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-[metadata] -lock-version = "2.0" -python-versions = "^3.9" -content-hash = "bb583d8b1ca433374294d22ecf19a04cd051f1e7443703ff58ebe5d473fa0852" diff --git a/pyproject.toml b/pyproject.toml index 92844f8..ea5efb2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ name = "cellmap-schemas" dynamic = ["version"] description = 'Schemas for data used by the Cellmap project team at Janelia Research Campus.' readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.10" license = "MIT" keywords = ["cellmap", "ngff", "n5", "zarr"] authors = [ @@ -16,7 +16,6 @@ authors = [ classifiers = [ "Development Status :: 4 - Beta", "Programming Language :: Python", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", @@ -45,7 +44,7 @@ dependencies = [ ] [[tool.hatch.envs.test.matrix]] -python = ["3.9", "3.10", "3.11"] +python = ["3.10", "3.11"] [tool.hatch.envs.test.scripts] run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov=tests" diff --git a/src/cellmap_schemas/annotation.py b/src/cellmap_schemas/annotation.py index 7751c03..0306e80 100644 --- a/src/cellmap_schemas/annotation.py +++ b/src/cellmap_schemas/annotation.py @@ -247,14 +247,24 @@ class AnnotationArrayAttrs(BaseModel, Generic[TName]): class_name: TName # a mapping from values to frequencies - complement_counts: Optional[dict[Possibility, int]] + complement_counts: dict[Possibility, int] | None # a mapping from class names to values # this is array metadata because labels might disappear during downsampling annotation_type: AnnotationType @model_validator(mode="after") def check_encoding(self: "AnnotationArrayAttrs"): - assert set(self.annotation_type.encoding.keys()).issuperset((self.complement_counts.keys())) + if isinstance(self.annotation_type, SemanticSegmentation): + if self.complement_counts is not None: + if not set(self.annotation_type.encoding.keys()).issuperset( + (self.complement_counts.keys()) + ): + msg = ( + "The keys in annotation_type.encoding must be a superset of the keys in complement_counts." + f"Got {tuple(self.annotation_type.encoding.keys())} for annotation_type.encoding, and" + f"{tuple(self.complement_counts.keys())} for complement_counts." + ) + raise ValueError(msg) return self @@ -327,11 +337,15 @@ class CropGroupAttrs(BaseModel, Generic[TName], validate_assignment=True): class_names: list[TName] @field_serializer("start_date") - def ser_end_date(value: date): + def ser_end_date(value: date | None) -> None | str: + if value is None: + return None return serialize_date(value) @field_serializer("end_date") - def ser_start_date(value: date): + def ser_start_date(value: date | None) -> None | str: + if value is None: + return None return serialize_date(value) From 2c55f207b0a1ba9d15ba10363f66034fa4a89bfc Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Fri, 20 Sep 2024 22:44:35 +0200 Subject: [PATCH 2/3] add more elaborate tests + corresponding logic in from_array --- src/cellmap_schemas/annotation.py | 44 ++++++++++++++++++++----------- tests/test_annotation.py | 43 +++++++++++++++++++++++++++--- 2 files changed, 68 insertions(+), 19 deletions(-) diff --git a/src/cellmap_schemas/annotation.py b/src/cellmap_schemas/annotation.py index 295646d..3ba5c0e 100644 --- a/src/cellmap_schemas/annotation.py +++ b/src/cellmap_schemas/annotation.py @@ -181,7 +181,7 @@ class SemanticSegmentation(BaseModel, extra="forbid"): type: Literal["semantic_segmentation"] Must be the string 'semantic_segmentation'. - encoding: dict[Union[Possibility, Literal["present"]], int] + encoding: dict[SemanticPossibility, int] This dict represents the mapping from possibilities to numeric values. The keys must be strings in the set `{'unknown', 'absent', 'present'}`, and the values must be numeric values contained in the array described by this metadata. @@ -280,24 +280,36 @@ def from_array( if complement_counts == "auto": complement_counts_parsed: dict[SemanticPossibility, int] | dict[ InstancePossibility, int - ] - num_unknown = (array == annotation_type.encoding["unknown"]).sum() - num_absent = (array == annotation_type.encoding["absent"]).sum() - num_present = array.size - (num_unknown + num_absent) + ] = {} + + num_unknown: int = 0 + num_absent: int = 0 + num_present: int = 0 + + if "unknown" in annotation_type.encoding: + num_unknown = (array == annotation_type.encoding["unknown"]).sum() + + if "absent" in annotation_type.encoding: + num_absent = (array == annotation_type.encoding["absent"]).sum() + + if "present" in annotation_type.encoding: + num_present = array.size - (num_unknown + num_absent) if isinstance(annotation_type, SemanticSegmentation): - complement_counts_parsed: dict[SemanticPossibility, int] = { - "unknown": num_unknown, - "absent": num_absent, - "present": num_present, - } + if "unknown" in annotation_type.encoding: + complement_counts_parsed["unknown"] = num_unknown + if "absent" in annotation_type.encoding: + complement_counts_parsed["absent"] = num_absent + if "present" in annotation_type.encoding: + complement_counts_parsed["present"] = num_present + elif isinstance(annotation_type, InstanceSegmentation): - complement_counts_parsed: dict[InstancePossibility, int] = { - "unknown": num_unknown, - "absent": num_absent, - } - else: - complement_counts_parsed = complement_counts # type: ignore + if "unknown" in annotation_type.encoding: + complement_counts_parsed["unknown"] = num_unknown + if "absent" in annotation_type.encoding: + complement_counts_parsed["absent"] = num_absent + else: + complement_counts_parsed = complement_counts # type: ignore return cls( class_name=class_name, diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 4af489b..cc095b0 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -9,6 +9,9 @@ AnnotationGroupAttrs, CropGroup, CropGroupAttrs, + InstancePossibility, + InstanceSegmentation, + SemanticPossibility, SemanticSegmentation, wrap_attributes, ) @@ -16,10 +19,23 @@ import zarr -def test_cropgroup(): +@pytest.mark.parametrize( + "annotation_cls, encoding", + [ + (SemanticSegmentation, {"absent": 0}), + (SemanticSegmentation, {"absent": 0, "present": 1}), + (SemanticSegmentation, {"absent": 0, "present": 1, "unknown": 3}), + (InstanceSegmentation, {"absent": 0}), + (InstanceSegmentation, {"absent": 0, "unknown": 3}), + ], +) +def test_cropgroup( + annotation_cls: type[SemanticSegmentation] | type[InstanceSegmentation], + encoding: dict[SemanticPossibility, int] | dict[InstancePossibility, int], +): ClassNamesT = Literal["foo", "bar"] - class_names = ["foo", "bar"] - ann_type = SemanticSegmentation(encoding={"absent": 0}) + class_names: list[Literal["foo", "bar"]] = ["foo", "bar"] + ann_type = annotation_cls(encoding=encoding) # type: ignore arrays = [np.zeros(10) for class_name in class_names] crop_group_attrs = CropGroupAttrs[ClassNamesT]( name="foo", @@ -79,3 +95,24 @@ def test_cropgroup(): ) with pytest.raises(ValueError, match=match): CropGroup.from_zarr(stored) + + +@pytest.mark.parametrize( + "annotation_cls, encoding", + [ + (SemanticSegmentation, {"absent": 0}), + (SemanticSegmentation, {"absent": 0, "present": 1}), + (SemanticSegmentation, {"absent": 0, "present": 1, "unknown": 3}), + (InstanceSegmentation, {"absent": 0}), + (InstanceSegmentation, {"absent": 0, "unknown": 3}), + ], +) +def test_annotation_attrs_from_array(annotation_cls, encoding) -> None: + array = np.array([0, 1, 0, 3]) + attrs = AnnotationArrayAttrs.from_array( + array, + class_name="foo", + annotation_type=annotation_cls(encoding=encoding), + complement_counts="auto", + ) + assert attrs.complement_counts["absent"] == 2 From 78222f4fb14c72edec584c5b8a56bde5a99c394a Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Fri, 20 Sep 2024 22:53:43 +0200 Subject: [PATCH 3/3] version bump --- src/cellmap_schemas/__about__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cellmap_schemas/__about__.py b/src/cellmap_schemas/__about__.py index c97254c..9752c56 100644 --- a/src/cellmap_schemas/__about__.py +++ b/src/cellmap_schemas/__about__.py @@ -1,4 +1,4 @@ # SPDX-FileCopyrightText: 2022-present Howard Hughes Medical Institute # # SPDX-License-Identifier: MIT -__version__ = "0.7.1" +__version__ = "0.8.1"