Materials Analysis Using Diffraction: A Rietveld extended program to perform combined analyses. It can be used to fit diffraction, fluorescence and reflectivity data using X-ray, neutron, TOF or electrons
Mosflm can process diffraction images from a wide range of detectors and produces, as output, an MTZ file of reflection indices with their intensities and standard deviations (and other parameters). This MTZ file is passed onto other programs of the CCP4 program suite (SORTMTZ, SCALA, TRUNCATE) for further data reduction.
MXAN performs a quantitative analysis of the XANES energy range. This is based on a comparison between experimental data and many theoretical spectra that are calculated by varying selected structural parameters of an initial putative structure, i.e. a well defined initial geometrical configurations around the absorber. Hundreds of different geometrical configurations are needed to obtain the best fit of the experimental data. The calculations are performed in the energy space without involving any Fourier transform algorithm; polarized spectra can be easily analysed because the calculations are performed within the full multiple scattering approach. Recently, MXAN has been developed in the framework of the multiple scattering theory and successfully applied to the analysis of several system, both in solid and liquid state. The MXAN procedure,encompasses also the phenomenological broadening and the electronic charge fitting.
A set of Python tools and widgets for handling and visualizing scanning imaging data at the NanoMAX (MAX IV) beamline.
NeXpy provides a high-level python interface to NeXus data contained within a simple GUI. It is designed to provide an intuitive interactive toolbox allowing users both to access existing NeXus files and to create new NeXus-conforming data structures without expert knowledge of the file format. The underlying Python API for reading and writing NeXus files is provided by the nexusformat package, which is also described here.
nxtomomill provide a set of applications to convert tomography acquisition made from bliss (@ESRF) from their original file format (.edf, .h5) to a Nexus compliant file format (using NXtomo)
OCEAN is a versatile package for performing first-principles calculations of core edge spectroscopy. The many-body method is based on ground-state density-functional theory (DFT) and uses the Bethe-Salpeter equation. OCEAN utilizes the programs ABINIT or QuantumESPRESSO for ground-state DFT portion of the calculations. OCEAN is capable of producing various spectra including X-ray absorption near-edge spectra (XANES), X-ray emission spectra (XES), and non-resonant inelastic X-ray scatter (NRIXS or XRS). OCEAN is the result of collaboration between the Rehr group at the University of Washington and Eric Shirley at the National Institute of Standards and Technology (USA).
Combined EXAFS and XRPD data analysis with EXAFS full multiple scattering calculations and whole-spectrum fitting. A code designed to maximise the usefulness of the EXAFS technique in the investigation of crystalline materials which powder diffraction (PD) methods could not uniquely resolve. The program retains many of the features of EXCURVE (s. the related web pages) and provides most of the PD features of the program GSAS. For EXAFS this includes full multiple scattering calculations and whole-spectrum fitting, but at present it cannot deal with EXAFS polarisation dependence. PD calculations currently exclude calculation of the thermal diffuse scattering contribution, which is included in the background.
PHENIX is a software suite for automated macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This has been made possible by the development of novel algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a set of crystallographic libraries that have been built and made available to the community.
Pore3D is a software toolbox for quantitative analysis of three-dimensional images. The core of Pore3D consists in a set of state-of-the-art functions and procedures for performing filtering, segmentation, skeletonization and quantitative analysis of three-dimensional data. Although three-dimensional data can be produced by several techniques (for instance: magnetic resonance, x-ray scattering or confocal microscopy), the library was developed and optimized for micro-CT (Computed Tomography) data. Pore3D features are available through the high-level scripting environment IDL. Pore3D has been tested with IDL 64-bit from versions 6.4 to 8.5.
Framework for scientific ptychography including suitable classes for many concepts of ptychography
pyFAI is an azimuthal integration library that tries to be fast (as fast as C and even more using OpenCL and GPU). It is based on histogramming of the 2theta/Q positions of each (center of) pixel weighted by the intensity of each pixel, but parallel version uses a SparseMatrix-DenseVector multiplication
Hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities. PyHST2 (formerly known as PyHST) has been engineered to sustain the high data flow typical of the third generation synchrotron facilities (10 terabytes per experiment) by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a-priori knowledge. The latter are used to improve the reconstruction quality or in order to reduce the required data volume and reach a given quality goal. The implemented a-priori knowledge techniques are based on the total variation penalisation and a new recently found convex functional which is based on overlapping patches.
X-ray Fluorescence Toolkit (visualization and analysis of energy-dispersive X-ray fluorescence data). . The program allows both interactive and batch processing of large data sets and is particularly well suited for X-ray imaging. Its implementation of a complete description of the M shell is particularly helpful for analysis of data collected at low energies. It features, among many other things, the fundamental parameters method
Python toolkit for accelerated Nano-structures Crystallography and Coherent X-ray Imaging techniques. The software included in this package can be used for: 1. the computing of X-ray scattering using graphical processing units 2. X-ray wavefield propagation (from near to far field) 3. simulation and GPU-accelerated analysis of experiments using the ptychography and coherent diffraction imaging techniques See the full documentation at: http://ftp.esrf.fr/pub/scisoft/PyNX/doc/