The Python Programming Language and HDF5: H5Py

The Python Programming Language and HDF5: H5py.
Application to Satellite Remote Sensing Data Processing.
Needs of satellite remote sensing data processing and
programming languages.
Introduction to some Python elements.
Introduction to Numerical Python with Numpy.
Tying them together with H5py.
Examples.
Daniel Kahn, Science Systems and Applications Inc.
HDF/HDF-EOS Workshop XIII, Riverdale, MD
3 Nov 2009

Where credit is due:

Andrew Collette, UCLA, author of h5py
Francesc Alted, author of PyTables and the
HDF5 1.6 Pyrex definitions (i.e Python-C defs
used in H5py)
Andrew also requested acknowledgment for Darren
Dale (Cornell) and Armando Sole (ESRF) for their
suggestions, patches and encouragement.

Modern remote sensing satellite data and data processing
needs have several characteristics.
1) The data need to be subjected to numerical algorithms. The
algorithms vary in their sophistication but few, if any, require
supercomputer architectures. E.g. Computing a zonal mean.
(Fortran, C, C++)
2) The data need to be subjected to non-numerical “bookkeeping”
algorithms. Associated metadata needs to be read, matched, sliced,
diced, acted upon and committed to databases. (Perl)
3) Modern systems automatically the schedule processing on to
lots of inexpensive, commodity CPUs. This complicates using
managed (i.e. licensed) commercial runtime environments, e.g.
IDL, Matlab, Mathematica.
4) Satellite processing systems are dynamic. They need
customization several times over the course of each instrument's
life. Development time needs to be short. (Perl, IDL, Matlab,
Mathematica)
5) Data processing systems need to track data provenance.

A Remote Sensing Data Processing Challenge...

Problem:
We lack a programming language which spans the breath of
our remote sensing data processing needs, i.e. Which can
handle both numerical and non-numerical processing
(including HDF5) and that has a short development cycle.
Goal:
Find a programming language which allows fast development
and is adept at numerical processing as well as non-numerical
processing. “Adept” doesn't mean “best”, just pretty good.

...and the Python Programming Language
Why Python fits the bill better than:
Fortran
As an interpreted language with dynamic variable bindings
Python offers more flexibility during development. The
multidimensional array extension (numpy) provides efficient and
competitive array operations. It is more similar to IDL or
Matlab...
IDL or Matlab
No license required which can save money on several levels.
Python language can be more well suited to non-numerical
data processing tasks such as are encountered in production
processing of remote sensing. It is more similar to Perl...
Perl/PDL
Nicer syntax for array operations.
More complete HDF5 support (h5py vs PDL HDF5).

Some elements of Python
Python is an interpreted language. Python
statements can easily be run from an interactive
prompt. Python programs are written in ASCII files.

Python has many of the same elements as programming
languages used for numerical processing (I.e. loops,
conditionals, etc) plus...
Name spaces
Lists
Dictionaries

Python has name spaces
Name spaces allow related functions and data to be grouped together
in a way that will not conflict with unrelated functions and data which
happens to be named the same.
Name space are very useful, but are only relevant here because
Python name spaces correspond to Python modules. The
numerical and HDF5 routines we will see later are implemented
as Python modules.
For example, to open an HDF5 file in Python we first import the h5py
module and then we open the file using the File function of the h5py
module.

import h5py # First import the module.
FileID = h5py.File('hdf5_test.h5','r')#Now use the File function,
#note the module name in red.
.
.
.

We could import other modules simultaneously which have an unrelated
function called File and there would be no conflict or error.

Python has Lists:
These are 1D arrays which are useful for solving many problems.
List index notation looks like 1D array notation in many languages.

>>> MyList = [1.0,70] # initialize variable to 2 element list
>>> MyList.append("Demo Data!") # Append an element, NOT like fortran
>>> MyList.append(MyList[0] + MyList[1]) # Append sum of first 2 elements
>>> print MyList
[1.0, 70, 'Demo Data!', 71.0]

Python has Dictionaries:
(Aka hash tables) These map symbols to objects in analogy to
how a 1D list maps an integer index value to an object.
>>>
>>>
>>>
>>>
>>>
>>>
{0:

MyDictionary = {} # Initialize empty Dictionary
MyDictionary[0] = 1
MyDictionary['Gadzooks'] = 70
MyDictionary['Kind of Data'] = 'Demo Data!'
MyDictionary['Result'] = MyDictionary[0] + MyDictionary['Gadzooks']
print MyDictionary
1, 'Kind of Data': 'Demo Data!', 'Result': 71, 'Gadzooks': 70}

Python Lists vs Python Dictionaries vs Arrays in Fortran
Index to a List must be an integer, but a Dictionary can be
indexed by an integer or string.
MyList[Integer] vs. MyDictionary[Integer or String]

The objects referenced by a List or Dictionary can be any Python
object. This is in contrast to more traditional languages, eg. The
elements Fortran array must be of a particular type such as
real*4.
MyList = [34,”String Datum”]
or
MyDictionary={'FirstKey':34,'SecondKey':”String Datum”}

The List and Dictionary data structures make it possible to write
flexible programs very quickly. However, they are not good for
numerical computation. The variety of objects (number, string, etc)
which they can reference makes computation slow.
For example, adding array elements: MyList[0] + MyList[1]
Python must check at run time if MyList[0] and MyList[1] are
objects that can be added together, and not, say, a number and a
string. In a loop this check is performed at every iteration!
What to do?

Enter Numpy
Numpy is a package for use with Python which provides
multidimensional arrays of numeric (and other) types and extends
Python syntax to provide a familiar interface to the arrays.
Numpy extends Python syntax to allow the expression of vector
operations similar to those in IDL, Matlab, or Fortran (>=90).

Numpy Example: Create, Print, and add two 2D arrays
Build from Python lists of lists of elements (the module name is numpy)...
>>>
>>>
[[1
[4

a = numpy.array([[1,2,3],[4,5,6]])
print a
2 3]
5 6]]

Build from dimension sizes...
>>> b = numpy.ones([2,3])
>>> print b
[[ 1. 1. 1.]
[ 1. 1. 1.]]

Print a selected element...
>>> print a[1,2]
6

Example: Add two dimensional arrays.
>>> print a+b
[[ 2. 3. 4.]
[ 5. 6. 7.]]
>>>

The HDF5 connection: H5py
H5py is an Python-HDF5 interface is a Python module
written by Andrew Collette. Its design allows the use of
familiar Python structures for working with HDF5 files.

The interface maps Python syntax for familiar Python
objects to similar objects in the HDF5 file.

Here is a familiar example HDF5 file
from the HDFView distribution:
Here is how to read the 3D int array using
h5py.

>>> import h5py
>>> fid = h5py.File('hdf5_test.h5','r')
>>> group = fid['arrays']
>>> The3DArray = group['3D int array'].value
>>> fid.close()
>>> The3DArray
array([[[
174,
27,
0, ...,
102,
[
171,
27,
0, ...,
194,
[
172,
27,
0, ...,
102,
...,

71,
79,
55,

100009
100109
100209

Equivalence of HDF5 Groups and Python Dictionaries
Print value of dictionary entry:
>>> MyDictionary =
{'RandArray':numpy.random.random([2,2])}
>>> print MyDictionary['RandArray']
[[ 0.82066938 0.39219683]
[ 0.86546443 0.91276533]]
Print value of HDF5 file entry:
>>> fid = h5py.File('RandomArray.h5','r')
>>> print fid['RandArray'].value
[[ 0.1
3.14152908]
[ 2.71828008 0.
]]

Simple Real world example:
Goal: Retrieve HDF5 file from Configuration Management (CM)
and insert CM metadata into HDF5 file.
We want to place the CM path and revision number inside the
HDF5 file as an attribute.

Python script to retrieve file from CM and store Rev
number as attribute.
#! /usr/bin/env python
import sys
import os
import h5py
Rev = sys.argv[1] # Specifiy CM path on command line
SVNFilepath = sys.argv[2] # Specify revision number on
#comand line.
command = 'svn export -r ' + Rev + ' ' + SVNFilepath #Subversion
# Command
InStream = os.popen(command,'r')
ExportString = InStream.read()
ExportReturnCode = InStream.close()
Elements = SVNFilepath.split('/')
# HDF5 code
fid = h5py.File(Elements[-1]) # Elements[-1] is file name
fid.attrs['SVN Path and Revision'] = SVNFilepath + '@' + Rev
fid.close()

H5py code in red. Note the minimal effort coding HDF5 calls.

Another real world example (if NPOESS is your real world).
We have had several occasions to do data aggregation on HDF5 files for the
OMPS Limb instrument.
Our retrieval code (Fortran) processes an orbit of data as 480 distinct pieces
and places the results into 480 distinct HDF5 files. We wish to aggregate the
files such that an N dimensional array in a unaggregated file becomes a N+1
dimensional array in the aggregated HDF5 file.
The Fortran code is (mostly) the product of the retrieval scientist, while the
aggregation is a requirement of the production data processing system. It makes
sense to aggregate as a post-processing step to the Fortran code so as to
minimize changes to the original Fortran code.

Aggregation Algorithm
1) Input is list of HDF5 files
2) Analyze structure of one file to generate list of fully qualified dataset names,
dimensions, and type (In the code I use a Python Dictionary and not a list).
3) Assume all files have that structure. Read corresponding datasets (of dim N)
from each file into aggregation variable (of dim N+1).
4) After corresponding datasets have been read from all files write aggregation
variable to HDF5 file.
5) Repeat 3 until all datasets have been aggregated.
File 1 Array

Array 4
Array 3
File 4 Array
Array 2
Array 1

File 2 Array File 3 Array

+

+

+

Schematic of Array Aggregation for One Dataset

# Data Aggregator. This script takes a set of HDF5 files as input.
# The files are expected to have identical struture. All the
# corresponding arrays in the input files are combined into an array
# which has dimensions N+1, where N is the number of dimensions in the
# original, constituent arrays.
import sys
import h5py
import numpy
Files = sys.argv[1:] # Get file names from command line
# First step is to select one file and create a map of the shape and
# data type of all datasets. This is naturally done via a recursive
# function, called VisitAllObjects
FirstFid = h5py.File(Files[0],'r') # Open first HDF5 file
FileInfo = {} # Initialize FileInfo to be a dictionary. We will use it to build a mapping from
# dataset name to a tuple containing shape and type of dataset.
# EVALUATE HDF5 HIERARCHY
# Evaluating a a hierarchy is naturally a recursive process so we define a function....
def VisitAllObjects(Group,Path):
for i in Group.items():
if isinstance(i[1],h5py.Group):
VisitAllObjects(i[1],Path + '/' + i[0])
else:
DatasetName = Path + '/' + i[0]
FileInfo[DatasetName] = (Group[DatasetName].shape, Group[DatasetName].dtype)
VisitAllObjects(FirstFid,'')
FirstFid.close()

# Print dataset paths and info to screen
for (k,v) in FileInfo.items():
print k,v
# AGGREGATE DATA
# Now that we understand the file structure we can perform the aggregation.
OutputFileID = h5py.File('AggregatedData.h5','w')
NumberOfFiles = len(Files)
# Here is the meat of the code. The outer loop is over datasets, the inner
over all files.
for Dataset in FileInfo.keys():
AggregatedData = numpy.ndarray(FileInfo[Dataset][0]+
(NumberOfFiles,),dtype = FileInfo[Dataset][1])
for FileNumber in range(NumberOfFiles):
# Open file, read data into aggregation array, and close
fid = h5py.File(Files[FileNumber],'r')
AggregatedData[...,FileNumber] = fid[Dataset].value
fid.close()
Path = Dataset.split('/')
map((lambda(x): OutputFileID.require_group(x)), Path[1:-1])
#OutputFileID[Dataset] = AggregatedData
OutputFileID.create_dataset(Dataset,data=AggregatedData,compression=5,chunks=
FileInfo[Dataset][0]+(1,))
OutputFileID.close()

Original, Unaggregated Data Field
$ h5dump -H -d /ANCILLARY_DATA/GeopotentialHeight_NCEP
Data/OMPS_LP_SDR_20041121_55_146_-69_-119.h5
HDF5 "Data/OMPS_LP_SDR_20041121_55_146_-69_-119.h5" {
DATASET "/ANCILLARY_DATA/GeopotentialHeight_NCEP" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 5, 3, 21 ) / ( 5, 3, 21 ) }
ATTRIBUTE "Title" {
DATATYPE H5T_STRING {
STRSIZE 25;
Note 3 dimensions
}
DATASPACE SCALAR
}
ATTRIBUTE "Units" {
STRSIZE 2;
}
DATASPACE SCALAR
}
ATTRIBUTE "_FillValue" {
DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
}
}

Aggregated Data Field

AggregatedData.h5
HDF5 "AggregatedData.h5" {
DATASPACE SIMPLE { ( 5, 3, 21, 4 ) / ( 5, 3, 21, 4 ) }
}
}

Now we have 4 dimensions. The new
dimension has extent 4, corresponding to
the number of input files.
Note that none of the attributes were copied.
This is a bug, but easily fixed.

To fix the bug, I assume attributes (like “Units”) are not
aggregated, and I take attributes and values from first file.
New code consists of only 2+ additional lines, shown below
in green.

def VisitAllObjects(Group,Path):
for i in Group.items():
if isinstance(i[1],h5py.Group):
VisitAllObjects(i[1],Path + '/' + i[0])
else:
DatasetName = Path + '/' + i[0]
FileInfo[DatasetName] = (Group[DatasetName].shape,
Group[DatasetName].dtype,
Group[DatasetName].attrs.listitems())

And also....

DS=OutputFileID.create_dataset(Dataset,data=AggregatedData,compression=5,chunks=F
[DS.attrs.__setitem__(Attribute[0],Attribute[1]) for Attribute in
FileInfo[Dataset][2]]

Fixed output:
AggregatedDataWithAttributes.h5
HDF5 "AggregatedDataWithAttributes.h5" {
DATASPACE SIMPLE { ( 5, 3, 21, 4 ) / ( 5, 3, 21, 4 ) }
ATTRIBUTE "Title" {
STRSIZE 25;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
Now we have attributes.
}
ATTRIBUTE "Units" {
STRSIZE 2;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "_FillValue" {
DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
}
}

}

Summary:
Python offers a high degree of flexibility for code
development, combined with the ability to do easy
text, numerical array and HDF5 coding make it a
good candidate for solving problems in satellite
remote sensing data processing.
Few, if any, other computer languages offer this
combination of benefits making it uniquely suited for
this task.
Future
Work:
Tracking module version provenance is likely one of the
outstanding questions for Python use in production.
Acknowledgment:
Curt Tilmes at NASA Goddard funded this work via
contract NNG06HX18C task 614.5-01-07

The Python Programming Language and HDF5: H5Py

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