From 357f0031225602d22c372dffec7c0245e84550e2 Mon Sep 17 00:00:00 2001
From: Mike Tyszka <jmt@caltech.edu>
Date: Thu, 12 Jan 2023 14:55:59 -0800
Subject: [PATCH] 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

---
 bidskit/__main__.py                     | 2 +-
 bidskit/bidstree.py                     | 2 +-
 bidskit/io.py                           | 4 ++--
 bidskit/json.py                         | 2 +-
 bidskit/templates/{README.MD => README} | 0
 bidskit/templates/bidsignore            | 3 ++-
 docs/Flywheel.md                        | 4 ++--
 7 files changed, 9 insertions(+), 8 deletions(-)
 rename bidskit/templates/{README.MD => README} (100%)

diff --git a/bidskit/__main__.py b/bidskit/__main__.py
index fd7fbac..0e7ed1e 100755
--- a/bidskit/__main__.py
+++ b/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:
diff --git a/bidskit/bidstree.py b/bidskit/bidstree.py
index 1e4ddfd..4e41ec4 100644
--- a/bidskit/bidstree.py
+++ b/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')
diff --git a/bidskit/io.py b/bidskit/io.py
index 79f073c..ebc5892 100644
--- a/bidskit/io.py
+++ b/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:
diff --git a/bidskit/json.py b/bidskit/json.py
index da13aac..be2a438 100644
--- a/bidskit/json.py
+++ b/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')
diff --git a/bidskit/templates/README.MD b/bidskit/templates/README
similarity index 100%
rename from bidskit/templates/README.MD
rename to bidskit/templates/README
diff --git a/bidskit/templates/bidsignore b/bidskit/templates/bidsignore
index 8dfdfec..cff3db9 100644
--- a/bidskit/templates/bidsignore
+++ b/bidskit/templates/bidsignore
@@ -1,4 +1,5 @@
 exclude/
 derivatives/
 work/
-incoming/
\ No newline at end of file
+incoming/
+*.tar
\ No newline at end of file
diff --git a/docs/Flywheel.md b/docs/Flywheel.md
index 77f6642..0520841 100644
--- a/docs/Flywheel.md
+++ b/docs/Flywheel.md
@@ -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
\ No newline at end of file