From 81dd1e6620c20bebb4e1155d60f56411e11fef5a Mon Sep 17 00:00:00 2001 From: John Wilkie <124276291+JBWilkie@users.noreply.github.com> Date: Mon, 4 Nov 2024 11:09:41 +0000 Subject: [PATCH] E2E tests for converting annotations (#949) --- .gitignore | 1 - e2e_tests/cli/{convert => }/test_convert.py | 57 +- .../coco/from/base_annotation.json | 0 .../data/{ => convert}/coco/to/output.json | 0 .../data/convert/cvat/from/000000021295.json | 67 ++ e2e_tests/data/convert/cvat/to/output.xml | 1 + .../instance_mask/from/000000021295.json | 155 +++ .../to/masks/000000021295_00000.png | Bin 0 -> 1163 bytes .../to/masks/000000021295_00001.png | Bin 0 -> 940 bytes .../to/masks/000000021295_00002.png | Bin 0 -> 1198 bytes .../hippocampus_001_mpr_1_test_hippo.nii.json | 945 ++++++++++++++++++ ..._mpr_1_test_hippo_test_mask_basic_m.nii.gz | Bin 0 -> 1022 bytes ...mpr_1_test_hippo_test_polygon_basic.nii.gz | Bin 0 -> 974 bytes .../convert/pascalvoc/from/000000021295.json | 81 ++ .../convert/pascalvoc/to/000000021295.xml | 1 + .../semantic_mask/from/221b-2.json | 0 .../semantic_mask/to/class_mapping.csv | 0 .../test_input_with_bboxes_and_polys.json | 0 .../data/{ => convert}/yolo/to/darknet.labels | 0 .../test_input_with_bboxes_and_polys.json | 0 .../{ => convert}/yolov8/to/darknet.labels | 0 .../to/test_input_with_bboxes_and_polys.txt | 5 - .../to/test_input_with_bboxes_and_polys.txt | 5 - 23 files changed, 1300 insertions(+), 18 deletions(-) rename e2e_tests/cli/{convert => }/test_convert.py (65%) rename e2e_tests/data/{ => convert}/coco/from/base_annotation.json (100%) rename e2e_tests/data/{ => convert}/coco/to/output.json (100%) create mode 100644 e2e_tests/data/convert/cvat/from/000000021295.json create mode 100644 e2e_tests/data/convert/cvat/to/output.xml create mode 100644 e2e_tests/data/convert/instance_mask/from/000000021295.json create mode 100644 e2e_tests/data/convert/instance_mask/to/masks/000000021295_00000.png create mode 100644 e2e_tests/data/convert/instance_mask/to/masks/000000021295_00001.png create mode 100644 e2e_tests/data/convert/instance_mask/to/masks/000000021295_00002.png create mode 100644 e2e_tests/data/convert/nifti/from/hippocampus_001_mpr_1_test_hippo.nii.json create mode 100644 e2e_tests/data/convert/nifti/to/hippocampus_001_mpr_1_test_hippo_test_mask_basic_m.nii.gz create mode 100644 e2e_tests/data/convert/nifti/to/hippocampus_001_mpr_1_test_hippo_test_polygon_basic.nii.gz create mode 100644 e2e_tests/data/convert/pascalvoc/from/000000021295.json create mode 100644 e2e_tests/data/convert/pascalvoc/to/000000021295.xml rename e2e_tests/data/{ => convert}/semantic_mask/from/221b-2.json (100%) rename e2e_tests/data/{ => convert}/semantic_mask/to/class_mapping.csv (100%) rename e2e_tests/data/{ => convert}/yolo/from/test_input_with_bboxes_and_polys.json (100%) rename e2e_tests/data/{ => convert}/yolo/to/darknet.labels (100%) rename e2e_tests/data/{ => convert}/yolov8/from/test_input_with_bboxes_and_polys.json (100%) rename e2e_tests/data/{ => convert}/yolov8/to/darknet.labels (100%) delete mode 100644 e2e_tests/data/yolo/to/test_input_with_bboxes_and_polys.txt delete mode 100644 e2e_tests/data/yolov8/to/test_input_with_bboxes_and_polys.txt diff --git a/.gitignore b/.gitignore index 5d4b4611b..54f37a022 100644 --- a/.gitignore +++ b/.gitignore @@ -9,7 +9,6 @@ data/ !tests/darwin/data darwin_py.egg-info/PKG-INFO -*.png *.jpeg *.jpg *.bpm diff --git a/e2e_tests/cli/convert/test_convert.py b/e2e_tests/cli/test_convert.py similarity index 65% rename from e2e_tests/cli/convert/test_convert.py rename to e2e_tests/cli/test_convert.py index 188d93635..aadbc1612 100644 --- a/e2e_tests/cli/convert/test_convert.py +++ b/e2e_tests/cli/test_convert.py @@ -4,13 +4,14 @@ import orjson as json import pytest +import xml.etree.ElementTree as ET from e2e_tests.helpers import assert_cli, run_cli_command class TestExportCli: this_file_path = Path(dirname(__file__)).absolute() - data_path = (this_file_path / ".." / ".." / "data").resolve() + data_path = (this_file_path / ".." / "data" / "convert").resolve() @pytest.fixture(autouse=True) def config(self) -> None: @@ -33,10 +34,10 @@ def compare_directories(self, path: Path, expected_path: Path) -> None: continue # Compare files - with file.open("r") as f: + with file.open("rb") as f: content = f.read() - with Path(expected_path / file.name).open() as f: + with Path(expected_path / file.name).open("rb") as f: expected_content = f.read() if content != expected_content: @@ -52,6 +53,14 @@ def compare_directories(self, path: Path, expected_path: Path) -> None: [ ("yolo_segmented", data_path / "yolov8/from", data_path / "yolov8/to"), ("yolo", data_path / "yolo/from", data_path / "yolo/to"), + ("cvat", data_path / "cvat/from", data_path / "cvat/to"), + ("pascalvoc", data_path / "pascalvoc/from", data_path / "pascalvoc/to"), + ("nifti", data_path / "nifti/from", data_path / "nifti/to"), + ( + "instance_mask", + data_path / "instance_mask/from", + data_path / "instance_mask/to", + ), pytest.param( "coco", data_path / "coco/from", @@ -87,23 +96,34 @@ def test_darwin_convert( result = run_cli_command( f"darwin convert {format} {str(input_path)} {str(tmp_path)}" ) - if format == "coco": - self.patch_coco(tmp_path / "output.json") + self.patch_format(format, tmp_path) assert_cli(result, 0) self.compare_directories(expectation_path, tmp_path) + def patch_format(self, format: str, path: Path) -> None: + """ + Patch files based on format to match the expected output. + """ + patch_methods = { + "coco": self.patch_coco, + "cvat": self.patch_cvat, + } + patch_method = patch_methods.get(format) + if patch_method: + patch_method(path) + def patch_coco(self, path: Path) -> None: """ Patch coco file to match the expected output, includes changes to year and date_created, wrapped in try except so that format errors are still caught later with correct error messages """ try: - with open(path, "r") as f: + with open(path / "output.json", "r") as f: contents = f.read() temp = json.loads(contents) temp["info"]["year"] = 2023 temp["info"]["date_created"] = "2023/12/05" - with open(path, "w") as f: + with open(path / "output.json", "w") as f: op = json.dumps( temp, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY ).decode("utf-8") @@ -111,6 +131,29 @@ def patch_coco(self, path: Path) -> None: except Exception: print(f"Error patching {path}") + def patch_cvat(self, path: Path) -> None: + """ + Patch cvat file to match the expected output. + """ + try: + tree = ET.parse(path / "output.xml") + root = tree.getroot() + # Adjust the required fields + dumped_elem = root.find(".//meta/dumped") + if dumped_elem is not None: + dumped_elem.text = "2024-10-25 10:33:01.789498+00:00" + created_elem = root.find(".//meta/task/created") + if created_elem is not None: + created_elem.text = "2024-10-25 10:33:01.789603+00:00" + updated_elem = root.find(".//meta/task/updated") + if updated_elem is not None: + updated_elem.text = "2024-10-25 10:33:01.789608+00:00" + tree.write(path / "output.xml") + except ET.ParseError: + print(f"Error parsing XML in {path}") + except Exception as e: + print(f"Error patching {path}: {e}") + if __name__ == "__main__": pytest.main(["-vv", "-s", __file__]) diff --git a/e2e_tests/data/coco/from/base_annotation.json b/e2e_tests/data/convert/coco/from/base_annotation.json similarity index 100% rename from e2e_tests/data/coco/from/base_annotation.json rename to e2e_tests/data/convert/coco/from/base_annotation.json diff --git a/e2e_tests/data/coco/to/output.json b/e2e_tests/data/convert/coco/to/output.json similarity index 100% rename from e2e_tests/data/coco/to/output.json rename to e2e_tests/data/convert/coco/to/output.json diff --git a/e2e_tests/data/convert/cvat/from/000000021295.json b/e2e_tests/data/convert/cvat/from/000000021295.json new file mode 100644 index 000000000..5e428560d --- /dev/null +++ b/e2e_tests/data/convert/cvat/from/000000021295.json @@ -0,0 +1,67 @@ +{ + "version": "2.0", + "schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/2.0/schema.json", + "item": { + "name": "000000021295.jpg", + "path": "/", + "source_info": { + "item_id": "0192c338-2dc8-bb9f-8dde-9c4a8714c957", + "dataset": { + "name": "tmp", + "slug": "tmp", + "dataset_management_url": "https://staging.v7labs.com/datasets/426200/dataset-management" + }, + "team": { + "name": "E2E Testing", + "slug": "e2e-testing" + }, + "workview_url": "https://staging.v7labs.com/workview?dataset=426200&item=0192c338-2dc8-bb9f-8dde-9c4a8714c957" + }, + "slots": [ + { + "type": "image", + "slot_name": "0", + "width": 640, + "height": 427, + "thumbnail_url": "https://staging.v7labs.com/api/v2/teams/e2e-testing/files/6c554c31-8bf6-4fc7-9f31-394fd775b2a6/thumbnail", + "source_files": [ + { + "file_name": "000000021295.jpg", + "url": "https://staging.v7labs.com/api/v2/teams/e2e-testing/uploads/ade5f1e3-a165-4a07-989f-86ee342499c9" + } + ] + } + ] + }, + "annotations": [ + { + "bounding_box": { + "h": 43.7181, + "w": 71.2665, + "x": 166.0884, + "y": 113.1879 + }, + "id": "46b33c9c-7453-4722-8b43-91bbb3fc247f", + "name": "test_bounding_box_basic", + "properties": [], + "slot_names": [ + "0" + ] + }, + { + "bounding_box": { + "h": 31.7405, + "w": 58.0912, + "x": 360.1248, + "y": 259.913 + }, + "id": "2b7c85ed-74b3-4111-a5d6-073da56d0072", + "name": "test_bounding_box_basic", + "properties": [], + "slot_names": [ + "0" + ] + } + ], + "properties": [] +} \ No newline at end of file diff --git a/e2e_tests/data/convert/cvat/to/output.xml b/e2e_tests/data/convert/cvat/to/output.xml new file mode 100644 index 000000000..66a9982e1 --- /dev/null +++ b/e2e_tests/data/convert/cvat/to/output.xml @@ -0,0 +1 @@ +1.12024-10-25 10:33:01.789498+00:001exported_task_from_darwin1annotation0NoneFalse2024-10-25 10:33:01.789603+00:002024-10-25 10:33:01.789608+00:00111not applicableexample_usernameuser@example.com \ No newline at end of file diff --git a/e2e_tests/data/convert/instance_mask/from/000000021295.json b/e2e_tests/data/convert/instance_mask/from/000000021295.json new file mode 100644 index 000000000..34cac389b --- /dev/null +++ b/e2e_tests/data/convert/instance_mask/from/000000021295.json @@ -0,0 +1,155 @@ +{ + "version": "2.0", + "schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/2.0/schema.json", + "item": { + "name": "000000021295.jpg", + "path": "/", + "source_info": { + "item_id": "0192c338-2dc8-bb9f-8dde-9c4a8714c957", + "team": { + "name": "E2E Testing", + "slug": "e2e-testing" + }, + "dataset": { + "name": "tmp", + "slug": "tmp", + "dataset_management_url": "https://staging.v7labs.com/datasets/426200/dataset-management" + }, + "workview_url": "https://staging.v7labs.com/workview?dataset=426200&item=0192c338-2dc8-bb9f-8dde-9c4a8714c957" + }, + "slots": 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