qc cov csv for std atlas

scripts/stats_csvs.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+#
+# Stats file conversions for XCP_D when standard atlas used
+
+import argparse
+import bids
+import os
+import pandas
+import sys
+
+parser.add_argument('--xcpd_dir', required=True, 
+    help='Absolute path of xcpd output (must match subject/session/etc of fmriprep)')
+parser.add_argument('--atlas', required=True, 
+    help='Atlas used')
+parser.add_argument('--out_dir', default='/OUTPUTS', 
+    help='Output directory for stats CSVs')
+args = parser.parse_args()
+
+# Process BIDS dir
+bids_xcpd = bids.layout.BIDSLayout(args.xcpd_dir, validate=False)
+
+# Find QC file and convert to CSV
+# Fail if more than one because we can't handle that right now
+qc_tsv = bids_xcpd.get(
+    extension='tsv',
+    desc='linc',
+    suffix='qc',
+    )
+if len(qc_tsv)!=1:
+    raise Exception(f'Found {len(qc_tsv)} qc .tsv instead of 1')
+qc = qc_tsv[0].get_df()
+qc.to_csv(os.path.join(args.out_dir, 'qc.csv'), index=False)
+
+# Find coverage file
+# Base this on QC filename because 'stat' is not a valid standard BIDS
+# entity and I don't know how to use the xcp-d extended entities
+cov_tsv_fname = qc_tsv.path.replace(
+    f'_desc-linc_qc.tsv',
+    f'_seg-{args.atlas}_stat-coverage_bold.tsv'
+)
+cov = pandas.read_csv(cov_tsv_fname, sep='\t')
+cov.transpose().to_csv(
+    os.path.join(args.out_dir, 'coverage.csv'), 
+    index=False, 
+    header=False
+    )