Merge pull request #66 from neuropoly/remove-unused-arguments

Remove unused arguments
neuropoly · Oct 2, 2024 · 68bef13 · 68bef13
2 parents 6c98d77 + 80a3e5a
commit 68bef13
Show file tree

Hide file tree

Showing 15 changed files with 30 additions and 381 deletions.
diff --git a/scripts/prepare_datasets.sh b/scripts/prepare_datasets.sh
@@ -75,8 +75,8 @@ for dsp in "$bids"/*; do
     echo "Working on $dsn"
 
     echo "Adding label-canal_seg and label-SC_seg to label-spine_dseg"
-    totalspineseg_map_labels -m 1:2 -s "$bids"/$dsn/derivatives/labels_iso -o "$bids"/$dsn/derivatives/labels_iso  --update-segs-dir "$bids"/$dsn/derivatives/labels_iso --seg-suffix "_label-canal_seg" --output-seg-suffix "_label-spine_dseg" --update-seg-suffix "_label-spine_dseg" -d "sub-" -u "anat" -r -w $JOBS
-    totalspineseg_map_labels -m 1:1 -s "$bids"/$dsn/derivatives/labels_iso -o "$bids"/$dsn/derivatives/labels_iso  --update-segs-dir "$bids"/$dsn/derivatives/labels_iso --seg-suffix "_label-SC_seg" --output-seg-suffix "_label-spine_dseg" --update-seg-suffix "_label-spine_dseg" -d "sub-" -u "anat" -r -w $JOBS
+    totalspineseg_map_labels -m 1:2 -s "$bids"/$dsn/derivatives/labels_iso -o "$bids"/$dsn/derivatives/labels_iso  --update-segs-dir "$bids"/$dsn/derivatives/labels_iso --seg-suffix "_label-canal_seg" --output-seg-suffix "_label-spine_dseg" --update-seg-suffix "_label-spine_dseg" -p "sub-*/anat/" -r -w $JOBS
+    totalspineseg_map_labels -m 1:1 -s "$bids"/$dsn/derivatives/labels_iso -o "$bids"/$dsn/derivatives/labels_iso  --update-segs-dir "$bids"/$dsn/derivatives/labels_iso --seg-suffix "_label-SC_seg" --output-seg-suffix "_label-spine_dseg" --update-seg-suffix "_label-spine_dseg" -p "sub-*/anat/" -r -w $JOBS
 
     echo "Copy images and labels into the nnUNet dataset folder"
     totalspineseg_cpdir "$bids"/$dsn "$nnUNet_raw"/$SRC_DATASET/imagesTr -p "sub-*/anat/sub-*.nii.gz" -f -t sub-:sub-${dsw} .nii.gz:_0000.nii.gz -r -w $JOBS

diff --git a/totalspineseg/utils/augment.py b/totalspineseg/utils/augment.py
@@ -27,7 +27,7 @@ def main():
             Examples:
             augment -i images -s labels -o images -g labels --labels2image --seg-classes 1 2 11-50 63-100
             For BIDS:
-            augment -i . -s derivatives/labels -o . -g derivatives/labels --image-suffix "" --output-image-suffix "" --seg-suffix "_seg" --output-seg-suffix "_seg" -d "sub-" -u "anat" --labels2image --seg-classes 1 2 11-50 63-100
+            augment -i . -s derivatives/labels -o . -g derivatives/labels --image-suffix "" --output-image-suffix "" --seg-suffix "_seg" --output-seg-suffix "_seg" -p "sub-*/anat/" --labels2image --seg-classes 1 2 11-50 63-100
         '''),
         formatter_class=argparse.RawTextHelpFormatter
     )
@@ -47,18 +47,6 @@ def main():
         '--output-segs-dir', '-g', type=Path, required=True,
         help='The folder where output augmented segmentation will be saved with _a1, _a2 etc. suffixes (required).'
     )
-    parser.add_argument(
-        '--subject-dir', '-d', type=str, default=None, nargs='?', const='',
-        help=' '.join(f'''
-            Is every subject has its oen direcrory.
-            If this argument will be provided without value it will look for any directory in the segmentation directory.
-            If value also provided it will be used as a prefix to subject directory, defaults to False (no subjet directory).
-        '''.split()),
-    )
-    parser.add_argument(
-        '--subject-subdir', '-u', type=str, default='',
-        help='Subfolder inside subject folder containing masks, defaults to no subfolder.'
-    )
     parser.add_argument(
         '--prefix', '-p', type=str, default='',
         help='File prefix to work on.'
@@ -112,8 +100,6 @@ def main():
     segs_path = args.segs_dir
     output_images_path = args.output_images_dir
     output_segs_path = args.output_segs_dir
-    subject_dir = args.subject_dir
-    subject_subdir = args.subject_subdir
     prefix = args.prefix
     image_suffix = args.image_suffix
     seg_suffix = args.seg_suffix
@@ -134,8 +120,6 @@ def main():
             segs_path = "{segs_path}"
             output_images_path = "{output_images_path}"
             output_segs_path = "{output_segs_path}"
-            subject_dir = "{subject_dir}"
-            subject_subdir = "{subject_subdir}"
             prefix = "{prefix}"
             image_suffix = "{image_suffix}"
             seg_suffix = "{seg_suffix}"
@@ -154,8 +138,6 @@ def main():
         segs_path=segs_path,
         output_images_path=output_images_path,
         output_segs_path=output_segs_path,
-        subject_dir=subject_dir,
-        subject_subdir=subject_subdir,
         prefix=prefix,
         image_suffix=image_suffix,
         seg_suffix=seg_suffix,
@@ -174,8 +156,6 @@ def augment_mp(
         segs_path,
         output_images_path,
         output_segs_path,
-        subject_dir=None,
-        subject_subdir='',
         prefix='',
         image_suffix='_0000',
         seg_suffix='',
@@ -196,12 +176,7 @@ def augment_mp(
     output_images_path = Path(output_images_path)
     output_segs_path = Path(output_segs_path)
 
-    glob_pattern = ""
-    if subject_dir is not None:
-        glob_pattern += f"{subject_dir}*/"
-    if len(subject_subdir) > 0:
-        glob_pattern += f"{subject_subdir}/"
-    glob_pattern += f'{prefix}*{image_suffix}.nii.gz'
+    glob_pattern = f'{prefix}*{image_suffix}.nii.gz'
 
     # Process the NIfTI image and segmentation files
     image_path_list = list(images_path.glob(glob_pattern))

diff --git a/totalspineseg/utils/average4d.py b/totalspineseg/utils/average4d.py
@@ -21,7 +21,7 @@ def main():
             Examples:
             average4d -i images -o images
             For BIDS:
-            average4d -i . -o . --image-suffix "" --output-image-suffix "" -d "sub-" -u "anat"
+            average4d -i . -o . --image-suffix "" --output-image-suffix "" -p "sub-*/anat/"
         '''),
         formatter_class=argparse.RawTextHelpFormatter
     )
@@ -33,18 +33,6 @@ def main():
         '--output-images-dir', '-o', type=Path, required=True,
         help='The folder where output images will be saved (required).'
     )
-    parser.add_argument(
-        '--subject-dir', '-d', type=str, default=None, nargs='?', const='',
-        help=' '.join(f'''
-            Is every subject has its oen direcrory.
-            If this argument will be provided without value it will look for any directory in the segmentation directory.
-            If value also provided it will be used as a prefix to subject directory, defaults to False (no subjet directory).
-        '''.split())
-    )
-    parser.add_argument(
-        '--subject-subdir', '-u', type=str, default='',
-        help='Subfolder inside subject folder containing masks, defaults to no subfolder.'
-    )
     parser.add_argument(
         '--prefix', '-p', type=str, default='',
         help='File prefix to work on.'
@@ -76,8 +64,6 @@ def main():
     # Get the command-line argument values
     images_path = args.images_dir
     output_images_path = args.output_images_dir
-    subject_dir = args.subject_dir
-    subject_subdir = args.subject_subdir
     prefix = args.prefix
     image_suffix = args.image_suffix
     output_image_suffix = args.output_image_suffix
@@ -91,8 +77,6 @@ def main():
             Running {Path(__file__).stem} with the following params:
             images_path = "{images_path}"
             output_images_path = "{output_images_path}"
-            subject_dir = "{subject_dir}"
-            subject_subdir = "{subject_subdir}"
             prefix = "{prefix}"
             image_suffix = "{image_suffix}"
             output_image_suffix = "{output_image_suffix}"
@@ -104,8 +88,6 @@ def main():
     average4d_mp(
         images_path=images_path,
         output_images_path=output_images_path,
-        subject_dir=subject_dir,
-        subject_subdir=subject_subdir,
         prefix=prefix,
         image_suffix=image_suffix,
         output_image_suffix=output_image_suffix,
@@ -117,8 +99,6 @@ def main():
 def average4d_mp(
         images_path,
         output_images_path,
-        subject_dir=None,
-        subject_subdir='',
         prefix='',
         image_suffix='_0000',
         output_image_suffix='_0000',
@@ -132,12 +112,7 @@ def average4d_mp(
     images_path = Path(images_path)
     output_images_path = Path(output_images_path)
 
-    glob_pattern = ""
-    if subject_dir is not None:
-        glob_pattern += f"{subject_dir}*/"
-    if len(subject_subdir) > 0:
-        glob_pattern += f"{subject_subdir}/"
-    glob_pattern += f'{prefix}*{image_suffix}.nii.gz'
+    glob_pattern = f'{prefix}*{image_suffix}.nii.gz'
 
     # Process the NIfTI image and segmentation files
     image_path_list = list(images_path.glob(glob_pattern))

diff --git a/totalspineseg/utils/crop_image2seg.py b/totalspineseg/utils/crop_image2seg.py
@@ -23,7 +23,7 @@ def main():
             Examples:
             crop_image2seg -i images -s labels -o images -m 50
             For BIDS:
-            crop_image2seg -i . -s derivatives/labels -o . --image-suffix "" --output-image-suffix "" --seg-suffix "_seg" -d "sub-" -u "anat" -m 50
+            crop_image2seg -i . -s derivatives/labels -o . --image-suffix "" --output-image-suffix "" --seg-suffix "_seg" -p "sub-*/anat/" -m 50
         '''),
         formatter_class=argparse.RawTextHelpFormatter
     )
@@ -39,18 +39,6 @@ def main():
         '--output-images-dir', '-o', type=Path, required=True,
         help='The folder where output augmented images will be saved with _a1, _a2 etc. suffixes (required).'
     )
-    parser.add_argument(
-        '--subject-dir', '-d', type=str, default=None, nargs='?', const='',
-        help=' '.join(f'''
-            Is every subject has its oen direcrory.
-            If this argument will be provided without value it will look for any directory in the segmentation directory.
-            If value also provided it will be used as a prefix to subject directory, defaults to False (no subjet directory).
-        '''.split())
-    )
-    parser.add_argument(
-        '--subject-subdir', '-u', type=str, default='',
-        help='Subfolder inside subject folder containing masks, defaults to no subfolder.'
-    )
     parser.add_argument(
         '--prefix', '-p', type=str, default='',
         help='File prefix to work on.'
@@ -91,8 +79,6 @@ def main():
     images_path = args.images_dir
     segs_path = args.segs_dir
     output_images_path = args.output_images_dir
-    subject_dir = args.subject_dir
-    subject_subdir = args.subject_subdir
     prefix = args.prefix
     image_suffix = args.image_suffix
     seg_suffix = args.seg_suffix
@@ -109,8 +95,6 @@ def main():
             images_path = "{images_path}"
             segs_path = "{segs_path}"
             output_images_path = "{output_images_path}"
-            subject_dir = "{subject_dir}"
-            subject_subdir = "{subject_subdir}"
             prefix = "{prefix}"
             image_suffix = "{image_suffix}"
             seg_suffix = "{seg_suffix}"
@@ -125,8 +109,6 @@ def main():
         images_path=images_path,
         segs_path=segs_path,
         output_images_path=output_images_path,
-        subject_dir=subject_dir,
-        subject_subdir=subject_subdir,
         prefix=prefix,
         image_suffix=image_suffix,
         seg_suffix=seg_suffix,
@@ -141,8 +123,6 @@ def crop_image2seg_mp(
         images_path,
         segs_path,
         output_images_path,
-        subject_dir=None,
-        subject_subdir='',
         prefix='',
         image_suffix='_0000',
         seg_suffix='',
@@ -159,12 +139,7 @@ def crop_image2seg_mp(
     segs_path = Path(segs_path)
     output_images_path = Path(output_images_path)
 
-    glob_pattern = ""
-    if subject_dir is not None:
-        glob_pattern += f"{subject_dir}*/"
-    if len(subject_subdir) > 0:
-        glob_pattern += f"{subject_subdir}/"
-    glob_pattern += f'{prefix}*{image_suffix}.nii.gz'
+    glob_pattern = f'{prefix}*{image_suffix}.nii.gz'
 
     # Process the NIfTI image and segmentation files
     image_path_list = list(images_path.glob(glob_pattern))

diff --git a/totalspineseg/utils/extract_alternate.py b/totalspineseg/utils/extract_alternate.py
@@ -25,7 +25,7 @@ def main():
             Examples:
             extract_alternate -s labels -o levels --labels 60-100 -r
             For BIDS:
-            extract_alternate -s derivatives/labels -o derivatives/labels --seg-suffix "_seg" --output-seg-suffix "_levels" -d "sub-" -u "anat" --labels 60-100 -r
+            extract_alternate -s derivatives/labels -o derivatives/labels --seg-suffix "_seg" --output-seg-suffix "_levels" -p "sub-*/anat/" --labels 60-100 -r
         '''),
         formatter_class=argparse.RawTextHelpFormatter
     )
@@ -38,18 +38,6 @@ def main():
         '--output-segs-dir', '-o', type=Path, required=True,
         help='Folder to save output segmentations.'
     )
-    parser.add_argument(
-        '--subject-dir', '-d', type=str, default=None, nargs='?', const='',
-        help=' '.join(f'''
-            Is every subject has its oen direcrory.
-            If this argument will be provided without value it will look for any directory in the segmentation directory.
-            If value also provided it will be used as a prefix to subject directory (for example "sub-"), defaults to False (no subjet directory).
-        '''.split())
-    )
-    parser.add_argument(
-        '--subject-subdir', '-u', type=str, default='',
-        help='Subfolder inside subject folder containing masks (for example "anat"), defaults to no subfolder.'
-    )
     parser.add_argument(
         '--prefix', '-p', type=str, default='',
         help='File prefix to work on.'
@@ -89,8 +77,6 @@ def main():
     # Get arguments
     segs_path = args.segs_dir
     output_segs_path = args.output_segs_dir
-    subject_dir = args.subject_dir
-    subject_subdir = args.subject_subdir
     prefix = args.prefix
     seg_suffix = args.seg_suffix
     output_seg_suffix = args.output_seg_suffix
@@ -106,8 +92,6 @@ def main():
             Running {Path(__file__).stem} with the following params:
             segs_dir = "{segs_path}"
             output_segs_dir = "{output_segs_path}"
-            subject_dir = "{subject_dir}"
-            subject_subdir = "{subject_subdir}"
             prefix = "{prefix}"
             seg_suffix = "{seg_suffix}"
             output_seg_suffix = "{output_seg_suffix}"
@@ -121,8 +105,6 @@ def main():
     extract_alternate_mp(
         segs_path=segs_path,
         output_segs_path=output_segs_path,
-        subject_dir=subject_dir,
-        subject_subdir=subject_subdir,
         prefix=prefix,
         seg_suffix=seg_suffix,
         output_seg_suffix=output_seg_suffix,
@@ -136,8 +118,6 @@ def main():
 def extract_alternate_mp(
         segs_path,
         output_segs_path,
-        subject_dir=None,
-        subject_subdir='',
         prefix='',
         seg_suffix='',
         output_seg_suffix='',
@@ -153,12 +133,7 @@ def extract_alternate_mp(
     segs_path = Path(segs_path)
     output_segs_path = Path(output_segs_path)
 
-    glob_pattern = ""
-    if subject_dir is not None:
-        glob_pattern += f"{subject_dir}*/"
-    if len(subject_subdir) > 0:
-        glob_pattern += f"{subject_subdir}/"
-    glob_pattern += f'{prefix}*{seg_suffix}.nii.gz'
+    glob_pattern = f'{prefix}*{seg_suffix}.nii.gz'
 
     # Process the NIfTI image and segmentation files
     seg_path_list = list(segs_path.glob(glob_pattern))