[DAR-2504][External] Generate empty NifTI volumes when no polygons ar…

…e present (#863)

* Update EVENT_merge_to_master.yml with V3 > V7 github-script changes

* temp test

* temp test

* Undo temp changes

* Improved NifTI import dependency failure error message

* Undid GHA workflow changes

* ga .

* WIP

* Correct error message

* Corrected test failure output message

* Output empty file if no annotations & unit tests

.github/workflows/EVENT_merge_to_master.yml

@@ -49,6 +49,4 @@ jobs:
               repo: context.repo.repo,
               sha: context.sha,
               state: 'success'
-            })
-
-
+            })

darwin/exporter/formats/nifti.py

@@ -72,10 +72,17 @@ def export(annotation_files: Iterable[dt.AnnotationFile], output_dir: Path) -> N
             for ann in video_annotation.annotations
             if ann.annotation_class.annotation_type == "polygon"
         ]
+        # Check if there are any rasters in the annotation, these are created with a _m suffix
+        # in addition to those created from polygons.
+        annotation_types = [
+            a.annotation_class.annotation_type for a in video_annotation.annotations
+        ]
+        mask_present = "raster_layer" in annotation_types and "mask" in annotation_types
         output_volumes = build_output_volumes(
             video_annotation,
             class_names_to_export=polygon_class_names,
             from_raster_layer=False,
+            mask_present=mask_present,
         )
         slot_map = {slot.name: slot for slot in video_annotation.slots}
         polygon_annotations = [
@@ -90,13 +97,8 @@ def export(annotation_files: Iterable[dt.AnnotationFile], output_dir: Path) -> N
         write_output_volume_to_disk(
             output_volumes, image_id=image_id, output_dir=output_dir
         )
-        # Check if there are any rasters in the annotation, these are created with a _m suffix
-        # in addition to those created from polygons.
-        annotation_types = [
-            a.annotation_class.annotation_type for a in video_annotation.annotations
-        ]
         # Need to map raster layers to SeriesInstanceUIDs
-        if "raster_layer" in annotation_types and "mask" in annotation_types:
+        if mask_present:
             mask_id_to_classname = {
                 ann.id: ann.annotation_class.name
                 for ann in video_annotation.annotations
@@ -130,6 +132,7 @@ def build_output_volumes(
     video_annotation: dt.AnnotationFile,
     from_raster_layer: bool = False,
     class_names_to_export: List[str] = None,
+    mask_present: Optional[bool] = False,
 ) -> Dict:
     """
     This is a function to create the output volumes based on the whole annotation file
@@ -142,6 +145,8 @@ def build_output_volumes(
         Whether the output volumes are being built from raster layers or not
     class_names_to_export : List[str]
         The list of class names to export
+    mask_present: bool
+        If mask annotations are present in the annotation
     Returns
     -------
     output_volumes: Dict
@@ -160,6 +165,10 @@ def build_output_volumes(
         )
         # Builds output volumes per class
         volume_dims, pixdims, affine, original_affine = process_metadata(slot.metadata)
+        if not mask_present and not class_names_to_export:
+            class_names_to_export = [
+                ""
+            ]  # If there are no annotations to export, we still need to create an empty volume
         output_volumes[series_instance_uid] = {
             class_name: Volume(
                 pixel_array=np.zeros(volume_dims),

darwin/importer/formats/nifti.py

@@ -16,8 +16,8 @@
     from scipy.ndimage import zoom
 except ImportError:
     import_fail_string = """
-    You must install darwin-py with pip install nibabel connected-components-3d
-    in order to import with using nifti format
+    You must install darwin-py with pip install darwin-py\[medical]
+    in order to import using nifti format
     """
     console.print(import_fail_string)
     sys.exit(1)

tests/darwin/exporter/formats/export_nifti_test.py

@@ -102,7 +102,7 @@ def test_export_calls_populate_output_volumes_from_polygons(
                 / team_slug_darwin_json_v2
                 / "nifti/releases/latest/annotations"
             )
-            video_annotation_filepaths = [annotations_dir / "polygon_no_mask.json"]
+            video_annotation_filepaths = [annotations_dir / "polygon_only.json"]
             video_annotations = list(
                 darwin_to_dt_gen(video_annotation_filepaths, False)
             )
@@ -124,9 +124,48 @@ def test_export_calls_populate_output_volumes_from_raster_layer(
                 / team_slug_darwin_json_v2
                 / "nifti/releases/latest/annotations"
             )
-            video_annotation_filepaths = [annotations_dir / "mask_no_polygon.json"]
+            video_annotation_filepaths = [annotations_dir / "mask_only.json"]
             video_annotations = list(
                 darwin_to_dt_gen(video_annotation_filepaths, False)
             )
             nifti.export(video_annotations, output_dir=Path(tmpdir))
             mock.assert_called()
+
+
+def test_export_creates_file_for_polygons_and_masks(
+    team_slug_darwin_json_v2: str,
+):
+    with tempfile.TemporaryDirectory() as tmpdir:
+        with ZipFile("tests/data.zip") as zfile:
+            zfile.extractall(tmpdir)
+            annotations_dir = (
+                Path(tmpdir)
+                / team_slug_darwin_json_v2
+                / "nifti/releases/latest/annotations"
+            )
+            video_annotation_files = {
+                "mask_only.json": ["hippocampus_multislot_3_test_hippo_LOIN_m.nii.gz"],
+                "polygon_only.json": [
+                    "hippocampus_multislot_3_test_hippo_create_class_1.nii.gz"
+                ],
+                "polygon_and_mask.json": [
+                    "hippocampus_multislot_3_test_hippo_create_class_1.nii.gz",
+                    "hippocampus_multislot_3_test_hippo_LOIN_m.nii.gz",
+                ],
+                "empty.json": ["hippocampus_multislot_3_test_hippo_.nii.gz"],
+            }
+            for video_annotation_file in video_annotation_files:
+                video_annotation_filepaths = [annotations_dir / video_annotation_file]
+                video_annotations = list(
+                    darwin_to_dt_gen(video_annotation_filepaths, False)
+                )
+                nifti.export(video_annotations, output_dir=Path(tmpdir))
+                for output_file in video_annotation_files[video_annotation_file]:
+                    assert (
+                        Path(tmpdir) / output_file
+                    ).exists(), (
+                        f"Expected file {output_file} does not exist in {tmpdir}"
+                    )
+                # Empty the directory for the next test
+                for output_file in video_annotation_files[video_annotation_file]:
+                    (Path(tmpdir) / output_file).unlink()