/XRF

Scripts used to process XRF data collected at synchrotrons

Primary LanguagePython

XRF

Scripts used to process XRF data collected at synchrotrons

Contents:

  1. Convert_to_h5
  2. Transformtxt
  3. Matlab-scripts

Descriptions:

1: Convert_to_h5

This folder contains scripts used to convert XRF data recorded at the Canadian Light Source VESPERS beamline to an H5 file format such that it can be read by the data analysis program pyXRF. Two versions are included. The first is the updated python3 compatable script implemented via command line and the second is a more user-friendly gui whereby the two files are selected and loaded via a browser window. NOTE: The gui is VERY outdated. It is not python3 compatable and lacks error handling for input files. This is only included for historical purposes in the hopes I find time to convert it to the python3-compatable distribution. Use at your own risk.

Installation:

  1. CLone the git repo to a location of your choice (git clone https://github.com/davidkuter/XRF)
  2. CD into the convert_to_h5 folder
  3. pip install -r requirements.txt
  4. pip install -e .

Usage:

h5conversion <datafile1> <datafile2>

Here datafile1 is the ROI file that contains information regarding the step sizes used in the collection and datafile2 is the file containing the raw data.

2: Transformtxt

This folder contains scripts used to concatenate files output from pyXRF into a single csv file such that it can be plot in Origin. The script is implement from the command line and needs to be run in the folder containing the output data files. The script just needs to be run - no additional arguments are needed. The folder contains sample data obtained from pyXRF analysis on data obtained from the Canadian Light Sources VESPERS beamline and from the Brookhaven National Synchrotron Light Source SRX beamline. The script automatically determines which beamline the data has been obtained from by identifying the names of the normalization files which differ between the two.

3: Matlab-scripts

This folder contains two Matlab scripts which allow XRF data obtained from synchrotrons to be visualized using Matlab. The two scripts are run sequentially, first importxrfdata.m followed by plotxrfdata. The former prompts the user to select an element to visualize, following which it loads the data file (obtained after pyXRF deconvolution). It normalizes the data (using a filename that must be changed depending on whether CLS or NSLS was used to record the data) and then creates a frequency distribution of the values that are used to determine the upper and lower limits necessary for the plot. Once complete, the second script plots the normalized data using the upper and lower limits specified from the user (which is obtained by looking at the frequency distribution). The number of contour levels is also specified for by the user.