v2023.1.12 add support for Flywheel DICOM download tarballs in top-level BIDS directory. Rename README.md to README for validation. Add tarballs to bidsignore

Author: jmtyszka

bidskit/__main__.py

@@ -117,7 +117,7 @@ def main():
         'Recon': args.recon
     }
 
-    # Read version from setup.py
+    # Read installed version number
     ver = pkg_resources.get_distribution('bidskit').version
 
     if args.version:

bidskit/bidstree.py

@@ -61,7 +61,7 @@ def __init__(self, dataset_dir, overwrite=False):
         print('Creating file templates required for BIDS compliance')
 
         # Copy BIDS-compliant JSON templates to BIDS directory root
-        self.copy_template('README.md', 'README.md')
+        self.copy_template('README', 'README')
         self.copy_template('CHANGES', 'CHANGES')
         self.copy_template('dataset_description.json', 'dataset_description.json')
         self.copy_template('participants.json', 'participants.json')

bidskit/io.py

@@ -175,11 +175,11 @@ def parse_dcm2niix_fname(fname):
     # Filename format: <PatientName>--<SeriesDescription>--s<SeriesNo>--e<EchoNo>[_ph].<ext>
     info['SubjName'] = vals[0]
     info['SerDesc'] = vals[1]
-    info['SerNo'] = np.int(vals[2].replace('s', ''))
+    info['SerNo'] = int(vals[2].replace('s', ''))
 
     # Check for phase image suffix after echo number (eg "e2_ph")
     bits = vals[3].split('_', 1)
-    info['EchoNo'] = np.int(bits[0].replace('e', ''))
+    info['EchoNo'] = int(bits[0].replace('e', ''))
 
     # Record any suffix after the echo number key (typically "ph" if anything)
     if len(bits) > 1:

bidskit/json.py

@@ -42,7 +42,7 @@ def acqtime_mins(json_file):
     if 'AcquisitionTime' in info:
         t1 = dt.datetime.strptime(info['AcquisitionTime'], '%H:%M:%S.%f0')
         t0 = dt.datetime(1900, 1, 1)
-        t_mins = np.float((t1 - t0).total_seconds() / 60.0)
+        t_mins = float((t1 - t0).total_seconds() / 60.0)
     else:
         print(f'* WARNING: AcquisitionTime not found in {json_file} (deidentified?)')
         print(f'* WARNING: Automatic fieldmap binding will not work correctly')

bidskit/templates/README.MD bidskit/templates/READMEbidskit/templates/README.MD renamed to bidskit/templates/README

@@ -1,4 +1,5 @@
 exclude/
 derivatives/
 work/
-incoming/
+incoming/
+*.tar

bidskit/templates/bidsignore

@@ -42,8 +42,8 @@ folder and build the template BIDS files and folders (Phase 1)
 $ bidskit --flywheel <other command line arguments>
 ```
 3. Edit `code/Protocol_Translator.json` manually or use the `--auto` option to autofill the translator file
-4. Run bidskit again (Phase 2) to complete the curation
+4. Run bidskit again (Phase 2) without the `--flywheel` option to complete the curation
 ```
-$ bidskit --flywheel <other command line arguments>
+$ bidskit <other command line arguments>
 ```
 5. Delete the original Flywheel tarball