debugging

SPIDER.py

@@ -66,7 +66,8 @@ def subset_file_list(all_files: List[str], subset_ids: Set[int]):
 
 def standardize_3D_image(
     image: np.ndarray,
-    resize_shape: Tuple[int, int, int]
+    resize_shape: Tuple[int, int, int],
+    nearest_neighbor_interpolation: bool = False,
 ) -> np.ndarray:
     """Aligns dimensions of image to be (height, width, channels); resizes
     images to values specified in resize_shape; and rescales pixel values
@@ -75,12 +76,14 @@ def standardize_3D_image(
     if image.shape[0] < image.shape[2]:
         image = np.transpose(image, axes=[1, 2, 0])
     # Resize image
-    image = skimage.transform.resize(image, resize_shape)
+    order = 0 if nearest_neighbor_interpolation else 1
+    image = skimage.transform.resize(image, resize_shape, order=order)
     # Rescale to UInt8 type (required for PyArrow and PIL)
     image = skimage.img_as_ubyte(image)
     return image
 
 
+
 # Define constants
 MIN_IVD = 0
 MAX_IVD = 9
@@ -494,6 +497,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             image_array_standardized = standardize_3D_image(
                 image_array_original,
                 resize_shape,
+                nearest_neighbor_interpolation=False,
             )
 
             # Load .mha mask file
@@ -511,6 +515,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             mask_array_standardized = standardize_3D_image(
                 mask_array_standardized,
                 resize_shape,
+                nearest_neighbor_interpolation=True,
             )
 
             # Extract overview data corresponding to image