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Python

Specific support for the cansas1d/1.1 data standard in Python (http://danse.us/trac/sans) is being developed by NIST/NCNR (http://www.ncnr.nist.gov) as part of their contribution to the DANSE project (http://wiki.cacr.caltech.edu/danse).

Here are some extremeley terse instructions (circa 2008) to get you started on a UNIX or Linux system:

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svn co http://danse.us/trac/sans/browser/trunk/DataLoader DataLoader
cd DataLoader
python setup.py install

The release notes (http://danse.us/trac/sans/browser/trunk/DataLoader/release_notes.txt) have a list of the dependencies.

Comments

Other constructive suggestions (that predate the NIST/NCNR support) have been gathered on this page.

gnosis.xml.objectify

The GnosisUtils (http://freecode.com/projects/gnosisxml/) offer a method to read any XML file into Python data structures. This utility does not validate the XML against a specific XML Schema which can be both good (flexible, especially when XML Foreign Namespace elements are used) and not so good (XML content not guaranteed to be valid by the rules).

A quick test of this turned up an acceptable result in that it was able to read several of the canSAS test XML files, including those with foreign namespaces. And it was very easy. (Especially with some help from http://www.xml.com/pub/a/2003/07/02/py-xml.html)

Here is a quick example.

Installation

Here is the condensed GnosisUtils installation (without all that output) steps. Your system may have gnosis already installed. You may also need sysAdmin privileges. You may need ...

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cd /tmp
wget http://freshmeat.net/redir/gnosisxml/22028/url_tgz/Gnosis_Utils-1.2.2.tar.gz
tar xzf Gnosis_Utils-1.2.2.tar.gz
cd Gnosis_Utils-1.2.2/
python setup.py install_all

Alternatively, it might be simpler to install from the PyPI repository (http://pypi.python.org/pypi/Gnosis%20Utilities):

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easy_install -U gnosis_utils

Quick test in Python

Conclusion: OK

The GnosisUtils have the promise of being a useful tool to support reading this format in Python. Now, how to write back out... ? From the website, it appears the development of GnosisUtils has stagnated in 2007 at v1.2.2.

Here is the Python code (without all that output) (called python-test.py):

python-test.py

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import gnosis.xml.objectify

sasxml = gnosis.xml.objectify.XML_Objectify('bimodal-test1.xml').make_instance()
print sasxml.SASentry.Title.PCDATA
print sasxml.SASentry.Run.PCDATA
print sasxml.SASentry.SASinstrument.name.PCDATA
data0 = sasxml.SASentry.SASdata.Idata[0]
print data0.Q.unit,  data0.I.unit
print data0.Q.PCDATA,  data0.I.PCDATA,  data0.Idev.PCDATA

Output from python-test.py

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[Pete@ubuntu,2441,cansas1dwg]$ ./python-test.py
SAS bimodal test1
1992
simulated SAS calculation
1/A 1/cm
0.0040157139 3497.473 90.72816

Full session output

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[Pete@ubuntu,2429,/tmp]$ cd /tmp
/tmp
[Pete@ubuntu,2430,/tmp]$ wget http://freshmeat.net/redir/gnosisxml/22028/url_tgz/Gnosis_Utils-1.2.2.tar.gz
--11:43:16--  http://freshmeat.net/redir/gnosisxml/22028/url_tgz/Gnosis_Utils-1.2.2.tar.gz
           => `Gnosis_Utils-1.2.2.tar.gz'
Resolving freshmeat.net... 66.35.250.168
Connecting to freshmeat.net|66.35.250.168|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://www.gnosis.cx/download/Gnosis_Utils.More/Gnosis_Utils-1.2.2.tar.gz [following]
--11:43:16--  http://www.gnosis.cx/download/Gnosis_Utils.More/Gnosis_Utils-1.2.2.tar.gz
           => `Gnosis_Utils-1.2.2.tar.gz'
Resolving www.gnosis.cx... 64.41.64.172
Connecting to www.gnosis.cx|64.41.64.172|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 287,989 (281K) [application/x-tar]

100%[==============================================================================>] 287,989       --.--K/s

11:43:16 (2.47 MB/s) - `Gnosis_Utils-1.2.2.tar.gz' saved [287989/287989]

[Pete@ubuntu,2431,/tmp]$ tar xzf Gnosis_Utils-1.2.2.tar.gz
[Pete@ubuntu,2432,/tmp]$ cd Gnosis_Utils-1.2.2/
/tmp/Gnosis_Utils-1.2.2
[Pete@ubuntu,2433,Gnosis_Utils-1.2.2]$ python setup.py install_all
[Pete@ubuntu,2434,Gnosis_Utils-1.2.2]$ cd ~/workspace/cansas1dwg-regitte
[Pete@ubuntu,2435,cansas1dwg-regitte]$ python
Python 2.5.1 (r251:54863, May 18 2007, 16:56:43)
[GCC 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)] on cygwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gnosis.xml.objectify
>>> sasxml = gnosis.xml.objectify.XML_Objectify('bimodal-test1.xml').make_instance()
>>> print sasxml.SASentry.Title.PCDATA
SAS bimodal test1
>>> print sasxml.SASentry.Run.PCDATA
1992
>>> print sasxml.SASentry.SASinstrument.name.PCDATA
simulated SAS calculation
>>> data0 = sasxml.SASentry.SASdata.Idata[0]
>>> print data0.Q.unit
1/A
>>> print data0.I.unit
1/cm
>>> print data0.Q.PCDATA,  data0.I.PCDATA,  data0.Idev.PCDATA
0.0040157139 3497.473 90.72816

generateDS.py

Conclusion: not ready yet (2008-05-16)

Either the canSAS standard (by means of the cansas1d.xsd XML Schema) is not ready or generateDS.py does not cover the XML Schema requirements we have at this time. Either way, this is not a viable tool to use now.

generateDS.py (http://www.rexx.com/~dkuhlman/, http://www.rexx.com/~dkuhlman/generateDS.html) can build a binding (map the structure of the XML file directly into a Python data structure) for Python from an XML Schema. However, the cansas1d/1.1 XML schema (cansas1d.xsd) does not seem to fit the model.It seems, for now, that generateDS-1.12a fails on a certain annotate line.

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[Pete@ubuntu,2402,cansas1dwg]$ python  \
                ~/generateDS-1.12a/generateDS.py  \
                -p CS1D_  \
                -o cansas1d.py  \
                -s cansas1dsubs.py  \
                cansas1d.xsd
Traceback (most recent call last):
  File "/home/Pete/generateDS-1.12a/generateDS.py", line 3997, in <module>
    main()
  File "/home/Pete/generateDS-1.12a/generateDS.py", line 3993, in main
    processIncludes, superModule=superModule)
  File "/home/Pete/generateDS-1.12a/generateDS.py", line 3909, in parseAndGenerate
    root.annotate()
AttributeError: 'NoneType' object has no attribute 'annotate'

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