update to using generate by

yeatmanlab · Nov 11, 2022 · c447c8d · c447c8d
1 parent 14315a3
commit c447c8d
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Showing 4 changed files with 15 additions and 12 deletions.
diff --git a/AFQ/api/group.py b/AFQ/api/group.py
@@ -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')
 

diff --git a/AFQ/data/fetch.py b/AFQ/data/fetch.py
@@ -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)
@@ -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):
@@ -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(
@@ -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)
diff --git a/AFQ/tests/test_api.py b/AFQ/tests/test_api.py
@@ -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:
@@ -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]
@@ -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']:
@@ -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(
@@ -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"

diff --git a/examples/plot_bids_layout.py b/examples/plot_bids_layout.py
@@ -107,7 +107,7 @@
 afd.to_bids_description(
     tractography_path,
     **{"Name": "my_tractography",
-        "PipelineDescription": {"Name": "my_tractography"}})
+        "GeneratedBy": [{"Name": "my_tractography"}]})
 
 
 ###########################################################################