diff --git a/darwin/importer/formats/nifti.py b/darwin/importer/formats/nifti.py index c575e029f..54821c48a 100644 --- a/darwin/importer/formats/nifti.py +++ b/darwin/importer/formats/nifti.py @@ -3,7 +3,7 @@ import warnings from collections import OrderedDict, defaultdict from pathlib import Path -from typing import Dict, List, Optional, Sequence, Tuple, Union +from typing import Dict, List, Optional, Tuple from rich.console import Console @@ -13,6 +13,7 @@ try: import cc3d import nibabel as nib + from scipy.ndimage import zoom except ImportError: import_fail_string = """ You must install darwin-py with pip install nibabel connected-components-3d @@ -133,6 +134,7 @@ def _parse_nifti( img, processed_class_map, slot_names, + pixdims=pixdims, ) if mode in ["video", "instances"]: annotation_classes = { @@ -197,13 +199,21 @@ def get_polygon_video_annotations( def get_mask_video_annotations( - volume: np.ndarray, processed_class_map: Dict, slot_names: List[str] + volume: np.ndarray, + processed_class_map: Dict, + slot_names: List[str], + pixdims: Tuple[int, int, int] = (1, 1, 1), ) -> Optional[List[dt.VideoAnnotation]]: """ The function takes a volume and a class map and returns a list of video annotations We write a single raster layer for the volume but K mask annotations, where K is the number of classes. + + Assumptions: + - Importing annotation from Axial view only (view_idx=2) """ + new_size = get_new_axial_size(volume, pixdims) + frame_annotations = OrderedDict() all_mask_annotations = defaultdict(lambda: OrderedDict()) # This is a dictionary of class_names to generated mask_annotation_ids @@ -239,6 +249,10 @@ def get_mask_video_annotations( slice_mask = volume[:, :, i].astype( np.uint8 ) # Product requirement: We only support 255 classes! + slice_mask = zoom( + slice_mask, (new_size[0] / volume.shape[0], new_size[1] / volume.shape[1]) + ) + # We need to convert from nifti_idx to raster_idx slice_mask = np.vectorize( lambda key: map_from_nifti_idx_to_raster_idx.get(key, 0) @@ -247,7 +261,7 @@ def get_mask_video_annotations( raster_annotation = dt.make_raster_layer( class_name="__raster_layer__", mask_annotation_ids_mapping=mask_annotation_ids_mapping, - total_pixels=class_mask.size, + total_pixels=slice_mask.size, dense_rle=dense_rle, slot_names=slot_names, ) @@ -505,3 +519,24 @@ def convert_to_dense_rle(raster: np.ndarray) -> List[int]: prev_val, cnt = val, 1 dense_rle.extend([int(prev_val), int(cnt)]) return dense_rle + + +def get_new_axial_size( + volume: np.ndarray, pixdims: Tuple[int, int, int] +) -> Tuple[int, int]: + """Get the new size of the Axial plane after resizing to isotropic pixel dimensions. + + Args: + volume: Input volume. + pixdims: The pixel dimensions / spacings of the volume. + + Returns: + Tuple[int, int]: The new size of the Axial plane. + """ + original_size = volume.shape + original_spacing = pixdims + min_spacing = min(pixdims[0], pixdims[1]) + return ( + int(round(original_size[0] * (original_spacing[0] / min_spacing))), + int(round(original_size[1] * (original_spacing[1] / min_spacing))), + ) diff --git a/poetry.lock b/poetry.lock index 6517080a1..a4bc72ce2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,28 +1,25 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] dev = ["black", "debugpy", "isort", "mypy", "pytest", "pytest-rerunfailures", "responses", "ruff", "validate-pyproject"] @@ -2135,4 +2129,4 @@ test = ["pytest", "responses"] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.12" -content-hash = "be48163c2e599a525f547b745d2c833345996c7abc615c46322b123068dd0157" +content-hash = "ee9cc940af2b89243b3074aa35eb6be2c52d5d390f3a7cf6c2b201ca27abe9b3" diff --git a/pyproject.toml b/pyproject.toml index fda43302e..db055928d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,19 +1,19 @@ [build-system] -requires = [ "poetry-core",] build-backend = "poetry.core.masonry.api" +requires = ["poetry-core"] [tool.poetry] -name = "darwin-py" -version = "0.8.59" +authors = ["V7 "] +classifiers = ["Programming Language :: Python :: 3", "License :: OSI Approved :: MIT License"] description = "Library and command line interface for darwin.v7labs.com" -homepage = "https://docs.v7labs.com/reference/getting-started-2" documentation = "https://darwin-py-sdk.v7labs.com/index.html" -repository = "https://github.com/v7labs/darwin-py" -authors = [ "V7 ",] -readme = "README.md" -license = "MIT" +homepage = "https://docs.v7labs.com/reference/getting-started-2" keywords = [] -classifiers = [ "Programming Language :: Python :: 3", "License :: OSI Approved :: MIT License",] +license = "MIT" +name = "darwin-py" +readme = "README.md" +repository = "https://github.com/v7labs/darwin-py" +version = "0.8.59" [[tool.poetry.packages]] include = "darwin" @@ -21,28 +21,28 @@ include = "darwin" profile = "black" [tool.mypy] -plugins = [ "pydantic.mypy",] -follow_imports = "silent" -warn_redundant_casts = true -warn_unused_ignores = true check_untyped_defs = true -no_implicit_reexport = true -ignore_missing_imports = true -disallow_any_unimported = true -disallow_any_expr = false disallow_any_decorated = false disallow_any_explicit = true +disallow_any_expr = false +disallow_any_unimported = true +disallow_incomplete_defs = true disallow_subclassing_any = true -python_version = "3.10" disallow_untyped_calls = true -disallow_untyped_defs = true -disallow_incomplete_defs = true disallow_untyped_decorators = true +disallow_untyped_defs = true +follow_imports = "silent" +ignore_missing_imports = true +implicit_reexport = true no_implicit_optional = true +no_implicit_reexport = true +plugins = ["pydantic.mypy"] +pretty = true +python_version = "3.10" +warn_redundant_casts = true warn_return_any = false warn_unreachable = true -pretty = true -implicit_reexport = true +warn_unused_ignores = true [tool.pydantic-mypy] init_forbid_extra = true @@ -51,122 +51,122 @@ warn_required_dynamic_aliases = true warn_untyped_fields = true [tool.ruff] -select = [ "E", "F", "C",] -ignore = [ "E203", "E402", "E501",] +ignore = ["E203", "E402", "E501"] line-length = 88 +select = ["E", "F", "C"] [tool.flake8] +ignore = ["E203", "W503", "E402"] max-line-length = 88 -ignore = [ "E203", "W503", "E402",] [tool.black] line-length = 88 [tool.poetry.dependencies] -python = ">=3.8.0,<3.12" argcomplete = "^2.0.0" +deprecation = "^2.1.0" humanize = "^4.4.0" +json-stream = "^2.3.2" +jsonschema = ">=4.0.0" +numpy = "*" +orjson = "^3.8.5" pillow = "^10.1.0" +pydantic = "^2.0.0" +python = ">=3.8.0,<3.12" +pyyaml = "^6.0.1" requests = "^2.28.1" rich = "^13.0.1" -upolygon = "0.1.10" -jsonschema = ">=4.0.0" -deprecation = "^2.1.0" -pydantic = "^2.0.0" -orjson = "^3.8.5" -numpy = "*" toml = "^0.10.2" -types-requests = "^2.28.11.8" tqdm = "^4.64.1" types-pyyaml = "^6.0.12.9" -pyyaml = "^6.0.1" -json-stream = "^2.3.2" +types-requests = "^2.28.11.8" +upolygon = "0.1.10" [tool.poetry.extras] -dev = [ "black", "isort", "flake8", "mypy", "debugpy", "responses", "pytest", "flake8-pyproject", "pytest-rerunfailures", "ruff", "validate-pyproject",] -test = [ "responses", "pytest", "flake8-pyproject",] -ml = [ "torch", "torchvision", "scikit-learn", "albumentations",] -medical = [ "nibabel", "connected-components-3d",] -ocv = [ "opencv-python-headless",] +dev = ["black", "isort", "flake8", "mypy", "debugpy", "responses", "pytest", "flake8-pyproject", "pytest-rerunfailures", "ruff", "validate-pyproject"] +medical = ["nibabel", "connected-components-3d", "scipy"] +ml = ["torch", "torchvision", "scikit-learn", "albumentations"] +ocv = ["opencv-python-headless"] +test = ["responses", "pytest", "flake8-pyproject"] [tool.poetry.scripts] darwin = "darwin.cli:main" [tool.ruff.per-file-ignores] -"__init__.py" = [ "E402", "F401",] -"**/{tests,docs,tools}/*" = [ "E402", "F403",] +"**/{tests,docs,tools}/*" = ["E402", "F403"] +"__init__.py" = ["E402", "F401"] [tool.poetry.dependencies.nibabel] -version = "^5.0.0" -python = ">=3.8.1" optional = true +python = ">=3.8.1" +version = "^5.0.0" [tool.poetry.dependencies.connected-components-3d] -version = "^3.10.3" optional = true +version = "^3.10.3" [tool.poetry.dependencies.scikit-learn] -version = "^1.2.0" -python = ">=3.8.1,<3.12" optional = true +python = ">=3.8.1,<3.12" +version = "^1.2.0" [tool.poetry.dependencies.albumentations] -version = "^1.3.1" -python = ">=3.8" optional = true +python = ">=3.8" +version = "^1.3.1" [tool.poetry.dependencies.torch] -version = "^2.0.0" optional = true +version = "^2.0.0" [tool.poetry.dependencies.torchvision] -version = "^0.15.0" optional = true +version = "^0.15.0" [tool.poetry.dependencies.black] -version = ">=22.12,<25.0" optional = true +version = ">=22.12,<25.0" [tool.poetry.dependencies.isort] -version = "^5.11.4" optional = true +version = "^5.11.4" [tool.poetry.dependencies.mypy] -version = "^1.5" optional = true python = ">=3.8" +version = "^1.5" [tool.poetry.dependencies.responses] -version = "^0.22.0" optional = true +version = "^0.22.0" [tool.poetry.dependencies.pytest] -version = "^7.2.1" optional = true +version = "^7.2.1" [tool.poetry.dependencies.debugpy] -version = "1.8.1" optional = true +version = "1.8.1" [tool.poetry.dependencies.mpire] version = "^2.7.0" [tool.poetry.dependencies.python-dotenv] -version = "^1.0.0" python = ">3.8" +version = "^1.0.0" [tool.poetry.dependencies.opencv-python-headless] -version = "^4.8.0.76" optional = true +version = "^4.8.0.76" [tool.poetry.dependencies.pytest-rerunfailures] -version = "^12.0" optional = true +version = "^12.0" [tool.poetry.dependencies.ruff] -version = ">=0.0.292,<0.3.8" optional = true +version = ">=0.0.292,<0.3.8" [tool.poetry.dependencies.validate-pyproject] -version = "^0.15" optional = true +version = "^0.15" diff --git a/tests/darwin/importer/formats/import_nifti_test.py b/tests/darwin/importer/formats/import_nifti_test.py index 5d1c2d02e..d5dbbe537 100644 --- a/tests/darwin/importer/formats/import_nifti_test.py +++ b/tests/darwin/importer/formats/import_nifti_test.py @@ -3,8 +3,12 @@ import tempfile from pathlib import Path from typing import Union +from unittest.mock import patch from zipfile import ZipFile +import numpy as np +from scipy import ndimage + from darwin.datatypes import ( Annotation, AnnotationClass, @@ -12,7 +16,7 @@ SubAnnotation, VideoAnnotation, ) -from darwin.importer.formats.nifti import parse_path +from darwin.importer.formats.nifti import get_new_axial_size, parse_path from tests.fixtures import * @@ -92,6 +96,7 @@ def test_image_annotation_nifti_import_multi_slot(team_slug_darwin_json_v2: str) upload_json.write_text( json.dumps(input_dict, indent=4, sort_keys=True, default=str) ) + annotation_files = parse_path(path=upload_json) annotation_file = annotation_files[0] output_json_string = json.loads( @@ -178,34 +183,51 @@ def test_image_annotation_nifti_import_single_slot_to_mask( upload_json.write_text( json.dumps(input_dict, indent=4, sort_keys=True, default=str) ) - annotation_files = parse_path(path=upload_json) - annotation_file = annotation_files[0] - output_json_string = json.loads( - serialise_annotation_file(annotation_file, as_dict=False) - ) - expected_json_string = json.load( - open( - Path(tmpdir) - / team_slug_darwin_json_v2 - / "nifti" - / "vol0_annotation_file_to_mask.json", - "r", + + with patch("darwin.importer.formats.nifti.zoom") as mock_zoom: + mock_zoom.side_effect = ndimage.zoom + + annotation_files = parse_path(path=upload_json) + annotation_file = annotation_files[0] + output_json_string = json.loads( + serialise_annotation_file(annotation_file, as_dict=False) ) - ) - # This needs to not check for mask_annotation_ids_mapping as these - # are randomly generated - [ - frame.get("raster_layer", {}).pop("mask_annotation_ids_mapping") - for frame in output_json_string["annotations"][0]["frames"].values() - ] - [ - frame.get("raster_layer", {}).pop("mask_annotation_ids_mapping") - for frame in expected_json_string["annotations"][0]["frames"].values() - ] - assert ( - output_json_string["annotations"][0]["frames"] - == expected_json_string["annotations"][0]["frames"] - ) + expected_json_string = json.load( + open( + Path(tmpdir) + / team_slug_darwin_json_v2 + / "nifti" + / "vol0_annotation_file_to_mask.json", + "r", + ) + ) + # This needs to not check for mask_annotation_ids_mapping as these + # are randomly generated + [ + frame.get("raster_layer", {}).pop("mask_annotation_ids_mapping") + for frame in output_json_string["annotations"][0]["frames"].values() + ] + [ + frame.get("raster_layer", {}).pop("mask_annotation_ids_mapping") + for frame in expected_json_string["annotations"][0][ + "frames" + ].values() + ] + + assert mock_zoom.call_count == len( + expected_json_string["annotations"][0]["frames"] + ) + assert ( + output_json_string["annotations"][0]["frames"] + == expected_json_string["annotations"][0]["frames"] + ) + + +def test_get_new_axial_size(): + volume = np.zeros((10, 10, 10)) + pixdims = (1, 0.5, 0.5) + new_size = get_new_axial_size(volume, pixdims) + assert new_size == (20, 10) def serialise_annotation_file(