This interactive jupyter notebook is designed to produce heatmaps for data visualisation of operando electrochemical NPD collected on the POLARIS instrument at ISIS Neutron and Muon source, though it could be adapted to most other ToF (or even CW) neutron diffractometers.
You will need:
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A folder containing all collected NPD scans (on POLARIS we recommend collections every 2 minutes to give more flexibility, since you can always add more scans into a slice, but you cannot seperate them out)
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The lab notebook log text file exported from journal viewer. (You can export this from the POLARIS data analysis PC by highlighting the relevant scans, and exporting selected only).
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The electrochemical data file. (We used a biologic potentiostat, but the navani package used in this code is compatible with most potentiostat file types).
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The measured background scan of choice. (This notebook assumes you have collected a scan of the cell - the cathode film, but you could use an empirical background fit for example with winplotr if you do not have this).
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The python modules used in this notebook (The two you will likely be missing are navani, and the specific version of bokeh plot required. Instructions for installing these are given below).
The navani module can be installed via git as below, or via the other methods listed at https://github.com/be-smith/navani Note that after installation of the modules, you will need to restart the jupyter notebook kernel for the changes to take effect.
This script was adapted by James Steele (jmas5@cam.ac.uk) from an original script that takes a log file with XRD scan timings, matching XRD files, and an echem file to plot XRD patterns as a heatmap. This version is for operando NPD echem experiments at POLARIS, ISIS, using biologic cycler files, diffraction files, and IBEX notebook CSV output.
Original code by Josh Bocarsly jdbocars@uhouston.edu, tidied by Matthew Evans git@ml-evs.science.
authors = [ "James Steele jmas5@cam.ac.uk", "Josh Bocarsly jdbocars@uhouston.edu", "Matthew Evans git@ml-evs.science" ]