regae-utils

Python scripts for data processing at REGAE - Deutsches Elektronen-Synchrotron (DESY).

Dependencies:

• Python 3.10
• requirements.txt

JF1M conversion:

Access the regae-utils/jungfrau/conversion directory

Convert and merge dark files

./convert_pedestals.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype

Example:

./convert_pedestals.sh 231023_mos_c3_ms_004/ed_rot_step_001/231023_mos_c3_ms_004_001 step

Convert images

• Step scan

sbatch convert_step.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype start_file_index end_file_index

Example:

sbatch convert_step.sh 231023_membran_back/ed_rot_step_001/231023_membran_back_001 step 0 1000

• Fly scan

sbatch convert_fly.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype 

Example:

sbatch convert_fly.sh 231023_membran_back/ed_rot_step_001/231023_membran_back_001 fly

• Step + Fly scan

After accumulating the frames of each position using convert_step.sh, run the following script to merge sub steps in order to have each frame corresponding to 0.1 deg rotation.

sbatch merge_sub.sh folder_on_raw/ed_rot_scantype_00*/file_label n_frames_to_merge

Example:

sbatch merge_sub.sh 231222_c3b_mica_020/ed_rot_step_001/231222_c3b_mica_020_001 20 

Assemble images

python save_assembled_images.py -i /asap3/fs-bmx/gpfs/regae/2023/data/11018148/processed/converted/folder_on_raw/ed_rot_scantype_00*/file_label -g /asap3/fs-bmx/gpfs/regae/2023/data/11018148/scratch_cc/yefanov/geom/JF_regae_v4.geom -m /asap3/fs-bmx/gpfs/regae/2023/data/11018148/scratch_cc/yefanov/mask/mask_edges.h5 -o /asap3/fs-bmx/gpfs/regae/2023/data/11018148/processed/assembled/folder_on_raw/ed_rot_scantype_00* -f cbf &

Example:

python save_assembled_images.py -i /asap3/fs-bmx/gpfs/regae/2023/data/11018148/processed/converted/231019_mos_c3_ms_001/ed_rot_step_001/231019_mos_c3_ms_001_001 -g /asap3/fs-bmx/gpfs/regae/2023/data/11018148/scratch_cc/yefanov/geom/JF_regae_v4.geom -m /asap3/fs-bmx/gpfs/regae/2023/data/11018148/scratch_cc/yefanov/mask/mask_edges.h5 -o /asap3/fs-bmx/gpfs/regae/2023/data/11018148/processed/assembled/231019_mos_c3_ms_001/ed_rot_step_001 -f cbf &

Center refinement

Check on https://github.com/anananacr/beambusters

Optmize Sol67 current for maximum sharpness of the diffraction pattern

Example:

python optimize_magnet_powder.py /path/to/converted/file/ current_increment min_peak_height peak_width

python optimize_magnet_powder.py /asap3/fs-bmx/gpfs/regae/2023/data/11018148/processed/converted/231221_au_ref_scan/ed_magnet_step_001/231221_au_ref_scan_001_master.h5 0.1 130 4

Authors:

Ana Carolina Rodrigues (2021 - 2024)

Mail: [email protected] / [email protected]