xrayscatteringtools 0.3.0

A library for gas phase analysis at the CXI endstation

X-Ray Scattering Tools

xrayscatteringtools is a Python library designed for advanced X-ray scattering data analysis. It provides tools for data processing, visualization, calibration, and theoretical modeling. Specifically, it works alongside the CXI-Template repository for analyzing data from the Linac Coherent Light Source's Coherent X-ray Imaging hutch.

Features

• Data I/O: Read and write various data formats, including .xyz and .mol files, and handle experimental data stored in HDF5.
• Visualization: Generate plots for detector data.
• Calibration: Perform geometry calibration and create masks for X-ray scattering experiments.
• Theoretical Modeling: Compute scattering patterns using theoretical models and atomic data.
• Utilities: A collection of helper functions for unit conversions, azimuthal binning, and more.

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Installation

To install the latest version, use pip:

pip install xrayscatteringtools

or install manually

git clone https://github.com/Weber-Group/xrayscatteringtools.git
cd xrayscatteringtools
pip install -r requirements.txt

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Modules Overview

1. xrayscatteringtools.io

Handles data input and output operations:

• Key Functions:
  • combineRuns: Combine data from multiple experimental runs.
  • read_xyz, write_xyz: Read and write .xyz files.
  • get_data_paths: Retrieve paths to data files.
  • get_config: Load configuration files for experiments.

2. xrayscatteringtools.plotting

Provides tools for visualizing X-ray scattering data:

• Key Functions:
  • plot_j4m: Plot Jungfrau 4M detector data.

3. xrayscatteringtools.utils

A collection of utility functions:

• Key Functions
  • Unit conversions, azimuthal binning, transformations, ipython ease-of-use.

4. xrayscatteringtools.calib

Tools for calibration and masking:

• Submodules:
  • geometry_calibration: Perform geometry calibration using theoretical scattering patterns.
  • masking: Create and manage masks for X-ray scattering data.
  • scattering_corrections: Compute correction factors for scattering experiments.

5. xrayscatteringtools.theory

Theoretical modeling of X-ray scattering:

• Submodules:
  • geometries: Load and manage molecular geometries from HDF5 files.
  • iam: Compute elastic X-ray scattering patterns using the Independent Atom Model (IAM).
  • patterns : Load and manage ab initio scattering data from HDF5 files.

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Contributing

Contributions are welcome! Please fork the repository and submit a pull request with your changes.

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License

This project is licensed under the MIT License. See the LICENSE file for details.

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Acknowledgments

This library was created by David J. Romano based of compiling and standardizing code from previous data analysis piplines. Maintained by the Weber Research Group and developed by collaborators to facilitate X-ray scattering research.