ngio 0.2.0b2__tar.gz → 0.2.0b3__tar.gz

{ngio-0.2.0b2 → ngio-0.2.0b3}/.github/workflows/build_docs.yml

@@ -56,5 +56,6 @@ jobs:
             echo "Deployed stable version"
           else
             mike deploy --push dev
+            mike set-default --push dev
             echo "Deployed development version"
-          fi
+          fi

{ngio-0.2.0b2 → ngio-0.2.0b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0b2
+Version: 0.2.0b3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -61,7 +61,7 @@ Description-Content-Type: text/markdown
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
+[![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
 NGIO is a Python library to streamline OME-Zarr image analysis workflows.
@@ -97,3 +97,4 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
 | Full Documentation | Not started | 2025 | Complete Documentation |
 | Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |
+

{ngio-0.2.0b2 → ngio-0.2.0b3}/README.md

@@ -3,7 +3,7 @@
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
+[![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
 NGIO is a Python library to streamline OME-Zarr image analysis workflows.
@@ -39,3 +39,4 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
 | Full Documentation | Not started | 2025 | Complete Documentation |
 | Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |
+

{ngio-0.2.0b2 → ngio-0.2.0b3}/src/ngio/common/_array_pipe.py

@@ -179,13 +179,6 @@ def _mask_pipe_common(
         **slice_kwargs,
     )
 
-    if "c" in slice_kwargs.keys():
-        # This makes the strong assumption that the
-        # user is passing the channel axis as "c"
-        # This will fail if the channel axis is queried
-        # with a different on-disk name
-        slice_kwargs.pop("c")
-
     label_patch = get_pipe(
         label_array,
         dimensions=dimensions_label,

{ngio-0.2.0b2 → ngio-0.2.0b3}/src/ngio/images/abstract_image.py

@@ -99,6 +99,36 @@ class AbstractImage(Generic[_image_handler]):
         """Return the dimensions of the image."""
         return self._dimensions
 
+    @property
+    def is_3d(self) -> bool:
+        """Return True if the image is 3D."""
+        return self.dimensions.is_3d
+
+    @property
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.dimensions.is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.dimensions.is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.dimensions.is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.dimensions.is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.dimensions.is_multi_channels
+
     @property
     def pixel_size(self) -> PixelSize:
         """Return the pixel size of the image."""

{ngio-0.2.0b2 → ngio-0.2.0b3}/src/ngio/images/omezarr_container.py

@@ -125,6 +125,36 @@ class OmeZarrContainer:
         """Return the paths of the levels in the image."""
         return self._images_container.levels_paths
 
+    @property
+    def is_3d(self) -> bool:
+        """Return True if the image is 3D."""
+        return self.get_image().is_3d
+
+    @property
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.get_image().is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.get_image().is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.get_image().is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.get_image().is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.get_image().is_multi_channels
+
     def initialize_channel_meta(
         self,
         labels: Collection[str] | int | None = None,

{ngio-0.2.0b2 → ngio-0.2.0b3}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -342,12 +342,6 @@ class NgioLabelMeta(AbstractNgioImageMeta):
     ) -> None:
         """Initialize the ImageMeta object."""
         super().__init__(version, name, datasets)
-
-        # Make sure that there are no channel axes
-        channel_axis = self.axes_mapper.get_axis("c")
-        if channel_axis is not None:
-            raise NgioValidationError("Label metadata must not have channel axes.")
-
         image_label = (
             ImageLabelSource.default_init(self.version)
             if image_label is None

{ngio-0.2.0b2 → ngio-0.2.0b3}/tests/unit/images/test_omezarr_container.py

@@ -79,6 +79,11 @@ def test_create_omezarr_container(tmp_path: Path, array_mode: str):
     assert isinstance(omezarr.__repr__(), str)
     assert omezarr.levels == 3
     assert omezarr.levels_paths == ["0", "1", "2"]
+    assert omezarr.is_3d
+    assert not omezarr.is_time_series
+    assert not omezarr.is_multi_channels
+    assert not omezarr.is_2d_time_series
+    assert not omezarr.is_3d_time_series
 
     image = omezarr.get_image()
 

{ngio-0.2.0b2 → ngio-0.2.0b3}/tests/unit/test_ome_zarr_meta/test_unit_ngio_specs.py

@@ -438,7 +438,7 @@ def test_label_meta():
     assert label_meta.get_dataset(pixel_size=datasets[-1].pixel_size).path == "3"
 
 
-def test_fail_label_meta():
+def test_channels_label_meta():
     on_disk_axes = [
         Axis(on_disk_name="t", axis_type=AxisType.time, unit=TimeUnits.s),
         Axis(on_disk_name="c"),
@@ -465,9 +465,4 @@ def test_fail_label_meta():
             s * f for s, f in zip(on_disk_scale, [1, 1, 1, 2, 2], strict=True)
         ]
 
-    with pytest.raises(ValueError):
-        NgioLabelMeta(
-            version="0.4",
-            name="test",
-            datasets=datasets,
-        )
+    _ = NgioLabelMeta(version="0.4", name="test", datasets=datasets)