From 8d4f4cec2dc9149a21219aa6ae40ebc5f789cf33 Mon Sep 17 00:00:00 2001 From: Jan Eglinger Date: Tue, 1 Oct 2024 18:12:16 +0200 Subject: [PATCH 1/2] Return DataArray from NdInfo --- .gitattributes | 2 + .github/workflows/test.yml | 40 +- .gitignore | 3 + pixi.lock | 7804 +++++++++++++++++ pyproject.toml | 71 +- src/metamorph_mda_parser/nd.py | 15 + src/metamorph_mda_parser/xarray.py | 51 + .../resources/data/sample_3ch_2pos_mixed-z.nd | 21 + .../sample_3ch_2pos_mixed-z_w1Conf640_s1.tif | Bin 0 -> 342 bytes .../sample_3ch_2pos_mixed-z_w1Conf640_s2.tif | Bin 0 -> 342 bytes .../sample_3ch_2pos_mixed-z_w2Conf561_s1.stk | Bin 0 -> 1046 bytes .../sample_3ch_2pos_mixed-z_w2Conf561_s2.stk | Bin 0 -> 1046 bytes .../sample_3ch_2pos_mixed-z_w3Conf488_s1.stk | Bin 0 -> 1046 bytes .../sample_3ch_2pos_mixed-z_w3Conf488_s2.stk | Bin 0 -> 1046 bytes tests/test_xarray.py | 25 + 15 files changed, 7991 insertions(+), 41 deletions(-) create mode 100644 .gitattributes create mode 100644 pixi.lock create mode 100644 src/metamorph_mda_parser/xarray.py create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z.nd create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z_w1Conf640_s1.tif create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z_w1Conf640_s2.tif create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z_w2Conf561_s1.stk create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z_w2Conf561_s2.stk create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z_w3Conf488_s1.stk create mode 100644 tests/resources/data/sample_3ch_2pos_mixed-z_w3Conf488_s2.stk create mode 100644 tests/test_xarray.py diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..07fe41c --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# GitHub syntax highlighting +pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a772c7d..01ec0da 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -2,9 +2,9 @@ name: test on: push: - branches: [main, master] + branches: [main] pull_request: - branches: [main, master] + branches: [main] concurrency: group: test-${{ github.head_ref }} @@ -16,27 +16,27 @@ env: jobs: run: - name: Python ${{ matrix.python-version }} on ${{ startsWith(matrix.os, 'macos-') && 'macOS' || startsWith(matrix.os, 'windows-') && 'Windows' || 'Linux' }} + name: ${{ matrix.pixi-environment }} - ${{ matrix.os }} runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python-version: ['3.10', '3.11', '3.12'] - + pixi-environment: + - py310-base + - py310-xarray + - py311-base + - py311-xarray + - py312-base + - py312-xarray steps: - - uses: actions/checkout@v3 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - - - name: Install Hatch - run: pip install --upgrade hatch - - - name: Run static analysis - run: hatch fmt --check - - - name: Run tests - run: hatch run cov + - uses: actions/checkout@v4 + + - name: Set up Pixi + uses: prefix-dev/setup-pixi@v0.8.1 + with: + cache: true + environments: ${{ matrix.pixi-environment }} + + - name: Run tests + run: pixi run --environment ${{ matrix.pixi-environment }} test diff --git a/.gitignore b/.gitignore index d5a91c2..791c590 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ dist __pycache__ .coverage* +# pixi environments +.pixi +*.egg-info diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..d0a0d1a --- /dev/null +++ b/pixi.lock @@ -0,0 +1,7804 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + 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100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,6 +28,15 @@ dependencies = [ "pydantic", ] +[project.optional-dependencies] +xarray = [ + "dask", + "numpy<2", + "tifffile", + "xarray", + "zarr", +] + [project.urls] Documentation = "https://github.com/fmi-faim/metamorph-mda-parser#readme" Issues = "https://github.com/fmi-faim/metamorph-mda-parser/issues" @@ -41,27 +50,6 @@ dependencies = [ "coverage[toml]>=6.5", "pytest", ] -[tool.hatch.envs.default.scripts] -test = "pytest {args:tests}" -test-cov = "coverage run -m pytest {args:tests}" -cov-report = [ - "- coverage combine", - "coverage report", -] -cov = [ - "test-cov", - "cov-report", -] - -[[tool.hatch.envs.all.matrix]] -python = ["3.10", "3.11", "3.12"] - -[tool.hatch.envs.types] -dependencies = [ - "mypy>=1.0.0", -] -[tool.hatch.envs.types.scripts] -check = "mypy --install-types --non-interactive {args:src/metamorph_mda_parser tests}" [tool.coverage.run] source_pkgs = ["metamorph_mda_parser", "tests"] @@ -93,3 +81,44 @@ runtime-evaluated-base-classes = ["pydantic.BaseModel"] addopts = [ "--import-mode=importlib", ] + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["win-64", "linux-64", "osx-arm64"] + +[tool.pixi.pypi-dependencies] +metamorph-mda-parser = { path = ".", editable = true } + +[tool.pixi.environments] +default = { solve-group = "py312" } +xarray = { features = ["xarray"], solve-group = "py312" } +jupyter = { features = ["jupyter", "xarray"], solve-group = "py312" } +py310-base = { features = ["py310", "test"], solve-group = "py310" } +py310-xarray = { features = ["py310", "test", "xarray"], solve-group = "py310" } +py311-base = { features = ["py311", "test"], solve-group = "py311" } +py311-xarray = { features = ["py311", "test", "xarray"], solve-group = "py311" } +py312-base = { features = ["py312", "test"], solve-group = "py312" } +py312-xarray = { features = ["py312", "test", "xarray"], solve-group = "py312" } + +[tool.pixi.tasks] + +[tool.pixi.feature.jupyter.dependencies] +jupyter = "*" + +[tool.pixi.feature.jupyter.tasks] +jupyter = "jupyter lab" + +[tool.pixi.feature.test.dependencies] +pytest = "*" + +[tool.pixi.feature.test.tasks] +test = "pytest" + +[tool.pixi.feature.py310.dependencies] +python = "==3.10" + +[tool.pixi.feature.py311.dependencies] +python = "==3.11" + +[tool.pixi.feature.py312.dependencies] +python = "==3.12" diff --git a/src/metamorph_mda_parser/nd.py b/src/metamorph_mda_parser/nd.py index e7f5987..1efb825 100644 --- a/src/metamorph_mda_parser/nd.py +++ b/src/metamorph_mda_parser/nd.py @@ -89,3 +89,18 @@ def get_files(self) -> pd.DataFrame: "time", ], ) + + def get_data_array(self, channels=None, positions=None, timepoints=None): + from metamorph_mda_parser.xarray import HAS_XARRAY + if HAS_XARRAY: + from metamorph_mda_parser.xarray import dataarray_from_dataframe + else: + raise ValueError("Dependencies for data array creation not found.") + files = self.get_files() + if channels: + files = files[files["channel"].isin(channels)] + if positions: + files = files[files["position"].isin(positions)] + if timepoints: + files = files[files["time"].isin(timepoints)] + return dataarray_from_dataframe(files, self.wave_do_z) diff --git a/src/metamorph_mda_parser/xarray.py b/src/metamorph_mda_parser/xarray.py new file mode 100644 index 0000000..ea8456e --- /dev/null +++ b/src/metamorph_mda_parser/xarray.py @@ -0,0 +1,51 @@ +try: + import dask.array as da + import xarray as xr + from tifffile.tifffile import imread + from pandas import DataFrame + HAS_XARRAY = True +except ImportError: + HAS_XARRAY = False + + +def dataarray_from_dataframe(df: "DataFrame", channels_3d: list[bool]): + required_columns = ["path", "channel", "position", "time"] + missing_columns = [col for col in required_columns if col not in df.columns] + if missing_columns: + msg = f"Missing columns: {missing_columns}" + raise ValueError(msg) + if df["channel"].max() > len(channels_3d): + msg = f"No dimension information available for certain channels." + raise ValueError(msg) + data_arrays = [_load_file(row, channels_3d) for _, row in df.iterrows()] + return xr.combine_by_coords(data_arrays)["intensity"] + + +def _load_file(row, channels_3d: list[bool]): + path = row['path'] + position = row['position'] + time = row['time'] + channel = row['channel'] + + chunks = (-1,) * (3 if channels_3d[channel] else 2) + with imread(path, aszarr=True) as store: + data = da.from_zarr(store, chunks=chunks) + + # Determine if the array is 2D or 3D + if data.ndim == 2: + data = data[None, ...] # Add a dummy Z dimension + + data_array = xr.DataArray( + data[None, None, None, ...], # Add singleton dimensions for position, time, and channel + dims=['position', 'time', 'channel', 'z', 'y', 'x'], + coords={ + 'position': [int(position)], + 'time': [int(time)], + 'channel': [int(channel)], + 'z': range(data.shape[0]), + 'y': range(data.shape[1]), + 'x': range(data.shape[2]) + } + ) + + return xr.Dataset({'intensity': data_array}) diff --git a/tests/resources/data/sample_3ch_2pos_mixed-z.nd b/tests/resources/data/sample_3ch_2pos_mixed-z.nd new file mode 100644 index 0000000..a9aa926 --- /dev/null +++ b/tests/resources/data/sample_3ch_2pos_mixed-z.nd @@ -0,0 +1,21 @@ +"NDInfoFile", Version 1.0 +"Description", File recreated from images. +"StartTime1", 20241001 12:00:00.000 +"DoTimelapse", FALSE +"DoStage", TRUE +"NStagePositions", 2 +"Stage1", "Position1" +"Stage2", "Position2" +"DoWave", TRUE +"NWavelengths", 3 +"WaveName1", "Conf640" +"WaveDoZ1", FALSE +"WaveName2", "Conf561" +"WaveDoZ2", TRUE +"WaveName3", "Conf488" +"WaveDoZ3", TRUE +"DoZSeries", TRUE +"NZSteps", 42 +"ZStepSize", 3 +"WaveInFileName", TRUE +"EndFile" diff --git a/tests/resources/data/sample_3ch_2pos_mixed-z_w1Conf640_s1.tif b/tests/resources/data/sample_3ch_2pos_mixed-z_w1Conf640_s1.tif new file mode 100644 index 0000000000000000000000000000000000000000..d32adbe3ff25a7b942ab55ba60edec6f0085d425 GIT binary 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Path("tests/resources/data/sample_3ch_2pos_mixed-z.nd") + +def test_data_array_from_nd(sample_3ch_2pos_mixed_z): + ndinfo = NdInfo.from_path(sample_3ch_2pos_mixed_z) + dataarray2d = ndinfo.get_data_array(channels=[0]) + dataarray3d = ndinfo.get_data_array(channels=[1, 2]) + + assert dataarray2d.dims == ("position", "time", "channel", "z", "y", "x") + assert dataarray2d[0, 0, 0, 0, :, :].data.compute().tolist() == [[0,0], [0,128], [0,0]] + assert dataarray2d[1, 0, 0, 0, :, :].data.compute().tolist() == [[0,1], [0,128], [0,0]] + + assert dataarray3d.dims == ("position", "time", "channel", "z", "y", "x") + assert dataarray3d[0, 0, 0, 0, :, :].data.compute().tolist() == [[1,0], [0,128], [0,0]] + assert dataarray3d[0, 0, 1, 0, :, :].data.compute().tolist() == [[2,0], [0,128], [0,0]] + assert dataarray3d[1, 0, 0, 0, :, :].data.compute().tolist() == [[1,1], [0,128], [0,0]] + assert dataarray3d[1, 0, 1, 0, :, :].data.compute().tolist() == [[2,1], [0,128], [0,0]] From 019b1ee143a4bd9cfaa248f15f581c0388574db2 Mon Sep 17 00:00:00 2001 From: Jan Eglinger Date: Tue, 8 Oct 2024 14:33:20 +0200 Subject: [PATCH 2/2] README: add pixi badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index f86ca4a..d7536b6 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ [![PyPI - Version](https://img.shields.io/pypi/v/metamorph-mda-parser.svg)](https://pypi.org/project/metamorph-mda-parser) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/metamorph-mda-parser.svg)](https://pypi.org/project/metamorph-mda-parser) +[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) -----