Difference between revisions of "Software"

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* '''[[GIXSGUI]]''': Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang ([[APS]]).
 
* '''[[GIXSGUI]]''': Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang ([[APS]]).
 
** Citation: Z. Jiang [http://scripts.iucr.org/cgi-bin/paper?S1600576715004434 GIXSGUI: a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films] ''J. Appl. Cryst.'' '''2015''', 48, 3, 917-926. [http://dx.doi.org/10.1107/S1600576715004434 doi: 10.1107/S1600576715004434]
 
** Citation: Z. Jiang [http://scripts.iucr.org/cgi-bin/paper?S1600576715004434 GIXSGUI: a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films] ''J. Appl. Cryst.'' '''2015''', 48, 3, 917-926. [http://dx.doi.org/10.1107/S1600576715004434 doi: 10.1107/S1600576715004434]
−
** [https://www1.aps.anl.gov/Sectors/Sector-8/8-ID/Operations-and-Schedules/Useful-Links/Sector-8-GIXSGUI Official site.]
+
** [https://www.aps.anl.gov/Sector-8/8-ID/Operations-and-Schedules/Useful-Links/Sector-8-GIXSGUI Official site.]
 
* '''[[GISAXSshop]]''': 2D visualization and reduction for GISAXS. Requires the Igor (Wavemetrics). Written by Byeongdu Lee ([[APS]]).
 
* '''[[GISAXSshop]]''': 2D visualization and reduction for GISAXS. Requires the Igor (Wavemetrics). Written by Byeongdu Lee ([[APS]]).
 
** [https://sites.google.com/site/byeongdu/software Official site.]
 
** [https://sites.google.com/site/byeongdu/software Official site.]
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* '''DPDAK''': Open-source Python tool for analyzing large sets of SAXS data. Works on Linux and Windows.
 
* '''DPDAK''': Open-source Python tool for analyzing large sets of SAXS data. Works on Linux and Windows.
 
** [https://dpdak.desy.de/index.php/Hauptseite Official site.]
 
** [https://dpdak.desy.de/index.php/Hauptseite Official site.]
 +
* '''SAS-cam''': SAXS data reduction, using the [https://bio.tools/sastbx SASTBX package].
 +
** Citation: H. Wu, Y. Li, G. Liu, H. Liu and N. Li [http://scripts.iucr.org/cgi-bin/paper?ei5058 SAS-cam: a program for automatic processing and analysis of small-angle scattering data] ''J. Appl. Cryst.'' '''2020''', 53, 1147-1153. [https://doi.org/10.1107/S1600576720008985 doi: 10.1107/S1600576720008985]
  
 
==Data Modeling and Fitting==
 
==Data Modeling and Fitting==
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* '''[[BornAgain]]''': Python/C++ implementation of DWBA modeling (similar to IsGISAXS, but more modern and with lots of extensions). Allows for polarized [[GISANS]] and GISAXS simulation and fitting. Available on Linux, MacOS and Windows. 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/C++ implementation of DWBA modeling (similar to IsGISAXS, but more modern and with lots of extensions). Allows for polarized [[GISANS]] and GISAXS simulation and fitting. Available on Linux, MacOS and Windows. Written by the [http://apps.jcns.fz-juelich.de/doku/sc/start Scientific Computing Group] at [http://www.mlz-garching.de/ MLZ Garching].
 
** Citation: C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke (2015), BornAgain - Software for simulating and fitting X-ray and neutron small-angle scattering at grazing incidence, http://www.bornagainproject.org
 
** Citation: C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke (2015), BornAgain - Software for simulating and fitting X-ray and neutron small-angle scattering at grazing incidence, http://www.bornagainproject.org
 +
** Citation: G. Pospelov, W. Van Herck, J. Burle, J. M. Carmona Loaiza, C. Durniak, J. M. Fisher, M. Ganeva, D. Yurov and J. Wuttke [https://scripts.iucr.org/cgi-bin/paper?ge5067 BornAgain: software for simulating and fitting grazing-incidence small-angle scattering] ''J. Appl. Cryst.'' '''2020''',  53, 262-276. [https://doi.org/10.1107/S1600576719016789 doi: 10.1107/S1600576719016789]
 
** [http://www.bornagainproject.org/ Official site.]
 
** [http://www.bornagainproject.org/ Official site.]
 
* '''[[HipGISAXS]]''': A high-performance (massively parallel) C++ software for simulating GISAXS data.
 
* '''[[HipGISAXS]]''': A high-performance (massively parallel) C++ software for simulating GISAXS data.
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** Citation: A.K. Hailey, A.M. Hiszpanski, D.-M. Smilgies and Y.-L. Loo [http://scripts.iucr.org/cgi-bin/paper?fs5084 The Diffraction Pattern Calculator (DPC) toolkit: a user-friendly approach to unit-cell lattice parameter identification of two-dimensional grazing-incidence wide-angle X-ray scattering data] ''Journal of Applied Crystallography'' '''2014''', 47. [http://dx.doi.org/10.1107/S1600576714022006 doi: 10.1107/S1600576714022006]
 
** Citation: A.K. Hailey, A.M. Hiszpanski, D.-M. Smilgies and Y.-L. Loo [http://scripts.iucr.org/cgi-bin/paper?fs5084 The Diffraction Pattern Calculator (DPC) toolkit: a user-friendly approach to unit-cell lattice parameter identification of two-dimensional grazing-incidence wide-angle X-ray scattering data] ''Journal of Applied Crystallography'' '''2014''', 47. [http://dx.doi.org/10.1107/S1600576714022006 doi: 10.1107/S1600576714022006]
 
** [http://www.princeton.edu/cbe/people/faculty/loo/group/software Official site.]
 
** [http://www.princeton.edu/cbe/people/faculty/loo/group/software Official site.]
 +
* '''Indexing''': Python code for overlaying peak positions for a particular unit cell on a detector image.
 +
** Code available on [https://github.com/esther279/Indexing github].
  
 
===[[Reflectivity]]===
 
===[[Reflectivity]]===
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** [http://genx.sourceforge.net/ Official site.]
 
** [http://genx.sourceforge.net/ Official site.]
 
* '''Aurore''': Open source Matlab code for neutron reflectivity, including error estimates.
 
* '''Aurore''': Open source Matlab code for neutron reflectivity, including error estimates.
−
** Citation: Y. Gerelli [http://scripts.iucr.org/cgi-bin/paper?rg5094 Aurore: new software for neutron reflectivity data analysis] ''J. Appl. Cryst.'' '''2016''', 49, 330-339. [http://dx.doi.org/10.1107/S1600576716000108 10.1107/S1600576716000108]
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** Citation: Y. Gerelli [http://scripts.iucr.org/cgi-bin/paper?rg5094 Aurore: new software for neutron reflectivity data analysis] ''J. Appl. Cryst.'' '''2016''', 49, 330-339. [http://dx.doi.org/10.1107/S1600576716000108 doi: 10.1107/S1600576716000108]
 
** [https://sourceforge.net/projects/aurorenr/ Official site.]
 
** [https://sourceforge.net/projects/aurorenr/ Official site.]
 
* '''Web Reflectivity Calculator''': Interactive, Web-Based Calculator of Neutron and X-ray Reflectivity.
 
* '''Web Reflectivity Calculator''': Interactive, Web-Based Calculator of Neutron and X-ray Reflectivity.
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** [https://github.com/refnx/refnx Available on github]
 
** [https://github.com/refnx/refnx Available on github]
 
** Citation:  A.R.J. Nelson and S.W. Prescott [http://scripts.iucr.org/cgi-bin/paper?rg5158 refnx: neutron and X-ray reflectometry analysis in Python] ''J. Appl. Cryst.'' '''2019'''. [https://doi.org/10.1107/S1600576718017296 doi: 10.1107/S1600576718017296]
 
** Citation:  A.R.J. Nelson and S.W. Prescott [http://scripts.iucr.org/cgi-bin/paper?rg5158 refnx: neutron and X-ray reflectometry analysis in Python] ''J. Appl. Cryst.'' '''2019'''. [https://doi.org/10.1107/S1600576718017296 doi: 10.1107/S1600576718017296]
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* '''Multifitting''': Reflectivity calculations for multilayer systems
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** Citation: M. Svechnikov [http://scripts.iucr.org/cgi-bin/paper?te5051 Multifitting: software for the reflectometric reconstruction of multilayer nanofilms] ''J. Appl. Cryst.'' '''2019''' [https://doi.org/10.1107/S160057671901584X doi: 10.1107/S160057671901584X]
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* '''MLReflect''': Machine-learning method for reflectivity curves
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** [https://mlreflect.readthedocs.io/en/latest/ Docs] and [https://github.com/schreiber-lab/mlreflect/tree/master code]
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** Citation: [https://arxiv.org/abs/2202.11609 arxiv]
  
 
===[[Crystallography]]===
 
===[[Crystallography]]===
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** Toby, B. H., & Von Dreele, R. B. [http://scripts.iucr.org/cgi-bin/paper?S0021889813003531 GSAS-II: the genesis of a modern open-source all purpose crystallography software package] ''Journal of Applied Crystallography'' '''2013''', 46(2), 544-549. [http://dx.doi.org/10.1107/S0021889813003531 doi: 10.1107/S0021889813003531]
 
** Toby, B. H., & Von Dreele, R. B. [http://scripts.iucr.org/cgi-bin/paper?S0021889813003531 GSAS-II: the genesis of a modern open-source all purpose crystallography software package] ''Journal of Applied Crystallography'' '''2013''', 46(2), 544-549. [http://dx.doi.org/10.1107/S0021889813003531 doi: 10.1107/S0021889813003531]
 
** [https://subversion.xor.aps.anl.gov/trac/pyGSAS Official site.]
 
** [https://subversion.xor.aps.anl.gov/trac/pyGSAS Official site.]
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* '''Jana2006''': Reconstruct electron density modulation from powder or single-crystal data.
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** Citations: Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features ''Z. Kristallogr.'' '''2014''', 229(5), 345-352. [10.1515/zkri-2014-1737 doi: 10.1515/zkri-2014-1737]
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** [http://jana.fzu.cz/ Official site.]
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* '''τompas''': TEM online multi-purpose analyzing system
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** Citation: R.-X. Xie and W.-Z. Zhang [http://scripts.iucr.org/cgi-bin/paper?ks5644 τompas: a free and integrated tool for online crystallographic analysis in transmission electron microscopy] ''J. Appl. Cryst.'' '''2020''', 53. [https://doi.org/10.1107/S1600576720000801 doi: 10.1107/S1600576720000801]
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* '''UnitCell Tools''': Determine unit-cell parameters from a single electron diffraction pattern.
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** Citation: Hong-Long Shi and Zi-An Li [https://journals.iucr.org/m/issues/2021/05/00/gq5014/index.html UnitCell Tools, a package to determine unit-cell parameters from a single electron diffraction pattern] ''IUCrJ'' '''2020''' [https://doi.org/10.1107/S2052252521007867 doi: 10.1107/S2052252521007867]
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===Wave/Matter interaction===
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====X-rays====
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These software packages directly simulation the propagation of an EM field, and/or the interaction between EM waves and material:
 +
* '''SRW''' (Synchrotron Radiation Workshop): Fast numerical simulation of near-field and far-field of radiation generated by electron beams traveling through magnetic fields. I.e. can be used to simulate x-ray emission from [[synchrotron]] sources (e.g. [[undulator]]).
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** [https://www.esrf.fr/Accelerators/Groups/InsertionDevices/Software/SRW Official site.]
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* '''Shadow''': X-ray optics simulation package for coherent x-ray wavefront propagation simulations​​.
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** Citation: Niccolo Canestrari, Oleg Chubar and Manuel Sanchez del Rio [https://iopscience.iop.org/article/10.1088/1742-6596/425/16/162007 Improved models for synchrotron radiation sources in SHADOW] ''J. Phys.: Conf. Ser.'' '''2013''', 425 162007. [http://dx.doi.org/10.1088/1742-6596/425/16/162007 doi: 10.1088/1742-6596/425/16/162007]
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* '''WPG''' (WavePropaGator): Software package for simulating coherent and partially coherent X-ray wavefront propagation, especially intended for simulating [[XFEL]]
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** [https://wpg.readthedocs.io/en/stable/wpg.html Docs.]
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** [https://github.com/samoylv/WPG Code.]
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====General EM field====
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* [https://github.com/flaport/fdtd Python 3D FDTD Simulator]
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* [https://github.com/kc-ml2/meent Meent]
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* [https://github.com/stefanmeili/FastFD FastFD]
  
 
==Computing [[Materials]] Properties==
 
==Computing [[Materials]] Properties==
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* '''DANSE Periodic Table''': Python library for x-ray and neutron elemental scattering properties.
 
* '''DANSE Periodic Table''': Python library for x-ray and neutron elemental scattering properties.
 
** [http://www.reflectometry.org/danse/elements.html Official site].
 
** [http://www.reflectometry.org/danse/elements.html Official site].
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* '''MultiSciView''': Web-based tool for looking at arbitrary arrays of 2D image data. Convenient for looking at scattering images arranged based on metadata (coordinates, annealing history, etc.).
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** Citation: [https://www.sciencedirect.com/science/article/pii/S2468502X18300093 MultiSciView: Multivariate Scientific X-ray Image Visual Exploration with Cross-Data Space Views] ''Visual Informatics'' '''2018''', 1(2), 14-25 [http://dx.doi.org/10.1016/j.visinf.2018.04.003 doi: 10.1016/j.visinf.2018.04.003]
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==Synchrotron==
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* '''[https://github.com/silx-kit/silx SILX]''': Data reading/writing for synchrotron data formats.
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* '''[https://nsls-ii.github.io/bluesky/ BlueSky]''': Instrument control, including data saving into a database and access via databroker.
  
 
==General==
 
==General==

Latest revision as of 08:40, 9 April 2024

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.

Data Viewing, Reduction, and Simple Analysis

These packages provide ways to view data, and perform simple operations (linecuts, etc.).

Geared towards 2D data

Geared towards 1D data

Data Modeling and Fitting

These packages can predict scattering curves for various possible nano- or molecular- structures. Some of the packages allow fitting of experimental data.

SAXS

BioSAXS

GISAXS

Reflectivity

Crystallography

Wave/Matter interaction

X-rays

These software packages directly simulation the propagation of an EM field, and/or the interaction between EM waves and material:

  • SRW (Synchrotron Radiation Workshop): Fast numerical simulation of near-field and far-field of radiation generated by electron beams traveling through magnetic fields. I.e. can be used to simulate x-ray emission from synchrotron sources (e.g. undulator).
  • Shadow: X-ray optics simulation package for coherent x-ray wavefront propagation simulations​​.
  • WPG (WavePropaGator): Software package for simulating coherent and partially coherent X-ray wavefront propagation, especially intended for simulating XFEL

General EM field

Computing Materials Properties

Synchrotron

  • SILX: Data reading/writing for synchrotron data formats.
  • BlueSky: Instrument control, including data saving into a database and access via databroker.

General

  • SciStreams: Simple workflow/pipeline software (building on Dask and Streams), intended for asynchronous and distributed computations at a beamline.
  • ParaView: Generalized GUI for visualizing scientific data, such as 3D images (uses Python and QT).
  • Mantid: Framework for computing and visualizing materials science data.
    • Official site.
    • Citation: O. Arnold, et al., Mantid—Data analysis and visualization package for neutron scattering and μSR experiments, Nuclear Instruments and Methods in Physics Research Section A, Volume 764, 11 November 2014, Pages 156-166. doi: 10.1016/j.nima.2014.07.029
  • DAWN (Data Analysis WorkbeNch): An application (based on Eclipse) for general scientific data analysis. It is mainly developed by the Diamond Light Source and is well-optimized for analysis of x-ray data, including SAXS-specific features.

Custom

It is of course possible to code your own software for modeling or fitting scattering data. This is not as difficult as it may at first seem. The fundamental scattering equations are well-known (c.f. scattering, Fourier transform, Form Factor, Structure Factor, Lattice Factor), and can be brute-force solved numerically. Or, they can be solved (or simplified) analytically for a particular case. Many modern programming languages provide libraries for numerical integration, fitting, minimizing multi-dimensional parameter spaces, etc. (e.g. Python is particularly clean and powerful).

See Also

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