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

 

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 also written for Igor Pro, version 5 from Wavemetrics, Inc. It should be now compatible with Igor Pro version 6 also.

  

Current version

Nika version 1.18 is available here - Nika v 1.18

This version is adds support of more image types - thanks to Jonathan Tishler and his code we add support for Princeton (*.spe, aka WinView) file format. This is _very_ flexible file format and quite complicated, so this is very good news. Further, this version adds on Mac OSX platform ability to use FIt2D (which has OSX/X11 version) as file convertor. To my surprise it works _very_ well...

This version has been modified to store temp data to system temp directory, so the user can run even when he/she is measly no-permission user, who cannot write in Igor folder.

Manual is still stale, sorry.

Note, that the command “Load Nika macros” is located in Macros menu.

Install files from the zip file according to the included folder structure - one single file goes into "Igor Procedures", rest of the files go in the "User procedures" in the included subfolders.

New/Fixed stuff:

1.18 9/15/2007
Changed Rigaku loader format - yet another size of images found with different offset. Now I search for the first non-zero byte after the header to find the right offset. Hopefully this will work. I now have Rigaku latest C code and will look into this again soon...
ADSC loader - added wavelength and energy to be loaded from the header.
Added loader for WinView (Princeton CCD) .spe file format (using code by Jon Tischler).
Added ability to use Fit2d on Mac as file loader. Download Mac version of Fit2d, install (chmod +x it so it can be run). Due to limitations the temp tiff file will be created in data file area.

1.17 7/15/2007
Fix to problem with "Geometry corrections" which failed. Added one file loader.

1.16 4/11/2007 Fix to make also back compatible with Igor 5.05A

1.15 3/29/2007 Fix to make compatible with Igor 6.0
Fixed code for many popup controls, as it was still failing in Igor 6. Should be fixed now. Tested briefly controls and functionality in Igor 6.01beta11.
Fixed one bug in Make mask, where the slider ranges were not set correctly on load of new file
Fixed Bug when wrong extension for flood image was called. The file is always tiff (created by Nika package) but was called with extension of user data.

ver 1.14, 2/28/2007
Igor 6 compatible - had to fix few lines of code. <--- 3/29/07 ... Did nto fix all bug, use version 1.15 on Igor 6, please...
Added option to modify imported image by user defined hook function... If this function does not exist, it is not run and all behaves as previously... User can create function which has one parameter (wave) and modifies the same wave. The name has to be as exactly : ModifyImportedImageHook. Example is in the "Modification history.txt". This function is run for all imports, except for mask, as that is special created wave. All others will be passed through this function - that includes data import, import of dark and empty and of waves for beam center and mask creation. User needs to make this function inaccessible (rename it), if it should not be run...

ver 1.13 (7/1/2006 - well, it was probably never really posted for general download)...
Added separate checkbox for solid angle correction AND polarization correction. Fixed Solid angle correction (it should be 1/cos(angle)^3, matches NIST routines and Fit2D). Placed in routines to be done with 2D data (just after all calibration steps)... Fixed routine NI1A_SolidangleCorrection and added new routine NI1A_GenerateGeometryCorr2DWave. Fixed loader for Rigaku, so it should work on both Max and PCs... Weird, the binary file has Mac-like bit order...

ver 1.12, 4/23/2006
Requested feature: Add into the "Make mask" tool capability to automatically mask off points with really low intensity. Useful for detectors which have circular active area, so points in corners are set to 0 intensity.
Added built in loader for Rigaku R-axis data format. The format header contains a lot of principally useful info. Some of it is parsed to the rest of the code (number of points, wavelength, pizel size in mm). All of it is saved in the wave note of the image. Note: Beam center and detector distance are not parsed, as I am worried that it would overwrite any optimized values user may have.

ver 1.11, 1/18/2006
Bug fix: fixed safe configuration routines (bug introduced in previous versions). Now the popumenus should be synced also and all pramaters for main tool and beam center utility should be included.
Added Ag behenate secodn line in calibrants.

ver 1.10 beta
Tilts reworked and should work now... It is very difficult to verify the proper functionality. Need some real test case with known tilts (and significant)...
Added fix to fileLoaders to load standard tiff files, which load as 3 layer files (24 bit tiff). Still for B/W images ONLY, dumps the other dimensions...

ver 1.09, 3/29/2004:
Added option to save image within Igor experiment - can create VERY large files (some images may be 40 Mb large or even more in double precision...)
Added some support (create image, delete saved images, changing the color table and range) for saved images.
Fixed bug which tripped debugger when nofile existed in selected external image data folder
Added option to skip files witgh low intensity in them. Will be developing further, so this tool will change!
Added mpa/asc ascii type of data for Molecular Metrology SAXS system at the University of Tennessee-Knoxville data type. ASCII header, two lineout blocks and the ASCII 2d data. Takes forever to load... Binary data are better choise. You were warned...
Start workign on detector tilts, but these are at this time removed from GUIs

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.