Merge pull request #73 from BrainLesion/71-enhancement-fails-on-cpu-only-machines-when-not-explicitly-setting-to-cpu

71 enhancement fails on cpu only machines when not explicitly setting to cpu

Author: neuronflow

brainles_preprocessing/brain_extraction/brain_extractor.py

@@ -1,5 +1,6 @@
 # TODO add typing and docs
 from abc import abstractmethod
+from pathlib import Path
 from shutil import copyfile
 
 from auxiliary.nifti.io import read_nifti, write_nifti
@@ -82,13 +83,10 @@ def extract(
         )
 
         hdbet_mask_path = (
-            masked_image_path.parent
-            + "/"
-            + name_extractor(masked_image_path)
-            + "_mask.nii.gz"
+            Path(masked_image_path).parent
+            / f"{name_extractor(masked_image_path)}_mask.nii.gz"
         )
-
-        if hdbet_mask_path != brain_mask_path:
+        if hdbet_mask_path.resolve() != Path(brain_mask_path).resolve():
             copyfile(
                 src=hdbet_mask_path,
                 dst=brain_mask_path,

pyproject.toml

@@ -50,7 +50,7 @@ nibabel = "^3.2.1"
 numpy = "^1.23.0"
 
 # hd-bet reqs
-BrainLes-HD-BET = ">=0.0.5"
+brainles_hd_bet = "*" #= ">=0.0.5"
 
 # utils
 tqdm = "^4.64.1"