Simpler implementation

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), legacy=legacy)
+    img, pixdims = process_nifti(nib.load(nifti_path))
 
     processed_class_map = process_class_map(class_map)
     video_annotations = []
@@ -513,10 +513,9 @@ 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 RAS orientation (if legacy), then converts to the passed ornt orientation.
+    Function that converts a nifti object to the RAS orientation, then converts to the passed ornt orientation.
     The default ornt is LPI.
 
     Args:
@@ -530,20 +529,8 @@ 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)
-    else:
-        current_ornt = nib.orientations.io_orientation(img.affine)
-        adjusted_ornt = []
-        for idx, (target_axis, target_direction) in enumerate(ornt):
-            _, current_direction = current_ornt[idx]
-            if current_direction == target_direction:
-                adjusted_ornt.append([target_axis, 1])
-            else:
-                adjusted_ornt.append([target_axis, -1])
-        data_array = nib.orientations.apply_orientation(img.get_fdata(), adjusted_ornt)
-
+    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
 

tests/darwin/importer/formats/import_nifti_test.py

@@ -239,12 +239,7 @@ def test_get_new_axial_size_with_isotropic():
     assert new_size == (20, 10)
 
 
-def test_process_nifti_orientation_legacy(team_slug_darwin_json_v2):
-    pass
-    # It's not yet clear how to write this as the desired behaviour isn't known
-
-
-def test_process_nifti_orinetation_no_legacy(team_slug_darwin_json_v2):
+def test_process_nifti_orinetation(team_slug_darwin_json_v2):
     with tempfile.TemporaryDirectory() as tmpdir:
         with ZipFile("tests/data.zip") as zfile:
             zfile.extractall(tmpdir)
@@ -259,12 +254,12 @@ def test_process_nifti_orinetation_no_legacy(team_slug_darwin_json_v2):
             )
             lpi_ornt = [[0.0, -1.0], [1.0, -1.0], [2.0, -1.0]]
             ras_file = nib.load(filepath)
-            las_transformed_file = nib.orientations.apply_orientation(
+            lpi_transformed_file = nib.orientations.apply_orientation(
                 ras_file.get_fdata(), lpi_ornt
             )
-            processed_file, _ = process_nifti(input_data=ras_file, legacy=False)
+            processed_file, _ = process_nifti(input_data=ras_file)
             assert not np.array_equal(processed_file, ras_file._dataobj)
-            assert np.array_equal(processed_file, las_transformed_file)
+            assert np.array_equal(processed_file, lpi_transformed_file)
 
 
 def serialise_annotation_file(