Merge pull request #94 from melonora/xarray_datatree

adjust to xarray datatree

.github/workflows/test.yml

@@ -9,7 +9,7 @@ jobs:
       max-parallel: 5
       matrix:
         os: [ubuntu-22.04, windows-2022, macos-12, macos-14]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

.gitignore

@@ -10,6 +10,7 @@ examples/sub-I46_ses-SPIM_sample-BrocaAreaS01_stain-GAD67_chunk-00_SPIM*
 examples/dask-worker-space/
 .pixi/
 examples/Cell_Colony.zarr/
+.idea/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

examples/ConvertTiffFile.ipynb

@@ -10,14 +10,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "cffe4de0",
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "jupyter": {
+     "is_executing": true
+    }
+   },
    "source": [
     "import sys\n",
     "!{sys.executable} -m pip install --upgrade multiscale-spatial-image matplotlib tifffile zarr ome-types dask_image 'dask[diagnostics]'"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
@@ -34,7 +38,7 @@
     "import zarr\n",
     "import ome_types\n",
     "import dask.array as da\n",
-    "import datatree\n",
+    "from xarray import open_datatree\n",
     "from numcodecs import Blosc"
    ]
   },
@@ -1296,7 +1300,7 @@
    "source": [
     "store = zarr.storage.DirectoryStore(f'{image_name}.zarr/0', dimension_separator='/')\n",
     "\n",
-    "new_multiscale = datatree.open_datatree(store, engine='zarr')\n",
+    "new_multiscale = open_datatree(store, engine='zarr')\n",
     "new_multiscale['scale2'].ds[name].isel(x=250).plot.imshow()"
    ]
   }

multiscale_spatial_image/multiscale_spatial_image.py

@@ -1,11 +1,10 @@
 from typing import Union
 
-from datatree import DataTree
+from xarray import DataTree, register_datatree_accessor
 import numpy as np
 from collections.abc import MutableMapping
 from pathlib import Path
 from zarr.storage import BaseStore
-from datatree import register_datatree_accessor
 
 
 @register_datatree_accessor("msi")

multiscale_spatial_image/to_multiscale/itk_image_to_multiscale.py

@@ -3,7 +3,7 @@
 from spatial_image import to_spatial_image
 
 from .to_multiscale import to_multiscale, Methods
-from datatree import DataTree
+from xarray import DataTree
 
 
 def itk_image_to_multiscale(

multiscale_spatial_image/to_multiscale/to_multiscale.py

@@ -4,7 +4,7 @@
 from spatial_image import SpatialImage  # type: ignore
 
 
-from datatree import DataTree
+from xarray import DataTree
 
 from ._xarray import _downsample_xarray_coarsen
 from ._itk import (
@@ -184,6 +184,6 @@ def to_multiscale(
             label="mode",
         )
 
-    multiscale = DataTree.from_dict(d=data_objects)
+    multiscale = DataTree.from_dict(data_objects)
 
     return multiscale

pyproject.toml

@@ -15,11 +15,10 @@ classifiers = [
     'Intended Audience :: Developers',
     'Intended Audience :: Science/Research',
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.8',
-    'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
+    'Programming Language :: Python :: 3.13',
    ]
 keywords = [
     "itk",
@@ -28,18 +27,17 @@ keywords = [
     "zarr",
     "dask",
     "imaging",
-    "visualization",
+    "visualization"
 ]
 dynamic = ["version"]
 
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
     "numpy",
     "dask",
     "python-dateutil",
     "spatial_image>=0.2.1",
-    "xarray",
-    "xarray-datatree>=0.0.5",
+    "xarray>=2024.10.0",
     "zarr",
 ]
 
@@ -71,7 +69,7 @@ dask-image = [
 imagej = [
   "pyimagej",
 ]
-notebooks = ["matplotlib>=3.9.1,<4", "ome-types>=0.5.1.post1,<0.6", "tqdm>=4.66.4,<5"]
+notebooks = ["matplotlib>=3.9.2,<4", "ome-types>=0.5.1.post1,<0.6", "tqdm>=4.66.4,<5"]
 
 [tool.black]
 line-length = 88
@@ -99,21 +97,21 @@ lint = { features = ["lint"], no-default-feature = true, solve-group = "default"
 test = { cmd = "pytest", description = "Run the test suite" }
 
 [tool.pixi.feature.test.dependencies]
-python = "3.9.*"
+python = "3.10.*"
 
 [tool.pixi.feature.notebooks.dependencies]
 openjdk = "8.*"
 maven = ">=3.9.8,<3.10"
 jupyterlab = ">=4.2.4,<4.3"
-python = "3.9.*"
+python = "3.10.*"
 
 [tool.pixi.feature.notebooks.tasks]
 init-imagej = { cmd = "python3 -c \"import imagej; ij = imagej.init('2.15.0'); print(ij.getVersion())\"", description = "Initialize the python imagej installation" }
 test-notebooks = { cmd = "pytest --nbmake --nbmake-timeout=3000 examples/ConvertImageioImageResource.ipynb examples/ConvertITKImage.ipynb examples/ConvertPyImageJDataset.ipynb examples/ConvertTiffFile.ipynb examples/HelloMultiscaleSpatialImageWorld.ipynb", depends-on = ["init-imagej"], description = "Test the notebooks" }
 dev-notebooks = { cmd = "jupyter lab examples", description = "Start Jupyter Lab" }
 
 [tool.pixi.feature.data.dependencies]
-python = ">=3.9.19,<4"
+python = ">=3.10.0,<4"
 pooch = ">=1.8.2,<2"
 
 [tool.pixi.feature.data.tasks]

test/_data.py

@@ -4,7 +4,6 @@
 import pooch
 from zarr.storage import DirectoryStore
 import xarray as xr
-from datatree import open_datatree
 
 test_data_ipfs_cid = "bafybeiaskr5fxg6rbcwlxl6ibzqhubdleacenrpbnymc6oblwoi7ceqzta"
 test_data_sha256 = "507dd779cba007c46ea68a5fe8865cabd5d8a7e00816470faae9195d1f1c3cd1"
@@ -58,7 +57,7 @@ def verify_against_baseline(dataset_name, baseline_name, multiscale):
         test_data_dir / f"baseline/{dataset_name}/{baseline_name}",
         dimension_separator="/",
     )
-    dt = open_datatree(store, engine="zarr", mode="r")
+    dt = xr.open_datatree(store, engine="zarr", mode="r")
     xr.testing.assert_equal(dt.ds, multiscale.ds)
     for scale in multiscale.children:
         xr.testing.assert_equal(dt[scale].ds, multiscale[scale].ds)

test/test_ngff_validation.py

@@ -5,7 +5,7 @@
 from referencing import Registry, Resource
 from jsonschema import Draft202012Validator
 
-from datatree import DataTree
+from xarray import DataTree
 
 from multiscale_spatial_image import to_multiscale, MultiscaleSpatialImage
 from spatial_image import to_spatial_image