ngio 0.2.0b1__py3-none-any.whl → 0.2.0b3__py3-none-any.whl

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/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/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/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/tables/backends/_anndata_utils.py

@@ -41,6 +41,9 @@ def custom_read_zarr(
     """
     group, _ = open_group_wrapper(store=store, mode="r")
 
+    if not isinstance(group.store, zarr.DirectoryStore):
+        elem_to_read = ["X", "obs", "var"]
+
     if elem_to_read is None:
         elem_to_read = [
             "X",

{ngio-0.2.0b1.dist-info → ngio-0.2.0b3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0b1
+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
@@ -41,6 +41,7 @@ Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: scikit-image; extra == 'dev'
 Provides-Extra: docs
+Requires-Dist: mike; extra == 'docs'
 Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs; extra == 'docs'
 Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
@@ -60,7 +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/lorenzocerrone/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.
@@ -96,3 +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-0.2.0b1.dist-info → ngio-0.2.0b3.dist-info}/RECORD

@@ -1,6 +1,6 @@
 ngio/__init__.py,sha256=8-5UcDEIPVIM3mk4GqyBJNteQo0WZNOox1-F6UJoHjg,1001
 ngio/common/__init__.py,sha256=4MLD3Xgr6-I6NwGoY7pa5qQfbfEobFCW3KvLybYcgOc,1373
-ngio/common/_array_pipe.py,sha256=TTdSGJp8eFFycfme_gtdSKk9vcu-A--PhpP4qSi7N40,7840
+ngio/common/_array_pipe.py,sha256=rZQMB3cgMSnpvZpLZEndNZVdWZIOMWgvYqeEOLz7XQ0,7576
 ngio/common/_axes_transforms.py,sha256=kWU0M5erNmgWBXdu5LNv-tLW3jqkT00MMYX7cz-kyHs,2035
 ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,129
 ngio/common/_dimensions.py,sha256=UV2XulWaROb3Y2f4fv27ZkTIu-MoS53U26aDkrv-_lk,3900
@@ -12,12 +12,12 @@ ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
 ngio/hcs/__init__.py,sha256=9YNmtHgCKhYSjmAE2-YVg5BycH-5cQGAE9xFrxxWo8c,188
 ngio/hcs/plate.py,sha256=b-EHns-OGQF_RXEa-GDzP2TJFqpRFc0rBKdgf4l7MwU,12409
 ngio/images/__init__.py,sha256=aijqG14eyqVgHtnlcKVNx37FRfT6QvKt8V6bwBpX_r8,526
-ngio/images/abstract_image.py,sha256=zA1LAZNAuBmZwInUhL33NiFLsCtfyEhI-4XPIRQgCIg,8770
+ngio/images/abstract_image.py,sha256=UQpcp--SzJITIZfSg_KZWU9_mIC11LdHTuITJdxCNTE,9671
 ngio/images/create.py,sha256=wQfoB9pmQkHFFYE3WNbhgQt36XhoTopGcPGcEXTNI-0,9764
 ngio/images/image.py,sha256=BL9TINwYrT2_HdkhCKoRcfy7XqiiwEIVQvHDFkF8ZWc,15246
 ngio/images/label.py,sha256=gvVuRUsrDBk-EpsuUMepC4M5hYPb5yTVvWwozaLM7-g,9333
 ngio/images/masked_image.py,sha256=4YYVqf8OtIp-wWGVGUKMHMTqod4p4F7ZyWrsUIXMjEs,7905
-ngio/images/omezarr_container.py,sha256=80bqjl3Km7lAp0p_eKOpslgCY1UEj-7kM8M67THUZHo,26469
+ngio/images/omezarr_container.py,sha256=db5KnWAfWoaEekNmWxVQPAI3xXXeQGItQ3gvBbr55VA,27376
 ngio/ome_zarr_meta/__init__.py,sha256=EfBX9ppb_wliSIcVb4NBDt3dFVldeIJ0h9tY9HELRY4,1075
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=BLvYt5PONYrWkEb2XgEiAXR_OX9rfeX_C0eEqen0jQA,25549
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=ZpghXfbq0r-YJklD7J76BRMTlzEIAJFzneYlsosdyTY,1548
@@ -25,7 +25,7 @@ ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=zgAE0-2DHzJfqGqBhyjY7y_6qAgDLdV9iu
 ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=ufZuYuTO5PJA1vcBrNAcuZCMgIEwF57buPloTHIzB1Q,14082
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=xT4GY2mdIsm6nAP8bXRj5E9-P6rS-iwzcXT_o3pZajo,4696
 ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=YQlobPYU7vbo9fShHQyCfzLlDUlP-mprAivay6W4-A0,11610
-ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=6bJNONxf1UbpxF635Dckm7RTG11zY0EWyRNtQAUkBYw,17004
+ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=74L3ibo0SurKnbkxt0Re9jEVcLf63ZJouL2ZHpHZDbc,16776
 ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=QZy94THDBkeLgOtN6o_jF3oXSewRxdM2E7ZTSBTo7RU,3878
 ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=G4GGarkktjdsIzHUhaoZEL69-r-ZLpLz6y5TDVsN4W0,15939
@@ -34,7 +34,7 @@ ngio/tables/_validators.py,sha256=RzF09YrlUSb-xdVlosuU-_BaLswtvhpduHfzLaWu2mY,64
 ngio/tables/tables_container.py,sha256=FXp-s_zKqbMcBFh4515kbSdxYaFK1ULE2Pf0pzlnpEE,9845
 ngio/tables/backends/__init__.py,sha256=NlOXmZXDA1kOCVONUyo_aqSjdMHmfqk-3xuKBLXpaUM,217
 ngio/tables/backends/_abstract_backend.py,sha256=JlaHqLjDm2uVnXFWxsHMojNeKo3leg6uauzoFMSF5O4,2256
-ngio/tables/backends/_anndata_utils.py,sha256=TnrjOI70tSRl0bYJvVzvMSMojD61GDK3Uo8wS6EOXZg,6816
+ngio/tables/backends/_anndata_utils.py,sha256=zo85K0bwgyQKBj8hQASfOSWugdd4BPUTyT6_tRO58fI,6917
 ngio/tables/backends/_anndata_v1.py,sha256=hhEwoBybWFDHqajOk_JEazniYmhAlCehOYTtmcYJfyY,2615
 ngio/tables/backends/_json_v1.py,sha256=9ZC0d_tMiiugm-VXDL3sRFfESzSnnY9kAtSxoXYV-dY,1910
 ngio/tables/backends/_table_backends.py,sha256=XXtnZqVDbMqFkbUkHbf9IBNz4teCouLpa5fWgEgVtfg,3269
@@ -48,7 +48,7 @@ ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=7qoGLiLi8JQFh9Ej_z5WNwQQuWrujb0f6p9nj8ocsS8,548
 ngio/utils/_logger.py,sha256=HIuqD_2ShfFGDswBddcouStbKfL0Vz_ah8cAIFGhbS8,888
 ngio/utils/_zarr_utils.py,sha256=r075cNpr-JHZ1PaDHX1KlENIGMvLf-WTTYwpODACWm4,12924
-ngio-0.2.0b1.dist-info/METADATA,sha256=J-tCuj8BXolhGSU57DFUkgm3dvFkyQq9JQy5MrXznTs,4933
-ngio-0.2.0b1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.0b1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.0b1.dist-info/RECORD,,
+ngio-0.2.0b3.dist-info/METADATA,sha256=hvC4PR-EEJBiDvSHl4Bq_0I924a0ifhf0r1vdVsiQ6k,4995
+ngio-0.2.0b3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.0b3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.0b3.dist-info/RECORD,,