cansas1d binding Python - Revision history

Jemian: identify NIST/NCNR Python work for DANSE

2008-10-15T23:01:15Z

identify NIST/NCNR Python work for DANSE

@@ Line 1: / Line 1: @@
 == 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.
+Other constructive suggestions (that predate the NIST/NCNR support) have been gathered on this page.
 == gnosis.xml.objectify ==

Jemian: /* quick test in Python */

2008-05-16T17:15:25Z

quick test in Python

← Older revision		Revision as of 17:15, 16 May 2008
Line 43:		Line 43:
	print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA		print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA
	</pre>		</pre>

			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 ===		=== execution of that Python code ===

Jemian: /* Other suggestions */

2008-05-16T16:54:04Z

Other suggestions

← Older revision		Revision as of 16:54, 16 May 2008
Line 137:		Line 137:
	* http://www.devx.com/ibm/Article/20261		* http://www.devx.com/ibm/Article/20261
	* http://mail.python.org/pipermail/xml-sig/2002-April/007559.html		* http://mail.python.org/pipermail/xml-sig/2002-April/007559.html
			* http://pywebsvcs.sourceforge.net/

Jemian at 16:46, 16 May 2008

2008-05-16T16:46:37Z

← Older revision		Revision as of 16:46, 16 May 2008
Line 19:		Line 19:
	=== installation ===		=== installation ===

	Here is the condensed installation (without all that output)		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 ...

	<pre>		<pre>
Line 31:		Line 31:
	=== quick test in Python ===		=== quick test in Python ===

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

	<pre>		<pre>
Line 42:		Line 42:
	print sasxml.SASentry.SASdata.Idata[0].Q.unit, sasxml.SASentry.SASdata.Idata[0].I.unit		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		print sasxml.SASentry.SASdata.Idata[0].Q.PCDATA, sasxml.SASentry.SASdata.Idata[0].I.PCDATA, sasxml.SASentry.SASdata.Idata[0].Idev.PCDATA
			</pre>

			=== execution of that Python code ===

			<pre>
			[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
	</pre>		</pre>

Jemian: initial documentation

2008-05-16T16:40:55Z

initial documentation

New page

== 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)

<pre>
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
</pre>

=== quick test in Python ===

Here is the Python code (without all that output)

<pre>
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
</pre>

=== full session output ===

<pre>
[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
</pre>

=== 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.

<pre>
[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'
</pre>

=== 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)

== Other suggestions ==

* http://www.devx.com/ibm/Article/20261
* http://mail.python.org/pipermail/xml-sig/2002-April/007559.html