Implemented requested changes

CerebNet/apply_warp.py

@@ -35,19 +35,14 @@ def save_nii_image(img_data, save_path, header, affine):
         The header information for the NIfTI file.
     affine : ndarray
         The affine matrix for the NIfTI file.
-
-    Returns
-    -------
-    None
-        This function returns nothing.
     """
 
     img_out = nib.Nifti1Image(img_data, header=header, affine=affine)
     print(f"Saving {save_path}")
     nib.save(img_out, save_path)
 
 
-def store_warped_data(img_path, lbl_path, warp_path, result_path, patch_size):
+def main(img_path, lbl_path, warp_path, result_path, patch_size):
 
     """
     Load, warp, crop, and save both an image and its corresponding label based on a given warp field.
@@ -64,11 +59,6 @@ def store_warped_data(img_path, lbl_path, warp_path, result_path, patch_size):
         Directory path where the warped and cropped images will be saved.
     patch_size : tuple of int
         The dimensions (height, width, depth) cropped images after warping.
-
-    Returns
-    -------
-    None
-        This function returns nothing.
     """
 
     img, img_file = utils.load_reorient_rescale_image(img_path)
@@ -120,7 +110,7 @@ def store_warped_data(img_path, lbl_path, warp_path, result_path, patch_size):
 
     args = parser.parse_args()
     warp_path = join(args.result_path, args.warp_filename)
-    store_warped_data(args.img_path,
+    main(args.img_path,
                       args.lbl_path,
                       warp_path=warp_path,
                       result_path=args.result_path,

CerebNet/run_prediction.py

@@ -104,6 +104,7 @@ def setup_options():
 def main(args):
     """
     Main function to run the inference based on the given command line arguments.
+    This implementation is inspired by methods described in CerebNet for cerebellum sub-segmentation.
 
     Parameters
     ----------
@@ -112,8 +113,16 @@ def main(args):
 
     Returns
     -------
-    str or None
-        A message indicating the failure reason in case of an exception, otherwise `None`.
+    int 
+        Returns 0 upon successful execution to indicate success.
+    str
+        A message indicating the failure reason in case of an exception.
+
+    References
+    ----------
+    Faber J, Kuegler D, Bahrami E, et al. CerebNet: A fast and reliable deep-learning 
+    pipeline for detailed cerebellum sub-segmentation. NeuroImage 264 (2022), 119703. 
+    https://doi.org/10.1016/j.neuroimage.2022.119703
     """
     cfg = get_config(args)
     cfg.TEST.ENABLE = True

doc/conf.py

@@ -21,12 +21,6 @@
 import os
 sys.path.append(os.path.dirname(__file__) + '/..') 
 sys.path.append(os.path.dirname(__file__) + '/../recon_surf') 
-# sys.path.append(os.path.dirname(__file__) + '/../CerebNet') 
-
-# sys.path.insert(0, '..') #after
-
-# autodoc_mock_imports = ["torch", "yacs"]
-
 
 project = 'FastSurfer'
 copyright = '2023, Martin Reuter'

recon_surf/N4_bias_correct.py

@@ -15,17 +15,21 @@
 
 
 # IMPORTS
-import image_io as iio
+# Group 1: Python native modules
 import argparse
-import sys
 import logging
-import SimpleITK as sitk
-import numpy as np
-
+import sys
 from pathlib import Path
 from typing import Optional, cast, Tuple
+
+# Group 2: External modules
+import SimpleITK as sitk
+import numpy as np
 from numpy import typing as npt
 
+# Group 3: Internal modules
+import image_io as iio
+
 HELPTEXT = """
 
 Script to call SITK N4 Bias Correction
@@ -104,7 +108,7 @@ def options_parse():
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = argparse.ArgumentParser(
         description=HELPTEXT,
@@ -277,7 +281,8 @@ def normalize_wm_aseg(
         target_bg: float = 3.
 ) -> sitk.Image:
     """
-    Normalize WM image [MISSING].
+    Normalize WM image so the white matter has a mean 
+    intensity of target_wm and the backgroud has intensity target_bg.
 
     Parameters
     ----------
@@ -323,8 +328,8 @@ def normalize_wm_aseg(
 def normalize_img(
         itk_image: sitk.Image,
         itk_mask: Optional[sitk.Image],
-        source_intensity: Tuple[float, float],
-        target_intensity: Tuple[float, float]
+        source_intensity: tuple[float, float],
+        target_intensity: tuple[float, float]
 ) -> sitk.Image:
     """
     Normalize image by source and target intensity values.
@@ -334,10 +339,11 @@ def normalize_img(
     itk_image : sitk.Image
         Input image to be normalized.
     itk_mask : sitk.Image | None
-        [MISSING].
-    source_intensity : Tuple[float, float]
+        Brain mask, voxels inside the mask are guaranteed to be > 0,
+        None is optional.
+    source_intensity : tuple[float, float]
         Source intensity range.
-    target_intensity : Tuple[float, float]
+    target_intensity : tuple[float, float]
         Target intensity range.
 
     Returns
@@ -474,12 +480,12 @@ def get_image_mean(image: sitk.Image, mask: Optional[sitk.Image] = None) -> floa
 
 def get_brain_centroid(itk_mask: sitk.Image) -> np.ndarray:
     """
-    Get the brain centroid from the itk_mask
+    Get the brain centroid from a binary image.
 
     Parameters
     ----------
     itk_mask : sitk.Image
-        [MISSING].
+        Binary image to compute the centroid of its labeled region.
 
     Returns
     -------

recon_surf/fs_balabels.py

@@ -75,12 +75,12 @@
 
 def options_parse():
     """
-    Command line option parser.
+    Create a command line interface and return command line options.
 
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = optparse.OptionParser(
         version="$Id:fs_balabels.py,v 1.0 2022/08/24 21:22:08 mreuter Exp $",

recon_surf/lta.py

@@ -29,7 +29,7 @@ def writeLTA(
         dst_header: Dict
 ) -> None:
     """
-    Write linear transform array info to a .lta file.
+    An .lta file.
 
     Parameters
     ----------

recon_surf/map_surf_label.py

@@ -60,12 +60,12 @@
 
 def options_parse():
     """
-    Command line option parser.
+    Create a command line interface and return command line options.
 
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = optparse.OptionParser(
         version="$Id:map_surf_label.py,v 1.0 2022/08/24 21:22:08 mreuter Exp $",

recon_surf/paint_cc_into_pred.py

@@ -14,11 +14,11 @@
 
 
 # IMPORTS
-import numpy as np
-import nibabel as nib
+
 import sys
 import argparse
-
+import numpy as np
+import nibabel as nib
 from numpy import typing as npt
 
 HELPTEXT = """
@@ -44,12 +44,12 @@
 
 def argument_parse():
     """
-    Command line option parser.
+    Create a command line interface and return command line options.
 
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = argparse.ArgumentParser(usage=HELPTEXT)
     parser.add_argument(
@@ -87,14 +87,14 @@ def paint_in_cc(pred: npt.ArrayLike, aseg_cc: npt.ArrayLike) -> npt.ArrayLike:
 
     Parameters
     ----------
-    pred : npt.ArrayLike
+    asegdt : npt.ArrayLike
         Deep-learning prediction.
     aseg_cc : npt.ArrayLike
         Aseg segmentation with CC.
 
     Returns
     -------
-    pred
+    asegdt
         Prediction with added CC.
     """
     cc_mask = (aseg_cc >= 251) & (aseg_cc <= 255)
@@ -116,3 +116,6 @@ def paint_in_cc(pred: npt.ArrayLike, aseg_cc: npt.ArrayLike) -> npt.ArrayLike:
     pred_with_cc_fin.to_filename(options.output)
 
     sys.exit(0)
+
+
+# TODO: Rename the file (paint_cc_into_asegdkt or similar) and functions.

recon_surf/rewrite_mc_surface.py

@@ -22,12 +22,12 @@
 
 def options_parse():
     """
-    Command line option parser.
+    Create a command line interface and return command line options.
 
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = optparse.OptionParser(
         version="$Id: rewrite_mc_surface,v 1.1 2020/06/23 15:42:08 henschell $",

recon_surf/rotate_sphere.py

@@ -18,11 +18,12 @@
 
 # IMPORTS
 import optparse
-import numpy as np
 import sys
+
+import numpy as np
 import nibabel.freesurfer.io as fs
-import align_points as align
 
+import align_points as align
 from numpy import typing as npt
 
 
@@ -68,12 +69,12 @@
 
 def options_parse():
     """
-    Command line option parser.
+    Create a command line interface and return command line options.
 
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = optparse.OptionParser(
         version="$Id: rotate_sphere.py,v 1.0 2022/03/18 21:22:08 mreuter Exp $",
@@ -125,7 +126,7 @@ def align_aparc_centroids(
 
     Returns
     -------
-    R
+    R : npt.NDArray[float]
         Rotation Matrix.
     """
     #nferiorparietal, inferiortemporal, lateraloccipital, postcentral, posteriorsingulate

recon_surf/sample_parc.py

@@ -19,11 +19,13 @@
 # IMPORTS
 import optparse
 import sys
+
 import numpy as np
 import nibabel.freesurfer.io as fs
 import nibabel as nib
 from scipy import sparse
 from scipy.sparse.csgraph import connected_components
+
 from lapy import TriaMesh
 from smooth_aparc import smooth_aparc
 from numpy import typing as npt
@@ -65,12 +67,12 @@
 
 def options_parse():
     """
-    Command line option parser.
+    Create a command line interface and return command line options.
 
     Returns
     -------
     options
-        Object holding options.
+        Namespace object holding options.
     """
     parser = optparse.OptionParser(
         version="$Id: smooth_aparc,v 1.0 2018/06/24 11:34:08 mreuter Exp $",
@@ -102,7 +104,7 @@ def options_parse():
 
 def construct_adj_cluster(tria, annot):
     """
-    Adjacency matrix of edges from same annotation label only.
+    Compute adjacency matrix of edges from same annotation label only.
 
     Operates only on triangles and removes edges that cross annotation
     label boundaries.
@@ -268,7 +270,7 @@ def sample_img(surf, img, cortex=None, projmm=0.0, radius=None):
         Filename of cortex label or np.array with cortex indices.
     projmm : float
         Sample projmm mm along the surface vertex normals (default=0).
-    radius : float [optional] | None
+    radius : float, optional 
         If given and if the sample is equal to zero, then consider
         all voxels inside this radius to find a non-zero value.
 
@@ -389,7 +391,7 @@ def sample_parc (surf, seg, imglut, surflut, outaparc, cortex=None, projmm=0.0,
         Filename of cortex label or np.ndarray with cortex indices.
     projmm : float
         Sample projmm mm along the surface vertex normals (default=0).
-    radius : float [optional] | None
+    radius : float, optional
         If given and if the sample is equal to zero, then consider
         all voxels inside this radius to find a non-zero value.
     """