XPCS_FitLab

XPCS_FitLab is a toolset designed for analyzing X-ray Photon Correlation Spectroscopy (XPCS) data stored in HDF5 files. The tool includes both a Jupyter notebook (hdf5_xpcs_fitlab.ipynb) and a Python script (hdf5_xpcs_fitlab.py), both of which provide the same functionality. They offer a graphical interface (GUI) for managing input files and analyzing multiple HDF5 datasets efficiently.

The tool relies on functions defined in the XPCS_functions.py file, which must be located in the same directory as the main script or notebook for proper execution.

Features

• HDF5 Data Handling: Reads XPCS data from HDF5 files using the h5py library.
• Autocorrelation Function Fitting: Fits precomputed $g_2(t)$ functions from the HDF5 files to three different models:
  • Single Exponential
  • Stretched Exponential
  • Cumulant Method
• Diffusion Coefficient Calculation: Calculates the diffusion coefficient ($D_0$) using two methods:
  • Direct calculation from the relaxation rate ($C$).
  • Linear fit of $C$ vs $q²$.
• Graphical Interface: Provides a GUI for selecting input files, setting parameters, and visualizing results.

Installation

Before running XPCS_FitLab, ensure you have Python 3.6 or later installed. You can download it from Python Downloads.

To install the required Python packages, run the following command in your terminal or command prompt:

pip install h5py numpy scipy scikit-learn matplotlib qtpy pandas PyQt5 tk

How to Use

Running with Jupyter Notebook

1. Open hdf5_xpcs_fitlab.ipynb in Jupyter Notebook or JupyterLab.
2. Follow the instructions within the notebook to configure and run your analysis.

Running with Python Script

1. Ensure that hdf5_xpcs_fitlab.py and XPCS_functions.py are located in the same directory.

2. Run hdf5_xpcs_fitlab.py from the terminal:

   python hdf5_xpcs_fitlab.py

   The GUI will open, allowing you to select files and perform the analysis.

Important Notes

• The XPCS_functions.py file contains all the necessary functions used by both the notebook and script. Make sure it is located in the same directory as hdf5_xpcs_fitlab.py for the script to work correctly.
• You can define the $R²$ threshold for selecting fitted curves to include in the diffusion coefficient calculations. Both the direct calculation and linear fit methods will use this threshold.

Dependencies

• Python (>= 3.6)
• h5py
• numpy
• scipy
• scikit-learn
• matplotlib
• qtpy
• pandas
• PyQt5
• tk

License

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