PAN Blend diffraction packages

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

This is the common documentation package.

A program that computes structure factors |F^2| for neutrons, x-rays, and electrons from CIF/CFL/SHX/PCR crystallographic descriptions. This is useful to compute the diffraction pattern from materials.

This package contains the executable.

This metapackage will install packages for crystallography which might be useful for chemists.

The program density-fitness calculates electron density metrics, for main- (includes Cβ atom) and side-chain atoms of individual residues.

For this calculation, the program uses the structure model in either PDB or mmCIF format and the electron density from the 2mFo-DFc and mFo-DFc maps. If these maps are not readily available, the MTZ file and model can be used to calculate maps clipper. Density-fitness support both X-ray and electron diffraction data.

This program is essentially a reimplementation of edstats, a program available from the CCP4 suite. However, the output now contains only the RSR, SRSR and RSCC fields as in edstats with the addition of EDIAm and OPIA and no longer requires pre-calculated map coefficients.

A GUI program for fast analysis of powder X-ray diffraction Images. It provides the capability of calibrating, creating masks, having pattern overlays and showing phase lines.

Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.

It was developed for analyzing diffraction patterns, but can be also used in other fields, since concepts and operations specific for crystallography are separated from the rest of the program.

Fityk offers various nonlinear fitting methods, subtracting background, calibrating data, easy placement of peaks and changing peak parameters, automation of common tasks with scripts, and much more. The main advantage of the program is flexibility - parameters of peaks can be arbitrarily bound to each other, eg. the width of a peak can be an independent variable, can be the same as the width of another peak or can be given by a complicated - common to all peaks - formula.

libjs-sphinxdoc is necessary for the Javascript stuff in the documentation.

GNOME Crystal is a light model visualizer for crystal-structures. It is based on the GNOME Chemistry Utils and should display models of all sorts of crystal microscopic structures using OpenGL.

The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

This package provides a gui on top of the hkl library.

The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

 This package can be used by other packages using the GIRepository format to
generate dynamic bindings.

The CCP4 software suite is based around a library of routines which cover common tasks, such as file opening, parsing keyworded input, reading and writing of standard data formats, applying symmetry operations, etc. Programs in the suite call these routines which, as well as saving the programmer some effort, ensure that the varied programs in the suite have a similar look-and-feel.

The library contains several sub components:

• CMTZ library -- Contains a variety of functions for manipulating the data structure, for example adding crystals, datasets or columns. The data structure can be dumped to an output MTZ data file.

• CMAP library -- Functions defining the C-level API for accessing CCP4 map files.

• CSYM library -- a collection of functions centered around a data file syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox of cctbx).

• CCP4 utility library -- many utility functions which either give specific CCP4 or platform independent functionality.

• CCP4 Parser library -- provides CCP4-style parsing, as used for processing keywords of CCP4 programs, MTZ header records, etc.

• CCP4 resizable arrays -- defines an object and methods which looks just like a simple C array, but can be resized at will without incurring excessive overheads.

This package provides the common files for the CCP4 library.

The CCP4 software suite is based around a library of routines which cover common tasks, such as file opening, parsing keyworded input, reading and writing of standard data formats, applying symmetry operations, etc. Programs in the suite call these routines which, as well as saving the programmer some effort, ensure that the varied programs in the suite have a similar look-and-feel.

The library contains several sub components:

• CMTZ library -- Contains a variety of functions for manipulating the data structure, for example adding crystals, datasets or columns. The data structure can be dumped to an output MTZ data file.

• CMAP library -- Functions defining the C-level API for accessing CCP4 map files.

• CSYM library -- a collection of functions centered around a data file syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox of cctbx).

• CCP4 utility library -- many utility functions which either give specific CCP4 or platform independent functionality.

• CCP4 Parser library -- provides CCP4-style parsing, as used for processing keywords of CCP4 programs, MTZ header records, etc.

• CCP4 resizable arrays -- defines an object and methods which looks just like a simple C array, but can be resized at will without incurring excessive overheads.

The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

This package provides everything needed to link against hkl.

The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

This package provides the documentation for hkl.

xylib is a C++ library for reading files that contain x-y data from powder diffraction, spectroscopy and other experimental methods.

This package contains a small program xyconv that converts files supported by the xylib library to TSV (tab-separated values).

Development files for xylib.

xylib is a C++ library for reading files that contain x-y data from powder diffraction, spectroscopy and other experimental methods.

FOX is a program for the ab initio structure determination from powder diffraction (neutrons, X-Ray). The crystal structure can be described as any combination of atoms, molecules or polyhedra, without a priori information about the connectivity of these 'building block'. Fox can make multi-pattern global optimizations, and automatically correct special positions.

FOX could also be used for educational purposes, to display Crystal Structures in 3D with the associated powder diffraction pattern.

PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

This is the common documentation package.

The silx project aims at providing a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. It aims at providing reading/writing different file formats, data reduction routines and a set of Qt widgets to browse and visualize data.

The current version provides :

• reading HDF5 file format (with support of SPEC file format)
• histogramming
• fitting
• 1D and 2D visualization using multiple backends (matplotlib or OpenGL)
• image plot widget with a set of associated tools (See changelog file).
• Unified browser for HDF5, SPEC and image file formats supporting inspection and visualization of n-dimensional datasets.
• Unified viewer (silx view filename) for HDF5, SPEC and image file formats
• OpenGL-based widget to display 3D scalar field with isosurface and cutting plane.

This is the common documentation package.

xrayutilities is a collection of scripts used to analyze x-ray diffraction data. It consists of a Python package and several routines coded in C. It especially useful for the reciprocal space conversion of diffraction data taken with linear and area detectors.

This package includes the manual in HTML format.

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

This is the Python 3 version of the package.

CodraFT is a generic signal and image processing software based on Python scientific libraries (such as NumPy, SciPy or scikit-image) and Qt graphical user interfaces (thanks to guidata and guiqwt.

CodraFT stands for "CODRA Filtering Tool".

CodraFT is available as a stand-alone application or as an addon to your Python-Qt application thanks to advanced automation and embedding features.

DENSS is an algorithm used for calculating ab initio electron density maps directly from solution scattering data. DENSS implements a novel iterative structure factor retrieval algorithm to cycle between real space density and reciprocal space structure factors, applying appropriate restraints in each domain to obtain a set of structure factors whose intensities are consistent with experimental data and whose electron density is consistent with expected real space properties of particles.

DENSS utilizes the NumPy Fast Fourier Transform for moving between real and reciprocal space domains. Each domain is represented by a grid of points (Cartesian), N x N x N. N is determined by the size of the system and the desired resolution. The real space size of the box is determined by the maximum dimension of the particle, D, and the desired sampling ratio. Larger sampling ratio results in a larger real space box and therefore a higher sampling in reciprocal space (i.e. distance between data points in q). Smaller voxel size in real space corresponds to higher spatial resolution and therefore to larger q values in reciprocal space.

Lightweight, simple Python(-only) package. It is used to provide access to data files used in regression tests, but does not contain any of those data files itself.

Although it is envisaged as mostly being used in a cctbx/DIALS environment for tests in DIALS, dxtbx, xia2 and related packages, it has no dependencies on either cctbx or DIALS, in fact all dependencies are explicitly declared in the setup.py file and are installable via standard setuptools/pip methods. This means dials_data can easily be used in other projects accessing the same data, and can be used in temporary environments such as Travis containers.

MoviePy is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.

PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

This is the Python 3 version of the package.

Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library.

Some examples offer 3D support which can use python3-ipywidgets.

This package installs the library for Python 3.

python implementation of the matrix algorithm for computer modeling of X-ray diffraction (XRD) patterns of disordered lamellar structures. It's goals are to:

• provide an easy user-interface for end-users
• provide basic tools for displaying and manipulating XRD patterns
• produce high-quality (publication-grade) figures
• make modelling of XRD patterns for mixed-layer clay minerals 'easy'
• be free and open-source (open box instead of closed box model)

PyXRD was written with the multi-specimen full-profile fitting method in mind. A direct result is the ability to 'share' parameters among similar phases. This allows for instance to have an air-dry and a glycolated illite-smectite share their coherent scattering domain size, but still have different basal spacings and interlayer compositions for the smectite component. Or play with the di/tri-octahedral composition of a chlorite with ease.

The silx project aims at providing a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. It aims at providing reading/writing different file formats, data reduction routines and a set of Qt widgets to browse and visualize data.

The current version provides :

• reading HDF5 file format (with support of SPEC file format)
• histogramming
• fitting
• 1D and 2D visualization using multiple backends (matplotlib or OpenGL)
• image plot widget with a set of associated tools (See changelog file).
• Unified browser for HDF5, SPEC and image file formats supporting inspection and visualization of n-dimensional datasets.
• Unified viewer (silx view filename) for HDF5, SPEC and image file formats
• OpenGL-based widget to display 3D scalar field with isosurface and cutting plane.

This is the Python 3 version of the package.

xrayutilities is a collection of scripts used to analyze X-rays diffraction data. It consists of a Python package and several routines coded in C. It especially useful for the reciprocal space conversion of diffraction data taken with linear and area detectors.

This is the Python 3 version of the package.

The silx project aims at providing a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. It aims at providing reading/writing different file formats, data reduction routines and a set of Qt widgets to browse and visualize data.

The current version provides :

• reading HDF5 file format (with support of SPEC file format)
• histogramming
• fitting
• 1D and 2D visualization using multiple backends (matplotlib or OpenGL)
• image plot widget with a set of associated tools (See changelog file).
• Unified browser for HDF5, SPEC and image file formats supporting inspection and visualization of n-dimensional datasets.
• Unified viewer (silx view filename) for HDF5, SPEC and image file formats
• OpenGL-based widget to display 3D scalar field with isosurface and cutting plane.

This uses the Python 3 version of the package.

Nebula is a scalable overlay networking tool with a focus on performance, simplicity and security. It is intended to be more robust than current virtual networking solutions by providing peer-to-peer connectivity and NAT traversal mechanisms. Nebula uses state-of-the-art cryptography based on the "Noise" protocol.

This package provide the binaries and default configuration for Nebula.

PyNX stands for Python tools for Nano-structures Crystallography. It is a python library with the following main modules:

1) pynx.scattering: X-ray scattering computing using graphical processing units, allowing up to 2.5x10^11 reflections/atoms/seconds (single nVidia Titan X). The sub-modulepynx.scattering.gid can be used for Grazing Incidence Diffraction calculations, using the Distorted Wave Born Approximation

2) pynx.ptycho : simulation and analysis of experiments using the ptychography technique, using either CPU (deprecated) or GPU using OpenCL. Examples are available in the pynx/Examples directory. Scripts for analysis of raw data from beamlines are also available, as well as using or producing ptychography data sets in CXI (Coherent X-ray Imaging) format.

3) pynx.wavefront: X-ray wavefront propagation in the near, far field, or continuous (examples available at the end of wavefront.py). Also provided are sub-modules for Fresnel propagation and simulation of the illumination from a Fresnel Zone Plate, both using OpenCL for high performance computing.

4) pynx.cdi: Coherent Diffraction Imaging reconstruction algorithms using GPU.

In addition, it includes :doc:scripts <scripts/index> for command-line processing of ptychography data from generic CXI data (pynx-ptycho-cxi) or specific to beamlines (pynx-ptycho-id01, pynx-ptycho-id13,...).