Metadata fixes (#170)

* Fix use of ZOffsetInSlideCoordinateSystem * Fix skip serialization of empty PrimaryAnatomicStructureSequence * Fix skip serialization of empty ContainerComponentSequence * Fix missing WholeSlideMicroscopyImageFrameTypeSequence for some image types * Fix skip setting SpacingBetweenSlices if no focal planes * Use defined slice_thickness * Test for serializing full json metadata * Update version
imi-bigpicture · Oct 28, 2024 · 08045d4 · 08045d4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.21.3] - 2024-10-28
+
+### Fixed
+
+- Missing `WholeSlideMicroscopyImageFrameTypeSequence` in produced DICOM dataset for some image types.
+- Do not insert empty `ContainerComponentSequence` and `PrimaryAnatomicStructureSequence` into produced DICOM dataset.
+- Only insert `SpacingBetweenSlices` into produced DICOM dataset if multiple focal planes.
+- Prefer use of `ZOffsetInSlideCoordinateSystem` in main DICOM dataset to attribute in `SharedFunctionalGroupsSequence`/`PlanePositionSlideSequence`.
+
 ## [0.21.2] - 2024-10-21
 
 ### Fixed
@@ -405,7 +414,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Initial release of wsidicom
 
-[Unreleased]: https://github.com/imi-bigpicture/wsidicom/compare/0.21.2..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/wsidicom/compare/v0.21.3..HEAD
+[0.21.3]: https://github.com/imi-bigpicture/wsidicom/compare/v0.21.2..v0.21.3
 [0.21.2]: https://github.com/imi-bigpicture/wsidicom/compare/v0.21.1..v0.21.2
 [0.21.1]: https://github.com/imi-bigpicture/wsidicom/compare/v0.21.0..v0.21.1
 [0.21.0]: https://github.com/imi-bigpicture/wsidicom/compare/v0.20.6..v0.21.0

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "wsidicom"
-version = "0.21.2"
+version = "0.21.3"
 description = "Tools for handling DICOM based whole scan images"
 authors = ["Erik O Gabrielsson <[email protected]>"]
 license = "Apache-2.0"

diff --git a/tests/metadata/conftest.py b/tests/metadata/conftest.py
@@ -36,7 +36,8 @@
     SpecimenSamplingProcedureCode,
     SpecimenStainsCode,
 )
-from wsidicom.geometry import SizeMm
+from wsidicom.geometry import PointMm, SizeMm
+from wsidicom.instance.dataset import ImageType
 from wsidicom.metadata import (
     Equipment,
     ExtendedDepthOfField,
@@ -536,6 +537,51 @@ def study():
     )
 
 
+@pytest.fixture()
+def illumination():
+    yield IlluminationColorCode("Full Spectrum")
+
+
+@pytest.fixture()
+def acquisition_datetime():
+    yield datetime.datetime(2023, 8, 5)
+
+
+@pytest.fixture()
+def focus_method():
+    yield FocusMethod.AUTO
+
+
+@pytest.fixture()
+def extended_depth_of_field():
+    yield ExtendedDepthOfField(5, 0.5)
+
+
+@pytest.fixture()
+def image_coordinate_system():
+    yield ImageCoordinateSystem(PointMm(20.0, 30.0), 90.0)
+
+
+@pytest.fixture()
+def pixel_spacing():
+    yield None
+
+
+@pytest.fixture()
+def focal_plane_spacing():
+    yield None
+
+
+@pytest.fixture()
+def depth_of_field():
+    yield None
+
+
+@pytest.fixture()
+def image_type():
+    yield ImageType.VOLUME
+
+
 @pytest.fixture()
 def wsi_metadata(
     study: Study,

diff --git a/tests/metadata/dicom_schema/conftest.py b/tests/metadata/dicom_schema/conftest.py
@@ -12,7 +12,6 @@
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-from datetime import datetime
 
 import pytest
 from pydicom import Dataset
@@ -24,7 +23,6 @@
     code_to_code_dataset,
 )
 from wsidicom.conceptcode import IlluminationColorCode
-from wsidicom.geometry import PointMm
 from wsidicom.instance import ImageType
 from wsidicom.metadata import (
     Equipment,
@@ -37,11 +35,6 @@
     Study,
     WsiMetadata,
 )
-from wsidicom.metadata.image import (
-    ExtendedDepthOfField,
-    FocusMethod,
-    ImageCoordinateSystem,
-)
 from wsidicom.metadata.schema.dicom.optical_path import LutDicomFormatter
 from wsidicom.metadata.schema.dicom.slide import SlideDicomSchema
 
@@ -74,6 +67,10 @@ def dicom_image(image: Image, valid_dicom: bool):
         origin = Dataset()
         origin.XOffsetInSlideCoordinateSystem = image.image_coordinate_system.origin.x
         origin.YOffsetInSlideCoordinateSystem = image.image_coordinate_system.origin.y
+        if image.image_coordinate_system.z_offset is not None:
+            origin.ZOffsetInSlideCoordinateSystem = (
+                image.image_coordinate_system.z_offset
+            )
 
         dataset.TotalPixelMatrixOriginSequence = [origin]
     elif not valid_dicom:
@@ -313,48 +310,3 @@ def dicom_wsi_metadata(
     dataset.DimensionOrganizationSequence = dimension_organization_sequence
     dataset.FrameOfReferenceUID = wsi_metadata.default_frame_of_reference_uid
     yield dataset
-
-
-@pytest.fixture()
-def illumination():
-    yield IlluminationColorCode("Full Spectrum")
-
-
-@pytest.fixture()
-def acquisition_datetime():
-    yield datetime(2023, 8, 5)
-
-
-@pytest.fixture()
-def focus_method():
-    yield FocusMethod.AUTO
-
-
-@pytest.fixture()
-def extended_depth_of_field():
-    yield ExtendedDepthOfField(5, 0.5)
-
-
-@pytest.fixture()
-def image_coordinate_system():
-    yield ImageCoordinateSystem(PointMm(20.0, 30.0), 90.0)
-
-
-@pytest.fixture()
-def pixel_spacing():
-    yield None
-
-
-@pytest.fixture()
-def focal_plane_spacing():
-    yield None
-
-
-@pytest.fixture()
-def depth_of_field():
-    yield None
-
-
-@pytest.fixture()
-def image_type():
-    yield ImageType.VOLUME
diff --git a/tests/metadata/dicom_schema/helpers.py b/tests/metadata/dicom_schema/helpers.py
@@ -172,6 +172,13 @@ def assert_dicom_image_equals_image(dicom_image: Dataset, image: Image):
         assert dicom_image.ImageOrientationSlide == list(
             image.image_coordinate_system.orientation.values
         )
+        if image.image_coordinate_system.z_offset is not None:
+            assert (
+                dicom_image.TotalPixelMatrixOriginSequence[
+                    0
+                ].ZOffsetInSlideCoordinateSystem
+                == image.image_coordinate_system.z_offset
+            )
     if any(
         item is not None
         for item in [
@@ -762,7 +769,7 @@ def create_description_dataset(
             issuer_of_identifier_dataset
         ]
 
-    if primary_anatomic_structures is not None:
+    if primary_anatomic_structures is not None and len(primary_anatomic_structures) > 0:
         description.PrimaryAnatomicStructureSequence = [
             create_code_dataset(item) for item in primary_anatomic_structures
         ]

diff --git a/tests/metadata/dicom_schema/sample/test_dicom_sample.py b/tests/metadata/dicom_schema/sample/test_dicom_sample.py
@@ -115,6 +115,9 @@ class TestSampleDicom:
             ],
         ],
     )
+    @pytest.mark.parametrize(
+        "primary_anatomic_structures", ([], [Code("value", "schema", "meaning")])
+    )
     def test_slide_sample_from_dataset(
         self,
         slide_sample_ids: Sequence[str],
@@ -269,6 +272,9 @@ def test_slide_sample_from_dataset(
             ],
         ],
     )
+    @pytest.mark.parametrize(
+        "primary_anatomic_structures", ([], [Code("value", "schema", "meaning")])
+    )
     def test_slide_sample_to_dataset(
         self,
         slide_sample_ids: Sequence[str],
@@ -361,26 +367,29 @@ def test_slide_sample_to_dataset(
                 assert description.SpecimenDetailedDescription == detailed_description
             else:
                 assert "SpecimenDetailedDescription" not in description
-            assert len(description.PrimaryAnatomicStructureSequence) == len(
-                primary_anatomic_structures
-            )
-            for index, primary_anatomic_structure in enumerate(
-                primary_anatomic_structures
-            ):
-                assert (
-                    description.PrimaryAnatomicStructureSequence[index].CodeValue
-                    == primary_anatomic_structure.value
-                )
-                assert (
-                    description.PrimaryAnatomicStructureSequence[
-                        index
-                    ].CodingSchemeDesignator
-                    == primary_anatomic_structure.scheme_designator
-                )
-                assert (
-                    description.PrimaryAnatomicStructureSequence[index].CodeMeaning
-                    == primary_anatomic_structure.meaning
+            if len(primary_anatomic_structures) > 0:
+                assert len(description.PrimaryAnatomicStructureSequence) == len(
+                    primary_anatomic_structures
                 )
+                for index, primary_anatomic_structure in enumerate(
+                    primary_anatomic_structures
+                ):
+                    assert (
+                        description.PrimaryAnatomicStructureSequence[index].CodeValue
+                        == primary_anatomic_structure.value
+                    )
+                    assert (
+                        description.PrimaryAnatomicStructureSequence[
+                            index
+                        ].CodingSchemeDesignator
+                        == primary_anatomic_structure.scheme_designator
+                    )
+                    assert (
+                        description.PrimaryAnatomicStructureSequence[index].CodeMeaning
+                        == primary_anatomic_structure.meaning
+                    )
+            else:
+                assert "PrimaryAnatomicStructureSequence" not in description
 
             step_iterator = iter(description.SpecimenPreparationSequence)
 

diff --git a/tests/metadata/dicom_schema/test_dicom_schema.py b/tests/metadata/dicom_schema/test_dicom_schema.py
@@ -159,7 +159,7 @@ def test_deserialize_equipment(
                 datetime(2023, 8, 5, 12, 13, 14, 150),
                 FocusMethod.MANUAL,
                 ExtendedDepthOfField(15, 0.5),
-                ImageCoordinateSystem(PointMm(50.0, 20.0), 180.0),
+                ImageCoordinateSystem(PointMm(50.0, 20.0), 180.0, 1.0),
                 SizeMm(0.5, 0.5),
                 0.25,
                 2.5,
@@ -226,7 +226,7 @@ def test_serialize_default_image(self):
                 datetime(2023, 8, 5, 12, 13, 14, 150),
                 FocusMethod.MANUAL,
                 ExtendedDepthOfField(15, 0.5),
-                ImageCoordinateSystem(PointMm(50.0, 20.0), 180.0),
+                ImageCoordinateSystem(PointMm(50.0, 20.0), 180.0, 1.0),
                 SizeMm(0.5, 0.5),
                 0.25,
                 2.5,

diff --git a/tests/metadata/json_schema/test_json_schema.py b/tests/metadata/json_schema/test_json_schema.py
@@ -48,6 +48,8 @@
     SeriesJsonSchema,
     StudyJsonSchema,
 )
+from wsidicom.metadata.schema.json.wsi import WsiMetadataJsonSchema
+from wsidicom.metadata.wsi import WsiMetadata
 
 
 class TestJsonSchema:
@@ -181,6 +183,14 @@ def test_image_serialize(self, image: Image):
                 dumped["image_coordinate_system"]["rotation"]
                 == image.image_coordinate_system.rotation
             )
+            if image.image_coordinate_system.z_offset is None:
+                assert dumped["image_coordinate_system"]["z_offset"] is None
+            else:
+                assert (
+                    dumped["image_coordinate_system"]["z_offset"]
+                    == image.image_coordinate_system.z_offset
+                )
+
         if image.pixel_spacing is None:
             assert dumped["pixel_spacing"] is None
         else:
@@ -216,6 +226,7 @@ def test_image_deserialize(self):
             "image_coordinate_system": {
                 "origin": {"x": 20.0, "y": 30.0},
                 "rotation": 90.0,
+                "z_offset": 1.0,
             },
             "pixel_spacing": {"width": 0.01, "height": 0.01},
             "focal_plane_spacing": 0.001,
@@ -261,6 +272,10 @@ def test_image_deserialize(self):
             loaded.image_coordinate_system.rotation
             == dumped["image_coordinate_system"]["rotation"]
         )
+        assert (
+            loaded.image_coordinate_system.z_offset
+            == dumped["image_coordinate_system"]["z_offset"]
+        )
         assert loaded.pixel_spacing.width == dumped["pixel_spacing"]["width"]
         assert loaded.pixel_spacing.height == dumped["pixel_spacing"]["height"]
         assert loaded.focal_plane_spacing == dumped["focal_plane_spacing"]
@@ -709,3 +724,23 @@ def test_study_deserialize(self):
         assert loaded.time == time.fromisoformat(dumped["time"])
         assert loaded.accession_number == dumped["accession_number"]
         assert loaded.referring_physician_name == dumped["referring_physician_name"]
+
+    def test_metadata_serialize(
+        self,
+        wsi_metadata: WsiMetadata,
+    ):
+        # Arrange
+
+        # Act
+        dumped = WsiMetadataJsonSchema().dump(wsi_metadata)
+
+        # Assert
+        assert isinstance(dumped, dict)
+        assert "study" in dumped
+        assert "series" in dumped
+        assert "patient" in dumped
+        assert "equipment" in dumped
+        assert "optical_paths" in dumped
+        assert "slide" in dumped
+        assert "label" in dumped
+        assert "image" in dumped
diff --git a/wsidicom/__init__.py b/wsidicom/__init__.py
@@ -30,7 +30,7 @@
 from wsidicom.web import WsiDicomWebClient
 from wsidicom.wsidicom import WsiDicom
 
-__version__ = "0.21.2"
+__version__ = "0.21.3"
 
 __all__ = [
     "settings",