CHESS-ID3A-FAST

Running a CHAP EDD Pipeline (Map + Strain)

These instructions walk through copying the example pipeline files, editing the few fields that need to change for your sample, and running the pipeline.

1. Copy the pipeline files

Copy both pipeline .yaml files from the example folder into your own working directory:

cp /nfs/chess/aux/cycles/*cycle_num*/id1a3/*btr*/reduced_data/*previous_sample_name*/*.yaml /nfs/chess/aux/cycles/*cycle_num*/id1a3/*btr*/reduced_data/*current_sample_name*/
cd /nfs/chess/aux/cycles/*cycle_num*/id1a3/*btr*/reduced_data/*current_sample_name*/

You should now have something like pipeline_map.yaml and pipeline_strain.yaml.

2. Edit `pipeline_map.yaml`

Update the `.par` file

map:
  - edd.EddMapReader:
      filename: /nfs/chess/aux/cycles/.../raw_data/<sample-name>/<scan-name>.par

Point this to your sample’s .par file. To find it:

find /nfs/chess/aux/cycles/2026-2/id1a3/<your-experiment-folder>/raw_data/ -name "*.par"

Leave the detector config (eta angles) unchanged unless your detector setup differs from the example.

6. Run the pipelines in order

run_chap_edd_dev pipeline_map.yaml
run_chap_edd_dev pipeline_strain.yaml

The map step produces map.nxs, which the strain step reads as input — it must be run first and must be in the same working directory (or update common.NexusReader.filename in pipeline_strain.yaml to point to it).

7. Check the output

With interactive: false, the pipeline runs straight through without popping up plots. Check:

The terminal for errors / tracebacks
output_<...>/strain_full.nxs — the main strain results
output_<...>/saved_figures/ — diagnostic plots (peak fits, etc.)

Summary of what to change per run

File	Field	Set it to
`pipeline_map.yaml`	`EddMapReader.filename`	your sample’s `.par` file

Everything else (detector configs, find_peak_cutoff, rel_height_cutoff, etc.) should stay as the example provides unless you have a specific reason to change it.

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