Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/azazellochg/tfs_epu_parser
Parse EPU sessions
https://github.com/azazellochg/tfs_epu_parser
Last synced: about 1 hour ago
JSON representation
Parse EPU sessions
- Host: GitHub
- URL: https://github.com/azazellochg/tfs_epu_parser
- Owner: azazellochg
- License: gpl-3.0
- Created: 2023-07-26T09:41:50.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2024-03-08T14:29:27.000Z (8 months ago)
- Last Synced: 2024-10-13T01:29:24.034Z (about 1 month ago)
- Language: Python
- Homepage:
- Size: 35.2 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# TFS_EPU_parser
A simple Python 3 script to parse EPU session files. No dependencies or installation is required!
This script can be useful to analyze EPU parameters from sessions of different facility users. It will analyze **EpuSession.dm** (one per session) and a FoilHole data xml file (from a first found movie), then create a CSV table.
How to use
----------
1) Locate *EpuSession.dm* files. You can use **get_files.sh** as an example script to find all files modified in 2023. This script will output a list of file paths (see **examples/scope0**).
2) Run the main script:
``python3 parse_epu_session.py /path/to/scope0``
It will generate **scope0.csv** which you can see in examples folder.
3) PROFIT!! You are done. You can analyse the output CSV in any way you like with downstream tools.
CSV columns
-----------
* Autofocus distance (um)
* Autofocus recurrence
* BeamSize (um)
* Binning
* C2Aperture (um)
* ClusteringMode
* ClusteringRadius (um)
* Defocus list (um)
* DelayAfterImageShift (s)
* DelayAfterStageShift (s)
* Detector
* Dose (e/A^2)
* DoseFractionsOutputFormat
* DoseOnCamera (e/unbinned_px/s)
* DosePerFrame (e/A^2/frame)
* Drift recurrence
* Drift threshold (m/s)
* EnergySelectionSlitWidth (eV)
* EPUversion
* ExposureTime (s)
* ExtractorVoltage (V)
* GunLens
* HoleSize (um)
* HoleSpacing (um)
* Magnification
* MicroscopeID
* Mode
* Name
* Number of exposures (per hole)
* NumSubFrames
* ObjAperture (um)
* PhasePlateEnabled
* PhasePlateUsed
* PixelSpacing (A)
* ProbeMode
* SpecimenCarrierType
* SpotSize
* StartDateTime
* Voltage (kV)
