fix: Do not convert mask nifti to RAS but to ornt

darwin/importer/formats/nifti.py

@@ -103,7 +103,7 @@ def _parse_nifti(
     is_mpr: bool,
     legacy: bool = False,
 ) -> dt.AnnotationFile:
-    img, pixdims = process_nifti(nib.load(nifti_path))
+    img, pixdims = process_nifti(nib.load(nifti_path), legacy=legacy)
 
     processed_class_map = process_class_map(class_map)
     video_annotations = []
@@ -367,7 +367,7 @@ def nifti_to_video_polygon_annotation(
 def mask_to_polygon(
     mask: np.ndarray, class_name: str, pixdims: List[float], legacy: bool = False
 ) -> Optional[dt.Annotation]:
-    def adjust_for_pixdims(x, y, pixdims, legacy):
+    def adjust_for_pixdims(x, y, pixdims):
         if legacy:
             if pixdims[1] > pixdims[0]:
                 return {"x": y, "y": x * pixdims[1] / pixdims[0]}
@@ -386,7 +386,7 @@ def adjust_for_pixdims(x, y, pixdims, legacy):
             if len(external_path) // 2 <= 2:
                 continue
             path = [
-                adjust_for_pixdims(x, y, pixdims, legacy=legacy)
+                adjust_for_pixdims(x, y, pixdims)
                 for x, y in zip(external_path[0::2], external_path[1::2])
             ]
             paths.append(path)
@@ -406,7 +406,7 @@ def adjust_for_pixdims(x, y, pixdims, legacy):
         polygon = dt.make_polygon(
             class_name,
             point_paths=[
-                adjust_for_pixdims(x, y, pixdims, legacy=legacy)
+                adjust_for_pixdims(x, y, pixdims)
                 for x, y in zip(external_path[0::2], external_path[1::2])
             ],
         )
@@ -513,9 +513,10 @@ def correct_nifti_header_if_necessary(img_nii):
 def process_nifti(
     input_data: nib.nifti1.Nifti1Image,
     ornt: Optional[List[List[float]]] = [[0.0, -1.0], [1.0, -1.0], [2.0, -1.0]],
+    legacy: bool = False,
 ) -> Tuple[np.ndarray, Tuple[float]]:
     """
-    Function that converts a nifti object to the passed ornt orientation.
+    Function that converts a nifti object to RAS orientation (if legacy), then converts to the passed ornt orientation.
     The default ornt is for LPI.
 
     Args:
@@ -529,6 +530,8 @@ def process_nifti(
         pixdims: tuple of nifti header zoom values.
     """
     img = correct_nifti_header_if_necessary(input_data)
+    if legacy:
+        img = nib.funcs.as_closest_canonical(img)
     data_array = nib.orientations.apply_orientation(img.get_fdata(), ornt)
     pixdims = img.header.get_zooms()
     return data_array, pixdims