Spectral SAXS PCD data Analysis Tool

Overview:

This is an open-source data analysis tool to analyze spectroscopic photon counting detector data for spectral small angle x-ray scattering (sSAXS) application.

Data Input:

This application assumes that the input files a 3D array of detector counts at each energy level. In order to work properly the data should be formatted as [energyDetected,xPixel,yPixel]

Each functions requires some experimental parameters as well:

Parameter	Units	Description
Sample to Detector Distance	mm	The distance between the scanned sample and the surface of the detector
q Range	nm-1	The region of momentum transfer values to analyze across
Transmission Beam Location	pixels	The approximate location where the incident beam strikes the detector

This application allows two primary functions:

1D Spectral Analysis and Energy Windowing

Users have the options to plot spectra from thier collected x-ray scattering data and separate into energy windows of interest.

Parameter	Units	Description
Energy Range	keV	Total range of energies you wish to analyze
Bin Width	keV	The size of the steps between energy values
Energy Window Width	keV	The size of the sub-ranges you wish to analyze

Output:

-Plots of the individual spectra -A single plot of the background subtracted spectrum -A plot of the angles corresponding to each detector pixel -A heatmap of the background subtracted detector data across the whole energy range -Heatmaps of the background subtrated detector data in each energy window -A 3D plot of the background subtracted spectra in each energy window

2D scanning analysis to generate spatially resolved scattering map

Users can map the relative intensity of scattering signals across multiple data set from 2D scanning sSAXS experiments to generate a planar image.

Parameter	Units	Description
Energy Range	keV	Total range of energies you wish to analyze
Integral q Range	nm-1	The start and end of the q-peak of interest
Scans Per Row	pixels	The width of the final map you wish to create, if this is a 2D scan it is the number of collections you took per row

Output:

-A 3D plot of the background subtracted spectra for each file -A heatmap of each file's intensity at the specified q region of interest

Installation:

• Clone this repository: https://github.com/<REPO> and navigate to its root directory

• Install python 3.9.19 (or any version greater than 3.9)

• Create a virtual environtment named pcd (or any name of your choosing)

  • python -m venv <chosen_env_name>

• Activate the environment (Ensure you replace <chosen_env_name> with your chosen venv name)

  • Windows: <chosen_env_name>\Scripts\activate
  • Unix: source <chosen_env_name>/bin/activate

• Install the required dependencies: pip install -r requirements.txt

Usage

From your activated virtual environment run: python main.py

Credits: