index 7b149c1cee..13a3154a57 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistBrainMp2rageDuraEstimation +from ....testing import assert_equal +from ..developer import JistBrainMp2rageDuraEstimation def test_JistBrainMp2rageDuraEstimation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): ) inputs = JistBrainMp2rageDuraEstimation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistBrainMp2rageDuraEstimation_outputs(): @@ -45,7 +45,7 @@ def test_JistBrainMp2rageDuraEstimation_outputs(): ) outputs = JistBrainMp2rageDuraEstimation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index f4926e910d..9535b7d171 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistBrainMp2rageSkullStripping +from ....testing import assert_equal +from ..developer import JistBrainMp2rageSkullStripping def test_JistBrainMp2rageSkullStripping_inputs(): input_map = dict(args=dict(argstr='%s', @@ -47,8 +47,8 @@ def test_JistBrainMp2rageSkullStripping_inputs(): ) inputs = JistBrainMp2rageSkullStripping.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistBrainMp2rageSkullStripping_outputs(): @@ -59,7 +59,7 @@ def test_JistBrainMp2rageSkullStripping_outputs(): ) outputs = JistBrainMp2rageSkullStripping.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 120373b261..487bb25bfb 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistBrainPartialVolumeFilter +from ....testing import assert_equal +from ..developer import JistBrainPartialVolumeFilter def test_JistBrainPartialVolumeFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_JistBrainPartialVolumeFilter_inputs(): ) inputs = JistBrainPartialVolumeFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistBrainPartialVolumeFilter_outputs(): @@ -43,7 +43,7 @@ def test_JistBrainPartialVolumeFilter_outputs(): ) outputs = JistBrainPartialVolumeFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index d87de79b2f..caec86fbf4 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistCortexSurfaceMeshInflation +from ....testing import assert_equal +from ..developer import JistCortexSurfaceMeshInflation def test_JistCortexSurfaceMeshInflation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_JistCortexSurfaceMeshInflation_inputs(): ) inputs = JistCortexSurfaceMeshInflation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistCortexSurfaceMeshInflation_outputs(): @@ -55,7 +55,7 @@ def test_JistCortexSurfaceMeshInflation_outputs(): ) outputs = JistCortexSurfaceMeshInflation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index 4001c00998..9ad0e07868 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistIntensityMp2rageMasking +from ....testing import assert_equal +from ..developer import JistIntensityMp2rageMasking def test_JistIntensityMp2rageMasking_inputs(): input_map = dict(args=dict(argstr='%s', @@ -49,8 +49,8 @@ def test_JistIntensityMp2rageMasking_inputs(): ) inputs = JistIntensityMp2rageMasking.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistIntensityMp2rageMasking_outputs(): @@ -61,7 +61,7 @@ def test_JistIntensityMp2rageMasking_outputs(): ) outputs = JistIntensityMp2rageMasking.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index ad15fe15d8..360bc1cb9a 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistLaminarProfileCalculator +from ....testing import assert_equal +from ..developer import JistLaminarProfileCalculator def test_JistLaminarProfileCalculator_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_JistLaminarProfileCalculator_inputs(): ) inputs = JistLaminarProfileCalculator.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistLaminarProfileCalculator_outputs(): @@ -43,7 +43,7 @@ def test_JistLaminarProfileCalculator_outputs(): ) outputs = JistLaminarProfileCalculator.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index c8f3d67020..91612a6106 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistLaminarProfileGeometry +from ....testing import assert_equal +from ..developer import JistLaminarProfileGeometry def test_JistLaminarProfileGeometry_inputs(): input_map = dict(args=dict(argstr='%s', @@ -38,8 +38,8 @@ def test_JistLaminarProfileGeometry_inputs(): ) inputs = JistLaminarProfileGeometry.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistLaminarProfileGeometry_outputs(): @@ -47,7 +47,7 @@ def test_JistLaminarProfileGeometry_outputs(): ) outputs = JistLaminarProfileGeometry.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index 22ba4fe7d0..b33903f1e8 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistLaminarProfileSampling +from ....testing import assert_equal +from ..developer import JistLaminarProfileSampling def test_JistLaminarProfileSampling_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_JistLaminarProfileSampling_inputs(): ) inputs = JistLaminarProfileSampling.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistLaminarProfileSampling_outputs(): @@ -47,7 +47,7 @@ def test_JistLaminarProfileSampling_outputs(): ) outputs = JistLaminarProfileSampling.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index 19ec0f46fa..a2f684e95d 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistLaminarROIAveraging +from ....testing import assert_equal +from ..developer import JistLaminarROIAveraging def test_JistLaminarROIAveraging_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_JistLaminarROIAveraging_inputs(): ) inputs = JistLaminarROIAveraging.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistLaminarROIAveraging_outputs(): @@ -45,7 +45,7 @@ def test_JistLaminarROIAveraging_outputs(): ) outputs = JistLaminarROIAveraging.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index f7792e1626..4ad3f30476 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import JistLaminarVolumetricLayering +from ....testing import assert_equal +from ..developer import JistLaminarVolumetricLayering def test_JistLaminarVolumetricLayering_inputs(): input_map = dict(args=dict(argstr='%s', @@ -56,8 +56,8 @@ def test_JistLaminarVolumetricLayering_inputs(): ) inputs = JistLaminarVolumetricLayering.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JistLaminarVolumetricLayering_outputs(): @@ -67,7 +67,7 @@ def test_JistLaminarVolumetricLayering_outputs(): ) outputs = JistLaminarVolumetricLayering.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index ea49dddccf..6252555653 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import MedicAlgorithmImageCalculator +from ....testing import assert_equal +from ..developer import MedicAlgorithmImageCalculator def test_MedicAlgorithmImageCalculator_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_MedicAlgorithmImageCalculator_inputs(): ) inputs = MedicAlgorithmImageCalculator.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedicAlgorithmImageCalculator_outputs(): @@ -43,7 +43,7 @@ def test_MedicAlgorithmImageCalculator_outputs(): ) outputs = MedicAlgorithmImageCalculator.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 87d149e837..7b03410be4 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import MedicAlgorithmLesionToads +from ....testing import assert_equal +from ..developer import MedicAlgorithmLesionToads def test_MedicAlgorithmLesionToads_inputs(): input_map = dict(args=dict(argstr='%s', @@ -94,8 +94,8 @@ def test_MedicAlgorithmLesionToads_inputs(): ) inputs = MedicAlgorithmLesionToads.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedicAlgorithmLesionToads_outputs(): @@ -111,7 +111,7 @@ def test_MedicAlgorithmLesionToads_outputs(): ) outputs = MedicAlgorithmLesionToads.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index 06a9f0e867..b288aabc2f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import MedicAlgorithmMipavReorient +from ....testing import assert_equal +from ..developer import MedicAlgorithmMipavReorient def test_MedicAlgorithmMipavReorient_inputs(): input_map = dict(args=dict(argstr='%s', @@ -47,15 +47,15 @@ def test_MedicAlgorithmMipavReorient_inputs(): ) inputs = MedicAlgorithmMipavReorient.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedicAlgorithmMipavReorient_outputs(): output_map = dict() outputs = MedicAlgorithmMipavReorient.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index 294264bee7..344e6924bb 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import MedicAlgorithmN3 +from ....testing import assert_equal +from ..developer import MedicAlgorithmN3 def test_MedicAlgorithmN3_inputs(): input_map = dict(args=dict(argstr='%s', @@ -49,8 +49,8 @@ def test_MedicAlgorithmN3_inputs(): ) inputs = MedicAlgorithmN3.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedicAlgorithmN3_outputs(): @@ -59,7 +59,7 @@ def test_MedicAlgorithmN3_outputs(): ) outputs = MedicAlgorithmN3.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index 25d7ee4282..f3edf74136 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import MedicAlgorithmSPECTRE2010 +from ....testing import assert_equal +from ..developer import MedicAlgorithmSPECTRE2010 def test_MedicAlgorithmSPECTRE2010_inputs(): input_map = dict(args=dict(argstr='%s', @@ -120,8 +120,8 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): ) inputs = MedicAlgorithmSPECTRE2010.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedicAlgorithmSPECTRE2010_outputs(): @@ -137,7 +137,7 @@ def test_MedicAlgorithmSPECTRE2010_outputs(): ) outputs = MedicAlgorithmSPECTRE2010.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py index d883bdfda1..95db54b4c6 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import MedicAlgorithmThresholdToBinaryMask +from ....testing import assert_equal +from ..developer import MedicAlgorithmThresholdToBinaryMask def test_MedicAlgorithmThresholdToBinaryMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,15 +37,15 @@ def test_MedicAlgorithmThresholdToBinaryMask_inputs(): ) inputs = MedicAlgorithmThresholdToBinaryMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedicAlgorithmThresholdToBinaryMask_outputs(): output_map = dict() outputs = MedicAlgorithmThresholdToBinaryMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index c0a9c902d7..0fd32c6296 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mipav.developer import RandomVol +from ....testing import assert_equal +from ..developer import RandomVol def test_RandomVol_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_RandomVol_inputs(): ) inputs = RandomVol.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_RandomVol_outputs(): @@ -55,7 +55,7 @@ def test_RandomVol_outputs(): ) outputs = RandomVol.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mne/__init__.py b/nipype/interfaces/mne/__init__.py index 063ab95b3e..16d95f8454 100644 --- a/nipype/interfaces/mne/__init__.py +++ b/nipype/interfaces/mne/__init__.py @@ -1 +1 @@ -from nipype.interfaces.mne.base import WatershedBEM +from .base import WatershedBEM diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index 609dcd2246..59938d1af9 100644 --- a/nipype/interfaces/mne/base.py +++ b/nipype/interfaces/mne/base.py @@ -1,15 +1,15 @@ -from nipype.interfaces.base import (traits, File, Directory, TraitedSpec, - OutputMultiPath) + import os.path as op import glob -from nipype.interfaces.freesurfer.base import FSCommand, FSTraitedSpec -from nipype.utils.filemanip import list_to_filename -from nipype.external import six import logging - logging.basicConfig() iflogger = logging.getLogger('interface') +from ..base import (traits, File, Directory, TraitedSpec, OutputMultiPath) +from ..freesurfer.base import FSCommand, FSTraitedSpec +from ...external.six import string_types +from ...utils.filemanip import list_to_filename + class WatershedBEMInputSpec(FSTraitedSpec): subject_id = traits.Str(argstr='--subject %s', mandatory=True, @@ -79,7 +79,7 @@ def _list_outputs(self): subject_path = op.join(subjects_dir, self.inputs.subject_id) output_traits = self._outputs() mesh_paths = [] - for k in outputs.keys(): + for k in list(outputs.keys()): if k != 'mesh_files': val = self._get_files(subject_path, k, output_traits.traits()[k].loc, @@ -90,7 +90,7 @@ def _list_outputs(self): out_files = [] for value in value_list: out_files.append(op.abspath(value)) - elif isinstance(value_list, six.string_types): + elif isinstance(value_list, string_types): out_files = op.abspath(value_list) else: raise TypeError diff --git a/nipype/interfaces/mne/tests/__init__.py b/nipype/interfaces/mne/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 267ebb025f..745cc8b99a 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mne.base import WatershedBEM +from ....testing import assert_equal +from ..base import WatershedBEM def test_WatershedBEM_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_WatershedBEM_inputs(): ) inputs = WatershedBEM.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_WatershedBEM_outputs(): @@ -53,7 +53,7 @@ def test_WatershedBEM_outputs(): ) outputs = WatershedBEM.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py index cb22ce194f..b6e7d7df69 100644 --- a/nipype/interfaces/mrtrix/convert.py +++ b/nipype/interfaces/mrtrix/convert.py @@ -9,6 +9,8 @@ """ +from __future__ import division + # -*- coding: utf-8 -*- import os.path as op import nibabel as nb, nibabel.trackvis as trk @@ -26,7 +28,7 @@ have_dipy = True try: package_check('dipy') -except Exception, e: +except Exception as e: False else: from dipy.tracking.utils import move_streamlines, affine_from_fsl_mat_file @@ -37,17 +39,17 @@ iflogger = logging.getLogger('interface') def transform_to_affine(streams, header, affine): - rotation, scale = np.linalg.qr(affine) - streams = move_streamlines(streams, rotation) - scale[0:3,0:3] = np.dot(scale[0:3,0:3], np.diag(1./header['voxel_size'])) - scale[0:3,3] = abs(scale[0:3,3]) - streams = move_streamlines(streams, scale) - return streams + rotation, scale = np.linalg.qr(affine) + streams = move_streamlines(streams, rotation) + scale[0:3,0:3] = np.dot(scale[0:3,0:3], np.diag(1. / header['voxel_size'])) + scale[0:3,3] = abs(scale[0:3,3]) + streams = move_streamlines(streams, scale) + return streams def read_mrtrix_tracks(in_file, as_generator=True): - header = read_mrtrix_header(in_file) - streamlines = read_mrtrix_streamlines(in_file, header, as_generator) - return header, streamlines + header = read_mrtrix_header(in_file) + streamlines = read_mrtrix_streamlines(in_file, header, as_generator) + return header, streamlines def read_mrtrix_header(in_file): fileobj = open(in_file,'r') @@ -84,7 +86,7 @@ def points_per_track(offset): track_points = [] iflogger.info('Identifying the number of points per tract...') all_str = fileobj.read() - num_triplets = len(all_str)/bytesize + num_triplets = int(len(all_str) / bytesize) pts = np.ndarray(shape=(num_triplets,pt_cols), dtype='f4',buffer=all_str) nonfinite_list = np.where(np.isfinite(pts[:,2]) == False) nonfinite_list = list(nonfinite_list[0])[0:-1] # Converts numpy array to list, removes the last value @@ -131,7 +133,7 @@ def track_gen(track_points): if n_streams == stream_count: iflogger.info('100% : {n} tracks read'.format(n=n_streams)) raise StopIteration - if n_streams % (float(stream_count)/100) == 0: + if n_streams % int(stream_count / 100) == 0: percent = int(float(n_streams)/float(stream_count)*100) iflogger.info('{p}% : {n} tracks read'.format(p=percent, n=n_streams)) track_points, nonfinite_list = points_per_track(offset) @@ -200,7 +202,7 @@ def _run_interface(self, runtime): trk_header['dim'] = [r_dx,r_dy,r_dz] trk_header['voxel_size'] = [r_vx,r_vy,r_vz] - affine = np.dot(affine,np.diag(1./np.array([vx, vy, vz, 1]))) + affine = np.dot(affine,np.diag(1. / np.array([vx, vy, vz, 1]))) transformed_streamlines = transform_to_affine(streamlines, trk_header, affine) aff = affine_from_fsl_mat_file(xfm, [vx,vy,vz], [r_vx,r_vy,r_vz]) @@ -233,11 +235,11 @@ def _list_outputs(self): outputs['out_file'] = op.abspath(self.inputs.out_filename) return outputs - def _gen_filename(self, name): - if name is 'out_filename': - return self._gen_outfilename() - else: - return None - def _gen_outfilename(self): - _, name , _ = split_filename(self.inputs.in_file) - return name + '.trk' + def _gen_filename(self, name): + if name is 'out_filename': + return self._gen_outfilename() + else: + return None + def _gen_outfilename(self): + _, name , _ = split_filename(self.inputs.in_file) + return name + '.trk' diff --git a/nipype/interfaces/mrtrix/preprocess.py b/nipype/interfaces/mrtrix/preprocess.py index f7ca17c13f..68f16c237f 100644 --- a/nipype/interfaces/mrtrix/preprocess.py +++ b/nipype/interfaces/mrtrix/preprocess.py @@ -8,11 +8,13 @@ >>> os.chdir(datadir) """ - -from nipype.interfaces.base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File, InputMultiPath, isdefined -from nipype.utils.filemanip import split_filename import os.path as op +from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, + File, InputMultiPath, isdefined) +from ...utils.filemanip import split_filename + + class MRConvertInputSpec(CommandLineInputSpec): in_file = File(exists=True, argstr='%s', mandatory=True, position=-2, desc='voxel-order data filename') diff --git a/nipype/interfaces/mrtrix/tensors.py b/nipype/interfaces/mrtrix/tensors.py index f301da13fb..9307cde264 100644 --- a/nipype/interfaces/mrtrix/tensors.py +++ b/nipype/interfaces/mrtrix/tensors.py @@ -8,16 +8,18 @@ >>> os.chdir(datadir) """ - -from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, BaseInterface, BaseInterfaceInputSpec, - traits, File, TraitedSpec, Directory, InputMultiPath, OutputMultiPath, isdefined) -from nipype.utils.filemanip import split_filename import os.path as op + import numpy as np +from ..base import (CommandLineInputSpec, CommandLine, BaseInterface, + BaseInterfaceInputSpec, traits, File, TraitedSpec, + Directory, InputMultiPath, OutputMultiPath, isdefined) +from ...utils.filemanip import split_filename from ... import logging iflogger = logging.getLogger('interface') + class DWI2SphericalHarmonicsImageInputSpec(CommandLineInputSpec): in_file = File(exists=True, argstr='%s', mandatory=True, position=-2, desc='Diffusion-weighted images') out_filename = File(genfile=True, argstr='%s', position=-1, desc='Output filename') diff --git a/nipype/interfaces/mrtrix/tests/__init__.py b/nipype/interfaces/mrtrix/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 5f24d6906e..2261a9c887 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import ConstrainedSphericalDeconvolution +from ....testing import assert_equal +from ..tensors import ConstrainedSphericalDeconvolution def test_ConstrainedSphericalDeconvolution_inputs(): input_map = dict(args=dict(argstr='%s', @@ -53,8 +53,8 @@ def test_ConstrainedSphericalDeconvolution_inputs(): ) inputs = ConstrainedSphericalDeconvolution.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ConstrainedSphericalDeconvolution_outputs(): @@ -62,7 +62,7 @@ def test_ConstrainedSphericalDeconvolution_outputs(): ) outputs = ConstrainedSphericalDeconvolution.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 5d3d3b7b79..86d9d6259d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import DWI2SphericalHarmonicsImage +from ....testing import assert_equal +from ..tensors import DWI2SphericalHarmonicsImage def test_DWI2SphericalHarmonicsImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_DWI2SphericalHarmonicsImage_inputs(): ) inputs = DWI2SphericalHarmonicsImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWI2SphericalHarmonicsImage_outputs(): @@ -42,7 +42,7 @@ def test_DWI2SphericalHarmonicsImage_outputs(): ) outputs = DWI2SphericalHarmonicsImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 2052a2ea1f..a8e0e1f3d8 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import DWI2Tensor +from ....testing import assert_equal +from ..preprocess import DWI2Tensor def test_DWI2Tensor_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_DWI2Tensor_inputs(): ) inputs = DWI2Tensor.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWI2Tensor_outputs(): @@ -52,7 +52,7 @@ def test_DWI2Tensor_outputs(): ) outputs = DWI2Tensor.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 839bc9c42b..3cb6d42bc1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tracking import DiffusionTensorStreamlineTrack +from ....testing import assert_equal +from ..tracking import DiffusionTensorStreamlineTrack def test_DiffusionTensorStreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', @@ -103,8 +103,8 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ) inputs = DiffusionTensorStreamlineTrack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DiffusionTensorStreamlineTrack_outputs(): @@ -112,7 +112,7 @@ def test_DiffusionTensorStreamlineTrack_outputs(): ) outputs = DiffusionTensorStreamlineTrack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index 715a6721dc..5fedacb20b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import Directions2Amplitude +from ....testing import assert_equal +from ..tensors import Directions2Amplitude def test_Directions2Amplitude_inputs(): input_map = dict(args=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_Directions2Amplitude_inputs(): ) inputs = Directions2Amplitude.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Directions2Amplitude_outputs(): @@ -49,7 +49,7 @@ def test_Directions2Amplitude_outputs(): ) outputs = Directions2Amplitude.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 67460ba69e..3a159ae5e6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import Erode +from ....testing import assert_equal +from ..preprocess import Erode def test_Erode_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_Erode_inputs(): ) inputs = Erode.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Erode_outputs(): @@ -44,7 +44,7 @@ def test_Erode_outputs(): ) outputs = Erode.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index 4ac1c46fd4..5b595183bc 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import EstimateResponseForSH +from ....testing import assert_equal +from ..tensors import EstimateResponseForSH def test_EstimateResponseForSH_inputs(): input_map = dict(args=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_EstimateResponseForSH_inputs(): ) inputs = EstimateResponseForSH.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EstimateResponseForSH_outputs(): @@ -49,7 +49,7 @@ def test_EstimateResponseForSH_outputs(): ) outputs = EstimateResponseForSH.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index 6f8e7f8976..46a63b32c8 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import FSL2MRTrix +from ....testing import assert_equal +from ..tensors import FSL2MRTrix def test_FSL2MRTrix_inputs(): input_map = dict(bval_file=dict(mandatory=True, @@ -18,8 +18,8 @@ def test_FSL2MRTrix_inputs(): ) inputs = FSL2MRTrix.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FSL2MRTrix_outputs(): @@ -27,7 +27,7 @@ def test_FSL2MRTrix_outputs(): ) outputs = FSL2MRTrix.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index e8e78ebc9c..1947787160 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tracking import FilterTracks +from ....testing import assert_equal +from ..tracking import FilterTracks def test_FilterTracks_inputs(): input_map = dict(args=dict(argstr='%s', @@ -57,8 +57,8 @@ def test_FilterTracks_inputs(): ) inputs = FilterTracks.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FilterTracks_outputs(): @@ -66,7 +66,7 @@ def test_FilterTracks_outputs(): ) outputs = FilterTracks.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 52291693a0..37a82e7433 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import FindShPeaks +from ....testing import assert_equal +from ..tensors import FindShPeaks def test_FindShPeaks_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_FindShPeaks_inputs(): ) inputs = FindShPeaks.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FindShPeaks_outputs(): @@ -55,7 +55,7 @@ def test_FindShPeaks_outputs(): ) outputs = FindShPeaks.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index ddd3831f2e..ccd0fdf3f3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tensors import GenerateDirections +from ....testing import assert_equal +from ..tensors import GenerateDirections def test_GenerateDirections_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_GenerateDirections_inputs(): ) inputs = GenerateDirections.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateDirections_outputs(): @@ -45,7 +45,7 @@ def test_GenerateDirections_outputs(): ) outputs = GenerateDirections.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 7b6c593f50..b4c2b7fdda 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import GenerateWhiteMatterMask +from ....testing import assert_equal +from ..preprocess import GenerateWhiteMatterMask def test_GenerateWhiteMatterMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_GenerateWhiteMatterMask_inputs(): ) inputs = GenerateWhiteMatterMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateWhiteMatterMask_outputs(): @@ -43,7 +43,7 @@ def test_GenerateWhiteMatterMask_outputs(): ) outputs = GenerateWhiteMatterMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index aa87e2637c..87304f7e64 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import MRConvert +from ....testing import assert_equal +from ..preprocess import MRConvert def test_MRConvert_inputs(): input_map = dict(args=dict(argstr='%s', @@ -58,8 +58,8 @@ def test_MRConvert_inputs(): ) inputs = MRConvert.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRConvert_outputs(): @@ -67,7 +67,7 @@ def test_MRConvert_outputs(): ) outputs = MRConvert.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index f9fbfd6eee..edd6fd187e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import MRMultiply +from ....testing import assert_equal +from ..preprocess import MRMultiply def test_MRMultiply_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_MRMultiply_inputs(): ) inputs = MRMultiply.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRMultiply_outputs(): @@ -39,7 +39,7 @@ def test_MRMultiply_outputs(): ) outputs = MRMultiply.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index 15157a5f26..1786a3c305 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import MRTransform +from ....testing import assert_equal +from ..preprocess import MRTransform def test_MRTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -48,8 +48,8 @@ def test_MRTransform_inputs(): ) inputs = MRTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRTransform_outputs(): @@ -57,7 +57,7 @@ def test_MRTransform_outputs(): ) outputs = MRTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index 701731fa46..57318ad01b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.convert import MRTrix2TrackVis +from ....testing import assert_equal +from ..convert import MRTrix2TrackVis def test_MRTrix2TrackVis_inputs(): input_map = dict(image_file=dict(), @@ -14,8 +14,8 @@ def test_MRTrix2TrackVis_inputs(): ) inputs = MRTrix2TrackVis.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRTrix2TrackVis_outputs(): @@ -23,7 +23,7 @@ def test_MRTrix2TrackVis_outputs(): ) outputs = MRTrix2TrackVis.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index d8bc24f5c8..321c5bac12 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import MRTrixInfo +from ....testing import assert_equal +from ..preprocess import MRTrixInfo def test_MRTrixInfo_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,15 +20,15 @@ def test_MRTrixInfo_inputs(): ) inputs = MRTrixInfo.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRTrixInfo_outputs(): output_map = dict() outputs = MRTrixInfo.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index b7d92de549..783dc90bcb 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import MRTrixViewer +from ....testing import assert_equal +from ..preprocess import MRTrixViewer def test_MRTrixViewer_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,15 +26,15 @@ def test_MRTrixViewer_inputs(): ) inputs = MRTrixViewer.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MRTrixViewer_outputs(): output_map = dict() outputs = MRTrixViewer.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 62baaa17fc..670a88c038 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import MedianFilter3D +from ....testing import assert_equal +from ..preprocess import MedianFilter3D def test_MedianFilter3D_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_MedianFilter3D_inputs(): ) inputs = MedianFilter3D.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedianFilter3D_outputs(): @@ -39,7 +39,7 @@ def test_MedianFilter3D_outputs(): ) outputs = MedianFilter3D.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 5382ade143..9bb78f5ff2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tracking import ProbabilisticSphericallyDeconvolutedStreamlineTrack +from ....testing import assert_equal +from ..tracking import ProbabilisticSphericallyDeconvolutedStreamlineTrack def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', @@ -101,8 +101,8 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ) inputs = ProbabilisticSphericallyDeconvolutedStreamlineTrack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): @@ -110,7 +110,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): ) outputs = ProbabilisticSphericallyDeconvolutedStreamlineTrack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index e8ed23a7d9..74085472c5 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tracking import SphericallyDeconvolutedStreamlineTrack +from ....testing import assert_equal +from ..tracking import SphericallyDeconvolutedStreamlineTrack def test_SphericallyDeconvolutedStreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', @@ -99,8 +99,8 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ) inputs = SphericallyDeconvolutedStreamlineTrack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SphericallyDeconvolutedStreamlineTrack_outputs(): @@ -108,7 +108,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_outputs(): ) outputs = SphericallyDeconvolutedStreamlineTrack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index 0233311ec0..9c4e24c857 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tracking import StreamlineTrack +from ....testing import assert_equal +from ..tracking import StreamlineTrack def test_StreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', @@ -99,8 +99,8 @@ def test_StreamlineTrack_inputs(): ) inputs = StreamlineTrack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_StreamlineTrack_outputs(): @@ -108,7 +108,7 @@ def test_StreamlineTrack_outputs(): ) outputs = StreamlineTrack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 6faa03bc3b..7c23f3234a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import Tensor2ApparentDiffusion +from ....testing import assert_equal +from ..preprocess import Tensor2ApparentDiffusion def test_Tensor2ApparentDiffusion_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_Tensor2ApparentDiffusion_inputs(): ) inputs = Tensor2ApparentDiffusion.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Tensor2ApparentDiffusion_outputs(): @@ -39,7 +39,7 @@ def test_Tensor2ApparentDiffusion_outputs(): ) outputs = Tensor2ApparentDiffusion.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index d58df7954a..64b71e3f3c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import Tensor2FractionalAnisotropy +from ....testing import assert_equal +from ..preprocess import Tensor2FractionalAnisotropy def test_Tensor2FractionalAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_Tensor2FractionalAnisotropy_inputs(): ) inputs = Tensor2FractionalAnisotropy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Tensor2FractionalAnisotropy_outputs(): @@ -39,7 +39,7 @@ def test_Tensor2FractionalAnisotropy_outputs(): ) outputs = Tensor2FractionalAnisotropy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 32ab730d6c..06dec919ca 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import Tensor2Vector +from ....testing import assert_equal +from ..preprocess import Tensor2Vector def test_Tensor2Vector_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_Tensor2Vector_inputs(): ) inputs = Tensor2Vector.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Tensor2Vector_outputs(): @@ -39,7 +39,7 @@ def test_Tensor2Vector_outputs(): ) outputs = Tensor2Vector.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index b4ed8b44b8..daebdfbadf 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.preprocess import Threshold +from ....testing import assert_equal +from ..preprocess import Threshold def test_Threshold_inputs(): input_map = dict(absolute_threshold_value=dict(argstr='-abs %s', @@ -40,8 +40,8 @@ def test_Threshold_inputs(): ) inputs = Threshold.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Threshold_outputs(): @@ -49,7 +49,7 @@ def test_Threshold_outputs(): ) outputs = Threshold.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index c074720eee..2c91ba9052 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix.tracking import Tracks2Prob +from ....testing import assert_equal +from ..tracking import Tracks2Prob def test_Tracks2Prob_inputs(): input_map = dict(args=dict(argstr='%s', @@ -44,8 +44,8 @@ def test_Tracks2Prob_inputs(): ) inputs = Tracks2Prob.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Tracks2Prob_outputs(): @@ -53,7 +53,7 @@ def test_Tracks2Prob_outputs(): ) outputs = Tracks2Prob.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix/tracking.py b/nipype/interfaces/mrtrix/tracking.py index ebb5997e98..c07fd166ca 100644 --- a/nipype/interfaces/mrtrix/tracking.py +++ b/nipype/interfaces/mrtrix/tracking.py @@ -8,11 +8,12 @@ >>> os.chdir(datadir) """ - -from nipype.interfaces.base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File -from nipype.utils.filemanip import split_filename import os, os.path as op -from nipype.interfaces.traits_extension import isdefined + +from ..base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename + class FilterTracksInputSpec(CommandLineInputSpec): in_file = File(exists=True, argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/mrtrix3/__init__.py b/nipype/interfaces/mrtrix3/__init__.py index ec7d02aecb..d5ef942b12 100644 --- a/nipype/interfaces/mrtrix3/__init__.py +++ b/nipype/interfaces/mrtrix3/__init__.py @@ -1,10 +1,11 @@ +from __future__ import absolute_import # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: # -*- coding: utf-8 -*- -from utils import (Mesh2PVE, Generate5tt, BrainMask, TensorMetrics, +from .utils import (Mesh2PVE, Generate5tt, BrainMask, TensorMetrics, ComputeTDI, TCK2VTK) -from preprocess import ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST -from tracking import Tractography -from reconst import FitTensor, EstimateFOD -from connectivity import LabelConfig, BuildConnectome +from .preprocess import ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST +from .tracking import Tractography +from .reconst import FitTensor, EstimateFOD +from .connectivity import LabelConfig, BuildConnectome diff --git a/nipype/interfaces/mrtrix3/base.py b/nipype/interfaces/mrtrix3/base.py index 18432d760a..40a8e93a88 100644 --- a/nipype/interfaces/mrtrix3/base.py +++ b/nipype/interfaces/mrtrix3/base.py @@ -14,13 +14,10 @@ import os import os.path as op -from nipype.interfaces.base import ( - CommandLineInputSpec, CommandLine, traits, TraitedSpec, File, - InputMultiPath) - -from nipype.utils.filemanip import split_filename -from nipype.interfaces.traits_extension import isdefined - +from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, File, + InputMultiPath) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename from ... import logging logger = logging.getLogger('interface') diff --git a/nipype/interfaces/mrtrix3/connectivity.py b/nipype/interfaces/mrtrix3/connectivity.py index af09ae36bc..64e73f8069 100644 --- a/nipype/interfaces/mrtrix3/connectivity.py +++ b/nipype/interfaces/mrtrix3/connectivity.py @@ -14,12 +14,10 @@ import os import os.path as op -from base import MRTrix3BaseInputSpec, MRTrix3Base -from nipype.interfaces.base import ( - CommandLineInputSpec, CommandLine, traits, TraitedSpec, File) - -from nipype.utils.filemanip import split_filename -from nipype.interfaces.traits_extension import isdefined +from .base import MRTrix3BaseInputSpec, MRTrix3Base +from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, File) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename class BuildConnectomeInputSpec(CommandLineInputSpec): diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index aea3ef97f9..e52c84071d 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -14,12 +14,11 @@ import os import os.path as op -from base import MRTrix3BaseInputSpec, MRTrix3Base -from nipype.interfaces.base import ( - CommandLineInputSpec, CommandLine, traits, TraitedSpec, File) - -from nipype.utils.filemanip import split_filename -from nipype.interfaces.traits_extension import isdefined +from .base import MRTrix3BaseInputSpec, MRTrix3Base +from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, + File) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename class ResponseSDInputSpec(MRTrix3BaseInputSpec): diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 2916b4bdac..ce023fbdef 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -11,16 +11,16 @@ >>> os.chdir(datadir) """ + +from __future__ import absolute_import import os import os.path as op -from base import MRTrix3BaseInputSpec, MRTrix3Base -from nipype.interfaces.base import ( - CommandLineInputSpec, CommandLine, traits, TraitedSpec, File, - InputMultiPath) - -from nipype.utils.filemanip import split_filename -from nipype.interfaces.traits_extension import isdefined +from .base import MRTrix3BaseInputSpec, MRTrix3Base +from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, + File, InputMultiPath) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename class FitTensorInputSpec(MRTrix3BaseInputSpec): diff --git a/nipype/interfaces/mrtrix3/tests/__init__.py b/nipype/interfaces/mrtrix3/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index 7a8c4a54a0..9661a59842 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.preprocess import ACTPrepareFSL +from ....testing import assert_equal +from ..preprocess import ACTPrepareFSL def test_ACTPrepareFSL_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_ACTPrepareFSL_inputs(): ) inputs = ACTPrepareFSL.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ACTPrepareFSL_outputs(): @@ -34,7 +34,7 @@ def test_ACTPrepareFSL_outputs(): ) outputs = ACTPrepareFSL.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 58b6184044..5e6713290d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.utils import BrainMask +from ....testing import assert_equal +from ..utils import BrainMask def test_BrainMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_BrainMask_inputs(): ) inputs = BrainMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BrainMask_outputs(): @@ -46,7 +46,7 @@ def test_BrainMask_outputs(): ) outputs = BrainMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 68ea51ede8..24dd8d2d62 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.connectivity import BuildConnectome +from ....testing import assert_equal +from ..connectivity import BuildConnectome def test_BuildConnectome_inputs(): input_map = dict(args=dict(argstr='%s', @@ -49,8 +49,8 @@ def test_BuildConnectome_inputs(): ) inputs = BuildConnectome.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BuildConnectome_outputs(): @@ -58,7 +58,7 @@ def test_BuildConnectome_outputs(): ) outputs = BuildConnectome.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 25c36d0265..9112ece997 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.utils import ComputeTDI +from ....testing import assert_equal +from ..utils import ComputeTDI def test_ComputeTDI_inputs(): input_map = dict(args=dict(argstr='%s', @@ -60,8 +60,8 @@ def test_ComputeTDI_inputs(): ) inputs = ComputeTDI.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeTDI_outputs(): @@ -69,7 +69,7 @@ def test_ComputeTDI_outputs(): ) outputs = ComputeTDI.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index 10ef4b33d0..142283a10f 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.reconst import EstimateFOD +from ....testing import assert_equal +from ..reconst import EstimateFOD def test_EstimateFOD_inputs(): input_map = dict(args=dict(argstr='%s', @@ -58,8 +58,8 @@ def test_EstimateFOD_inputs(): ) inputs = EstimateFOD.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EstimateFOD_outputs(): @@ -67,7 +67,7 @@ def test_EstimateFOD_outputs(): ) outputs = EstimateFOD.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 2dc23a5a3a..7102d75fbf 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.reconst import FitTensor +from ....testing import assert_equal +from ..reconst import FitTensor def test_FitTensor_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_FitTensor_inputs(): ) inputs = FitTensor.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FitTensor_outputs(): @@ -52,7 +52,7 @@ def test_FitTensor_outputs(): ) outputs = FitTensor.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index a6e4e76989..417a0b487f 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.utils import Generate5tt +from ....testing import assert_equal +from ..utils import Generate5tt def test_Generate5tt_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_Generate5tt_inputs(): ) inputs = Generate5tt.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Generate5tt_outputs(): @@ -37,7 +37,7 @@ def test_Generate5tt_outputs(): ) outputs = Generate5tt.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index f559920ab1..895da00071 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.connectivity import LabelConfig +from ....testing import assert_equal +from ..connectivity import LabelConfig def test_LabelConfig_inputs(): input_map = dict(args=dict(argstr='%s', @@ -41,8 +41,8 @@ def test_LabelConfig_inputs(): ) inputs = LabelConfig.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_LabelConfig_outputs(): @@ -50,7 +50,7 @@ def test_LabelConfig_outputs(): ) outputs = LabelConfig.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py index 3595f3acd9..7a82b5f98d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.base import MRTrix3Base +from ....testing import assert_equal +from ..base import MRTrix3Base def test_MRTrix3Base_inputs(): input_map = dict(args=dict(argstr='%s', @@ -16,7 +16,7 @@ def test_MRTrix3Base_inputs(): ) inputs = MRTrix3Base.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index a019f52eb7..5c4ef045aa 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.utils import Mesh2PVE +from ....testing import assert_equal +from ..utils import Mesh2PVE def test_Mesh2PVE_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_Mesh2PVE_inputs(): ) inputs = Mesh2PVE.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Mesh2PVE_outputs(): @@ -40,7 +40,7 @@ def test_Mesh2PVE_outputs(): ) outputs = Mesh2PVE.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index fd5b38bc42..a32cc65902 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.preprocess import ReplaceFSwithFIRST +from ....testing import assert_equal +from ..preprocess import ReplaceFSwithFIRST def test_ReplaceFSwithFIRST_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_ReplaceFSwithFIRST_inputs(): ) inputs = ReplaceFSwithFIRST.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ReplaceFSwithFIRST_outputs(): @@ -41,7 +41,7 @@ def test_ReplaceFSwithFIRST_outputs(): ) outputs = ReplaceFSwithFIRST.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 6bbc14c195..628981abb3 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.preprocess import ResponseSD +from ....testing import assert_equal +from ..preprocess import ResponseSD def test_ResponseSD_inputs(): input_map = dict(args=dict(argstr='%s', @@ -58,8 +58,8 @@ def test_ResponseSD_inputs(): ) inputs = ResponseSD.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ResponseSD_outputs(): @@ -68,7 +68,7 @@ def test_ResponseSD_outputs(): ) outputs = ResponseSD.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index 6e7c5c193f..aa3b05036c 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.utils import TCK2VTK +from ....testing import assert_equal +from ..utils import TCK2VTK def test_TCK2VTK_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_TCK2VTK_inputs(): ) inputs = TCK2VTK.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TCK2VTK_outputs(): @@ -40,7 +40,7 @@ def test_TCK2VTK_outputs(): ) outputs = TCK2VTK.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 4c0f6f97eb..1dd22ef0aa 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.utils import TensorMetrics +from ....testing import assert_equal +from ..utils import TensorMetrics def test_TensorMetrics_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_TensorMetrics_inputs(): ) inputs = TensorMetrics.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TensorMetrics_outputs(): @@ -47,7 +47,7 @@ def test_TensorMetrics_outputs(): ) outputs = TensorMetrics.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index 03154c5d8a..60fae0c3d7 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.mrtrix3.tracking import Tractography +from ....testing import assert_equal +from ..tracking import Tractography def test_Tractography_inputs(): input_map = dict(act_file=dict(argstr='-act %s', @@ -109,8 +109,8 @@ def test_Tractography_inputs(): ) inputs = Tractography.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Tractography_outputs(): @@ -119,7 +119,7 @@ def test_Tractography_outputs(): ) outputs = Tractography.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/mrtrix3/tracking.py b/nipype/interfaces/mrtrix3/tracking.py index b90ad6aab7..7495211543 100644 --- a/nipype/interfaces/mrtrix3/tracking.py +++ b/nipype/interfaces/mrtrix3/tracking.py @@ -11,15 +11,16 @@ >>> os.chdir(datadir) """ + +from __future__ import absolute_import import os import os.path as op -from base import MRTrix3BaseInputSpec, MRTrix3Base -from nipype.interfaces.base import ( - CommandLineInputSpec, CommandLine, traits, TraitedSpec, File) - -from nipype.utils.filemanip import split_filename -from nipype.interfaces.traits_extension import isdefined +from .base import MRTrix3BaseInputSpec, MRTrix3Base +from ..base import (CommandLineInputSpec, CommandLine, traits, + TraitedSpec, File) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename class TractographyInputSpec(MRTrix3BaseInputSpec): diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index fe542f8000..0667353a9c 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -11,16 +11,16 @@ >>> os.chdir(datadir) """ + +from __future__ import absolute_import import os import os.path as op -from base import MRTrix3BaseInputSpec, MRTrix3Base -from nipype.interfaces.base import ( - CommandLineInputSpec, CommandLine, traits, TraitedSpec, File, - InputMultiPath) - -from nipype.utils.filemanip import split_filename -from nipype.interfaces.traits_extension import isdefined +from .base import MRTrix3BaseInputSpec, MRTrix3Base +from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, + File,InputMultiPath) +from ..traits_extension import isdefined +from ...utils.filemanip import split_filename class BrainMaskInputSpec(MRTrix3BaseInputSpec): @@ -210,7 +210,7 @@ class TensorMetrics(CommandLine): def _list_outputs(self): outputs = self.output_spec().get() - for k in outputs.keys(): + for k in list(outputs.keys()): if isdefined(getattr(self.inputs, k)): outputs[k] = op.abspath(getattr(self.inputs, k)) diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py index ebbe394fdc..cf45ae0c6d 100644 --- a/nipype/interfaces/nipy/model.py +++ b/nipype/interfaces/nipy/model.py @@ -1,17 +1,17 @@ -import warnings +from __future__ import division +from builtins import range import os import nibabel as nb import numpy as np -from nipype.external import six - from ...utils.misc import package_check +from ...external.six import string_types have_nipy = True try: package_check('nipy') -except Exception, e: +except Exception as e: have_nipy = False else: import nipy.modalities.fmri.design_matrix as dm @@ -81,7 +81,7 @@ def _run_interface(self, runtime): session_info = self.inputs.session_info functional_runs = self.inputs.session_info[0]['scans'] - if isinstance(functional_runs, six.string_types): + if isinstance(functional_runs, string_types): functional_runs = [functional_runs] nii = nb.load(functional_runs[0]) data = nii.get_data() @@ -105,7 +105,7 @@ def _run_interface(self, runtime): nscans = timeseries.shape[1] - if 'hpf' in session_info[0].keys(): + if 'hpf' in list(session_info[0].keys()): hpf = session_info[0]['hpf'] drift_model=self.inputs.drift_model else: @@ -147,7 +147,9 @@ def _run_interface(self, runtime): ) if self.inputs.normalize_design_matrix: for i in range(len(self._reg_names)-1): - design_matrix[:,i] = (design_matrix[:,i]-design_matrix[:,i].mean())/design_matrix[:,i].std() + design_matrix[:,i] = ((design_matrix[:,i] - + design_matrix[:,i].mean()) / + design_matrix[:,i].std()) if self.inputs.plot_design_matrix: import pylab diff --git a/nipype/interfaces/nipy/preprocess.py b/nipype/interfaces/nipy/preprocess.py index f4b506717f..8efdce940d 100644 --- a/nipype/interfaces/nipy/preprocess.py +++ b/nipype/interfaces/nipy/preprocess.py @@ -19,7 +19,7 @@ have_nipy = True try: package_check('nipy') -except Exception, e: +except Exception as e: have_nipy = False else: import nipy @@ -53,7 +53,7 @@ class ComputeMask(BaseInterface): def _run_interface(self, runtime): from nipy.labs.mask import compute_mask args = {} - for key in [k for k, _ in self.inputs.items() + for key in [k for k, _ in list(self.inputs.items()) if k not in BaseInterfaceInputSpec().trait_names()]: value = getattr(self.inputs, key) if isdefined(value): @@ -129,7 +129,7 @@ class FmriRealign4d(BaseInterface): >>> realigner = FmriRealign4d() >>> realigner.inputs.in_file = ['functional.nii'] >>> realigner.inputs.tr = 2 - >>> realigner.inputs.slice_order = range(0,67) + >>> realigner.inputs.slice_order = list(range(0,67)) >>> res = realigner.run() # doctest: +SKIP References @@ -256,7 +256,7 @@ class SpaceTimeRealigner(BaseInterface): >>> realigner = SpaceTimeRealigner() >>> realigner.inputs.in_file = ['functional.nii'] >>> realigner.inputs.tr = 2 - >>> realigner.inputs.slice_times = range(0, 3, 67) + >>> realigner.inputs.slice_times = list(range(0, 3, 67)) >>> realigner.inputs.slice_info = 2 >>> res = realigner.run() # doctest: +SKIP diff --git a/nipype/interfaces/nipy/tests/__init__.py b/nipype/interfaces/nipy/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 18b416b991..057c1d46f0 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.preprocess import ComputeMask +from ....testing import assert_equal +from ..preprocess import ComputeMask def test_ComputeMask_inputs(): input_map = dict(M=dict(), @@ -15,8 +15,8 @@ def test_ComputeMask_inputs(): ) inputs = ComputeMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ComputeMask_outputs(): @@ -24,7 +24,7 @@ def test_ComputeMask_outputs(): ) outputs = ComputeMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index c617d192f6..f2ed249b8b 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.model import EstimateContrast +from ....testing import assert_equal +from ..model import EstimateContrast def test_EstimateContrast_inputs(): input_map = dict(axis=dict(mandatory=True, @@ -26,8 +26,8 @@ def test_EstimateContrast_inputs(): ) inputs = EstimateContrast.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EstimateContrast_outputs(): @@ -37,7 +37,7 @@ def test_EstimateContrast_outputs(): ) outputs = EstimateContrast.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 09e70280fe..7524597ecd 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.model import FitGLM +from ....testing import assert_equal +from ..model import FitGLM def test_FitGLM_inputs(): input_map = dict(TR=dict(mandatory=True, @@ -28,8 +28,8 @@ def test_FitGLM_inputs(): ) inputs = FitGLM.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FitGLM_outputs(): @@ -45,7 +45,7 @@ def test_FitGLM_outputs(): ) outputs = FitGLM.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index c3b3ccb4c8..605dfc839a 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.preprocess import FmriRealign4d +from ....testing import assert_equal +from ..preprocess import FmriRealign4d def test_FmriRealign4d_inputs(): input_map = dict(between_loops=dict(usedefault=True, @@ -27,8 +27,8 @@ def test_FmriRealign4d_inputs(): ) inputs = FmriRealign4d.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FmriRealign4d_outputs(): @@ -37,7 +37,7 @@ def test_FmriRealign4d_outputs(): ) outputs = FmriRealign4d.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index 548fe5f117..7f39019026 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.utils import Similarity +from ....testing import assert_equal +from ..utils import Similarity def test_Similarity_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -17,8 +17,8 @@ def test_Similarity_inputs(): ) inputs = Similarity.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Similarity_outputs(): @@ -26,7 +26,7 @@ def test_Similarity_outputs(): ) outputs = Similarity.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index 3786e760b0..e04a9d1b0b 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.preprocess import SpaceTimeRealigner +from ....testing import assert_equal +from ..preprocess import SpaceTimeRealigner def test_SpaceTimeRealigner_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -17,8 +17,8 @@ def test_SpaceTimeRealigner_inputs(): ) inputs = SpaceTimeRealigner.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SpaceTimeRealigner_outputs(): @@ -27,7 +27,7 @@ def test_SpaceTimeRealigner_outputs(): ) outputs = SpaceTimeRealigner.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index 0b9b3f881f..843774e686 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nipy.preprocess import Trim +from ....testing import assert_equal +from ..preprocess import Trim def test_Trim_inputs(): input_map = dict(begin_index=dict(usedefault=True, @@ -18,8 +18,8 @@ def test_Trim_inputs(): ) inputs = Trim.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Trim_outputs(): @@ -27,7 +27,7 @@ def test_Trim_outputs(): ) outputs = Trim.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/nipy/utils.py b/nipype/interfaces/nipy/utils.py index 8a6af7de96..82e80c32c3 100644 --- a/nipype/interfaces/nipy/utils.py +++ b/nipype/interfaces/nipy/utils.py @@ -15,7 +15,7 @@ have_nipy = True try: package_check('nipy') -except Exception, e: +except Exception as e: have_nipy = False else: from nipy.algorithms.registration.histogram_registration import HistogramRegistration diff --git a/nipype/interfaces/nitime/analysis.py b/nipype/interfaces/nitime/analysis.py index a83b85432d..740f56cde7 100644 --- a/nipype/interfaces/nitime/analysis.py +++ b/nipype/interfaces/nitime/analysis.py @@ -10,6 +10,9 @@ """ +from builtins import zip +from builtins import object + import warnings import numpy as np import tempfile @@ -23,7 +26,7 @@ have_nitime = True try: package_check('nitime') -except Exception, e: +except Exception as e: have_nitime = False else: import nitime.analysis as nta @@ -143,7 +146,7 @@ def _run_interface(self, runtime): TS = self.inputs.in_TS # deal with creating or storing ROI names: - if not TS.metadata.has_key('ROIs'): + if 'ROIs' not in TS.metadata: self.ROIs = ['roi_%d' % x for x, _ in enumerate(TS.data)] else: self.ROIs = TS.metadata['ROIs'] @@ -245,14 +248,14 @@ def _make_output_figures(self): suffix='_delay')) -class GetTimeSeriesInputSpec(): +class GetTimeSeriesInputSpec(object): pass -class GetTimeSeriesOutputSpec(): +class GetTimeSeriesOutputSpec(object): pass -class GetTimeSeries(): +class GetTimeSeries(object): # getting time series data from nifti files and ROIs pass diff --git a/nipype/interfaces/nitime/tests/__init__.py b/nipype/interfaces/nitime/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 0c0f134af3..bda6746b44 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.nitime.analysis import CoherenceAnalyzer +from ....testing import assert_equal +from ..analysis import CoherenceAnalyzer def test_CoherenceAnalyzer_inputs(): input_map = dict(NFFT=dict(usedefault=True, @@ -23,8 +23,8 @@ def test_CoherenceAnalyzer_inputs(): ) inputs = CoherenceAnalyzer.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CoherenceAnalyzer_outputs(): @@ -37,7 +37,7 @@ def test_CoherenceAnalyzer_outputs(): ) outputs = CoherenceAnalyzer.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/__init__.py b/nipype/interfaces/semtools/__init__.py index f6fe1a743c..33a57faab6 100644 --- a/nipype/interfaces/semtools/__init__.py +++ b/nipype/interfaces/semtools/__init__.py @@ -1,10 +1,11 @@ -from diffusion import * -from featurecreator import GenerateCsfClippedFromClassifiedImage -from segmentation import * -from filtering import * -from brains import * -from testing import * -from utilities import * -from legacy import * -from registration import * -from converters import DWISimpleCompare, DWICompare +from __future__ import absolute_import +from .diffusion import * +from .featurecreator import GenerateCsfClippedFromClassifiedImage +from .segmentation import * +from .filtering import * +from .brains import * +from .testing import * +from .utilities import * +from .legacy import * +from .registration import * +from .converters import DWISimpleCompare, DWICompare diff --git a/nipype/interfaces/semtools/brains/__init__.py b/nipype/interfaces/semtools/brains/__init__.py index c20ce97e81..a14dc3ba13 100644 --- a/nipype/interfaces/semtools/brains/__init__.py +++ b/nipype/interfaces/semtools/brains/__init__.py @@ -1,3 +1,4 @@ -from segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask -from utilities import HistogramMatchingFilter -from classify import BRAINSPosteriorToContinuousClass +from __future__ import absolute_import +from .segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask +from .utilities import HistogramMatchingFilter +from .classify import BRAINSPosteriorToContinuousClass diff --git a/nipype/interfaces/semtools/brains/classify.py b/nipype/interfaces/semtools/brains/classify.py index 5be4ad9ddf..191284b104 100644 --- a/nipype/interfaces/semtools/brains/classify.py +++ b/nipype/interfaces/semtools/brains/classify.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class BRAINSPosteriorToContinuousClassInputSpec(CommandLineInputSpec): inputWhiteVolume = File(desc="White Matter Posterior Volume", exists=True, argstr="--inputWhiteVolume %s") diff --git a/nipype/interfaces/semtools/brains/segmentation.py b/nipype/interfaces/semtools/brains/segmentation.py index 7f1b1bbaf4..a5f5c0031c 100644 --- a/nipype/interfaces/semtools/brains/segmentation.py +++ b/nipype/interfaces/semtools/brains/segmentation.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class SimilarityIndexInputSpec(CommandLineInputSpec): outputCSVFilename = File(desc="output CSV Filename", exists=True, argstr="--outputCSVFilename %s") diff --git a/nipype/interfaces/semtools/brains/tests/__init__.py b/nipype/interfaces/semtools/brains/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index a13b86fbf6..6d989a9493 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.brains.classify import BRAINSPosteriorToContinuousClass +from .....testing import assert_equal +from ..classify import BRAINSPosteriorToContinuousClass def test_BRAINSPosteriorToContinuousClass_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): ) inputs = BRAINSPosteriorToContinuousClass.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSPosteriorToContinuousClass_outputs(): @@ -42,7 +42,7 @@ def test_BRAINSPosteriorToContinuousClass_outputs(): ) outputs = BRAINSPosteriorToContinuousClass.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index 077f5a3fd6..53363df141 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.brains.segmentation import BRAINSTalairach +from .....testing import assert_equal +from ..segmentation import BRAINSTalairach def test_BRAINSTalairach_inputs(): input_map = dict(AC=dict(argstr='--AC %s', @@ -44,8 +44,8 @@ def test_BRAINSTalairach_inputs(): ) inputs = BRAINSTalairach.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSTalairach_outputs(): @@ -54,7 +54,7 @@ def test_BRAINSTalairach_outputs(): ) outputs = BRAINSTalairach.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index 90ce166d78..6b94a9535e 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.brains.segmentation import BRAINSTalairachMask +from .....testing import assert_equal +from ..segmentation import BRAINSTalairachMask def test_BRAINSTalairachMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_BRAINSTalairachMask_inputs(): ) inputs = BRAINSTalairachMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSTalairachMask_outputs(): @@ -38,7 +38,7 @@ def test_BRAINSTalairachMask_outputs(): ) outputs = BRAINSTalairachMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 2297969edd..8d360f2e58 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.brains.utilities import HistogramMatchingFilter +from .....testing import assert_equal +from ..utilities import HistogramMatchingFilter def test_HistogramMatchingFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_HistogramMatchingFilter_inputs(): ) inputs = HistogramMatchingFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_HistogramMatchingFilter_outputs(): @@ -46,7 +46,7 @@ def test_HistogramMatchingFilter_outputs(): ) outputs = HistogramMatchingFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 9411fb7393..2b8f058872 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.brains.segmentation import SimilarityIndex +from .....testing import assert_equal +from ..segmentation import SimilarityIndex def test_SimilarityIndex_inputs(): input_map = dict(ANNContinuousVolume=dict(argstr='--ANNContinuousVolume %s', @@ -24,15 +24,15 @@ def test_SimilarityIndex_inputs(): ) inputs = SimilarityIndex.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SimilarityIndex_outputs(): output_map = dict() outputs = SimilarityIndex.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/brains/utilities.py b/nipype/interfaces/semtools/brains/utilities.py index 0955968a7d..a296be671c 100644 --- a/nipype/interfaces/semtools/brains/utilities.py +++ b/nipype/interfaces/semtools/brains/utilities.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class HistogramMatchingFilterInputSpec(CommandLineInputSpec): inputVolume = File(desc="The Input image to be computed for statistics", exists=True, argstr="--inputVolume %s") diff --git a/nipype/interfaces/semtools/converters.py b/nipype/interfaces/semtools/converters.py index edfc322898..01ef06967b 100644 --- a/nipype/interfaces/semtools/converters.py +++ b/nipype/interfaces/semtools/converters.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ..base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class DWISimpleCompareInputSpec(CommandLineInputSpec): inputVolume1 = File(desc="First input volume (.nhdr or .nrrd)", exists=True, argstr="--inputVolume1 %s") diff --git a/nipype/interfaces/semtools/diffusion/__init__.py b/nipype/interfaces/semtools/diffusion/__init__.py index 46a5793f6f..f7b207f039 100644 --- a/nipype/interfaces/semtools/diffusion/__init__.py +++ b/nipype/interfaces/semtools/diffusion/__init__.py @@ -1,4 +1,5 @@ -from diffusion import dtiaverage, dtiestim, dtiprocess, DWIConvert -from tractography import * -from gtract import gtractTransformToDisplacementField, gtractInvertBSplineTransform, gtractConcatDwi, gtractAverageBvalues, gtractCoregBvalues, gtractResampleAnisotropy, gtractResampleCodeImage, gtractCopyImageOrientation, gtractCreateGuideFiber, gtractAnisotropyMap, gtractClipAnisotropy, gtractResampleB0, gtractInvertRigidTransform, gtractImageConformity, compareTractInclusion, gtractFastMarchingTracking, gtractInvertDisplacementField, gtractCoRegAnatomy, gtractResampleDWIInPlace, gtractCostFastMarching, gtractFiberTracking, extractNrrdVectorIndex, gtractResampleFibers, gtractTensor -from maxcurvature import maxcurvature +from __future__ import absolute_import +from .diffusion import dtiaverage, dtiestim, dtiprocess, DWIConvert +from .tractography import * +from .gtract import gtractTransformToDisplacementField, gtractInvertBSplineTransform, gtractConcatDwi, gtractAverageBvalues, gtractCoregBvalues, gtractResampleAnisotropy, gtractResampleCodeImage, gtractCopyImageOrientation, gtractCreateGuideFiber, gtractAnisotropyMap, gtractClipAnisotropy, gtractResampleB0, gtractInvertRigidTransform, gtractImageConformity, compareTractInclusion, gtractFastMarchingTracking, gtractInvertDisplacementField, gtractCoRegAnatomy, gtractResampleDWIInPlace, gtractCostFastMarching, gtractFiberTracking, extractNrrdVectorIndex, gtractResampleFibers, gtractTensor +from .maxcurvature import maxcurvature diff --git a/nipype/interfaces/semtools/diffusion/diffusion.py b/nipype/interfaces/semtools/diffusion/diffusion.py index 7522257296..6d30e1fc44 100644 --- a/nipype/interfaces/semtools/diffusion/diffusion.py +++ b/nipype/interfaces/semtools/diffusion/diffusion.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class dtiaverageInputSpec(CommandLineInputSpec): inputs = InputMultiPath(File(exists=True), desc="List of all the tensor fields to be averaged", argstr="--inputs %s...") diff --git a/nipype/interfaces/semtools/diffusion/gtract.py b/nipype/interfaces/semtools/diffusion/gtract.py index 7553ee93d4..c7f2db432c 100644 --- a/nipype/interfaces/semtools/diffusion/gtract.py +++ b/nipype/interfaces/semtools/diffusion/gtract.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class gtractTransformToDisplacementFieldInputSpec(CommandLineInputSpec): inputTransform = File(desc="Input Transform File Name", exists=True, argstr="--inputTransform %s") diff --git a/nipype/interfaces/semtools/diffusion/maxcurvature.py b/nipype/interfaces/semtools/diffusion/maxcurvature.py index 7b4711e58d..4206844ea2 100644 --- a/nipype/interfaces/semtools/diffusion/maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/maxcurvature.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class maxcurvatureInputSpec(CommandLineInputSpec): image = File(desc="FA Image", exists=True, argstr="--image %s") diff --git a/nipype/interfaces/semtools/diffusion/tests/__init__.py b/nipype/interfaces/semtools/diffusion/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index f9efbcc921..4b4d692385 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.diffusion import DWIConvert +from .....testing import assert_equal +from ..diffusion import DWIConvert def test_DWIConvert_inputs(): input_map = dict(args=dict(argstr='%s', @@ -53,8 +53,8 @@ def test_DWIConvert_inputs(): ) inputs = DWIConvert.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWIConvert_outputs(): @@ -66,7 +66,7 @@ def test_DWIConvert_outputs(): ) outputs = DWIConvert.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index 73ccecf241..1b8a841b75 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import compareTractInclusion +from .....testing import assert_equal +from ..gtract import compareTractInclusion def test_compareTractInclusion_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,15 +32,15 @@ def test_compareTractInclusion_inputs(): ) inputs = compareTractInclusion.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_compareTractInclusion_outputs(): output_map = dict() outputs = compareTractInclusion.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index 6ab3b98b1d..4306c604b8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.diffusion import dtiaverage +from .....testing import assert_equal +from ..diffusion import dtiaverage def test_dtiaverage_inputs(): input_map = dict(DTI_double=dict(argstr='--DTI_double ', @@ -25,8 +25,8 @@ def test_dtiaverage_inputs(): ) inputs = dtiaverage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_dtiaverage_outputs(): @@ -34,7 +34,7 @@ def test_dtiaverage_outputs(): ) outputs = dtiaverage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 77d8b6e50c..220d80ba9c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.diffusion import dtiestim +from .....testing import assert_equal +from ..diffusion import dtiestim def test_dtiestim_inputs(): input_map = dict(B0=dict(argstr='--B0 %s', @@ -57,8 +57,8 @@ def test_dtiestim_inputs(): ) inputs = dtiestim.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_dtiestim_outputs(): @@ -69,7 +69,7 @@ def test_dtiestim_outputs(): ) outputs = dtiestim.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index 01acf5488e..7d77c6d799 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.diffusion import dtiprocess +from .....testing import assert_equal +from ..diffusion import dtiprocess def test_dtiprocess_inputs(): input_map = dict(DTI_double=dict(argstr='--DTI_double ', @@ -89,8 +89,8 @@ def test_dtiprocess_inputs(): ) inputs = dtiprocess.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_dtiprocess_outputs(): @@ -112,7 +112,7 @@ def test_dtiprocess_outputs(): ) outputs = dtiprocess.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index 7c7ff4230e..081858b122 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import extractNrrdVectorIndex +from .....testing import assert_equal +from ..gtract import extractNrrdVectorIndex def test_extractNrrdVectorIndex_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_extractNrrdVectorIndex_inputs(): ) inputs = extractNrrdVectorIndex.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_extractNrrdVectorIndex_outputs(): @@ -36,7 +36,7 @@ def test_extractNrrdVectorIndex_outputs(): ) outputs = extractNrrdVectorIndex.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index 1ee04e4d55..779a9f4155 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractAnisotropyMap +from .....testing import assert_equal +from ..gtract import gtractAnisotropyMap def test_gtractAnisotropyMap_inputs(): input_map = dict(anisotropyType=dict(argstr='--anisotropyType %s', @@ -25,8 +25,8 @@ def test_gtractAnisotropyMap_inputs(): ) inputs = gtractAnisotropyMap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractAnisotropyMap_outputs(): @@ -34,7 +34,7 @@ def test_gtractAnisotropyMap_outputs(): ) outputs = gtractAnisotropyMap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 4636fe4623..25dfb3e1f7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractAverageBvalues +from .....testing import assert_equal +from ..gtract import gtractAverageBvalues def test_gtractAverageBvalues_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_gtractAverageBvalues_inputs(): ) inputs = gtractAverageBvalues.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractAverageBvalues_outputs(): @@ -36,7 +36,7 @@ def test_gtractAverageBvalues_outputs(): ) outputs = gtractAverageBvalues.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index de93e5f2af..66827b5129 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractClipAnisotropy +from .....testing import assert_equal +from ..gtract import gtractClipAnisotropy def test_gtractClipAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_gtractClipAnisotropy_inputs(): ) inputs = gtractClipAnisotropy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractClipAnisotropy_outputs(): @@ -36,7 +36,7 @@ def test_gtractClipAnisotropy_outputs(): ) outputs = gtractClipAnisotropy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 9f57db005f..b08543b760 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractCoRegAnatomy +from .....testing import assert_equal +from ..gtract import gtractCoRegAnatomy def test_gtractCoRegAnatomy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -66,8 +66,8 @@ def test_gtractCoRegAnatomy_inputs(): ) inputs = gtractCoRegAnatomy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractCoRegAnatomy_outputs(): @@ -75,7 +75,7 @@ def test_gtractCoRegAnatomy_outputs(): ) outputs = gtractCoRegAnatomy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 7d89297359..a553336672 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractConcatDwi +from .....testing import assert_equal +from ..gtract import gtractConcatDwi def test_gtractConcatDwi_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_gtractConcatDwi_inputs(): ) inputs = gtractConcatDwi.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractConcatDwi_outputs(): @@ -34,7 +34,7 @@ def test_gtractConcatDwi_outputs(): ) outputs = gtractConcatDwi.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index 44bd535411..ef8dacf00f 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractCopyImageOrientation +from .....testing import assert_equal +from ..gtract import gtractCopyImageOrientation def test_gtractCopyImageOrientation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_gtractCopyImageOrientation_inputs(): ) inputs = gtractCopyImageOrientation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractCopyImageOrientation_outputs(): @@ -34,7 +34,7 @@ def test_gtractCopyImageOrientation_outputs(): ) outputs = gtractCopyImageOrientation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index f44f69e270..c210e61cbd 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractCoregBvalues +from .....testing import assert_equal +from ..gtract import gtractCoregBvalues def test_gtractCoregBvalues_inputs(): input_map = dict(args=dict(argstr='%s', @@ -50,8 +50,8 @@ def test_gtractCoregBvalues_inputs(): ) inputs = gtractCoregBvalues.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractCoregBvalues_outputs(): @@ -60,7 +60,7 @@ def test_gtractCoregBvalues_outputs(): ) outputs = gtractCoregBvalues.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 7bc5a1ccf5..7faf8558f3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractCostFastMarching +from .....testing import assert_equal +from ..gtract import gtractCostFastMarching def test_gtractCostFastMarching_inputs(): input_map = dict(anisotropyWeight=dict(argstr='--anisotropyWeight %f', @@ -38,8 +38,8 @@ def test_gtractCostFastMarching_inputs(): ) inputs = gtractCostFastMarching.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractCostFastMarching_outputs(): @@ -48,7 +48,7 @@ def test_gtractCostFastMarching_outputs(): ) outputs = gtractCostFastMarching.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index 6e6ea6ecc1..1ff8663d6c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractCreateGuideFiber +from .....testing import assert_equal +from ..gtract import gtractCreateGuideFiber def test_gtractCreateGuideFiber_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_gtractCreateGuideFiber_inputs(): ) inputs = gtractCreateGuideFiber.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractCreateGuideFiber_outputs(): @@ -36,7 +36,7 @@ def test_gtractCreateGuideFiber_outputs(): ) outputs = gtractCreateGuideFiber.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index 9173b5d840..d7ab24874b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractFastMarchingTracking +from .....testing import assert_equal +from ..gtract import gtractFastMarchingTracking def test_gtractFastMarchingTracking_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_gtractFastMarchingTracking_inputs(): ) inputs = gtractFastMarchingTracking.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractFastMarchingTracking_outputs(): @@ -54,7 +54,7 @@ def test_gtractFastMarchingTracking_outputs(): ) outputs = gtractFastMarchingTracking.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index 01839b5f18..a634895777 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractFiberTracking +from .....testing import assert_equal +from ..gtract import gtractFiberTracking def test_gtractFiberTracking_inputs(): input_map = dict(args=dict(argstr='%s', @@ -73,8 +73,8 @@ def test_gtractFiberTracking_inputs(): ) inputs = gtractFiberTracking.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractFiberTracking_outputs(): @@ -82,7 +82,7 @@ def test_gtractFiberTracking_outputs(): ) outputs = gtractFiberTracking.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index 1d8cc5b6b3..1f555d1afd 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractImageConformity +from .....testing import assert_equal +from ..gtract import gtractImageConformity def test_gtractImageConformity_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_gtractImageConformity_inputs(): ) inputs = gtractImageConformity.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractImageConformity_outputs(): @@ -34,7 +34,7 @@ def test_gtractImageConformity_outputs(): ) outputs = gtractImageConformity.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index 7a6ac478ef..84a5b8c6d0 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractInvertBSplineTransform +from .....testing import assert_equal +from ..gtract import gtractInvertBSplineTransform def test_gtractInvertBSplineTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_gtractInvertBSplineTransform_inputs(): ) inputs = gtractInvertBSplineTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractInvertBSplineTransform_outputs(): @@ -37,7 +37,7 @@ def test_gtractInvertBSplineTransform_outputs(): ) outputs = gtractInvertBSplineTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index fcc3aacd98..d1cf84126c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractInvertDisplacementField +from .....testing import assert_equal +from ..gtract import gtractInvertDisplacementField def test_gtractInvertDisplacementField_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_gtractInvertDisplacementField_inputs(): ) inputs = gtractInvertDisplacementField.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractInvertDisplacementField_outputs(): @@ -36,7 +36,7 @@ def test_gtractInvertDisplacementField_outputs(): ) outputs = gtractInvertDisplacementField.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index b5b14f1364..c76a097da9 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractInvertRigidTransform +from .....testing import assert_equal +from ..gtract import gtractInvertRigidTransform def test_gtractInvertRigidTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_gtractInvertRigidTransform_inputs(): ) inputs = gtractInvertRigidTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractInvertRigidTransform_outputs(): @@ -32,7 +32,7 @@ def test_gtractInvertRigidTransform_outputs(): ) outputs = gtractInvertRigidTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index 5b6e9ddbac..a373d9802b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractResampleAnisotropy +from .....testing import assert_equal +from ..gtract import gtractResampleAnisotropy def test_gtractResampleAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_gtractResampleAnisotropy_inputs(): ) inputs = gtractResampleAnisotropy.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractResampleAnisotropy_outputs(): @@ -38,7 +38,7 @@ def test_gtractResampleAnisotropy_outputs(): ) outputs = gtractResampleAnisotropy.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index 00af0fa8b0..1eaf64701f 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractResampleB0 +from .....testing import assert_equal +from ..gtract import gtractResampleB0 def test_gtractResampleB0_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_gtractResampleB0_inputs(): ) inputs = gtractResampleB0.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractResampleB0_outputs(): @@ -40,7 +40,7 @@ def test_gtractResampleB0_outputs(): ) outputs = gtractResampleB0.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index dc4d16911e..e66f094f90 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractResampleCodeImage +from .....testing import assert_equal +from ..gtract import gtractResampleCodeImage def test_gtractResampleCodeImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_gtractResampleCodeImage_inputs(): ) inputs = gtractResampleCodeImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractResampleCodeImage_outputs(): @@ -38,7 +38,7 @@ def test_gtractResampleCodeImage_outputs(): ) outputs = gtractResampleCodeImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index e4426642a9..3e1d5011e1 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractResampleDWIInPlace +from .....testing import assert_equal +from ..gtract import gtractResampleDWIInPlace def test_gtractResampleDWIInPlace_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_gtractResampleDWIInPlace_inputs(): ) inputs = gtractResampleDWIInPlace.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractResampleDWIInPlace_outputs(): @@ -47,7 +47,7 @@ def test_gtractResampleDWIInPlace_outputs(): ) outputs = gtractResampleDWIInPlace.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index acfa2ab1fa..483d52d89c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractResampleFibers +from .....testing import assert_equal +from ..gtract import gtractResampleFibers def test_gtractResampleFibers_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_gtractResampleFibers_inputs(): ) inputs = gtractResampleFibers.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractResampleFibers_outputs(): @@ -38,7 +38,7 @@ def test_gtractResampleFibers_outputs(): ) outputs = gtractResampleFibers.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 7f12791f9e..890b1dc9af 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractTensor +from .....testing import assert_equal +from ..gtract import gtractTensor def test_gtractTensor_inputs(): input_map = dict(applyMeasurementFrame=dict(argstr='--applyMeasurementFrame ', @@ -43,8 +43,8 @@ def test_gtractTensor_inputs(): ) inputs = gtractTensor.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractTensor_outputs(): @@ -52,7 +52,7 @@ def test_gtractTensor_outputs(): ) outputs = gtractTensor.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 60ee624968..75f4671bdc 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.gtract import gtractTransformToDisplacementField +from .....testing import assert_equal +from ..gtract import gtractTransformToDisplacementField def test_gtractTransformToDisplacementField_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_gtractTransformToDisplacementField_inputs(): ) inputs = gtractTransformToDisplacementField.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_gtractTransformToDisplacementField_outputs(): @@ -34,7 +34,7 @@ def test_gtractTransformToDisplacementField_outputs(): ) outputs = gtractTransformToDisplacementField.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index cf3d76aca1..84f476b1a7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.maxcurvature import maxcurvature +from .....testing import assert_equal +from ..maxcurvature import maxcurvature def test_maxcurvature_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_maxcurvature_inputs(): ) inputs = maxcurvature.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_maxcurvature_outputs(): @@ -34,7 +34,7 @@ def test_maxcurvature_outputs(): ) outputs = maxcurvature.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tractography/__init__.py b/nipype/interfaces/semtools/diffusion/tractography/__init__.py index 6d15f2b6a8..2d170ebcfe 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/__init__.py +++ b/nipype/interfaces/semtools/diffusion/tractography/__init__.py @@ -1,4 +1,5 @@ -from commandlineonly import fiberstats -from fiberprocess import fiberprocess -from fibertrack import fibertrack -from ukftractography import UKFTractography +from __future__ import absolute_import +from .commandlineonly import fiberstats +from .fiberprocess import fiberprocess +from .fibertrack import fibertrack +from .ukftractography import UKFTractography diff --git a/nipype/interfaces/semtools/diffusion/tractography/commandlineonly.py b/nipype/interfaces/semtools/diffusion/tractography/commandlineonly.py index 71971ec4a2..edf2f089a9 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/commandlineonly.py +++ b/nipype/interfaces/semtools/diffusion/tractography/commandlineonly.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ....base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class fiberstatsInputSpec(CommandLineInputSpec): fiber_file = File(desc="DTI Fiber File", exists=True, argstr="--fiber_file %s") diff --git a/nipype/interfaces/semtools/diffusion/tractography/fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/fiberprocess.py index ccba1d081f..28fbac5b24 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/fiberprocess.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ....base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class fiberprocessInputSpec(CommandLineInputSpec): fiber_file = File(desc="DTI fiber file", exists=True, argstr="--fiber_file %s") diff --git a/nipype/interfaces/semtools/diffusion/tractography/fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/fibertrack.py index 1599f1e30d..893f3a9b7b 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/fibertrack.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ....base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class fibertrackInputSpec(CommandLineInputSpec): input_tensor_file = File(desc="Tensor Image", exists=True, argstr="--input_tensor_file %s") diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py b/nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 24bdf31507..98c9a05add 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.tractography.ukftractography import UKFTractography +from ......testing import assert_equal +from ..ukftractography import UKFTractography def test_UKFTractography_inputs(): input_map = dict(Ql=dict(argstr='--Ql %f', @@ -85,8 +85,8 @@ def test_UKFTractography_inputs(): ) inputs = UKFTractography.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_UKFTractography_outputs(): @@ -95,7 +95,7 @@ def test_UKFTractography_outputs(): ) outputs = UKFTractography.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index 012e2d1cd8..a1ba70176c 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.tractography.fiberprocess import fiberprocess +from ......testing import assert_equal +from ..fiberprocess import fiberprocess def test_fiberprocess_inputs(): input_map = dict(args=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_fiberprocess_inputs(): ) inputs = fiberprocess.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_fiberprocess_outputs(): @@ -56,7 +56,7 @@ def test_fiberprocess_outputs(): ) outputs = fiberprocess.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index 91f1bbc7a4..f2c5af669d 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.tractography.commandlineonly import fiberstats +from ......testing import assert_equal +from ..commandlineonly import fiberstats def test_fiberstats_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,15 +20,15 @@ def test_fiberstats_inputs(): ) inputs = fiberstats.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_fiberstats_outputs(): output_map = dict() outputs = fiberstats.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index bd496c309d..a903b0fa7d 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.diffusion.tractography.fibertrack import fibertrack +from ......testing import assert_equal +from ..fibertrack import fibertrack def test_fibertrack_inputs(): input_map = dict(args=dict(argstr='%s', @@ -43,8 +43,8 @@ def test_fibertrack_inputs(): ) inputs = fibertrack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_fibertrack_outputs(): @@ -52,7 +52,7 @@ def test_fibertrack_outputs(): ) outputs = fibertrack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py b/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py index 9457621445..63b1ecb33c 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ....base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class UKFTractographyInputSpec(CommandLineInputSpec): dwiFile = File(desc="Input DWI volume", exists=True, argstr="--dwiFile %s") diff --git a/nipype/interfaces/semtools/featurecreator.py b/nipype/interfaces/semtools/featurecreator.py index cfd8f49cdd..4147832b77 100644 --- a/nipype/interfaces/semtools/featurecreator.py +++ b/nipype/interfaces/semtools/featurecreator.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ..base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class GenerateCsfClippedFromClassifiedImageInputSpec(CommandLineInputSpec): inputCassifiedVolume = File(desc="Required: input tissue label image", exists=True, argstr="--inputCassifiedVolume %s") diff --git a/nipype/interfaces/semtools/filtering/__init__.py b/nipype/interfaces/semtools/filtering/__init__.py index 3abc3c3bd1..7631224429 100644 --- a/nipype/interfaces/semtools/filtering/__init__.py +++ b/nipype/interfaces/semtools/filtering/__init__.py @@ -1,2 +1,3 @@ -from denoising import UnbiasedNonLocalMeans -from featuredetection import GenerateSummedGradientImage, CannySegmentationLevelSetImageFilter, DilateImage, TextureFromNoiseImageFilter, FlippedDifference, ErodeImage, GenerateBrainClippedImage, NeighborhoodMedian, GenerateTestImage, NeighborhoodMean, HammerAttributeCreator, TextureMeasureFilter, DilateMask, DumpBinaryTrainingVectors, DistanceMaps, STAPLEAnalysis, GradientAnisotropicDiffusionImageFilter, CannyEdge +from __future__ import absolute_import +from .denoising import UnbiasedNonLocalMeans +from .featuredetection import GenerateSummedGradientImage, CannySegmentationLevelSetImageFilter, DilateImage, TextureFromNoiseImageFilter, FlippedDifference, ErodeImage, GenerateBrainClippedImage, NeighborhoodMedian, GenerateTestImage, NeighborhoodMean, HammerAttributeCreator, TextureMeasureFilter, DilateMask, DumpBinaryTrainingVectors, DistanceMaps, STAPLEAnalysis, GradientAnisotropicDiffusionImageFilter, CannyEdge diff --git a/nipype/interfaces/semtools/filtering/denoising.py b/nipype/interfaces/semtools/filtering/denoising.py index fc4d0b13eb..03536fd643 100644 --- a/nipype/interfaces/semtools/filtering/denoising.py +++ b/nipype/interfaces/semtools/filtering/denoising.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class UnbiasedNonLocalMeansInputSpec(CommandLineInputSpec): sigma = traits.Float(desc="The root power of noise (sigma) in the complex Gaussian process the Rician comes from. If it is underestimated, the algorithm fails to remove the noise. If it is overestimated, over-blurring is likely to occur.", argstr="--sigma %f") diff --git a/nipype/interfaces/semtools/filtering/featuredetection.py b/nipype/interfaces/semtools/filtering/featuredetection.py index 651dd2c4f6..6f66a39ae4 100644 --- a/nipype/interfaces/semtools/filtering/featuredetection.py +++ b/nipype/interfaces/semtools/filtering/featuredetection.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class GenerateSummedGradientImageInputSpec(CommandLineInputSpec): inputVolume1 = File(desc="input volume 1, usally t1 image", exists=True, argstr="--inputVolume1 %s") diff --git a/nipype/interfaces/semtools/filtering/tests/__init__.py b/nipype/interfaces/semtools/filtering/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index a8dd94e1f1..49f6caeaa7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import CannyEdge +from .....testing import assert_equal +from ..featuredetection import CannyEdge def test_CannyEdge_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_CannyEdge_inputs(): ) inputs = CannyEdge.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CannyEdge_outputs(): @@ -36,7 +36,7 @@ def test_CannyEdge_outputs(): ) outputs = CannyEdge.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index 4ec3aa3936..d8d4af7c35 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import CannySegmentationLevelSetImageFilter +from .....testing import assert_equal +from ..featuredetection import CannySegmentationLevelSetImageFilter def test_CannySegmentationLevelSetImageFilter_inputs(): input_map = dict(advectionWeight=dict(argstr='--advectionWeight %f', @@ -36,8 +36,8 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): ) inputs = CannySegmentationLevelSetImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CannySegmentationLevelSetImageFilter_outputs(): @@ -46,7 +46,7 @@ def test_CannySegmentationLevelSetImageFilter_outputs(): ) outputs = CannySegmentationLevelSetImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 5148b42e35..f419053ea4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import DilateImage +from .....testing import assert_equal +from ..featuredetection import DilateImage def test_DilateImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_DilateImage_inputs(): ) inputs = DilateImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DilateImage_outputs(): @@ -34,7 +34,7 @@ def test_DilateImage_outputs(): ) outputs = DilateImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 03826fe162..40e1e30a33 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import DilateMask +from .....testing import assert_equal +from ..featuredetection import DilateMask def test_DilateMask_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_DilateMask_inputs(): ) inputs = DilateMask.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DilateMask_outputs(): @@ -36,7 +36,7 @@ def test_DilateMask_outputs(): ) outputs = DilateMask.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index d760101acc..866b57d539 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import DistanceMaps +from .....testing import assert_equal +from ..featuredetection import DistanceMaps def test_DistanceMaps_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_DistanceMaps_inputs(): ) inputs = DistanceMaps.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DistanceMaps_outputs(): @@ -34,7 +34,7 @@ def test_DistanceMaps_outputs(): ) outputs = DistanceMaps.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index 43e01b047a..a00278d312 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import DumpBinaryTrainingVectors +from .....testing import assert_equal +from ..featuredetection import DumpBinaryTrainingVectors def test_DumpBinaryTrainingVectors_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,15 +20,15 @@ def test_DumpBinaryTrainingVectors_inputs(): ) inputs = DumpBinaryTrainingVectors.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DumpBinaryTrainingVectors_outputs(): output_map = dict() outputs = DumpBinaryTrainingVectors.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index 7f71dc0661..f041f1857e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import ErodeImage +from .....testing import assert_equal +from ..featuredetection import ErodeImage def test_ErodeImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_ErodeImage_inputs(): ) inputs = ErodeImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ErodeImage_outputs(): @@ -34,7 +34,7 @@ def test_ErodeImage_outputs(): ) outputs = ErodeImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 1b65bdefec..bde8e2d405 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import FlippedDifference +from .....testing import assert_equal +from ..featuredetection import FlippedDifference def test_FlippedDifference_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_FlippedDifference_inputs(): ) inputs = FlippedDifference.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FlippedDifference_outputs(): @@ -32,7 +32,7 @@ def test_FlippedDifference_outputs(): ) outputs = FlippedDifference.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 65c9a32583..b85e616ff8 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import GenerateBrainClippedImage +from .....testing import assert_equal +from ..featuredetection import GenerateBrainClippedImage def test_GenerateBrainClippedImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_GenerateBrainClippedImage_inputs(): ) inputs = GenerateBrainClippedImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateBrainClippedImage_outputs(): @@ -34,7 +34,7 @@ def test_GenerateBrainClippedImage_outputs(): ) outputs = GenerateBrainClippedImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index c873f6c278..5873f1e8a7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import GenerateSummedGradientImage +from .....testing import assert_equal +from ..featuredetection import GenerateSummedGradientImage def test_GenerateSummedGradientImage_inputs(): input_map = dict(MaximumGradient=dict(argstr='--MaximumGradient ', @@ -27,8 +27,8 @@ def test_GenerateSummedGradientImage_inputs(): ) inputs = GenerateSummedGradientImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateSummedGradientImage_outputs(): @@ -36,7 +36,7 @@ def test_GenerateSummedGradientImage_outputs(): ) outputs = GenerateSummedGradientImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index e893f928a1..cd786d6097 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import GenerateTestImage +from .....testing import assert_equal +from ..featuredetection import GenerateTestImage def test_GenerateTestImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_GenerateTestImage_inputs(): ) inputs = GenerateTestImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateTestImage_outputs(): @@ -36,7 +36,7 @@ def test_GenerateTestImage_outputs(): ) outputs = GenerateTestImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index 93aac5134e..cf0f3ccca1 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import GradientAnisotropicDiffusionImageFilter +from .....testing import assert_equal +from ..featuredetection import GradientAnisotropicDiffusionImageFilter def test_GradientAnisotropicDiffusionImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): ) inputs = GradientAnisotropicDiffusionImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GradientAnisotropicDiffusionImageFilter_outputs(): @@ -36,7 +36,7 @@ def test_GradientAnisotropicDiffusionImageFilter_outputs(): ) outputs = GradientAnisotropicDiffusionImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 00d259e3ac..4c8813a1c4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import HammerAttributeCreator +from .....testing import assert_equal +from ..featuredetection import HammerAttributeCreator def test_HammerAttributeCreator_inputs(): input_map = dict(Scale=dict(argstr='--Scale %d', @@ -28,15 +28,15 @@ def test_HammerAttributeCreator_inputs(): ) inputs = HammerAttributeCreator.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_HammerAttributeCreator_outputs(): output_map = dict() outputs = HammerAttributeCreator.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index a5bbfad695..5d9cfae916 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import NeighborhoodMean +from .....testing import assert_equal +from ..featuredetection import NeighborhoodMean def test_NeighborhoodMean_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_NeighborhoodMean_inputs(): ) inputs = NeighborhoodMean.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NeighborhoodMean_outputs(): @@ -34,7 +34,7 @@ def test_NeighborhoodMean_outputs(): ) outputs = NeighborhoodMean.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 7818ab39c6..1f59a35b07 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import NeighborhoodMedian +from .....testing import assert_equal +from ..featuredetection import NeighborhoodMedian def test_NeighborhoodMedian_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_NeighborhoodMedian_inputs(): ) inputs = NeighborhoodMedian.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NeighborhoodMedian_outputs(): @@ -34,7 +34,7 @@ def test_NeighborhoodMedian_outputs(): ) outputs = NeighborhoodMedian.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 1d0204aaf4..2cc852cefe 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import STAPLEAnalysis +from .....testing import assert_equal +from ..featuredetection import STAPLEAnalysis def test_STAPLEAnalysis_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_STAPLEAnalysis_inputs(): ) inputs = STAPLEAnalysis.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_STAPLEAnalysis_outputs(): @@ -32,7 +32,7 @@ def test_STAPLEAnalysis_outputs(): ) outputs = STAPLEAnalysis.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index 5ac7c1100a..1c29c32681 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import TextureFromNoiseImageFilter +from .....testing import assert_equal +from ..featuredetection import TextureFromNoiseImageFilter def test_TextureFromNoiseImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_TextureFromNoiseImageFilter_inputs(): ) inputs = TextureFromNoiseImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TextureFromNoiseImageFilter_outputs(): @@ -32,7 +32,7 @@ def test_TextureFromNoiseImageFilter_outputs(): ) outputs = TextureFromNoiseImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index 188df83ff7..74f3adfe9f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.featuredetection import TextureMeasureFilter +from .....testing import assert_equal +from ..featuredetection import TextureMeasureFilter def test_TextureMeasureFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_TextureMeasureFilter_inputs(): ) inputs = TextureMeasureFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TextureMeasureFilter_outputs(): @@ -36,7 +36,7 @@ def test_TextureMeasureFilter_outputs(): ) outputs = TextureMeasureFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index fe83efcc85..9d1ec355c4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.filtering.denoising import UnbiasedNonLocalMeans +from .....testing import assert_equal +from ..denoising import UnbiasedNonLocalMeans def test_UnbiasedNonLocalMeans_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_UnbiasedNonLocalMeans_inputs(): ) inputs = UnbiasedNonLocalMeans.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_UnbiasedNonLocalMeans_outputs(): @@ -45,7 +45,7 @@ def test_UnbiasedNonLocalMeans_outputs(): ) outputs = UnbiasedNonLocalMeans.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/legacy/__init__.py b/nipype/interfaces/semtools/legacy/__init__.py index f1d96b6e99..e026aab90e 100644 --- a/nipype/interfaces/semtools/legacy/__init__.py +++ b/nipype/interfaces/semtools/legacy/__init__.py @@ -1 +1,2 @@ -from registration import scalartransform +from __future__ import absolute_import +from .registration import scalartransform diff --git a/nipype/interfaces/semtools/legacy/registration.py b/nipype/interfaces/semtools/legacy/registration.py index 0ca985a69c..8af1e20bfd 100644 --- a/nipype/interfaces/semtools/legacy/registration.py +++ b/nipype/interfaces/semtools/legacy/registration.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class scalartransformInputSpec(CommandLineInputSpec): input_image = File(desc="Image to tranform", exists=True, argstr="--input_image %s") diff --git a/nipype/interfaces/semtools/legacy/tests/__init__.py b/nipype/interfaces/semtools/legacy/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 3afac31c98..1d49041ea6 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.legacy.registration import scalartransform +from .....testing import assert_equal +from ..registration import scalartransform def test_scalartransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_scalartransform_inputs(): ) inputs = scalartransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_scalartransform_outputs(): @@ -42,7 +42,7 @@ def test_scalartransform_outputs(): ) outputs = scalartransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/registration/__init__.py b/nipype/interfaces/semtools/registration/__init__.py index b4e74350cd..2471436c7a 100644 --- a/nipype/interfaces/semtools/registration/__init__.py +++ b/nipype/interfaces/semtools/registration/__init__.py @@ -1,4 +1,5 @@ -from specialized import VBRAINSDemonWarp, BRAINSDemonWarp, BRAINSTransformFromFiducials -from brainsresample import BRAINSResample -from brainsfit import BRAINSFit -from brainsresize import BRAINSResize +from __future__ import absolute_import +from .specialized import VBRAINSDemonWarp, BRAINSDemonWarp, BRAINSTransformFromFiducials +from .brainsresample import BRAINSResample +from .brainsfit import BRAINSFit +from .brainsresize import BRAINSResize diff --git a/nipype/interfaces/semtools/registration/brainsfit.py b/nipype/interfaces/semtools/registration/brainsfit.py index d15b321dae..f80750d09a 100644 --- a/nipype/interfaces/semtools/registration/brainsfit.py +++ b/nipype/interfaces/semtools/registration/brainsfit.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class BRAINSFitInputSpec(CommandLineInputSpec): fixedVolume = File(desc="Input fixed image (the moving image will be transformed into this image space).", exists=True, argstr="--fixedVolume %s") diff --git a/nipype/interfaces/semtools/registration/brainsresample.py b/nipype/interfaces/semtools/registration/brainsresample.py index 88d4d0806f..9a14b48589 100644 --- a/nipype/interfaces/semtools/registration/brainsresample.py +++ b/nipype/interfaces/semtools/registration/brainsresample.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class BRAINSResampleInputSpec(CommandLineInputSpec): inputVolume = File(desc="Image To Warp", exists=True, argstr="--inputVolume %s") diff --git a/nipype/interfaces/semtools/registration/brainsresize.py b/nipype/interfaces/semtools/registration/brainsresize.py index 24d238ac54..dac094b6e4 100644 --- a/nipype/interfaces/semtools/registration/brainsresize.py +++ b/nipype/interfaces/semtools/registration/brainsresize.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class BRAINSResizeInputSpec(CommandLineInputSpec): inputVolume = File(desc="Image To Scale", exists=True, argstr="--inputVolume %s") diff --git a/nipype/interfaces/semtools/registration/specialized.py b/nipype/interfaces/semtools/registration/specialized.py index d67ea80e74..ed6e6c76d7 100644 --- a/nipype/interfaces/semtools/registration/specialized.py +++ b/nipype/interfaces/semtools/registration/specialized.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class VBRAINSDemonWarpInputSpec(CommandLineInputSpec): movingVolume = InputMultiPath(File(exists=True), desc="Required: input moving image", argstr="--movingVolume %s...") diff --git a/nipype/interfaces/semtools/registration/tests/__init__.py b/nipype/interfaces/semtools/registration/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index f1869db48b..6bb0b716cc 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.registration.specialized import BRAINSDemonWarp +from .....testing import assert_equal +from ..specialized import BRAINSDemonWarp def test_BRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -106,8 +106,8 @@ def test_BRAINSDemonWarp_inputs(): ) inputs = BRAINSDemonWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSDemonWarp_outputs(): @@ -117,7 +117,7 @@ def test_BRAINSDemonWarp_outputs(): ) outputs = BRAINSDemonWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 9e3db7f262..8a3c229d99 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.registration.brainsfit import BRAINSFit +from .....testing import assert_equal +from ..brainsfit import BRAINSFit def test_BRAINSFit_inputs(): input_map = dict(ROIAutoClosingSize=dict(argstr='--ROIAutoClosingSize %f', @@ -159,8 +159,8 @@ def test_BRAINSFit_inputs(): ) inputs = BRAINSFit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSFit_outputs(): @@ -175,7 +175,7 @@ def test_BRAINSFit_outputs(): ) outputs = BRAINSFit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 7c27434aa4..9dd1c3c00a 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.registration.brainsresample import BRAINSResample +from .....testing import assert_equal +from ..brainsresample import BRAINSResample def test_BRAINSResample_inputs(): input_map = dict(args=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_BRAINSResample_inputs(): ) inputs = BRAINSResample.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSResample_outputs(): @@ -49,7 +49,7 @@ def test_BRAINSResample_outputs(): ) outputs = BRAINSResample.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 7b3f8c8ee3..e1180bd075 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.registration.brainsresize import BRAINSResize +from .....testing import assert_equal +from ..brainsresize import BRAINSResize def test_BRAINSResize_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_BRAINSResize_inputs(): ) inputs = BRAINSResize.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSResize_outputs(): @@ -34,7 +34,7 @@ def test_BRAINSResize_outputs(): ) outputs = BRAINSResize.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index 3ff80654b6..69abf621d3 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.registration.specialized import BRAINSTransformFromFiducials +from .....testing import assert_equal +from ..specialized import BRAINSTransformFromFiducials def test_BRAINSTransformFromFiducials_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_BRAINSTransformFromFiducials_inputs(): ) inputs = BRAINSTransformFromFiducials.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSTransformFromFiducials_outputs(): @@ -40,7 +40,7 @@ def test_BRAINSTransformFromFiducials_outputs(): ) outputs = BRAINSTransformFromFiducials.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index ca20239f47..b0445a4380 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.registration.specialized import VBRAINSDemonWarp +from .....testing import assert_equal +from ..specialized import VBRAINSDemonWarp def test_VBRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -109,8 +109,8 @@ def test_VBRAINSDemonWarp_inputs(): ) inputs = VBRAINSDemonWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VBRAINSDemonWarp_outputs(): @@ -120,7 +120,7 @@ def test_VBRAINSDemonWarp_outputs(): ) outputs = VBRAINSDemonWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/__init__.py b/nipype/interfaces/semtools/segmentation/__init__.py index c0f122307e..c35f11739a 100644 --- a/nipype/interfaces/semtools/segmentation/__init__.py +++ b/nipype/interfaces/semtools/segmentation/__init__.py @@ -1 +1,2 @@ -from specialized import BRAINSCut, BRAINSROIAuto, BRAINSConstellationDetector, BRAINSCreateLabelMapFromProbabilityMaps, BinaryMaskEditorBasedOnLandmarks, BRAINSMultiSTAPLE, BRAINSABC, ESLR +from __future__ import absolute_import +from .specialized import BRAINSCut, BRAINSROIAuto, BRAINSConstellationDetector, BRAINSCreateLabelMapFromProbabilityMaps, BinaryMaskEditorBasedOnLandmarks, BRAINSMultiSTAPLE, BRAINSABC, ESLR diff --git a/nipype/interfaces/semtools/segmentation/specialized.py b/nipype/interfaces/semtools/segmentation/specialized.py index 7d29c59dfd..2454cd3c18 100644 --- a/nipype/interfaces/semtools/segmentation/specialized.py +++ b/nipype/interfaces/semtools/segmentation/specialized.py @@ -2,9 +2,12 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + class BRAINSCutInputSpec(CommandLineInputSpec): netConfiguration = File(desc="XML File defining BRAINSCut parameters. OLD NAME. PLEASE USE modelConfigurationFilename instead.", exists=True, argstr="--netConfiguration %s") diff --git a/nipype/interfaces/semtools/segmentation/tests/__init__.py b/nipype/interfaces/semtools/segmentation/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 7f9ac18c5a..30d070119d 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BRAINSABC +from .....testing import assert_equal +from ..specialized import BRAINSABC def test_BRAINSABC_inputs(): input_map = dict(args=dict(argstr='%s', @@ -87,8 +87,8 @@ def test_BRAINSABC_inputs(): ) inputs = BRAINSABC.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSABC_outputs(): @@ -103,7 +103,7 @@ def test_BRAINSABC_outputs(): ) outputs = BRAINSABC.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index c9f0b2e95c..208f6ceba9 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BRAINSConstellationDetector +from .....testing import assert_equal +from ..specialized import BRAINSConstellationDetector def test_BRAINSConstellationDetector_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', @@ -111,8 +111,8 @@ def test_BRAINSConstellationDetector_inputs(): ) inputs = BRAINSConstellationDetector.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSConstellationDetector_outputs(): @@ -129,7 +129,7 @@ def test_BRAINSConstellationDetector_outputs(): ) outputs = BRAINSConstellationDetector.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 3284ccf294..d583f7458c 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BRAINSCreateLabelMapFromProbabilityMaps +from .....testing import assert_equal +from ..specialized import BRAINSCreateLabelMapFromProbabilityMaps def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): ) inputs = BRAINSCreateLabelMapFromProbabilityMaps.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): @@ -44,7 +44,7 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): ) outputs = BRAINSCreateLabelMapFromProbabilityMaps.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index d0c5396682..ce6273d108 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BRAINSCut +from .....testing import assert_equal +from ..specialized import BRAINSCut def test_BRAINSCut_inputs(): input_map = dict(NoTrainingVectorShuffling=dict(argstr='--NoTrainingVectorShuffling ', @@ -50,15 +50,15 @@ def test_BRAINSCut_inputs(): ) inputs = BRAINSCut.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSCut_outputs(): output_map = dict() outputs = BRAINSCut.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 56969b572d..ad12b7a00d 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BRAINSMultiSTAPLE +from .....testing import assert_equal +from ..specialized import BRAINSMultiSTAPLE def test_BRAINSMultiSTAPLE_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,8 +34,8 @@ def test_BRAINSMultiSTAPLE_inputs(): ) inputs = BRAINSMultiSTAPLE.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSMultiSTAPLE_outputs(): @@ -44,7 +44,7 @@ def test_BRAINSMultiSTAPLE_outputs(): ) outputs = BRAINSMultiSTAPLE.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index dc0c3264dd..10b4df6a6a 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BRAINSROIAuto +from .....testing import assert_equal +from ..specialized import BRAINSROIAuto def test_BRAINSROIAuto_inputs(): input_map = dict(ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', @@ -40,8 +40,8 @@ def test_BRAINSROIAuto_inputs(): ) inputs = BRAINSROIAuto.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSROIAuto_outputs(): @@ -50,7 +50,7 @@ def test_BRAINSROIAuto_outputs(): ) outputs = BRAINSROIAuto.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index 3c9307af94..d6dcaee899 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import BinaryMaskEditorBasedOnLandmarks +from .....testing import assert_equal +from ..specialized import BinaryMaskEditorBasedOnLandmarks def test_BinaryMaskEditorBasedOnLandmarks_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): ) inputs = BinaryMaskEditorBasedOnLandmarks.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BinaryMaskEditorBasedOnLandmarks_outputs(): @@ -44,7 +44,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_outputs(): ) outputs = BinaryMaskEditorBasedOnLandmarks.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 136b34b20c..8903cb7a29 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.segmentation.specialized import ESLR +from .....testing import assert_equal +from ..specialized import ESLR def test_ESLR_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_ESLR_inputs(): ) inputs = ESLR.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ESLR_outputs(): @@ -44,7 +44,7 @@ def test_ESLR_outputs(): ) outputs = ESLR.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/testing/__init__.py b/nipype/interfaces/semtools/testing/__init__.py index 2ceae41133..83ddac53d7 100644 --- a/nipype/interfaces/semtools/testing/__init__.py +++ b/nipype/interfaces/semtools/testing/__init__.py @@ -1,3 +1,4 @@ -from featuredetection import SphericalCoordinateGeneration -from landmarkscompare import LandmarksCompare -from generateaveragelmkfile import GenerateAverageLmkFile +from __future__ import absolute_import +from .featuredetection import SphericalCoordinateGeneration +from .landmarkscompare import LandmarksCompare +from .generateaveragelmkfile import GenerateAverageLmkFile diff --git a/nipype/interfaces/semtools/tests/__init__.py b/nipype/interfaces/semtools/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 6429a25e73..107767e57e 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.converters import DWICompare +from ....testing import assert_equal +from ..converters import DWICompare def test_DWICompare_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,15 +20,15 @@ def test_DWICompare_inputs(): ) inputs = DWICompare.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWICompare_outputs(): output_map = dict() outputs = DWICompare.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index b1ec948644..6160e9f642 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.converters import DWISimpleCompare +from ....testing import assert_equal +from ..converters import DWISimpleCompare def test_DWISimpleCompare_inputs(): input_map = dict(args=dict(argstr='%s', @@ -22,15 +22,15 @@ def test_DWISimpleCompare_inputs(): ) inputs = DWISimpleCompare.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWISimpleCompare_outputs(): output_map = dict() outputs = DWISimpleCompare.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index 8651a8abcc..48a7310d00 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.featurecreator import GenerateCsfClippedFromClassifiedImage +from ....testing import assert_equal +from ..featurecreator import GenerateCsfClippedFromClassifiedImage def test_GenerateCsfClippedFromClassifiedImage_inputs(): input_map = dict(args=dict(argstr='%s', @@ -21,8 +21,8 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): ) inputs = GenerateCsfClippedFromClassifiedImage.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateCsfClippedFromClassifiedImage_outputs(): @@ -30,7 +30,7 @@ def test_GenerateCsfClippedFromClassifiedImage_outputs(): ) outputs = GenerateCsfClippedFromClassifiedImage.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/__init__.py b/nipype/interfaces/semtools/utilities/__init__.py index 2416b5ee42..5bf1a40e4a 100644 --- a/nipype/interfaces/semtools/utilities/__init__.py +++ b/nipype/interfaces/semtools/utilities/__init__.py @@ -1 +1,2 @@ -from brains import BRAINSConstellationModeler, landmarksConstellationWeights, BRAINSTrimForegroundInDirection, BRAINSLmkTransform, BRAINSMush, BRAINSTransformConvert, landmarksConstellationAligner, BRAINSEyeDetector, BRAINSLinearModelerEPCA, BRAINSInitializedControlPoints, CleanUpOverlapLabels, BRAINSClipInferior, GenerateLabelMapFromProbabilityMap, BRAINSAlignMSP, BRAINSLandmarkInitializer, insertMidACPCpoint, BRAINSSnapShotWriter, JointHistogram, ShuffleVectorsModule, ImageRegionPlotter +from __future__ import absolute_import +from .brains import BRAINSConstellationModeler, landmarksConstellationWeights, BRAINSTrimForegroundInDirection, BRAINSLmkTransform, BRAINSMush, BRAINSTransformConvert, landmarksConstellationAligner, BRAINSEyeDetector, BRAINSLinearModelerEPCA, BRAINSInitializedControlPoints, CleanUpOverlapLabels, BRAINSClipInferior, GenerateLabelMapFromProbabilityMap, BRAINSAlignMSP, BRAINSLandmarkInitializer, insertMidACPCpoint, BRAINSSnapShotWriter, JointHistogram, ShuffleVectorsModule, ImageRegionPlotter diff --git a/nipype/interfaces/semtools/utilities/brains.py b/nipype/interfaces/semtools/utilities/brains.py index 7ac72ddf19..e7402da5a4 100644 --- a/nipype/interfaces/semtools/utilities/brains.py +++ b/nipype/interfaces/semtools/utilities/brains.py @@ -2,9 +2,13 @@ """Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.""" -from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath import os +from ...base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, + TraitedSpec, File, Directory, traits, isdefined, + InputMultiPath, OutputMultiPath) + + class BRAINSConstellationModelerInputSpec(CommandLineInputSpec): verbose = traits.Bool(desc=", Show more verbose output, ", argstr="--verbose ") inputTrainingList = File(desc=", Setup file, giving all parameters for training up a template model for each landmark., ", exists=True, argstr="--inputTrainingList %s") diff --git a/nipype/interfaces/semtools/utilities/tests/__init__.py b/nipype/interfaces/semtools/utilities/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index c0f421a594..2d04886661 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSAlignMSP +from .....testing import assert_equal +from ..brains import BRAINSAlignMSP def test_BRAINSAlignMSP_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', @@ -43,8 +43,8 @@ def test_BRAINSAlignMSP_inputs(): ) inputs = BRAINSAlignMSP.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSAlignMSP_outputs(): @@ -53,7 +53,7 @@ def test_BRAINSAlignMSP_outputs(): ) outputs = BRAINSAlignMSP.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index 8d0dcac4a5..9952b24563 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSClipInferior +from .....testing import assert_equal +from ..brains import BRAINSClipInferior def test_BRAINSClipInferior_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', @@ -27,8 +27,8 @@ def test_BRAINSClipInferior_inputs(): ) inputs = BRAINSClipInferior.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSClipInferior_outputs(): @@ -36,7 +36,7 @@ def test_BRAINSClipInferior_outputs(): ) outputs = BRAINSClipInferior.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index 7ac11bfedb..f18173e992 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSConstellationModeler +from .....testing import assert_equal +from ..brains import BRAINSConstellationModeler def test_BRAINSConstellationModeler_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', @@ -45,8 +45,8 @@ def test_BRAINSConstellationModeler_inputs(): ) inputs = BRAINSConstellationModeler.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSConstellationModeler_outputs(): @@ -55,7 +55,7 @@ def test_BRAINSConstellationModeler_outputs(): ) outputs = BRAINSConstellationModeler.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index 2003b3d976..83a26253c6 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSEyeDetector +from .....testing import assert_equal +from ..brains import BRAINSEyeDetector def test_BRAINSEyeDetector_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_BRAINSEyeDetector_inputs(): ) inputs = BRAINSEyeDetector.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSEyeDetector_outputs(): @@ -34,7 +34,7 @@ def test_BRAINSEyeDetector_outputs(): ) outputs = BRAINSEyeDetector.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index 0311d80ce9..70672b58a6 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSInitializedControlPoints +from .....testing import assert_equal +from ..brains import BRAINSInitializedControlPoints def test_BRAINSInitializedControlPoints_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_BRAINSInitializedControlPoints_inputs(): ) inputs = BRAINSInitializedControlPoints.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSInitializedControlPoints_outputs(): @@ -40,7 +40,7 @@ def test_BRAINSInitializedControlPoints_outputs(): ) outputs = BRAINSInitializedControlPoints.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 9b39687ce0..e006d86724 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSLandmarkInitializer +from .....testing import assert_equal +from ..brains import BRAINSLandmarkInitializer def test_BRAINSLandmarkInitializer_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_BRAINSLandmarkInitializer_inputs(): ) inputs = BRAINSLandmarkInitializer.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSLandmarkInitializer_outputs(): @@ -34,7 +34,7 @@ def test_BRAINSLandmarkInitializer_outputs(): ) outputs = BRAINSLandmarkInitializer.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index a75aa8c0b0..8738c68876 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSLinearModelerEPCA +from .....testing import assert_equal +from ..brains import BRAINSLinearModelerEPCA def test_BRAINSLinearModelerEPCA_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,15 +20,15 @@ def test_BRAINSLinearModelerEPCA_inputs(): ) inputs = BRAINSLinearModelerEPCA.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSLinearModelerEPCA_outputs(): output_map = dict() outputs = BRAINSLinearModelerEPCA.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 4b10a5bcf3..71643b90d3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSLmkTransform +from .....testing import assert_equal +from ..brains import BRAINSLmkTransform def test_BRAINSLmkTransform_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_BRAINSLmkTransform_inputs(): ) inputs = BRAINSLmkTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSLmkTransform_outputs(): @@ -42,7 +42,7 @@ def test_BRAINSLmkTransform_outputs(): ) outputs = BRAINSLmkTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 795554ecd1..1137807abc 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSMush +from .....testing import assert_equal +from ..brains import BRAINSMush def test_BRAINSMush_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_BRAINSMush_inputs(): ) inputs = BRAINSMush.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSMush_outputs(): @@ -65,7 +65,7 @@ def test_BRAINSMush_outputs(): ) outputs = BRAINSMush.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index 94dfc6ca06..c3dc623af4 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSSnapShotWriter +from .....testing import assert_equal +from ..brains import BRAINSSnapShotWriter def test_BRAINSSnapShotWriter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_BRAINSSnapShotWriter_inputs(): ) inputs = BRAINSSnapShotWriter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSSnapShotWriter_outputs(): @@ -44,7 +44,7 @@ def test_BRAINSSnapShotWriter_outputs(): ) outputs = BRAINSSnapShotWriter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index af1e3cb03e..262c752e4b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSTransformConvert +from .....testing import assert_equal +from ..brains import BRAINSTransformConvert def test_BRAINSTransformConvert_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_BRAINSTransformConvert_inputs(): ) inputs = BRAINSTransformConvert.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSTransformConvert_outputs(): @@ -40,7 +40,7 @@ def test_BRAINSTransformConvert_outputs(): ) outputs = BRAINSTransformConvert.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index 6f1d120891..e9da3f550d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import BRAINSTrimForegroundInDirection +from .....testing import assert_equal +from ..brains import BRAINSTrimForegroundInDirection def test_BRAINSTrimForegroundInDirection_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', @@ -33,8 +33,8 @@ def test_BRAINSTrimForegroundInDirection_inputs(): ) inputs = BRAINSTrimForegroundInDirection.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSTrimForegroundInDirection_outputs(): @@ -42,7 +42,7 @@ def test_BRAINSTrimForegroundInDirection_outputs(): ) outputs = BRAINSTrimForegroundInDirection.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py index 1a307e6436..d946909659 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import CleanUpOverlapLabels +from .....testing import assert_equal +from ..brains import CleanUpOverlapLabels def test_CleanUpOverlapLabels_inputs(): input_map = dict(args=dict(argstr='%s', @@ -21,8 +21,8 @@ def test_CleanUpOverlapLabels_inputs(): ) inputs = CleanUpOverlapLabels.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CleanUpOverlapLabels_outputs(): @@ -30,7 +30,7 @@ def test_CleanUpOverlapLabels_outputs(): ) outputs = CleanUpOverlapLabels.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index 9defff49a1..4000b9b184 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import FindCenterOfBrain +from .....testing import assert_equal +from ..brains import FindCenterOfBrain def test_FindCenterOfBrain_inputs(): input_map = dict(args=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_FindCenterOfBrain_inputs(): ) inputs = FindCenterOfBrain.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FindCenterOfBrain_outputs(): @@ -68,7 +68,7 @@ def test_FindCenterOfBrain_outputs(): ) outputs = FindCenterOfBrain.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index a247997044..92fe22f2aa 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import GenerateLabelMapFromProbabilityMap +from .....testing import assert_equal +from ..brains import GenerateLabelMapFromProbabilityMap def test_GenerateLabelMapFromProbabilityMap_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): ) inputs = GenerateLabelMapFromProbabilityMap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GenerateLabelMapFromProbabilityMap_outputs(): @@ -32,7 +32,7 @@ def test_GenerateLabelMapFromProbabilityMap_outputs(): ) outputs = GenerateLabelMapFromProbabilityMap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 290c4faddf..290476cc71 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import ImageRegionPlotter +from .....testing import assert_equal +from ..brains import ImageRegionPlotter def test_ImageRegionPlotter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -34,15 +34,15 @@ def test_ImageRegionPlotter_inputs(): ) inputs = ImageRegionPlotter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageRegionPlotter_outputs(): output_map = dict() outputs = ImageRegionPlotter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index 9cdd69595c..f78ebbb4ec 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import JointHistogram +from .....testing import assert_equal +from ..brains import JointHistogram def test_JointHistogram_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,15 +28,15 @@ def test_JointHistogram_inputs(): ) inputs = JointHistogram.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JointHistogram_outputs(): output_map = dict() outputs = JointHistogram.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 98dfd45f23..9fce96a5e1 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import ShuffleVectorsModule +from .....testing import assert_equal +from ..brains import ShuffleVectorsModule def test_ShuffleVectorsModule_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_ShuffleVectorsModule_inputs(): ) inputs = ShuffleVectorsModule.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ShuffleVectorsModule_outputs(): @@ -32,7 +32,7 @@ def test_ShuffleVectorsModule_outputs(): ) outputs = ShuffleVectorsModule.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index f35f0a2ad3..274ed3460d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import fcsv_to_hdf5 +from .....testing import assert_equal +from ..brains import fcsv_to_hdf5 def test_fcsv_to_hdf5_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_fcsv_to_hdf5_inputs(): ) inputs = fcsv_to_hdf5.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_fcsv_to_hdf5_outputs(): @@ -40,7 +40,7 @@ def test_fcsv_to_hdf5_outputs(): ) outputs = fcsv_to_hdf5.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index 9a5f9c184f..27be5441f5 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import insertMidACPCpoint +from .....testing import assert_equal +from ..brains import insertMidACPCpoint def test_insertMidACPCpoint_inputs(): input_map = dict(args=dict(argstr='%s', @@ -21,8 +21,8 @@ def test_insertMidACPCpoint_inputs(): ) inputs = insertMidACPCpoint.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_insertMidACPCpoint_outputs(): @@ -30,7 +30,7 @@ def test_insertMidACPCpoint_outputs(): ) outputs = insertMidACPCpoint.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index 5f9d02ad2f..c8246f482c 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import landmarksConstellationAligner +from .....testing import assert_equal +from ..brains import landmarksConstellationAligner def test_landmarksConstellationAligner_inputs(): input_map = dict(args=dict(argstr='%s', @@ -21,8 +21,8 @@ def test_landmarksConstellationAligner_inputs(): ) inputs = landmarksConstellationAligner.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_landmarksConstellationAligner_outputs(): @@ -30,7 +30,7 @@ def test_landmarksConstellationAligner_outputs(): ) outputs = landmarksConstellationAligner.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index 5424ec92e4..e4db760aab 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.semtools.utilities.brains import landmarksConstellationWeights +from .....testing import assert_equal +from ..brains import landmarksConstellationWeights def test_landmarksConstellationWeights_inputs(): input_map = dict(LLSModel=dict(argstr='--LLSModel %s', @@ -25,8 +25,8 @@ def test_landmarksConstellationWeights_inputs(): ) inputs = landmarksConstellationWeights.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_landmarksConstellationWeights_outputs(): @@ -34,7 +34,7 @@ def test_landmarksConstellationWeights_outputs(): ) outputs = landmarksConstellationWeights.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/__init__.py b/nipype/interfaces/slicer/__init__.py index 5261e22ebc..84fd7de4b7 100644 --- a/nipype/interfaces/slicer/__init__.py +++ b/nipype/interfaces/slicer/__init__.py @@ -1,9 +1,10 @@ -from diffusion import * -from segmentation import * -from filtering import * -from utilities import EMSegmentTransformToNewFormat -from surface import MergeModels, ModelToLabelMap, GrayscaleModelMaker, ProbeVolumeWithModel, LabelMapSmoothing, ModelMaker -from quantification import * -from legacy import * -from registration import * -from converters import DicomToNrrdConverter, OrientScalarVolume +from __future__ import absolute_import +from .diffusion import * +from .segmentation import * +from .filtering import * +from .utilities import EMSegmentTransformToNewFormat +from .surface import MergeModels, ModelToLabelMap, GrayscaleModelMaker, ProbeVolumeWithModel, LabelMapSmoothing, ModelMaker +from .quantification import * +from .legacy import * +from .registration import * +from .converters import DicomToNrrdConverter, OrientScalarVolume diff --git a/nipype/interfaces/slicer/diffusion/__init__.py b/nipype/interfaces/slicer/diffusion/__init__.py index 346997356d..e8ba6f01c9 100644 --- a/nipype/interfaces/slicer/diffusion/__init__.py +++ b/nipype/interfaces/slicer/diffusion/__init__.py @@ -1 +1,2 @@ -from diffusion import ResampleDTIVolume, DWIRicianLMMSEFilter, TractographyLabelMapSeeding, DWIJointRicianLMMSEFilter, DiffusionWeightedVolumeMasking, DTIimport, DWIToDTIEstimation, DiffusionTensorScalarMeasurements, DTIexport +from __future__ import absolute_import +from .diffusion import ResampleDTIVolume, DWIRicianLMMSEFilter, TractographyLabelMapSeeding, DWIJointRicianLMMSEFilter, DiffusionWeightedVolumeMasking, DTIimport, DWIToDTIEstimation, DiffusionTensorScalarMeasurements, DTIexport diff --git a/nipype/interfaces/slicer/diffusion/tests/__init__.py b/nipype/interfaces/slicer/diffusion/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index e411517e5b..31635cae6c 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DTIexport +from .....testing import assert_equal +from ..diffusion import DTIexport def test_DTIexport_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_DTIexport_inputs(): ) inputs = DTIexport.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTIexport_outputs(): @@ -33,7 +33,7 @@ def test_DTIexport_outputs(): ) outputs = DTIexport.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index cc452ebf56..5b5fd34acc 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DTIimport +from .....testing import assert_equal +from ..diffusion import DTIimport def test_DTIimport_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_DTIimport_inputs(): ) inputs = DTIimport.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DTIimport_outputs(): @@ -35,7 +35,7 @@ def test_DTIimport_outputs(): ) outputs = DTIimport.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index 41653ee907..c37d94420e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DWIJointRicianLMMSEFilter +from .....testing import assert_equal +from ..diffusion import DWIJointRicianLMMSEFilter def test_DWIJointRicianLMMSEFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_DWIJointRicianLMMSEFilter_inputs(): ) inputs = DWIJointRicianLMMSEFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWIJointRicianLMMSEFilter_outputs(): @@ -43,7 +43,7 @@ def test_DWIJointRicianLMMSEFilter_outputs(): ) outputs = DWIJointRicianLMMSEFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index d8570c6d25..a608997e0c 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DWIRicianLMMSEFilter +from .....testing import assert_equal +from ..diffusion import DWIRicianLMMSEFilter def test_DWIRicianLMMSEFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_DWIRicianLMMSEFilter_inputs(): ) inputs = DWIRicianLMMSEFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWIRicianLMMSEFilter_outputs(): @@ -55,7 +55,7 @@ def test_DWIRicianLMMSEFilter_outputs(): ) outputs = DWIRicianLMMSEFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index fd9c07352b..ce150df698 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DWIToDTIEstimation +from .....testing import assert_equal +from ..diffusion import DWIToDTIEstimation def test_DWIToDTIEstimation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_DWIToDTIEstimation_inputs(): ) inputs = DWIToDTIEstimation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWIToDTIEstimation_outputs(): @@ -45,7 +45,7 @@ def test_DWIToDTIEstimation_outputs(): ) outputs = DWIToDTIEstimation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index ae73730f34..c7598a94ee 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DiffusionTensorScalarMeasurements +from .....testing import assert_equal +from ..diffusion import DiffusionTensorScalarMeasurements def test_DiffusionTensorScalarMeasurements_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_DiffusionTensorScalarMeasurements_inputs(): ) inputs = DiffusionTensorScalarMeasurements.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DiffusionTensorScalarMeasurements_outputs(): @@ -35,7 +35,7 @@ def test_DiffusionTensorScalarMeasurements_outputs(): ) outputs = DiffusionTensorScalarMeasurements.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index f0993de70c..b6f8e07d8a 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import DiffusionWeightedVolumeMasking +from .....testing import assert_equal +from ..diffusion import DiffusionWeightedVolumeMasking def test_DiffusionWeightedVolumeMasking_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_DiffusionWeightedVolumeMasking_inputs(): ) inputs = DiffusionWeightedVolumeMasking.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DiffusionWeightedVolumeMasking_outputs(): @@ -43,7 +43,7 @@ def test_DiffusionWeightedVolumeMasking_outputs(): ) outputs = DiffusionWeightedVolumeMasking.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 87c9baaf6a..976409cd75 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import ResampleDTIVolume +from .....testing import assert_equal +from ..diffusion import ResampleDTIVolume def test_ResampleDTIVolume_inputs(): input_map = dict(Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', @@ -75,8 +75,8 @@ def test_ResampleDTIVolume_inputs(): ) inputs = ResampleDTIVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ResampleDTIVolume_outputs(): @@ -85,7 +85,7 @@ def test_ResampleDTIVolume_outputs(): ) outputs = ResampleDTIVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index c2f31abb9b..b9ec5ec713 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.diffusion.diffusion import TractographyLabelMapSeeding +from .....testing import assert_equal +from ..diffusion import TractographyLabelMapSeeding def test_TractographyLabelMapSeeding_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -54,8 +54,8 @@ def test_TractographyLabelMapSeeding_inputs(): ) inputs = TractographyLabelMapSeeding.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TractographyLabelMapSeeding_outputs(): @@ -65,7 +65,7 @@ def test_TractographyLabelMapSeeding_outputs(): ) outputs = TractographyLabelMapSeeding.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/__init__.py b/nipype/interfaces/slicer/filtering/__init__.py index 3cce465777..33c18db51a 100644 --- a/nipype/interfaces/slicer/filtering/__init__.py +++ b/nipype/interfaces/slicer/filtering/__init__.py @@ -1,11 +1,12 @@ -from morphology import GrayscaleGrindPeakImageFilter, GrayscaleFillHoleImageFilter -from denoising import GradientAnisotropicDiffusion, CurvatureAnisotropicDiffusion, GaussianBlurImageFilter, MedianImageFilter -from arithmetic import MultiplyScalarVolumes, MaskScalarVolume, SubtractScalarVolumes, AddScalarVolumes, CastScalarVolume -from extractskeleton import ExtractSkeleton -from histogrammatching import HistogramMatching -from thresholdscalarvolume import ThresholdScalarVolume -from n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection -from checkerboardfilter import CheckerBoardFilter -from imagelabelcombine import ImageLabelCombine -from votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter -from resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume +from __future__ import absolute_import +from .morphology import GrayscaleGrindPeakImageFilter, GrayscaleFillHoleImageFilter +from .denoising import GradientAnisotropicDiffusion, CurvatureAnisotropicDiffusion, GaussianBlurImageFilter, MedianImageFilter +from .arithmetic import MultiplyScalarVolumes, MaskScalarVolume, SubtractScalarVolumes, AddScalarVolumes, CastScalarVolume +from .extractskeleton import ExtractSkeleton +from .histogrammatching import HistogramMatching +from .thresholdscalarvolume import ThresholdScalarVolume +from .n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection +from .checkerboardfilter import CheckerBoardFilter +from .imagelabelcombine import ImageLabelCombine +from .votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter +from .resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume diff --git a/nipype/interfaces/slicer/filtering/tests/__init__.py b/nipype/interfaces/slicer/filtering/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 45a9c3db16..b251028a8f 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.arithmetic import AddScalarVolumes +from .....testing import assert_equal +from ..arithmetic import AddScalarVolumes def test_AddScalarVolumes_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_AddScalarVolumes_inputs(): ) inputs = AddScalarVolumes.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AddScalarVolumes_outputs(): @@ -38,7 +38,7 @@ def test_AddScalarVolumes_outputs(): ) outputs = AddScalarVolumes.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index 2b8908610d..e3785f9724 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.arithmetic import CastScalarVolume +from .....testing import assert_equal +from ..arithmetic import CastScalarVolume def test_CastScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_CastScalarVolume_inputs(): ) inputs = CastScalarVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CastScalarVolume_outputs(): @@ -35,7 +35,7 @@ def test_CastScalarVolume_outputs(): ) outputs = CastScalarVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 594810dbe9..4852564e6d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.checkerboardfilter import CheckerBoardFilter +from .....testing import assert_equal +from ..checkerboardfilter import CheckerBoardFilter def test_CheckerBoardFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_CheckerBoardFilter_inputs(): ) inputs = CheckerBoardFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CheckerBoardFilter_outputs(): @@ -39,7 +39,7 @@ def test_CheckerBoardFilter_outputs(): ) outputs = CheckerBoardFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index e9180820e6..d0e36b88cd 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.denoising import CurvatureAnisotropicDiffusion +from .....testing import assert_equal +from ..denoising import CurvatureAnisotropicDiffusion def test_CurvatureAnisotropicDiffusion_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_CurvatureAnisotropicDiffusion_inputs(): ) inputs = CurvatureAnisotropicDiffusion.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CurvatureAnisotropicDiffusion_outputs(): @@ -39,7 +39,7 @@ def test_CurvatureAnisotropicDiffusion_outputs(): ) outputs = CurvatureAnisotropicDiffusion.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index d10f92fcfe..453bea8ff9 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.extractskeleton import ExtractSkeleton +from .....testing import assert_equal +from ..extractskeleton import ExtractSkeleton def test_ExtractSkeleton_inputs(): input_map = dict(InputImageFileName=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_ExtractSkeleton_inputs(): ) inputs = ExtractSkeleton.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ExtractSkeleton_outputs(): @@ -41,7 +41,7 @@ def test_ExtractSkeleton_outputs(): ) outputs = ExtractSkeleton.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index 0241d3539e..efdfea9eea 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.denoising import GaussianBlurImageFilter +from .....testing import assert_equal +from ..denoising import GaussianBlurImageFilter def test_GaussianBlurImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_GaussianBlurImageFilter_inputs(): ) inputs = GaussianBlurImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GaussianBlurImageFilter_outputs(): @@ -35,7 +35,7 @@ def test_GaussianBlurImageFilter_outputs(): ) outputs = GaussianBlurImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index c91c154cd7..58b51833ee 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.denoising import GradientAnisotropicDiffusion +from .....testing import assert_equal +from ..denoising import GradientAnisotropicDiffusion def test_GradientAnisotropicDiffusion_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_GradientAnisotropicDiffusion_inputs(): ) inputs = GradientAnisotropicDiffusion.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GradientAnisotropicDiffusion_outputs(): @@ -39,7 +39,7 @@ def test_GradientAnisotropicDiffusion_outputs(): ) outputs = GradientAnisotropicDiffusion.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 33224894d3..81bf49025e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.morphology import GrayscaleFillHoleImageFilter +from .....testing import assert_equal +from ..morphology import GrayscaleFillHoleImageFilter def test_GrayscaleFillHoleImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_GrayscaleFillHoleImageFilter_inputs(): ) inputs = GrayscaleFillHoleImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GrayscaleFillHoleImageFilter_outputs(): @@ -33,7 +33,7 @@ def test_GrayscaleFillHoleImageFilter_outputs(): ) outputs = GrayscaleFillHoleImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 75ab253327..6b940e03f3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.morphology import GrayscaleGrindPeakImageFilter +from .....testing import assert_equal +from ..morphology import GrayscaleGrindPeakImageFilter def test_GrayscaleGrindPeakImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): ) inputs = GrayscaleGrindPeakImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GrayscaleGrindPeakImageFilter_outputs(): @@ -33,7 +33,7 @@ def test_GrayscaleGrindPeakImageFilter_outputs(): ) outputs = GrayscaleGrindPeakImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index dfdece81ce..bdf83e33e0 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.histogrammatching import HistogramMatching +from .....testing import assert_equal +from ..histogrammatching import HistogramMatching def test_HistogramMatching_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_HistogramMatching_inputs(): ) inputs = HistogramMatching.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_HistogramMatching_outputs(): @@ -42,7 +42,7 @@ def test_HistogramMatching_outputs(): ) outputs = HistogramMatching.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 82cc80a21a..1841c77696 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.imagelabelcombine import ImageLabelCombine +from .....testing import assert_equal +from ..imagelabelcombine import ImageLabelCombine def test_ImageLabelCombine_inputs(): input_map = dict(InputLabelMap_A=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_ImageLabelCombine_inputs(): ) inputs = ImageLabelCombine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ImageLabelCombine_outputs(): @@ -38,7 +38,7 @@ def test_ImageLabelCombine_outputs(): ) outputs = ImageLabelCombine.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index 217766f1d7..abbd67bf79 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.arithmetic import MaskScalarVolume +from .....testing import assert_equal +from ..arithmetic import MaskScalarVolume def test_MaskScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_MaskScalarVolume_inputs(): ) inputs = MaskScalarVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MaskScalarVolume_outputs(): @@ -40,7 +40,7 @@ def test_MaskScalarVolume_outputs(): ) outputs = MaskScalarVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 1f152ba57b..feb020d09b 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.denoising import MedianImageFilter +from .....testing import assert_equal +from ..denoising import MedianImageFilter def test_MedianImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_MedianImageFilter_inputs(): ) inputs = MedianImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MedianImageFilter_outputs(): @@ -36,7 +36,7 @@ def test_MedianImageFilter_outputs(): ) outputs = MedianImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index 4d9e6e3136..619af34f5e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.arithmetic import MultiplyScalarVolumes +from .....testing import assert_equal +from ..arithmetic import MultiplyScalarVolumes def test_MultiplyScalarVolumes_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_MultiplyScalarVolumes_inputs(): ) inputs = MultiplyScalarVolumes.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MultiplyScalarVolumes_outputs(): @@ -38,7 +38,7 @@ def test_MultiplyScalarVolumes_outputs(): ) outputs = MultiplyScalarVolumes.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index 2f9c553dd3..fe815b8c4e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection +from .....testing import assert_equal +from ..n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection def test_N4ITKBiasFieldCorrection_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,8 +45,8 @@ def test_N4ITKBiasFieldCorrection_inputs(): ) inputs = N4ITKBiasFieldCorrection.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_N4ITKBiasFieldCorrection_outputs(): @@ -55,7 +55,7 @@ def test_N4ITKBiasFieldCorrection_outputs(): ) outputs = N4ITKBiasFieldCorrection.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index 20c565eb08..b8fe840c58 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume +from .....testing import assert_equal +from ..resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume def test_ResampleScalarVectorDWIVolume_inputs(): input_map = dict(Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', @@ -71,8 +71,8 @@ def test_ResampleScalarVectorDWIVolume_inputs(): ) inputs = ResampleScalarVectorDWIVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ResampleScalarVectorDWIVolume_outputs(): @@ -81,7 +81,7 @@ def test_ResampleScalarVectorDWIVolume_outputs(): ) outputs = ResampleScalarVectorDWIVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 10b748c4d1..74d7d15497 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.arithmetic import SubtractScalarVolumes +from .....testing import assert_equal +from ..arithmetic import SubtractScalarVolumes def test_SubtractScalarVolumes_inputs(): input_map = dict(args=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_SubtractScalarVolumes_inputs(): ) inputs = SubtractScalarVolumes.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SubtractScalarVolumes_outputs(): @@ -38,7 +38,7 @@ def test_SubtractScalarVolumes_outputs(): ) outputs = SubtractScalarVolumes.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index 95ef07b0e8..fcbd6ceb2d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.thresholdscalarvolume import ThresholdScalarVolume +from .....testing import assert_equal +from ..thresholdscalarvolume import ThresholdScalarVolume def test_ThresholdScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -33,8 +33,8 @@ def test_ThresholdScalarVolume_inputs(): ) inputs = ThresholdScalarVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ThresholdScalarVolume_outputs(): @@ -43,7 +43,7 @@ def test_ThresholdScalarVolume_outputs(): ) outputs = ThresholdScalarVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 3d7becb51a..314873e5e3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.filtering.votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter +from .....testing import assert_equal +from ..votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter def test_VotingBinaryHoleFillingImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): ) inputs = VotingBinaryHoleFillingImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VotingBinaryHoleFillingImageFilter_outputs(): @@ -42,7 +42,7 @@ def test_VotingBinaryHoleFillingImageFilter_outputs(): ) outputs = VotingBinaryHoleFillingImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py index e801f9b7cf..d784e6f5fe 100644 --- a/nipype/interfaces/slicer/generate_classes.py +++ b/nipype/interfaces/slicer/generate_classes.py @@ -3,15 +3,18 @@ in the cli_modules.py file (and imported in __init__.py). For this to work correctly you must have your CLI executabes in $PATH""" +from __future__ import print_function + import xml.dom.minidom import subprocess import os from shutil import rmtree -from nipype.external import six import keyword python_keywords = keyword.kwlist # If c++ SEM module uses one of these key words as a command line parameter, we need to modify variable +from ...external.six import string_types + def force_to_valid_python_variable_name(old_name): """ Valid c++ names are not always valid in python, so @@ -47,8 +50,8 @@ def add_class_to_package(class_codes, class_names, module_name, package_dir): def crawl_code_struct(code_struct, package_dir): subpackages = [] - for k, v in code_struct.iteritems(): - if isinstance(v, six.string_types) or isinstance(v, unicode): + for k, v in code_struct.items(): + if isinstance(v, str) or isinstance(v, string_types): module_name = k.lower() class_name = k class_code = v @@ -57,8 +60,8 @@ def crawl_code_struct(code_struct, package_dir): else: l1 = {} l2 = {} - for key in v.keys(): - if (isinstance(v[key], six.string_types) or isinstance(v[key], unicode)): + for key in list(v.keys()): + if (isinstance(v[key], str) or isinstance(v[key], string_types)): l1[key] = v[key] else: l2[key] = v[key] @@ -74,13 +77,13 @@ def crawl_code_struct(code_struct, package_dir): os.mkdir(new_pkg_dir) crawl_code_struct(v, new_pkg_dir) if l1: - for ik, iv in l1.iteritems(): + for ik, iv in l1.items(): crawl_code_struct({ik: {ik: iv}}, new_pkg_dir) elif l1: v = l1 module_name = k.lower() add_class_to_package( - v.values(), v.keys(), module_name, package_dir) + list(v.values()), list(v.keys()), module_name, package_dir) if subpackages: f = open(os.path.join(package_dir, "setup.py"), 'w') f.write("""# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- @@ -292,7 +295,7 @@ def generate_class(module, launcher, strip_module_name_prefix=True, redirect_x = output_filenames_code = "_outputs_filenames = {" output_filenames_code += ",".join(["'%s':'%s'" % ( - key, value) for key, value in outputs_filenames.iteritems()]) + key, value) for key, value in outputs_filenames.items()]) output_filenames_code += "}" input_spec_code += "\n\n" @@ -344,8 +347,8 @@ def grab_xml(module, launcher, mipav_hacks=False): xmlReturnValue = xmlReturnValue.strip()[len("Error: Unable to set default atlas"):] try: dom = xml.dom.minidom.parseString(xmlReturnValue.strip()) - except Exception, e: - print xmlReturnValue.strip() + except Exception as e: + print(xmlReturnValue.strip()) raise e return dom # if ret.runtime.returncode == 0: @@ -356,8 +359,8 @@ def grab_xml(module, launcher, mipav_hacks=False): def parse_params(params): list = [] - for key, value in params.iteritems(): - if isinstance(value, six.string_types) or isinstance(value, unicode): + for key, value in params.items(): + if isinstance(value, string_types): list.append('%s="%s"' % (key, value.replace('"', "'"))) else: list.append('%s=%s' % (key, value)) diff --git a/nipype/interfaces/slicer/legacy/__init__.py b/nipype/interfaces/slicer/legacy/__init__.py index 800fa5a056..8071dab173 100644 --- a/nipype/interfaces/slicer/legacy/__init__.py +++ b/nipype/interfaces/slicer/legacy/__init__.py @@ -1,5 +1,6 @@ -from diffusion import * -from segmentation import OtsuThresholdSegmentation -from filtering import OtsuThresholdImageFilter, ResampleScalarVolume -from converters import BSplineToDeformationField -from registration import BSplineDeformableRegistration, AffineRegistration, MultiResolutionAffineRegistration, RigidRegistration, LinearRegistration, ExpertAutomatedRegistration +from __future__ import absolute_import +from .diffusion import * +from .segmentation import OtsuThresholdSegmentation +from .filtering import OtsuThresholdImageFilter, ResampleScalarVolume +from .converters import BSplineToDeformationField +from .registration import BSplineDeformableRegistration, AffineRegistration, MultiResolutionAffineRegistration, RigidRegistration, LinearRegistration, ExpertAutomatedRegistration diff --git a/nipype/interfaces/slicer/legacy/diffusion/__init__.py b/nipype/interfaces/slicer/legacy/diffusion/__init__.py index c1a762993e..f57a40fd2b 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/__init__.py +++ b/nipype/interfaces/slicer/legacy/diffusion/__init__.py @@ -1 +1,2 @@ -from denoising import DWIUnbiasedNonLocalMeansFilter +from __future__ import absolute_import +from .denoising import DWIUnbiasedNonLocalMeansFilter diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py b/nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index 51c72f7eb4..331399e3f2 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.diffusion.denoising import DWIUnbiasedNonLocalMeansFilter +from ......testing import assert_equal +from ..denoising import DWIUnbiasedNonLocalMeansFilter def test_DWIUnbiasedNonLocalMeansFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): ) inputs = DWIUnbiasedNonLocalMeansFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DWIUnbiasedNonLocalMeansFilter_outputs(): @@ -46,7 +46,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_outputs(): ) outputs = DWIUnbiasedNonLocalMeansFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/__init__.py b/nipype/interfaces/slicer/legacy/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index 9d8c24aa98..89be9520be 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.registration import AffineRegistration +from .....testing import assert_equal +from ..registration import AffineRegistration def test_AffineRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_AffineRegistration_inputs(): ) inputs = AffineRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_AffineRegistration_outputs(): @@ -52,7 +52,7 @@ def test_AffineRegistration_outputs(): ) outputs = AffineRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 9b83cfe88b..9210e0238c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.registration import BSplineDeformableRegistration +from .....testing import assert_equal +from ..registration import BSplineDeformableRegistration def test_BSplineDeformableRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', @@ -47,8 +47,8 @@ def test_BSplineDeformableRegistration_inputs(): ) inputs = BSplineDeformableRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BSplineDeformableRegistration_outputs(): @@ -58,7 +58,7 @@ def test_BSplineDeformableRegistration_outputs(): ) outputs = BSplineDeformableRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 840479b249..d955a87e03 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.converters import BSplineToDeformationField +from .....testing import assert_equal +from ..converters import BSplineToDeformationField def test_BSplineToDeformationField_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_BSplineToDeformationField_inputs(): ) inputs = BSplineToDeformationField.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BSplineToDeformationField_outputs(): @@ -32,7 +32,7 @@ def test_BSplineToDeformationField_outputs(): ) outputs = BSplineToDeformationField.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 26547da373..194c9889ae 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.registration import ExpertAutomatedRegistration +from .....testing import assert_equal +from ..registration import ExpertAutomatedRegistration def test_ExpertAutomatedRegistration_inputs(): input_map = dict(affineMaxIterations=dict(argstr='--affineMaxIterations %d', @@ -76,8 +76,8 @@ def test_ExpertAutomatedRegistration_inputs(): ) inputs = ExpertAutomatedRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ExpertAutomatedRegistration_outputs(): @@ -86,7 +86,7 @@ def test_ExpertAutomatedRegistration_outputs(): ) outputs = ExpertAutomatedRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index 90cc0bb7c7..4a305cf83f 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.registration import LinearRegistration +from .....testing import assert_equal +from ..registration import LinearRegistration def test_LinearRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', @@ -46,8 +46,8 @@ def test_LinearRegistration_inputs(): ) inputs = LinearRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_LinearRegistration_outputs(): @@ -56,7 +56,7 @@ def test_LinearRegistration_outputs(): ) outputs = LinearRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index 0f997c9c82..ad5d7a1c6d 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.registration import MultiResolutionAffineRegistration +from .....testing import assert_equal +from ..registration import MultiResolutionAffineRegistration def test_MultiResolutionAffineRegistration_inputs(): input_map = dict(args=dict(argstr='%s', @@ -42,8 +42,8 @@ def test_MultiResolutionAffineRegistration_inputs(): ) inputs = MultiResolutionAffineRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MultiResolutionAffineRegistration_outputs(): @@ -52,7 +52,7 @@ def test_MultiResolutionAffineRegistration_outputs(): ) outputs = MultiResolutionAffineRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index de858e3a4f..35be781ab1 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.filtering import OtsuThresholdImageFilter +from .....testing import assert_equal +from ..filtering import OtsuThresholdImageFilter def test_OtsuThresholdImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_OtsuThresholdImageFilter_inputs(): ) inputs = OtsuThresholdImageFilter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_OtsuThresholdImageFilter_outputs(): @@ -39,7 +39,7 @@ def test_OtsuThresholdImageFilter_outputs(): ) outputs = OtsuThresholdImageFilter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index 4c447abc86..98a54e95c9 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.segmentation import OtsuThresholdSegmentation +from .....testing import assert_equal +from ..segmentation import OtsuThresholdSegmentation def test_OtsuThresholdSegmentation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_OtsuThresholdSegmentation_inputs(): ) inputs = OtsuThresholdSegmentation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_OtsuThresholdSegmentation_outputs(): @@ -41,7 +41,7 @@ def test_OtsuThresholdSegmentation_outputs(): ) outputs = OtsuThresholdSegmentation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 76d6b1307b..ccaaed954d 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.filtering import ResampleScalarVolume +from .....testing import assert_equal +from ..filtering import ResampleScalarVolume def test_ResampleScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_ResampleScalarVolume_inputs(): ) inputs = ResampleScalarVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ResampleScalarVolume_outputs(): @@ -38,7 +38,7 @@ def test_ResampleScalarVolume_outputs(): ) outputs = ResampleScalarVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index b42c294b92..17a3e41a43 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.legacy.registration import RigidRegistration +from .....testing import assert_equal +from ..registration import RigidRegistration def test_RigidRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', @@ -48,8 +48,8 @@ def test_RigidRegistration_inputs(): ) inputs = RigidRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_RigidRegistration_outputs(): @@ -58,7 +58,7 @@ def test_RigidRegistration_outputs(): ) outputs = RigidRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/quantification/__init__.py b/nipype/interfaces/slicer/quantification/__init__.py index 3ebd3c71df..3a0d67b038 100644 --- a/nipype/interfaces/slicer/quantification/__init__.py +++ b/nipype/interfaces/slicer/quantification/__init__.py @@ -1,2 +1,3 @@ -from changequantification import IntensityDifferenceMetric -from petstandarduptakevaluecomputation import PETStandardUptakeValueComputation +from __future__ import absolute_import +from .changequantification import IntensityDifferenceMetric +from .petstandarduptakevaluecomputation import PETStandardUptakeValueComputation diff --git a/nipype/interfaces/slicer/quantification/tests/__init__.py b/nipype/interfaces/slicer/quantification/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index 4ff8f9d794..a0211daff0 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.quantification.changequantification import IntensityDifferenceMetric +from .....testing import assert_equal +from ..changequantification import IntensityDifferenceMetric def test_IntensityDifferenceMetric_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_IntensityDifferenceMetric_inputs(): ) inputs = IntensityDifferenceMetric.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_IntensityDifferenceMetric_outputs(): @@ -47,7 +47,7 @@ def test_IntensityDifferenceMetric_outputs(): ) outputs = IntensityDifferenceMetric.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index c500c5a8c5..75f63d3e47 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.quantification.petstandarduptakevaluecomputation import PETStandardUptakeValueComputation +from .....testing import assert_equal +from ..petstandarduptakevaluecomputation import PETStandardUptakeValueComputation def test_PETStandardUptakeValueComputation_inputs(): input_map = dict(OutputLabel=dict(argstr='--OutputLabel %s', @@ -37,8 +37,8 @@ def test_PETStandardUptakeValueComputation_inputs(): ) inputs = PETStandardUptakeValueComputation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PETStandardUptakeValueComputation_outputs(): @@ -46,7 +46,7 @@ def test_PETStandardUptakeValueComputation_outputs(): ) outputs = PETStandardUptakeValueComputation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/registration/__init__.py b/nipype/interfaces/slicer/registration/__init__.py index 9be7a69b1c..1d5349c291 100644 --- a/nipype/interfaces/slicer/registration/__init__.py +++ b/nipype/interfaces/slicer/registration/__init__.py @@ -1,3 +1,4 @@ -from specialized import ACPCTransform, FiducialRegistration, VBRAINSDemonWarp, BRAINSDemonWarp -from brainsresample import BRAINSResample -from brainsfit import BRAINSFit +from __future__ import absolute_import +from .specialized import ACPCTransform, FiducialRegistration, VBRAINSDemonWarp, BRAINSDemonWarp +from .brainsresample import BRAINSResample +from .brainsfit import BRAINSFit diff --git a/nipype/interfaces/slicer/registration/tests/__init__.py b/nipype/interfaces/slicer/registration/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 6a6a1f435d..972f70b17c 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.registration.specialized import ACPCTransform +from .....testing import assert_equal +from ..specialized import ACPCTransform def test_ACPCTransform_inputs(): input_map = dict(acpc=dict(argstr='--acpc %s...', @@ -25,8 +25,8 @@ def test_ACPCTransform_inputs(): ) inputs = ACPCTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ACPCTransform_outputs(): @@ -34,7 +34,7 @@ def test_ACPCTransform_outputs(): ) outputs = ACPCTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index ee72e72202..6bb0b716cc 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.registration.specialized import BRAINSDemonWarp +from .....testing import assert_equal +from ..specialized import BRAINSDemonWarp def test_BRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -106,8 +106,8 @@ def test_BRAINSDemonWarp_inputs(): ) inputs = BRAINSDemonWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSDemonWarp_outputs(): @@ -117,7 +117,7 @@ def test_BRAINSDemonWarp_outputs(): ) outputs = BRAINSDemonWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index 29a5987249..6aa9e0762e 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.registration.brainsfit import BRAINSFit +from .....testing import assert_equal +from ..brainsfit import BRAINSFit def test_BRAINSFit_inputs(): input_map = dict(NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ', @@ -151,8 +151,8 @@ def test_BRAINSFit_inputs(): ) inputs = BRAINSFit.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSFit_outputs(): @@ -166,7 +166,7 @@ def test_BRAINSFit_outputs(): ) outputs = BRAINSFit.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index dbc8897d75..9dd1c3c00a 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.registration.brainsresample import BRAINSResample +from .....testing import assert_equal +from ..brainsresample import BRAINSResample def test_BRAINSResample_inputs(): input_map = dict(args=dict(argstr='%s', @@ -40,8 +40,8 @@ def test_BRAINSResample_inputs(): ) inputs = BRAINSResample.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSResample_outputs(): @@ -49,7 +49,7 @@ def test_BRAINSResample_outputs(): ) outputs = BRAINSResample.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index 626bdb1751..24be6492df 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.registration.specialized import FiducialRegistration +from .....testing import assert_equal +from ..specialized import FiducialRegistration def test_FiducialRegistration_inputs(): input_map = dict(args=dict(argstr='%s', @@ -29,8 +29,8 @@ def test_FiducialRegistration_inputs(): ) inputs = FiducialRegistration.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FiducialRegistration_outputs(): @@ -38,7 +38,7 @@ def test_FiducialRegistration_outputs(): ) outputs = FiducialRegistration.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index c2bddf3bda..b0445a4380 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.registration.specialized import VBRAINSDemonWarp +from .....testing import assert_equal +from ..specialized import VBRAINSDemonWarp def test_VBRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', @@ -109,8 +109,8 @@ def test_VBRAINSDemonWarp_inputs(): ) inputs = VBRAINSDemonWarp.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VBRAINSDemonWarp_outputs(): @@ -120,7 +120,7 @@ def test_VBRAINSDemonWarp_outputs(): ) outputs = VBRAINSDemonWarp.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/segmentation/__init__.py b/nipype/interfaces/slicer/segmentation/__init__.py index d98c3767de..a88073aceb 100644 --- a/nipype/interfaces/slicer/segmentation/__init__.py +++ b/nipype/interfaces/slicer/segmentation/__init__.py @@ -1,2 +1,3 @@ -from specialized import RobustStatisticsSegmenter, EMSegmentCommandLine, BRAINSROIAuto -from simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation +from __future__ import absolute_import +from .specialized import RobustStatisticsSegmenter, EMSegmentCommandLine, BRAINSROIAuto +from .simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation diff --git a/nipype/interfaces/slicer/segmentation/tests/__init__.py b/nipype/interfaces/slicer/segmentation/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 7c1f2db24e..478804d4b3 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.segmentation.specialized import BRAINSROIAuto +from .....testing import assert_equal +from ..specialized import BRAINSROIAuto def test_BRAINSROIAuto_inputs(): input_map = dict(ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', @@ -36,8 +36,8 @@ def test_BRAINSROIAuto_inputs(): ) inputs = BRAINSROIAuto.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_BRAINSROIAuto_outputs(): @@ -46,7 +46,7 @@ def test_BRAINSROIAuto_outputs(): ) outputs = BRAINSROIAuto.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 0f3f6bcd75..defce68ae1 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.segmentation.specialized import EMSegmentCommandLine +from .....testing import assert_equal +from ..specialized import EMSegmentCommandLine def test_EMSegmentCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -61,8 +61,8 @@ def test_EMSegmentCommandLine_inputs(): ) inputs = EMSegmentCommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EMSegmentCommandLine_outputs(): @@ -72,7 +72,7 @@ def test_EMSegmentCommandLine_outputs(): ) outputs = EMSegmentCommandLine.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index dfe48a7a41..4754fafbab 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.segmentation.specialized import RobustStatisticsSegmenter +from .....testing import assert_equal +from ..specialized import RobustStatisticsSegmenter def test_RobustStatisticsSegmenter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -36,8 +36,8 @@ def test_RobustStatisticsSegmenter_inputs(): ) inputs = RobustStatisticsSegmenter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_RobustStatisticsSegmenter_outputs(): @@ -46,7 +46,7 @@ def test_RobustStatisticsSegmenter_outputs(): ) outputs = RobustStatisticsSegmenter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 23f1fc9fdb..2d8329724c 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.segmentation.simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation +from .....testing import assert_equal +from ..simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation def test_SimpleRegionGrowingSegmentation_inputs(): input_map = dict(args=dict(argstr='%s', @@ -37,8 +37,8 @@ def test_SimpleRegionGrowingSegmentation_inputs(): ) inputs = SimpleRegionGrowingSegmentation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SimpleRegionGrowingSegmentation_outputs(): @@ -47,7 +47,7 @@ def test_SimpleRegionGrowingSegmentation_outputs(): ) outputs = SimpleRegionGrowingSegmentation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/__init__.py b/nipype/interfaces/slicer/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index 15b5fe792f..a559ed194c 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.converters import DicomToNrrdConverter +from ....testing import assert_equal +from ..converters import DicomToNrrdConverter def test_DicomToNrrdConverter_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_DicomToNrrdConverter_inputs(): ) inputs = DicomToNrrdConverter.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DicomToNrrdConverter_outputs(): @@ -40,7 +40,7 @@ def test_DicomToNrrdConverter_outputs(): ) outputs = DicomToNrrdConverter.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 4393a16ca4..96b8a229dd 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.utilities import EMSegmentTransformToNewFormat +from ....testing import assert_equal +from ..utilities import EMSegmentTransformToNewFormat def test_EMSegmentTransformToNewFormat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -23,8 +23,8 @@ def test_EMSegmentTransformToNewFormat_inputs(): ) inputs = EMSegmentTransformToNewFormat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EMSegmentTransformToNewFormat_outputs(): @@ -32,7 +32,7 @@ def test_EMSegmentTransformToNewFormat_outputs(): ) outputs = EMSegmentTransformToNewFormat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index b965d5c309..6e724e0d1a 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.surface import GrayscaleModelMaker +from ....testing import assert_equal +from ..surface import GrayscaleModelMaker def test_GrayscaleModelMaker_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -35,8 +35,8 @@ def test_GrayscaleModelMaker_inputs(): ) inputs = GrayscaleModelMaker.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GrayscaleModelMaker_outputs(): @@ -45,7 +45,7 @@ def test_GrayscaleModelMaker_outputs(): ) outputs = GrayscaleModelMaker.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index 8f67dd65ed..00dfbb55c7 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.surface import LabelMapSmoothing +from ....testing import assert_equal +from ..surface import LabelMapSmoothing def test_LabelMapSmoothing_inputs(): input_map = dict(args=dict(argstr='%s', @@ -31,8 +31,8 @@ def test_LabelMapSmoothing_inputs(): ) inputs = LabelMapSmoothing.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_LabelMapSmoothing_outputs(): @@ -41,7 +41,7 @@ def test_LabelMapSmoothing_outputs(): ) outputs = LabelMapSmoothing.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 6ba6173a20..3d76bb87a1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.surface import MergeModels +from ....testing import assert_equal +from ..surface import MergeModels def test_MergeModels_inputs(): input_map = dict(Model1=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_MergeModels_inputs(): ) inputs = MergeModels.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MergeModels_outputs(): @@ -36,7 +36,7 @@ def test_MergeModels_outputs(): ) outputs = MergeModels.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index fa534ab87e..a3cfc53d86 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.surface import ModelMaker +from ....testing import assert_equal +from ..surface import ModelMaker def test_ModelMaker_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -55,8 +55,8 @@ def test_ModelMaker_inputs(): ) inputs = ModelMaker.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ModelMaker_outputs(): @@ -64,7 +64,7 @@ def test_ModelMaker_outputs(): ) outputs = ModelMaker.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 6cfdfbfa11..021ecb0738 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.surface import ModelToLabelMap +from ....testing import assert_equal +from ..surface import ModelToLabelMap def test_ModelToLabelMap_inputs(): input_map = dict(InputVolume=dict(argstr='%s', @@ -28,8 +28,8 @@ def test_ModelToLabelMap_inputs(): ) inputs = ModelToLabelMap.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ModelToLabelMap_outputs(): @@ -38,7 +38,7 @@ def test_ModelToLabelMap_outputs(): ) outputs = ModelToLabelMap.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index 5443d6be11..cb44b3685d 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.converters import OrientScalarVolume +from ....testing import assert_equal +from ..converters import OrientScalarVolume def test_OrientScalarVolume_inputs(): input_map = dict(args=dict(argstr='%s', @@ -25,8 +25,8 @@ def test_OrientScalarVolume_inputs(): ) inputs = OrientScalarVolume.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_OrientScalarVolume_outputs(): @@ -35,7 +35,7 @@ def test_OrientScalarVolume_outputs(): ) outputs = OrientScalarVolume.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index 4f9192417e..6a50d3364b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.surface import ProbeVolumeWithModel +from ....testing import assert_equal +from ..surface import ProbeVolumeWithModel def test_ProbeVolumeWithModel_inputs(): input_map = dict(InputModel=dict(argstr='%s', @@ -26,8 +26,8 @@ def test_ProbeVolumeWithModel_inputs(): ) inputs = ProbeVolumeWithModel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ProbeVolumeWithModel_outputs(): @@ -36,7 +36,7 @@ def test_ProbeVolumeWithModel_outputs(): ) outputs = ProbeVolumeWithModel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index 505bd12cc5..9002270b19 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.slicer.base import SlicerCommandLine +from ....testing import assert_equal +from ..base import SlicerCommandLine def test_SlicerCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -16,7 +16,7 @@ def test_SlicerCommandLine_inputs(): ) inputs = SlicerCommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index db56ef661d..cc31a7ad58 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -14,6 +14,10 @@ spm.SPMCommand().version """ +from __future__ import print_function +from builtins import range +from builtins import object + __docformat__ = 'restructuredtext' # Standard library imports @@ -24,14 +28,13 @@ from nibabel import load import numpy as np from scipy.io import savemat -from nipype.external import six # Local imports from ..base import (BaseInterface, traits, isdefined, InputMultiPath, BaseInterfaceInputSpec, Directory, Undefined) from ..matlab import MatlabCommand from ...utils import spm_docs as sd - +from ...external.six import string_types from ... import logging logger = logging.getLogger('interface') @@ -181,7 +184,7 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): """ try: out = mlab.run() - except (IOError, RuntimeError), e: + except (IOError, RuntimeError) as e: # if no Matlab at all -- exception could be raised # No Matlab -- no spm logger.debug(str(e)) @@ -200,7 +203,7 @@ def no_spm(): used with nosetests skipif to skip tests that will fail if spm is not installed""" - if Info.version() is None or 'NIPYPE_NO_MATLAB' in os.environ: + if 'NIPYPE_NO_MATLAB' in os.environ or Info.version() is None: return True else: return False @@ -330,7 +333,7 @@ def _format_arg(self, opt, spec, val): def _parse_inputs(self, skip=()): spmdict = {} metadata = dict(field=lambda t: t is not None) - for name, spec in self.inputs.traits(**metadata).items(): + for name, spec in list(self.inputs.traits(**metadata).items()): if skip and name in skip: continue value = getattr(self.inputs, name) @@ -341,7 +344,7 @@ def _parse_inputs(self, skip=()): fields = field.split('.') dictref = spmdict for f in fields[:-1]: - if f not in dictref.keys(): + if f not in list(dictref.keys()): dictref[f] = {} dictref = dictref[f] dictref[fields[-1]] = self._format_arg(name, spec, value) @@ -366,7 +369,7 @@ def _reformat_dict_for_savemat(self, contents): """ newdict = {} try: - for key, value in contents.items(): + for key, value in list(contents.items()): if isinstance(value, dict): if value: newdict[key] = self._reformat_dict_for_savemat(value) @@ -376,7 +379,7 @@ def _reformat_dict_for_savemat(self, contents): return [newdict] except TypeError: - print 'Requires dict input' + print('Requires dict input') def _generate_job(self, prefix='', contents=None): """Recursive function to generate spm job specification as a string @@ -403,7 +406,7 @@ def _generate_job(self, prefix='', contents=None): jobstring += self._generate_job(newprefix, value) return jobstring if isinstance(contents, dict): - for key, value in contents.items(): + for key, value in list(contents.items()): newprefix = "%s.%s" % (prefix, key) jobstring += self._generate_job(newprefix, value) return jobstring @@ -417,7 +420,7 @@ def _generate_job(self, prefix='', contents=None): if isinstance(val, np.ndarray): jobstring += self._generate_job(prefix=None, contents=val) - elif isinstance(val, six.string_types): + elif isinstance(val, string_types): jobstring += '\'%s\';...\n' % (val) else: jobstring += '%s;...\n' % str(val) @@ -432,7 +435,7 @@ def _generate_job(self, prefix='', contents=None): jobstring += self._generate_job(newprefix, val[field]) return jobstring - if isinstance(contents, six.string_types): + if isinstance(contents, string_types): jobstring += "%s = '%s';\n" % (prefix, contents) return jobstring jobstring += "%s = %s;\n" % (prefix, str(contents)) diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py index 8585147765..71fc268565 100644 --- a/nipype/interfaces/spm/model.py +++ b/nipype/interfaces/spm/model.py @@ -20,16 +20,15 @@ # Third-party imports import numpy as np import scipy.io as sio -from nipype.external import six # Local imports -from nipype.interfaces.base import (Bunch, traits, TraitedSpec, File, Directory, - OutputMultiPath, InputMultiPath, isdefined) -from nipype.interfaces.spm.base import (SPMCommand, SPMCommandInputSpec, - scans_for_fnames) -from nipype.utils.filemanip import (filename_to_list, list_to_filename, - split_filename) - +from .base import (SPMCommand, SPMCommandInputSpec, + scans_for_fnames) +from ..base import (Bunch, traits, TraitedSpec, File, Directory, + OutputMultiPath, InputMultiPath, isdefined) +from ...external.six import string_types +from ...utils.filemanip import (filename_to_list, list_to_filename, + split_filename) from ... import logging logger = logging.getLogger('interface') @@ -201,7 +200,7 @@ def _format_arg(self, opt, spec, val): if opt == 'spm_mat_file': return np.array([str(val)], dtype=object) if opt == 'estimation_method': - if isinstance(val, six.string_types): + if isinstance(val, string_types): return {'%s' % val: 1} else: return val @@ -765,7 +764,7 @@ def _format_arg(self, opt, spec, val): 'centering': 'iCC'} for dictitem in val: outdict = {} - for key, keyval in dictitem.items(): + for key, keyval in list(dictitem.items()): outdict[mapping[key]] = keyval outlist.append(outdict) return outlist @@ -921,7 +920,7 @@ def _format_arg(self, opt, spec, val): 'centering': 'iCC'} for dictitem in val: outdict = {} - for key, keyval in dictitem.items(): + for key, keyval in list(dictitem.items()): outdict[mapping[key]] = keyval outlist.append(outdict) return outlist diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py index f6c9307d52..77f460e2c1 100644 --- a/nipype/interfaces/spm/preprocess.py +++ b/nipype/interfaces/spm/preprocess.py @@ -9,6 +9,8 @@ >>> os.chdir(datadir) """ +from builtins import range + __docformat__ = 'restructuredtext' # Standard library imports @@ -74,7 +76,7 @@ class SliceTiming(SPMCommand): >>> st.inputs.num_slices = 32 >>> st.inputs.time_repetition = 6.0 >>> st.inputs.time_acquisition = 6. - 6./32. - >>> st.inputs.slice_order = range(32,0,-1) + >>> st.inputs.slice_order = list(range(32,0,-1)) >>> st.inputs.ref_slice = 1 >>> st.run() # doctest: +SKIP @@ -209,7 +211,7 @@ def _list_outputs(self): outputs = self._outputs().get() resliced_all = self.inputs.write_which[0] > 0 resliced_mean = self.inputs.write_which[1] > 0 - + if self.inputs.jobtype != "write": if isdefined(self.inputs.in_files): outputs['realignment_parameters'] = [] @@ -765,7 +767,7 @@ class Segment(SPMCommand): input_spec = SegmentInputSpec output_spec = SegmentOutputSpec - + def __init__(self, **inputs): _local_version = SPMCommand().version if _local_version and '12.' in _local_version: @@ -774,7 +776,7 @@ def __init__(self, **inputs): else: self._jobtype = 'spatial' self._jobname = 'preproc' - + SPMCommand.__init__(self, **inputs) def _format_arg(self, opt, spec, val): @@ -894,7 +896,7 @@ class NewSegment(SPMCommand): input_spec = NewSegmentInputSpec output_spec = NewSegmentOutputSpec - + def __init__(self, **inputs): _local_version = SPMCommand().version if _local_version and '12.' in _local_version: @@ -903,7 +905,7 @@ def __init__(self, **inputs): else: self._jobtype = 'tools' self._jobname = 'preproc8' - + SPMCommand.__init__(self, **inputs) def _format_arg(self, opt, spec, val): diff --git a/nipype/interfaces/spm/tests/__init__.py b/nipype/interfaces/spm/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index 808a8ad374..9444246881 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import Analyze2nii +from ....testing import assert_equal +from ..utils import Analyze2nii def test_Analyze2nii_inputs(): input_map = dict(analyze_file=dict(mandatory=True, @@ -19,8 +19,8 @@ def test_Analyze2nii_inputs(): ) inputs = Analyze2nii.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Analyze2nii_outputs(): @@ -39,7 +39,7 @@ def test_Analyze2nii_outputs(): ) outputs = Analyze2nii.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index caeeb179b8..c67359d5fc 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import ApplyDeformations +from ....testing import assert_equal +from ..preprocess import ApplyDeformations def test_ApplyDeformations_inputs(): input_map = dict(deformation_field=dict(field='comp{1}.def', @@ -28,8 +28,8 @@ def test_ApplyDeformations_inputs(): ) inputs = ApplyDeformations.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyDeformations_outputs(): @@ -37,7 +37,7 @@ def test_ApplyDeformations_outputs(): ) outputs = ApplyDeformations.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index c7fe241ce8..36117f1136 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import ApplyInverseDeformation +from ....testing import assert_equal +from ..utils import ApplyInverseDeformation def test_ApplyInverseDeformation_inputs(): input_map = dict(bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', @@ -34,8 +34,8 @@ def test_ApplyInverseDeformation_inputs(): ) inputs = ApplyInverseDeformation.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyInverseDeformation_outputs(): @@ -43,7 +43,7 @@ def test_ApplyInverseDeformation_outputs(): ) outputs = ApplyInverseDeformation.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index bff1d7466e..3b1c3ea7e5 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import ApplyTransform +from ....testing import assert_equal +from ..utils import ApplyTransform def test_ApplyTransform_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -24,8 +24,8 @@ def test_ApplyTransform_inputs(): ) inputs = ApplyTransform.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ApplyTransform_outputs(): @@ -33,7 +33,7 @@ def test_ApplyTransform_outputs(): ) outputs = ApplyTransform.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 325838471a..0fda6df16d 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import CalcCoregAffine +from ....testing import assert_equal +from ..utils import CalcCoregAffine def test_CalcCoregAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -24,8 +24,8 @@ def test_CalcCoregAffine_inputs(): ) inputs = CalcCoregAffine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CalcCoregAffine_outputs(): @@ -34,7 +34,7 @@ def test_CalcCoregAffine_outputs(): ) outputs = CalcCoregAffine.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 1e64bba9cc..27147d8996 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import Coregister +from ....testing import assert_equal +from ..preprocess import Coregister def test_Coregister_inputs(): input_map = dict(apply_to_files=dict(copyfile=True, @@ -47,8 +47,8 @@ def test_Coregister_inputs(): ) inputs = Coregister.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Coregister_outputs(): @@ -57,7 +57,7 @@ def test_Coregister_outputs(): ) outputs = Coregister.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index 1b26bbe09c..dff0490643 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import CreateWarped +from ....testing import assert_equal +from ..preprocess import CreateWarped def test_CreateWarped_inputs(): input_map = dict(flowfield_files=dict(copyfile=False, @@ -31,8 +31,8 @@ def test_CreateWarped_inputs(): ) inputs = CreateWarped.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CreateWarped_outputs(): @@ -40,7 +40,7 @@ def test_CreateWarped_outputs(): ) outputs = CreateWarped.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index 4637f65556..30b0146191 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import DARTEL +from ....testing import assert_equal +from ..preprocess import DARTEL def test_DARTEL_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -30,8 +30,8 @@ def test_DARTEL_inputs(): ) inputs = DARTEL.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DARTEL_outputs(): @@ -41,7 +41,7 @@ def test_DARTEL_outputs(): ) outputs = DARTEL.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index 80cce2b51f..037d50eead 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import DARTELNorm2MNI +from ....testing import assert_equal +from ..preprocess import DARTELNorm2MNI def test_DARTELNorm2MNI_inputs(): input_map = dict(apply_to_files=dict(copyfile=False, @@ -36,8 +36,8 @@ def test_DARTELNorm2MNI_inputs(): ) inputs = DARTELNorm2MNI.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DARTELNorm2MNI_outputs(): @@ -46,7 +46,7 @@ def test_DARTELNorm2MNI_outputs(): ) outputs = DARTELNorm2MNI.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index 6fe2bbc65a..8b5c3f9107 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import DicomImport +from ....testing import assert_equal +from ..utils import DicomImport def test_DicomImport_inputs(): input_map = dict(format=dict(field='convopts.format', @@ -32,8 +32,8 @@ def test_DicomImport_inputs(): ) inputs = DicomImport.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DicomImport_outputs(): @@ -41,7 +41,7 @@ def test_DicomImport_outputs(): ) outputs = DicomImport.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index e8eda5c50a..09dc2740b3 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import EstimateContrast +from ....testing import assert_equal +from ..model import EstimateContrast def test_EstimateContrast_inputs(): input_map = dict(beta_images=dict(copyfile=False, @@ -33,8 +33,8 @@ def test_EstimateContrast_inputs(): ) inputs = EstimateContrast.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EstimateContrast_outputs(): @@ -46,7 +46,7 @@ def test_EstimateContrast_outputs(): ) outputs = EstimateContrast.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index bb4af3a99e..aa1d2ce320 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import EstimateModel +from ....testing import assert_equal +from ..model import EstimateModel def test_EstimateModel_inputs(): input_map = dict(estimation_method=dict(field='method', @@ -25,8 +25,8 @@ def test_EstimateModel_inputs(): ) inputs = EstimateModel.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_EstimateModel_outputs(): @@ -38,7 +38,7 @@ def test_EstimateModel_outputs(): ) outputs = EstimateModel.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 9dd4b77790..9c56e98132 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import FactorialDesign +from ....testing import assert_equal +from ..model import FactorialDesign def test_FactorialDesign_inputs(): input_map = dict(covariates=dict(field='cov', @@ -47,8 +47,8 @@ def test_FactorialDesign_inputs(): ) inputs = FactorialDesign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FactorialDesign_outputs(): @@ -56,7 +56,7 @@ def test_FactorialDesign_outputs(): ) outputs = FactorialDesign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index d5086b728c..7172a87736 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import Level1Design +from ....testing import assert_equal +from ..model import Level1Design def test_Level1Design_inputs(): input_map = dict(bases=dict(field='bases', @@ -47,8 +47,8 @@ def test_Level1Design_inputs(): ) inputs = Level1Design.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Level1Design_outputs(): @@ -56,7 +56,7 @@ def test_Level1Design_outputs(): ) outputs = Level1Design.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index b200958cdd..0bdb5ccb97 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import MultipleRegressionDesign +from ....testing import assert_equal +from ..model import MultipleRegressionDesign def test_MultipleRegressionDesign_inputs(): input_map = dict(covariates=dict(field='cov', @@ -55,8 +55,8 @@ def test_MultipleRegressionDesign_inputs(): ) inputs = MultipleRegressionDesign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MultipleRegressionDesign_outputs(): @@ -64,7 +64,7 @@ def test_MultipleRegressionDesign_outputs(): ) outputs = MultipleRegressionDesign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 051b92695f..9ca6703a97 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import NewSegment +from ....testing import assert_equal +from ..preprocess import NewSegment def test_NewSegment_inputs(): input_map = dict(affine_regularization=dict(field='warp.affreg', @@ -33,8 +33,8 @@ def test_NewSegment_inputs(): ) inputs = NewSegment.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_NewSegment_outputs(): @@ -50,7 +50,7 @@ def test_NewSegment_outputs(): ) outputs = NewSegment.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index 67619b3613..91e9af91ea 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import Normalize +from ....testing import assert_equal +from ..preprocess import Normalize def test_Normalize_inputs(): input_map = dict(DCT_period_cutoff=dict(field='eoptions.cutoff', @@ -68,8 +68,8 @@ def test_Normalize_inputs(): ) inputs = Normalize.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Normalize_outputs(): @@ -79,7 +79,7 @@ def test_Normalize_outputs(): ) outputs = Normalize.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index eb93c5d432..e9f3e2c80d 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import Normalize12 +from ....testing import assert_equal +from ..preprocess import Normalize12 def test_Normalize12_inputs(): input_map = dict(affine_regularization_type=dict(field='eoptions.affreg', @@ -54,8 +54,8 @@ def test_Normalize12_inputs(): ) inputs = Normalize12.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Normalize12_outputs(): @@ -65,7 +65,7 @@ def test_Normalize12_outputs(): ) outputs = Normalize12.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 6ff8bdc031..5153531b84 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import OneSampleTTestDesign +from ....testing import assert_equal +from ..model import OneSampleTTestDesign def test_OneSampleTTestDesign_inputs(): input_map = dict(covariates=dict(field='cov', @@ -50,8 +50,8 @@ def test_OneSampleTTestDesign_inputs(): ) inputs = OneSampleTTestDesign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_OneSampleTTestDesign_outputs(): @@ -59,7 +59,7 @@ def test_OneSampleTTestDesign_outputs(): ) outputs = OneSampleTTestDesign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index 71045cccdf..840b0ea963 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import PairedTTestDesign +from ....testing import assert_equal +from ..model import PairedTTestDesign def test_PairedTTestDesign_inputs(): input_map = dict(ancova=dict(field='des.pt.ancova', @@ -54,8 +54,8 @@ def test_PairedTTestDesign_inputs(): ) inputs = PairedTTestDesign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_PairedTTestDesign_outputs(): @@ -63,7 +63,7 @@ def test_PairedTTestDesign_outputs(): ) outputs = PairedTTestDesign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 3f37f846fe..277ada55c1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import Realign +from ....testing import assert_equal +from ..preprocess import Realign def test_Realign_inputs(): input_map = dict(fwhm=dict(field='eoptions.fwhm', @@ -51,8 +51,8 @@ def test_Realign_inputs(): ) inputs = Realign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Realign_outputs(): @@ -63,7 +63,7 @@ def test_Realign_outputs(): ) outputs = Realign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 79dbd7a095..75fc35c8d4 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import Reslice +from ....testing import assert_equal +from ..utils import Reslice def test_Reslice_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -24,8 +24,8 @@ def test_Reslice_inputs(): ) inputs = Reslice.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Reslice_outputs(): @@ -33,7 +33,7 @@ def test_Reslice_outputs(): ) outputs = Reslice.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index a79e81bd71..6eba2f6aee 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.utils import ResliceToReference +from ....testing import assert_equal +from ..utils import ResliceToReference def test_ResliceToReference_inputs(): input_map = dict(bounding_box=dict(field='comp{2}.idbbvox.bb', @@ -28,8 +28,8 @@ def test_ResliceToReference_inputs(): ) inputs = ResliceToReference.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ResliceToReference_outputs(): @@ -37,7 +37,7 @@ def test_ResliceToReference_outputs(): ) outputs = ResliceToReference.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index 105fe06fec..3408497e0b 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.base import SPMCommand +from ....testing import assert_equal +from ..base import SPMCommand def test_SPMCommand_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -17,7 +17,7 @@ def test_SPMCommand_inputs(): ) inputs = SPMCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index 022fa279c1..bd8e7a0f4e 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import Segment +from ....testing import assert_equal +from ..preprocess import Segment def test_Segment_inputs(): input_map = dict(affine_regularization=dict(field='opts.regtype', @@ -49,8 +49,8 @@ def test_Segment_inputs(): ) inputs = Segment.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Segment_outputs(): @@ -72,7 +72,7 @@ def test_Segment_outputs(): ) outputs = Segment.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index 4a1812759e..18ee3dc537 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import SliceTiming +from ....testing import assert_equal +from ..preprocess import SliceTiming def test_SliceTiming_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -39,8 +39,8 @@ def test_SliceTiming_inputs(): ) inputs = SliceTiming.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SliceTiming_outputs(): @@ -48,7 +48,7 @@ def test_SliceTiming_outputs(): ) outputs = SliceTiming.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index e0d54046c1..b4fce66cd9 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import Smooth +from ....testing import assert_equal +from ..preprocess import Smooth def test_Smooth_inputs(): input_map = dict(data_type=dict(field='dtype', @@ -30,8 +30,8 @@ def test_Smooth_inputs(): ) inputs = Smooth.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Smooth_outputs(): @@ -39,7 +39,7 @@ def test_Smooth_outputs(): ) outputs = Smooth.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index 8d2aecb6b8..e9afc7fa94 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import Threshold +from ....testing import assert_equal +from ..model import Threshold def test_Threshold_inputs(): input_map = dict(contrast_index=dict(mandatory=True, @@ -39,8 +39,8 @@ def test_Threshold_inputs(): ) inputs = Threshold.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Threshold_outputs(): @@ -53,7 +53,7 @@ def test_Threshold_outputs(): ) outputs = Threshold.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index 42837d595a..04560e6178 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import ThresholdStatistics +from ....testing import assert_equal +from ..model import ThresholdStatistics def test_ThresholdStatistics_inputs(): input_map = dict(contrast_index=dict(mandatory=True, @@ -29,8 +29,8 @@ def test_ThresholdStatistics_inputs(): ) inputs = ThresholdStatistics.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_ThresholdStatistics_outputs(): @@ -43,7 +43,7 @@ def test_ThresholdStatistics_outputs(): ) outputs = ThresholdStatistics.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index ff21621c32..0bd2c399b3 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.model import TwoSampleTTestDesign +from ....testing import assert_equal +from ..model import TwoSampleTTestDesign def test_TwoSampleTTestDesign_inputs(): input_map = dict(covariates=dict(field='cov', @@ -57,8 +57,8 @@ def test_TwoSampleTTestDesign_inputs(): ) inputs = TwoSampleTTestDesign.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_TwoSampleTTestDesign_outputs(): @@ -66,7 +66,7 @@ def test_TwoSampleTTestDesign_outputs(): ) outputs = TwoSampleTTestDesign.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index 1e9f0d58b6..b4f9de6761 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.spm.preprocess import VBMSegment +from ....testing import assert_equal +from ..preprocess import VBMSegment def test_VBMSegment_inputs(): input_map = dict(bias_corrected_affine=dict(field='estwrite.output.bias.affine', @@ -113,8 +113,8 @@ def test_VBMSegment_inputs(): ) inputs = VBMSegment.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VBMSegment_outputs(): @@ -134,7 +134,7 @@ def test_VBMSegment_outputs(): ) outputs = VBMSegment.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/__init__.py b/nipype/interfaces/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/tests/test_auto_AssertEqual.py b/nipype/interfaces/tests/test_auto_AssertEqual.py index c0dd821b0c..ebe528ff2f 100644 --- a/nipype/interfaces/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/tests/test_auto_AssertEqual.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import AssertEqual +from ...testing import assert_equal +from ..utility import AssertEqual def test_AssertEqual_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -13,7 +13,7 @@ def test_AssertEqual_inputs(): ) inputs = AssertEqual.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/tests/test_auto_BaseInterface.py index de4c191e36..e47c27a9aa 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/tests/test_auto_BaseInterface.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.base import BaseInterface +from ...testing import assert_equal +from ..base import BaseInterface def test_BaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -9,7 +9,7 @@ def test_BaseInterface_inputs(): ) inputs = BaseInterface.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 7569c70fbb..efd5cb6d73 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.c3 import C3dAffineTool +from ...testing import assert_equal +from ..c3 import C3dAffineTool def test_C3dAffineTool_inputs(): input_map = dict(args=dict(argstr='%s', @@ -32,8 +32,8 @@ def test_C3dAffineTool_inputs(): ) inputs = C3dAffineTool.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_C3dAffineTool_outputs(): @@ -41,7 +41,7 @@ def test_C3dAffineTool_outputs(): ) outputs = C3dAffineTool.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_CSVReader.py b/nipype/interfaces/tests/test_auto_CSVReader.py index 82a92508c3..2d950112f8 100644 --- a/nipype/interfaces/tests/test_auto_CSVReader.py +++ b/nipype/interfaces/tests/test_auto_CSVReader.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import CSVReader +from ...testing import assert_equal +from ..utility import CSVReader def test_CSVReader_inputs(): input_map = dict(header=dict(usedefault=True, @@ -10,15 +10,15 @@ def test_CSVReader_inputs(): ) inputs = CSVReader.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CSVReader_outputs(): output_map = dict() outputs = CSVReader.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/tests/test_auto_CommandLine.py index 064620a113..48e2716557 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/tests/test_auto_CommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.base import CommandLine +from ...testing import assert_equal +from ..base import CommandLine def test_CommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -16,7 +16,7 @@ def test_CommandLine_inputs(): ) inputs = CommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index 8bfff5fb85..e71481a5af 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import CopyMeta +from ...testing import assert_equal +from ..dcmstack import CopyMeta def test_CopyMeta_inputs(): input_map = dict(dest_file=dict(mandatory=True, @@ -12,8 +12,8 @@ def test_CopyMeta_inputs(): ) inputs = CopyMeta.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_CopyMeta_outputs(): @@ -21,7 +21,7 @@ def test_CopyMeta_outputs(): ) outputs = CopyMeta.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index 039b41ba94..946a7497d4 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import DataFinder +from ...testing import assert_equal +from ..io import DataFinder def test_DataFinder_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -18,15 +18,15 @@ def test_DataFinder_inputs(): ) inputs = DataFinder.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DataFinder_outputs(): output_map = dict() outputs = DataFinder.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index 1d630a8941..4af03c2ddf 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import DataGrabber +from ...testing import assert_equal +from ..io import DataGrabber def test_DataGrabber_inputs(): input_map = dict(base_directory=dict(), @@ -17,15 +17,15 @@ def test_DataGrabber_inputs(): ) inputs = DataGrabber.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DataGrabber_outputs(): output_map = dict() outputs = DataGrabber.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 15305f3694..0e43c7727e 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import DataSink +from ...testing import assert_equal +from ..io import DataSink def test_DataSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, @@ -20,8 +20,8 @@ def test_DataSink_inputs(): ) inputs = DataSink.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DataSink_outputs(): @@ -29,7 +29,7 @@ def test_DataSink_outputs(): ) outputs = DataSink.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index f5e61e103e..ae556e8bdc 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcm2nii import Dcm2nii +from ...testing import assert_equal +from ..dcm2nii import Dcm2nii def test_Dcm2nii_inputs(): input_map = dict(anonymize=dict(argstr='-a', @@ -71,8 +71,8 @@ def test_Dcm2nii_inputs(): ) inputs = Dcm2nii.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Dcm2nii_outputs(): @@ -84,7 +84,7 @@ def test_Dcm2nii_outputs(): ) outputs = Dcm2nii.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index c2678f9dac..ef364f6696 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import DcmStack +from ...testing import assert_equal +from ..dcmstack import DcmStack def test_DcmStack_inputs(): input_map = dict(dicom_files=dict(mandatory=True, @@ -17,8 +17,8 @@ def test_DcmStack_inputs(): ) inputs = DcmStack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_DcmStack_outputs(): @@ -26,7 +26,7 @@ def test_DcmStack_outputs(): ) outputs = DcmStack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index e447e354da..c9e71c3886 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import FreeSurferSource +from ...testing import assert_equal +from ..io import FreeSurferSource def test_FreeSurferSource_inputs(): input_map = dict(hemi=dict(usedefault=True, @@ -15,8 +15,8 @@ def test_FreeSurferSource_inputs(): ) inputs = FreeSurferSource.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_FreeSurferSource_outputs(): @@ -99,7 +99,7 @@ def test_FreeSurferSource_outputs(): ) outputs = FreeSurferSource.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_Function.py b/nipype/interfaces/tests/test_auto_Function.py index e627635a7f..7454cdec84 100644 --- a/nipype/interfaces/tests/test_auto_Function.py +++ b/nipype/interfaces/tests/test_auto_Function.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import Function +from ...testing import assert_equal +from ..utility import Function def test_Function_inputs(): input_map = dict(function_str=dict(mandatory=True, @@ -11,15 +11,15 @@ def test_Function_inputs(): ) inputs = Function.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Function_outputs(): output_map = dict() outputs = Function.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_GroupAndStack.py b/nipype/interfaces/tests/test_auto_GroupAndStack.py index 530ee42cb2..cab06d673b 100644 --- a/nipype/interfaces/tests/test_auto_GroupAndStack.py +++ b/nipype/interfaces/tests/test_auto_GroupAndStack.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import GroupAndStack +from ...testing import assert_equal +from ..dcmstack import GroupAndStack def test_GroupAndStack_inputs(): input_map = dict(dicom_files=dict(mandatory=True, @@ -17,8 +17,8 @@ def test_GroupAndStack_inputs(): ) inputs = GroupAndStack.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_GroupAndStack_outputs(): @@ -26,7 +26,7 @@ def test_GroupAndStack_outputs(): ) outputs = GroupAndStack.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index e2f9541d95..1bcd8a8c0e 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import IOBase +from ...testing import assert_equal +from ..io import IOBase def test_IOBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -9,7 +9,7 @@ def test_IOBase_inputs(): ) inputs = IOBase.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_IdentityInterface.py b/nipype/interfaces/tests/test_auto_IdentityInterface.py index 9821b3bcf1..8a4ce3f464 100644 --- a/nipype/interfaces/tests/test_auto_IdentityInterface.py +++ b/nipype/interfaces/tests/test_auto_IdentityInterface.py @@ -1,20 +1,20 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import IdentityInterface +from ...testing import assert_equal +from ..utility import IdentityInterface def test_IdentityInterface_inputs(): input_map = dict() inputs = IdentityInterface.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_IdentityInterface_outputs(): output_map = dict() outputs = IdentityInterface.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index f1872e791a..d7a7684f4d 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import JSONFileGrabber +from ...testing import assert_equal +from ..io import JSONFileGrabber def test_JSONFileGrabber_inputs(): input_map = dict(defaults=dict(), @@ -11,15 +11,15 @@ def test_JSONFileGrabber_inputs(): ) inputs = JSONFileGrabber.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JSONFileGrabber_outputs(): output_map = dict() outputs = JSONFileGrabber.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 7c8cd80f98..9632906e97 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import JSONFileSink +from ...testing import assert_equal +from ..io import JSONFileSink def test_JSONFileSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, @@ -14,8 +14,8 @@ def test_JSONFileSink_inputs(): ) inputs = JSONFileSink.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_JSONFileSink_outputs(): @@ -23,7 +23,7 @@ def test_JSONFileSink_outputs(): ) outputs = JSONFileSink.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index 7ae4c19491..276362520c 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import LookupMeta +from ...testing import assert_equal +from ..dcmstack import LookupMeta def test_LookupMeta_inputs(): input_map = dict(in_file=dict(mandatory=True, @@ -10,15 +10,15 @@ def test_LookupMeta_inputs(): ) inputs = LookupMeta.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_LookupMeta_outputs(): output_map = dict() outputs = LookupMeta.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index 335174df4a..e82fc2d665 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.matlab import MatlabCommand +from ...testing import assert_equal +from ..matlab import MatlabCommand def test_MatlabCommand_inputs(): input_map = dict(args=dict(argstr='%s', @@ -45,7 +45,7 @@ def test_MatlabCommand_inputs(): ) inputs = MatlabCommand.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_Merge.py b/nipype/interfaces/tests/test_auto_Merge.py index 161fe247f6..3a68555612 100644 --- a/nipype/interfaces/tests/test_auto_Merge.py +++ b/nipype/interfaces/tests/test_auto_Merge.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import Merge +from ...testing import assert_equal +from ..utility import Merge def test_Merge_inputs(): input_map = dict(axis=dict(usedefault=True, @@ -13,8 +13,8 @@ def test_Merge_inputs(): ) inputs = Merge.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Merge_outputs(): @@ -22,7 +22,7 @@ def test_Merge_outputs(): ) outputs = Merge.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index c9df264d36..efa8dfdae9 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import MergeNifti +from ...testing import assert_equal +from ..dcmstack import MergeNifti def test_MergeNifti_inputs(): input_map = dict(in_files=dict(mandatory=True, @@ -14,8 +14,8 @@ def test_MergeNifti_inputs(): ) inputs = MergeNifti.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MergeNifti_outputs(): @@ -23,7 +23,7 @@ def test_MergeNifti_outputs(): ) outputs = MergeNifti.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 1b4262c6d6..f1452ef49c 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.meshfix import MeshFix +from ...testing import assert_equal +from ..meshfix import MeshFix def test_MeshFix_inputs(): input_map = dict(args=dict(argstr='%s', @@ -90,8 +90,8 @@ def test_MeshFix_inputs(): ) inputs = MeshFix.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_MeshFix_outputs(): @@ -99,7 +99,7 @@ def test_MeshFix_outputs(): ) outputs = MeshFix.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/tests/test_auto_MpiCommandLine.py index bf4e629465..cd715de2e2 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/tests/test_auto_MpiCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.base import MpiCommandLine +from ...testing import assert_equal +from ..base import MpiCommandLine def test_MpiCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -19,7 +19,7 @@ def test_MpiCommandLine_inputs(): ) inputs = MpiCommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 58869d63b8..c731c08151 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import MySQLSink +from ...testing import assert_equal +from ..io import MySQLSink def test_MySQLSink_inputs(): input_map = dict(config=dict(mandatory=True, @@ -23,7 +23,7 @@ def test_MySQLSink_inputs(): ) inputs = MySQLSink.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 848f94990c..2fa8d50ffe 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import NiftiGeneratorBase +from ...testing import assert_equal +from ..dcmstack import NiftiGeneratorBase def test_NiftiGeneratorBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -9,7 +9,7 @@ def test_NiftiGeneratorBase_inputs(): ) inputs = NiftiGeneratorBase.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_Rename.py b/nipype/interfaces/tests/test_auto_Rename.py index 758191e890..4df470a6ed 100644 --- a/nipype/interfaces/tests/test_auto_Rename.py +++ b/nipype/interfaces/tests/test_auto_Rename.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import Rename +from ...testing import assert_equal +from ..utility import Rename def test_Rename_inputs(): input_map = dict(format_string=dict(mandatory=True, @@ -14,8 +14,8 @@ def test_Rename_inputs(): ) inputs = Rename.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Rename_outputs(): @@ -23,7 +23,7 @@ def test_Rename_outputs(): ) outputs = Rename.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py new file mode 100644 index 0000000000..d675d60cae --- /dev/null +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -0,0 +1,39 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from ...testing import assert_equal +from ..io import S3DataGrabber + +def test_S3DataGrabber_inputs(): + input_map = dict(anon=dict(usedefault=True, + ), + bucket=dict(mandatory=True, + ), + bucket_path=dict(usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + local_directory=dict(), + raise_on_empty=dict(usedefault=True, + ), + region=dict(usedefault=True, + ), + sort_filelist=dict(mandatory=True, + ), + template=dict(mandatory=True, + ), + template_args=dict(), + ) + inputs = S3DataGrabber.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(inputs.traits()[key], metakey), value + +def test_S3DataGrabber_outputs(): + output_map = dict() + outputs = S3DataGrabber.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_S3DataSink.py b/nipype/interfaces/tests/test_auto_S3DataSink.py new file mode 100644 index 0000000000..add9ddb5c2 --- /dev/null +++ b/nipype/interfaces/tests/test_auto_S3DataSink.py @@ -0,0 +1,43 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from ...testing import assert_equal +from ..io import S3DataSink + +def test_S3DataSink_inputs(): + input_map = dict(_outputs=dict(usedefault=True, + ), + anon=dict(usedefault=True, + ), + base_directory=dict(), + bucket=dict(mandatory=True, + ), + bucket_path=dict(usedefault=True, + ), + container=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + parameterization=dict(usedefault=True, + ), + regexp_substitutions=dict(), + remove_dest_dir=dict(usedefault=True, + ), + strip_dir=dict(), + substitutions=dict(), + testing=dict(usedefault=True, + ), + ) + inputs = S3DataSink.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(inputs.traits()[key], metakey), value + +def test_S3DataSink_outputs(): + output_map = dict(out_file=dict(), + ) + outputs = S3DataSink.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py index 842ded8b2a..5c42df7910 100644 --- a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.base import SEMLikeCommandLine +from ...testing import assert_equal +from ..base import SEMLikeCommandLine def test_SEMLikeCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -16,7 +16,7 @@ def test_SEMLikeCommandLine_inputs(): ) inputs = SEMLikeCommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 6a7a064291..5017acac00 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import SQLiteSink +from ...testing import assert_equal +from ..io import SQLiteSink def test_SQLiteSink_inputs(): input_map = dict(database_file=dict(mandatory=True, @@ -13,7 +13,7 @@ def test_SQLiteSink_inputs(): ) inputs = SQLiteSink.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py index 6f936eb756..0ab83b764b 100644 --- a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import SSHDataGrabber +from ...testing import assert_equal +from ..io import SSHDataGrabber def test_SSHDataGrabber_inputs(): input_map = dict(base_directory=dict(mandatory=True, @@ -28,15 +28,15 @@ def test_SSHDataGrabber_inputs(): ) inputs = SSHDataGrabber.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SSHDataGrabber_outputs(): output_map = dict() outputs = SSHDataGrabber.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_Select.py b/nipype/interfaces/tests/test_auto_Select.py index 85649f42e6..6509148edf 100644 --- a/nipype/interfaces/tests/test_auto_Select.py +++ b/nipype/interfaces/tests/test_auto_Select.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import Select +from ...testing import assert_equal +from ..utility import Select def test_Select_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -13,8 +13,8 @@ def test_Select_inputs(): ) inputs = Select.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Select_outputs(): @@ -22,7 +22,7 @@ def test_Select_outputs(): ) outputs = Select.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index edec59dbe5..b30a53d899 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import SelectFiles +from ...testing import assert_equal +from ..io import SelectFiles def test_SelectFiles_inputs(): input_map = dict(base_directory=dict(), @@ -16,15 +16,15 @@ def test_SelectFiles_inputs(): ) inputs = SelectFiles.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SelectFiles_outputs(): output_map = dict() outputs = SelectFiles.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index 71872d3833..f2a8e4b717 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dynamic_slicer import SlicerCommandLine +from ...testing import assert_equal +from ..dynamic_slicer import SlicerCommandLine def test_SlicerCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -17,15 +17,15 @@ def test_SlicerCommandLine_inputs(): ) inputs = SlicerCommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SlicerCommandLine_outputs(): output_map = dict() outputs = SlicerCommandLine.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_Split.py b/nipype/interfaces/tests/test_auto_Split.py index 2a694655b4..596d6a51da 100644 --- a/nipype/interfaces/tests/test_auto_Split.py +++ b/nipype/interfaces/tests/test_auto_Split.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.utility import Split +from ...testing import assert_equal +from ..utility import Split def test_Split_inputs(): input_map = dict(ignore_exception=dict(nohash=True, @@ -15,15 +15,15 @@ def test_Split_inputs(): ) inputs = Split.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Split_outputs(): output_map = dict() outputs = Split.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index e494d2cea3..bcd389a0ca 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.dcmstack import SplitNifti +from ...testing import assert_equal +from ..dcmstack import SplitNifti def test_SplitNifti_inputs(): input_map = dict(in_file=dict(mandatory=True, @@ -13,8 +13,8 @@ def test_SplitNifti_inputs(): ) inputs = SplitNifti.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_SplitNifti_outputs(): @@ -22,7 +22,7 @@ def test_SplitNifti_outputs(): ) outputs = SplitNifti.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py index fee9a4cb27..e7a3089553 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.base import StdOutCommandLine +from ...testing import assert_equal +from ..base import StdOutCommandLine def test_StdOutCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', @@ -20,7 +20,7 @@ def test_StdOutCommandLine_inputs(): ) inputs = StdOutCommandLine.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index 5fd01e583d..ee35b059ca 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import XNATSink +from ...testing import assert_equal +from ..io import XNATSink def test_XNATSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, @@ -33,7 +33,7 @@ def test_XNATSink_inputs(): ) inputs = XNATSink.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index ab86a880f4..1744ce7eb5 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.io import XNATSource +from ...testing import assert_equal +from ..io import XNATSource def test_XNATSource_inputs(): input_map = dict(cache_dir=dict(), @@ -23,15 +23,15 @@ def test_XNATSource_inputs(): ) inputs = XNATSource.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_XNATSource_outputs(): output_map = dict() outputs = XNATSource.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/tests/test_base.py b/nipype/interfaces/tests/test_base.py index 04b88e7593..edc51035ae 100644 --- a/nipype/interfaces/tests/test_base.py +++ b/nipype/interfaces/tests/test_base.py @@ -1,8 +1,13 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import print_function +from future import standard_library +standard_library.install_aliases() + import os import tempfile import shutil +import warnings from nipype.testing import (assert_equal, assert_not_equal, assert_raises, assert_true, assert_false, with_setup, package_check, @@ -12,7 +17,8 @@ from nipype.interfaces.base import Undefined, config from traits.testing.nose_tools import skip import traits.api as traits -#test Bunch + + def test_bunch(): b = nib.Bunch() yield assert_equal, b.__dict__,{} @@ -52,9 +58,8 @@ def test_bunch_hash(): yield assert_equal, bhash, 'ddcc7b4ec5675df8cf317a48bd1857fa' # Make sure the hash stored in the json file for `infile` is correct. jshash = nib.md5() - fp = file(json_pth) - jshash.update(fp.read()) - fp.close() + with open(json_pth) as fp: + jshash.update(fp.read().encode('utf-8')) yield assert_equal, newbdict['infile'][0][1], jshash.hexdigest() yield assert_equal, newbdict['yat'], True @@ -67,7 +72,8 @@ def setup_file(): #global tmp_infile, tmp_dir tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo.txt') - open(tmp_infile, 'w').writelines('123456789') + with open(tmp_infile, 'w') as fp: + fp.writelines(['123456789']) return tmp_infile def teardown_file(tmp_dir): @@ -95,7 +101,7 @@ class spec(nib.TraitedSpec): @skip def test_TraitedSpec_dynamic(): - from cPickle import dumps, loads + from pickle import dumps, loads a = nib.BaseTraitedSpec() a.add_trait('foo', nib.traits.Int) a.foo = 1 @@ -134,43 +140,67 @@ class MyInterface(nib.BaseInterface): yield assert_equal, myif.inputs.kung, 2.0 def test_deprecation(): - class DeprecationSpec1(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='0.1') - spec_instance = DeprecationSpec1() - set_foo = lambda : setattr(spec_instance, 'foo', 1) - yield assert_raises, nib.TraitError, set_foo - class DeprecationSpec1numeric(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='0.1') - spec_instance = DeprecationSpec1numeric() - set_foo = lambda : setattr(spec_instance, 'foo', 1) - yield assert_raises, nib.TraitError, set_foo - class DeprecationSpec2(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='100', new_name='bar') - spec_instance = DeprecationSpec2() - set_foo = lambda : setattr(spec_instance, 'foo', 1) - yield assert_raises, nib.TraitError, set_foo - class DeprecationSpec3(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='1000', new_name='bar') - bar = nib.traits.Int() - spec_instance = DeprecationSpec3() - not_raised = True - try: - spec_instance.foo = 1 - except nib.TraitError: - not_raised = False - yield assert_true, not_raised - class DeprecationSpec3(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='1000', new_name='bar') - bar = nib.traits.Int() - spec_instance = DeprecationSpec3() - not_raised = True - try: - spec_instance.foo = 1 - except nib.TraitError: - not_raised = False - yield assert_true, not_raised - yield assert_equal, spec_instance.foo, Undefined - yield assert_equal, spec_instance.bar, 1 + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec1(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='0.1') + spec_instance = DeprecationSpec1() + set_foo = lambda : setattr(spec_instance, 'foo', 1) + yield assert_raises, nib.TraitError, set_foo + yield assert_equal, len(w), 0, 'no warnings, just errors' + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec1numeric(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='0.1') + spec_instance = DeprecationSpec1numeric() + set_foo = lambda : setattr(spec_instance, 'foo', 1) + yield assert_raises, nib.TraitError, set_foo + yield assert_equal, len(w), 0, 'no warnings, just errors' + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec2(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='100', new_name='bar') + spec_instance = DeprecationSpec2() + set_foo = lambda : setattr(spec_instance, 'foo', 1) + yield assert_raises, nib.TraitError, set_foo + yield assert_equal, len(w), 0, 'no warnings, just errors' + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec3(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='1000', new_name='bar') + bar = nib.traits.Int() + spec_instance = DeprecationSpec3() + not_raised = True + try: + spec_instance.foo = 1 + except nib.TraitError: + not_raised = False + yield assert_true, not_raised + yield assert_equal, len(w), 1, 'deprecated warning 1 %s' % [w1.message for w1 in w] + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec3(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='1000', new_name='bar') + bar = nib.traits.Int() + spec_instance = DeprecationSpec3() + not_raised = True + try: + spec_instance.foo = 1 + except nib.TraitError: + not_raised = False + yield assert_true, not_raised + yield assert_equal, spec_instance.foo, Undefined + yield assert_equal, spec_instance.bar, 1 + yield assert_equal, len(w), 1, 'deprecated warning 2 %s' % [w1.message for w1 in w] def test_namesource(): @@ -285,7 +315,7 @@ class TestCycle(nib.CommandLine): res = to1.cmdline except nib.NipypeInterfaceError: not_raised = False - print res + print(res) yield assert_true, not_raised yield assert_true, '%s' % tmp_infile in res @@ -407,24 +437,21 @@ def _run_interface(self, runtime): nib.BaseInterface.input_spec = None yield assert_raises, Exception, nib.BaseInterface +def assert_not_raises(fn, *args, **kwargs): + fn(*args, **kwargs) + return True + def test_input_version(): class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', min_ver='0.9') class DerivedInterface1(nib.BaseInterface): input_spec = InputSpec obj = DerivedInterface1() - not_raised = True - try: - obj._check_version_requirements(obj.inputs) - except: - not_raised = False - yield assert_true, not_raised + yield assert_not_raises, obj._check_version_requirements, obj.inputs + config.set('execution', 'stop_on_unknown_version', True) - try: - obj._check_version_requirements(obj.inputs) - except: - not_raised = False - yield assert_false, not_raised + yield assert_raises, Exception, obj._check_version_requirements, obj.inputs + config.set_default_config() class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', min_ver='0.9') @@ -434,18 +461,15 @@ class DerivedInterface1(nib.BaseInterface): obj = DerivedInterface1() obj.inputs.foo = 1 yield assert_raises, Exception, obj._check_version_requirements + class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', min_ver='0.9') class DerivedInterface1(nib.BaseInterface): input_spec = InputSpec _version = '0.10' obj = DerivedInterface1() - not_raised = True - try: - obj._check_version_requirements(obj.inputs) - except: - not_raised = False - yield assert_true, not_raised + yield assert_not_raises, obj._check_version_requirements, obj.inputs + class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', min_ver='0.9') class DerivedInterface1(nib.BaseInterface): @@ -454,11 +478,8 @@ class DerivedInterface1(nib.BaseInterface): obj = DerivedInterface1() obj.inputs.foo = 1 not_raised = True - try: - obj._check_version_requirements(obj.inputs) - except: - not_raised = False - yield assert_true, not_raised + yield assert_not_raises, obj._check_version_requirements, obj.inputs + class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', max_ver='0.7') class DerivedInterface2(nib.BaseInterface): @@ -467,6 +488,7 @@ class DerivedInterface2(nib.BaseInterface): obj = DerivedInterface2() obj.inputs.foo = 1 yield assert_raises, Exception, obj._check_version_requirements + class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', max_ver='0.9') class DerivedInterface1(nib.BaseInterface): @@ -475,11 +497,7 @@ class DerivedInterface1(nib.BaseInterface): obj = DerivedInterface1() obj.inputs.foo = 1 not_raised = True - try: - obj._check_version_requirements(obj.inputs) - except: - not_raised = False - yield assert_true, not_raised + yield assert_not_raises, obj._check_version_requirements, obj.inputs def test_output_version(): class InputSpec(nib.TraitedSpec): @@ -603,6 +621,7 @@ def test_CommandLine_output(): ci.inputs.terminal_output = 'file' res = ci.run() yield assert_true, 'stdout.nipype' in res.runtime.stdout + yield assert_equal, type(res.runtime.stdout), type('hi') ci = nib.CommandLine(command='ls -l') ci.inputs.terminal_output = 'none' res = ci.run() diff --git a/nipype/interfaces/tests/test_io.py b/nipype/interfaces/tests/test_io.py index 8c19ea0503..598621b5d8 100644 --- a/nipype/interfaces/tests/test_io.py +++ b/nipype/interfaces/tests/test_io.py @@ -1,5 +1,10 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import print_function +from builtins import zip +from builtins import range +from builtins import open + import os import glob import shutil @@ -208,7 +213,13 @@ def test_s3datasink_substitutions(): # run fakes3 server and set up bucket fakes3dir = op.expanduser('~/fakes3') - proc = Popen(['fakes3', '-r', fakes3dir, '-p', '4567'], stdout=open(os.devnull, 'wb')) + try: + proc = Popen(['fakes3', '-r', fakes3dir, '-p', '4567'], stdout=open(os.devnull, 'wb')) + except OSError as ose: + if 'No such file or directory' in str(ose): + return # fakes3 not installed. OK! + raise ose + conn = S3Connection(anon=True, is_secure=False, port=4567, host='localhost', calling_format=OrdinaryCallingFormat()) @@ -270,7 +281,7 @@ def _temp_analyze_files(): """Generate temporary analyze file pair.""" fd, orig_img = mkstemp(suffix='.img', dir=mkdtemp()) orig_hdr = orig_img[:-4] + '.hdr' - fp = file(orig_hdr, 'w+') + fp = open(orig_hdr, 'w+') fp.close() return orig_img, orig_hdr @@ -356,7 +367,7 @@ def test_datafinder_unpack(): df.inputs.match_regex = '.+/(?P.+)\.txt' df.inputs.unpack_single = True result = df.run() - print result.outputs.out_paths + print(result.outputs.out_paths) yield assert_equal, result.outputs.out_paths, single_res @@ -368,7 +379,7 @@ def test_freesurfersource(): def test_jsonsink(): - import json + import simplejson import os ds = nio.JSONFileSink() @@ -387,7 +398,7 @@ def test_jsonsink(): res = js.run() with open(res.outputs.out_file, 'r') as f: - data = json.load(f) + data = simplejson.load(f) yield assert_true, data == {"contrasts": {"alt": "someNestedValue"}, "foo": "var", "new_entry": "someValue"} js = nio.JSONFileSink(infields=['test'], in_dict={'foo': 'var'}) @@ -397,7 +408,7 @@ def test_jsonsink(): res = js.run() with open(res.outputs.out_file, 'r') as f: - data = json.load(f) + data = simplejson.load(f) yield assert_true, data == {"test": "testInfields", "contrasts": {"alt": "someNestedValue"}, "foo": "var", "new_entry": "someValue"} os.chdir(curdir) diff --git a/nipype/interfaces/tests/test_matlab.py b/nipype/interfaces/tests/test_matlab.py index 423f8f9a0b..36facb8038 100644 --- a/nipype/interfaces/tests/test_matlab.py +++ b/nipype/interfaces/tests/test_matlab.py @@ -14,9 +14,17 @@ mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd) +def clean_workspace_and_get_default_script_file(): + # Make sure things are clean. + default_script_file = mlab.MatlabInputSpec().script_file + if os.path.exists(default_script_file): + os.remove(default_script_file) # raise Exception('Default script file needed for tests; please remove %s!' % default_script_file) + return default_script_file + @skipif(no_matlab) def test_cmdline(): - basedir = mkdtemp() + default_script_file = clean_workspace_and_get_default_script_file() + mi = mlab.MatlabCommand(script='whos', script_file='testscript', mfile=False) @@ -31,13 +39,13 @@ def test_cmdline(): yield assert_equal, mi.inputs.script, 'whos' yield assert_equal, mi.inputs.script_file, 'testscript' - path_exists = os.path.exists(os.path.join(basedir, 'testscript.m')) - yield assert_false, path_exists - rmtree(basedir) + yield assert_false, os.path.exists(mi.inputs.script_file), 'scriptfile should not exist' + yield assert_false, os.path.exists(default_script_file), 'default scriptfile should not exist.' @skipif(no_matlab) def test_mlab_inputspec(): + default_script_file = clean_workspace_and_get_default_script_file() spec = mlab.MatlabInputSpec() for k in ['paths', 'script', 'nosplash', 'mfile', 'logfile', 'script_file', 'nodesktop']: @@ -45,11 +53,13 @@ def test_mlab_inputspec(): yield assert_true, spec.nodesktop yield assert_true, spec.nosplash yield assert_true, spec.mfile - yield assert_equal, spec.script_file, 'pyscript.m' + yield assert_equal, spec.script_file, default_script_file @skipif(no_matlab) def test_mlab_init(): + default_script_file = clean_workspace_and_get_default_script_file() + yield assert_equal, mlab.MatlabCommand._cmd, 'matlab' yield assert_equal, mlab.MatlabCommand.input_spec, mlab.MatlabInputSpec @@ -60,26 +70,48 @@ def test_mlab_init(): @skipif(no_matlab) def test_run_interface(): + default_script_file = clean_workspace_and_get_default_script_file() + mc = mlab.MatlabCommand(matlab_cmd='foo_m') + yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 1.' yield assert_raises, ValueError, mc.run # script is mandatory + yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 2.' + if os.path.exists(default_script_file): # cleanup + os.remove(default_script_file) + mc.inputs.script = 'a=1;' + yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 3.' yield assert_raises, IOError, mc.run # foo_m is not an executable + yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 3.' + if os.path.exists(default_script_file): # cleanup + os.remove(default_script_file) + cwd = os.getcwd() basedir = mkdtemp() os.chdir(basedir) + # bypasses ubuntu dash issue mc = mlab.MatlabCommand(script='foo;', paths=[basedir], mfile=True) + yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 4.' yield assert_raises, RuntimeError, mc.run + yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 4.' + if os.path.exists(default_script_file): # cleanup + os.remove(default_script_file) + # bypasses ubuntu dash issue res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run() yield assert_equal, res.runtime.returncode, 0 + yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 5.' os.chdir(cwd) rmtree(basedir) @skipif(no_matlab) def test_set_matlabcmd(): + default_script_file = clean_workspace_and_get_default_script_file() + mi = mlab.MatlabCommand() mi.set_default_matlab_cmd('foo') + yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist.' yield assert_equal, mi._default_matlab_cmd, 'foo' mi.set_default_matlab_cmd(matlab_cmd) diff --git a/nipype/interfaces/tests/test_utility.py b/nipype/interfaces/tests/test_utility.py index ff1f308011..b9b61fbf0f 100644 --- a/nipype/interfaces/tests/test_utility.py +++ b/nipype/interfaces/tests/test_utility.py @@ -1,3 +1,5 @@ +from __future__ import print_function +from builtins import range # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: import os @@ -106,7 +108,7 @@ def test_function_with_imports(): function=make_random_array, imports=["import numpy as np"]), name="should_not_fail") - print node.inputs.function_str + print(node.inputs.function_str) try: node.inputs.size = 10 node.run() @@ -121,14 +123,14 @@ def test_split(): os.chdir(tempdir) try: - node = pe.Node(utility.Split(inlist=range(4), + node = pe.Node(utility.Split(inlist=list(range(4)), splits=[1, 3]), name='split_squeeze') res = node.run() yield assert_equal, res.outputs.out1, [0] yield assert_equal, res.outputs.out2, [1, 2, 3] - node = pe.Node(utility.Split(inlist=range(4), + node = pe.Node(utility.Split(inlist=list(range(4)), splits=[1, 3], squeeze=True), name='split_squeeze') @@ -147,7 +149,7 @@ def test_csvReader(): "baz,goodbye,0.3\n"] for x in range(2): fd, name = mkstemp(suffix=".csv") - with open(name, 'w+b') as fid: + with open(name, 'w') as fid: reader = utility.CSVReader() if x % 2 == 0: fid.write(header) diff --git a/nipype/interfaces/traits_extension.py b/nipype/interfaces/traits_extension.py index 6cb6fdd252..994488284c 100644 --- a/nipype/interfaces/traits_extension.py +++ b/nipype/interfaces/traits_extension.py @@ -15,7 +15,6 @@ (usually by Robert Kern). """ - import os # perform all external trait imports here @@ -109,7 +108,7 @@ def __init__ ( self, value = '', filter = None, auto_set = False, """ if not exists: # Define the C-level fast validator to use: - fast_validate = ( 11, basestring ) + fast_validate = ( 11, str ) super( File, self ).__init__( value, filter, auto_set, entries, exists, **metadata ) @@ -195,7 +194,7 @@ def __init__ ( self, value = '', auto_set = False, entries = 0, # Define the C-level fast validator to use if the directory existence # test is not required: if not exists: - self.fast_validate = ( 11, basestring ) + self.fast_validate = ( 11, str ) super( Directory, self ).__init__( value, auto_set, entries, exists, **metadata ) @@ -235,7 +234,7 @@ def has_metadata(trait, metadata, value=None, recursive=True): Checks if a given trait has a metadata (and optionally if it is set to particular value) ''' count = 0 - if hasattr(trait, "_metadata") and metadata in trait._metadata.keys() and (trait._metadata[metadata] == value or value==None): + if hasattr(trait, "_metadata") and metadata in list(trait._metadata.keys()) and (trait._metadata[metadata] == value or value==None): count += 1 if recursive: if hasattr(trait, 'inner_traits'): diff --git a/nipype/interfaces/utility.py b/nipype/interfaces/utility.py index ca2bb5ba69..fb1cb628c3 100644 --- a/nipype/interfaces/utility.py +++ b/nipype/interfaces/utility.py @@ -9,20 +9,26 @@ >>> os.chdir(datadir) """ +from future import standard_library +standard_library.install_aliases() +from builtins import zip +from builtins import range + import os import re -from cPickle import dumps, loads +from pickle import dumps +from textwrap import dedent import numpy as np import nibabel as nb -from nipype.external import six -from nipype.utils.filemanip import (filename_to_list, copyfile, split_filename) -from nipype.interfaces.base import (traits, TraitedSpec, DynamicTraitedSpec, File, - Undefined, isdefined, OutputMultiPath, - InputMultiPath, BaseInterface, BaseInterfaceInputSpec) -from nipype.interfaces.io import IOBase, add_traits -from nipype.testing import assert_equal -from nipype.utils.misc import getsource, create_function_from_source +from .base import (traits, TraitedSpec, DynamicTraitedSpec, File, + Undefined, isdefined, OutputMultiPath, + InputMultiPath, BaseInterface, BaseInterfaceInputSpec) +from .io import IOBase, add_traits +from ..external.six import string_types +from ..testing import assert_equal +from ..utils.filemanip import (filename_to_list, copyfile, split_filename) +from ..utils.misc import getsource, create_function_from_source class IdentityInterface(IOBase): @@ -188,7 +194,7 @@ class Rename(IOBase): >>> rename1.inputs.in_file = "zstat1.nii.gz" >>> rename1.inputs.format_string = "Faces-Scenes.nii.gz" >>> res = rename1.run() # doctest: +SKIP - >>> print res.outputs.out_file # doctest: +SKIP + >>> res.outputs.out_file # doctest: +SKIP 'Faces-Scenes.nii.gz" # doctest: +SKIP >>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d") @@ -197,7 +203,7 @@ class Rename(IOBase): >>> rename2.inputs.subject_id = "subj_201" >>> rename2.inputs.run = 2 >>> res = rename2.run() # doctest: +SKIP - >>> print res.outputs.out_file # doctest: +SKIP + >>> res.outputs.out_file # doctest: +SKIP 'subj_201_func_run02.nii' # doctest: +SKIP >>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii") @@ -206,7 +212,7 @@ class Rename(IOBase): >>> rename3.inputs.subject_id = "subj_201" >>> rename3.inputs.run = 2 >>> res = rename3.run() # doctest: +SKIP - >>> print res.outputs.out_file # doctest: +SKIP + >>> res.outputs.out_file # doctest: +SKIP 'subj_201_epi_run02.nii' # doctest: +SKIP """ @@ -401,8 +407,8 @@ def __init__(self, input_names, output_names, function=None, imports=None, raise Exception('Interface Function does not accept ' \ 'function objects defined interactively ' \ 'in a python session') - elif isinstance(function, six.string_types): - self.inputs.function_str = dumps(function) + elif isinstance(function, string_types): + self.inputs.function_str = function else: raise Exception('Unknown type of function') self.inputs.on_trait_change(self._set_function_string, @@ -419,8 +425,8 @@ def _set_function_string(self, obj, name, old, new): if name == 'function_str': if hasattr(new, '__call__'): function_source = getsource(new) - elif isinstance(new, six.string_types): - function_source = dumps(new) + elif isinstance(new, string_types): + function_source = new self.inputs.trait_set(trait_change_notify=False, **{'%s' % name: function_source}) diff --git a/nipype/interfaces/vista/tests/__init__.py b/nipype/interfaces/vista/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index b16fa51926..4996b2b8de 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.vista.vista import Vnifti2Image +from ....testing import assert_equal +from ..vista import Vnifti2Image def test_Vnifti2Image_inputs(): input_map = dict(args=dict(argstr='%s', @@ -30,8 +30,8 @@ def test_Vnifti2Image_inputs(): ) inputs = Vnifti2Image.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_Vnifti2Image_outputs(): @@ -39,7 +39,7 @@ def test_Vnifti2Image_outputs(): ) outputs = Vnifti2Image.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 4bca4a88c6..713dd9dbc6 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.vista.vista import VtoMat +from ....testing import assert_equal +from ..vista import VtoMat def test_VtoMat_inputs(): input_map = dict(args=dict(argstr='%s', @@ -27,8 +27,8 @@ def test_VtoMat_inputs(): ) inputs = VtoMat.input_spec() - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value def test_VtoMat_outputs(): @@ -36,7 +36,7 @@ def test_VtoMat_outputs(): ) outputs = VtoMat.output_spec() - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/pipeline/__init__.py b/nipype/pipeline/__init__.py index 7edd081511..b7a6afe20e 100644 --- a/nipype/pipeline/__init__.py +++ b/nipype/pipeline/__init__.py @@ -4,5 +4,7 @@ Package contains modules for generating pipelines using interfaces """ + +from __future__ import absolute_import __docformat__ = 'restructuredtext' -from engine import Node, MapNode, JoinNode, Workflow +from .engine import Node, MapNode, JoinNode, Workflow diff --git a/nipype/pipeline/engine.py b/nipype/pipeline/engine.py index 70b8e71754..c4d621a5e0 100644 --- a/nipype/pipeline/engine.py +++ b/nipype/pipeline/engine.py @@ -12,15 +12,20 @@ """ +from future import standard_library +standard_library.install_aliases() +from builtins import range +from builtins import object + from datetime import datetime from nipype.utils.misc import flatten, unflatten -from nipype.interfaces.traits_extension import File try: from collections import OrderedDict except ImportError: from ordereddict import OrderedDict + from copy import deepcopy -import cPickle +import pickle from glob import glob import gzip import inspect @@ -29,20 +34,18 @@ import re import shutil import errno +import socket from shutil import rmtree -from socket import gethostname -from string import Template import sys from tempfile import mkdtemp from warnings import warn from hashlib import sha1 -from nipype.external import six import numpy as np +import networkx as nx from ..utils.misc import package_check, str2bool package_check('networkx', '1.3') -import networkx as nx from .. import config, logging logger = logging.getLogger('workflow') @@ -50,14 +53,15 @@ Undefined, TraitedSpec, DynamicTraitedSpec, Bunch, InterfaceResult, md5, Interface, TraitDictObject, TraitListObject, isdefined) -from ..utils.misc import getsource, create_function_from_source +from ..utils.misc import (getsource, create_function_from_source, + flatten, unflatten) from ..utils.filemanip import (save_json, FileNotFoundError, filename_to_list, list_to_filename, copyfiles, fnames_presuffix, loadpkl, split_filename, load_json, savepkl, write_rst_header, write_rst_dict, write_rst_list) - +from ..external.six import string_types from .utils import (generate_expanded_graph, modify_paths, export_graph, make_output_dir, write_workflow_prov, clean_working_directory, format_dot, topological_sort, @@ -67,18 +71,18 @@ def _write_inputs(node): lines = [] nodename = node.fullname.replace('.', '_') - for key, _ in node.inputs.items(): + for key, _ in list(node.inputs.items()): val = getattr(node.inputs, key) if isdefined(val): if type(val) == str: try: func = create_function_from_source(val) - except RuntimeError, e: + except RuntimeError as e: lines.append("%s.inputs.%s = '%s'" % (nodename, key, val)) else: - funcname = [name for name in func.func_globals + funcname = [name for name in func.__globals__ if name != '__builtins__'][0] - lines.append(cPickle.loads(val)) + lines.append(pickle.loads(val)) if funcname == nodename: lines[-1] = lines[-1].replace(' %s(' % funcname, ' %s_1(' % funcname) @@ -101,7 +105,7 @@ def format_node(node, format='python', include_config=False): importline = 'from %s import %s' % (klass.__module__, klass.__class__.__name__) comment = '# Node: %s' % node.fullname - spec = inspect.getargspec(node._interface.__init__) + spec = inspect.signature(node._interface.__init__) args = spec.args[1:] if args: filled_args = [] @@ -364,7 +368,7 @@ def connect(self, *args, **kwargs): # handles the case that source is specified # with a function sourcename = source[0] - elif isinstance(source, six.string_types): + elif isinstance(source, string_types): sourcename = source else: raise Exception(('Unknown source specification in ' @@ -385,7 +389,7 @@ def connect(self, *args, **kwargs): # turn functions into strings for srcnode, destnode, connects in connection_list: for idx, (src, dest) in enumerate(connects): - if isinstance(src, tuple) and not isinstance(src[1], six.string_types): + if isinstance(src, tuple) and not isinstance(src[1], string_types): function_source = getsource(src[1]) connects[idx] = ((src[0], function_source, src[2:]), dest) @@ -626,7 +630,7 @@ def export(self, filename=None, prefix="output", format="python", funcname = functions[args[1]] else: func = create_function_from_source(args[1]) - funcname = [name for name in func.func_globals + funcname = [name for name in func.__globals__ if name != '__builtins__'][0] functions[args[1]] = funcname args[1] = funcname @@ -642,7 +646,7 @@ def export(self, filename=None, prefix="output", format="python", lines.append(connect_template2 % line_args) functionlines = ['# Functions'] for function in functions: - functionlines.append(cPickle.loads(function).rstrip()) + functionlines.append(pickle.loads(function).rstrip()) all_lines = importlines + functionlines + lines if not filename: @@ -665,7 +669,7 @@ def run(self, plugin=None, plugin_args=None, updatehash=False): """ if plugin is None: plugin = config.get('execution', 'plugin') - if type(plugin) is not str: + if not isinstance(plugin, string_types): runner = plugin else: name = 'nipype.pipeline.plugins' @@ -775,13 +779,10 @@ def _set_needed_outputs(self, graph): node.needed_outputs = [] for edge in graph.out_edges_iter(node): data = graph.get_edge_data(*edge) - for sourceinfo, _ in sorted(data['connect']): - if isinstance(sourceinfo, tuple): - input_name = sourceinfo[0] - else: - input_name = sourceinfo - if input_name not in node.needed_outputs: - node.needed_outputs += [input_name] + sourceinfo = [v1[0] if isinstance(v1, tuple) else v1 + for v1, v2 in data['connect']] + node.needed_outputs += [v for v in sourceinfo + if v not in node.needed_outputs] if node.needed_outputs: node.needed_outputs = sorted(node.needed_outputs) @@ -865,7 +866,7 @@ def _get_inputs(self): for cd in d['connect']: taken_inputs.append(cd[1]) unconnectedinputs = TraitedSpec() - for key, trait in node.inputs.items(): + for key, trait in list(node.inputs.items()): if key not in taken_inputs: unconnectedinputs.add_trait(key, traits.Trait(trait, @@ -886,7 +887,7 @@ def _get_outputs(self): setattr(outputdict, node.name, node.outputs) elif node.outputs: outputs = TraitedSpec() - for key, _ in node.outputs.items(): + for key, _ in list(node.outputs.items()): outputs.add_trait(key, traits.Any(node=node)) setattr(outputs, key, None) setattr(outputdict, node.name, outputs) @@ -899,7 +900,7 @@ def _set_input(self, object, name, newvalue): def _set_node_input(self, node, param, source, sourceinfo): """Set inputs of a node given the edge connection""" - if isinstance(sourceinfo, six.string_types): + if isinstance(sourceinfo, string_types): val = source.get_output(sourceinfo) elif isinstance(sourceinfo, tuple): if callable(sourceinfo[1]): @@ -1467,9 +1468,9 @@ def _get_hashval(self): rm_extra = self.config['execution']['remove_unnecessary_outputs'] if str2bool(rm_extra) and self.needed_outputs: hashobject = md5() - hashobject.update(hashvalue) + hashobject.update(hashvalue.encode()) sorted_outputs = sorted(self.needed_outputs) - hashobject.update(str(sorted_outputs)) + hashobject.update(str(sorted_outputs).encode()) hashvalue = hashobject.hexdigest() hashed_inputs.append(('needed_outputs', sorted_outputs)) return hashed_inputs, hashvalue @@ -1483,9 +1484,9 @@ def _save_hashfile(self, hashfile, hashed_inputs): # XXX - SG current workaround is to just # create the hashed file and not put anything # in it - fd = open(hashfile, 'wt') - fd.writelines(str(hashed_inputs)) - fd.close() + with open(hashfile, 'wt') as fd: + fd.writelines(str(hashed_inputs)) + logger.debug(('Unable to write a particular type to the json ' 'file')) else: @@ -1499,7 +1500,7 @@ def _get_inputs(self): other data sources (e.g., XNAT, HTTP, etc.,.) """ logger.debug('Setting node inputs') - for key, info in self.input_source.items(): + for key, info in list(self.input_source.items()): logger.debug('input: %s' % key) results_file = info[0] logger.debug('results file: %s' % results_file) @@ -1521,7 +1522,7 @@ def _get_inputs(self): logger.debug('output: %s' % output_name) try: self.set_input(key, deepcopy(output_value)) - except traits.TraitError, e: + except traits.TraitError as e: msg = ['Error setting node input:', 'Node: %s' % self.name, 'input: %s' % key, @@ -1578,8 +1579,8 @@ def _load_resultfile(self, cwd): if op.exists(resultsoutputfile): pkl_file = gzip.open(resultsoutputfile, 'rb') try: - result = cPickle.load(pkl_file) - except (traits.TraitError, AttributeError, ImportError), err: + result = pickle.load(pkl_file) + except (traits.TraitError, AttributeError, ImportError) as err: if isinstance(err, (AttributeError, ImportError)): attribute_error = True logger.debug(('attribute error: %s probably using ' @@ -1619,8 +1620,8 @@ def _load_results(self, cwd): needed_outputs=self.needed_outputs) runtime = Bunch(cwd=cwd, returncode=0, - environ=deepcopy(os.environ.data), - hostname=gethostname()) + environ=dict(os.environ), + hostname=socket.gethostname()) result = InterfaceResult( interface=self._interface.__class__, runtime=runtime, @@ -1639,8 +1640,8 @@ def _run_command(self, execute, copyfiles=True): self._originputs = deepcopy(self._interface.inputs) if execute: runtime = Bunch(returncode=1, - environ=deepcopy(os.environ.data), - hostname=gethostname()) + environ=dict(os.environ), + hostname=socket.gethostname()) result = InterfaceResult( interface=self._interface.__class__, runtime=runtime, @@ -1652,7 +1653,7 @@ def _run_command(self, execute, copyfiles=True): if issubclass(self._interface.__class__, CommandLine): try: cmd = self._interface.cmdline - except Exception, msg: + except Exception as msg: self._result.runtime.stderr = msg raise cmdfile = op.join(cwd, 'command.txt') @@ -1662,7 +1663,7 @@ def _run_command(self, execute, copyfiles=True): logger.info('Running: %s' % cmd) try: result = self._interface.run() - except Exception, msg: + except Exception as msg: self._result.runtime.stderr = msg raise @@ -1847,7 +1848,7 @@ def __init__(self, interface, name, joinsource, joinfield=None, if not joinfield: # default is the interface fields joinfield = self._interface.inputs.copyable_trait_names() - elif isinstance(joinfield, six.string_types): + elif isinstance(joinfield, string_types): joinfield = [joinfield] self.joinfield = joinfield """the fields to join""" @@ -1944,7 +1945,7 @@ def _override_join_traits(self, basetraits, fields): if not basetraits.trait(field): raise ValueError("The JoinNode %s does not have a field" " named %s" % (self.name, field)) - for name, trait in basetraits.items(): + for name, trait in list(basetraits.items()): # if a join field has a single inner trait, then the item # trait is that inner trait. Otherwise, the item trait is # a new Any trait. @@ -2057,7 +2058,7 @@ def __init__(self, interface, iterfield, name, serial=False, nested=False, **kwa super(MapNode, self).__init__(interface, name, **kwargs) - if isinstance(iterfield, six.string_types): + if isinstance(iterfield, string_types): iterfield = [iterfield] self.iterfield = iterfield self.nested = nested @@ -2073,7 +2074,7 @@ def _create_dynamic_traits(self, basetraits, fields=None, nitems=None): output = DynamicTraitedSpec() if fields is None: fields = basetraits.copyable_trait_names() - for name, spec in basetraits.items(): + for name, spec in list(basetraits.items()): if name in fields and ((nitems is None) or (nitems > 1)): logger.debug('adding multipath trait: %s' % name) if self.nested: @@ -2132,9 +2133,9 @@ def _get_hashval(self): rm_extra = self.config['execution']['remove_unnecessary_outputs'] if str2bool(rm_extra) and self.needed_outputs: hashobject = md5() - hashobject.update(hashvalue) + hashobject.update(hashvalue.encode()) sorted_outputs = sorted(self.needed_outputs) - hashobject.update(str(sorted_outputs)) + hashobject.update(str(sorted_outputs).encode()) hashvalue = hashobject.hexdigest() hashed_inputs.append(('needed_outputs', sorted_outputs)) return hashed_inputs, hashvalue @@ -2183,7 +2184,7 @@ def _node_runner(self, nodes, updatehash=False): err = None try: node.run(updatehash=updatehash) - except Exception, err: + except Exception as err: if str2bool(self.config['execution']['stop_on_first_crash']): self._result = node.result raise @@ -2205,7 +2206,7 @@ def _collate_results(self, nodes): self._result.provenance.insert(i, node.result.provenance) returncode.insert(i, err) if self.outputs: - for key, _ in self.outputs.items(): + for key, _ in list(self.outputs.items()): rm_extra = (self.config['execution'] ['remove_unnecessary_outputs']) if str2bool(rm_extra) and self.needed_outputs: @@ -2223,7 +2224,7 @@ def _collate_results(self, nodes): setattr(self._result.outputs, key, values) if self.nested: - for key, _ in self.outputs.items(): + for key, _ in list(self.outputs.items()): values = getattr(self._result.outputs, key) if isdefined(values): values = unflatten(values, filename_to_list(getattr(self.inputs, self.iterfield[0]))) diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index b987dcfc13..1413ba2c75 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -3,6 +3,9 @@ """Common graph operations for execution """ +from builtins import range +from builtins import object + from copy import deepcopy from glob import glob import os @@ -513,7 +516,7 @@ def _get_result(self, taskid): glob(os.path.join(node_dir, 'result_*.pklz')).pop() timed_out = False break - except Exception, e: + except Exception as e: logger.debug(e) sleep(2) if timed_out: @@ -529,7 +532,7 @@ def _get_result(self, taskid): 'Node working directory: ({2}) '.format( taskid,timeout,node_dir) ) raise IOError(error_message) - except IOError, e: + except IOError as e: result_data['traceback'] = format_exc() else: results_file = glob(os.path.join(node_dir, 'result_*.pklz'))[0] diff --git a/nipype/pipeline/plugins/condor.py b/nipype/pipeline/plugins/condor.py index 00db00ef74..19f2b68ba1 100644 --- a/nipype/pipeline/plugins/condor.py +++ b/nipype/pipeline/plugins/condor.py @@ -95,7 +95,7 @@ def _submit_batchtask(self, scriptfile, node): while True: try: result = cmd.run() - except Exception, e: + except Exception as e: if tries < self._max_tries: tries += 1 sleep(self._retry_timeout) # sleep 2 seconds and try again. diff --git a/nipype/pipeline/plugins/ipython.py b/nipype/pipeline/plugins/ipython.py index 87cb0d686d..10576d8e5c 100644 --- a/nipype/pipeline/plugins/ipython.py +++ b/nipype/pipeline/plugins/ipython.py @@ -3,7 +3,10 @@ """Parallel workflow execution via IPython controller """ -from cPickle import dumps +from future import standard_library +standard_library.install_aliases() + +from pickle import dumps import sys @@ -27,7 +30,7 @@ def execute_task(pckld_task, node_config, updatehash): try: config.update_config(node_config) logging.update_logging(config) - from cPickle import loads + from pickle import loads task = loads(pckld_task) result = task.run(updatehash=updatehash) except: @@ -63,7 +66,7 @@ def run(self, graph, config, updatehash=False): "will be unavailable") try: self.taskclient = self.iparallel.Client() - except Exception, e: + except Exception as e: if isinstance(e, TimeoutError): raise Exception("No IPython clients found.") if isinstance(e, IOError): diff --git a/nipype/pipeline/plugins/ipythonx.py b/nipype/pipeline/plugins/ipythonx.py index 28418f142f..38066589a2 100644 --- a/nipype/pipeline/plugins/ipythonx.py +++ b/nipype/pipeline/plugins/ipythonx.py @@ -40,7 +40,7 @@ def run(self, graph, config, updatehash=False): "will be unavailable") try: self.taskclient = self.ipyclient.TaskClient() - except Exception, e: + except Exception as e: if isinstance(e, ConnectionRefusedError): raise Exception("No IPython clients found.") if isinstance(e, ValueError): diff --git a/nipype/pipeline/plugins/lsf.py b/nipype/pipeline/plugins/lsf.py index 94f75802e4..5b03ab6a73 100644 --- a/nipype/pipeline/plugins/lsf.py +++ b/nipype/pipeline/plugins/lsf.py @@ -96,7 +96,7 @@ def _submit_batchtask(self, scriptfile, node): while True: try: result = cmd.run() - except Exception, e: + except Exception as e: if tries < self._max_tries: tries += 1 sleep( diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py index 61d2f165d2..089a8288e8 100644 --- a/nipype/pipeline/plugins/pbs.py +++ b/nipype/pipeline/plugins/pbs.py @@ -89,7 +89,7 @@ def _submit_batchtask(self, scriptfile, node): while True: try: result = cmd.run() - except Exception, e: + except Exception as e: if tries < self._max_tries: tries += 1 sleep(self._retry_timeout) # sleep 2 seconds and try again. diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index c2495a831f..8005cd5a08 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -1,6 +1,8 @@ """Parallel workflow execution via SGE """ +from builtins import object + import os import pwd import re @@ -24,7 +26,7 @@ def sge_debug_print(message): # print DEBUGGING_PREFIX + " " + "=!" * 3 + " " + message -class QJobInfo: +class QJobInfo(object): """Information about a single job created by OGE/SGE or similar Each job is responsible for knowing it's own refresh state @@ -95,7 +97,7 @@ def set_state(self, new_state): self._job_queue_state = new_state -class QstatSubstitute: +class QstatSubstitute(object): """A wrapper for Qstat to avoid overloading the SGE/OGS server with rapid continuous qstat requests""" @@ -209,7 +211,7 @@ def _parse_qstat_job_list(self, xml_job_list): # were started and finished, and pushed out of the window of review # before their state being recorded. The qacct command is slower, but # much more robust for ensuring that a job has completed. - for dictionary_job in self._task_dictionary.keys(): + for dictionary_job in list(self._task_dictionary.keys()): if dictionary_job not in current_jobs_parsed: is_completed = self._qacct_verified_complete(dictionary_job) if is_completed: @@ -271,7 +273,7 @@ def _run_qstat(self, reason_for_qstat, force_instant=True): def print_dictionary(self): """For debugging""" - for vv in self._task_dictionary.values(): + for vv in list(self._task_dictionary.values()): sge_debug_print(str(vv)) def is_job_pending(self, task_id): @@ -398,7 +400,7 @@ def _submit_batchtask(self, scriptfile, node): while True: try: result = cmd.run() - except Exception, e: + except Exception as e: if tries < self._max_tries: tries += 1 time.sleep( diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index cd3803157b..04218589c3 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -106,7 +106,7 @@ def _submit_batchtask(self, scriptfile, node): while True: try: result = cmd.run() - except Exception, e: + except Exception as e: if tries < self._max_tries: tries += 1 sleep(self._retry_timeout) # sleep 2 seconds and try again. diff --git a/nipype/pipeline/plugins/somaflow.py b/nipype/pipeline/plugins/somaflow.py index b54262d4aa..915b0e373e 100644 --- a/nipype/pipeline/plugins/somaflow.py +++ b/nipype/pipeline/plugins/somaflow.py @@ -31,7 +31,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes): jobs.append(Job(command=[sys.executable, fname], name=name)) - for key, values in dependencies.items(): + for key, values in list(dependencies.items()): for val in values: soma_deps.append((jobs[val], jobs[key])) diff --git a/nipype/pipeline/plugins/tests/test_callback.py b/nipype/pipeline/plugins/tests/test_callback.py index d70c65a012..db02bc889b 100644 --- a/nipype/pipeline/plugins/tests/test_callback.py +++ b/nipype/pipeline/plugins/tests/test_callback.py @@ -3,6 +3,8 @@ """Tests for workflow callbacks """ + +from builtins import object from tempfile import mkdtemp from shutil import rmtree @@ -19,7 +21,7 @@ def bad_func(): raise Exception -class Status: +class Status(object): def __init__(self): self.statuses = [] diff --git a/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py b/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py index 472b4dd158..0b9dc3af0b 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py +++ b/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py @@ -1,3 +1,4 @@ +from builtins import range import os from tempfile import mkdtemp from shutil import rmtree @@ -42,7 +43,7 @@ def dummyFunction(filename): with open(filename, 'w') as f: f.write(str(j)) - for n in xrange(numberOfThreads): + for n in range(numberOfThreads): # mark thread as alive a[n] = True @@ -62,7 +63,7 @@ def dummyFunction(filename): time.sleep(1) - for n in xrange(numberOfThreads): + for n in range(numberOfThreads): a[n] = t[n].is_alive() diff --git a/nipype/pipeline/tests/test_engine.py b/nipype/pipeline/tests/test_engine.py index 944e583c31..020476fbda 100644 --- a/nipype/pipeline/tests/test_engine.py +++ b/nipype/pipeline/tests/test_engine.py @@ -2,6 +2,8 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Tests for the engine module """ + +from __future__ import print_function from copy import deepcopy from glob import glob import os @@ -13,7 +15,7 @@ from nipype.testing import (assert_raises, assert_equal, assert_true, assert_false) import nipype.interfaces.base as nib import nipype.pipeline.engine as pe -from nipype import logging + class InputSpec(nib.TraitedSpec): input1 = nib.traits.Int(desc='a random int') @@ -228,34 +230,46 @@ def test_synchronize_expansion(): def test_synchronize_tuples_expansion(): import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(),name='node1') - node2 = pe.Node(TestInterface(),name='node2') - node1.iterables = [('input1','input2'), [(1,3), (2,4), (None,5)]] + + node1 = pe.Node(TestInterface(), name='node1') + node2 = pe.Node(TestInterface(), name='node2') + node1.iterables = [('input1', 'input2'), [(1, 3), (2, 4), (None, 5)]] + node1.synchronize = True - wf1.connect(node1,'output1', node2, 'input2') + + wf1.connect(node1, 'output1', node2, 'input2') + wf3 = pe.Workflow(name='group') - for i in [0,1,2]: + for i in [0, 1, 2]: wf3.add_nodes([wf1.clone(name='test%d'%i)]) + wf3._flatgraph = wf3._create_flat_graph() # Identical to test_synchronize_expansion yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 18 def test_itersource_expansion(): import nipype.pipeline.engine as pe + wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(),name='node1') - node1.iterables = ('input1',[1,2]) - node2 = pe.Node(TestInterface(),name='node2') - wf1.connect(node1,'output1', node2, 'input1') - node3 = pe.Node(TestInterface(),name='node3') + node1 = pe.Node(TestInterface(), name='node1') + node1.iterables = ('input1', [1, 2]) + + node2 = pe.Node(TestInterface(), name='node2') + wf1.connect(node1, 'output1', node2, 'input1') + + node3 = pe.Node(TestInterface(), name='node3') node3.itersource = ('node1', 'input1') - node3.iterables = [('input1', {1:[3,4], 2:[5,6,7]})] - wf1.connect(node2,'output1', node3, 'input1') - node4 = pe.Node(TestInterface(),name='node4') - wf1.connect(node3,'output1', node4, 'input1') + node3.iterables = [('input1', {1: [3, 4], 2: [5, 6, 7]})] + + wf1.connect(node2, 'output1', node3, 'input1') + node4 = pe.Node(TestInterface(), name='node4') + + wf1.connect(node3, 'output1', node4, 'input1') + wf3 = pe.Workflow(name='group') - for i in [0,1,2]: + for i in [0, 1, 2]: wf3.add_nodes([wf1.clone(name='test%d'%i)]) + wf3._flatgraph = wf3._create_flat_graph() # each expanded graph clone has: @@ -272,14 +286,14 @@ def test_itersource_synchronize1_expansion(): import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') node1 = pe.Node(TestInterface(),name='node1') - node1.iterables = [('input1',[1,2]), ('input2',[3,4])] + node1.iterables = [('input1', [1, 2]), ('input2', [3, 4])] node1.synchronize = True node2 = pe.Node(TestInterface(),name='node2') - wf1.connect(node1,'output1', node2, 'input1') + wf1.connect(node1, 'output1', node2, 'input1') node3 = pe.Node(TestInterface(),name='node3') node3.itersource = ('node1', ['input1', 'input2']) - node3.iterables = [('input1', {(1,3):[5,6]}), - ('input2', {(1,3):[7,8], (2,4): [9]})] + node3.iterables = [('input1', {(1, 3): [5, 6]}), + ('input2', {(1, 3): [7, 8], (2, 4): [9]})] wf1.connect(node2,'output1', node3, 'input1') node4 = pe.Node(TestInterface(),name='node4') wf1.connect(node3,'output1', node4, 'input1') @@ -301,6 +315,7 @@ def test_itersource_synchronize1_expansion(): def test_itersource_synchronize2_expansion(): import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') + node1 = pe.Node(TestInterface(),name='node1') node1.iterables = [('input1',[1,2]), ('input2',[3,4])] node1.synchronize = True @@ -390,8 +405,8 @@ def test_doubleconnect(): import nipype.pipeline.engine as pe import nipype.interfaces.spm as spm import os +from nipype.external.six import StringIO from nipype.utils.config import config -from StringIO import StringIO config.readfp(StringIO(""" [execution] @@ -485,7 +500,7 @@ def func1(in1): name='n1') n1.inputs.in1 = [[1,[2]],3,[4,5]] n1.run() - print n1.get_output('out') + print(n1.get_output('out')) yield assert_equal, n1.get_output('out'), [[2,[3]],4,[5,6]] n2 = MapNode(Function(input_names=['in1'], @@ -498,7 +513,7 @@ def func1(in1): error_raised = False try: n2.run() - except Exception, e: + except Exception as e: pe.logger.info('Exception: %s' % str(e)) error_raised = True yield assert_true, error_raised @@ -539,7 +554,7 @@ def _submit_job(self, node, updatehash=False): raise Exception('Submit called') try: w1.run(plugin=RaiseError()) - except Exception, e: + except Exception as e: pe.logger.info('Exception: %s' % str(e)) error_raised = True yield assert_true, error_raised @@ -553,7 +568,7 @@ def _submit_job(self, node, updatehash=False): error_raised = False try: w1.run(plugin=RaiseError()) - except Exception, e: + except Exception as e: pe.logger.info('Exception: %s' % str(e)) error_raised = True yield assert_false, error_raised @@ -588,7 +603,7 @@ def func2(a): error_raised = False try: w1.run(plugin='Linear') - except Exception, e: + except Exception as e: pe.logger.info('Exception: %s' % str(e)) error_raised = True yield assert_false, error_raised @@ -670,7 +685,7 @@ def func1(in1): error_raised = False try: w1.run(plugin='MultiProc') - except Exception, e: + except Exception as e: pe.logger.info('Exception: %s' % str(e)) error_raised = True yield assert_false, error_raised @@ -683,7 +698,7 @@ def func1(in1): error_raised = False try: w1.run(plugin='MultiProc') - except Exception, e: + except Exception as e: pe.logger.info('Exception: %s' % str(e)) error_raised = True yield assert_false, error_raised diff --git a/nipype/pipeline/tests/test_join.py b/nipype/pipeline/tests/test_join.py index 00293fb816..ab58fbacb5 100644 --- a/nipype/pipeline/tests/test_join.py +++ b/nipype/pipeline/tests/test_join.py @@ -2,13 +2,11 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Tests for join expansion """ -from copy import deepcopy + import os from shutil import rmtree from tempfile import mkdtemp -import networkx as nx - from nipype.testing import (assert_equal, assert_true) import nipype.interfaces.base as nib import nipype.pipeline.engine as pe @@ -399,7 +397,7 @@ def test_multifield_join_node(): assert_equal(len(result.nodes()), 10, "The number of expanded nodes is incorrect.") # the product inputs are [2, 4], [2, 5], [3, 4], [3, 5] - assert_equal(_products, [8, 10, 12, 15], + assert_equal(set(_products), set([8, 10, 12, 15]), "The post-join products is incorrect: %s." % _products) os.chdir(cwd) diff --git a/nipype/pipeline/tests/test_utils.py b/nipype/pipeline/tests/test_utils.py index 129a654418..6c7f19d160 100644 --- a/nipype/pipeline/tests/test_utils.py +++ b/nipype/pipeline/tests/test_utils.py @@ -2,6 +2,8 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Tests for the engine utils module """ + +from builtins import range import os from copy import deepcopy from tempfile import mkdtemp diff --git a/nipype/pipeline/utils.py b/nipype/pipeline/utils.py index 73f251049a..d6bb996140 100644 --- a/nipype/pipeline/utils.py +++ b/nipype/pipeline/utils.py @@ -3,20 +3,34 @@ """Utility routines for workflow graphs """ +from future import standard_library +standard_library.install_aliases() + +from builtins import map +from builtins import next +from builtins import zip +from builtins import range + +try: + import itertools.imap as map +except ImportError: + pass + +from collections import OrderedDict from copy import deepcopy from glob import glob from collections import defaultdict import os import re - import numpy as np from nipype.utils.misc import package_check -from nipype.external import six +from functools import reduce package_check('networkx', '1.3') import networkx as nx +from ..external.six import string_types from ..utils.filemanip import (fname_presuffix, FileNotFoundError, filename_to_list, get_related_files) from ..utils.misc import create_function_from_source, str2bool @@ -100,7 +114,7 @@ def modify_paths(object, relative=True, basedir=None): out = tuple(out) else: if isdefined(object): - if isinstance(object, six.string_types) and os.path.isfile(object): + if isinstance(object, string_types) and os.path.isfile(object): if relative: if config.getboolean('execution', 'use_relative_paths'): out = relpath(object, start=basedir) @@ -183,7 +197,7 @@ def _write_detailed_dot(graph, dotfilename): inports = [] for u, v, d in graph.in_edges_iter(nbunch=n, data=True): for cd in d['connect']: - if isinstance(cd[0], six.string_types): + if isinstance(cd[0], string_types): outport = cd[0] else: outport = cd[0][0] @@ -203,7 +217,7 @@ def _write_detailed_dot(graph, dotfilename): outports = [] for u, v, d in graph.out_edges_iter(nbunch=n, data=True): for cd in d['connect']: - if isinstance(cd[0], six.string_types): + if isinstance(cd[0], string_types): outport = cd[0] else: outport = cd[0][0] @@ -252,7 +266,7 @@ def expand_iterables(iterables, synchronize=False): if synchronize: return synchronize_iterables(iterables) else: - return list(walk(iterables.items())) + return list(walk(list(iterables.items()))) def count_iterables(iterables, synchronize=False): """Return the number of iterable expansion nodes. @@ -266,7 +280,7 @@ def count_iterables(iterables, synchronize=False): op = max else: op = lambda x,y: x*y - return reduce(op, [len(func()) for _, func in iterables.iteritems()]) + return reduce(op, [len(func()) for _, func in iterables.items()]) def walk(children, level=0, path=None, usename=True): """Generate all the full paths in a tree, as a dict. @@ -275,8 +289,10 @@ def walk(children, level=0, path=None, usename=True): -------- >>> from nipype.pipeline.utils import walk >>> iterables = [('a', lambda: [1, 2]), ('b', lambda: [3, 4])] - >>> list(walk(iterables)) - [{'a': 1, 'b': 3}, {'a': 1, 'b': 4}, {'a': 2, 'b': 3}, {'a': 2, 'b': 4}] + >>> [val['a'] for val in walk(iterables)] + [1, 1, 2, 2] + >>> [val['b'] for val in walk(iterables)] + [3, 4, 3, 4] """ # Entry point if level == 0: @@ -315,14 +331,22 @@ def synchronize_iterables(iterables): >>> synced == [{'a': 1, 'b': 3, 'c': 4}, {'a': 2, 'c': 5}, {'c': 6}] True """ - # Convert the (field, function) tuples into (field, value) lists - pair_lists = [[(field, value) for value in func()] - for field, func in iterables.iteritems()] - # A factory to make a dictionary from the mapped (field, value) - # key-value pairs. The filter removes any unmapped None items. - factory = lambda *pairs: dict(filter(None, pairs)) - # Make a dictionary for each of the correlated (field, value) items - return map(factory, *pair_lists) + out_list = [] + iterable_items = [(field, iter(fvals())) + for field, fvals in sorted(iterables.items())] + while True: + cur_dict = {} + for field, iter_values in iterable_items: + try: + cur_dict[field] = next(iter_values) + except StopIteration: + pass + if cur_dict: + out_list.append(cur_dict) + else: + break + + return out_list def evaluate_connect_function(function_source, args, first_arg): func = create_function_from_source(function_source) @@ -483,7 +507,7 @@ def _remove_identity_node(graph, node): """Remove identity nodes from an execution graph """ portinputs, portoutputs = _node_ports(graph, node) - for field, connections in portoutputs.items(): + for field, connections in list(portoutputs.items()): if portinputs: _propagate_internal_output(graph, node, field, connections, portinputs) @@ -594,8 +618,12 @@ def generate_expanded_graph(graph_in): jedge_dict = {} for jnode in jnodes: in_edges = jedge_dict[jnode] = {} + edges2remove = [] for src, dest, data in graph_in.in_edges_iter(jnode, True): in_edges[src._id] = data + edges2remove.append((src, dest)) + + for src, dest in edges2remove: graph_in.remove_edge(src, dest) logger.debug("Excised the %s -> %s join node in-edge." % (src, dest)) @@ -604,7 +632,7 @@ def generate_expanded_graph(graph_in): # the itersource is a (node name, fields) tuple src_name, src_fields = inode.itersource # convert a single field to a list - if isinstance(src_fields, six.string_types): + if isinstance(src_fields, string_types): src_fields = [src_fields] # find the unique iterable source node in the graph try: @@ -634,9 +662,10 @@ def generate_expanded_graph(graph_in): iter_dict = dict([(field, lookup[key]) for field, lookup in inode.iterables if key in lookup]) # convert the iterables to the standard {field: function} format - iter_items = map(lambda(field, value): (field, lambda: value), - iter_dict.iteritems()) - iterables = dict(iter_items) + def make_field_func(*pair): + return pair[0], lambda: pair[1] + + iterables = dict([make_field_func(*pair) for pair in iter_dict.items()]) else: iterables = inode.iterables.copy() inode.iterables = None @@ -674,14 +703,14 @@ def generate_expanded_graph(graph_in): # the edge source node replicates expansions = defaultdict(list) for node in graph_in.nodes_iter(): - for src_id, edge_data in old_edge_dict.iteritems(): + for src_id, edge_data in list(old_edge_dict.items()): if node._id.startswith(src_id): expansions[src_id].append(node) - for in_id, in_nodes in expansions.iteritems(): + for in_id, in_nodes in list(expansions.items()): logger.debug("The join node %s input %s was expanded" " to %d nodes." %(jnode, in_id, len(in_nodes))) # preserve the node iteration order by sorting on the node id - for in_nodes in expansions.itervalues(): + for in_nodes in list(expansions.values()): in_nodes.sort(key=lambda node: node._id) # the number of join source replicates. @@ -697,7 +726,7 @@ def generate_expanded_graph(graph_in): # field 'in' are qualified as ('out_file', 'in1') and # ('out_file', 'in2'), resp. This preserves connection port # integrity. - for old_id, in_nodes in expansions.iteritems(): + for old_id, in_nodes in list(expansions.items()): # reconnect each replication of the current join in-edge # source for in_idx, in_node in enumerate(in_nodes): @@ -771,7 +800,6 @@ def _iterable_nodes(graph_in): def _standardize_iterables(node): """Converts the given iterables to a {field: function} dictionary, if necessary, where the function returns a list.""" - # trivial case if not node.iterables: return iterables = node.iterables @@ -786,7 +814,7 @@ def _standardize_iterables(node): if node.synchronize: if len(iterables) == 2: first, last = iterables - if all((isinstance(item, six.string_types) and item in fields + if all((isinstance(item, string_types) and item in fields for item in first)): iterables = _transpose_iterables(first, last) @@ -800,8 +828,10 @@ def _standardize_iterables(node): # Convert a values list to a function. This is a legacy # Nipype requirement with unknown rationale. if not node.itersource: - iter_items = map(lambda(field, value): (field, lambda: value), - iterables) + def make_field_func(*pair): + return pair[0], lambda: pair[1] + + iter_items = [make_field_func(*field_value1) for field_value1 in iterables] iterables = dict(iter_items) node.iterables = iterables @@ -815,7 +845,7 @@ def _validate_iterables(node, iterables, fields): """ # The iterables can be a {field: value list} dictionary. if isinstance(iterables, dict): - iterables = iterables.items() + iterables = list(iterables.items()) elif not isinstance(iterables, tuple) and not isinstance(iterables, list): raise ValueError("The %s iterables type is not a list or a dictionary:" " %s" % (node.name, iterables.__class__)) @@ -824,7 +854,7 @@ def _validate_iterables(node, iterables, fields): if len(item) != 2: raise ValueError("The %s iterables is not a [(field, values)]" " list" % node.name) - except TypeError, e: + except TypeError as e: raise TypeError("A %s iterables member is not iterable: %s" % (node.name, e)) field, _ = item @@ -844,15 +874,15 @@ def _transpose_iterables(fields, values): """ if isinstance(values, dict): transposed = dict([(field, defaultdict(list)) for field in fields]) - for key, tuples in values.iteritems(): + for key, tuples in list(values.items()): for kvals in tuples: for idx, val in enumerate(kvals): if val != None: transposed[fields[idx]][key].append(val) - return transposed.items() + return list(transposed.items()) else: - return zip(fields, [filter(lambda(v): v != None, list(transpose)) - for transpose in zip(*values)]) + return list(zip(fields, [[v for v in list(transpose) if v != None] + for transpose in zip(*values)])) def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False, show_connectinfo=False, dotfilename='graph.dot', format='png', @@ -916,9 +946,17 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False, def format_dot(dotfilename, format=None): + """Dump a directed graph (Linux only; install via `brew` on OSX)""" cmd = 'dot -T%s -O \'%s\'' % (format, dotfilename) - CommandLine(cmd).run() - logger.info('Converting dotfile: %s to %s format' % (dotfilename, format)) + try: + CommandLine(cmd).run() + except IOError as ioe: + if "could not be found" in str(ioe): + raise IOError("Cannot draw directed graph; executable 'dot' is unavailable") + else: + raise ioe + else: + logger.info('Converting dotfile: %s to %s format' % (dotfilename, format)) def make_output_dir(outdir): @@ -958,7 +996,7 @@ def walk_outputs(object): if isdefined(val): out.extend(walk_outputs(val)) else: - if isdefined(object) and isinstance(object, six.string_types): + if isdefined(object) and isinstance(object, string_types): if os.path.islink(object) or os.path.isfile(object): out = [(filename, 'f') for filename in get_all_files(object)] elif os.path.isdir(object): @@ -978,7 +1016,7 @@ def clean_working_directory(outputs, cwd, inputs, needed_outputs, config, """ if not outputs: return - outputs_to_keep = outputs.get().keys() + outputs_to_keep = list(outputs.get().keys()) if needed_outputs and \ str2bool(config['execution']['remove_unnecessary_outputs']): outputs_to_keep = needed_outputs @@ -1048,10 +1086,17 @@ def merge_dict(d1, d2, merge=lambda x, y: y): Examples: >>> d1 = {'a': 1, 'c': 3, 'b': 2} - >>> merge_dict(d1, d1) - {'a': 1, 'c': 3, 'b': 2} - >>> merge_dict(d1, d1, lambda x,y: x+y) - {'a': 2, 'c': 6, 'b': 4} + >>> d2 = merge_dict(d1, d1) + >>> len(d2) + 3 + >>> [d2[k] for k in ['a', 'b', 'c']] + [1, 2, 3] + + >>> d3 = merge_dict(d1, d1, lambda x,y: x+y) + >>> len(d3) + 3 + >>> [d3[k] for k in ['a', 'b', 'c']] + [2, 4, 6] """ if not isinstance(d1, dict): @@ -1059,7 +1104,7 @@ def merge_dict(d1, d2, merge=lambda x, y: y): result = dict(d1) if d2 is None: return result - for k, v in d2.iteritems(): + for k, v in list(d2.items()): if k in result: result[k] = merge_dict(result[k], v, merge=merge) else: @@ -1100,7 +1145,7 @@ def write_workflow_prov(graph, filename=None, format='turtle'): if idx < len(result.inputs): subresult.inputs = result.inputs[idx] if result.outputs: - for key, value in result.outputs.items(): + for key, value in list(result.outputs.items()): values = getattr(result.outputs, key) if isdefined(values) and idx < len(values): subresult.outputs[key] = values[idx] diff --git a/nipype/pkg_info.py b/nipype/pkg_info.py index e107bcd622..b3982bb4cb 100644 --- a/nipype/pkg_info.py +++ b/nipype/pkg_info.py @@ -1,13 +1,18 @@ +from future import standard_library +standard_library.install_aliases() + import os import sys import subprocess + try: - from ConfigParser import ConfigParser + from configparser import ConfigParser except ImportError: from configparser import ConfigParser # python 3 COMMIT_INFO_FNAME = 'COMMIT_INFO.txt' + def pkg_commit_hash(pkg_path): ''' Get short form of commit hash given directory `pkg_path` diff --git a/nipype/testing/data/pyscript.m b/nipype/testing/data/pyscript.m deleted file mode 100644 index 8bf3ece9f1..0000000000 --- a/nipype/testing/data/pyscript.m +++ /dev/null @@ -1,16 +0,0 @@ -fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now)); -ver, -try, -if isempty(which('spm')), -throw(MException('SPMCheck:NotFound','SPM not in matlab path')); -end; -spm_path = spm('dir'); -[name, version] = spm('ver'); -fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version); -exit; - -,catch ME, -fprintf(2,'MATLAB code threw an exception:\n'); -fprintf(2,'%s\n',ME.message); -if length(ME.stack) ~= 0, fprintf(2,'File:%s\nName:%s\nLine:%d\n',ME.stack.file,ME.stack.name,ME.stack.line);, end; -end; \ No newline at end of file diff --git a/nipype/testing/decorators.py b/nipype/testing/decorators.py index 2591b76ea1..d225f5d1e9 100644 --- a/nipype/testing/decorators.py +++ b/nipype/testing/decorators.py @@ -5,7 +5,6 @@ """ from numpy.testing.decorators import * -from nipype.external import six from nibabel.data import DataError @@ -31,7 +30,7 @@ def make_label_dec(label, ds=None): Examples -------- >>> slow = make_label_dec('slow') - >>> print slow.__doc__ + >>> slow.__doc__ Labels a test as 'slow' >>> rare = make_label_dec(['slow','hard'], @@ -45,7 +44,7 @@ def make_label_dec(label, ds=None): >>> f.hard True """ - if isinstance(label,six.string_types): + if isinstance(label,str): labels = [label] else: labels = label diff --git a/nipype/utils/__init__.py b/nipype/utils/__init__.py index 80efb1a20a..93b967edb8 100644 --- a/nipype/utils/__init__.py +++ b/nipype/utils/__init__.py @@ -1,4 +1,5 @@ +from __future__ import absolute_import -from onetime import OneTimeProperty, setattr_on_read -from tmpdirs import TemporaryDirectory, InTemporaryDirectory +from .onetime import OneTimeProperty, setattr_on_read +from .tmpdirs import TemporaryDirectory, InTemporaryDirectory diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 0a86d1af26..c07136ecf7 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -8,16 +8,20 @@ @author: Chris Filo Gorgolewski ''' +from future import standard_library +standard_library.install_aliases() +from builtins import object -import ConfigParser +import configparser from json import load, dump import os import shutil import errno -from StringIO import StringIO from warnings import warn from ..external import portalocker +from ..external.six import StringIO + # Get home directory in platform-agnostic way homedir = os.path.expanduser('~') @@ -74,7 +78,7 @@ class NipypeConfig(object): """ def __init__(self, *args, **kwargs): - self._config = ConfigParser.ConfigParser() + self._config = configparser.ConfigParser() config_dir = os.path.expanduser('~/.nipype') mkdir_p(config_dir) old_config_file = os.path.expanduser('~/.nipype.cfg') @@ -121,6 +125,9 @@ def get(self, section, option): return self._config.get(section, option) def set(self, section, option, value): + if isinstance(value, bool): + value = str(value) + return self._config.set(section, option, value) def getboolean(self, section, option): @@ -157,7 +164,7 @@ def save_data(self, key, value): def update_config(self, config_dict): for section in ['execution', 'logging', 'check']: if section in config_dict: - for key, val in config_dict[section].items(): + for key, val in list(config_dict[section].items()): if not key.startswith('__'): self._config.set(section, key, str(val)) diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index 2a60d257e1..e5cf459ce0 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -16,7 +16,8 @@ import subprocess from nipype.interfaces.base import CommandLine from nipype.utils.misc import is_container -from nipype.external import six +from nipype.external.six import string_types + def grab_doc(cmd, trap_error=True): """Run cmd without args and grab documentation. @@ -72,7 +73,7 @@ def reverse_opt_map(opt_map): # if (k != 'flags' and v) , key must not be flags as it is generic, # v must not be None or it cannot be parsed by this line revdict = {} - for key, value in opt_map.items(): + for key, value in list(opt_map.items()): if is_container(value): # The value is a tuple where the first element is the # format string and the second element is a docstring. @@ -146,7 +147,7 @@ def insert_doc(doc, new_items): >>> new_items = ['infile : str', ' The name of the input file'] >>> new_items.extend(['outfile : str', ' The name of the output file']) >>> newdoc = insert_doc(doc, new_items) - >>> print newdoc + >>> print(newdoc) Parameters ---------- infile : str @@ -278,7 +279,7 @@ def _parse_doc(doc, style=['--']): # individual flag/option. doclist = doc.split('\n') optmap = {} - if isinstance(style,six.string_types): + if isinstance(style, string_types): style = [style] for line in doclist: linelist = line.split() @@ -360,6 +361,6 @@ def replace_opts(rep_doc, opts): """ # Replace flags with attribute names - for key, val in opts.items(): + for key, val in list(opts.items()): rep_doc = rep_doc.replace(key, val) return rep_doc diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index c9b2f14d20..9249dc294b 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -4,21 +4,24 @@ """ -import cPickle -from glob import glob +from future import standard_library +standard_library.install_aliases() + +import pickle import gzip import hashlib from hashlib import md5 -import json +import simplejson import os import re import shutil import numpy as np -from ..interfaces.traits_extension import isdefined from .misc import is_container from .config import mkdir_p +from ..external.six import string_types +from ..interfaces.traits_extension import isdefined from .. import logging, config fmlogger = logging.getLogger("filemanip") @@ -172,13 +175,12 @@ def hash_infile(afile, chunk_len=8192, crypto=hashlib.md5): hex = None if os.path.isfile(afile): crypto_obj = crypto() - fp = file(afile, 'rb') - while True: - data = fp.read(chunk_len) - if not data: - break - crypto_obj.update(data) - fp.close() + with open(afile, 'rb') as fp: + while True: + data = fp.read(chunk_len) + if not data: + break + crypto_obj.update(data) hex = crypto_obj.hexdigest() return hex @@ -189,8 +191,8 @@ def hash_timestamp(afile): if os.path.isfile(afile): md5obj = md5() stat = os.stat(afile) - md5obj.update(str(stat.st_size)) - md5obj.update(str(stat.st_mtime)) + md5obj.update(str(stat.st_size).encode()) + md5obj.update(str(stat.st_mtime).encode()) md5hex = md5obj.hexdigest() return md5hex @@ -270,7 +272,7 @@ def copyfile(originalfile, newfile, copy=False, create_new=False, nipype_hardlink_wrapper(originalfile, newfile) else: shutil.copyfile(originalfile, newfile) - except shutil.Error, e: + except shutil.Error as e: fmlogger.warn(e.message) else: fmlogger.debug("File: %s already exists, not overwriting, copy:%d" @@ -348,7 +350,7 @@ def copyfiles(filelist, dest, copy=False, create_new=False): def filename_to_list(filename): """Returns a list given either a string or a list """ - if isinstance(filename, (str, unicode)): + if isinstance(filename, (str, string_types)): return [filename] elif isinstance(filename, list): return filename @@ -380,9 +382,8 @@ def save_json(filename, data): """ - fp = file(filename, 'w') - json.dump(data, fp, sort_keys=True, indent=4) - fp.close() + with open(filename, 'w') as fp: + simplejson.dump(data, fp, sort_keys=True, indent=4) def load_json(filename): @@ -399,9 +400,8 @@ def load_json(filename): """ - fp = file(filename, 'r') - data = json.load(fp) - fp.close() + with open (filename, 'r') as fp: + data = simplejson.load(fp) return data def loadcrash(infile, *args): @@ -427,7 +427,7 @@ def loadpkl(infile): pkl_file = gzip.open(infile, 'rb') else: pkl_file = open(infile) - return cPickle.load(pkl_file) + return pickle.load(pkl_file) def savepkl(filename, record): @@ -435,7 +435,7 @@ def savepkl(filename, record): pkl_file = gzip.open(filename, 'wb') else: pkl_file = open(filename, 'wb') - cPickle.dump(record, pkl_file) + pickle.dump(record, pkl_file) pkl_file.close() rst_levels = ['=', '-', '~', '+'] diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index fed263bbf4..4088ec117d 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -1,3 +1,4 @@ +from builtins import object # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: @@ -108,7 +109,7 @@ def logdebug_dict_differences(self, dold, dnew, prefix=""): # tuples, we might need to cast them into the same type # as the last resort. And lets try to be more generic same = old.__class__(new) == old - except Exception, e: + except Exception as e: same = False if not same: msgs += ["%s: %r != %r" diff --git a/nipype/utils/matlabtools.py b/nipype/utils/matlabtools.py index 7e5b4e0d35..ad1daced57 100644 --- a/nipype/utils/matlabtools.py +++ b/nipype/utils/matlabtools.py @@ -2,6 +2,8 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """ Useful Functions for working with matlab""" +from builtins import range + # Stdlib imports import os import re diff --git a/nipype/utils/misc.py b/nipype/utils/misc.py index df932ec9e8..cccb0cc86d 100644 --- a/nipype/utils/misc.py +++ b/nipype/utils/misc.py @@ -2,7 +2,11 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Miscellaneous utility functions """ -from cPickle import dumps, loads + +from future import standard_library +standard_library.install_aliases() +from builtins import next +from pickle import dumps, loads import inspect from distutils.version import LooseVersion @@ -10,7 +14,10 @@ from textwrap import dedent import sys import re -from nipype.external.six import Iterator +from collections import Iterator + +from ..external.six import string_types + def human_order_sorted(l): """Sorts string in human order (i.e. 'stat10' will go after 'stat2')""" @@ -31,14 +38,14 @@ def trim(docstring, marker=None): # and split into a list of lines: lines = docstring.expandtabs().splitlines() # Determine minimum indentation (first line doesn't count): - indent = sys.maxint + indent = sys.maxsize for line in lines[1:]: stripped = line.lstrip() if stripped: indent = min(indent, len(line) - len(stripped)) # Remove indentation (first line is special): trimmed = [lines[0].strip()] - if indent < sys.maxint: + if indent < sys.maxsize: for line in lines[1:]: # replace existing REST marker with doc level marker stripped = line.lstrip().strip().rstrip() @@ -57,7 +64,7 @@ def trim(docstring, marker=None): def getsource(function): """Returns the source code of a function""" - src = dumps(dedent(inspect.getsource(function))) + src = dedent(inspect.getsource(function)) return src def create_function_from_source(function_source, imports=None): @@ -76,12 +83,11 @@ def create_function_from_source(function_source, imports=None): try: if imports is not None: for statement in imports: - exec statement in ns - import_keys = ns.keys() + exec(statement, ns) + import_keys = list(ns.keys()) + exec(function_source, ns) - exec loads(function_source) in ns - - except Exception, msg: + except Exception as msg: msg = str(msg) + '\nError executing function:\n %s\n'%function_source msg += '\n'.join(["Functions in connection strings have to be standalone.", "They cannot be declared either interactively or inside", @@ -114,7 +120,9 @@ def is_container(item): True if container False if not (eg string) """ - if hasattr(item, '__iter__'): + if isinstance(item, string_types): + return False + elif hasattr(item, '__iter__'): return True else: return False @@ -139,10 +147,10 @@ def container_to_string(cont): Container elements joined into a string. """ - if hasattr(cont, '__iter__'): - return ' '.join(cont) - else: - return str(cont) + if hasattr(cont, '__iter__') and not isinstance(cont, string_types): + return str(' '.join(cont)) + + return str(cont) # Dependency checks. Copied this from Nipy, with some modificiations @@ -205,7 +213,7 @@ def str2bool(v): elif lower in ("no", "false", "n", "f", "0"): return False else: - raise ValueError("%s cannot be converted to bool"%v) + raise ValueError("%s cannot be converted to bool" % v) def flatten(S): if S == []: @@ -219,7 +227,7 @@ def unflatten(in_list, prev_structure): in_list = iter(in_list) if not isinstance(prev_structure, list): - return in_list.next() + return next(in_list) else: out = [] for item in prev_structure: diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py index 0ca21e76a6..6b41e7a5ab 100644 --- a/nipype/utils/nipype2boutiques.py +++ b/nipype/utils/nipype2boutiques.py @@ -1,3 +1,4 @@ +from __future__ import print_function # This tool exports a Nipype interface in the Boutiques (https://github.com/boutiques) JSON format. # Boutiques tools can be imported in CBRAIN (https://github.com/aces/cbrain) among other platforms. # @@ -14,7 +15,7 @@ import argparse import inspect import sys -import json +import simplejson import tempfile from nipype.interfaces.base import Interface @@ -86,7 +87,7 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input tool_desc['inputs'].append(input) tool_desc['command-line']+= input['command-line-key']+" " if verbose: - print "-> Adding input "+input['name'] + print("-> Adding input "+input['name']) # Generates tool outputs for name,spec in sorted(outputs.traits(transient=None).items()): @@ -94,9 +95,9 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input if output['path-template'] != "": tool_desc['outputs'].append(output) if verbose: - print "-> Adding output "+output['name'] + print("-> Adding output "+output['name']) elif verbose: - print "xx Skipping output "+output['name']+" with no path template." + print("xx Skipping output "+output['name']+" with no path template.") if tool_desc['outputs'] == []: raise Exception("Tool has no output.") @@ -105,7 +106,7 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input for input in tool_desc['inputs']: del input['tempvalue'] - return json.dumps(tool_desc, indent=4, separators=(',', ': ')) + return simplejson.dumps(tool_desc, indent=4, separators=(',', ': ')) def get_boutiques_input(inputs,interface,input_name,spec,ignored_template_inputs,verbose,ignore_template_numbers): """ @@ -152,7 +153,7 @@ def get_boutiques_input(inputs,interface,input_name,spec,ignored_template_inputs setattr(interface.inputs,input_name,tempvalue) input['tempvalue'] = tempvalue if verbose: - print "oo Path-template creation using "+input['id']+"="+str(tempvalue) + print("oo Path-template creation using "+input['id']+"="+str(tempvalue)) # Now that temp values have been generated, set Boolean types to # Number (there is no Boolean type in Boutiques) diff --git a/nipype/utils/nipype_cmd.py b/nipype/utils/nipype_cmd.py index 749650ef51..66fb12f199 100644 --- a/nipype/utils/nipype_cmd.py +++ b/nipype/utils/nipype_cmd.py @@ -1,3 +1,4 @@ +from __future__ import print_function import os import argparse import inspect @@ -9,16 +10,16 @@ def listClasses(module=None): if module: __import__(module) pkg = sys.modules[module] - print "Available Interfaces:" - for k,v in pkg.__dict__.items(): + print("Available Interfaces:") + for k, v in sorted(list(pkg.__dict__.items())): if inspect.isclass(v) and issubclass(v, Interface): - print "\t%s"%k + print("\t%s"%k) def add_options(parser=None, module=None, function=None): interface = None if parser and module and function: __import__(module) - interface = getattr(sys.modules[module],function)() + interface = getattr(sys.modules[module], function)() inputs = interface.input_spec() for name, spec in sorted(interface.inputs.traits(transient=None).items()): @@ -30,20 +31,20 @@ def add_options(parser=None, module=None, function=None): if hasattr(spec, "mandatory") and spec.mandatory: if spec.is_trait_type(InputMultiPath): - args["nargs"]="+" + args["nargs"] = "+" parser.add_argument(name, help=desc, **args) else: if spec.is_trait_type(InputMultiPath): - args["nargs"]="*" + args["nargs"] = "*" parser.add_argument("--%s"%name, dest=name, help=desc, **args) return parser, interface def run_instance(interface, options): if interface: - print "setting function inputs" + print("setting function inputs") - for input_name, _ in interface.inputs.items(): + for input_name, _ in list(interface.inputs.items()): if getattr(options, input_name) != None: value = getattr(options, input_name) if not isinstance(value, bool): @@ -60,12 +61,12 @@ def run_instance(interface, options): try: setattr(interface.inputs, input_name, value) - except ValueError, e: - print "Error when setting the value of %s: '%s'"%(input_name, str(e)) + except ValueError as e: + print("Error when setting the value of %s: '%s'"%(input_name, str(e))) - print interface.inputs + print(interface.inputs) res = interface.run() - print res.outputs + print(res.outputs) def main(argv): diff --git a/nipype/utils/onetime.py b/nipype/utils/onetime.py index 972d12c221..f40560dedb 100644 --- a/nipype/utils/onetime.py +++ b/nipype/utils/onetime.py @@ -17,6 +17,8 @@ [2] Python data model, http://docs.python.org/reference/datamodel.html """ +from builtins import object + class OneTimeProperty(object): """A descriptor to make special properties that become normal attributes. """ @@ -32,7 +34,7 @@ def __init__(self, func): the value of this computation. """ self.getter = func - self.name = func.func_name + self.name = func.__name__ def __get__(self, obj, type=None): """ Called on attribute access on the class or instance. """ diff --git a/nipype/utils/provenance.py b/nipype/utils/provenance.py index 79b1f43b01..16dd645cfe 100644 --- a/nipype/utils/provenance.py +++ b/nipype/utils/provenance.py @@ -1,10 +1,13 @@ -from cPickle import dumps -import json +from future import standard_library +standard_library.install_aliases() +from builtins import object + +from pickle import dumps +import simplejson import os import getpass from socket import getfqdn from uuid import uuid1 -from nipype.external import six import numpy as np try: @@ -12,10 +15,11 @@ except ImportError: from ordereddict import OrderedDict -try: - import prov.model as pm -except ImportError: - from ..external import provcopy as pm +#try: +# import prov.model as pm +#except ImportError: +from ..external import provcopy as pm +from ..external.six import string_types from .. import get_info from .filemanip import (md5, hashlib, hash_infile) @@ -95,7 +99,7 @@ def _get_sorteddict(object, dictwithhash=False): if isinstance(object, tuple): out = tuple(out) else: - if isinstance(object, six.string_types) and os.path.isfile(object): + if isinstance(object, string_types) and os.path.isfile(object): hash = hash_infile(object) if dictwithhash: out = (object, hash) @@ -118,7 +122,7 @@ def safe_encode(x, as_literal=True): else: return value try: - if isinstance(x, (str, unicode)): + if isinstance(x, (str, string_types)): if os.path.exists(x): value = 'file://%s%s' % (getfqdn(), x) if not as_literal: @@ -135,47 +139,47 @@ def safe_encode(x, as_literal=True): if not as_literal: return value return pm.Literal(value, pm.XSD['string']) - if isinstance(x, (int,)): + if isinstance(x, int): if not as_literal: return x return pm.Literal(int(x), pm.XSD['integer']) - if isinstance(x, (float,)): + if isinstance(x, float): if not as_literal: return x return pm.Literal(x, pm.XSD['float']) if isinstance(x, dict): outdict = {} - for key, value in x.items(): + for key, value in list(x.items()): encoded_value = safe_encode(value, as_literal=False) - if isinstance(encoded_value, (pm.Literal,)): + if isinstance(encoded_value, pm.Literal): outdict[key] = encoded_value.json_representation() else: outdict[key] = encoded_value if not as_literal: - return json.dumps(outdict) - return pm.Literal(json.dumps(outdict), pm.XSD['string']) + return simplejson.dumps(outdict) + return pm.Literal(simplejson.dumps(outdict), pm.XSD['string']) if isinstance(x, list): try: nptype = np.array(x).dtype if nptype == np.dtype(object): raise ValueError('dtype object') - except ValueError, e: + except ValueError as e: outlist = [] for value in x: encoded_value = safe_encode(value, as_literal=False) - if isinstance(encoded_value, (pm.Literal,)): + if isinstance(encoded_value, pm.Literal): outlist.append(encoded_value.json_representation()) else: outlist.append(encoded_value) else: outlist = x if not as_literal: - return json.dumps(outlist) - return pm.Literal(json.dumps(outlist), pm.XSD['string']) + return simplejson.dumps(outlist) + return pm.Literal(simplejson.dumps(outlist), pm.XSD['string']) if not as_literal: return dumps(x) return pm.Literal(dumps(x), nipype_ns['pickle']) - except TypeError, e: + except TypeError as e: iflogger.info(e) value = "Could not encode: " + str(e) if not as_literal: @@ -198,7 +202,7 @@ def prov_encode(graph, value, create_container=True): entities.append(item_entity) if isinstance(item, list): continue - if not isinstance(item_entity.get_value()[0], basestring): + if not isinstance(item_entity.get_value()[0], string_types): raise ValueError('Not a string literal') if 'file://' not in item_entity.get_value()[0]: raise ValueError('No file found') @@ -206,7 +210,7 @@ def prov_encode(graph, value, create_container=True): entity = graph.collection(identifier=id) for item_entity in entities: graph.hadMember(id, item_entity) - except ValueError, e: + except ValueError as e: iflogger.debug(e) entity = prov_encode(graph, value, create_container=False) else: @@ -214,7 +218,7 @@ def prov_encode(graph, value, create_container=True): else: encoded_literal = safe_encode(value) attr = {pm.PROV['value']: encoded_literal} - if isinstance(value, six.string_types) and os.path.exists(value): + if isinstance(value, string_types) and os.path.exists(value): attr.update({pm.PROV['location']: encoded_literal}) if not os.path.isdir(value): sha512 = hash_infile(value, crypto=hashlib.sha512) @@ -369,7 +373,7 @@ def add_results(self, results): agent_attr = {pm.PROV["type"]: pm.PROV["SoftwareAgent"], pm.PROV["label"]: "Nipype", foaf["name"]: safe_encode("Nipype")} - for key, value in get_info().items(): + for key, value in list(get_info().items()): agent_attr.update({nipype_ns[key]: safe_encode(value)}) software_agent = self.g.agent(get_attr_id(agent_attr), agent_attr) self.g.wasAssociatedWith(a0, user_agent, None, None, @@ -389,5 +393,5 @@ def write_provenance(self, filename='provenance', format='turtle'): fp.writelines(self.g.get_provn()) if format in ['json', 'all']: with open(filename + '.json', 'wt') as fp: - pm.json.dump(self.g, fp, cls=pm.ProvBundle.JSONEncoder) + pm.simplejson.dump(self.g, fp, cls=pm.ProvBundle.JSONEncoder) return self.g diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py index 368dc7cbf8..11af7b2ccc 100644 --- a/nipype/utils/tests/test_cmd.py +++ b/nipype/utils/tests/test_cmd.py @@ -1,10 +1,14 @@ #!/usr/bin/env python -from StringIO import StringIO +from future import standard_library +standard_library.install_aliases() + import unittest, sys -from nipype.utils import nipype_cmd from contextlib import contextmanager +from nipype.external.six import PY2, PY3, StringIO +from nipype.utils import nipype_cmd + @contextmanager def capture_sys_output(): caputure_out, capture_err = StringIO(), StringIO() @@ -26,10 +30,17 @@ def test_main_returns_2_on_empty(self): exit_exception = cm.exception self.assertEqual(exit_exception.code, 2) - self.assertEqual(stderr.getvalue(), + if PY2: + self.assertEqual(stderr.getvalue(), """usage: nipype_cmd [-h] module interface nipype_cmd: error: too few arguments """) + elif PY3: + self.assertEqual(stderr.getvalue(), +"""usage: nipype_cmd [-h] module interface +nipype_cmd: error: the following arguments are required: module, interface +""") + self.assertEqual(stdout.getvalue(), '') def test_main_returns_0_on_help(self): @@ -69,12 +80,12 @@ def test_list_nipy_interfacesp(self): self.assertEqual(stderr.getvalue(), '') self.assertEqual(stdout.getvalue(), """Available Interfaces: - SpaceTimeRealigner - Similarity ComputeMask - FitGLM EstimateContrast + FitGLM FmriRealign4d + Similarity + SpaceTimeRealigner """) def test_run_4d_realign_without_arguments(self): @@ -85,8 +96,7 @@ def test_run_4d_realign_without_arguments(self): exit_exception = cm.exception self.assertEqual(exit_exception.code, 2) - self.assertEqual(stderr.getvalue(), -"""usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h] + error_message = """usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h] [--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]] [--ignore_exception] [--loops [LOOPS [LOOPS ...]]] @@ -96,9 +106,18 @@ def test_run_4d_realign_without_arguments(self): [--time_interp TIME_INTERP] [--tr_slices TR_SLICES] in_file [in_file ...] - tr + tr""" + + if PY2: + error_message += """ nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments -""") +""" + elif PY3: + error_message += """ +nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr +""" + + self.assertEqual(stderr.getvalue(), error_message) self.assertEqual(stdout.getvalue(), '') def test_run_4d_realign_help(self): diff --git a/nipype/utils/tests/test_docparse.py b/nipype/utils/tests/test_docparse.py index 251302eee6..0138f92c9d 100644 --- a/nipype/utils/tests/test_docparse.py +++ b/nipype/utils/tests/test_docparse.py @@ -1,3 +1,4 @@ +from builtins import object # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: from nipype.testing import * diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py index 9ab07f9923..0c958f3da6 100644 --- a/nipype/utils/tests/test_filemanip.py +++ b/nipype/utils/tests/test_filemanip.py @@ -1,5 +1,7 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from builtins import open + import os from tempfile import mkstemp, mkdtemp @@ -63,7 +65,7 @@ def _temp_analyze_files(): """Generate temporary analyze file pair.""" fd, orig_img = mkstemp(suffix = '.img') orig_hdr = orig_img[:-4] + '.hdr' - fp = file(orig_hdr, 'w+') + fp = open(orig_hdr, 'w+') fp.close() return orig_img, orig_hdr diff --git a/nipype/utils/tests/test_misc.py b/nipype/utils/tests/test_misc.py index 17f2fe2564..5a0f6bd382 100644 --- a/nipype/utils/tests/test_misc.py +++ b/nipype/utils/tests/test_misc.py @@ -1,18 +1,24 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from future import standard_library +standard_library.install_aliases() + +from builtins import next + from nipype.testing import assert_equal, assert_true, assert_false from nipype.utils.misc import (container_to_string, getsource, create_function_from_source, str2bool, flatten, - unflatten) + unflatten) + def test_cont_to_str(): # list x = ['a', 'b'] - yield assert_equal, container_to_string(x), 'a b' + yield assert_true, container_to_string(x) == 'a b' # tuple x = tuple(x) - yield assert_equal, container_to_string(x), 'a b' + yield assert_true, container_to_string(x) == 'a b' # set x = set(x) y = container_to_string(x) @@ -22,10 +28,10 @@ def test_cont_to_str(): y = container_to_string(x) yield assert_true, (y == 'a b') or (y == 'b a') # string - yield assert_equal, container_to_string('foobar'), 'foobar' + yield assert_true, container_to_string('foobar') == 'foobar' # int. Integers are not the main intent of this function, but see # no reason why they shouldn't work. - yield assert_equal, container_to_string(123), '123' + yield assert_true, (container_to_string(123) == '123') def _func1(x): return x**3 diff --git a/nipype/utils/tmpdirs.py b/nipype/utils/tmpdirs.py index c850311c1b..274c08caed 100644 --- a/nipype/utils/tmpdirs.py +++ b/nipype/utils/tmpdirs.py @@ -1,3 +1,4 @@ +from builtins import object # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: import os diff --git a/nipype/workflows/dmri/__init__.py b/nipype/workflows/dmri/__init__.py index 6a9323a26c..d138c9e02e 100644 --- a/nipype/workflows/dmri/__init__.py +++ b/nipype/workflows/dmri/__init__.py @@ -1 +1,2 @@ -import camino, mrtrix, fsl, dipy +from __future__ import absolute_import +from . import camino, mrtrix, fsl, dipy diff --git a/nipype/workflows/dmri/camino/__init__.py b/nipype/workflows/dmri/camino/__init__.py index 5b3f9db5e0..ef72229cde 100644 --- a/nipype/workflows/dmri/camino/__init__.py +++ b/nipype/workflows/dmri/camino/__init__.py @@ -1,4 +1,5 @@ -from diffusion import create_camino_dti_pipeline -from connectivity_mapping import create_connectivity_pipeline -from group_connectivity import create_group_connectivity_pipeline +from __future__ import absolute_import +from .diffusion import create_camino_dti_pipeline +from .connectivity_mapping import create_connectivity_pipeline +from .group_connectivity import create_group_connectivity_pipeline diff --git a/nipype/workflows/dmri/camino/connectivity_mapping.py b/nipype/workflows/dmri/camino/connectivity_mapping.py index a0b83b4ee3..838aa2371d 100644 --- a/nipype/workflows/dmri/camino/connectivity_mapping.py +++ b/nipype/workflows/dmri/camino/connectivity_mapping.py @@ -1,14 +1,15 @@ -import nipype.interfaces.io as nio # Data i/o -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine -import nipype.interfaces.camino as camino -import nipype.interfaces.fsl as fsl -import nipype.interfaces.camino2trackvis as cam2trk -import nipype.interfaces.freesurfer as fs # freesurfer -import nipype.interfaces.cmtk as cmtk -import nipype.algorithms.misc as misc import inspect import os.path as op + +from ....interfaces import io as nio # Data i/o +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine +from ....interfaces import camino as camino +from ....interfaces import fsl as fsl +from ....interfaces import camino2trackvis as cam2trk +from ....interfaces import freesurfer as fs # freesurfer +from ....interfaces import cmtk as cmtk +from ....algorithms import misc as misc from ...misc.utils import (get_affine, get_data_dims, get_vox_dims, select_aparc, select_aparc_annot) diff --git a/nipype/workflows/dmri/camino/diffusion.py b/nipype/workflows/dmri/camino/diffusion.py index c7a8e97ff4..cf0a5ffd51 100644 --- a/nipype/workflows/dmri/camino/diffusion.py +++ b/nipype/workflows/dmri/camino/diffusion.py @@ -1,11 +1,12 @@ -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine -import nipype.interfaces.camino as camino -import nipype.interfaces.fsl as fsl -import nipype.interfaces.camino2trackvis as cam2trk -import nipype.algorithms.misc as misc +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine +from ....interfaces import camino as camino +from ....interfaces import fsl as fsl +from ....interfaces import camino2trackvis as cam2trk +from ....algorithms import misc as misc from ...misc.utils import get_affine, get_data_dims, get_vox_dims + def create_camino_dti_pipeline(name="dtiproc"): """Creates a pipeline that does the same diffusion processing as in the :doc:`../../users/examples/dmri_camino_dti` example script. Given a diffusion-weighted image, diff --git a/nipype/workflows/dmri/camino/group_connectivity.py b/nipype/workflows/dmri/camino/group_connectivity.py index c09f771bfd..92b2eeb21b 100644 --- a/nipype/workflows/dmri/camino/group_connectivity.py +++ b/nipype/workflows/dmri/camino/group_connectivity.py @@ -1,9 +1,9 @@ import os.path as op # system functions -import nipype.interfaces.io as nio # Data i/o -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine from .connectivity_mapping import create_connectivity_pipeline +from ....interfaces import io as nio # Data i/o +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_dir, output_dir, template_args_dict=0): @@ -55,7 +55,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_ info = template_args_dict datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/nipype/workflows/dmri/connectivity/__init__.py b/nipype/workflows/dmri/connectivity/__init__.py index 303582286d..78434ae883 100644 --- a/nipype/workflows/dmri/connectivity/__init__.py +++ b/nipype/workflows/dmri/connectivity/__init__.py @@ -1,5 +1,6 @@ -from nx import (create_networkx_pipeline, create_cmats_to_csv_pipeline) -from group_connectivity import (create_merge_networks_by_group_workflow, +from __future__ import absolute_import +from .nx import (create_networkx_pipeline, create_cmats_to_csv_pipeline) +from .group_connectivity import (create_merge_networks_by_group_workflow, create_merge_network_results_by_group_workflow, create_merge_group_networks_workflow, create_merge_group_network_results_workflow, diff --git a/nipype/workflows/dmri/connectivity/group_connectivity.py b/nipype/workflows/dmri/connectivity/group_connectivity.py index 71ebd05719..5afe2983d3 100644 --- a/nipype/workflows/dmri/connectivity/group_connectivity.py +++ b/nipype/workflows/dmri/connectivity/group_connectivity.py @@ -1,16 +1,19 @@ +from __future__ import print_function + import os.path as op -import nipype.interfaces.io as nio # Data i/o -import nipype.interfaces.utility as util # utility -import nipype.interfaces.cmtk as cmtk -import nipype.algorithms.misc as misc -import nipype.pipeline.engine as pe # pypeline engine -from nipype.interfaces.utility import Function -from nipype.utils.misc import package_check + +from ....interfaces import io as nio # Data i/o +from ....interfaces import utility as util # utility +from ....interfaces import cmtk as cmtk +from ....algorithms import misc as misc +from ....pipeline import engine as pe # pypeline engine +from ....interfaces.utility import Function +from ....utils.misc import package_check have_cmp = True try: package_check('cmp') -except Exception, e: +except Exception as e: have_cmp = False else: import cmp @@ -33,7 +36,7 @@ def pullnodeIDs(in_network, name_key='dn_name'): nodedata = ntwk.node ids = [] integer_nodelist = [] - for node in nodedata.keys(): + for node in list(nodedata.keys()): integer_nodelist.append(int(node)) for node in np.sort(integer_nodelist): try: @@ -314,7 +317,7 @@ def create_merge_group_networks_workflow(group_list, data_dir, subjects_dir, out """ l3infosource = pe.Node(interface=util.IdentityInterface( fields=['group_id']), name='l3infosource') - l3infosource.inputs.group_id = group_list.keys() + l3infosource.inputs.group_id = list(group_list.keys()) l3source = pe.Node(nio.DataGrabber( infields=['group_id'], outfields=['CFFfiles']), name='l3source') @@ -348,35 +351,35 @@ def create_merge_group_networks_workflow(group_list, data_dir, subjects_dir, out def create_merge_group_network_results_workflow(group_list, data_dir, subjects_dir, output_dir, title='group'): """Creates a third-level pipeline to merge the Connectome File Format (CFF) outputs from each group - and combines them into a single CFF file for each group. This version of the third-level pipeline also - concatenates the comma-separated value files for the NetworkX metrics and the connectivity matrices - into single files. - - Example - ------- - - >>> import nipype.workflows.dmri.connectivity.group_connectivity as groupwork - >>> from nipype.testing import example_data - >>> subjects_dir = '.' - >>> data_dir = '.' - >>> output_dir = '.' - >>> group_list = {} - >>> group_list['group1'] = ['subj1', 'subj2'] - >>> group_list['group2'] = ['subj3', 'subj4'] - >>> l3pipeline = groupwork.create_merge_group_network_results_workflow(group_list, data_dir, subjects_dir, output_dir) - >>> l3pipeline.run() # doctest: +SKIP - - Inputs:: - - group_list: Dictionary of subject lists, keyed by group name - data_dir: Path to the data directory - subjects_dir: Path to the Freesurfer 'subjects' directory - output_dir: Path for the output files - title: String to use as a title for the output merged CFF file (default 'group') - """ + and combines them into a single CFF file for each group. This version of the third-level pipeline also + concatenates the comma-separated value files for the NetworkX metrics and the connectivity matrices + into single files. + + Example + ------- + + >>> import nipype.workflows.dmri.connectivity.group_connectivity as groupwork + >>> from nipype.testing import example_data + >>> subjects_dir = '.' + >>> data_dir = '.' + >>> output_dir = '.' + >>> group_list = {} + >>> group_list['group1'] = ['subj1', 'subj2'] + >>> group_list['group2'] = ['subj3', 'subj4'] + >>> l3pipeline = groupwork.create_merge_group_network_results_workflow(group_list, data_dir, subjects_dir, output_dir) + >>> l3pipeline.run() # doctest: +SKIP + + Inputs:: + + group_list: Dictionary of subject lists, keyed by group name + data_dir: Path to the data directory + subjects_dir: Path to the Freesurfer 'subjects' directory + output_dir: Path for the output files + title: String to use as a title for the output merged CFF file (default 'group') + """ l3infosource = pe.Node(interface=util.IdentityInterface( - fields=['group_id']), name='l3infosource') - l3infosource.inputs.group_id = group_list.keys() + fields=['group_id']), name='l3infosource') + l3infosource.inputs.group_id = list(group_list.keys()) l3source = pe.Node(nio.DataGrabber(infields=['group_id'], outfields=['CFFfiles', 'CSVnodemetrics', 'CSVglobalmetrics', 'CSVmatrices']), name='l3source') l3source.inputs.template_args = dict(CFFfiles=[['group_id']], CSVnodemetrics=[['group_id']], CSVglobalmetrics=[['group_id']], CSVmatrices=[['group_id']]) @@ -384,8 +387,8 @@ def create_merge_group_network_results_workflow(group_list, data_dir, subjects_d l3source.inputs.sort_filelist = True l3source.inputs.field_template = dict( - CFFfiles=op.join(output_dir, '%s/*.cff'), CSVnodemetrics=op.join(output_dir, '%s/node_csv/*.csv'), - CSVglobalmetrics=op.join(output_dir, '%s/global_csv/*.csv'), CSVmatrices=op.join(output_dir, '%s/cmatrices_csv/*/*.csv')) + CFFfiles=op.join(output_dir, '%s/*.cff'), CSVnodemetrics=op.join(output_dir, '%s/node_csv/*.csv'), + CSVglobalmetrics=op.join(output_dir, '%s/global_csv/*.csv'), CSVmatrices=op.join(output_dir, '%s/cmatrices_csv/*/*.csv')) l3inputnode = pe.Node(interface=util.IdentityInterface(fields=['Group_CFFs', 'Group_CSVnodemetrics', 'Group_CSVglobalmetrics', 'Group_CSVmatrices']), name='l3inputnode') @@ -398,18 +401,18 @@ def create_merge_group_network_results_workflow(group_list, data_dir, subjects_d l3pipeline = pe.Workflow(name="l3output") l3pipeline.base_dir = output_dir l3pipeline.connect([ - (l3infosource, l3source, [('group_id', 'group_id')]), - (l3source, l3inputnode, [('CFFfiles', 'Group_CFFs')]), - (l3source, l3inputnode, [('CSVnodemetrics', 'Group_CSVnodemetrics')]), - (l3source, l3inputnode, [('CSVglobalmetrics', 'Group_CSVglobalmetrics')]), - (l3source, l3inputnode, [('CSVmatrices', 'Group_CSVmatrices')]), - ]) + (l3infosource, l3source, [('group_id', 'group_id')]), + (l3source, l3inputnode, [('CFFfiles', 'Group_CFFs')]), + (l3source, l3inputnode, [('CSVnodemetrics', 'Group_CSVnodemetrics')]), + (l3source, l3inputnode, [('CSVglobalmetrics', 'Group_CSVglobalmetrics')]), + (l3source, l3inputnode, [('CSVmatrices', 'Group_CSVmatrices')]), + ]) l3pipeline.connect([(l3inputnode, MergeCNetworks_grp, [('Group_CFFs', 'in_files')])]) l3pipeline.connect([(MergeCNetworks_grp, l3datasink, [('connectome_file', '@l3output')])]) concat_csv_interface = Function(input_names=["in_files"], output_names=["out_name"], - function=concatcsv) + function=concatcsv) concat_node_csvs = pe.Node(interface=concat_csv_interface, name='concat_node_csvs') concat_global_csvs = pe.Node(interface=concat_csv_interface, name='concat_global_csvs') @@ -455,16 +458,16 @@ def create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir """ l4infosource = pe.Node(interface=util.IdentityInterface(fields=['group_id1', 'group_id2']), name='l4infosource') try: - l4infosource.inputs.group_id1 = group_list.keys()[0] - l4infosource.inputs.group_id2 = group_list.keys()[1] + l4infosource.inputs.group_id1 = list(group_list.keys())[0] + l4infosource.inputs.group_id2 = list(group_list.keys())[1] except IndexError: - print 'The create_average_networks_by_group_workflow requires 2 groups' + print('The create_average_networks_by_group_workflow requires 2 groups') raise Exception l4info = dict(networks=[['group_id', '']], CMatrices=[['group_id', '']], fibmean=[['group_id', 'mean_fiber_length']], fibdev=[['group_id', 'fiber_length_std']]) - l4source_grp1 = pe.Node(nio.DataGrabber(infields=['group_id'], outfields=l4info.keys()), name='l4source_grp1') + l4source_grp1 = pe.Node(nio.DataGrabber(infields=['group_id'], outfields=list(l4info.keys())), name='l4source_grp1') l4source_grp1.inputs.template = '%s/%s' l4source_grp1.inputs.field_template = dict(networks=op.join(output_dir, '%s/networks/*/*%s*intersections*.pck'), CMatrices=op.join(output_dir, '%s/cmatrix/*/*%s*.mat'), fibmean=op.join(output_dir, '%s/mean_fiber_length/*/*%s*.mat'), fibdev=op.join(output_dir, '%s/fiber_length_std/*/*%s*.mat')) diff --git a/nipype/workflows/dmri/connectivity/nx.py b/nipype/workflows/dmri/connectivity/nx.py index 576e08cbda..29b23e42f3 100644 --- a/nipype/workflows/dmri/connectivity/nx.py +++ b/nipype/workflows/dmri/connectivity/nx.py @@ -1,9 +1,9 @@ -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as util -import nipype.interfaces.cmtk as cmtk -import nipype.algorithms.misc as misc +from ....pipeline import engine as pe +from ....interfaces import utility as util +from ....interfaces import cmtk as cmtk +from ....algorithms import misc as misc +from ....algorithms.misc import remove_identical_paths from .group_connectivity import pullnodeIDs -from nipype.algorithms.misc import remove_identical_paths def add_global_to_filename(in_file): from nipype.utils.filemanip import split_filename diff --git a/nipype/workflows/dmri/dipy/__init__.py b/nipype/workflows/dmri/dipy/__init__.py index 2d5ec4f70b..04b751f203 100644 --- a/nipype/workflows/dmri/dipy/__init__.py +++ b/nipype/workflows/dmri/dipy/__init__.py @@ -2,4 +2,5 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -from denoise import nlmeans_pipeline +from __future__ import absolute_import +from .denoise import nlmeans_pipeline diff --git a/nipype/workflows/dmri/dipy/denoise.py b/nipype/workflows/dmri/dipy/denoise.py index 850f4b9cd9..08269d015d 100644 --- a/nipype/workflows/dmri/dipy/denoise.py +++ b/nipype/workflows/dmri/dipy/denoise.py @@ -2,10 +2,10 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as niu -from nipype.interfaces import fsl -from nipype.interfaces import dipy +from builtins import range +from ....pipeline import engine as pe +from ....interfaces import utility as niu +from ....interfaces import dipy def nlmeans_pipeline(name='Denoise', @@ -79,7 +79,7 @@ def csf_mask(in_file, in_mask, out_file=None): structure=np.ones((2, 2, 2))).astype(np.uint8) label_im, nb_labels = label(imdata) - sizes = nd.sum(imdata, label_im, range(nb_labels + 1)) + sizes = nd.sum(imdata, label_im, list(range(nb_labels + 1))) mask_size = sizes != sizes.max() remove_pixel = mask_size[label_im] label_im[remove_pixel] = 0 diff --git a/nipype/workflows/dmri/fsl/__init__.py b/nipype/workflows/dmri/fsl/__init__.py index 645c70bc52..b477b29a76 100644 --- a/nipype/workflows/dmri/fsl/__init__.py +++ b/nipype/workflows/dmri/fsl/__init__.py @@ -1,13 +1,14 @@ -from dti import create_bedpostx_pipeline, bedpostx_parallel +from __future__ import absolute_import +from .dti import create_bedpostx_pipeline, bedpostx_parallel -from artifacts import (all_fmb_pipeline, all_peb_pipeline, all_fsl_pipeline, +from .artifacts import (all_fmb_pipeline, all_peb_pipeline, all_fsl_pipeline, hmc_pipeline, ecc_pipeline, sdc_fmb, sdc_peb, remove_bias) -from epi import (fieldmap_correction, topup_correction, +from .epi import (fieldmap_correction, topup_correction, create_eddy_correct_pipeline, create_epidewarp_pipeline, create_dmri_preprocessing) -from tbss import (create_tbss_1_preproc, create_tbss_2_reg, +from .tbss import (create_tbss_1_preproc, create_tbss_2_reg, create_tbss_3_postreg, create_tbss_4_prestats, create_tbss_all, create_tbss_non_FA) diff --git a/nipype/workflows/dmri/fsl/artifacts.py b/nipype/workflows/dmri/fsl/artifacts.py index a6c5b78092..9579d55d02 100644 --- a/nipype/workflows/dmri/fsl/artifacts.py +++ b/nipype/workflows/dmri/fsl/artifacts.py @@ -1,16 +1,19 @@ # coding: utf-8 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import os - -import nipype.pipeline.engine as pe -from nipype.interfaces.io import JSONFileGrabber -from nipype.interfaces import utility as niu -from nipype.interfaces import freesurfer as fs -from nipype.interfaces import ants -from nipype.interfaces import fsl -from .utils import * - +from __future__ import division + +from ....interfaces.io import JSONFileGrabber +from ....interfaces import utility as niu +from ....interfaces import ants +from ....interfaces import fsl +from ....pipeline import engine as pe +from .utils import (b0_indices, time_avg, apply_all_corrections, b0_average, + hmc_split, dwi_flirt, eddy_rotate_bvecs, rotate_bvecs, + insert_mat, extract_bval, recompose_dwi, recompose_xfm, + siemens2rads, rads2radsec, demean_image, + cleanup_edge_pipeline, add_empty_vol, vsm2warp, + compute_readout,) def all_fmb_pipeline(name='hmc_sdc_ecc', fugue_params=dict(smooth3d=2.0)): """ @@ -535,7 +538,7 @@ def sdc_fmb(name='fmb_correction', interp='Linear', >>> from nipype.workflows.dmri.fsl.artifacts import sdc_fmb >>> fmb = sdc_fmb() >>> fmb.inputs.inputnode.in_file = 'diffusion.nii' - >>> fmb.inputs.inputnode.in_ref = range(0, 30, 6) + >>> fmb.inputs.inputnode.in_ref = list(range(0, 30, 6)) >>> fmb.inputs.inputnode.in_mask = 'mask.nii' >>> fmb.inputs.inputnode.bmap_mag = 'magnitude.nii' >>> fmb.inputs.inputnode.bmap_pha = 'phase.nii' diff --git a/nipype/workflows/dmri/fsl/dti.py b/nipype/workflows/dmri/fsl/dti.py index e375804e9e..a0a5d2db94 100644 --- a/nipype/workflows/dmri/fsl/dti.py +++ b/nipype/workflows/dmri/fsl/dti.py @@ -1,13 +1,14 @@ # coding: utf-8 -import nipype.pipeline.engine as pe -from nipype.interfaces import utility as niu -from nipype.interfaces import fsl -from nipype.algorithms import misc -import os +from __future__ import absolute_import + +from ....pipeline import engine as pe +from ....interfaces import utility as niu +from ....interfaces import fsl +from ....algorithms import misc #backwards compatibility -from epi import create_eddy_correct_pipeline +from .epi import create_eddy_correct_pipeline def transpose(samples_over_fibres): diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py index f4dc8afb35..9f267f8a7e 100644 --- a/nipype/workflows/dmri/fsl/epi.py +++ b/nipype/workflows/dmri/fsl/epi.py @@ -1,11 +1,15 @@ # coding: utf-8 -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as niu -import nipype.interfaces.fsl as fsl -import os +from __future__ import division + import warnings +from ....pipeline import engine as pe +from ....interfaces import utility as niu +from ....interfaces import fsl as fsl + + + def create_dmri_preprocessing(name='dMRI_preprocessing', use_fieldmap=True, fieldmap_registration=False): """ Creates a workflow that chains the necessary pipelines to @@ -704,7 +708,7 @@ def _cat_logs(in_files): def _compute_dwelltime(dwell_time=0.68, pi_factor=1.0, is_reverse_encoding=False): - dwell_time *= (1.0/pi_factor) + dwell_time *= (1.0 / pi_factor) if is_reverse_encoding: dwell_time *= -1.0 @@ -712,7 +716,7 @@ def _compute_dwelltime(dwell_time=0.68, pi_factor=1.0, is_reverse_encoding=False return dwell_time def _effective_echospacing( dwell_time, pi_factor=1.0 ): - dwelltime = 1.0e-3 * dwell_time * ( 1.0/pi_factor ) + dwelltime = 1.0e-3 * dwell_time * (1.0 / pi_factor) return dwelltime @@ -723,7 +727,7 @@ def _prepare_phasediff(in_file): img = nib.load(in_file) max_diff = np.max(img.get_data().reshape(-1)) min_diff = np.min(img.get_data().reshape(-1)) - A = (2.0 * np.pi)/(max_diff-min_diff) + A = (2.0 * np.pi) / (max_diff-min_diff) B = np.pi - (A * max_diff) diff_norm = img.get_data() * A + B diff --git a/nipype/workflows/dmri/fsl/tbss.py b/nipype/workflows/dmri/fsl/tbss.py index 781a3a3861..071ad70d9d 100644 --- a/nipype/workflows/dmri/fsl/tbss.py +++ b/nipype/workflows/dmri/fsl/tbss.py @@ -4,9 +4,9 @@ import os from warnings import warn -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as util -import nipype.interfaces.fsl as fsl +from ....pipeline import engine as pe +from ....interfaces import utility as util +from ....interfaces import fsl as fsl def tbss1_op_string(in_files): diff --git a/nipype/workflows/dmri/fsl/utils.py b/nipype/workflows/dmri/fsl/utils.py index 562cdee464..e89696418f 100644 --- a/nipype/workflows/dmri/fsl/utils.py +++ b/nipype/workflows/dmri/fsl/utils.py @@ -2,10 +2,15 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as niu -from nipype.interfaces import fsl -from nipype.interfaces import ants +from __future__ import division +from builtins import zip +from builtins import next +from builtins import range + +from ....pipeline import engine as pe +from ....interfaces import utility as niu +from ....interfaces import fsl +from ....interfaces import ants def cleanup_edge_pipeline(name='Cleanup'): @@ -373,7 +378,7 @@ def recompose_xfm(in_bval, in_xfms): if b == 0.0: mat = np.eye(4) else: - mat = xfms.next() + mat = next(xfms) out_name = op.abspath('eccor_%04d.mat' % i) out_files.append(out_name) @@ -545,7 +550,7 @@ def eddy_rotate_bvecs(in_bvec, eddy_params): invrot = np.linalg.inv(R) newbvec = invrot.dot(bvec) - new_bvecs.append((newbvec / np.linalg.norm(newbvec))) + new_bvecs.append(newbvec / np.linalg.norm(newbvec)) np.savetxt(out_file, np.array(new_bvecs).T, fmt='%0.15f') return out_file @@ -785,7 +790,7 @@ def _checkinitxfm(in_bval, excl_nodiff, in_xfms=None): if excl_nodiff: dws = np.where(bvals != 0)[0].tolist() else: - dws = range(len(bvals)) + dws = list(range(len(bvals))) if gen_id: for i in dws: diff --git a/nipype/workflows/dmri/mrtrix/__init__.py b/nipype/workflows/dmri/mrtrix/__init__.py index 1264b0b7c2..044007abb1 100644 --- a/nipype/workflows/dmri/mrtrix/__init__.py +++ b/nipype/workflows/dmri/mrtrix/__init__.py @@ -1,3 +1,4 @@ -from diffusion import create_mrtrix_dti_pipeline -from connectivity_mapping import create_connectivity_pipeline -from group_connectivity import (create_group_connectivity_pipeline) +from __future__ import absolute_import +from .diffusion import create_mrtrix_dti_pipeline +from .connectivity_mapping import create_connectivity_pipeline +from .group_connectivity import (create_group_connectivity_pipeline) diff --git a/nipype/workflows/dmri/mrtrix/connectivity_mapping.py b/nipype/workflows/dmri/mrtrix/connectivity_mapping.py index ef293bfd80..ec09fbc8c3 100644 --- a/nipype/workflows/dmri/mrtrix/connectivity_mapping.py +++ b/nipype/workflows/dmri/mrtrix/connectivity_mapping.py @@ -1,17 +1,18 @@ -import nipype.interfaces.io as nio # Data i/o -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine -import nipype.interfaces.fsl as fsl -import nipype.interfaces.freesurfer as fs # freesurfer -import nipype.interfaces.mrtrix as mrtrix -import nipype.interfaces.cmtk as cmtk -import nipype.interfaces.dipy as dipy -import nipype.algorithms.misc as misc import inspect -import os, os.path as op # system functions +import os.path as op # system functions + +from ....interfaces import io as nio # Data i/o +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine +from ....interfaces import fsl as fsl +from ....interfaces import freesurfer as fs # freesurfer +from ....interfaces import mrtrix as mrtrix +from ....interfaces import cmtk as cmtk +from ....interfaces import dipy as dipy +from ....algorithms import misc as misc from ..fsl.epi import create_eddy_correct_pipeline from ..connectivity.nx import create_networkx_pipeline, create_cmats_to_csv_pipeline -from nipype.interfaces.utility import Function +from ....interfaces.utility import Function from ...misc.utils import select_aparc_annot diff --git a/nipype/workflows/dmri/mrtrix/diffusion.py b/nipype/workflows/dmri/mrtrix/diffusion.py index e049339ea8..f6c9b1af51 100644 --- a/nipype/workflows/dmri/mrtrix/diffusion.py +++ b/nipype/workflows/dmri/mrtrix/diffusion.py @@ -1,7 +1,7 @@ -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine -import nipype.interfaces.fsl as fsl -import nipype.interfaces.mrtrix as mrtrix +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine +from ....interfaces import fsl as fsl +from ....interfaces import mrtrix as mrtrix def create_mrtrix_dti_pipeline(name="dtiproc", tractography_type = 'probabilistic'): """Creates a pipeline that does the same diffusion processing as in the diff --git a/nipype/workflows/dmri/mrtrix/group_connectivity.py b/nipype/workflows/dmri/mrtrix/group_connectivity.py index 8a6c13c209..16e9e276c7 100644 --- a/nipype/workflows/dmri/mrtrix/group_connectivity.py +++ b/nipype/workflows/dmri/mrtrix/group_connectivity.py @@ -1,15 +1,17 @@ import os.path as op -import nipype.interfaces.io as nio # Data i/o -import nipype.interfaces.utility as util # utility -import nipype.interfaces.cmtk as cmtk -import nipype.algorithms.misc as misc -import nipype.pipeline.engine as pe # pypeline engine -from .connectivity_mapping import create_connectivity_pipeline -from nipype.utils.misc import package_check import warnings + +from ....interfaces import io as nio # Data i/o +from ....interfaces import utility as util # utility +from ....interfaces import cmtk as cmtk +from ....algorithms import misc as misc +from ....pipeline import engine as pe # pipeline engine +from ....utils.misc import package_check +from .connectivity_mapping import create_connectivity_pipeline + try: package_check('cmp') -except Exception, e: +except Exception as e: warnings.warn('cmp not installed') else: import cmp @@ -71,7 +73,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_ info = template_args_dict datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'], - outfields=info.keys()), + outfields=list(info.keys())), name = 'datasource') datasource.inputs.template = "%s/%s" diff --git a/nipype/workflows/fmri/fsl/estimate.py b/nipype/workflows/fmri/fsl/estimate.py index 2f5c712a70..beb48847af 100644 --- a/nipype/workflows/fmri/fsl/estimate.py +++ b/nipype/workflows/fmri/fsl/estimate.py @@ -1,10 +1,12 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import nipype.interfaces.fsl as fsl # fsl -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine +from builtins import range -from nipype import LooseVersion +from ....interfaces import fsl as fsl # fsl +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine + +from .... import LooseVersion def create_modelfit_workflow(name='modelfit', f_contrasts=False): diff --git a/nipype/workflows/fmri/fsl/preprocess.py b/nipype/workflows/fmri/fsl/preprocess.py index 7a08670919..608ab97e8d 100644 --- a/nipype/workflows/fmri/fsl/preprocess.py +++ b/nipype/workflows/fmri/fsl/preprocess.py @@ -1,16 +1,16 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import division import os -import nipype.interfaces.fsl as fsl # fsl -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine -import nipype.interfaces.freesurfer as fs # freesurfer -import nipype.interfaces.spm as spm - -from nipype import LooseVersion +from ....interfaces import fsl as fsl # fsl +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine +from ....interfaces import freesurfer as fs # freesurfer +from ....interfaces import spm as spm from ...smri.freesurfer.utils import create_getmask_flow +from .... import LooseVersion def getthreshop(thresh): return ['-thr %.10f -Tmin -bin'%(0.1*val[1]) for val in thresh] @@ -26,7 +26,7 @@ def pickmiddle(files): import numpy as np middlevol = [] for f in files: - middlevol.append(int(np.ceil(load(f).get_shape()[3]/2))) + middlevol.append(int(np.ceil(load(f).get_shape()[3] / 2))) return middlevol def pickvol(filenames, fileidx, which): @@ -35,7 +35,7 @@ def pickvol(filenames, fileidx, which): if which.lower() == 'first': idx = 0 elif which.lower() == 'middle': - idx = int(np.ceil(load(filenames[fileidx]).get_shape()[3]/2)) + idx = int(np.ceil(load(filenames[fileidx]).get_shape()[3] / 2)) elif which.lower() == 'last': idx = load(filenames[fileidx]).get_shape()[3]-1 else: @@ -52,10 +52,10 @@ def chooseindex(fwhm): return [1] def getmeanscale(medianvals): - return ['-mul %.10f'%(10000./val) for val in medianvals] + return ['-mul %.10f' % (10000. / val) for val in medianvals] def getusans(x): - return [[tuple([val[0],0.75*val[1]])] for val in x] + return [[tuple([val[0], 0.75 * val[1]])] for val in x] tolist = lambda x: [x] highpass_operand = lambda x:'-bptf %.10f -1'%x diff --git a/nipype/workflows/fmri/spm/preprocess.py b/nipype/workflows/fmri/spm/preprocess.py index fb21877200..9c67d4c307 100644 --- a/nipype/workflows/fmri/spm/preprocess.py +++ b/nipype/workflows/fmri/spm/preprocess.py @@ -3,15 +3,15 @@ import os -import nipype.algorithms.rapidart as ra -import nipype.interfaces.spm as spm -import nipype.interfaces.utility as niu -import nipype.pipeline.engine as pe -logger = pe.logger +from ....algorithms import rapidart as ra +from ....interfaces import spm as spm +from ....interfaces import utility as niu +from ....pipeline import engine as pe from ....interfaces.matlab import no_matlab - from ...smri.freesurfer.utils import create_getmask_flow +logger = pe.logger + def create_spm_preproc(name='preproc'): """Create an spm preprocessing workflow with freesurfer registration and artifact detection. diff --git a/nipype/workflows/misc/utils.py b/nipype/workflows/misc/utils.py index a4a7b4e72e..5e8d0ecef9 100644 --- a/nipype/workflows/misc/utils.py +++ b/nipype/workflows/misc/utils.py @@ -1,6 +1,10 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from builtins import map +from builtins import range + + def get_vox_dims(volume): import nibabel as nb if isinstance(volume, list): @@ -50,7 +54,7 @@ def region_list_from_volume(in_file): region_list = list(rois) region_list.sort() region_list.remove(0) - region_list = map(int, region_list) + region_list = list(map(int, region_list)) return region_list @@ -68,5 +72,5 @@ def id_list_from_lookup_table(lookup_file, region_list): for region in region_list: label = LUTlabelDict[region][0] id_list.append(label) - id_list = map(str, id_list) + id_list = list(map(str, id_list)) return id_list diff --git a/nipype/workflows/rsfmri/fsl/resting.py b/nipype/workflows/rsfmri/fsl/resting.py index b20ec2ec09..bd25829445 100644 --- a/nipype/workflows/rsfmri/fsl/resting.py +++ b/nipype/workflows/rsfmri/fsl/resting.py @@ -1,10 +1,12 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import division + +from ....interfaces import fsl as fsl # fsl +from ....interfaces import utility as util # utility +from ....pipeline import engine as pe # pypeline engine +from ....algorithms.misc import TSNR -import nipype.interfaces.fsl as fsl # fsl -from nipype.algorithms.misc import TSNR -import nipype.interfaces.utility as util # utility -import nipype.pipeline.engine as pe # pypeline engine def extract_noise_components(realigned_file, noise_mask_file, num_components): """Derive components most reflective of physiological noise @@ -25,7 +27,7 @@ def extract_noise_components(realigned_file, noise_mask_file, num_components): stdX[stdX == 0] = 1. stdX[np.isnan(stdX)] = 1. stdX[np.isinf(stdX)] = 1. - X = (X - np.mean(X, axis=0))/stdX + X = (X - np.mean(X, axis=0)) / stdX u, _, _ = sp.linalg.svd(X, full_matrices=False) if components is None: components = u[:, :num_components] @@ -43,7 +45,7 @@ def select_volume(filename, which): if which.lower() == 'first': idx = 0 elif which.lower() == 'middle': - idx = int(np.ceil(load(filename).get_shape()[3]/2)) + idx = int(np.ceil(load(filename).get_shape()[3] / 2)) else: raise Exception('unknown value for volume selection : %s'%which) return idx diff --git a/nipype/workflows/smri/ants/ANTSBuildTemplate.py b/nipype/workflows/smri/ants/ANTSBuildTemplate.py index a1ae3076ad..fa3b88f38f 100644 --- a/nipype/workflows/smri/ants/ANTSBuildTemplate.py +++ b/nipype/workflows/smri/ants/ANTSBuildTemplate.py @@ -9,22 +9,27 @@ ## PURPOSE. ## ################################################################################# +from __future__ import print_function +from builtins import map +from builtins import zip +from builtins import range -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as util -from nipype.interfaces.utility import Function +from ....pipeline import engine as pe +from ....interfaces import utility as util +from ....interfaces.utility import Function + +from ....interfaces.ants import (ANTS, + WarpImageMultiTransform, + AverageImages, MultiplyImages, + AverageAffineTransform) -from nipype.interfaces.ants import ( - ANTS, - WarpImageMultiTransform, - AverageImages, MultiplyImages, - AverageAffineTransform) def GetFirstListElement(this_list): return this_list[0] def MakeTransformListWithGradientWarps(averageAffineTranform, gradientStepWarp): return [averageAffineTranform, gradientStepWarp, gradientStepWarp, gradientStepWarp, gradientStepWarp] + def RenestDeformedPassiveImages(deformedPassiveImages,flattened_image_nametypes): import os """ Now make a list of lists of images where the outter list is per image type, @@ -44,14 +49,14 @@ def RenestDeformedPassiveImages(deformedPassiveImages,flattened_image_nametypes) curr_name=flattened_image_nametypes[index] curr_file=deformedPassiveImages[index] image_dictionary_of_lists[curr_name].append(curr_file) - for image_type,image_list in image_dictionary_of_lists.items(): + for image_type,image_list in list(image_dictionary_of_lists.items()): nested_imagetype_list.append(image_list) outputAverageImageName_list.append('AVG_'+image_type+'.nii.gz') image_type_list.append('WARP_AVG_'+image_type) - print "\n"*10 - print "HACK: ", nested_imagetype_list - print "HACK: ", outputAverageImageName_list - print "HACK: ", image_type_list + print("\n"*10) + print("HACK: ", nested_imagetype_list) + print("HACK: ", outputAverageImageName_list) + print("HACK: ", image_type_list) return nested_imagetype_list,outputAverageImageName_list,image_type_list ## Utility Function @@ -62,7 +67,7 @@ def RenestDeformedPassiveImages(deformedPassiveImages,flattened_image_nametypes) ## ll ##[['af1.mat', 'wp1.nii'], ['af2.mat', 'wp2.nii'], ['af3.mat', 'wp3.nii']] def MakeListsOfTransformLists(warpTransformList, AffineTransformList): - return map(list, zip(warpTransformList,AffineTransformList)) + return list(map(list, list(zip(warpTransformList,AffineTransformList)))) ## Flatten and return equal length transform and images lists. def FlattenTransformAndImagesList(ListOfPassiveImagesDictionaries,transformation_series): @@ -71,7 +76,7 @@ def FlattenTransformAndImagesList(ListOfPassiveImagesDictionaries,transformation subjCount=len(ListOfPassiveImagesDictionaries) tranCount=len(transformation_series) if subjCount != tranCount: - print "ERROR: subjCount must equal tranCount {0} != {1}".format(subjCount,tranCount) + print("ERROR: subjCount must equal tranCount {0} != {1}".format(subjCount,tranCount)) sys.exit(-1) flattened_images=list() flattened_image_nametypes=list() @@ -83,7 +88,7 @@ def FlattenTransformAndImagesList(ListOfPassiveImagesDictionaries,transformation # sys.exit(-1) subjImgDictionary=ListOfPassiveImagesDictionaries[subjIndex] subjToAtlasTransform=transformation_series[subjIndex] - for imgname,img in subjImgDictionary.items(): + for imgname,img in list(subjImgDictionary.items()): flattened_images.append(img) flattened_image_nametypes.append(imgname) flattened_transforms.append(subjToAtlasTransform) diff --git a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py index 5d5c190fea..46c95a4d96 100644 --- a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py +++ b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py @@ -9,16 +9,18 @@ ## PURPOSE. ## ################################################################################# +from __future__ import print_function +from builtins import range -import nipype.pipeline.engine as pe -import nipype.interfaces.utility as util -from nipype.interfaces.utility import Function +from ....pipeline import engine as pe +from ....interfaces import utility as util +from ....interfaces.utility import Function -from nipype.interfaces.ants import ( - Registration, - ApplyTransforms, - AverageImages, MultiplyImages, - AverageAffineTransform) +from ....interfaces.ants import ( + Registration, + ApplyTransforms, + AverageImages, MultiplyImages, + AverageAffineTransform) def makeListOfOneElement(inputFile): outputList=[inputFile] @@ -51,19 +53,19 @@ def RenestDeformedPassiveImages(deformedPassiveImages,flattened_image_nametypes, curr_name=flattened_image_nametypes[index] curr_file=deformedPassiveImages[index] image_dictionary_of_lists[curr_name].append(curr_file) - for image_type,image_list in image_dictionary_of_lists.items(): + for image_type,image_list in list(image_dictionary_of_lists.items()): nested_imagetype_list.append(image_list) outputAverageImageName_list.append('AVG_'+image_type+'.nii.gz') image_type_list.append('WARP_AVG_'+image_type) - if interpolationMapping.has_key(image_type): + if image_type in interpolationMapping: nested_interpolation_type.append(interpolationMapping[image_type]) else: nested_interpolation_type.append('Linear') #Linear is the default. - print "\n"*10 - print "HACK: ", nested_imagetype_list - print "HACK: ", outputAverageImageName_list - print "HACK: ", image_type_list - print "HACK: ", nested_interpolation_type + print("\n"*10) + print("HACK: ", nested_imagetype_list) + print("HACK: ", outputAverageImageName_list) + print("HACK: ", image_type_list) + print("HACK: ", nested_interpolation_type) return nested_imagetype_list,outputAverageImageName_list,image_type_list,nested_interpolation_type def SplitAffineAndWarpComponents(list_of_transforms_lists): @@ -74,7 +76,7 @@ def SplitAffineAndWarpComponents(list_of_transforms_lists): for transform in list_of_transforms_lists: affine_component_list.append(transform[0]) warp_component_list.append(transform[1]) - print "HACK ", affine_component_list, " ", warp_component_list + print("HACK ", affine_component_list, " ", warp_component_list) return affine_component_list, warp_component_list ## Flatten and return equal length transform and images lists. @@ -84,11 +86,11 @@ def FlattenTransformAndImagesList(ListOfPassiveImagesDictionaries,transforms,inv subjCount=len(ListOfPassiveImagesDictionaries) tranCount=len(transforms) if subjCount != tranCount: - print "ERROR: subjCount must equal tranCount {0} != {1}".format(subjCount,tranCount) + print("ERROR: subjCount must equal tranCount {0} != {1}".format(subjCount,tranCount)) sys.exit(-1) invertTfmsFlagsCount=len(invert_transform_flags) if subjCount != invertTfmsFlagsCount: - print "ERROR: subjCount must equal invertTfmsFlags {0} != {1}".format(subjCount,invertTfmsFlagsCount) + print("ERROR: subjCount must equal invertTfmsFlags {0} != {1}".format(subjCount,invertTfmsFlagsCount)) sys.exit(-1) flattened_images=list() flattened_image_nametypes=list() @@ -103,12 +105,12 @@ def FlattenTransformAndImagesList(ListOfPassiveImagesDictionaries,transforms,inv subjImgDictionary=ListOfPassiveImagesDictionaries[subjIndex] subjToAtlasTransform=transforms[subjIndex] subjToAtlasInvertFlags=invert_transform_flags[subjIndex] - for imgname,img in subjImgDictionary.items(): + for imgname,img in list(subjImgDictionary.items()): flattened_images.append(img) flattened_image_nametypes.append(imgname) flattened_transforms.append(subjToAtlasTransform) flattened_invert_transform_flags.append(subjToAtlasInvertFlags) - if interpolationMapping.has_key(imgname): + if imgname in interpolationMapping: flattened_interpolation_type.append(interpolationMapping[imgname]) else: flattened_interpolation_type.append('Linear') #Linear is the default. @@ -138,7 +140,7 @@ def GetPassiveImages(ListOfImagesDictionaries,registrationImageTypes): passive_images=list() for mdict in ListOfImagesDictionaries: ThisSubjectPassiveImages=dict() - for key,value in mdict.items(): + for key,value in list(mdict.items()): if key not in registrationImageTypes: ThisSubjectPassiveImages[key]=value passive_images.append(ThisSubjectPassiveImages) diff --git a/nipype/workflows/smri/freesurfer/bem.py b/nipype/workflows/smri/freesurfer/bem.py index fbaaeb551b..67857ed12d 100644 --- a/nipype/workflows/smri/freesurfer/bem.py +++ b/nipype/workflows/smri/freesurfer/bem.py @@ -1,11 +1,10 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import nipype.pipeline.engine as pe - -import nipype.interfaces.mne as mne -import nipype.interfaces.freesurfer as fs -import nipype.interfaces.utility as niu +from ....pipeline import engine as pe +from ....interfaces import mne as mne +from ....interfaces import freesurfer as fs +from ....interfaces import utility as niu def create_bem_flow(name='bem', out_format='stl'): diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py index 799a105a4a..2a2ea375cb 100644 --- a/nipype/workflows/smri/freesurfer/recon.py +++ b/nipype/workflows/smri/freesurfer/recon.py @@ -1,6 +1,7 @@ -import nipype.pipeline.engine as pe -import nipype.interfaces.freesurfer as fs -import nipype.interfaces.utility as niu +from ....pipeline import engine as pe +from ....interfaces import freesurfer as fs +from ....interfaces import utility as niu + def create_skullstripped_recon_flow(name="skullstripped_recon_all"): """Performs recon-all on voulmes that are already skull stripped. diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py index 01af326cc4..7e74fa044e 100644 --- a/nipype/workflows/smri/freesurfer/utils.py +++ b/nipype/workflows/smri/freesurfer/utils.py @@ -1,17 +1,15 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import nipype.pipeline.engine as pe - -import nipype.interfaces.fsl as fsl -import nipype.interfaces.freesurfer as fs -import nipype.interfaces.meshfix as mf -import nipype.interfaces.io as nio -import nipype.interfaces.utility as niu -import nipype.algorithms.misc as misc -from nipype.interfaces.utility import Function -from nipype.workflows.misc.utils import region_list_from_volume, id_list_from_lookup_table -import os, os.path as op +from ....pipeline import engine as pe +from ....interfaces import fsl as fsl +from ....interfaces import freesurfer as fs +from ....interfaces import meshfix as mf +from ....interfaces import io as nio +from ....interfaces import utility as niu +from ....algorithms import misc as misc +from ....interfaces.utility import Function +from ....workflows.misc.utils import region_list_from_volume, id_list_from_lookup_table def get_aparc_aseg(files): @@ -317,12 +315,12 @@ def create_tessellation_flow(name='tessellate', out_format='stl'): iterfield=['in_file'], name='surfconvert') smoother = pe.MapNode(mf.MeshFix(), - iterfield=['in_file1'], + iterfield=['in_file1'], name='smoother') if out_format == 'gii': - stl_to_gifti = pe.MapNode(fs.MRIsConvert(out_datatype=out_format), - iterfield=['in_file'], - name='stl_to_gifti') + stl_to_gifti = pe.MapNode(fs.MRIsConvert(out_datatype=out_format), + iterfield=['in_file'], + name='stl_to_gifti') smoother.inputs.save_as_stl = True smoother.inputs.laplacian_smoothing_steps = 1 @@ -352,7 +350,7 @@ def create_tessellation_flow(name='tessellate', out_format='stl'): (id_list_from_lookup_table_node, tessellate, [('id_list', 'out_file')]), (fssource, tessellate, [('aseg', 'in_file')]), (tessellate, surfconvert, [('surface','in_file')]), - (surfconvert, smoother, [('converted','in_file1')]), + (surfconvert, smoother, [('converted','in_file1')]), ]) """ @@ -360,17 +358,17 @@ def create_tessellation_flow(name='tessellate', out_format='stl'): """ outputnode = pe.Node(niu.IdentityInterface(fields=["meshes"]), - name="outputspec") + name="outputspec") if out_format == 'gii': - tessflow.connect([ - (smoother, stl_to_gifti, [("mesh_file", "in_file")]), - ]) - tessflow.connect([ - (stl_to_gifti, outputnode, [("converted", "meshes")]), - ]) + tessflow.connect([ + (smoother, stl_to_gifti, [("mesh_file", "in_file")]), + ]) + tessflow.connect([ + (stl_to_gifti, outputnode, [("converted", "meshes")]), + ]) else: - tessflow.connect([ - (smoother, outputnode, [("mesh_file", "meshes")]), + tessflow.connect([ + (smoother, outputnode, [("mesh_file", "meshes")]), ]) return tessflow diff --git a/requirements.txt b/requirements.txt index feb8f969b7..d3289968c5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,3 +5,5 @@ traits>=4.3 python-dateutil>=1.5 nibabel>=2.0.1 nose>=1.2 +future==0.15.2 +simplejson diff --git a/setup.py b/setup.py index 3345130f12..db042ba243 100755 --- a/setup.py +++ b/setup.py @@ -14,7 +14,6 @@ """Build helper.""" import os -from os.path import join as pjoin from glob import glob import sys from functools import partial @@ -36,7 +35,7 @@ ''' Distutils / setuptools helpers from nibabel.nisext''' import os -from os.path import join as pjoin, split as psplit, splitext +from os.path import join as pjoin import sys PY3 = sys.version_info[0] >= 3 if PY3: @@ -50,8 +49,6 @@ from distutils.version import LooseVersion from distutils.command.build_py import build_py -from distutils.command.install_scripts import install_scripts - from distutils import log def get_comrec_build(pkg_dir, build_cmd=build_py): @@ -273,6 +270,8 @@ def _package_status(pkg_name, version, version_getter, checker): pkg_chk('scipy', SCIPY_MIN_VERSION) pkg_chk('traits', TRAITS_MIN_VERSION) pkg_chk('nose', NOSE_MIN_VERSION) +pkg_chk('future', FUTURE_MIN_VERSION) +pkg_chk('simplejson', SIMPLEJSON_MIN_VERSION) custom_dateutil_messages = {'missing opt': ('Missing optional package "%s"' ' provided by package ' '"python-dateutil"')} diff --git a/setup_egg.py b/setup_egg.py index bbd439c728..1534f8a2c2 100755 --- a/setup_egg.py +++ b/setup_egg.py @@ -3,6 +3,7 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Wrapper to run setup.py using setuptools.""" +import os.path from setuptools import setup ################################################################################ @@ -15,8 +16,8 @@ if __name__ == '__main__': - execfile('setup.py', dict(__name__='__main__', - extra_setuptools_args=extra_setuptools_args)) - - - + setup_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'setup.py') + with open(setup_file) as f: + code = compile(f.read(), setup_file, 'exec') + exec(code, dict(__name__='__main__', + extra_setuptools_args=extra_setuptools_args)) diff --git a/tools/apigen.py b/tools/apigen.py index 1b332bea07..4e9d08bd72 100644 --- a/tools/apigen.py +++ b/tools/apigen.py @@ -21,6 +21,7 @@ # Stdlib imports from __future__ import print_function +from builtins import object import os import re diff --git a/tools/build_interface_docs.py b/tools/build_interface_docs.py index 8b22b74947..09f38cfc30 100755 --- a/tools/build_interface_docs.py +++ b/tools/build_interface_docs.py @@ -3,6 +3,8 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Script to auto-generate interface docs. """ + +from __future__ import print_function # stdlib imports import os import sys @@ -53,4 +55,4 @@ ] docwriter.write_api_docs(outdir) docwriter.write_index(outdir, 'gen', relative_to='interfaces') - print '%d files written' % len(docwriter.written_modules) + print('%d files written' % len(docwriter.written_modules)) diff --git a/tools/build_modref_templates.py b/tools/build_modref_templates.py index 637f34bfe2..a7bc309f08 100755 --- a/tools/build_modref_templates.py +++ b/tools/build_modref_templates.py @@ -3,6 +3,8 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Script to auto-generate our API docs. """ + +from __future__ import print_function # stdlib imports import os import sys @@ -36,4 +38,4 @@ ] docwriter.write_api_docs(outdir) docwriter.write_index(outdir, 'gen', relative_to='api') - print '%d files written' % len(docwriter.written_modules) + print('%d files written' % len(docwriter.written_modules)) diff --git a/tools/checkspecs.py b/tools/checkspecs.py index 55ea45375c..278ca102c2 100644 --- a/tools/checkspecs.py +++ b/tools/checkspecs.py @@ -4,16 +4,18 @@ """Attempt to check each interface in nipype """ +from __future__ import print_function +from builtins import object + # Stdlib imports -import inspect import os import re import sys -import tempfile import warnings -from nipype.external import six from nipype.interfaces.base import BaseInterface +from nipype.external.six import string_types + # Functions and classes class InterfaceChecker(object): @@ -206,8 +208,9 @@ def test_specs(self, uri): if not os.path.exists(nonautotest): with open(testfile, 'wt') as fp: cmd = ['# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT', - 'from nipype.testing import assert_equal', - 'from %s import %s' % (uri, c), + 'from %stesting import assert_equal' % + ('.' * len(uri.split('.'))), + 'from ..%s import %s' % (uri.split('.')[-1], c), ''] cmd.append('def test_%s_inputs():' % c) input_fields = '' @@ -216,7 +219,7 @@ def test_specs(self, uri): for key, value in sorted(trait.__dict__.items()): if key in in_built or key == 'desc': continue - if isinstance(value, six.string_types): + if isinstance(value, string_types): quote = "'" if "'" in value: quote = '"' @@ -228,8 +231,8 @@ def test_specs(self, uri): cmd += [' input_map = dict(%s)' % input_fields] cmd += [' inputs = %s.input_spec()' % c] cmd += [""" - for key, metadata in input_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value"""] fp.writelines('\n'.join(cmd) + '\n\n') else: @@ -241,7 +244,7 @@ def test_specs(self, uri): continue parent_metadata = [] if 'parent' in trait.__dict__: - parent_metadata = getattr(trait, 'parent').__dict__.keys() + parent_metadata = list(getattr(trait, 'parent').__dict__.keys()) if key not in allowed_keys + classinst._additional_metadata\ + parent_metadata: bad_specs.append([uri, c, 'Inputs', traitname, key]) @@ -260,7 +263,7 @@ def test_specs(self, uri): for key, value in sorted(trait.__dict__.items()): if key in in_built or key == 'desc': continue - if isinstance(value, six.string_types): + if isinstance(value, string_types): quote = "'" if "'" in value: quote = '"' @@ -272,8 +275,8 @@ def test_specs(self, uri): cmd += [' output_map = dict(%s)' % input_fields] cmd += [' outputs = %s.output_spec()' % c] cmd += [""" - for key, metadata in output_map.items(): - for metakey, value in metadata.items(): + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value"""] fp.writelines('\n'.join(cmd) + '\n\n') @@ -283,7 +286,7 @@ def test_specs(self, uri): continue parent_metadata = [] if 'parent' in trait.__dict__: - parent_metadata = getattr(trait, 'parent').__dict__.keys() + parent_metadata = list(getattr(trait, 'parent').__dict__.keys()) if key not in allowed_keys + classinst._additional_metadata\ + parent_metadata: bad_specs.append([uri, c, 'Outputs', traitname, key]) @@ -380,7 +383,7 @@ def check_modules(self): if bad_specs: checked_modules.extend(bad_specs) for bad_spec in checked_modules: - print ':'.join(bad_spec) + print(':'.join(bad_spec)) if __name__ == "__main__": package = 'nipype' diff --git a/tools/github.py b/tools/github.py index ea942e4ea1..9d7ceba1a1 100644 --- a/tools/github.py +++ b/tools/github.py @@ -1,6 +1,8 @@ -import httplib +from future import standard_library +standard_library.install_aliases() +import http.client import inspect -import json +import simplejson import os from subprocess import Popen, PIPE @@ -45,7 +47,7 @@ def create_hash_map(): from base64 import encodestring as base64 import pwd login_name = pwd.getpwuid(os.geteuid())[0] - conn = httplib.HTTPSConnection("api.github.com") + conn = http.client.HTTPSConnection("api.github.com") conn.request("GET", "/repos/nipy/nipype", headers={'Authorization': 'Basic %s' % base64(login_name)}) try: @@ -56,7 +58,7 @@ def create_hash_map(): r1 = conn.getresponse() if r1.reason != 'OK': raise Exception('HTTP Response %s:%s' % (r1.status, r1.reason)) - payload = json.loads(r1.read()) + payload = simplejson.loads(r1.read()) for infodict in payload['tree']: if infodict['type'] == "blob": hashmap[infodict['sha']] = infodict['path'] diff --git a/tools/gitwash_dumper.py b/tools/gitwash_dumper.py index 3a112b6eca..3431a0645a 100755 --- a/tools/gitwash_dumper.py +++ b/tools/gitwash_dumper.py @@ -1,5 +1,6 @@ #!/usr/bin/env python ''' Checkout gitwash repo into directory and do search replace on name ''' +from __future__ import print_function import os from os.path import join as pjoin @@ -79,7 +80,7 @@ def copy_replace(replace_pairs, for rep_glob in rep_globs: fnames += fnmatch.filter(out_fnames, rep_glob) if verbose: - print '\n'.join(fnames) + print('\n'.join(fnames)) for fname in fnames: filename_search_replace(replace_pairs, fname, False) for in_exp, out_exp in renames: diff --git a/tools/interfacedocgen.py b/tools/interfacedocgen.py index 4efc77e383..27ef425e31 100644 --- a/tools/interfacedocgen.py +++ b/tools/interfacedocgen.py @@ -19,6 +19,9 @@ PyMVPA project, which we've adapted for NIPY use. PyMVPA is an MIT-licensed project.""" +from __future__ import print_function +from builtins import object + # Stdlib imports import inspect import os @@ -260,7 +263,7 @@ def generate_api_doc(self, uri): workflows.append((workflow,function, finst)) if not classes and not workflows and not helper_functions: - print 'WARNING: Empty -',uri # dbg + print('WARNING: Empty -',uri) # dbg return '' # Make a shorter version of the uri that omits the package name for @@ -286,13 +289,13 @@ def generate_api_doc(self, uri): # self.rst_section_levels[2] * 7 + '\n' for c in classes: __import__(uri) - print c + print(c) try: with warnings.catch_warnings(): warnings.simplefilter("ignore") classinst = sys.modules[uri].__dict__[c] except Exception as inst: - print inst + print(inst) continue if not issubclass(classinst, BaseInterface): diff --git a/tools/make_examples.py b/tools/make_examples.py index a48a5a51ba..89fccf597a 100755 --- a/tools/make_examples.py +++ b/tools/make_examples.py @@ -3,6 +3,8 @@ This also creates the index.rst file appropriately, makes figures, etc. """ + +from past.builtins import execfile #----------------------------------------------------------------------------- # Library imports #----------------------------------------------------------------------------- diff --git a/tools/nipype_nightly.py b/tools/nipype_nightly.py index 5644cedf58..2355649350 100644 --- a/tools/nipype_nightly.py +++ b/tools/nipype_nightly.py @@ -4,6 +4,8 @@ to sourceforge. """ +from __future__ import print_function + import os import sys import subprocess @@ -11,7 +13,7 @@ dirname = '/home/cburns/src/nipy-sf/nipype/trunk/' def run_cmd(cmd): - print cmd + print(cmd) proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=os.environ, @@ -20,8 +22,8 @@ def run_cmd(cmd): returncode = proc.returncode if returncode: msg = 'Running cmd: %s\n Error: %s' % (cmd, error) - raise StandardError(msg) - print output + raise Exception(msg) + print(output) def update_repos(): """Update svn repository.""" diff --git a/tools/report_coverage.py b/tools/report_coverage.py index 95385243c7..c1a1fc2e66 100644 --- a/tools/report_coverage.py +++ b/tools/report_coverage.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +from __future__ import print_function import subprocess def run_tests(cmd): @@ -10,7 +11,7 @@ def run_tests(cmd): stdout, stderr = proc.communicate() if proc.returncode: msg = 'Running cmd: %s\n Error: %s' % (cmd, error) - raise StandardError(msg) + raise Exception(msg) # Nose returns the output in stderr return stderr @@ -41,10 +42,10 @@ def grab_coverage(output): def main(): cmd = 'nosetests --with-coverage --cover-package=nipype' - print 'From current directory, running cmd:' - print cmd, '\n' + print('From current directory, running cmd:') + print(cmd, '\n') output = run_tests(cmd) report = grab_coverage(output) - print report + print(report) main() diff --git a/tools/run_examples.py b/tools/run_examples.py index 53acb16474..1eb1f6e6ee 100644 --- a/tools/run_examples.py +++ b/tools/run_examples.py @@ -1,10 +1,11 @@ +from __future__ import print_function import os import sys from shutil import rmtree def run_examples(example, pipelines, plugin): - print 'running example: %s with plugin: %s'%(example, plugin) + print('running example: %s with plugin: %s'%(example, plugin)) from nipype import config config.enable_debug_mode() from nipype.interfaces.base import CommandLine diff --git a/tools/toollib.py b/tools/toollib.py index 95c4d42ae7..3f6f122ff3 100644 --- a/tools/toollib.py +++ b/tools/toollib.py @@ -1,5 +1,7 @@ """Various utilities common to IPython release and maintenance tools. """ + +from builtins import map # Library imports import os import sys