xanespy 0.3.3

Description:

xanespy 0.3.3

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.

32-ID-C - Advanced Photon Source
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.


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.