xanespy 0.1.5

Tools for analyzing X-ray absorbance spectroscopy data

Xanespy is a library for analyzing X-ray absorbance spectroscopy data for materials science, chemistry and similar fields. The major focus is on X-ray microscopy frames collected at multiple energies and over multiple timesteps. However, a design goal is for most (if not all) of the calculation routines to be applicable to bulk XAS data as well.

Motivation & Features

• Importing and analysis of transmission X-ray microscopy framesets

• Analysis of X-ray spectroscopy data (K-edge XANES and L-edge)

• Efficient analysis of large operando datasets

Installation

Xanespy can be installed from the python package index (PyPI) using pip

$ pip install xanespy

Usage

Each beamline generally has its own importer in the xanespy.importers module, which will process the data and create an HDF5 file ready for the rest of xanespy to use

import xanespy

# Example for importing from SSRL 6-2c
xanespy.import_ssrl_frameset('<data_dir>',
                             hdf_filename='imported_data.h5')

# Load a pre-defined XAS edge or create your own subclass xanespy.Edge
edge = xanespy.k_edges['Ni_NCA']
# Now load the newly created HDF5 file and the X-ray absorbance edge
fs = xanespy.XanesFrameset(filename='imported_data.h5', edge=edge)

# Perform automatic frame alignment
fs.align_frames(passes=5)
# Fit the absorbance spectra and extract the edge position (SLOW!)
fs.fit_spectra()

# Inspect the result with the built-in Qt5 GUI
fs.qt_viewer()

Beamlines

We currently have importers for data from the following beamlines. If you would like support a beamline that is not listed and are willing to share some test data publicly, please open an issue.

• 8-BM-B - Advanced Photon Source

• 6-2c - Stanford Synchrotron Radiation Lightsource

• 5.3.2.1 - Advanced Light Source (ptychography)

Ptychography

Xanespy has support for ptychography data from ALS beamline 5.3.2.1. Use xanespy.import_nanosurveyor_frameset to import the .cxi files and xanespy.PtychoFrameset to load the data.

Extended X-ray Absorbance Fine Structure (EXAFS)

Currently EXAFS analysis is NOT supported. While it would be nice to someday include this, this technique generally requires heavy user involvement and does not lend itself to batch processing; if you have expertise in automated analysis of EXAFS data, please get in touch.

License

This project is released under the GNU General Public License version 3.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Acknowledgement

This work was supported as part of the NorthEast Center for Chemical Energy Storage (NECCES), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012583.