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 section below.
Note
Note that this tool is not a true binding [1] in that the structure of the XML file is not replicated in IgorPro data structures. This tool reads the vectors of 1-D SAS data (Q, I, ...) into IgorPro waves (Qsas, Isas, ...). The tool also reads most of the metadata into an IgorPro textWave for use by other support in IgorPro.
| [1] | For example, see data binding from http://en.wikipedia.org/wiki/Binding_%28computer_science%29 |
Note
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).
| file: | http://www.cansas.org/trac/browser/1dwg/trunk/IgorPro/cansasXML.ipf |
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| author: | Pete R. Jemian <jemian@anl.gov> |
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| date: | 2013-03-29 |
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| version: | 1.12 (requires latest XMLutils XOP – see below) |
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| purpose: | Implement an IgorPro file reader to read the canSAS 1-D reduced SAS data in XML files that adhere to the cansas1d:1.1 standard. |
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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.
Here is the subversion checkout command:
svn co svn://svn.igorexchange.com/packages/XMLutils/ XMLutils
To retrieve an updated version of this support in the future, go into the XMLutils directory (created above) and type either of these commands:
svn update svn up
This will check the repository and update local 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://www.cansas.org/svn/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
To retrieve an updated version of this support in the future, go into the cansas-1dwg directory (created above) and type the command:
svn update
This will check the repository and update files as needed.
(should have already done this step by now)
Quit IgorPro if it is running
web browser, visit http://svn.igorexchange.com/viewvc/packages/XMLutils/trunk/
Install XMLutils XOP by double-clicking the installer for your operating system.
a web browser, copy cansasXML.ipf from the on-line subversion repository. (http://www.cansas.org/svn/1dwg/trunk/IgorPro/cansasXML.ipf)
(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 IgorPro 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.
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:1.1, 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, indicating 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. 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.
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 Case Study: Dry Chick Collagen.
metadata for the cs_collagen_full.xml case study
| row i | key: metadata[i][0] | value: metadata[i][1] |
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| 0 | xmlFile | cs_collagen_full.xml |
| 1 | namespace | cansas1d:1.1 |
| 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 |
| 6 | SASinstrument/SASsource/radiation | X-ray synchrotron |
| 7 | SASinstrument/SASsource/wavelength | 1.898 |
| 8 | SASinstrument/SASsource/wavelength/@unit | A |
| 9 | SASinstrument/SASdetector/@name | X6B PSD |
| 10 | SASnote | 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
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The XMLutils XOP package does not provide a method to insert the prescribed XML stylesheet processing-instruction into the XML data file.
<?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.
These are the important FUNCTIONS in the cansasXML.ipf code.
- CS_XmlReader(fileName)
- reads the named XML file and and loads SAS data
- prj_grabMyXmlData()
- demonstration function to show a usage example
- prjTest_cansas1d()
- demonstration function to show a usage example
Here is an example running the test routine prjTest_cansas1d().
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | *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:1.1 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:1.1 XML file
Title: standard can 12mm SANS
Completed in 0.0410387 seconds
W1W2.xml identified as: cansas1d:1.1 XML file
Title: standard can 12mm SANS
Title: TK49 standard 12mm SANS
Completed in 0.0669074 seconds
ill_sasxml_example.xml identified as: cansas1d:1.1 XML file
Title: ILL-D22 example: 7D1 2mm
Completed in 0.0332752 seconds
isis_sasxml_example.xml identified as: cansas1d:1.1 XML file
Title: LOQ TK49 Standard 12mm C9
Completed in 0.0388868 seconds
r586.xml identified as: cansas1d:1.1 XML file
Title: ILL-D11 example1: 2A 5mM 0%D2O
Completed in 0.0213737 seconds
r597.xml identified as: cansas1d:1.1 XML file
Title: ILL-D11 example2: 2A 5mM 0%D2O
Completed in 0.0221894 seconds
xg009036_001.xml identified as: cansas1d:1.1 XML file
Title: det corrn 5m
Completed in 0.0286721 seconds
cs_collagen.xml identified as: cansas1d:1.1 XML file
Title: dry chick collagen, d = 673 A, 6531 eV, X6B
Completed in 0.0296247 seconds
cs_collagen_full.xml identified as: cansas1d:1.1 XML file
Title: dry chick collagen, d = 673 A, 6531 eV, X6B
Completed in 0.0751836 seconds
cs_af1410.xml identified as: cansas1d:1.1 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:1.1 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:1.1 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:1.1 XML file
Title: S7 Neat Polyurea
Completed in 0.0361616 seconds
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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
Jan Ilavsky’s Irena tool suite for IgorPro has a GUI to load the data found in the XML file. Refer to http://usaxs.xor.aps.anl.gov/staff/ilavsky/irena.htm for more details.