Return DataArray from NdInfo

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.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/[email protected]
+        with:
+          cache: true
+          environments: ${{ matrix.pixi-environment }}
+
+      - name: Run tests
+        run: pixi run --environment ${{ matrix.pixi-environment }} test

.gitignore

@@ -1,3 +1,6 @@
 dist
 __pycache__
 .coverage*
+# pixi environments
+.pixi
+*.egg-info

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)
 
 -----
 

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"

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)

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})

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"

tests/test_xarray.py

@@ -0,0 +1,25 @@
+import pytest
+from pathlib import Path
+
+from metamorph_mda_parser.nd import NdInfo
+
+pytest.importorskip("xarray")
+
+@pytest.fixture
+def sample_3ch_2pos_mixed_z():
+    return 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]]