Experiment directory:

/gpfs/exfel/exp/SPB/202302/p004456

Put personal analysis code in usr/Shared, e.g. for user "amorgan"

/gpfs/exfel/exp/SPB/202302/p004456/usr/Shared/amorgan

Put any analysis files (bigger than a few megabytes) in /scratch:

/gpfs/exfel/exp/SPB/202302/p004456/scratch

• VDS: virtual h5 files that put all processed module data into a single cxi file.
  • e.g. sbatch --array=5 offline/slurm/vds_array.sh to generate a vds file for run 5 from processed data.
• Generate powder pattern
  • e.g. sbatch --array=40 offline/slurm/powder_sum_array.sh to sum all frames in run 40 using vds file.
• Get initial geometry (and test with extra-geom)
  • There is a usr/geometry/geom_v5.geom crystFEL geom file (probably from Oleksandr).
  • To have a look python tests/test_geom.py (output below)
• Jungfrau mask maker
  • Example python offline/tools/maskmaker.py /gpfs/exfel/exp/SPB/202302/p004456/scratch/powder/powder_r0040.h5/data
• Calculate number, location and intensity of streaks
  • Example sbatch --array=40 offline/slurm/streak_finder.sh. This outputs an "events" file here:

    h5ls -r /p004456/scratch/events/events_r0040.h5
    /                        Group
    /litpixels               Dataset {6066}
    /streak_list             Dataset {80173/Inf}
    /streaks                 Dataset {6066}
    /total_intens            Dataset {6066}
    

• Generate streakogram, and virtual powder from above
  • Example python offline/streaks_powder_plotter.py -e "/gpfs/exfel/u/scratch/SPB/202302/p004456/events/events_r0040.h5" -g "/gpfs/exfel/exp/XMPL/201750/p700000/proc/r0040/j4m-p2805_v03.geom" will create events_r0040.streaks_powder_plot.png and events_r0040.streakogram_plot.png in folder /gpfs/exfel/u/scratch/SPB/202302/p004456/events/
• Save hits to cxi file
• Write cxi file from scan runs, for the purpose of speckle-tracking
  • It seems Margarita already has a means of streaming scan data, with a modified scan log, to the ST software. It would be nice to include this code here.