Catalog of Data Analysis Software

Development of software for visualization, analysis, reduction and simulation of x-ray experimental work has been a major output from the APS. This page describes a number of projects, some mature and others in initial stages that are being actively developed by scientists with the X-ray Science Division, often aided by software engineers within the AES Software Services Group and sometimes in collaboration with other parts of Argonne or external laboratories.

Note other relevant web pages:

Beamline data collection packages.
Software Services Group software projects web page

Imaging

	HiSPoD: undulator white-beam diffraction analysis software HiSPoD is a Matlab® program, developed for simulating and analyzing undulator white-beam diffraction patterns. It is particularly useful for single-pulse diffraction patterns and where an area detector is not perpendicular to the beam and the transmission beam spot may not fall on the detector.
	LaueGo Provides a convenient means to view and analyze 1D, 2D, and 3D spatially-resolved diffraction data. It is capable of taking a multi-Terabyte set of images and automatically producing a view of the strain or orientation throughout a 3D volume. It can analyze either white or monochromatic x-ray data to obtain the orientation or strain information within an inhomogeneous material
	MANTiS: Multivariate Analysis Tool for Spectromicroscopy MANTiS (Multivariate ANalysis Tool for Spectromicroscopy) is a Python-based open source analysis code that uses a number of multivariate statistical analysis and classification techniques to find the dominant spectroscopic themes within a dataset.
	MapsPy: X-ray Fluorescence Imaging MAPS serves as the main analysis tool for XRF micro-probes (2-ID-B, 2-ID-D, 2-ID-E, 8-BM, 26-ID, 21-ID-D, GSECARS) at the APS. It features analysis methods for elemental maps, spectral, spectrum, and non-negative matrix data. It operates in batch mode, and also has an interactive GUI. MapsPy is a Python-based open source software package being developed to replace MAPS that will be easier to support, distribute and integrate into beamline workflows.
	MIDAS: Microstructural Imaging using Diffraction Analysis Software The Microstructural Imaging using Diffraction Analysis Software (MIDAS) software package allows users to non-destructively image the microstructures of crystalline materials. The output is a 3D map with information about each grain.
	TomoPy: tomographic reconstruction Provides multi-dimensional tomographic reconstruction from any type of X-ray transmission and/or emission dataset. Also provides functionality for pre- and post-processing functions, such as ring artifact correction, phase retrieval, optimal centering, zinger removal, etc.
	TXM Control System An experiment control and data processing system for tomography beamlines. Interfaces with EPICS for beamline control and provides live and offline data viewing, basic image manipulation features, and scan sequencing that coordinates EPICS-enabled apparatus.Displays live data as well as previously recorded data, offers graphical annotations and adjustable color maps. Scanning can be configured from the GUI.
	uProbeX Coordinates visible light microscopy scans with fluorescence scans performed at the APS. Users quickly acquire an overview of their sample with a commodity visible light microscope, and then acquire an elemental map on a selected a region-of-interest from the visible light image

Spectroscopy

Xclaim: Calculation of core-hole spectroscopies

Xclaim is a GUI and calculation tool for core-hole spectroscopy and ground state properties within a charge-transfer multiplet model, utilizing a many-body Hamiltonian with Coulomb, spin–orbit, crystal-field, and hybridization interactions. It uses Hartree–Fock limit Coulomb and spin–orbit parameters as wellas crystal-field, hybridization and charge-transfer energy ligand-field parameters. The program calculates XAS, XPS, PES, and IPES spectra and runs on all common platforms.

MANTiS: Multivariate Analysis Tool for Spectromicroscopy

MANTiS (Multivariate ANalysis Tool for Spectromicroscopy) is a Python-based open source analysis code that uses a number of multivariate statistical analysis and classification techniques to find the dominant spectroscopic themes within a dataset.

XRAPM, X-ray Atomic Physics Module

Simulates this interaction of an atom with an x-ray pulse using the Monte-Carlo Rate Equation approach, which is essential the applications of x-ray free electron laser (XFEL). It provides a complete tracking of all the electronic transitions undertaking by atom and predicts ion, electron and photo spectra for experimental conditions.

Scattering

HiSPoD: undulator white-beam diffraction analysis software

HiSPoD is a Matlab® program, developed for simulating and analyzing undulator white-beam diffraction patterns. It is particularly useful for single-pulse diffraction patterns and where an area detector is not perpendicular to the beam and the transmission beam spot may not fall on the detector.

Nika: 2-D Data Reduction for SAXS and WAXS

Area (2-D) detectors are widely used in small-angle and wide-angle scattering instruments (SAXS and WAXS) due to their efficiency. Nika accepts such data and reduces it to 1-dimensional scans – typically as intensity as function of scattering angle --suitable for most of the data analysis programs (e.g., Irena for SAXS data). It can also be used for grazing-incidence geometry SAXS or WAXS.

QXRD – Real Time Readout, Visualization and Data Reduction for powder diffraction and SAXS measurements.

QXRD provides an integrated readout, visualization and data reduction package for powder diffraction and SAXS measurements.It is mainly used in conjunction with a Perkin Elmer flat panel detector but has also been used in conjunction with marCCD, mar345 and Pilatus data.A major focus of the application is that it can perform simultaneous acquisition, visualization and data reduction in real time at the maximum acquisition rate of the detector used.

simSAXSLee: SAXS/WAXS scattering simulator

simSAXSLee provides simulations of small and wide angle scattering crystalline assemblies of particles, such as inorganic polyhedra, organic molecules, proteins or virus capsids.

	CCTW – Crystal Coordinate Transformation Workflow CCTW is part of a larger LDRD Grand Challenge project “Discovery Engines for Big Data” and is intended to provide real time, or near real time visualization and analysis ofsingle crystal diffuse scattering data.CCTW is responsible for transforming datasets from real to reciprocal coordinates.
	Dioptas - on-the-fly processing & exploration of 2D diffraction data Dioptas is a Python-based program for on-the-fly processing and exploration of area detector X-ray diffraction data, specifically designed for the large amount of data collected at synchrotron beamlines. Its fast data reduction algorithm and graphical data exploration capabilities make it ideal for online data processing during XRD experiments and batch post-processing of large numbers of images.
	GIXSGUI GIXSGUI is a Matlab-based toolbox for visualization, reduction, and analysis of 2D grazing-incidence X-ray scattering (GIXS) data taken from nanostructures that are either supported on surfaces or embedded in thin films.
	GSAS-II, GSAS and EXPGUI: Generalized Crystallographic Analysis Provides crystallographic determination of the atomic arrangement from any type of x-ray or neutron from diffraction measurements as well as materials characterization information. Multiple datasets may be combined for a single or parametric study. Can be used for all scales of complexity from materials characterization to proteins.

	Irena: Small-Angle Scattering Data Analysis Analysis tools for small-angle (X-ray and neutron) scattering data, primarily for complex, typically inorganic materials. Performs anumber of types of analysis: size distribution, unified fit model, direct modeling of scattering from disordered and ordered system, including fractal systems and small-angle diffraction, with number of supporting tools (data import/export, manipulation, plotting etc.). Includes scattering contrast calculator for both neutrons and X-rays (in free electron and Cromer-Lieberman approximations).
	LaueGo Provides a convenient means to view and analyze 1D, 2D, and 3D spatially-resolved diffraction data. It is capable of taking a multi-Terabyte set of images and automatically producing a view of the strain or orientation throughout a 3D volume. It can analyze either white or monochromatic x-ray data to obtain the orientation or strain information within an inhomogeneous material
	matSAXS & SAXSLee: SAXS/WAXS reduction, visualization and fitting A set of programs SAXS/WAXS data reduction, visualization and analysis.
	MIDAS: Microstructural Imaging using Diffraction Analysis Software The Microstructural Imaging using Diffraction Analysis Software (MIDAS) software package allows users to non-destructively image the microstructures of crystalline materials. The output is a 3D map with information about each grain.


	Real-time XPCS Multi-tau Analysis X-ray photoelectron correlation spectroscopy (XPCS) extracts length-scale dependent dynamical information for the sample being probed, by computing the time autocorrelation function using a series of 2D area detector images. To allow computation in real-time, the Hadoop MapReduce algorithm is employed to deploy this in a high-performance computing (HPC) environment. The resulting code can be used to process data irrespective of the geometry of the measurement such as small angle in transmission, grazing incidence or under diffraction conditions.
	rsMap3D Process diffraction data collected with area detectors at APS and represents the result as three-dimensional data sets as volumes in reciprocal space. Provides the means to look at various cuts through the map. The input for processing of this data consists of a series of area detector images collected over a range of diffractometer angles and/or input energy.
	Scedasticity: Model free ranked data analysis This package includes two computation methods ‘Correlation’ and ‘Scedasticity’ which are used to track the evolution of a set of data by looking for correlations. This method determines changes that occur in a parametric study by mining data from noise without imposition of a model.

	X-Ray Server: BRL, GID_sl, TER_sl, TRDS_sl, MAG_sl, and X0h The X-ray Server is a suite of WWW-accessed software for online modeling of X-ray diffraction, specular reflection and scattering, with possible applications to studying defects in surface layers of crystals, designing X-ray optics, and teaching the dynamical diffraction theory.The programs compute X-ray scattering factors, Bragg diffraction profiles from strained crystals, X-ray specular reflection, standing waves from multilayers, multiple Bragg diffraction, scattering from interface roughness and resonant specular reflection from magnetic multilayers

General

	APS Data Management System The APS Data Management system is being created to alleviate tedious data management tasks for beamline staff, while ensuring the integrity and security of beamline data. It will simplify remote electronic access to data for users and will provide an infrastructure for organizing the files that comprise these data sets and to tag these data sets with administrative information.
	Data Exchange A Python module to share scientific data and analysis tools through file conversion into HDF5. Implements the Data Exchange data standard.
	Fprime: X-ray cross-section estimators A series of utilities for computing the wavelength dependence for x-ray scattering and absorption. The utilities can be accessed through two GUI-based Python routines (for form factors or absorption) or via a web-based calculation routine tailored for powder diffraction sample evaluation
	HYBRID code for beamline simulation The HYBRID code simulates beamline optics by combining geometrical ray-tracing and wavefront propagation. It provides fast beamline performance calculation including diffraction effects, mirror figure errors and the partial coherence of synchrotron radiation sources. Two GUI implementations are available.
	Python-DTXRD A collection of Python tools developed to aid X-ray diffraction evaluation of single crystals and multi-crystal configurations used in x-ray optics. This calculates of reflectivity/transmissivity using the dynamical theory of x-ray diffraction, constructs rocking curve maps (for sequential x-ray diffraction topography), calculates x-ray flux based from PIN diodes and provides a few other helpful tools for x-ray crystal optics work.
	X-Ray Server: BRL, GID_sl, TER_sl, TRDS_sl, MAG_sl, and X0h The X-ray Server is a suite of WWW-accessed software for online modeling of X-ray diffraction, specular reflection and scattering, with possible applications to studying defects in surface layers of crystals, designing X-ray optics, and teaching the dynamical diffraction theory.The programs compute X-ray scattering factors, Bragg diffraction profiles from strained crystals, X-ray specular reflection, standing waves from multilayers, multiple Bragg diffraction, scattering from interface roughness and resonant specular reflection from magnetic multilayers
	XOP v2.4 X-ray Oriented Programs: a graphical-user-interface driven code for calculation of synchrotron radiation and its interaction with samples and optical elements. These programs allow for design of beamline instrumentation and experiments.

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