Irena 2 package of SAS data evaluation and modeling macros for Igor Pro

  This package contains macros for evaluation of small-angle scattering data. The package allows basic manipulation with data (import, export, modifications, and ploting), selected evaluation methods (mostly for particulate systems) and also includes reflectivity "Parratt's" code for evaluation of X-ray and neutron reflectivity. Same as with the software package for USAXS data analysis Indra 2, this one is also written for Igor Pro, version 6 from Wavemetrics, Inc.

Current version

Latest version is 2.30 for Igor 6.0 (released 9/1/2008) and 2.16 for Igor 5.0 (and 6.0) released on 9/15/2007.

You can download latest (version for only Igor 6.0) here (19Mb - manual is growing!): Irena_v2.30b.zip
Please NOTE, to load XML data files, you need to install one of platform-correct following xop files : PCxop or Macxop. The files in one of these zip files must be linked to (or located in) ".../Igor Pro Folder/Igor Extensions". Please make sure you install the correct version for your platform. You can also download latest versions of this xop from IgorExchange.

Current manual - note: it is included with the distribution zip file - for version 2.30 is here (18Mb): Irena manual.pdf

You can download previous version here (13Mb): Irena_v2.27.zip

Please note, that the version 2.16 is the last release for Igor 5.0. You can download it here: Irena_v2.16.zip

Irena 2.21 and higher can take advantage of two optional XOP files from Andrew Nelson (Abeles.xop and GenCurveFit.xop). These significantly (up to 10x) speed up Genetic optimizatiion and Reflectivity calculations. Latest versions can be downloaded from Andrew Nelsons web pages. I am posting here my current versions for download. Place these files in your ...Igor Pro Folder\Igor Extensions. Here is zip file for PC and here for Mac.

New for this version........:

Help movies. Examples how to use various features in Irena. Requires Quicktime. Check often - will be updated (hopefuly).

Pair distance distribution function! Using Regularization (similar to GNOM) or Indirect inverse Fourier Transformation (Moore, P. B. (1980). "Small-Angle Scattering - Information-Content and Error Analysis." Journal of Applied Crystallography 13(Apr): 168-175.)

Major improvements in Small-angle diffraction tool.

Current version of the package includes following tools:

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.

!!!!!!Please note! If you get error "IN2_GeneralProcedures.ipf is out of date", please dowload latest version here : IN2_GeneralProcedures.zip and replace one you have in ...Wavemetrics\Igor Pro Folder\User Procedures\Indra2 folder. Please make sure you place the file here and remove ALL other occurences of this file anywhere else in User procedures. This is important.

Note, that the command “Load Irena macros” is now located in Macros menu, not in separate SAS menu. SAS menu gets created after loading in the macros.

 Before installation I suggest you first remove (delete) folder “Irena 1” from “Wavemetrics\Igor Pro Folder\User procedures”. This will make sure no obsolete files are left behind.
 
Read modification history here: modification history.txt

New: Document with the description of form factors & structure factors included in the Irena package is available withing Igor (in the SAS menu) or here as pdf for download: FormFactorsList.pdf Included are also plots for each form factor and documentagion of the code used.

The last Igor 4 compatible version is release 1.70 from 4/14/2004, which you can download here: Irena1_v170.zip this is zip file with paths which indicate where to install the macros. The files are same for both Windows and Mac. 

 

 Few short comments to these various techniques:

Modeling II. Direct modeling of SAS from up to 6 populations of particles (in dilute limit, with 5 different Structure factors to use if appropriate). Allows up to 10 input data sets. Can be used to analyse multiple data sets collected on same sample with(for example) changing contrast, different q ranges, different instruments, etc... Each population can have (principally) for each input data set different contrast. Very flexible. Allows fitting of form factor & structrure factor parameters (which does not mean the data must support this fittng!!!).

Reflectivity code using Parrat's recursive method for X-ray and neutron reflectivity (many thanks to Andy Nelson, andyfaff@optusnet.com.au for providing the code doing the calculations). Note, Andy has made his more powerful Parrat's implementation for Igor available for free download (from SourceForge: http://motofit.sourceforge.net/) also, if you need more than my relatively simple tool (limited to 8 layers and one data set at a time), use Andy's code. Optionally now the package can (but does not require) use xop for faster calculations of reflectivity, prepared by Andy. You can download it from: http://members.optusnet.com.au/~andyfaff/. Please, use reference listed on his web site if using this code.

Data mining tool. Allows searching for information burried in different folders in variables, strings and wave notes (output to notebook or waves) and for aves themselves (output to notebook and graph). For now works well with Indra wave names and with Irena results. QRS data are more challenging, but I'll try.

Sizes. Significantly reworked. Added new options of creating errors by user. Not toally finished yet and does not really improve the capabilities, but allows users without errors or with clearly bad errors to use the tool more efficiently.

PDDF (also known as p(r)). Using two methods (regularization, used by GNOM, and indirect inverste Fourier transformation, see ref. by Moore in manual) one can produce this "staple" of bio-SAXS now in Irena. Results were checked against GNOM on limited set of test data.

   

Unified model.

For details about Unified model please see Gregg Beaucage web page and posted papers:

http://www.eng.uc.edu/~gbeaucag/

http://www.eng.uc.edu/~gbeaucag/PDFPapers/Beaucage2.pdf

http://www.eng.uc.edu/~gbeaucag/PDFPapers/Beaucage1.pdf

http://www.eng.uc.edu/~gbeaucag/PDFPapers/ma970373t.pdf

Generally, the SAS curve is described here using levels each created from Guinier region with Power law tail. Included are methods to address fractals, correlations between the particles etc. This is generic formula of this theory, which should be useable in most cases. Very flexible method.

 

Size distribution

Included is method for using Maximum entropy (MaxEnt), Regularization and Total-non negative least square method (TNNL) to evaluate size distribution from SAS data using various models (Form factors) of scatterers. The code was modified from MaxEnt C program provided by Pete Jemian with added TNNL method. For more details on the MaxEnt and Regularization methods, please see Pete Jemian web page….

References for MaxEnt method (the implementation used in this code or prior versions):
Potton, J. A., Daniell, G. J., and Rainford, B. D., Particle size distributions from SANS data using the maximum entropy method, J. Appl. Cryst. 21, 663-668 (1988).
P. Jemian, G. Long, F. Lofaj, and S. Wiederhorn, Anomalous ultra-small-angle x-ray scattering from evolving microstructures during tensile creep, Meeting of the Materials Research Society, Vol. 590, edited by S. Mini, D. Perry, and S. Stock, Boston, Massachusetts, 1999 (Materials Research Society), p. 131-136.

Reference for TNNLS method:
Michael Merrit and Yin Zhang, Technical report TR04-08, Department of Computational and Applied Mathematics Rice University, Houston, Texas, 77005, USA, (May 2004), http://www.caam.rice.edu/caam/trs/2004/TR04-08.pdf

Fractal model

This fractal model is by Andrew J. Allen from NIST. For details see included description.

 

Reflectivity model (aka "Parratt's recursive code")

This is relatively simple tool to model and fit X-ray and neutron reflectivity for up to 8 layers using recursive Parratt’s code (L. G. Parratt, Phys Rev, 95(2), 359-369, 1954), as implemented for example in older code called “Parratt”. The code itself was provided by Andrew Nelson (Andrew_Nelson@users.sourceforge.net ). I have implemented only the GUI in manner similar to the rest of the Irena code. I will provide basic support for this package. Please note, that Andy has made more complex and capable version of his package “Mottofit” available for free download to other Igor users through http://motofit.sourceforge.net/ under GNU license. If you need more complex fitting, than my code allows, please use Andy’s powerful code. You may, however, have to learn little bit more of Igor.