diff --git a/.vscode/settings.json b/.vscode/settings.json index f580f74a5..7343e13d9 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -14,7 +14,7 @@ "editor.tabSize": 2 }, "python.formatting.blackPath": "black", - "python.formatting.provider": "none", + "python.formatting.provider": "black", "python.formatting.blackArgs": [ "-l 120" ], diff --git a/darwin/exporter/formats/darwin.py b/darwin/exporter/formats/darwin.py index 0e7f33835..2e6193b4c 100644 --- a/darwin/exporter/formats/darwin.py +++ b/darwin/exporter/formats/darwin.py @@ -47,6 +47,7 @@ def build_image_annotation(annotation_file: dt.AnnotationFile) -> Dict[str, Any] } """ annotations: List[Dict[str, Any]] = [] + print(annotations) for annotation in annotation_file.annotations: payload = { annotation.annotation_class.annotation_type: _build_annotation_data(annotation), @@ -54,8 +55,7 @@ def build_image_annotation(annotation_file: dt.AnnotationFile) -> Dict[str, Any] } if ( - annotation.annotation_class.annotation_type == "complex_polygon" - or annotation.annotation_class.annotation_type == "polygon" + annotation.annotation_class.annotation_type == "complex_polygon" or annotation.annotation_class.annotation_type == "polygon" ) and "bounding_box" in annotation.data: payload["bounding_box"] = annotation.data["bounding_box"] diff --git a/darwin/exporter/formats/darwin_1_0.py b/darwin/exporter/formats/darwin_1_0.py index 8cff79fd3..d42505711 100644 --- a/darwin/exporter/formats/darwin_1_0.py +++ b/darwin/exporter/formats/darwin_1_0.py @@ -1,5 +1,5 @@ from pathlib import Path -from typing import Any, Dict, Iterable, List, Union +from typing import Iterable, List, Union import orjson as json @@ -34,14 +34,11 @@ def export(annotation_files: Iterable[AnnotationFile], output_dir: Path) -> None def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> None: - try: filename = annotation_file.path.parts[-1] output_file_path = (output_dir / filename).with_suffix(".json") except Exception as e: - raise ExportException_CouldNotAssembleOutputPath( - f"Could not export file {annotation_file.path} to {output_dir}" - ) from e + raise ExportException_CouldNotAssembleOutputPath(f"Could not export file {annotation_file.path} to {output_dir}") from e try: output: DictFreeForm = _build_json(annotation_file) @@ -50,9 +47,7 @@ def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> N try: with open(output_file_path, "w") as f: - op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode( - "utf-8" - ) + op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode("utf-8") f.write(op) except Exception as e: raise ExportException_CouldNotWriteFile(f"Could not write output for {annotation_file.path}") from e diff --git a/poetry.lock b/poetry.lock index 4e27775fc..f0ec35838 100644 --- a/poetry.lock +++ b/poetry.lock @@ 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[metadata] lock-version = "2.0" python-versions = ">=3.7.0,<3.11" -content-hash = "9865d21e7a68ded971e8b79d8d7c3b3ec669bb97eadce284fda60b892540ad2d" +content-hash = "1158b8ae2bbf51d84bc42543f93bc9bb6013df9dba67dec37a4963e477a143e9" diff --git a/pyproject.toml b/pyproject.toml index d0d834d87..89e73b70d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -88,6 +88,7 @@ toml = "^0.10.2" nibabel = { version = "^5.0.0", python = ">=3.8.1", optional = true } connected-components-3d = { version = "^3.10.3", optional = true } scikit-learn = { version = "^1.2.0", python = ">=3.8.1,<3.11", optional = true } +albumentations = { version = "^1.3.1", python = ">=3.8", optional = true } torch = { version = "^1.13.1", optional = true } torchvision = { version = "^0.14.1", optional = true } black = { version = "^22.12.0", optional = true } diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py new file mode 100644 index 000000000..099fbf241 --- /dev/null +++ b/tests/darwin/torch/transform_test.py @@ -0,0 +1,101 @@ +import pytest +import torch +from albumentations import BboxParams, Compose, HorizontalFlip, Resize +from PIL import Image + +from darwin.torch.transforms import AlbumentationsTransform + +# Sample data +SAMPLE_IMAGE = Image.new("RGB", (100, 100)) +SAMPLE_ANNOTATION = { + "boxes": torch.tensor([[25, 25, 75, 75]]), + "labels": torch.tensor([1]), + "area": torch.tensor([2500.0]), + "iscrowd": torch.tensor([0]), +} + +SAMPLE_ANNOTATION_OOB = { + "boxes": torch.tensor([[25, 25, 105, 105]]), # Out of bounds + "labels": torch.tensor([1]), + "area": torch.tensor([2500.0]), + "iscrowd": torch.tensor([0]), +} + +SAMPLE_ANNOTATION_WITH_MASKS = { + **SAMPLE_ANNOTATION, + "masks": torch.ones((1, 100, 100)), +} + +EXAMPLE_TRANSFORM = Compose( + [HorizontalFlip(p=1)], + bbox_params=BboxParams(format="coco", label_fields=["labels"]), +) +EXAMPLE_TRANSFORM_RESIZE = Compose( + [Resize(50, 50)], + bbox_params=BboxParams(format="coco", label_fields=["labels"]), +) + + +class TestAlbumentationsTransform: + def test_init(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + assert isinstance(at, AlbumentationsTransform) + + def test_from_path_invalid(self): + with pytest.raises(ValueError): + AlbumentationsTransform.from_path("invalid/path/to/config.yml") + + def test_from_dict_invalid(self): + with pytest.raises(ValueError): + AlbumentationsTransform.from_dict({"invalid": "config"}) + + def test_transformations(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + image, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + assert annotation["boxes"][0, 0] != SAMPLE_ANNOTATION["boxes"][0, 0] + + def test_transformations_resize(self): + transformations = EXAMPLE_TRANSFORM_RESIZE + at = AlbumentationsTransform(transformations) + image, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + assert image.shape[:2] == (50, 50) # We only check the height and width + + def test_boxes_out_of_bounds(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + with pytest.raises(ValueError): + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_OOB) # Expecting the ValueError due to out of bounds + + def test_transform_with_masks(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_WITH_MASKS) + assert "masks" in annotation + assert annotation["masks"].shape[0] == 1 + + def test_area_calculation_with_masks(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_WITH_MASKS) + assert annotation["area"] == torch.sum(annotation["masks"]) + + def test_area_calculation_without_masks(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + area = annotation["boxes"][0, 2] * annotation["boxes"][0, 3] + + assert torch.isclose(annotation["area"], area.unsqueeze(0), atol=1e-5) # Using isclose for floating point comparison + + def test_iscrowd_unchanged(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + assert "iscrowd" in annotation + assert annotation["iscrowd"] == SAMPLE_ANNOTATION["iscrowd"] + + +if __name__ == "__main__": + pytest.run()