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Add .h5 in extension using the 'same' reference in scil_tractogram_commit #1277

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Add .h5 in extension using the 'same' reference in scil_tractogram_commit #1277

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5 changes: 3 additions & 2 deletions src/scilpy/cli/scil_tractogram_commit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -238,8 +238,9 @@ def _save_results(args, tmp_dir, ext, in_hdf5_file, offsets_list, sub_dir,

# Loading the tractogram (we never did yet! Only sent the filename to
# commit). Reminder. If input was a hdf5, we have changed
# args.in_tractogram to our tmp_tractogram saved in tmp_dir.
if ext == '.trk' and args.reference is None:
# args.in_tractogram to our tmp_tractogram saved in tmp_dir. However,
# ext is still .h5 so we need to set the reference accordingly.
if ext in ['.trk', '.h5'] and args.reference is None:
args.reference = 'same'
logging.debug('Loading tractogram from {} with reference {}.'
.format(args.in_tractogram, args.reference))
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