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https://github.com/anananacr/regae-utils

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

https://github.com/anananacr/regae-utils

Science Score: 13.0%

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    Low similarity (4.6%) to scientific vocabulary

Keywords

electron-diffraction python
Last synced: 5 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: anananacr
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Homepage: https://regae.desy.de/
  • Size: 779 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
electron-diffraction python
Created almost 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

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

Owner

  • Name: Ana Carolina Rodrigues
  • Login: anananacr
  • Kind: user
  • Location: Hamburg, Germany
  • Company: CFEL - DESY

PhD student in Physics.

GitHub Events

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Dependencies

requirements.txt pypi
  • Cython ==0.29.33
  • HeapDict ==1.0.1
  • Jinja2 ==3.0.3
  • MarkupSafe ==2.0.1
  • PeakUtils ==1.3.4
  • Pillow ==8.4.0
  • PyCifRW ==4.4.5
  • PyQt5 ==5.15.6
  • PyQt5-Qt5 ==5.15.2
  • PyQt5-sip ==12.9.1
  • PyWavelets ==1.1.1
  • PyYAML ==6.0
  • astropy ==4.1
  • black ==22.8.0
  • bokeh ==2.3.3
  • cached-property ==1.5.2
  • certifi ==2022.12.7
  • charset-normalizer ==2.0.12
  • click ==8.0.4
  • cloudpickle ==2.2.1
  • contextvars ==2.4
  • crystals ==1.2.2
  • cycler ==0.11.0
  • dask ==2021.3.0
  • dataclasses ==0.8
  • decorator ==4.4.2
  • diffractem ==0.4.1
  • distributed ==2021.3.0
  • fabio ==0.14.0
  • fsspec ==2022.1.0
  • h5py ==3.1.0
  • hdf5plugin ==3.3.1
  • idna ==3.4
  • imageio ==2.15.0
  • immutables ==0.19
  • importlib-metadata ==4.8.3
  • joblib ==1.1.1
  • kiwisolver ==1.3.1
  • llvmlite ==0.36.0
  • locket ==1.0.0
  • matplotlib ==3.3.4
  • msgpack ==1.0.4
  • mypy-extensions ==1.0.0
  • networkx ==2.5.1
  • npstreams ==1.6.4
  • numba ==0.53.1
  • numpy ==1.19.5
  • ondamonitor ==21.5.0
  • opencv-python ==4.7.0.72
  • packaging ==21.3
  • pandas ==1.1.5
  • partd ==1.2.0
  • pathspec ==0.9.0
  • platformdirs ==2.4.0
  • psutil ==5.9.4
  • pyparsing ==3.0.9
  • pyqtgraph ==0.11.1
  • python-dateutil ==2.8.2
  • pytz ==2022.7.1
  • pyzmq ==25.0.0
  • requests ==2.27.1
  • scikit-image ==0.17.2
  • scikit-learn ==0.24.2
  • scikit-ued ==2.1.0
  • scipy ==1.5.4
  • six ==1.16.0
  • sortedcontainers ==2.4.0
  • spglib ==1.16.5
  • tblib ==1.7.0
  • threadpoolctl ==3.1.0
  • tifffile ==2020.9.3
  • tomli ==1.2.3
  • toolz ==0.12.0
  • tornado ==6.1
  • typed-ast ==1.5.4
  • typing_extensions ==4.1.1
  • urllib3 ==1.26.14
  • zict ==2.1.0
  • zipp ==3.6.0