Advanced Photon Source at Argonne National Laboratory   APS USAXS instrument
USAXS instrument at the Advanced Photon Source,
X-ray science division, beamline 15ID (ChemMatCARS)

Advanced Photon Source

A U.S. Department of Energy, Office of Science,
Office of Basic Energy Sciences national synchrotron x-ray research facility

 
 
Argonne Home > Advanced Photon Source > USAXS >

Important links:

USAXS web page

Irena 2 (software for SAS modeling)

Nika 1 (software for SAS area detector  data reduction )

Irena 2 movies & Handouts

Nika movies & Handouts

Indra 2 (software for USAXS data reduction)

Some other useful code for Igor Pro I wrote:


Cromer-Lieberman code for IgorPro (ver. 4.0): AtomicFormFactors

Clementine, package for modeling decay kinetics

Other useful links…

Home page of Pete Jemian (more SAS)

APS SAS web page

"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, two in 2013 and two in 2014. 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 September 18-19, 2014, here is registration page. To request to be put on waiting list for next workshops send e-mail to Connie.

Nika is one of my projects, which can reduce area detector (e.g., CCD) data into 1D "lineouts" for SAXS ortt WAXS. 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.

Current version : 1.66 (6.3x and higher) released 8/20/2014.

Distribution:

Current version
1.66
released 8/20/2014
     
Installation method
Link for download
Use only one of these methods
Igor - local copy

Universal Installer 1.24.pxp,
IgorCode.zip (~78Mb)

For Igor 6.3x and higher. Unzip the IgorCode.zip that to the same folder as "Universal installer 1.24.pxp". Open "Universal installer 1.24.pxp" installer in Igor Pro and select use "Local copy".
java - http

For default installation of Igor Pro 6.3x 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 1.24.pxp

Prior version (1.19)

Prior version for Igor 6.20: Universal Installer 1.14.pxp

For Igor version 6.3x 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.
Manual methods (not recommended, unless above methods fail)
zip files
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

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:

1.66 8/20/2014
Main panel - moved dezinering controls from tab4 to tab2, some users thought that dezinering was available only for Empty/dark and not for sample images…
Hook functions - added new: ImportedImageHookFunction which can be used to modify any image after load, AfterDisplayImageHook, which modifies detector images displayed by Nika. Fixed PilatusHookFunction.
Removed some print statements to reduce amount of information in history area.
Added Cbf file format importer (it has compression, so it was bit more work).
Added right click menus to most Listboxes,users can now refresh the content and there is also some more functionality where appropriate
Added Pilatus 3, 200k.
Added ability to import 2D calibrated data, for now ASCII (qx qy I dI) from EQSANS and NIST (DAT).
Added flexible support for CanSAS/Nexus (hdf5 file format). Can export to new or append to existing CanSAS/Nexus file - for now 2D calibrated data. Working on appending 1D data. Can also import a calibrated 2D data set from CanSAS/Nexus file.
Major new feature - export 2D calibrated data. Either full resolution or pseudo log-q rebinned data. Usable for 2D fitting programs.
15id support - change sector for pinSAXS & WAXS analysis from 10 to 30 degrees halfwidth.

1.65 2/20/2014
Fixed minor bug in LP profiles note handling. Matching release for Indra package.

1.64 1/5/2014
All files - extended copyright to 2005 - 2014
Installer - version 1.23 will handle stale links to hdf5 xops.
Beam center utils - added many more lines for Lab6, Si, and Ce standards. Modified to disable fitting both SDD and Wavelength, very unlikely this would be possible with most data

1.63 11/23/2013
Added calibration of Intensity popup and "Units=Arbitrary" or "cm2/cm3" or "cm2/g" for Intensity to help Irena to handle calibration of data.
Attempted to add cbf Pilatus file format, but example data provided by user were incorrect, so code has been disabled again.

1.62 7/23/2013
Added double click action to other list boxes in Main panel and in Beam center tool
Added *.mccd file format (tif, actually) and combined mpa file formats into the same loader. I am missing "csv" working example so that is not working, but asc, dat, and spe (internal names) are working now.
Mask tool - Added double click function and offset when Start mask draw is selected to accommodate tools.

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.


        

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This page last modified: 2014-08-20 10:57 AM