"Nika" package of 2D -> 1D SAS data reduction macros for Igor Pro

 

Please use following citiation when using Nika package:

Jan Ilavsky, "Nika - software for 2D data reduction", J. Appl. Cryst. (2012), vol. 45, pp. 324-328. DOI:10.1107/S0021889812004037 .

Workshops on using Irena & Nika packages... at APS we organized four workshops in 2012 and one in January 2013. In November 2012 was course at Australian Lightsource and one is scheduled at Brazilian lightsource in end of February 2013. Next workshop at APS is scheduled for May 9 - 10, 2013. To register please go to: http://www.regonline.com/saxssoftware_irenaandnika_spring

This package is one of my current projects, in which I am preparing package of macros for reduction of area detector (e.g., CCD) data into 1D "lineouts". Similarly to Irena package for 1D SAS data analysis and  USAXS data analysis Indra 2, this one is written for Igor Pro, version 6 from Wavemetrics, Inc. Version 1.31 is no more compatible with version 5 of Igor Pro.

Current version : 1.60 (6.22 and higher) released 1/3/2013.

Distribution:

Current version	1.61	released 4/8/2013
Installation method	Link for download	Use only one of these methods
java - http	Java installer	For default installation of Igor Pro 6.2x with standard locations of Igor folders (Mac or Windows). Seem to fail on non-English versions of Windows! Uses http and can check available/installed versions, uninstall the packages, and install/update to the latest versions. Report any problems.
Igor - http/ftp	Universal Installer 1.20.pxp Prior version (1.19) Prior version for Igor 6.20: Universal Installer 1.14.pxp	For Igor version 6.20 and higher. Can uninstall, install, or update to latest relased version of Irena using Igor. Uses http, ftp, or local copy; prior versions use only ftp or local copy.
Igor - local copy	Universal Installer 1.20.pxp and IgorCode.zip (~60Mb)	Use Igor installer and select use "Local copy". Unzip the IgorCode.zip to the same folder as is "Universal installer 1.18.pxp".
zip files	Nika_v1.61.zip	Download, unzip and install manually to proper places as indicated by folders in the zip file. Iinstall xop support manually (see below), including installing HDF5 support (provided by Wavemetrics, but not installed by default).
XOP zip files	WindowsXOPs, MacXOPs.	Install when using zip file installlation. Please make sure you install the correct version for your platform. You can also download latest versions of these xops from IgorExchange.
Manual		Is included in the zip file.
Prior versions	Nika v 1.31, Nika_v1.60	1.18 is the last release for Igor 5.0: Nika_v_1.18

Workshops on using Irena & Nika packages... first four workshops were May and September/August, 2012 at APS. In NOvember 2012 is one at Australian Lightsource and one is scheudled at Brazilian lightsourc ein end of February 2013. Next workshop at APS is scheduled for January 31 - February 1, 2013. To register please go to: http://www.regonline.com/saxssoftwarepackagesirenaandnika_winter

To request to be put on waiting list for later workshops (after January 2013) send e-mail to Connie.

New... Mailing group for Nika users: If you want to be informed about Nika updates and possibly have place to inquire about data reduction problems, visit the page: http://www.aps.anl.gov/mailman/listinfo/nika_users where you can join this group.

 

BUGs can be expected, please, let me know if something is not right!

Extending the code capabilities beyond design.

 

Modification history:

1.61 4/8/2013
Added monthly check for updates and reminder of references for publications.
Modified to compile on computers even without xop and abort & produce message when xop is called with instructions.
Fixed Pilatus ESRF edf file format. Header was set to 1024 bytes, which is incorrect, it is n*512Bytes. Changed to look for separator and cleaned up the header to match Nika/Irena wave note styles(removed unneeded spaces).
Modified 15IDD pinSAXS, WAXS support to use new Nexus data, fixed few bugs in calculations.
Added scroll buttons to enable scrolling of the main panel content for smaller displays.

1.60 1/4/2013
Added ability to trim name of data in end (default, same as before), in front (new) AND remove from the name string. Needed for some users who cannot be thought that name needs to be at most 20 characters long.
Fixed error message when processing 15idd pinSAXS data about empty name not matching USAXS empty. Introduced in last update to pinSAXS data processing.
Fixed bug which caused issues when exporting ASCII from lineprofile. Introduced during converting the export to use free waves.
Fixed problem when if beam center was way too far from detector the beam center alignment stopped working for higher order lines.

1.59 11/5/2012
Fixed Pilatus 300k import problem
Fixed Masking on Preview graph. Software bug introduced few updates ago.
Fixed minor bug in restore saved settings which caused problem to Image type popup.
Added three new NIST standards to Beam center & calibration tables

1.58 8/13/2012
Updated manual.
Added ability to "watch" folder with data and automatically display or process latest data set.
Added SSRL Material Science SAXS support. Tiff file with associated text file of the same name.
Added double click reaction to the 2D data (samples only).
GUI fonts control - fixed bug in Windows 7 which caused that fonts were not changed.
XMLutils xop updated to fix speed in loading xml data files
Fixed bug in Data selection "cleaning" which removed any file which had as second character "_".

1.57 5/30/2012
Added support for SSRLMatSAXS instrument. Lookup functions and ability to read their txt file containing records.
New nika_users mailing list. See: http://www.aps.anl.gov/mailman/listinfo/nika_users for details.
Fix BSL file - wrongly read detector size in pixels for non-square detectors (Pilatus).
Added small fix to catch debugger in case user creates movie, adds no frames and closes it.

1.56 4/30/2012
15ID pinSAXS support, fixed the slit length used to create _usx data for merging of 15ID USAXS data with pinSAXS data.
15ID SAXS support, added various functions to support our large SAXS camera.
Added option to add colorscale to the main image and to fix range of displayed intensities for the images. Requested features. Seems useful and fun.
Added more ColorTables as well as option to reverse them. Fit2D is closest to Geo32_R if anyone wants to get close to Fit2D.
Changed Match search to use GrepList - that means it uses now RegEx (regular expressions). Note: ^XYZ means start with XYZ, XYZ matches XYZ anywhere, etc.

Note:

These macros MAY produce Huge files. In my testing I have seen files well beyond 1 Gb. Conversion of CCD images at 3.5k x 3.5k level (Mar Image plate) and beyond takes some time and requires major CPU power. Make sure your hardware is up to the challenge. Note, I do not yet include any pixle splitting and do not provide any "bin width" data for q space smearing...

Testing:

I have been testing this package against Fit2D package. In my test cases I have been able to reproduce same Intensity vs q dependence. Nika provides statistical errors calculated simply from statistics of pixles included in any given q bin...
 If you believe, the results are incorrect, let me know ASAP.

Registration/e-mail list:

Please, if you are using these macros let me know via e-mail. This will allow me to have some idea who is interested in these macros and how much of my time is worth to invest in further development. Also, please, indicate if you would like to be included on e-mail list I would like to maintain – I can then sent e-mail announcements when a new version is available. I will not misuse the e-mail list in any way…

 Quick disclaimer:

This set of macros is currently being developed for use on any SAS data. Their use by anyone for open science is free of charge. If you want to use them for proprietary work, please contact me, the author, Jan Ilavsky, for permission. There are no warrantees with respect to functionality of these macros, please, verify all results by independent methods.