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Deutsches Elektronen-Synchrotron (DESY).\n\n## Dependencies:\n\n* Python 3.10\n* requirements.txt\n\n## JF1M conversion:\n\nAccess the `regae-utils/jungfrau/conversion` directory\n\n### Convert and merge dark files\n\n```bash\n./convert_pedestals.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype\n```\n\nExample:\n\n```bash\n./convert_pedestals.sh 231023_mos_c3_ms_004/ed_rot_step_001/231023_mos_c3_ms_004_001 step\n```\n\n### Convert images\n\n- Step scan\n  \n```bash\nsbatch convert_step.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype start_file_index end_file_index\n```\nExample:\n\n```bash\nsbatch convert_step.sh 231023_membran_back/ed_rot_step_001/231023_membran_back_001 step 0 1000\n```\n\n- Fly scan\n\n```bash\nsbatch convert_fly.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype \n```\n\nExample:\n\n```bash\nsbatch convert_fly.sh 231023_membran_back/ed_rot_step_001/231023_membran_back_001 fly\n```\n\n- Step + Fly scan\n\nAfter 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.\n\n```bash\nsbatch merge_sub.sh folder_on_raw/ed_rot_scantype_00*/file_label n_frames_to_merge\n```\n\nExample:\n```bash\nsbatch merge_sub.sh 231222_c3b_mica_020/ed_rot_step_001/231222_c3b_mica_020_001 20 \n```\n\n### Assemble images\n\n```bash\npython 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 \u0026\n```\n\nExample:\n\n```bash\npython 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 \u0026\n```\n## Center refinement\n\nCheck on https://github.com/anananacr/beambusters\n\n## Optmize Sol67 current for maximum sharpness of the diffraction pattern\n\nExample:\n```bash\npython optimize_magnet_powder.py /path/to/converted/file/ current_increment min_peak_height peak_width\n```\n```bash\npython 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\n```\n\n## Authors:\n\nAna Carolina Rodrigues (2021 - 2024)\n\nMail: ana.rodrigues@desy.de / sc.anarodrigue@gmail.com\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fanananacr%2Fregae-utils","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fanananacr%2Fregae-utils","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fanananacr%2Fregae-utils/lists"}