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
Procedure
- Connect to JupyterHub and start a job on a CLASSE node
- 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/)
- 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.
- 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.
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LouisaSmieska - 22 Feb 2023