From ebac050a4823304da457a8e03b0e50b57375ce3e Mon Sep 17 00:00:00 2001 From: Jan Eglinger Date: Mon, 2 Sep 2024 16:01:29 +0200 Subject: [PATCH] Resave with same dtype, save transforms --- .github/workflows/test.yml | 6 +- pixi.lock | 1753 ++++++++++++----------- pyproject.toml | 13 +- src/napari_save_transformed/__init__.py | 39 +- tests/__init__.py | 0 tests/test_napari_save_transformed.py | 16 +- 6 files changed, 971 insertions(+), 856 deletions(-) delete mode 100644 tests/__init__.py diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c95909d..23baef9 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -22,16 +22,16 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] + python-version: ['3.9', '3.10', '3.11', '3.12'] env: DISPLAY: ':99.0' steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/pixi.lock b/pixi.lock index 01ded8f..7020915 100644 --- a/pixi.lock +++ b/pixi.lock @@ -7,24 +7,24 @@ environments: - https://pypi.org/simple packages: win-64: - - conda: https://conda.anaconda.org/conda-forge/win-64/_libavif_api-1.0.4-h57928b3_4.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/win-64/_libavif_api-1.1.1-h57928b3_1.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-1.0.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/win-64/aom-3.9.1-he0c23c2_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/app-model-0.2.7-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/app-model-0.2.8-pyhd8ed1ab_0.conda - 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Beta", "Programming Language :: Python", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", @@ -58,6 +57,7 @@ napari_save_transformed = ["src/napari_save_transformed", "*/napari-save-transfo tests = ["tests", "*/napari-save-transformed/tests"] [tool.coverage.report] +show_missing = true exclude_lines = [ "no cov", "if __name__ == .__main__.:", @@ -80,6 +80,15 @@ pyqt = ">=5.15.9,<5.16" [tool.pixi.feature.napari.dependencies] napari = ">=0.4.19.post1,<0.4.20" pyqt = ">=5.15.9,<5.16" +pip = ">=24.0,<25" [tool.pixi.environments] napari = { features = ["napari"], no-default-feature = true } + +[tool.pytest.ini_options] +addopts = [ + "--import-mode=importlib", +] + +[tool.ruff.lint.extend-per-file-ignores] +"**/tests/*" = ["INP001"] diff --git a/src/napari_save_transformed/__init__.py b/src/napari_save_transformed/__init__.py index ac7f130..9ec2084 100644 --- a/src/napari_save_transformed/__init__.py +++ b/src/napari_save_transformed/__init__.py @@ -1,9 +1,12 @@ from __future__ import annotations +from pathlib import Path from typing import TYPE_CHECKING import numpy as np +import yaml from napari.utils.transforms import Affine +from pydantic import Field, RootModel from scipy.ndimage import affine_transform from skimage.transform import matrix_transform from tifffile.tifffile import imwrite @@ -12,14 +15,48 @@ from napari.types import FullLayerData +class TransformDict(RootModel): + root: dict[str, np.ndarray] = Field(default_factory=dict) + + model_config = {"arbitrary_types_allowed": True} # noqa: RUF012 + + def __getitem__(self, key): + return self.root[key] + + def __setitem__(self, key, value): + self.root[key] = value + + @classmethod + def from_yaml(cls, yaml_str: str) -> TransformDict: + loaded_data = yaml.safe_load(yaml_str) + return cls({k: np.array(v).reshape(3, 3) for k, v in loaded_data.items()}) + + def to_yaml(self) -> str: + return yaml.safe_dump(self.model_dump(), default_flow_style=None) + + @classmethod + def from_file(cls, file_path: str) -> TransformDict: + with open(file_path) as file: + return cls.from_yaml(file.read()) + + def to_file(self, file_path: str) -> None: + with open(file_path, "w") as file: + file.write(self.to_yaml()) + + def write_transformed_layers(path: str, layer_data: list[FullLayerData]) -> list[str]: images = [] transforms = [] + mapping = TransformDict() for data, attrs, _ in layer_data: images.append(data) + mapping[attrs["name"]] = attrs["affine"].tolist() transforms.append(Affine(affine_matrix=attrs["affine"])) results, out_shape = transform_arrays(images, transforms) - imwrite(path, np.stack(results).astype(np.float32), imagej=True) + imwrite(path, np.stack(results), imagej=True) + out_path = Path(path) + mapping_file = out_path.parent / f"{out_path.stem}_transforms.yml" + mapping.to_file(mapping_file) return path diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_napari_save_transformed.py b/tests/test_napari_save_transformed.py index 787f555..52acd91 100644 --- a/tests/test_napari_save_transformed.py +++ b/tests/test_napari_save_transformed.py @@ -1,13 +1,14 @@ import numpy as np from napari.layers import Image +from tifffile.tifffile import imread -from napari_save_transformed import write_transformed_layers +from napari_save_transformed import TransformDict, write_transformed_layers def test_write_transformed_layers(tmp_path): layers = [] shape = (100, 200) - image0 = np.ones(shape=shape) + image0 = np.ones(shape=shape, dtype=np.uint16) layers.append(Image(image0)) image1 = image0.copy() layers.append(Image(image1, affine=[[1, 0, 30], [0, 1, 10], [0, 0, 1]])) @@ -16,3 +17,14 @@ def test_write_transformed_layers(tmp_path): write_transformed_layers(path=out_path, layer_data=layer_data) assert out_path.exists() + + output = imread(out_path) + assert output.dtype == np.uint16 + assert output.shape == (2, 130, 210) + + transform_file = out_path.parent / f"{out_path.stem}_transforms.yml" + assert transform_file.exists() + + mapping = TransformDict.from_file(transform_file) + assert np.array_equal(mapping["image0"], [[1, 0, 0], [0, 1, 0], [0, 0, 1]]) + assert np.array_equal(mapping["image1"], [[1, 0, 30], [0, 1, 10], [0, 0, 1]])