We use cookies to ensure you get the best experience on our website
Home Verkennen Help News
Registreren Inloggen
RemiGau
/
example_ephys_bids_conversion
2
0
Vork 0
Bestanden Issues 0 Pull-aanvragen 0 Wiki
Aftakking: master
Aftakkingen Labels
example_ephy...
/
code
Remi Gau 05f5767537 [DATALAD] Recorded changes 2 jaren geleden
..
data 4746f00bfa update code, test, refactor and lint 2 jaren geleden
lib 05f5767537 [DATALAD] Recorded changes 2 jaren geleden
.gitignore b67b485b21 convert 50 samples 2 jaren geleden
.pre-commit-config.yaml 4746f00bfa update code, test, refactor and lint 2 jaren geleden
01_indexing_source_data.ipynb 29f8f6224f [DATALAD] Recorded changes 2 jaren geleden
02_BEP032_templater.ipynb 2de410cb56 refactor and add tests 2 jaren geleden
03_neo_conversion.ipynb b67b485b21 convert 50 samples 2 jaren geleden
README.md 4746f00bfa update code, test, refactor and lint 2 jaren geleden
config_bids_filename.json 4746f00bfa update code, test, refactor and lint 2 jaren geleden
config_pybids.json 4746f00bfa update code, test, refactor and lint 2 jaren geleden
convert.py 4746f00bfa update code, test, refactor and lint 2 jaren geleden
participants_map.csv 29f8f6224f [DATALAD] Recorded changes 2 jaren geleden
participants_map_short.csv 209856aba6 deal with scans TSVs 2 jaren geleden
requirements.txt 4746f00bfa update code, test, refactor and lint 2 jaren geleden
test_convert.py 4746f00bfa update code, test, refactor and lint 2 jaren geleden
test_utils.py 4746f00bfa update code, test, refactor and lint 2 jaren geleden
utils.py 4746f00bfa update code, test, refactor and lint 2 jaren geleden

README.md

Install

Inside a virtual environment (conda or virtualenv or whatever floats your boat ⛵)

This will install BEP032tools and the Neo "bleeding edge"

pip install -r requirements.txt
cd lib/BEP032tools
pip install .[tools]
cd ../python_neo
python setup.py install

pybids config

Because pybids does not yet support ephys or microscopy, we use a modified config for it.

running the conversion

code/01_indexing_source_data.ipynb goes through the sourcedata and creates a listing between each file to convert and the entities that will be associated with it.