InstantPlot to NetCDF

This step is in use as of 2022-2 and is used to convert the output of InstantPlot batch processing or the parallel_processing.py script (which may consist of many text files for a single scan) into a single .cdf file containing both the integrated 1D data as well as relevant spec data.

We recommend running this conversion using JupyterHub. Documentation from CLASSE IT: https://wiki.classe.cornell.edu/Computing/JupyterHub


  1. Connect to JupyterHub and start a job on a CLASSE node
  2. Use the file navigator on the left to locate your auxiliary area (e.g. /nfs/chess/auxiliary/reduced_data/cycles/2022-2/id3b/username-0000-A/)
  3. You will need:
    • A template .yaml file for netcdf conversion (this is different from the .yaml file used for parallel_processing.py batch integration)
    • A copy of our InstantPlot to netcdf jupyter notebook (.ipynb)
    • We usually place these in your "analysis" folder. If they are not present an FMB scientist can help you locate the versions you need.
  4. Open the InstantPlot to netcdf conversion jupyter notebook. Choose the HyperSpy kernel. Examples in the notebook will help you use a single .yaml file to batch convert your InstantPlot files to netcdf.
-- LouisaSmieska - 22 Feb 2023
Topic revision: r1 - 22 Feb 2023, LouisaSmieska
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