Fixes (#146)

* Add KeyError catch

* Allow missing ExtendedDepthOfField

* Lazy-load pyramid metadata

CHANGELOG.md

@@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.18.2] - 2023-11-12
+
+### Fixed
+
+- Missing KeyError in exception catch for Pyramid.get(), that made getting image data for non-existing levels (by downscaling) not work.
+- Handle loading metadata if `ExtendedDepthOfField` not set.
+- Metadata for pyramid is now lazy loaded.
+
 ## [0.18.1] - 2023-11-12
 
 ### Fixed
@@ -294,8 +302,9 @@ 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/0.18.1..HEAD
-[0.18.1]: https://github.com/imi-bigpicture/wsidicom/compare/v0.18.1..v0.18.1
+[Unreleased]: https://github.com/imi-bigpicture/wsidicom/compare/0.18.2..HEAD
+[0.18.2]: https://github.com/imi-bigpicture/wsidicom/compare/v0.18.1..v0.18.2
+[0.18.1]: https://github.com/imi-bigpicture/wsidicom/compare/v0.18.0..v0.18.1
 [0.18.0]: https://github.com/imi-bigpicture/wsidicom/compare/v0.17.0..v0.18.0
 [0.17.0]: https://github.com/imi-bigpicture/wsidicom/compare/v0.16.0..v0.17.0
 [0.16.0]: https://github.com/imi-bigpicture/wsidicom/compare/v0.15.2..v0.16.0

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "wsidicom"
-version = "0.18.1"
+version = "0.18.2"
 description = "Tools for handling DICOM based whole scan images"
 authors = ["Erik O Gabrielsson <erik.o.gabrielsson@sectra.com>"]
 license = "Apache-2.0"

tests/metadata/dicom_schema/conftest.py

@@ -46,6 +46,11 @@
 from wsidicom.metadata.schema.dicom.slide import SlideDicomSchema
 
 
+@pytest.fixture()
+def valid_dicom():
+    yield True
+
+
 @pytest.fixture()
 def dicom_equipment(equipment: Equipment):
     dataset = Dataset()
@@ -57,7 +62,7 @@ def dicom_equipment(equipment: Equipment):
 
 
 @pytest.fixture()
-def dicom_image(image: Image):
+def dicom_image(image: Image, valid_dicom: bool):
     dataset = Dataset()
     dataset.AcquisitionDateTime = DT(image.acquisition_datetime)
     if image.focus_method is not None:
@@ -79,7 +84,7 @@ def dicom_image(image: Image):
         dataset.DistanceBetweenFocalPlanes = (
             image.extended_depth_of_field.distance_between_focal_planes
         )
-    else:
+    elif valid_dicom:
         dataset.ExtendedDepthOfField = "NO"
     if any(
         item is not None

tests/metadata/dicom_schema/test_dicom_schema.py

@@ -240,6 +240,7 @@ def test_serialize_default_image(self):
             [None, None, None, None, None, None, None, None],
         ],
     )
+    @pytest.mark.parametrize("valid_dicom", [True, False])
     def test_deserialize_image(self, dicom_image: Dataset, image: Image):
         # Arrange
         schema = ImageDicomSchema()

wsidicom/__init__.py

@@ -51,4 +51,4 @@
 from wsidicom.web import WsiDicomWebClient
 from wsidicom.wsidicom import WsiDicom
 
-__version__ = "0.18.1"
+__version__ = "0.18.2"

wsidicom/metadata/schema/dicom/image.py

@@ -168,7 +168,9 @@ class ImageDicomSchema(ModuleDicomSchema[Image]):
         dump_default=Defaults.focus_method,
         load_default=None,
     )
-    extended_depth_of_field_bool = BooleanDicomField(data_key="ExtendedDepthOfField")
+    extended_depth_of_field_bool = BooleanDicomField(
+        data_key="ExtendedDepthOfField", load_default=False
+    )
     extended_depth_of_field = FlattenOnDumpNestedDicomField(
         ExtendedDepthOfFieldDicomSchema(),
         allow_none=True,

wsidicom/series/pyramid.py

@@ -14,7 +14,6 @@
 
 from typing import Iterable, List, Optional, OrderedDict
 
-
 from wsidicom.errors import (
     WsiDicomNotFoundError,
     WsiDicomOutOfBoundsError,
@@ -24,7 +23,6 @@
 from wsidicom.group.level import BaseLevel
 from wsidicom.instance import ImageType, WsiInstance
 from wsidicom.metadata import ImageCoordinateSystem
-from wsidicom.metadata.schema.dicom.wsi import WsiMetadataDicomSchema
 from wsidicom.series.series import Series
 from wsidicom.stringprinting import list_pretty_str
 
@@ -62,7 +60,6 @@ def __init__(self, levels: Iterable[Level]):
                 '"Volume" type'
             )
         self._mm_size = mm_size
-        self._metadata = WsiMetadataDicomSchema().load(self.datasets[0])
 
     def __repr__(self) -> str:
         return f"{type(self).__name__}({self._levels})"
@@ -96,7 +93,7 @@ def get(self, index: int, pyramid_index: bool = True) -> Level:
             if pyramid_index:
                 return self._levels[index]
             return self[index]
-        except IndexError:
+        except (KeyError, IndexError):
             raise WsiDicomNotFoundError(f"Level index {index}", "pyramid")
 
     @property