WIP: Fix/31 (use "All" instead of "-1" for karabo_da in notebooks)

Overview

This MR "fixes" https://git.xfel.eu/gitlab/detectors/pycalibration/issues/31

Most common setting: karabo_da is a list of strings and in practice, this is populated explicitly. However, the default catch-all value in the notebooks is ['-1'] which is a bit odd.

Note: modules is used to generate this karabo_da if the latter is "everythin" and in case modules is [-1], all are inserted. This merge request mainly changes the default for karabo_da from ['-1'] to ["all"]; as modules etc. are not lists of strings, their default value is left unchanged.

Additionally, the comment associated with modules is updated to reflect the fact that it is overridden when karabo_da is supplied (might be fairly obvious, but still).

Here are some potential changes not I did not make so far / some outliers which may require more insight than I currently have:

• AGIPD/AGIPD_FF_Histogramming only uses one karabo_da. The value is ["all"] by default (in line with other changes), but does not really make sense as a list given the current structure. Furthermore, it seems to be used only to infer the module.
• AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary listed karabo_da and modules in the settings variables cell, but never used the former and explicitly overwrites the latter. I removed the definitions in the settings cell for now.
• Notebooks in "playground" directories left alone
• FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode seems to be written to handle one karabo_da specifically (only touches karabo_da[0]). I have left this notebook alone for now.
  • The same goes for the two JUNGFRAU notebooks
  • And also pnCCD/Characterize_pnCCD_Dark_NBC.ipynb

How it has been tested

Overview of notebooks updated and testing status:

• notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
• notebooks/AGIPD/AGIPD_Correct_and_Verify_Summary_NBC.ipynb
• notebooks/AGIPD/AGIPD_FF_Histogramming.ipynb
• notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
• notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
• notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
• notebooks/DSSC/Characterize_DSSC_Darks_NBC.ipynb
• notebooks/DSSC/DSSC_Correct_and_Verify.ipynb
• notebooks/LPD/LPDChar_Darks_NBC.ipynb
• notebooks/LPD/LPD_Correct_and_Verify.ipynb

AGIPD DARK

The following invocation with and without --modules 0,1,2,3,4,5,6,7.

xfel-calibrate AGIPD DARK \
    --slurm-mem 750 \
    --slurm-name test_darks_mini_half \
    --report-to /gpfs/exfel/data/scratch/hammerd/test/agipd-dark-1 \
    --receiver-id {}CH0 \
    --karabo-id-control HED_EXP_AGIPD500K2G \
    --karabo-da-control AGIPD500K2G00 \
    --h5path-ctrl /CONTROL/{}/MDL/FPGA_COMP \
    --in-folder /gpfs/exfel/exp/HED/202031/p900174/raw/ \
    --out-folder /gpfs/exfel/data/scratch/hammerd/test/agipd-dark-1/runs \
    --karabo-id HED_DET_AGIPD500K2G \
    --run-high 10 \
    --run-med 11 \
    --run-low 12 \
    --sequences 0

AGIPD CORRECT

DSSC DARK

DSSC CORRECT