Difference between revisions of "cansas1d binding IgorPro"
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UPPER/lower case in the text '''cansas1d/1.0''' as this is a '''key component''' used to
UPPER/lower case in the text '''cansas1d/1.0''' as this is a '''key component''' used to
index through the XML file.
index through the XML file.
== List of Functions ==
== List of Functions ==
Latest revision as of 18:17, 26 December 2008
canSAS 1-D SAS XML format binding to IgorPro
An import tool (binding) for IgorPro has been created (cansasXML.ipf). You can check out the IgorPro working directory from the SVN server (see instructions below).
To use the canSASxml.ipf procedure, you must have the XMLutils XOP IGOR plugin installed. See the Usage Notes below.
Note that the code described here is not a complete user interface. (See further comments below.) It is expected that this code will be called by a graphical user interface routine and that routine will handle the work of copying the loaded SAS data in IgorPro from the root:Packages:CS_XMLreader data folder to the destination of choice (including any renaming of waves as desired).
|author||Pete R. Jemian <email@example.com>|
|version||1.10 (requires latest XMLutils XOP -- see below)|
|purpose||implement an IgorPro file reader to read the canSAS 1-D reduced SAS data in XML files |
adheres to the cansas1d/1.0 standard: http://www.smallangles.net/wgwiki/index.php/cansas1d_documentation
|URL||TRAC: http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/IgorPro/cansasXML.ipf |
|requires||IgorPro: http://www.wavemetrics.com |
XMLutils - XOP: http://www.igorexchange.com/project/XMLutils (IGOR.5.04.x-1.x-dev, 2008-Aug-22)
Checkout of support code in Subversion
Subversion (http://subversion.tigris.org/) is a program for managing software versions. There are command line and GUI clients for a variety of operating systems. We won't recommend any here but will show the command lines necessary.
The XMLutils XOP, written by Andrew Nelson (ANSTO), is hosted on the IgorExchange (http://www.igorexchange.com/).
One good location to place the checked out XMLutils directory is in the Wavemetrics directory, next to the Igor Pro Folder
In the future, to retrieve an updated version of this support, go into the XMLutils directory (created above) and type the command
This will check the repository and update files as needed. If the installer program was updated, you;ll need to run the new installer program. It is not necessary to uninstall first.
The installer executables contained in the download will do all the installation for you. They will place the XOP in the folder /User Procedures/motofit/XMLutils, and create a shortcut/alias to the plugin in /Igor Extensions. Packages from other facilities should place the XOP there as well.
Check out the canSAS 1d SAS XML reader from the subversion repository:
svn checkout http://svn.smallangles.net/svn/canSAS/1dwg/trunk cansas-1dwg
This will download lots of extra files. The file of interest is in the IgorPro directory and is called cansasXML.ipf
In the future, to retrieve an updated version of this support, go into the cansas-1dwg directory (created above) and type the command
This will check the repository and update files as needed.
- License and Install IgorPro (should have already been done by now)
- Quit IgorPro if it is running
- Download XMLutils XOP. Either checkout from subversion (see above) or, with a web browser, go to http://svn.igorexchange.com/viewvc/packages/XMLutils/trunk/
- Install XMLutils XOP by double-clicking the installer for you operating system.
- Download cansasXML.ipf. Either checkout from subversion (see above) or, with a web browser, copy cansasXML.ipf from on-line subversion repository: http://svn.smallangles.net/svn/canSAS/1dwg/trunk/IgorPro/cansasXML.ipf
- Copy cansasXML.ipf file to ...\Wavemetrics\Igor Pro Folder\User Procedures (or file system equivalent)
- Then, you should be able to restart IgorPro and progress from there
To use the canSASxml.ipf procedure, you must have the XMLutils XOP IGOR plugin installed. This may be downloaded from the IgorExchange Project site. There are installer executables contained in the download that will do all the installation for you. Each installer will place the XOP in the folder ...\Wavemetrics\Igor Pro Folder\User Procedures\motofit\XMLutils, and create a shortcut/alias to the plugin in ...\Wavemetrics\Igor Pro Folder\Igor Extensions.
What it does
Given an XML file, CS_XmlReader(fileName) attempts to open the file and read its contents as if it conformed to the canSAS XML standard for reduced 1-D SAS data (cansas1d/1.0, also known as SASXML). If the file is found to be non-conforming, then CS_XmlReader(fileName) returns with an error code (show below), otherwise it returns 0 that indicates no error. All data read by this code is left in the IgorPro data folder root:Packages:CS_XMLreader for pickup by the calling routine. (Two examples are provided to show how a routine might retrieve the data.)
After opening the XML file (with a file identifier fileID), control is passed to CS_1i_parseXml(fileID) which then walks through the XML elements. For each SASentry in the file, a new data folder is created with the name derived from the Title element (or best effort determination). Efforts are taken to avoid duplication of data folder names (using standard IgorPro routines). For SASentry elements that contain more than one SASdata element, a SASdata folder is created for each and the corresponding I(Q) is placed in that subfolder. When only one SASdata is found, the I(Q) data is placed in the main Title folder.
Each column of data in the SASdata/Idata/* table is placed into a single IgorPro wave. At present, the code does not check for non-standard data columns. (The capability is built into the code but is deactivated at present).
Additional metadata is collected into a single text wave (metadata) where the first column is an identifier (or key) and the second identifier is the value. Only those keys with non-empty values are retained in the metadata table. CAUTION: The values are not checked for characters that may cause trouble when placed in a wave note. This will be the responsibility of the calling routine to clean these up if the need arises.
The code checks for most metadata elements and will check for repeated elements where the standard permits.
Here is an example of the metadata for the cs_collagen_full.xml data:
|i (row)||metadata[i] (key)||metadata[i] (value)|
|2||Title||dry chick collagen, d = 673 A, 6531 eV, X6B|
|3||Run||Sep 19 1994 01:41:02 am|
|4||SASsample/ID||dry chick collagen, d = 673 A, 6531 eV, X6B|
|5||SASinstrument/name||X6B, NSLS, BNL|
Sep 19 1994 01:41:02 am Elt: 00090 Seconds ID: No spectrum identifier defined Memory Size: 8192 Chls Conversion Gain: 1024 Adc Offset: 0000 Chls dry chick collagen, d = 673 A 6531 eV, X6B
XML foreign namespace elements
These are ignored at this time.
XML namespace and header
The routine does a best-efforts check to ensure that the given XML file conforms to the required XML file header. If you take a minimalist view (a.k.a. a shortcut), it is likely that your file may be refused by this and other readers. Pay particular attention to UPPER/lower case in the text cansas1d/1.0 as this is a key component used to index through the XML file.
XML stylesheet processing-instruction is not generated
<?xml-stylesheet type="text/xsl" href="example.xsl" ?>
If this processing-instruction is desired, it must be added to each XML data file by other methods such as use of a text editor or application of an XSLT transformation.
List of Functions
These are (most of) the FUNCTIONS in the cansasXML.ipf code. The only functions of interest are CS_XmlReader(fileName) which reads the named XML file and and loads SAS data and the two demonstration functions prj_grabMyXmlData() and prjTest_cansas1d() that together show a usage example.
- open a canSAS 1-D reduced SAS XML data file
- input: fileName (string) name of canSAS XML file (can include file system path name to file)
- 0 successful
- -1: XML file not found
- -2: root element is not <SASroot> with valid canSAS namespace
- -3: <SASroot> version is not 1.0
- -4: no <SASentry> elements (NOT USED NOW)
- -5: XOPutils needs upgrade
- This is what guides the work, given a file ID returned from XMLOpenFile(), parses that file for SAS data and metadata
(1i in the function name signifies this is a function that supports INPUT from version 1.0 XML files)
- CS_1i_getOneSASdata(fileID, Title, SASdataPath)
- harvest the data and metadata in the specific SASdata element
- harvest just one column (vector) of data
- CS_1i_GetReducedSASdata(fileID, SASdataPath)
- grab the data and put it in the working data folder
- CS_1i_locateTitle(fileID, SASentryPath)
- determine the title for this experiment
- CS_appendMetaData(fileID, key, xpath, value)
- queries XML file for xpath. If value is not empty, appends it to metadata where last is the new last row: metadata[last]=key; metadata[last]=value
- CS_buildXpathStr(prefix, value)
- this function can be used only with very simple XPath constructions
- given a proposal string, returns a candidate folder name for immediate use
- looks for element index in structure W_ElementList returned from call to XmlElemList(fileID)
- returns the string containing the default namespace for the XML file
- Builds a table of all namespaces used in the XML file and appends W_ElementList with full namespace-xpath string for each element.
- CS_simpleXmlListXpath(fileID, prefix, value)
- Calls XMLlistXpath() with proper namespace prefix attached.
- CS_simpleXmlWaveFmXpath(fileID, prefix, value)
- Calls XMLwaveFmXpath() with proper namespace prefix attached.
- CS_updateWaveNote(wavName, key, value)
- adds (or replaces) definition of key=value in the wave note of wavName
- CS_XmlStrFmXpath(fileID, prefix, value)
- Calls XmlStrFmXpath() with proper namespace prefix attached. Trims the result string.
- this function adds namespace info as necessary to simpleStr (an XPath)
- Calls TrimWSL(TrimWSR(str))
- Trims white space from left (leading) end of str
- Trims white space from right (trailing) end of str
- Demonstration function that calls CS_XmlReader(fileName) for many of the test data sets.
- Demonstration function that moves loaded data from root:Packages:CS_XMLreader to a user's data folder. (In this example, that folder is root:PRJ_canSAS.)
- Demonstration function that reads an ISIS/LOQ file and copies the data to the root folder a la COLLETE
Example test case
Here is an example running the test routine prjTest_cansas1d().
•prjTest_cansas1d() XMLopenfile: File(path) to open doesn't exist, or file can't be opened elmo.xml either not found or cannot be opened for reading Completed in 0.00669666 seconds XMLopenfile: XML file was not parseable cansasXML.ipf: failed to parse XML Completed in 0.0133704 seconds root element is not <SASroot> with valid canSAS namespace Completed in 0.0134224 seconds bimodal-test1.xml identified as: cansas1d/1.0 XML file Title: SAS bimodal test1 Completed in 0.068654 seconds root element is not <SASroot> with valid canSAS namespace Completed in 0.0172572 seconds root element is not <SASroot> with valid canSAS namespace Completed in 0.0123102 seconds root element is not <SASroot> with valid canSAS namespace Completed in 0.00930118 seconds ISIS_SANS_Example.xml identified as: cansas1d/1.0 XML file Title: standard can 12mm SANS Completed in 0.0410387 seconds W1W2.xml identified as: cansas1d/1.0 XML file Title: standard can 12mm SANS Title: TK49 standard 12mm SANS Completed in 0.0669074 seconds ill_sasxml_example.xml identified as: cansas1d/1.0 XML file Title: ILL-D22 example: 7D1 2mm Completed in 0.0332752 seconds isis_sasxml_example.xml identified as: cansas1d/1.0 XML file Title: LOQ TK49 Standard 12mm C9 Completed in 0.0388868 seconds r586.xml identified as: cansas1d/1.0 XML file Title: ILL-D11 example1: 2A 5mM 0%D2O Completed in 0.0213737 seconds r597.xml identified as: cansas1d/1.0 XML file Title: ILL-D11 example2: 2A 5mM 0%D2O Completed in 0.0221894 seconds xg009036_001.xml identified as: cansas1d/1.0 XML file Title: det corrn 5m Completed in 0.0286721 seconds cs_collagen.xml identified as: cansas1d/1.0 XML file Title: dry chick collagen, d = 673 A, 6531 eV, X6B Completed in 0.0296247 seconds cs_collagen_full.xml identified as: cansas1d/1.0 XML file Title: dry chick collagen, d = 673 A, 6531 eV, X6B Completed in 0.0751836 seconds cs_af1410.xml identified as: cansas1d/1.0 XML file Title: AF1410-10 (AF1410 steel aged 10 h) Title: AF1410-8h (AF1410 steel aged 8 h) Title: AF1410-qu (AF1410 steel aged 0.25 h) Title: AF1410-cc (AF1410 steel aged 100 h) Title: AF1410-2h (AF1410 steel aged 2 h) Title: AF1410-50 (AF1410 steel aged 50 h) Title: AF1410-20 (AF1410 steel aged 20 h) Title: AF1410-5h (AF1410 steel aged 5 h) Title: AF1410-1h (AF1410 steel aged 1 h) Title: AF1410-hf (AF1410 steel aged 0.5 h) Completed in 0.338425 seconds XMLopenfile: File(path) to open doesn't exist, or file can't be opened cansas1d-template.xml either not found or cannot be opened for reading Completed in 0.00892823 seconds 1998spheres.xml identified as: cansas1d/1.0 XML file Title: 255 nm PS spheres Title: 460 nm PS spheres Completed in 2.87649 seconds XMLopenfile: File(path) to open doesn't exist, or file can't be opened does-not-exist-file.xml either not found or cannot be opened for reading Completed in 0.00404549 seconds cs_rr_polymers.xml identified as: cansas1d/1.0 XML file Title: Round Robin Polymer A Title: Round Robin Polymer B Title: Round Robin Polymer C Title: Round Robin Polymer D Completed in 0.0943477 seconds s81-polyurea.xml identified as: cansas1d/1.0 XML file Title: S7 Neat Polyurea Completed in 0.0361616 seconds
Graphical User Interface
At least two groups are working on graphical user interfaces that use the canSAS 1-D SAS XML format binding to IgorPro. The GUIs are intended to be used with their suites of SAS analysis tools (and hide the details of using this support code from the user).
NOTE: There is no support yet for writing the data back into the canSAS format. Several details need to be described, and these are being collected on the discussion page for the XML format
Irena tool suite
Jan Ilavsky's Irena tool suite (http://usaxs.xor.aps.anl.gov/staff/ilavsky/irena.html) for IgorPro has a GUI to load the data found in the XML file. Refer to the WWW site for more details.