ngio 0.5.0b3__tar.gz → 0.5.0b5__tar.gz

{ngio-0.5.0b3 → ngio-0.5.0b5}/.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-0.5.0b3 → ngio-0.5.0b5}/CHANGELOG.md

@@ -6,6 +6,7 @@
 - Add support for OME-NGFF v0.5
 - Move to zarr-python v3
 - API to delete labels and tables from OME-Zarr containers and HCS plates.
+- Allow to explicitly set axes order when building masking roi tables.
 
 ### API Breaking Changes
 
@@ -18,7 +19,13 @@
 - Internal changes to `ZarrGroupHandler` to support cleanup unused apis.
 - Remove `ngio_logger` in favor of standard warnings module.
 
-## [v0.4.6]
+### Bug Fixes
+- Fix bug in `consolidate` function when using corsening mode with non power-of-two shapes.
+
+## [v0.4.7]
+
+### Bug Fixes
+- Fix bug adding time axis to masking roi tables.
 
 ### Bug Fixes
 - Fix channel selection from `wavelength_id`

{ngio-0.5.0b3 → ngio-0.5.0b5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b3
+Version: 0.5.0b5
 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-0.5.0b3 → ngio-0.5.0b5}/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-0.5.0b3 → ngio-0.5.0b5}/src/ngio/common/_masking_roi.py

@@ -1,6 +1,7 @@
 """Utilities to build masking regions of interest (ROIs)."""
 
 import itertools
+from collections.abc import Sequence
 
 import dask.array as da
 import numpy as np
@@ -115,7 +116,9 @@ def lazy_compute_slices(segmentation: da.Array) -> dict[int, tuple[slice, ...]]:
 
 
 def compute_masking_roi(
-    segmentation: np.ndarray | da.Array, pixel_size: PixelSize
+    segmentation: np.ndarray | da.Array,
+    pixel_size: PixelSize,
+    axes_order: Sequence[str],
 ) -> list[Roi]:
     """Compute a ROIs for each label in a segmentation.
 
@@ -127,6 +130,12 @@ def compute_masking_roi(
     if segmentation.ndim not in [2, 3, 4]:
         raise NgioValueError("Only 2D, 3D, and 4D segmentations are supported.")
 
+    if len(axes_order) != segmentation.ndim:
+        raise NgioValueError(
+            "The length of axes_order must match the number of dimensions "
+            "of the segmentation."
+        )
+
     if isinstance(segmentation, da.Array):
         slices = lazy_compute_slices(segmentation)
     else:
@@ -134,24 +143,11 @@ def compute_masking_roi(
 
     rois = []
     for label, slice_ in slices.items():
-        if len(slice_) == 2:
-            slices = {"y": slice_[0], "x": slice_[1]}
-        elif len(slice_) == 3:
-            slices = {"z": slice_[0], "y": slice_[1], "x": slice_[2]}
-        elif len(slice_) == 4:
-            slices = {
-                "t": slice_[0],
-                "z": slice_[1],
-                "y": slice_[2],
-                "x": slice_[3],
-            }
-        else:
-            raise ValueError("Invalid slice length.")
-
+        assert len(slice_) == len(axes_order)
+        slices = dict(zip(axes_order, slice_, strict=True))
         roi = Roi.from_values(
             name=str(label), slices=slices, label=label, space="pixel"
         )
-
         roi = roi.to_world(pixel_size=pixel_size)
         rois.append(roi)
     return rois

{ngio-0.5.0b3 → ngio-0.5.0b5}/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-0.5.0b3 → ngio-0.5.0b5}/src/ngio/common/_roi.py

@@ -4,7 +4,7 @@ These are the interfaces bwteen the ROI tables / masking ROI tables and
     the ImageLikeHandler.
 """
 
-from collections.abc import Callable
+from collections.abc import Callable, Mapping
 from typing import Literal, Self
 
 from pydantic import BaseModel, ConfigDict, Field, field_validator
@@ -183,7 +183,7 @@ class Roi(BaseModel):
     @classmethod
     def from_values(
         cls,
-        slices: dict[str, float | tuple[float | None, float | None] | slice],
+        slices: Mapping[str, float | tuple[float | None, float | None] | slice],
         name: str | None,
         label: int | None = None,
         space: Literal["world", "pixel"] = "world",

{ngio-0.5.0b3 → ngio-0.5.0b5}/src/ngio/images/_abstract_image.py

@@ -615,7 +615,6 @@ def _shapes_from_ref_image(
     if len(shapes) == len(paths):
         return shapes
     missing_levels = len(paths) - len(shapes)
-    print(ref_image.meta.scaling_factor())
     extended_shapes = shapes_from_scaling_factors(
         base_shape=shapes[-1],
         scaling_factors=ref_image.meta.scaling_factor(),
@@ -918,7 +917,6 @@ def abstract_derive(
 
     if chunks is None:
         chunks = ref_image.zarr_array.chunks
-    print(chunks)
     if shards is None:
         shards = ref_image.zarr_array.shards
 

{ngio-0.5.0b3 → ngio-0.5.0b5}/src/ngio/images/_label.py

@@ -97,9 +97,11 @@ class Label(AbstractImage):
         meta = meta.to_units(space_unit=space_unit, time_unit=time_unit)
         self.meta_handler.update_meta(meta)
 
-    def build_masking_roi_table(self) -> MaskingRoiTable:
+    def build_masking_roi_table(
+        self, axes_order: Sequence[str] | None = None
+    ) -> MaskingRoiTable:
         """Compute the masking ROI table."""
-        return build_masking_roi_table(self)
+        return build_masking_roi_table(self, axes_order=axes_order)
 
     def consolidate(
         self,
@@ -405,8 +407,11 @@ def derive_label(
     return group_handler
 
 
-def build_masking_roi_table(label: Label) -> MaskingRoiTable:
+def build_masking_roi_table(
+    label: Label, axes_order: Sequence[str] | None = None
+) -> MaskingRoiTable:
     """Compute the masking ROI table for a label."""
-    array = label.get_as_dask(axes_order=["t", "z", "y", "x"])
-    rois = compute_masking_roi(array, label.pixel_size)
+    axes_order = axes_order or label.axes
+    array = label.get_as_dask(axes_order=axes_order)
+    rois = compute_masking_roi(array, label.pixel_size, axes_order=axes_order)
     return MaskingRoiTable(rois, reference_label=label.meta.name)

{ngio-0.5.0b3 → ngio-0.5.0b5}/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-0.5.0b3 → ngio-0.5.0b5}/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
@@ -225,7 +226,6 @@ def test_zoom_virtual_axes(
     assert img2_data.shape[0] == 1  # Virtual channel axis
 
     roi = img1.build_image_roi_table().rois()[0]
-    print(roi)
     img2_roi_data = img2.get_roi_as_numpy(roi, transforms=[zoom], axes_order="czyx")
     # Roi data should match exactly except for virtual axis
     assert img1_data.shape[1:] == img2_roi_data.shape[1:]
@@ -251,3 +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}"
+        )

{ngio-0.5.0b3 → ngio-0.5.0b5}/tests/unit/tables/test_backends.py

@@ -111,8 +111,6 @@ def test_csv_backend(tmp_path: Path):
 
     backend.write(test_table, metadata={"test": "test"})
     loaded_table = backend.load_as_pandas_df()
-    print(loaded_table)
-    print(test_table)
     assert loaded_table.equals(test_table), loaded_table
     meta = backend._group_handler.load_attrs()
     assert meta["test"] == "test"