Tests for identifying medical / MONAI slots

darwin/importer/importer.py

@@ -2487,28 +2487,26 @@ def _scale_coordinates_by_pixdims(
     if not remote_files_that_require_pixel_to_mm_transform:
         return maybe_parsed_files
     for file in maybe_parsed_files:
-        if Path(file.full_path) in remote_files_that_require_pixel_to_mm_transform:
+        if file.full_path in remote_files_that_require_pixel_to_mm_transform:
             for annotation in file.annotations:
                 slot_name = annotation.slot_names[0]
                 if (
                     slot_name
                     not in remote_files_that_require_pixel_to_mm_transform[
-                        Path(file.full_path)
+                        file.full_path
                     ]
                 ):
                     continue
                 pixdims = remote_files_that_require_pixel_to_mm_transform[
-                    Path(file.full_path)
+                    file.full_path
                 ][slot_name]
                 if isinstance(annotation, dt.VideoAnnotation):
                     for _, frame_annotation in annotation.frames.items():
                         frame_annotation.scale_coordinates(
-                            float(pixdims["x"]), float(pixdims["y"])
+                            float(pixdims[0]), float(pixdims[1])
                         )
                 elif isinstance(annotation, dt.Annotation):
-                    annotation.scale_coordinates(
-                        float(pixdims["x"]), float(pixdims["y"])
-                    )
+                    annotation.scale_coordinates(float(pixdims[0]), float(pixdims[1]))
     return maybe_parsed_files
 
 

tests/darwin/importer/importer_test.py

@@ -39,6 +39,8 @@
     _get_remote_files_targeted_by_import,
     _get_remote_medical_file_transform_requirements,
     _scale_coordinates_by_pixdims,
+    slot_is_medical,
+    slot_is_handled_by_monai,
 )
 from darwin.exceptions import RequestEntitySizeExceeded
 from darwin.datatypes import (
@@ -4240,15 +4242,15 @@ def test_scale_coordinates_by_pixdims():
     )
 
     remote_files_that_require_pixel_to_mm_transform: Dict[
-        Path, Dict[str, Dict[str, float]]
+        str, Dict[str, List[float]]
     ] = {
-        image_annotations_path: {
-            "slot1": {"x": 2.0, "y": 3.0},
-            "slot2": {"x": 1.5, "y": 2.5},
+        str(image_annotations_path): {
+            "slot1": [2.0, 3.0],
+            "slot2": [1.5, 2.5],
         },
-        video_annotations_path: {
-            "slot1": {"x": 4.0, "y": 6.0},
-            "slot2": {"x": 3.0, "y": 5.0},
+        str(video_annotations_path): {
+            "slot1": [4.0, 6.0],
+            "slot2": [3.0, 5.0],
         },
     }
 
@@ -4297,10 +4299,10 @@ def test_scale_coordinates_by_pixdims_no_scaling_needed():
     )
 
     remote_files_that_require_pixel_to_mm_transform: Dict[
-        Path, Dict[str, Dict[str, float]]
+        str, Dict[str, List[float]]
     ] = {
-        image_annotations_path: {
-            "slot2": {"x": 1.0, "y": 1.0},
+        str(image_annotations_path): {
+            "slot2": [1.0, 1.0],
         },
     }
 
@@ -4315,3 +4317,24 @@ def test_scale_coordinates_by_pixdims_no_scaling_needed():
         "w": 30,
         "h": 40,
     }
+
+
+def test_slot_is_medical():
+    """
+    Test that slot_is_medical returns True if the slot has medical metadata
+    """
+    medical_slot = {"metadata": {"medical": {}}}
+    non_medical_slot = {"metadata": {}}
+    assert slot_is_medical(medical_slot) is True
+    assert slot_is_medical(non_medical_slot) is False
+
+
+def test_slot_is_handled_by_monai():
+    """
+    Test that slot_is_handled_by_monai returns True if the slot has MONAI handler
+
+    """
+    monai_slot = {"metadata": {"medical": {"handler": "MONAI"}}}
+    non_monai_slot = {"metadata": {"medical": {}}}
+    assert slot_is_handled_by_monai(monai_slot) is True
+    assert slot_is_handled_by_monai(non_monai_slot) is False