https://github.com/anananacr/regae-utils
Scripts for data processing at REGAE - Deutsches Elektronen-Synchrotron (DESY).
https://github.com/anananacr/regae-utils
electron-diffraction python
Last synced: 3 months ago
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Scripts for data processing at REGAE - Deutsches Elektronen-Synchrotron (DESY).
- Host: GitHub
- URL: https://github.com/anananacr/regae-utils
- Owner: anananacr
- License: gpl-3.0
- Created: 2023-03-03T17:44:39.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-30T13:47:14.000Z (almost 2 years ago)
- Last Synced: 2025-09-09T06:40:52.220Z (7 months ago)
- Topics: electron-diffraction, python
- Language: Python
- Homepage: https://regae.desy.de/
- Size: 851 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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
```bash
./convert_pedestals.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype
```
Example:
```bash
./convert_pedestals.sh 231023_mos_c3_ms_004/ed_rot_step_001/231023_mos_c3_ms_004_001 step
```
### Convert images
- Step scan
```bash
sbatch convert_step.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype start_file_index end_file_index
```
Example:
```bash
sbatch convert_step.sh 231023_membran_back/ed_rot_step_001/231023_membran_back_001 step 0 1000
```
- Fly scan
```bash
sbatch convert_fly.sh folder_on_raw/ed_rot_scantype_00*/file_label scantype
```
Example:
```bash
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.
```bash
sbatch merge_sub.sh folder_on_raw/ed_rot_scantype_00*/file_label n_frames_to_merge
```
Example:
```bash
sbatch merge_sub.sh 231222_c3b_mica_020/ed_rot_step_001/231222_c3b_mica_020_001 20
```
### Assemble images
```bash
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:
```bash
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:
```bash
python optimize_magnet_powder.py /path/to/converted/file/ current_increment min_peak_height peak_width
```
```bash
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: ana.rodrigues@desy.de / sc.anarodrigue@gmail.com