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Update to generate by for BIDS #870

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Update to generate by for BIDS #870

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5 changes: 3 additions & 2 deletions AFQ/api/group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,8 +185,9 @@ def __init__(self,
pipeline_description = {
"Name": bids_description["Name"],
"BIDSVersion": bids_description["BIDSVersion"],
"PipelineDescription": {"Name": "pyAFQ",
"Version": pyafq_version}}
"GeneratedBy": [{
"Name": "pyAFQ",
"Version": pyafq_version}]}

pl_desc_file = op.join(self.afq_path, 'dataset_description.json')

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10 changes: 6 additions & 4 deletions AFQ/data/fetch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -722,6 +722,8 @@ def to_bids_description(path, fname='dataset_description.json',
BIDSVersion="1.4.0", **kwargs):
"""Dumps a dict into a bids description at the given location"""
kwargs.update({"BIDSVersion": BIDSVersion})
if "GeneratedBy" in kwargs and "DatasetType" not in kwargs:
kwargs["DatasetType"] = "derivative"
desc_file = op.join(path, fname)
with open(desc_file, 'w') as outfile:
json.dump(kwargs, outfile)
Expand Down Expand Up @@ -763,7 +765,7 @@ def organize_cfin_data(path=None):
to_bids_description(
dmriprep_folder,
**{"Name": "CFIN",
"PipelineDescription": {"Name": "dipy"}})
"GeneratedBy": [{"Name": "dipy"}]})


def organize_stanford_data(path=None, clear_previous_afq=False):
Expand Down Expand Up @@ -851,10 +853,10 @@ def organize_stanford_data(path=None, clear_previous_afq=False):
# And descriptions of the pipelines in the derivatives:
to_bids_description(dmriprep_folder,
**{"Name": "Stanford HARDI",
"PipelineDescription": {"Name": "vistasoft"}})
"GeneratedBy": [{"Name": "vistasoft"}]})
to_bids_description(freesurfer_folder,
**{"Name": "Stanford HARDI",
"PipelineDescription": {"Name": "freesurfer"}})
"GeneratedBy": [{"Name": "freesurfer"}]})


fetch_hcp_atlas_16_bundles = _make_reusable_fetcher(
Expand Down Expand Up @@ -1460,6 +1462,6 @@ def fetch_hcp(subjects,
to_bids_description(base_dir,
**{"Name": study,
"Acknowledgements": hcp_acknowledgements,
"PipelineDescription": {'Name': 'dmriprep'}})
"GeneratedBy": [{'Name': 'dmriprep'}]})

return data_files, op.join(my_path, study)
10 changes: 5 additions & 5 deletions AFQ/tests/test_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
afd.to_bids_description(
dmriprep_dir,
**{"Name": "Dummy",
"PipelineDescription": {"Name": "synthetic"}})
"GeneratedBy": [{"Name": "synthetic"}]})

for subject in subjects:
for session in sessions:
Expand All @@ -140,7 +140,7 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
afd.to_bids_description(
dmriprep_dir,
**{"Name": "Dummy",
"PipelineDescription": {"Name": "synthetic"}})
"GeneratedBy": [{"Name": "synthetic"}]})

for d in range(n_subjects):
subject = subjects[d]
Expand All @@ -163,7 +163,7 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
afd.to_bids_description(
dmriprep_dir,
**{"Name": "Dummy",
"PipelineDescription": {"Name": "synthetic"}})
"GeneratedBy": [{"Name": "synthetic"}]})

for subject in subjects:
for modality in ['anat', 'dwi']:
Expand Down Expand Up @@ -205,7 +205,7 @@ def test_AFQ_missing_files():
"otherDeriv"),
**{
"Name": "Missing",
"PipelineDescription": {"Name": "otherDeriv"}})
"GeneratedBy": [{"Name": "otherDeriv"}]})
touch(op.join(subses_folder, "sub-01_ses-01_dwi.nii.gz"))

with pytest.raises(
Expand All @@ -218,7 +218,7 @@ def test_AFQ_missing_files():
afd.to_bids_description(
op.join(bids_path, "missingPipe"), **{
"Name": "Missing",
"PipelineDescription": {"Name": "missingPipe"}})
"GeneratedBy": [{"Name": "missingPipe"}]})
with pytest.raises(
ValueError,
match="No non-json files recognized by pyBIDS"
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2 changes: 1 addition & 1 deletion examples/plot_bids_layout.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@
afd.to_bids_description(
tractography_path,
**{"Name": "my_tractography",
"PipelineDescription": {"Name": "my_tractography"}})
"GeneratedBy": [{"Name": "my_tractography"}]})


###########################################################################
Expand Down