/TFS_EPU_parser

Parse EPU sessions

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

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)

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