Fix output name for .nii.gz inputs

FNNDSC · Mar 31, 2022 · f392a8a · f392a8a
1 parent b07cf7a
commit f392a8a
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Showing 3 changed files with 12 additions and 1 deletion.
diff --git a/examples/out/sub-feta037_T2w.nii.png → examples/out/sub-feta037_T2w.png b/examples/out/sub-feta037_T2w.nii.png → examples/out/sub-feta037_T2w.png
diff --git a/examples/out/sub-feta037_T2w.nii.txt → examples/out/sub-feta037_T2w.txt b/examples/out/sub-feta037_T2w.nii.txt → examples/out/sub-feta037_T2w.txt
diff --git a/mri_preview.py b/mri_preview.py
@@ -103,10 +103,21 @@ def multi_mapper(inputdir: Path, outputdir: Path, file_extensions: str) -> Itera
  for file_extension in file_extensions.split(','):
  yield from PathMapper(
  inputdir, outputdir,
- glob=f'**/*{file_extension}', suffix='.out', fail_if_empty=False
+ glob=f'**/*{file_extension}',
+ name_mapper=_gz_aware_placeholder_mapper,
+ fail_if_empty=False
  )
 
 
+def _gz_aware_placeholder_mapper(input_file: Path, output_dir: Path) -> Path:
+ filename = str(input_file.name)
+ if filename.endswith('.gz'):
+ filename = filename[:-3] + '_gz'
+ if '.' not in filename:
+ raise ValueError(f'Unrecognized file extension in: {input_file}')
+ return (output_dir / filename).with_suffix('.out')
+
+
 def save_as(img, output: Path, num_voxels: int, total_vol: float, units: str) -> None:
  if output.name.endswith('.txt'):
  with output.open('w') as f: