Merge remote-tracking branch 'ancestor-mithril/dev-6'

MIC-DKFZ · Jul 2, 2024 · fee8c2d · fee8c2d
2 parents efab718 + f6e0248
commit fee8c2d
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Showing 4 changed files with 10 additions and 13 deletions.
diff --git a/nnunetv2/imageio/natural_image_reader_writer.py b/nnunetv2/imageio/natural_image_reader_writer.py
@@ -56,13 +56,13 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print('Image files:')
             print(image_fnames)
             raise RuntimeError()
-        return np.vstack(images).astype(np.float32), {'spacing': (999, 1, 1)}
+        return np.vstack(images, dtype=np.float32, casting='unsafe'), {'spacing': (999, 1, 1)}
 
     def read_seg(self, seg_fname: str) -> Tuple[np.ndarray, dict]:
         return self.read_images((seg_fname, ))
 
     def write_seg(self, seg: np.ndarray, output_fname: str, properties: dict) -> None:
-        io.imsave(output_fname, seg[0].astype(np.uint8), check_contrast=False)
+        io.imsave(output_fname, seg[0].astype(np.uint8, copy=False), check_contrast=False)
 
 
 if __name__ == '__main__':

diff --git a/nnunetv2/imageio/nibabel_reader_writer.py b/nnunetv2/imageio/nibabel_reader_writer.py
@@ -77,14 +77,13 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(image_fnames)
             raise RuntimeError()
 
-        stacked_images = np.vstack(images)
         dict = {
             'nibabel_stuff': {
                 'original_affine': original_affines[0],
             },
             'spacing': spacings_for_nnunet[0]
         }
-        return stacked_images.astype(np.float32), dict
+        return np.vstack(images, dtype=np.float32, casting='unsafe'), dict
 
     def read_seg(self, seg_fname: str) -> Tuple[np.ndarray, dict]:
         return self.read_images((seg_fname, ))
@@ -158,22 +157,21 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(image_fnames)
             raise RuntimeError()
 
-        stacked_images = np.vstack(images)
         dict = {
             'nibabel_stuff': {
                 'original_affine': original_affines[0],
                 'reoriented_affine': reoriented_affines[0],
             },
             'spacing': spacings_for_nnunet[0]
         }
-        return stacked_images.astype(np.float32), dict
+        return np.vstack(images, dtype=np.float32, casting='unsafe'), dict
 
     def read_seg(self, seg_fname: str) -> Tuple[np.ndarray, dict]:
         return self.read_images((seg_fname, ))
 
     def write_seg(self, seg: np.ndarray, output_fname: str, properties: dict) -> None:
         # revert transpose
-        seg = seg.transpose((2, 1, 0)).astype(np.uint8)
+        seg = seg.transpose((2, 1, 0)).astype(np.uint8, copy=False)
 
         seg_nib = nibabel.Nifti1Image(seg, affine=properties['nibabel_stuff']['reoriented_affine'])
         seg_nib_reoriented = seg_nib.as_reoriented(io_orientation(properties['nibabel_stuff']['original_affine']))

diff --git a/nnunetv2/imageio/simpleitk_reader_writer.py b/nnunetv2/imageio/simpleitk_reader_writer.py
@@ -98,7 +98,6 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(image_fnames)
             raise RuntimeError()
 
-        stacked_images = np.vstack(images)
         dict = {
             'sitk_stuff': {
                 # this saves the sitk geometry information. This part is NOT used by nnU-Net!
@@ -110,7 +109,7 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             # are returned x,y,z but spacing is returned z,y,x. Duh.
             'spacing': spacings_for_nnunet[0]
         }
-        return stacked_images.astype(np.float32), dict
+        return np.vstack(images, dtype=np.float32, casting='unsafe'), dict
 
     def read_seg(self, seg_fname: str) -> Tuple[np.ndarray, dict]:
         return self.read_images((seg_fname, ))
@@ -122,7 +121,7 @@ def write_seg(self, seg: np.ndarray, output_fname: str, properties: dict) -> Non
         if output_dimension == 2:
             seg = seg[0]
 
-        itk_image = sitk.GetImageFromArray(seg.astype(np.uint8))
+        itk_image = sitk.GetImageFromArray(seg.astype(np.uint8, copy=False))
         itk_image.SetSpacing(properties['sitk_stuff']['spacing'])
         itk_image.SetOrigin(properties['sitk_stuff']['origin'])
         itk_image.SetDirection(properties['sitk_stuff']['direction'])

diff --git a/nnunetv2/imageio/tif_reader_writer.py b/nnunetv2/imageio/tif_reader_writer.py
@@ -66,11 +66,11 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(image_fnames)
             raise RuntimeError()
 
-        return np.vstack(images).astype(np.float32), {'spacing': spacing}
+        return np.vstack(images, dtype=np.float32, casting='unsafe'), {'spacing': spacing}
 
     def write_seg(self, seg: np.ndarray, output_fname: str, properties: dict) -> None:
         # not ideal but I really have no clue how to set spacing/resolution information properly in tif files haha
-        tifffile.imwrite(output_fname, data=seg.astype(np.uint8), compression='zlib')
+        tifffile.imwrite(output_fname, data=seg.astype(np.uint8, copy=False), compression='zlib')
         file = os.path.basename(output_fname)
         out_dir = os.path.dirname(output_fname)
         ending = file.split('.')[-1]
@@ -97,4 +97,4 @@ def read_seg(self, seg_fname: str) -> Tuple[np.ndarray, dict]:
             print(f'WARNING no spacing file found for segmentation {seg_fname}\nAssuming spacing (1, 1, 1).')
             spacing = (1, 1, 1)
 
-        return seg.astype(np.float32), {'spacing': spacing}
+        return seg.astype(np.float32, copy=False), {'spacing': spacing}