Python

The Python binding to read canSAS 1-D data files has been implemented using the gnosis utils. It is very easy to use, once you have the gnosis utils installed. XML files are read by the readCanSasFile() routine from the cansas1d support file.

version	namespace
1.0	cansas1d/1.0
1.1	urn:cansas1d:1.1

If either namespace or version don’t match, an exception is raised.

If the version and namespace match this table, the data from the file is mapped into Python objects, as shown by the examples below. Otherwise, an appropriate exception is raised.

Interactive example using cansas1d

Here is an interactive example showing how to read a canSAS 1D data file using the canSAS 1D Python binding:

>>> from cansas1d import readCanSasFile
>>> sasxml = readCanSasFile('bimodal-test1.xml')
>>> print sasxml.SASentry.Title
<Title id="34b0470" >
>>> print sasxml.SASentry.Title.PCDATA
SAS bimodal test1
>>> print len(sasxml.SASentry.SASdata.Idata)
91
>>> print sasxml.SASentry.SASsample.ID.PCDATA
bimodal-test1
>>> source = sasxml.SASentry.SASinstrument.SASsource
>>> print source.radiation.PCDATA, source.wavelength.PCDATA, source.wavelength.unit
artificial 1.00 A

Interactive Example using gnosis.xml.objectify

Here is an interactive example showing how to read a canSAS 1D data file using gnosis.xml.objectify:

>>> from gnosis.xml.objectify import XML_Objectify
>>> sasxml = XML_Objectify('bimodal-test1.xml').make_instance()
>>> print sasxml.SASentry.Title.PCDATA
SAS bimodal test1
>>> sasxml.SASentry.Run.PCDATA
1992
>>> sasxml.SASentry.SASinstrument.name.PCDATA
simulated SAS calculation
>>> data0 = sasxml.SASentry.SASdata.Idata[0]
>>> print data0.Q.unit,  data0.I.unit
1/A 1/cm
>>> print data0.Q.PCDATA,  data0.I.PCDATA,  data0.Idev.PCDATA
0.0040157139 3497.473 90.72816

example: how to retrieve \(I(Q)\)

briefly (ignoring any exception handling):

>>> from cansas1d import readCanSasFile
>>> sasxml = readCanSasFile('bimodal-test1.xml')
>>> Q = [float(i.Q.PCDATA) for i in sasxml.SASentry.SASdata.Idata]
>>> I = [float(i.I.PCDATA) for i in sasxml.SASentry.SASdata.Idata]

cansas1d.py source code documentation

Here is the source code and documentation of the cansas1d.py Python binding. This file (and an example that calls this file and prints more data from the file) may be found in the canSAS subversion repository.

read canSAS 1-D XML data files (either v1.0 or v1.1)

requires:gnosis.xml.objectify # easy_install -U gnosis

basic use in a program:

import cansas1d
try:
    sasxml = cansas1d.readCanSasFile(xmlFile)
except cansas1d.Exception_canSAS_namespace, answer:
    print "wrong XML namespace:", answer
    return
except cansas1d.Exception_canSAS_version, answer:
    print "wrong version string:", answer
    return

Copyright (c) 2013, UChicago Argonne, LLC This file is distributed subject to a Software License Agreement found in the file LICENSE that is included with this distribution.

exception cansas1d.Exception_canSAS_namespace

Bases: exceptions.Exception

canSAS XML file namespace

exception cansas1d.Exception_canSAS_version

Bases: exceptions.Exception

version string of the canSAS standard

cansas1d.readCanSasFile(xmlFile)

open a canSAS XML data file as a gnosis file object

Parameters:

xmlFile (str) – name of canSAS 1D XML data file

Returns:

gnosis object with XML data structure

Raises:

• Exception_canSAS_namespace – if namespace does not match
• Exception_canSAS_version – if version does not match

gnosis utils

The Python binding to read canSAS 1-D data files has been implemented using the gnosis utilities. [1] Specifically, the gnosis.xml.objectify package turns arbitrary XML documents into Python objects. Since gnosis.xml.objectify is not aware of the XML Schema, it is necessary to check that the file read is a canSAS 1D file. Matching of the namespace and version should be sufficient to accept a canSAS 1D file. Appropriate exceptions are raised if the file does not pass these tests.

[1]	gnosis utilities: http://freecode.com/projects/gnosisxml/

You can install the gnosis utilities if you have the distutils package using:

easy_install -U gnosis