Difference between revisions of "Software"
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===Geared towards 2D data=== | ===Geared towards 2D data=== | ||
* '''Fit2D''': A well-known package for treatment and conversion 2D scattering images. | * '''Fit2D''': A well-known package for treatment and conversion 2D scattering images. | ||
| − | ** [http://www.esrf.eu/computing/scientific/FIT2D/ Official | + | ** [http://www.esrf.eu/computing/scientific/FIT2D/ Official site.] |
** [http://staff.chess.cornell.edu/~smilgies/D-lineNotes/GISAXS-at-D-line/fit2d-GIXS-primer.html Fit2D primer.] | ** [http://staff.chess.cornell.edu/~smilgies/D-lineNotes/GISAXS-at-D-line/fit2d-GIXS-primer.html Fit2D primer.] | ||
** [http://g-line.chess.cornell.edu/G-lineStatus/G-lineManuals/CheatSheets/FIT2D_MAIN.html Fit2D hints page.] | ** [http://g-line.chess.cornell.edu/G-lineStatus/G-lineManuals/CheatSheets/FIT2D_MAIN.html Fit2D hints page.] | ||
* '''ImageJ''': A generic tool for image treatment and analysis. Can be used to open and process x-ray detector images. | * '''ImageJ''': A generic tool for image treatment and analysis. Can be used to open and process x-ray detector images. | ||
| − | ** [http://rsb.info.nih.gov/ij/ Official | + | ** [http://rsb.info.nih.gov/ij/ Official site.] |
* '''[[view.gtk]]''': A simple interface for viewing 2D data, calibrating your data into ''q''-space, and extracting linecuts. Written by [[Lin Yang]] for the [[X9]] beamline at [[NSLS]]. | * '''[[view.gtk]]''': A simple interface for viewing 2D data, calibrating your data into ''q''-space, and extracting linecuts. Written by [[Lin Yang]] for the [[X9]] beamline at [[NSLS]]. | ||
** [Download here.] Installation requires GTK libraries. | ** [Download here.] Installation requires GTK libraries. | ||
* '''[[GIXSGUI]]''': Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang. | * '''[[GIXSGUI]]''': Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang. | ||
| − | ** [http://www.aps.anl.gov/Sectors/Sector8/Operations/GIXSGUI.html Official | + | ** [http://www.aps.anl.gov/Sectors/Sector8/Operations/GIXSGUI.html Official site.] |
===Geared towards 1D data=== | ===Geared towards 1D data=== | ||
* '''NCNR SANS/USANS Package''': Set of tools for reducing SANS and USANS data. Requires the commercial IgorPro software. | * '''NCNR SANS/USANS Package''': Set of tools for reducing SANS and USANS data. Requires the commercial IgorPro software. | ||
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** Citation: S.R. Kline "[http://www.ncnr.nist.gov/programs/sans/pdf/publications/0569.pdf Reduction and Analysis of SANS and USANS Data using Igor Pro]", ''J. Appl. Cryst.'' 2006, 39, 6, 895. [http://dx.doi.org/10.1107/S0021889806035059 doi:10.1107/S0021889806035059] | ** Citation: S.R. Kline "[http://www.ncnr.nist.gov/programs/sans/pdf/publications/0569.pdf Reduction and Analysis of SANS and USANS Data using Igor Pro]", ''J. Appl. Cryst.'' 2006, 39, 6, 895. [http://dx.doi.org/10.1107/S0021889806035059 doi:10.1107/S0021889806035059] | ||
* '''Irena''': Multiple tools for analyzing [[SAXS]], [[SANS]], [[USAXS]], and [[USANS]] data. Allows modeling of [[diffuse scattering]], form factors, reflctivity, etc. Requires the commerical IgorPro software. | * '''Irena''': Multiple tools for analyzing [[SAXS]], [[SANS]], [[USAXS]], and [[USANS]] data. Allows modeling of [[diffuse scattering]], form factors, reflctivity, etc. Requires the commerical IgorPro software. | ||
| − | ** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/irena.html Official | + | ** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/irena.html Official site.] |
* '''Scatter''': Targetted towards analysis of transmission-mode [[SAXS]] and [[SANS]]. Allows modeling of nano- and meso-structrue materials (surfactants, lipids, micelles, vesicles, block-copolymers, etc.). | * '''Scatter''': Targetted towards analysis of transmission-mode [[SAXS]] and [[SANS]]. Allows modeling of nano- and meso-structrue materials (surfactants, lipids, micelles, vesicles, block-copolymers, etc.). | ||
| − | ** [http://www.pci.uni-bayreuth.de/rg_foerster/en/Software/index.html Official | + | ** [http://www.pci.uni-bayreuth.de/rg_foerster/en/Software/index.html Official site.] |
===GISAXS=== | ===GISAXS=== | ||
* '''IsGISAXS''': GISAXS analysis and simulation software. Enables prediction of 2D scattering patterns, including the effects of [[DWBA]] and its variants. Written by Rémi Lazzari. | * '''IsGISAXS''': GISAXS analysis and simulation software. Enables prediction of 2D scattering patterns, including the effects of [[DWBA]] and its variants. Written by Rémi Lazzari. | ||
** Citation: R. Lazzari "[http://scripts.iucr.org/cgi-bin/paper?S0021889802006088 IsGISAXS: a program for grazing-incidence small-angle X-ray scattering analysis from supported islands]", ''J. Appl. Cryst.'' 2002, 35, 406-421. [http://dx.doi.org/10.1107/S0021889802006088 doi: 10.1107/S0021889802006088] | ** Citation: R. Lazzari "[http://scripts.iucr.org/cgi-bin/paper?S0021889802006088 IsGISAXS: a program for grazing-incidence small-angle X-ray scattering analysis from supported islands]", ''J. Appl. Cryst.'' 2002, 35, 406-421. [http://dx.doi.org/10.1107/S0021889802006088 doi: 10.1107/S0021889802006088] | ||
| − | ** [http://ln-www.insp.upmc.fr/axe4/Oxydes/IsGISAXS/isgisaxs.htm Official | + | ** [http://ln-www.insp.upmc.fr/axe4/Oxydes/IsGISAXS/isgisaxs.htm Official site.] |
* '''BornAgain''': Python implementation of DWBA modeling (similar to IsGISAXS, but more modern). Allows for [[GISANS]] and GISAXS simulation and fitting. Available on Linux and MacOS. Written by the [http://apps.jcns.fz-juelich.de/doku/sc/start Scientific Computing Group] at [http://www.mlz-garching.de/ MLZ Garching]. | * '''BornAgain''': Python implementation of DWBA modeling (similar to IsGISAXS, but more modern). Allows for [[GISANS]] and GISAXS simulation and fitting. Available on Linux and MacOS. Written by the [http://apps.jcns.fz-juelich.de/doku/sc/start Scientific Computing Group] at [http://www.mlz-garching.de/ MLZ Garching]. | ||
| − | ** [http://apps.jcns.fz-juelich.de/doku/sc/bornagain:start Official | + | ** [http://apps.jcns.fz-juelich.de/doku/sc/bornagain:start Official site.] |
* '''[[HipGISAXS]]''': A high-performance (GPU and massively parallel) C++ software for simulating GISAXS data. | * '''[[HipGISAXS]]''': A high-performance (GPU and massively parallel) C++ software for simulating GISAXS data. | ||
** Citation: S. Chourou, A. Sarje, X.S. Li, E. Chan, A. Hexemer, "[http://scripts.iucr.org/cgi-bin/paper?nb5076 HipGISAXS: A High Performance Computing Code for Simulating Grazing Incidence X-Ray Scattering Data]" ''Journal of Applied Crystallography'' 2013, 46, 6, 1781-1795. [http://dx.doi.org/10.1107/S0021889813025843 doi: 10.1107/S0021889813025843] | ** Citation: S. Chourou, A. Sarje, X.S. Li, E. Chan, A. Hexemer, "[http://scripts.iucr.org/cgi-bin/paper?nb5076 HipGISAXS: A High Performance Computing Code for Simulating Grazing Incidence X-Ray Scattering Data]" ''Journal of Applied Crystallography'' 2013, 46, 6, 1781-1795. [http://dx.doi.org/10.1107/S0021889813025843 doi: 10.1107/S0021889813025843] | ||
** Citation: A. Sarje, X.S. Li, S. Chourou, E. Chan, A. Hexemer, "Massively Parallel X-ray Scattering Simulations," in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (Supercomputing, SC'12), no. 46, pp. 46:1-46:11, November 2012. | ** Citation: A. Sarje, X.S. Li, S. Chourou, E. Chan, A. Hexemer, "Massively Parallel X-ray Scattering Simulations," in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (Supercomputing, SC'12), no. 46, pp. 46:1-46:11, November 2012. | ||
| − | ** [http://portal.nersc.gov/project/als/hipgisaxs/ Official | + | ** [http://portal.nersc.gov/project/als/hipgisaxs/ Official site.] |
===Reflectivity=== | ===Reflectivity=== | ||
* '''Reflfit''': NIST software for fitting neutron (or x-ray) reflectivity curves. | * '''Reflfit''': NIST software for fitting neutron (or x-ray) reflectivity curves. | ||
| − | ** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/ Official | + | ** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/ Official site.] |
* '''Motofit''': Co-refinement of multiple contrast reflectometry data (x-ray or neutron). Written by Andrew Nelson, ANSTO, Australia. | * '''Motofit''': Co-refinement of multiple contrast reflectometry data (x-ray or neutron). Written by Andrew Nelson, ANSTO, Australia. | ||
** Citation: Nelson, A. [http://www.iucr.org/cgi-bin/paper?ce5001 "Co-refinement of multiple contrast neutron / X-ray reflectivity data using MOTOFIT."] ''Journal of Applied Crystallography'' 2006, 39, 273-276. [http://dx.doi.org/10.1107/S0021889806005073 doi: 10.1107/S0021889806005073] | ** Citation: Nelson, A. [http://www.iucr.org/cgi-bin/paper?ce5001 "Co-refinement of multiple contrast neutron / X-ray reflectivity data using MOTOFIT."] ''Journal of Applied Crystallography'' 2006, 39, 273-276. [http://dx.doi.org/10.1107/S0021889806005073 doi: 10.1107/S0021889806005073] | ||
| − | ** '''[http://motofit.sourceforge.net/ Official | + | ** '''[http://motofit.sourceforge.net/ Official site.]''' |
* '''Yanera''': "Yet Another NEutron Reflectivity Analyzer", provides an open-source C++ implementation of the [[Parratt formalism]]. Written by Thad Harroun (Brock University), with contributions from [[Kevin Yager]]. | * '''Yanera''': "Yet Another NEutron Reflectivity Analyzer", provides an open-source C++ implementation of the [[Parratt formalism]]. Written by Thad Harroun (Brock University), with contributions from [[Kevin Yager]]. | ||
| − | ** [http://www.physics.brocku.ca/~tharroun/yanera/index.html Official | + | ** [http://www.physics.brocku.ca/~tharroun/yanera/index.html Official site.] |
* '''GA refl''': Simultaneous fitting of x-ray and neutron polarized reflectometry data. | * '''GA refl''': Simultaneous fitting of x-ray and neutron polarized reflectometry data. | ||
| − | ** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/garefl.html Official | + | ** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/garefl.html Official site.] |
* '''Simulreflec''': Calculate reflectivity of magnetic multiplayer systems. | * '''Simulreflec''': Calculate reflectivity of magnetic multiplayer systems. | ||
| − | ** [http://www-llb.cea.fr/prism/programs/simulreflec/simulreflec.html Official | + | ** [http://www-llb.cea.fr/prism/programs/simulreflec/simulreflec.html Official site.] |
* '''AFIT''': Fitting of reflectometry data. ([http://physchem.ox.ac.uk/%7erkt/AFit.zip download]) | * '''AFIT''': Fitting of reflectometry data. ([http://physchem.ox.ac.uk/%7erkt/AFit.zip download]) | ||
* '''Parratt32''': Windows GUI implementing the Parratt formalism. ([http://www.hmi.de/bensc/instrumentation/instrumente/v6/refl/parratt_en.htm link]) | * '''Parratt32''': Windows GUI implementing the Parratt formalism. ([http://www.hmi.de/bensc/instrumentation/instrumente/v6/refl/parratt_en.htm link]) | ||
Revision as of 10:12, 3 June 2014
A common question for new GISAXS users is: "What software can I use to analyze my data?" Unfortunately, there is no single package that will allow you to perform any possible analysis. This is in part due to the diversity of possible kinds of data analysis one might want to do on GISAXS or GIWAXS images. The following lists a variety of packages that are available.
Contents
Data Viewing, Reduction, and Simple Analysis
These packages provide ways to view data, and perform simple operations (linecuts, etc.).
Geared towards 2D data
- Fit2D: A well-known package for treatment and conversion 2D scattering images.
- ImageJ: A generic tool for image treatment and analysis. Can be used to open and process x-ray detector images.
- view.gtk: A simple interface for viewing 2D data, calibrating your data into q-space, and extracting linecuts. Written by Lin Yang for the X9 beamline at NSLS.
- [Download here.] Installation requires GTK libraries.
- GIXSGUI: Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang.
Geared towards 1D data
- NCNR SANS/USANS Package: Set of tools for reducing SANS and USANS data. Requires the commercial IgorPro software.
- Citation: S.R. Kline "Reduction and Analysis of SANS and USANS Data using Igor Pro", J. Appl. Cryst. 2006, 39, 6, 895. doi:10.1107/S0021889806035059
- Nika: Conversion of 2D images into 1D for SAS. Requires commercial IgorPro software.
- Indra 2: Reduction of USAXS data. Requires the commerical IgorPro software. Written for the 15ID instrument at APS.
- DPDAK: Open-source Python tool for analyzing large sets of SAXS data. Works on Linux and Windows.
- ATSAS: A suite of tools for small-angle scattering data of biological macromolecules.
Data Modeling and Fitting
SAXS
- NCNR SANS/USANS Package: Can model form factors for many common object shapes in solution. Requires the commercial IgorPro software.
- Citation: S.R. Kline "Reduction and Analysis of SANS and USANS Data using Igor Pro", J. Appl. Cryst. 2006, 39, 6, 895. doi:10.1107/S0021889806035059
- Irena: Multiple tools for analyzing SAXS, SANS, USAXS, and USANS data. Allows modeling of diffuse scattering, form factors, reflctivity, etc. Requires the commerical IgorPro software.
- Scatter: Targetted towards analysis of transmission-mode SAXS and SANS. Allows modeling of nano- and meso-structrue materials (surfactants, lipids, micelles, vesicles, block-copolymers, etc.).
GISAXS
- IsGISAXS: GISAXS analysis and simulation software. Enables prediction of 2D scattering patterns, including the effects of DWBA and its variants. Written by Rémi Lazzari.
- Citation: R. Lazzari "IsGISAXS: a program for grazing-incidence small-angle X-ray scattering analysis from supported islands", J. Appl. Cryst. 2002, 35, 406-421. doi: 10.1107/S0021889802006088
- Official site.
- BornAgain: Python implementation of DWBA modeling (similar to IsGISAXS, but more modern). Allows for GISANS and GISAXS simulation and fitting. Available on Linux and MacOS. Written by the Scientific Computing Group at MLZ Garching.
- HipGISAXS: A high-performance (GPU and massively parallel) C++ software for simulating GISAXS data.
- Citation: S. Chourou, A. Sarje, X.S. Li, E. Chan, A. Hexemer, "HipGISAXS: A High Performance Computing Code for Simulating Grazing Incidence X-Ray Scattering Data" Journal of Applied Crystallography 2013, 46, 6, 1781-1795. doi: 10.1107/S0021889813025843
- Citation: A. Sarje, X.S. Li, S. Chourou, E. Chan, A. Hexemer, "Massively Parallel X-ray Scattering Simulations," in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (Supercomputing, SC'12), no. 46, pp. 46:1-46:11, November 2012.
- Official site.
Reflectivity
- Reflfit: NIST software for fitting neutron (or x-ray) reflectivity curves.
- Motofit: Co-refinement of multiple contrast reflectometry data (x-ray or neutron). Written by Andrew Nelson, ANSTO, Australia.
- Citation: Nelson, A. "Co-refinement of multiple contrast neutron / X-ray reflectivity data using MOTOFIT." Journal of Applied Crystallography 2006, 39, 273-276. doi: 10.1107/S0021889806005073
- Official site.
- Yanera: "Yet Another NEutron Reflectivity Analyzer", provides an open-source C++ implementation of the Parratt formalism. Written by Thad Harroun (Brock University), with contributions from Kevin Yager.
- GA refl: Simultaneous fitting of x-ray and neutron polarized reflectometry data.
- Simulreflec: Calculate reflectivity of magnetic multiplayer systems.
- AFIT: Fitting of reflectometry data. (download)
- Parratt32: Windows GUI implementing the Parratt formalism. (link)
- Drydoc and Wetdoc: Multiple contrast data fitting. (link)
- Surface: Analysis of specular reflectivity. (link)
- Polly: Polarized neutron reflectometry. (link)
- Superfit: Specular and diffuse neutron reflectivity. (link)
