Merge pull request #1019 from yeatmanlab/pierre-nedelec/issue1018

add "GeneratedBy"s in `dataset_description.json` for BIDS 1.4+ compliance
yeatmanlab · Sep 13, 2023 · 75d360f · 75d360f
2 parents e9dfc21 + 921fdbd
commit 75d360f
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Showing 4 changed files with 27 additions and 13 deletions.
diff --git a/AFQ/api/group.py b/AFQ/api/group.py
@@ -187,7 +187,9 @@ def __init__(self,
             "Name": bids_description["Name"],
             "BIDSVersion": bids_description["BIDSVersion"],
             "PipelineDescription": {"Name": "pyAFQ",
-                                    "Version": pyafq_version}}
+                                    "Version": pyafq_version},
+            "GeneratedBy": [{"Name": op.basename(self.afq_path),
+                             "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
@@ -1020,7 +1020,8 @@ def organize_cfin_data(path=None):
     to_bids_description(
         dmriprep_folder,
         **{"Name": "CFIN",
-           "PipelineDescription": {"Name": "dipy"}})
+           "PipelineDescription": {"Name": "dipy"},
+           "GeneratedBy": [{"Name": "dipy"}]})
 
 
 def organize_stanford_data(path=None, clear_previous_afq=None):
@@ -1120,10 +1121,12 @@ def organize_stanford_data(path=None, clear_previous_afq=None):
     # And descriptions of the pipelines in the derivatives:
     to_bids_description(dmriprep_folder,
                         **{"Name": "Stanford HARDI",
-                           "PipelineDescription": {"Name": "vistasoft"}})
+                           "PipelineDescription": {"Name": "vistasoft"},
+                           "GeneratedBy": [{"Name": "vistasoft"}]})
     to_bids_description(freesurfer_folder,
                         **{"Name": "Stanford HARDI",
-                           "PipelineDescription": {"Name": "freesurfer"}})
+                           "PipelineDescription": {"Name": "freesurfer"},
+                           "GeneratedBy": [{"Name": "freesurfer"}]})
 
 
 fetch_stanford_hardi_lv1 = _make_reusable_fetcher(
@@ -1750,7 +1753,8 @@ def fetch_hcp(subjects,
     to_bids_description(base_dir,
                         **{"Name": study,
                            "Acknowledgements": hcp_acknowledgements,
-                           "PipelineDescription": {'Name': 'dmriprep'}})
+                           "PipelineDescription": {'Name': 'dmriprep'},
+                           "GeneratedBy": [{'Name': 'dmriprep'}]})
 
     return data_files, op.join(my_path, study)
 
@@ -1844,7 +1848,8 @@ def fetch_hbn_preproc(subjects, path=None):
     to_bids_description(base_dir,
                         **{"Name": "HBN",
                            "Acknowledgements": hbn_acknowledgements,
-                           "PipelineDescription": {'Name': 'qsiprep'}})
+                           "PipelineDescription": {'Name': 'qsiprep'},
+                           "GeneratedBy": [{'Name': 'qsiprep'}]})
 
     return data_files, op.join(my_path, "HBN")
 
@@ -1941,6 +1946,7 @@ def fetch_hbn_afq(subjects, path=None):
     # Create the BIDS derivatives description file text
     to_bids_description(base_dir,
                         **{"Name": "HBN",
-                           "PipelineDescription": {'Name': 'afq'}})
+                           "PipelineDescription": {'Name': 'afq'},
+                           "GeneratedBy": [{'Name': 'afq'}]})
 
     return data_files, op.join(my_path, "HBN")
diff --git a/AFQ/tests/test_api.py b/AFQ/tests/test_api.py
@@ -114,7 +114,8 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
             afd.to_bids_description(
                 dmriprep_dir,
                 **{"Name": "Dummy",
-                   "PipelineDescription": {"Name": "synthetic"}})
+                   "PipelineDescription": {"Name": "synthetic"},
+                   "GeneratedBy": [{"Name": "synthetic"}]})
 
             for subject in subjects:
                 for session in sessions:
@@ -140,7 +141,8 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
             afd.to_bids_description(
                 dmriprep_dir,
                 **{"Name": "Dummy",
-                   "PipelineDescription": {"Name": "synthetic"}})
+                   "PipelineDescription": {"Name": "synthetic"},
+                   "GeneratedBy": [{"Name": "synthetic"}]})
 
             for d in range(n_subjects):
                 subject = subjects[d]
@@ -163,7 +165,8 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
         afd.to_bids_description(
             dmriprep_dir,
             **{"Name": "Dummy",
-               "PipelineDescription": {"Name": "synthetic"}})
+               "PipelineDescription": {"Name": "synthetic"},
+               "GeneratedBy": [{"Name": "synthetic"}]})
 
         for subject in subjects:
             for modality in ['anat', 'dwi']:
@@ -205,7 +208,8 @@ def test_AFQ_missing_files():
             "otherDeriv"),
         **{
             "Name": "Missing",
-            "PipelineDescription": {"Name": "otherDeriv"}})
+            "PipelineDescription": {"Name": "otherDeriv"},
+            "GeneratedBy": [{"Name": "otherDeriv"}]})
     touch(op.join(subses_folder, "sub-01_ses-01_dwi.nii.gz"))
 
     with pytest.raises(
@@ -218,7 +222,8 @@ def test_AFQ_missing_files():
     afd.to_bids_description(
         op.join(bids_path, "missingPipe"), **{
             "Name": "Missing",
-            "PipelineDescription": {"Name": "missingPipe"}})
+            "PipelineDescription": {"Name": "missingPipe"},
+            "GeneratedBy": [{"Name": "missingPipe"}]})
     with pytest.raises(
             ValueError,
             match="No non-json files recognized by pyBIDS"

diff --git a/examples/tutorial_examples/plot_bids_layout.py b/examples/tutorial_examples/plot_bids_layout.py
@@ -107,7 +107,8 @@
 afd.to_bids_description(
     tractography_path,
     **{"Name": "my_tractography",
-        "PipelineDescription": {"Name": "my_tractography"}})
+       "PipelineDescription": {"Name": "my_tractography"},
+       "GeneratedBy": [{"Name": "my_tractography"}]})
 
 
 ###########################################################################