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Adding a BIDSification pipeline for an existing patchclamp data set #140

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Adding a BIDSification pipeline for an existing patchclamp data set #140

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d643b2c
First commit on this branch, creation of the inherited class dedicate…
SylvainTakerkart Oct 6, 2022
f850897
Merge remote-tracking branch 'origin/master' into patch_nw
SylvainTakerkart Oct 10, 2022
609ff74
New attempt at giving a working structure for the NW patch data bids …
SylvainTakerkart Oct 10, 2022
d38fe35
Full implementation of the previously proposed code structure... It w…
SylvainTakerkart Oct 18, 2022
7ebf5b0
a few attempts, not conclusive
SylvainTakerkart Oct 21, 2022
87e90d7
Updated the generate_csf_file_nw according to the plan
SylvainTakerkart Nov 9, 2022
fbfffdc
Updated the genrate_bids_dataset function to pass custom metadata sou…
SylvainTakerkart Nov 9, 2022
502202e
commiting before merging...
SylvainTakerkart Nov 29, 2022
34e7183
Merge branch 'master' of https://github.com/INT-NIT/BEP032tools into …
SylvainTakerkart Nov 29, 2022
65a01c9
commiting before merging the autoconvert code update...
SylvainTakerkart Nov 29, 2022
d07c883
Commit after conflict solving
SylvainTakerkart Nov 29, 2022
5641561
Progress to get all the parameters from the tsv file to register_data…
SylvainTakerkart Nov 29, 2022
fa54a9b
Updated BEP022Generator to better handle the task and run entities. …
SylvainTakerkart Nov 30, 2022
19deaea
Fixed a bug in BEP032NWConverter... Now, it handles the data from sev…
SylvainTakerkart Dec 5, 2022
45e2510
Small update on BEP032NWDataConverter
SylvainTakerkart Dec 7, 2022
27cf4a7
Merged from upstream after the PR on entities handling has been integ…
SylvainTakerkart Dec 7, 2022
f0534a6
Added reading of metadata xls file
SylvainTakerkart Dec 7, 2022
190b5b2
Merge branch 'master' into patch_nw
Dec 7, 2022
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10 changes: 10 additions & 0 deletions bep032tools/generator/BEP032Generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,10 @@ def register_data_sources(self, *sources, task=None, run=None):

sources = [Path(f) for f in sources]

# the run info is in self.custom_metadata_sources{'run'}
# let's go get it!


key = ''
if task is not None:
key += f'task-{task}'
Expand Down Expand Up @@ -208,6 +212,8 @@ def organize_data_files(self, mode='link', autoconvert=None):

data_folder = self.get_data_folder(mode='absolute')

converted_data_files = []

for key, sources in self.data.items():
converted_data_files = []

Expand Down Expand Up @@ -354,6 +360,10 @@ def generate_bids_dataset(cls, csv_file, pathToDir, autoconvert=None):
if not os.path.isdir(pathToDir):
os.makedirs(pathToDir)

#print(df.to_dict('index').values())
for data_kwargs in df.to_dict('index').values():
print(data_kwargs)

for data_kwargs in df.to_dict('index').values():
data_source = data_kwargs.pop('data_source', None)

Expand Down
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