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# MDCatch ## Still in development, but you are welcome to try! A simple PyQt5 app to fetch metadata from EPU or SerialEM. It parses the first found EPU xml and SerialEM mdoc file associated with a data collection session. In case of SerialEM you need to enable saving mdoc file for each movie.
- ### Prerequisites / installation:
Python 3 and PyQt5. If you don’t have PyQt5 module in your system python3 then create a virtual environment: ` python3 -m venv venv source venv/bin/activate pip install PyQt5 `
Relion 3.1 or Scipion 3.0 sourced in your PATH (at the moment Scipion 3 is not ready!)
Preprocessing templates: Schedules folder for Relion, template.json for Scipion
Edit config.py to adjust it to your settings
- ### Running
- Simply python3 run.py. User only needs to provide:
path to EPU session folder or path to folder with SerialEM movies/mdoc files
particle size (A)
username
### Working principle The idea is to launch the app on a separate OTF machine as soon as EPU/SerialEM starts data collection and the first movie is acquired.
check if username exists in the NIS database (ypmatch username passwd)
find and parse the first xml/mdoc file, getting all acquisition metadata
create a Relion/Scipion project folder username_microscope_date_time inside PROJECT_PATH (or inside Scipion default projects folder)
create symlinks for movies, gain reference, defects file, MTF in the project folder
modify existing Relion Schedules/Scipion templates then launch Relion/Scipion on-the-fly processing
### Screenshots
 
- ### TODO
beam tilt is parsed but not used since we parse only a single xml/mdoc for the whole session
SerialEM conversions: gain ref dm4->mrc, defects SerialEM->Relion
K3 EPU 2.6.1 gain file is a rubbish tif, to be fixed by TFS
use GAIN_DICT from config
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Release files for MDCatch 0.9.3
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Source distribution (sdist)
| File | Size | Uploaded | |
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| MDCatch-0.9.3.tar.gz | 42.0 kB | Details |
Release files / MDCatch-0.9.3.tar.gz
| Download URL | MDCatch-0.9.3.tar.gz |
|---|---|
| Size | 42.0 kB |
| Tags | Source |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.1.3 requests-toolbelt/0.9.1 tqdm/4.41.0 CPython/3.8.2
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