Fix name of overlay generator in warnings

MIC-DKFZ · Apr 11, 2024 · e0d5911 · e0d5911
1 parent 22945aa
commit e0d5911
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/nnunetv2/experiment_planning/verify_dataset_integrity.py b/nnunetv2/experiment_planning/verify_dataset_integrity.py
@@ -93,7 +93,7 @@ def check_cases(image_files: List[str], label_file: str, expected_num_channels:
         if not np.allclose(affine_image, affine_seg):
             print('WARNING: Affine is not the same for image and seg! \nAffine image: %s \nAffine seg: %s\n'
                   'Image files: %s. \nSeg file: %s.\nThis can be a problem but doesn\'t have to be. Please run '
-                  'nnUNet_plot_dataset_pngs to verify if everything is OK!\n'
+                  'nnUNetv2_plot_overlay_pngs to verify if everything is OK!\n'
                   % (affine_image, affine_seg, image_files, label_file))
 
     # sitk checks

diff --git a/nnunetv2/imageio/nibabel_reader_writer.py b/nnunetv2/imageio/nibabel_reader_writer.py
@@ -26,7 +26,7 @@ class NibabelIO(BaseReaderWriter):
     Nibabel loads the images in a different order than sitk. We convert the axes to the sitk order to be
     consistent. This is of course considered properly in segmentation export as well.
 
-    IMPORTANT: Run nnUNet_plot_dataset_pngs to verify that this did not destroy the alignment of data and seg!
+    IMPORTANT: Run nnUNetv2_plot_overlay_pngs to verify that this did not destroy the alignment of data and seg!
     """
     supported_file_endings = [
         '.nii.gz',
@@ -67,7 +67,7 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(original_affines)
             print('Image files:')
             print(image_fnames)
-            print('It is up to you to decide whether that\'s a problem. You should run nnUNet_plot_dataset_pngs to verify '
+            print('It is up to you to decide whether that\'s a problem. You should run nnUNetv2_plot_overlay_pngs to verify '
                   'that segmentations and data overlap.')
         if not self._check_all_same(spacings_for_nnunet):
             print('ERROR! Not all input images have the same spacing_for_nnunet! This might be caused by them not '
@@ -104,7 +104,7 @@ class NibabelIOWithReorient(BaseReaderWriter):
     Nibabel loads the images in a different order than sitk. We convert the axes to the sitk order to be
     consistent. This is of course considered properly in segmentation export as well.
 
-    IMPORTANT: Run nnUNet_plot_dataset_pngs to verify that this did not destroy the alignment of data and seg!
+    IMPORTANT: Run nnUNetv2_plot_overlay_pngs to verify that this did not destroy the alignment of data and seg!
     """
     supported_file_endings = [
         '.nii.gz',
@@ -149,7 +149,7 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(reoriented_affines)
             print('Image files:')
             print(image_fnames)
-            print('It is up to you to decide whether that\'s a problem. You should run nnUNet_plot_dataset_pngs to verify '
+            print('It is up to you to decide whether that\'s a problem. You should run nnUNetv2_plot_overlay_pngs to verify '
                   'that segmentations and data overlap.')
         if not self._check_all_same(spacings_for_nnunet):
             print('ERROR! Not all input images have the same spacing_for_nnunet! This might be caused by them not '

diff --git a/nnunetv2/imageio/simpleitk_reader_writer.py b/nnunetv2/imageio/simpleitk_reader_writer.py
@@ -78,15 +78,15 @@ def read_images(self, image_fnames: Union[List[str], Tuple[str, ...]]) -> Tuple[
             print(origins)
             print('Image files:')
             print(image_fnames)
-            print('It is up to you to decide whether that\'s a problem. You should run nnUNet_plot_dataset_pngs to verify '
+            print('It is up to you to decide whether that\'s a problem. You should run nnUNetv2_plot_overlay_pngs to verify '
                   'that segmentations and data overlap.')
         if not self._check_all_same(directions):
             print('WARNING! Not all input images have the same direction!')
             print('Directions:')
             print(directions)
             print('Image files:')
             print(image_fnames)
-            print('It is up to you to decide whether that\'s a problem. You should run nnUNet_plot_dataset_pngs to verify '
+            print('It is up to you to decide whether that\'s a problem. You should run nnUNetv2_plot_overlay_pngs to verify '
                   'that segmentations and data overlap.')
         if not self._check_all_same(spacings_for_nnunet):
             print('ERROR! Not all input images have the same spacing_for_nnunet! (This should not happen and must be a '