Author: J. K. Patel
Date: 04/11/2024

Title: Description of setup details and files contained in the Section 3: SciFi BPM dataset.

This dataset contains the raw image data, flat-field calibration data and flat-field calibration analysis for the scintillating fiber beam profile monitor
(SciFi BPM) data used in the results presented in Section 3 of the article "A scintillating fiber imaging spectrometer for active characterisation of laser-
driven proton beams". The Python analysis scripts in the Anlysis subdirectory calculate the calibrated profiles from the raw experimental data and the flat-
field calibration data, and plot the calibrated profiles in 'Figure4b-c).png' as output in the 'Section 3 dataeset/Figures/' directory.

See the main text of the article for details of the experimental setup and data analysis.


Files:

./RawData/20220721_0050_SciFi.tiff
        This is the raw image data from the experimental measurement with the SciFi BPM. The array of optical fibers are held in a 3D printed frame and the ends
        are image onto the camera, enabling quantification of the scintillation light generated in each scintillatig fiber.

./Flat-field calibration data/SciFi_UV_flat_field_calibration.tiff
        This is a calibration image captured while exposing the scintillating fibers to uniform illumination with a UV (380 nm) LED. See the Supplementary Materials 
        published alongside the main article for the complete details. This measurement enables compensation of any variation in the optical transport efficiency 
        of light from each scintillating fiber.

./Analysis/SciFi_flat_field_calibration_analysis.py
        This analysis script extracts the signals corresponding to each scintillating fiber in the raw image and the calibration image, using the regions-of-interest (ROI)
        corresponding to each fiber which are defined in the './Analysis/Fiber_ROI.pkl' file. The extracted signals are written to the files 'raw_SciFi_projections.pkl'
        and 'calibrated_SciFi_projections.pkl' The application of the calibration data to obtain a the calibrated SciFi BPM profiles is demonstrated by generating the 
        plots shown in Figure 4b-c) of the main article. This script was run using Python 3.9.19 and uses python packages: numpy-1.24.3, matplotlib-3.8.0, scikit-image-0.19.3 
        and tifffile-2023.8.30.

./Analysis/SciFi_flat_field_calibration_analysis.ipynb
        This notebook contains the same analysis as in './Analysis/SciFi_flat_field_calibration_analysis.py', but can be run in an interactive manner.

./Analysis/Fiber_ROI.pkl
        List of co-ordinates for the center of fiber ROI.

./Analysis/raw_SciFi_projections.pkl
        Array of summed pixel values in fiber ROIs from the raw image data, './RawData/20220721_0050_SciFi.tiff'

./Analysis/calibrated_SciFi_projections.pkl
        Array of summed pixel values in fiber ROIs from the calibraiton image data, './Flat-field calibration data/SciFi_UV_flat_field_calibration.tiff'