ngio 0.5.0b4__tar.gz → 0.5.0b6__tar.gz

{ngio-0.5.0b4 → ngio-0.5.0b6}/.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:

{ngio-0.5.0b4 → ngio-0.5.0b6}/CHANGELOG.md

@@ -19,6 +19,9 @@
 - Internal changes to `ZarrGroupHandler` to support cleanup unused apis.
 - Remove `ngio_logger` in favor of standard warnings module.
 
+### Bug Fixes
+- Fix bug in `consolidate` function when using corsening mode with non power-of-two shapes.
+
 ## [v0.4.7]
 
 ### Bug Fixes

{ngio-0.5.0b4 → ngio-0.5.0b6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b4
+Version: 0.5.0b6
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -13,8 +13,9 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Typing :: Typed
-Requires-Python: <3.14,>=3.11
+Requires-Python: <3.15,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata
 Requires-Dist: dask[array]<2025.11.0

{ngio-0.5.0b4 → ngio-0.5.0b6}/pyproject.toml

@@ -18,7 +18,7 @@ name = "ngio"
 dynamic = ["version"]
 description = "Next Generation file format IO"
 readme = "README.md"
-requires-python = ">=3.11,<3.14"
+requires-python = ">=3.11,<3.15"
 license = { text = "BSD-3-Clause" }
 authors = [{ name = "Lorenzo Cerrone", email = "lorenzo.cerrone@uzh.ch" }]
 # https://pypi.org/classifiers/
@@ -29,6 +29,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Typing :: Typed",
 ]
 # add your package dependencies here

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/common/_pyramid.py

@@ -92,16 +92,7 @@ def _on_disk_coarsen(
 
     coarsening_setup = {}
     for i, s in enumerate(_scale):
-        factor = 1 / s
-        # This check is very strict, but it is necessary to avoid
-        # a few pixels shift in the coarsening
-        # We could add a tolerance
-        if factor.is_integer():
-            coarsening_setup[i] = int(factor)
-        else:
-            raise NgioValueError(
-                f"Coarsening factor must be an integer, got {factor} on axis {i}"
-            )
+        coarsening_setup[i] = int(np.round(1 / s))
 
     out_target = da.coarsen(
         aggregation_function, source_array, coarsening_setup, trim_excess=True

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/common/_roi.py

@@ -1,6 +1,6 @@
 """Region of interest (ROI) metadata.
 
-These are the interfaces bwteen the ROI tables / masking ROI tables and
+These are the interfaces between the ROI tables / masking ROI tables and
     the ImageLikeHandler.
 """
 

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/images/_abstract_image.py

@@ -822,7 +822,6 @@ def abstract_derive(
         pixelsize (float | tuple[float, float] | None): The pixel size of the new image.
         z_spacing (float | None): The z spacing of the new image.
         time_spacing (float | None): The time spacing of the new image.
-        axes_names (Sequence[str] | None): The axes names of the new image.
         name (str | None): The name of the new image.
         channels_policy (Literal["squeeze", "same", "singleton"] | int):
             Possible policies:
@@ -837,7 +836,7 @@ def abstract_derive(
         chunks (ChunksLike | None): The chunk shape of the new image.
         shards (ShardsLike | None): The shard shape of the new image.
         dtype (str | None): The data type of the new image.
-        dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+        dimension_separator (Literal[".", "/"] | None): The separator to use for
             dimensions.
         compressors (CompressorLike | None): The compressors to use.
         extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/images/_image.py

@@ -656,7 +656,7 @@ class ImagesContainer:
             chunks (ChunksLike | None): The chunk shape of the new image.
             shards (ShardsLike | None): The shard shape of the new image.
             dtype (str | None): The data type of the new image.
-            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+            dimension_separator (Literal[".", "/"] | None): The separator to use for
                 dimensions.
             compressors (CompressorLike | None): The compressors to use.
             extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/images/_label.py

@@ -232,24 +232,18 @@ class LabelsContainer:
         labels: Sequence[str] | None = None,
         pixel_size: PixelSize | None = None,
     ) -> "Label":
-        """Create an empty OME-Zarr image from an existing image.
+        """Create an empty OME-Zarr label from an existing image or label.
 
         If a kwarg is not provided, the value from the reference image will be used.
 
         Args:
-            store (StoreOrGroup): The Zarr store or group to create the image in.
-            ref_image (Image | Label): The reference image to derive the new image from.
-            shape (Sequence[int] | None): The shape of the new image.
+            name (str): The name of the new label.
+            ref_image (Image | Label): The reference image to derive the new label from.
+            shape (Sequence[int] | None): The shape of the new label.
             pixelsize (float | tuple[float, float] | None): The pixel size of the new
-                image.
-            z_spacing (float | None): The z spacing of the new image.
-            time_spacing (float | None): The time spacing of the new image.
-            scaling_factors (Sequence[float] | Literal["auto"] | None): The scaling
-                factors of the new image.
-            axes_names (Sequence[str] | None): The axes names of the new image.
-            name (str | None): The name of the new image.
-            channels_meta (Sequence[str | Channel] | None): The channels metadata
-                of the new image.
+                label.
+            z_spacing (float | None): The z spacing of the new label.
+            time_spacing (float | None): The time spacing of the new label.
             channels_policy (Literal["squeeze", "same", "singleton"] | int):
                 Possible policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
@@ -258,19 +252,19 @@ class LabelsContainer:
                 - If an integer is provided, the channels axis will be changed to have
                     that size.
             ngff_version (NgffVersions | None): The NGFF version to use.
-            chunks (ChunksLike | None): The chunk shape of the new image.
-            shards (ShardsLike | None): The shard shape of the new image.
-            dtype (str | None): The data type of the new image.
-            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+            chunks (ChunksLike | None): The chunk shape of the new label.
+            shards (ShardsLike | None): The shard shape of the new label.
+            dtype (str | None): The data type of the new label.
+            dimension_separator (Literal[".", "/"] | None): The separator to use for
                 dimensions.
             compressors (CompressorLike | None): The compressors to use.
             extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to
                 the zarr array creation.
-            overwrite (bool): Whether to overwrite an existing image.
-            labels (Sequence[str] | None): The labels of the new image.
-                This argument is deprecated please use channels_meta instead.
-            pixel_size (PixelSize | None): The pixel size of the new image.
-                This argument is deprecated please use pixelsize, z_spacing,
+            overwrite (bool): Whether to overwrite an existing label.
+            labels (Sequence[str] | None): Deprecated. This argument is deprecated,
+                please use channels_meta instead.
+            pixel_size (PixelSize | None): Deprecated. The pixel size of the new label.
+                This argument is deprecated, please use pixelsize, z_spacing,
                 and time_spacing instead.
 
         Returns:

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/images/_ome_zarr_container.py

@@ -266,8 +266,8 @@ class OmeZarrContainer:
 
     def set_channel_meta(
         self,
-        labels: Sequence[str] | int | None = None,
-        wavelength_id: Sequence[str] | None = None,
+        labels: Sequence[str | None] | int | None = None,
+        wavelength_id: Sequence[str | None] | None = None,
         percentiles: tuple[float, float] | None = None,
         colors: Sequence[str] | None = None,
         active: Sequence[bool] | None = None,
@@ -462,7 +462,8 @@ class OmeZarrContainer:
             z_spacing (float | None): The z spacing of the new image.
             time_spacing (float | None): The time spacing of the new image.
             name (str | None): The name of the new image.
-            channels_policy (Literal["squeeze", "same"] | int): Possible policies:
+            channels_policy (Literal["squeeze", "same", "singleton"] | int): Possible
+                policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
                 - If "same", the channels axis will be kept as is (if it exists).
                 - If "singleton", the channels axis will be set to size 1.
@@ -814,7 +815,8 @@ class OmeZarrContainer:
                 label.
             z_spacing (float | None): The z spacing of the new label.
             time_spacing (float | None): The time spacing of the new label.
-            channels_policy (Literal["same", "squeeze"] | int): Possible policies:
+            channels_policy (Literal["same", "squeeze", "singleton"] | int): Possible
+                policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
                 - If "same", the channels axis will be kept as is (if it exists).
                 - If "singleton", the channels axis will be set to size 1.

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/ome_zarr_meta/__init__.py

@@ -15,6 +15,9 @@ from ngio.ome_zarr_meta._meta_handlers import (
 )
 from ngio.ome_zarr_meta.ngio_specs import (
     AxesHandler,
+    Channel,
+    ChannelsMeta,
+    ChannelVisualisation,
     Dataset,
     DefaultNgffVersion,
     ImageInWellPath,
@@ -31,6 +34,9 @@ from ngio.ome_zarr_meta.ngio_specs import (
 
 __all__ = [
     "AxesHandler",
+    "Channel",
+    "ChannelVisualisation",
+    "ChannelsMeta",
     "Dataset",
     "DefaultNgffVersion",
     "ImageInWellPath",

{ngio-0.5.0b4 → ngio-0.5.0b6}/src/ngio/utils/_datasets.py

@@ -155,5 +155,11 @@ def download_ome_zarr_dataset(
         path=download_dir,
         processor=processor,
         progressbar=progressbar,
+        # Add User-Agent to avoid 403 errors from Zenodo
+        downloader=pooch.HTTPDownloader(
+            headers={
+                "User-Agent": f"pooch/{pooch.__version__} (https://github.com/BioVisionCenter/ngio)"
+            }
+        ),
     )
     return processor.output_file()

{ngio-0.5.0b4 → ngio-0.5.0b6}/tests/unit/images/test_images.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 
 import pytest
+from zarr.storage import MemoryStore
 
 from ngio import Image, create_empty_ome_zarr, open_image
 from ngio.transforms import ZoomTransform
@@ -250,3 +251,37 @@ def test_derive_image_consistency(
 
     label = ome_zarr.derive_label("derived_label")
     assert label.path == "s0"
+
+
+@pytest.mark.parametrize(
+    ("shape", "factors"),
+    [
+        ((1, 1111, 1111), (1, 2, 2)),
+        ((1, 1111, 1111), (1, 4, 4)),
+        ((1, 1111, 1111), (1, 3, 3)),
+    ],
+)
+def test_consolidate_consistency(shape, factors):
+    store = MemoryStore()
+    ome_zarr = create_empty_ome_zarr(
+        store,
+        shape=shape,
+        axes_names="zyx",
+        xy_pixelsize=1.0,
+        scaling_factors=factors,
+        levels=3,
+    )
+    image = ome_zarr.get_image()
+    image.consolidate()
+
+    derived_store = MemoryStore()
+    derived_ome_zarr = ome_zarr.derive_image(derived_store)
+    derived_image = derived_ome_zarr.get_image()
+    derived_image.consolidate()
+
+    for level_path in ome_zarr.levels_paths:
+        img1 = ome_zarr.get_image(path=level_path)
+        img2 = derived_ome_zarr.get_image(path=level_path)
+        assert img1.shape == img2.shape, (
+            f"Shapes do not match at level {level_path}: {img1.shape} vs {img2.shape}"
+        )