cansas1d binding Python
Comments
Specific support for the cansas1d/1.0 data standard in Python has not been developed. However, some constructive suggestions are being gathered on this page.
gnosis.xml.objectify
The GnosisUtils (http://freshmeat.net/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 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 installation (without all that output) steps. Your system may have gnosis already installed. You may also need sysAdmin privileges. You may need ...
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
quick test in Python
Here is the Python code (without all that output) (called python-test.py):
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
print sasxml.SASentry.SASdata.Idata[0].Q.unit, sasxml.SASentry.SASdata.Idata[0].I.unit
print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA
A revision of this example is on the TRAC site: http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/python/python-test.py
execution of that Python code
[Pete@regitte,2441,cansas1dwg-regitte]$ ./python-test.py SAS bimodal test1 1992 simulated SAS calculation 1/A 1/cm 0.0040157139 3497.473 90.72816
full session output
[Pete@regitte,2429,/tmp]$ cd /tmp
/tmp
[Pete@regitte,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@regitte,2431,/tmp]$ tar xzf Gnosis_Utils-1.2.2.tar.gz
[Pete@regitte,2432,/tmp]$ cd Gnosis_Utils-1.2.2/
/tmp/Gnosis_Utils-1.2.2
[Pete@regitte,2433,Gnosis_Utils-1.2.2]$ python setup.py install_all
[Pete@regitte,2434,Gnosis_Utils-1.2.2]$ cd ~/workspace/cansas1dwg-regitte
[Pete@regitte,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
>>> print sasxml.SASentry.SASdata.Idata[0].Q.unit
1/A
>>> print sasxml.SASentry.SASdata.Idata[0].I.unit
1/cm
>>> print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA
0.0040157139 3497.473 90.72816
Conclusion: OK
This has the promise of being a useful approach to reading this format in Python. Now, how to write back out... ?
generateDS.py
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/1.0 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.
[Pete@regitte,2402,cansas1dwg-regitte]$ 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'
Conclusion: not ready yet
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. (2008-05-16)
