[DAR-4140][External] Fixed NifTI import orientation (#953)

* Fixed NifTI import orientation

* Simpler implementation

* Update tests/darwin/importer/formats/import_nifti_test.py

Co-authored-by: dorfmanrobert <[email protected]>

---------

Co-authored-by: dorfmanrobert <[email protected]>

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 = []
@@ -513,11 +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 RAS orientation (if legacy), then converts to the passed ornt orientation.
-    The default ornt is for LPI.
+    Function that converts a nifti object to the RAS orientation, then converts to the passed ornt orientation.
+    The default ornt is LPI.
 
     Args:
         input_data: nibabel nifti object.
@@ -530,8 +529,7 @@ 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)
+    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

@@ -9,6 +9,7 @@
 import numpy as np
 import pytest
 from scipy import ndimage
+import nibabel as nib
 
 from darwin.datatypes import (
     Annotation,
@@ -17,7 +18,7 @@
     SubAnnotation,
     VideoAnnotation,
 )
-from darwin.importer.formats.nifti import get_new_axial_size, parse_path
+from darwin.importer.formats.nifti import get_new_axial_size, parse_path, process_nifti
 from tests.fixtures import *
 from darwin.utils.utils import parse_darwin_json
 
@@ -239,6 +240,70 @@ def test_get_new_axial_size_with_isotropic():
     assert new_size == (20, 10)
 
 
+def test_process_nifti_orientation_ras_to_lpi(team_slug_darwin_json_v2):
+    """
+    Test that an input NifTI annotation file in the RAS orientation is correctly
+    transformed to the LPI orientation.
+
+    Do this by emulating the `process_nifti` function, which:
+    - 1: Transforms the input file into the RAS orientation
+    - 2: Transforms the transformed RAS file into the LPI orientation
+    """
+    with tempfile.TemporaryDirectory() as tmpdir:
+        with ZipFile("tests/data.zip") as zfile:
+            zfile.extractall(tmpdir)
+            filepath = (
+                Path(tmpdir)
+                / team_slug_darwin_json_v2
+                / "nifti"
+                / "releases"
+                / "latest"
+                / "annotations"
+                / "vol0_brain.nii.gz"
+            )
+            lpi_ornt = [[0.0, -1.0], [1.0, -1.0], [2.0, -1.0]]
+            ras_file = nib.load(filepath)
+            ras_transformed_file = nib.funcs.as_closest_canonical(ras_file)
+            lpi_transformed_file = nib.orientations.apply_orientation(
+                ras_transformed_file.get_fdata(), lpi_ornt
+            )
+            processed_file, _ = process_nifti(input_data=ras_file)
+            assert not np.array_equal(processed_file, ras_file._dataobj)
+            assert np.array_equal(processed_file, lpi_transformed_file)
+
+
+def test_process_nifti_orientation_las_to_lpi(team_slug_darwin_json_v2):
+    """
+    Test that an input NifTI annotation file in the LAS orientation is correctly
+    transformed to the LPI orientation.
+
+    Do this by emulating the `process_nifti` function, which:
+    - 1: Transforms the input file into the RAS orientation
+    - 2: Transforms the transformed RAS file into the LPI orientation
+    """
+    with tempfile.TemporaryDirectory() as tmpdir:
+        with ZipFile("tests/data.zip") as zfile:
+            zfile.extractall(tmpdir)
+            filepath = (
+                Path(tmpdir)
+                / team_slug_darwin_json_v2
+                / "nifti"
+                / "releases"
+                / "latest"
+                / "annotations"
+                / "BRAINIX_NIFTI_ROI.nii.gz"
+            )
+            lpi_ornt = [[0.0, -1.0], [1.0, -1.0], [2.0, -1.0]]
+            las_file = nib.load(filepath)
+            ras_transformed_file = nib.funcs.as_closest_canonical(las_file)
+            lpi_transformed_file = nib.orientations.apply_orientation(
+                ras_transformed_file.get_fdata(), lpi_ornt
+            )
+            processed_file, _ = process_nifti(input_data=las_file)
+            assert not np.array_equal(processed_file, las_file._dataobj)
+            assert np.array_equal(processed_file, lpi_transformed_file)
+
+
 def serialise_annotation_file(
     annotation_file: AnnotationFile, as_dict
 ) -> Union[str, dict]: