PAN Blend spectroscopy packages

DMRGPP / DMRG++ is an implementation of the Density matrix renormalization group algorithm which attempts to find the lowest-energy matrix product state wavefunction corresponding to the total energy of the system. DMRGPP embeds the PsimagLite utility to obtain codes for the simulation of strongly correlated electrons.

This package contains the dmrg executable and helpers, built using OpenBLAS.

The European Theoretical Spectroscopy Facility (ETSF) is a European network dedicated to providing support and services for ongoing research in academic, government and industrial laboratories.

The ETSF is divided into 7 beamlines, each of which is concerned with a specific scientific topic:

• Optics ;
• Energy Loss Spectroscopy ;
• Quantum Transport ;
• Time-resolved Spectroscopy ;
• Photo-emission Spectroscopy ;
• Vibrational Spectroscopy ;
• X-Rays Spectroscopy.

To allow the adoption of its recommendations about standardization, the ETSF proposes different libraries and tools implementing or using these specifications, as well as widely usable pieces of software.

ETSF_IO is a library of F90 routines to read/write the ETSF file format. This package contains the user tools to:

• check file conformance to the specifications;
• extract data from files;
• merge multiple files from parallel runs, as specified in the specifications.

Spectromicroscopy combines spectral data with microscopy, where typical datasets consist of a stack of microscopic images taken across an energy range. Due to the data complexity, manual analysis can be time consuming and inefficient, whereas multivariate analysis tools not only reduce the time needed but also can uncover hidden trends in the data.

Mantis is Multivariate ANalysis Tool for Spectromicroscopy developed in Python by 2nd Look Consulting. It uses principal component analysis and cluster analysis to classify pixels according to spectral similarity.

PyMca is set of applications and Python libraries for analysis of X-ray fluorescence spectra.

The applications included in this package are:

• edfviewer - Display and inspection of data files in ESRF Data Format
• elementsinfo - Displays element specific X-ray data
• mca2edf - Converts files from SPEC MCA format to EDF
• peakidentifier - Displays X-ray fluorescence peaks in a given energy range
• pymcabatch - Batch fitting of spectra
• pymcapostbatch - Post-processing of batch fitting results
• pymca - Interactive data-analysis
• pymcaroitool - Region-of-interest (ROI) imaging tool

The PyMca toolkit can read data files in SPEC, ESRF data file (EDF), OMNIC, HDF5, AIFIRA and SupaVisio formats.

This are the scripts of the package.

Collection of libraries, functions and tools related to ARPES data loading and analysis.

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.

Python parsers for Igor Binary Waves (.ibw) and Packed Experiment (.pxp) files written by WaveMetrics’ IGOR Pro software.

NavARP provides a navigation tool for Angle Resolved Photoemission spectroscopy data. NavARP is a companion app during ARPES data acquitision (as in beamtime) and set of dedicated libraries helping to get high quality figures for publication.

This package installs the navarp utility for Python 3.

Orange add-on for spectral data analysis. Provides spectra and hyperspectra plotting, interpolation, preprocessing (cutting, smoothing, normalization), and integration. Supports common spectral file formats.

Features

### Load and process data

• Load the spectroscopy data
• Preprocess and interpolate spectra
• Integrate spectra
• Average spectra
• Performs Fast Fourier Transform

### Visualisation

• Visually explore series of spectra
• Plots 2D map of hyperspectra

Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

This package contains Python 3 module.

Python Image Tool can be used to visualise analysis of data in microscopy (STM, SSM, optics), ARPES, XRD, or other multidimensional datasets on regularly gridded coordinates.

This package installs the module for Python 3 and an example helper script to create a writeable data cache.

Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis. These are some of the main features:

1.Highly flexible classes for the representation of Element, Site, Molecule, Structure objects.

1. Extensive input/output support, including support for VASP (http://cms.mpi.univie.ac.at/vasp/), ABINIT (http://www.abinit.org/), CIF, Gaussian, XYZ, and many other file formats.

2. Powerful analysis tools, including generation of phase diagrams, Pourbaix diagrams, diffusion analyses, reactions, etc.

3. Electronic structure analyses, such as density of states and band structure.

4. Integration with the Materials Project REST API, Crystallography Open Database.

This package provides the pymtgen module for Python 3.

Pure Python module for processing hyperspectral image data (imaging spectroscopy data). It has functions for reading, displaying, manipulating, and classifying hyperspectral imagery.

SPVIEW is a multiplatform Java application that allows graphical assignment of high-resolution molecular spectra. It is possible to load, display and manipulate experimental and simulated spectra (XY ASCII or OPUS formats) as well as stick spectra in various formats (including HITRAN format).

Collection of tools and Python3 modules to extract and analyze x-ray Raman scattering (XRS) data from ID20 of the European Synchrotron Radiation Facility

XRS_wizard is omitted until support is available for Qt5.

This package installs the library for Python 3.