ngio 0.3.0a1__py3-none-any.whl → 0.3.1__py3-none-any.whl

ngio/common/_array_pipe.py

@@ -1,10 +1,11 @@
 from collections.abc import Collection, Iterable
 from typing import Literal
 
-import dask
-import dask.delayed
+import dask.array as da
 import numpy as np
 import zarr
+from dask.array import Array as DaskArray
+from dask.delayed import Delayed, delayed
 
 from ngio.common._axes_transforms import transform_dask_array, transform_numpy_array
 from ngio.common._common_types import ArrayLike
@@ -55,26 +56,26 @@ def _numpy_get_pipe(
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
 ) -> np.ndarray:
-    array = numpy_get_slice(array, slices)
-    return transform_numpy_array(array, transformations)
+    _array = numpy_get_slice(array, slices)
+    return transform_numpy_array(_array, transformations)
 
 
 def _delayed_numpy_get_pipe(
     array: zarr.Array,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
-) -> dask.delayed:
-    array = dask.delayed(numpy_get_slice)(array, slices)
-    return dask.delayed(transform_numpy_array)(array, transformations)
+) -> Delayed:
+    _array = delayed(numpy_get_slice)(array, slices)
+    return delayed(transform_numpy_array)(_array, transformations)
 
 
 def _dask_get_pipe(
     array: zarr.Array,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
-) -> dask.array:
-    array = dask_get_slice(array, slices)
-    return transform_dask_array(array, transformations)
+) -> DaskArray:
+    _array = dask_get_slice(array, slices)
+    return transform_dask_array(_array, transformations)
 
 
 def _numpy_set_pipe(
@@ -89,22 +90,22 @@ def _numpy_set_pipe(
 
 def _dask_set_pipe(
     array: zarr.Array,
-    patch: np.ndarray,
+    patch: DaskArray,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
 ) -> None:
-    patch = transform_dask_array(patch, transformations)
-    dask_set_slice(array, patch, slices)
+    _patch = transform_dask_array(patch, transformations)
+    dask_set_slice(array, _patch, slices)
 
 
 def _delayed_numpy_set_pipe(
     array: zarr.Array,
-    patch: np.ndarray,
+    patch: np.ndarray | Delayed,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
-) -> dask.delayed:
-    patch = dask.delayed(transform_numpy_array)(patch, transformations)
-    return dask.delayed(numpy_set_slice)(array, patch, slices)
+) -> Delayed:
+    _patch = delayed(transform_numpy_array)(patch, transformations)
+    return delayed(numpy_set_slice)(array, _patch, slices)
 
 
 def get_pipe(
@@ -144,7 +145,7 @@ def set_pipe(
     slices, transformations = _compute_to_disk_transforms(
         dimensions=dimensions, axes_order=axes_order, **slice_kwargs
     )
-    if isinstance(patch, dask.array.Array):
+    if isinstance(patch, DaskArray):
         _dask_set_pipe(
             array=array, patch=patch, slices=slices, transformations=transformations
         )
@@ -152,7 +153,7 @@ def set_pipe(
         _numpy_set_pipe(
             array=array, patch=patch, slices=slices, transformations=transformations
         )
-    elif isinstance(patch, dask.delayed.Delayed):
+    elif isinstance(patch, Delayed):
         _delayed_numpy_set_pipe(
             array=array, patch=patch, slices=slices, transformations=transformations
         )
@@ -193,12 +194,15 @@ def _mask_pipe_common(
         **slice_kwargs,
     )
 
-    if isinstance(array_patch, np.ndarray):
+    if isinstance(array_patch, np.ndarray) and isinstance(label_patch, np.ndarray):
         label_patch = np.broadcast_to(label_patch, array_patch.shape)
-    elif isinstance(array_patch, dask.array.Array):
-        label_patch = dask.array.broadcast_to(label_patch, array_patch.shape)
+    elif isinstance(array_patch, DaskArray) and isinstance(label_patch, DaskArray):
+        label_patch = da.broadcast_to(label_patch, array_patch.shape)
     else:
-        raise NgioValueError(f"Mode {mode} not yet supported for masked array.")
+        raise NgioValueError(
+            "Incompatible types for array and label: "
+            f"{type(array_patch)} and {type(label_patch)}"
+        )
 
     mask = label_patch == label
     return array_patch, mask
@@ -225,7 +229,14 @@ def get_masked_pipe(
         mode=mode,
         **slice_kwargs,
     )
-    array_patch[~mask] = 0
+    if isinstance(array_patch, np.ndarray):
+        array_patch[~mask] = 0
+    elif isinstance(array_patch, DaskArray):
+        array_patch = da.where(mask, array_patch, 0)
+    else:
+        raise NgioValueError(
+            "Mode not yet supported for masked array. Expected a numpy or dask array."
+        )
     return array_patch
 
 
@@ -240,7 +251,7 @@ def set_masked_pipe(
     axes_order: Collection[str] | None = None,
     **slice_kwargs: slice | int | Iterable[int],
 ):
-    if isinstance(patch, dask.array.Array):
+    if isinstance(patch, DaskArray):
         mode = "dask"
     elif isinstance(patch, np.ndarray):
         mode = "numpy"
@@ -259,7 +270,19 @@ def set_masked_pipe(
         mode=mode,
         **slice_kwargs,
     )
-    patch = np.where(mask, patch, array_patch)
+    if isinstance(patch, np.ndarray):
+        assert isinstance(array_patch, np.ndarray)
+        _patch = np.where(mask, patch, array_patch)
+    elif isinstance(patch, DaskArray):
+        _patch = da.where(mask, patch, array_patch)
+    else:
+        raise NgioValueError(
+            "Mode not yet supported for masked array. Expected a numpy or dask array."
+        )
     set_pipe(
-        array, patch, dimensions=dimensions_array, axes_order=axes_order, **slice_kwargs
+        array,
+        _patch,
+        dimensions=dimensions_array,
+        axes_order=axes_order,
+        **slice_kwargs,
     )

ngio/common/_table_ops.py

@@ -9,7 +9,7 @@ from typing import Literal
 import pandas as pd
 import polars as pl
 
-from ngio.images.ome_zarr_container import OmeZarrContainer
+from ngio.images._ome_zarr_container import OmeZarrContainer
 from ngio.tables import Table, TableType
 
 

ngio/hcs/__init__.py

@@ -1,6 +1,6 @@
 """OME-Zarr HCS objects models."""
 
-from ngio.hcs.plate import (
+from ngio.hcs._plate import (
     OmeZarrPlate,
     OmeZarrWell,
     create_empty_plate,

ngio/hcs/{plate.py → _plate.py}

@@ -39,7 +39,6 @@ from ngio.tables import (
 )
 from ngio.utils import (
     AccessModeLiteral,
-    NgioValidationError,
     NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
@@ -805,22 +804,38 @@ class OmeZarrPlate:
             parallel_safe=parallel_safe,
         )
 
-    @property
-    def tables_container(self) -> TablesContainer:
+    def _get_tables_container(self) -> TablesContainer | None:
         """Return the tables container."""
         if self._tables_container is None:
-            self._tables_container = _default_table_container(self._group_handler)
-            if self._tables_container is None:
-                raise NgioValidationError("No tables found in the image.")
+            _tables_container = _default_table_container(self._group_handler)
+            if _tables_container is None:
+                return None
+            self._tables_container = _tables_container
         return self._tables_container
 
-    def list_tables(self, filter_types: str | None = None) -> list[str]:
+    @property
+    def tables_container(self) -> TablesContainer:
+        """Return the tables container."""
+        _table_container = self._get_tables_container()
+        if _table_container is None:
+            raise NgioValueError(
+                "No tables container found. Please add a tables container to the plate."
+            )
+        return _table_container
+
+    def list_tables(self, filter_types: TypedTable | str | None = None) -> list[str]:
         """List all tables in the image."""
         return self.tables_container.list(filter_types=filter_types)
 
     def list_roi_tables(self) -> list[str]:
         """List all ROI tables in the image."""
-        return self.tables_container.list_roi_tables()
+        masking_roi = self.tables_container.list(
+            filter_types="masking_roi_table",
+        )
+        roi = self.tables_container.list(
+            filter_types="roi_table",
+        )
+        return masking_roi + roi
 
     def get_roi_table(self, name: str) -> RoiTable:
         """Get a ROI table from the image.

ngio/images/__init__.py

@@ -1,8 +1,8 @@
 """OME-Zarr object models."""
 
-from ngio.images.image import Image, ImagesContainer
-from ngio.images.label import Label, LabelsContainer
-from ngio.images.ome_zarr_container import (
+from ngio.images._image import Image, ImagesContainer
+from ngio.images._label import Label, LabelsContainer
+from ngio.images._ome_zarr_container import (
     OmeZarrContainer,
     create_empty_ome_zarr,
     create_ome_zarr_from_array,

ngio/images/{image.py → _image.py}

@@ -3,11 +3,11 @@
 from collections.abc import Collection
 from typing import Literal
 
-from dask import array as da
+import dask.array as da
 
 from ngio.common import Dimensions
-from ngio.images.abstract_image import AbstractImage, consolidate_image
-from ngio.images.create import create_empty_image_container
+from ngio.images._abstract_image import AbstractImage, consolidate_image
+from ngio.images._create import create_empty_image_container
 from ngio.ome_zarr_meta import (
     ImageMetaHandler,
     NgioImageMeta,
@@ -152,31 +152,33 @@ class ImagesContainer:
 
     def set_channel_meta(
         self,
-        labels: Collection[str] | int | None = None,
-        wavelength_id: Collection[str] | None = None,
-        start: Collection[float] | None = None,
-        end: Collection[float] | None = None,
+        labels: Collection[str | None] | int | None = None,
+        wavelength_id: Collection[str | None] | None = None,
+        start: Collection[float | None] | None = None,
+        end: Collection[float | None] | None = None,
         percentiles: tuple[float, float] | None = None,
-        colors: Collection[str] | None = None,
-        active: Collection[bool] | None = None,
+        colors: Collection[str | None] | None = None,
+        active: Collection[bool | None] | None = None,
         **omero_kwargs: dict,
     ) -> None:
         """Create a ChannelsMeta object with the default unit.
 
         Args:
-            labels(Collection[str] | int): The list of channels names in the image.
-                If an integer is provided, the channels will be named "channel_i".
-            wavelength_id(Collection[str] | None): The wavelength ID of the channel.
+            labels(Collection[str | None] | int): The list of channels names
+                in the image. If an integer is provided, the channels will
+                be named "channel_i".
+            wavelength_id(Collection[str | None]): The wavelength ID of the channel.
                 If None, the wavelength ID will be the same as the channel name.
-            start(Collection[float] | None): The start value for each channel.
+            start(Collection[float | None]): The start value for each channel.
                 If None, the start value will be computed from the image.
-            end(Collection[float] | None): The end value for each channel.
+            end(Collection[float | None]): The end value for each channel.
                 If None, the end value will be computed from the image.
-            percentiles(tuple[float, float] | None): The start and end percentiles
-                for each channel. If None, the percentiles will not be computed.
-            colors(Collection[str, NgioColors] | None): The list of colors for the
+            percentiles(tuple[float, float] | None): The start and end
+                percentiles for each channel. If None, the percentiles will
+                not be computed.
+            colors(Collection[str | None]): The list of colors for the
                 channels. If None, the colors will be random.
-            active (Collection[bool] | None):active(bool): Whether the channel should
+            active (Collection[bool | None]): Whether the channel should
                 be shown by default.
             omero_kwargs(dict): Extra fields to store in the omero attributes.
         """
@@ -376,9 +378,12 @@ def compute_image_percentile(
     starts, ends = [], []
     for c in range(image.num_channels):
         if image.num_channels == 1:
-            data = image.get_array(mode="dask").ravel()
+            data = image.get_array(mode="dask")
         else:
-            data = image.get_array(c=c, mode="dask").ravel()
+            data = image.get_array(c=c, mode="dask")
+
+        assert isinstance(data, da.Array), "Data must be a Dask array."
+        data = da.ravel(data)
         # remove all the zeros
         mask = data > 1e-16
         data = data[mask]
@@ -391,7 +396,7 @@ def compute_image_percentile(
         # compute the percentiles
         _s_perc, _e_perc = da.percentile(
             data, [start_percentile, end_percentile], method="nearest"
-        ).compute()
+        ).compute()  # type: ignore
 
         starts.append(float(_s_perc))
         ends.append(float(_e_perc))

ngio/images/{label.py → _label.py}

@@ -3,10 +3,12 @@
 from collections.abc import Collection
 from typing import Literal
 
+import dask.array as da
+
 from ngio.common import compute_masking_roi
-from ngio.images.abstract_image import AbstractImage, consolidate_image
-from ngio.images.create import create_empty_label_container
-from ngio.images.image import Image
+from ngio.images._abstract_image import AbstractImage, consolidate_image
+from ngio.images._create import create_empty_label_container
+from ngio.images._image import Image
 from ngio.ome_zarr_meta import (
     LabelMetaHandler,
     NgioLabelMeta,
@@ -309,6 +311,6 @@ def build_masking_roi_table(label: Label) -> MaskingRoiTable:
         raise NgioValueError("Time series labels are not supported.")
 
     array = label.get_array(axes_order=["z", "y", "x"], mode="dask")
-
+    assert isinstance(array, da.Array), "Array must be a Dask array."
     rois = compute_masking_roi(array, label.pixel_size)
     return MaskingRoiTable(rois, reference_label=label.meta.name)

ngio/images/{masked_image.py → _masked_image.py}

@@ -4,8 +4,8 @@ from collections.abc import Collection, Iterable
 from typing import Literal
 
 from ngio.common import ArrayLike, get_masked_pipe, roi_to_slice_kwargs, set_masked_pipe
-from ngio.images.image import Image
-from ngio.images.label import Label
+from ngio.images._image import Image
+from ngio.images._label import Label
 from ngio.ome_zarr_meta import ImageMetaHandler, LabelMetaHandler
 from ngio.tables import MaskingRoiTable
 from ngio.utils import (

ngio/images/{ome_zarr_container.py → _ome_zarr_container.py}

@@ -5,10 +5,10 @@ from collections.abc import Collection
 
 import numpy as np
 
-from ngio.images.create import create_empty_image_container
-from ngio.images.image import Image, ImagesContainer
-from ngio.images.label import Label, LabelsContainer
-from ngio.images.masked_image import MaskedImage, MaskedLabel
+from ngio.images._create import create_empty_image_container
+from ngio.images._image import Image, ImagesContainer
+from ngio.images._label import Label, LabelsContainer
+from ngio.images._masked_image import MaskedImage, MaskedLabel
 from ngio.ome_zarr_meta import (
     NgioImageMeta,
     PixelSize,
@@ -68,7 +68,7 @@ class OmeZarrContainer:
         group_handler: ZarrGroupHandler,
         table_container: TablesContainer | None = None,
         label_container: LabelsContainer | None = None,
-        validate_arrays: bool = True,
+        validate_paths: bool = False,
     ) -> None:
         """Initialize the OmeZarrContainer."""
         self._group_handler = group_handler
@@ -77,6 +77,10 @@ class OmeZarrContainer:
         self._labels_container = label_container
         self._tables_container = table_container
 
+        if validate_paths:
+            for level_path in self._images_container.levels_paths:
+                self.get_image(path=level_path)
+
     def __repr__(self) -> str:
         """Return a string representation of the image."""
         num_labels = len(self.list_labels())
@@ -99,24 +103,40 @@ class OmeZarrContainer:
         """Return the image container."""
         return self._images_container
 
-    @property
-    def labels_container(self) -> LabelsContainer:
+    def _get_labels_container(self) -> LabelsContainer | None:
         """Return the labels container."""
         if self._labels_container is None:
-            self._labels_container = _default_label_container(self._group_handler)
-            if self._labels_container is None:
-                raise NgioValidationError("No labels found in the image.")
+            _labels_container = _default_label_container(self._group_handler)
+            if _labels_container is None:
+                return None
+            self._labels_container = _labels_container
         return self._labels_container
 
     @property
-    def tables_container(self) -> TablesContainer:
+    def labels_container(self) -> LabelsContainer:
+        """Return the labels container."""
+        _labels_container = self._get_labels_container()
+        if _labels_container is None:
+            raise NgioValidationError("No labels found in the image.")
+        return _labels_container
+
+    def _get_tables_container(self) -> TablesContainer | None:
         """Return the tables container."""
         if self._tables_container is None:
-            self._tables_container = _default_table_container(self._group_handler)
-            if self._tables_container is None:
-                raise NgioValidationError("No tables found in the image.")
+            _tables_container = _default_table_container(self._group_handler)
+            if _tables_container is None:
+                return None
+            self._tables_container = _tables_container
         return self._tables_container
 
+    @property
+    def tables_container(self) -> TablesContainer:
+        """Return the tables container."""
+        _tables_container = self._get_tables_container()
+        if _tables_container is None:
+            raise NgioValidationError("No tables found in the image.")
+        return _tables_container
+
     @property
     def image_meta(self) -> NgioImageMeta:
         """Return the image metadata."""
@@ -332,7 +352,7 @@ class OmeZarrContainer:
 
         new_ome_zarr = OmeZarrContainer(
             group_handler=handler,
-            validate_arrays=False,
+            validate_paths=False,
         )
 
         if copy_labels:
@@ -346,13 +366,25 @@ class OmeZarrContainer:
             )
         return new_ome_zarr
 
-    def list_tables(self, filter_types: str | None = None) -> list[str]:
+    def list_tables(self, filter_types: TypedTable | str | None = None) -> list[str]:
         """List all tables in the image."""
-        return self.tables_container.list(filter_types=filter_types)
+        table_container = self._get_tables_container()
+        if table_container is None:
+            return []
+
+        return table_container.list(
+            filter_types=filter_types,
+        )
 
     def list_roi_tables(self) -> list[str]:
         """List all ROI tables in the image."""
-        return self.tables_container.list_roi_tables()
+        masking_roi = self.tables_container.list(
+            filter_types="masking_roi_table",
+        )
+        roi = self.tables_container.list(
+            filter_types="roi_table",
+        )
+        return masking_roi + roi
 
     def get_roi_table(self, name: str) -> RoiTable:
         """Get a ROI table from the image.
@@ -479,7 +511,10 @@ class OmeZarrContainer:
 
     def list_labels(self) -> list[str]:
         """List all labels in the image."""
-        return self.labels_container.list()
+        label_container = self._get_labels_container()
+        if label_container is None:
+            return []
+        return label_container.list()
 
     def get_label(
         self,
@@ -597,7 +632,7 @@ def open_ome_zarr_container(
     handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     return OmeZarrContainer(
         group_handler=handler,
-        validate_arrays=validate_arrays,
+        validate_paths=validate_arrays,
     )
 
 

ngio/ome_zarr_meta/ngio_specs/_axes.py

@@ -2,15 +2,12 @@
 
 from collections.abc import Collection
 from enum import Enum
-from logging import Logger
 from typing import Literal, TypeVar
 
 import numpy as np
 from pydantic import BaseModel, ConfigDict, Field
 
-from ngio.utils import NgioValidationError, NgioValueError
-
-logger = Logger(__name__)
+from ngio.utils import NgioValidationError, NgioValueError, ngio_logger
 
 T = TypeVar("T")
 
@@ -102,20 +99,20 @@ class Axis(BaseModel):
     def implicit_type_cast(self, cast_type: AxisType) -> "Axis":
         unit = self.unit
         if self.axis_type != cast_type:
-            logger.warning(
+            ngio_logger.warning(
                 f"Axis {self.on_disk_name} has type {self.axis_type}. "
                 f"Casting to {cast_type}."
             )
 
         if cast_type == AxisType.time and unit is None:
-            logger.warning(
+            ngio_logger.warning(
                 f"Time axis {self.on_disk_name} has unit {self.unit}. "
                 f"Casting to {DefaultSpaceUnit}."
             )
             unit = DefaultTimeUnit
 
         if cast_type == AxisType.space and unit is None:
-            logger.warning(
+            ngio_logger.warning(
                 f"Space axis {self.on_disk_name} has unit {unit}. "
                 f"Casting to {DefaultSpaceUnit}."
             )

ngio/ome_zarr_meta/ngio_specs/_channels.py

@@ -329,33 +329,35 @@ class ChannelsMeta(BaseModel):
     @classmethod
     def default_init(
         cls,
-        labels: Collection[str] | int,
-        wavelength_id: Collection[str] | None = None,
-        colors: Collection[str | NgioColors] | None = None,
-        start: Collection[int | float] | int | float | None = None,
-        end: Collection[int | float] | int | float | None = None,
-        active: Collection[bool] | None = None,
+        labels: Collection[str | None] | int,
+        wavelength_id: Collection[str | None] | None = None,
+        colors: Collection[str | NgioColors | None] | None = None,
+        start: Collection[int | float | None] | int | float | None = None,
+        end: Collection[int | float | None] | int | float | None = None,
+        active: Collection[bool | None] | None = None,
         data_type: Any = np.uint16,
         **omero_kwargs: dict,
     ) -> "ChannelsMeta":
         """Create a ChannelsMeta object with the default unit.
 
         Args:
-            labels(Collection[str] | int): The list of channels names in the image.
-                If an integer is provided, the channels will be named "channel_i".
-            wavelength_id(Collection[str] | None): The wavelength ID of the channel.
-                If None, the wavelength ID will be the same as the channel name.
-            colors(Collection[str, NgioColors] | None): The list of colors for the
-                channels. If None, the colors will be random.
-            start(Collection[int | float] | int | float | None): The start value of the
-                channel. If None, the start value will be the minimum value of the
-                data type.
-            end(Collection[int | float] | int | float | None): The end value of the
-                channel. If None, the end value will be the maximum value of the
-                data type.
+            labels(Collection[str | None] | int): The list of channels names
+                in the image. If an integer is provided, the channels will be
+                named "channel_i".
+            wavelength_id(Collection[str | None] | None): The wavelength ID of the
+                channel. If None, the wavelength ID will be the same as the
+                channel name.
+            colors(Collection[str | NgioColors | None] | None): The list of
+                colors for the channels. If None, the colors will be random.
+            start(Collection[int | float | None] | int | float | None): The start
+                value of the channel. If None, the start value will be the
+                minimum value of the data type.
+            end(Collection[int | float | None] | int | float | None): The end
+                value of the channel. If None, the end value will be the
+                maximum value of the data type.
             data_type(Any): The data type of the channel. Will be used to set the
                 min and max values of the channel.
-            active (Collection[bool] | None):active(bool): Whether the channel should
+            active (Collection[bool | None] | None): Whether the channel should
                 be shown by default.
             omero_kwargs(dict): Extra fields to store in the omero attributes.
         """
@@ -366,25 +368,35 @@ class ChannelsMeta(BaseModel):
         labels = _check_unique(labels)
 
         _wavelength_id: Collection[str | None] = [None] * len(labels)
-        if isinstance(wavelength_id, Collection):
+        if wavelength_id is None:
+            _wavelength_id: Collection[str | None] = [None] * len(labels)
+        else:
             _wavelength_id = _check_elements(wavelength_id, str)
             _wavelength_id = _check_unique(wavelength_id)
 
-        _colors: Collection[str | NgioColors | None] = [None] * len(labels)
-        if isinstance(colors, Collection):
+        if colors is None:
+            _colors = [NgioColors.semi_random_pick(label) for label in labels]
+        else:
             _colors = _check_elements(colors, str | NgioColors)
 
-        _start: Collection[int | float | None] = [None] * len(labels)
-        if isinstance(start, Collection):
+        if start is None:
+            _start = [None] * len(labels)
+        elif isinstance(start, int | float):
+            _start = [start] * len(labels)
+        else:
             _start = _check_elements(start, (int, float))
 
-        _end: Collection[int | float | None] = [None] * len(labels)
-        if isinstance(end, Collection):
+        if end is None:
+            _end = [None] * len(labels)
+        elif isinstance(end, int | float):
+            _end = [end] * len(labels)
+        else:
             _end = _check_elements(end, (int, float))
 
-        _active: Collection[bool] = [True] * len(labels)
-        if isinstance(active, Collection):
-            _active = _check_elements(active, bool)
+        if active is None:
+            _active = [True] * len(labels)
+        else:
+            _active = _check_elements(active, (bool,))
 
         all_lengths = [
             len(labels),

ngio/tables/__init__.py

@@ -1,11 +1,6 @@
 """Ngio Tables implementations."""
 
-from ngio.tables.backends import (
-    ImplementedTableBackends,
-    TableBackend,
-    TableBackendProtocol,
-)
-from ngio.tables.tables_container import (
+from ngio.tables._tables_container import (
     ConditionTable,
     FeatureTable,
     GenericRoiTable,
@@ -19,6 +14,11 @@ from ngio.tables.tables_container import (
     open_table_as,
     open_tables_container,
 )
+from ngio.tables.backends import (
+    ImplementedTableBackends,
+    TableBackend,
+    TableBackendProtocol,
+)
 from ngio.tables.v1._generic_table import GenericTable
 
 __all__ = [

ngio/tables/{tables_container.py → _tables_container.py}

@@ -126,13 +126,18 @@ class Table(Protocol):
 
 
 TypedTable = Literal[
+    "generic_table",
     "roi_table",
     "masking_roi_table",
     "feature_table",
-    "generic_roi_table",
     "condition_table",
 ]
 
+TypedRoiTable = Literal[
+    "roi_table",
+    "masking_roi_table",
+]
+
 TableType = TypeVar("TableType", bound=Table)
 
 
@@ -192,19 +197,34 @@ class ImplementedTables:
         table = table_cls.from_handler(handler=handler, backend=backend)
         return table
 
-    def add_implementation(self, handler: type[Table], overwrite: bool = False):
+    def _add_implementation(
+        self, handler: type[Table], name: str, overwrite: bool = False
+    ) -> None:
+        """Register a new table handler."""
+        if name in self._implemented_tables and not overwrite:
+            raise NgioValueError(
+                f"Table handler for {name} already implemented. "
+                "Use overwrite=True to replace it."
+            )
+        self._implemented_tables[name] = handler
+
+    def add_implementation(
+        self,
+        handler: type[Table],
+        overwrite: bool = False,
+        aliases: list[str] | None = None,
+    ) -> None:
         """Register a new table handler."""
         meta = TableMeta(
             type=handler.table_type(),
             table_version=handler.version(),
         )
 
-        if meta.unique_name() in self._implemented_tables and not overwrite:
-            raise NgioValueError(
-                f"Table handler for {meta.unique_name()} already implemented. "
-                "Use overwrite=True to replace it."
-            )
-        self._implemented_tables[meta.unique_name()] = handler
+        self._add_implementation(handler, meta.unique_name(), overwrite)
+
+        if aliases is not None:
+            for alias in aliases:
+                self._add_implementation(handler, alias, overwrite)
 
 
 class TablesContainer:
@@ -240,14 +260,7 @@ class TablesContainer:
         handler = self._group_handler.derive_handler(path=name)
         return handler
 
-    def list_roi_tables(self) -> list[str]:
-        """List all ROI tables in the group."""
-        _tables = []
-        for _type in ["roi_table", "masking_roi_table"]:
-            _tables.extend(self.list(_type))
-        return _tables
-
-    def list(self, filter_types: str | None = None) -> list[str]:
+    def list(self, filter_types: TypedTable | str | None = None) -> list[str]:
         """List all labels in the group."""
         tables = self._get_tables_list()
         if filter_types is None:

ngio/tables/backends/_table_backends.py

@@ -180,24 +180,46 @@ class ImplementedTableBackends:
         )
         return backend
 
-    def add_backend(
+    def _add_backend(
         self,
-        table_beckend: type[TableBackendProtocol],
+        table_backend: type[TableBackendProtocol],
+        name: str,
         overwrite: bool = False,
-    ):
+    ) -> None:
         """Register a new handler."""
-        backend_name = table_beckend.backend_name()
-        if backend_name in self._implemented_backends and not overwrite:
+        if name in self._implemented_backends and not overwrite:
             raise NgioValueError(
-                f"Table backend {backend_name} already implemented. "
+                f"Table backend {name} already implemented. "
                 "Use the `overwrite=True` parameter to overwrite it."
             )
-        self._implemented_backends[backend_name] = table_beckend
-
+        self._implemented_backends[name] = table_backend
 
-ImplementedTableBackends().add_backend(AnnDataBackend)
-ImplementedTableBackends().add_backend(JsonTableBackend)
-ImplementedTableBackends().add_backend(CsvTableBackend)
-ImplementedTableBackends().add_backend(ParquetTableBackend)
+    def add_backend(
+        self,
+        table_backend: type[TableBackendProtocol],
+        overwrite: bool = False,
+        aliases: list[str] | None = None,
+    ) -> None:
+        """Register a new handler."""
+        self._add_backend(
+            table_backend=table_backend,
+            name=table_backend.backend_name(),
+            overwrite=overwrite,
+        )
+        if aliases is not None:
+            for alias in aliases:
+                self._add_backend(
+                    table_backend=table_backend, name=alias, overwrite=overwrite
+                )
+
+
+ImplementedTableBackends().add_backend(AnnDataBackend, aliases=["anndata_v1"])
+ImplementedTableBackends().add_backend(
+    JsonTableBackend, aliases=["experimental_json_v1"]
+)
+ImplementedTableBackends().add_backend(CsvTableBackend, aliases=["experimental_csv_v1"])
+ImplementedTableBackends().add_backend(
+    ParquetTableBackend, aliases=["experimental_parquet_v1"]
+)
 
 TableBackend = Literal["anndata", "json", "csv", "parquet"] | str | TableBackendProtocol

ngio/tables/v1/_condition_table.py

@@ -1,6 +1,6 @@
 """Implementation of a generic table class."""
 
-from ngio.tables.abstract_table import AbstractBaseTable
+from ngio.tables._abstract_table import AbstractBaseTable
 from ngio.tables.backends import (
     BackendMeta,
     TableBackend,

ngio/tables/v1/_feature_table.py

@@ -8,7 +8,7 @@ from typing import Literal
 
 from pydantic import BaseModel, Field
 
-from ngio.tables.abstract_table import AbstractBaseTable
+from ngio.tables._abstract_table import AbstractBaseTable
 from ngio.tables.backends import BackendMeta, TableBackend, TabularData
 from ngio.utils import NgioValueError
 from ngio.utils._zarr_utils import ZarrGroupHandler
@@ -26,7 +26,7 @@ class FeatureTableMeta(BackendMeta):
     table_version: Literal["1"] = "1"
     type: Literal["feature_table"] = "feature_table"
     region: RegionMeta | None = None
-    instance_key: str = "label" # Legacy field, kept for compatibility
+    instance_key: str = "label"  # Legacy field, kept for compatibility
     # Backend metadata
     index_key: str | None = "label"
     index_type: Literal["int", "str"] | None = "int"

ngio/tables/v1/_generic_table.py

@@ -1,6 +1,6 @@
 """Implementation of a generic table class."""
 
-from ngio.tables.abstract_table import AbstractBaseTable
+from ngio.tables._abstract_table import AbstractBaseTable
 from ngio.tables.backends import BackendMeta, TableBackend
 from ngio.utils import ZarrGroupHandler
 

ngio/tables/v1/_roi_table.py

@@ -13,7 +13,7 @@ import pandas as pd
 from pydantic import BaseModel
 
 from ngio.common import Roi
-from ngio.tables.abstract_table import (
+from ngio.tables._abstract_table import (
     AbstractBaseTable,
     TabularData,
 )

ngio/utils/_fractal_fsspec_store.py

@@ -37,6 +37,6 @@ def fractal_fsspec_store(
         raise NgioValueError(
             f"Store {url} can not be read. Possible problems are: \n"
             "- The url does not exist. \n"
-            f"- The url is not a valid .zarr. \n"
+            "- The url is not a valid .zarr. \n"
         )
     return store

{ngio-0.3.0a1.dist-info → ngio-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.0a1
+Version: 0.3.1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
 Project-URL: repository, https://github.com/fractal-analytics-platform/ngio
@@ -63,7 +63,7 @@ Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 
-# NGIO - Next Generation file format IO
+# Ngio - Next Generation file format IO
 
 [![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)
@@ -71,36 +71,69 @@ Description-Content-Type: text/markdown
 [![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.
-
-**Main Goals:**
-
-- Abstract object base API for handling OME-Zarr files
-- Powerful iterators for processing data using common access patterns
-- Tight integration with [Fractal's Table Fractal](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/)
-- Validation of OME-Zarr files
-
-To get started, check out the [Getting Started](https://fractal-analytics-platform.github.io/ngio/getting-started/) guide. Or checkout our [Documentation](https://fractal-analytics-platform.github.io/ngio/)
-
-## 🚧 Ngio is Under active Development 🚧
-
-### Roadmap
-
-| Feature | Status | ETA | Description |
-|---------|--------|-----|-------------|
-| Metadata Handling | ✅ | | Read, Write, Validate OME-Zarr Metadata (0.4 supported, 0.5 ready) |
-| OME-Zarr Validation | ✅ | | Validate OME-Zarr files for compliance with the OME-Zarr Specification + Compliance between Metadata and Data |
-| Base Image Handling | ✅ | | Load data from OME-Zarr files, retrieve basic metadata, and write data |
-| ROI Handling | ✅ | | Common ROI models |
-| Label Handling | ✅ | Mid-September | Based on Image Handling |
-| Table Validation | ✅ | Mid-September | Validate Table fractal V1 + Compliance between Metadata and Data |
-| Table Handling | ✅ | Mid-September | Read, Write ROI, Features, and Masked Tables |
-| Basic Iterators | Ongoing | End-September | Read and Write Iterators for common access patterns |
-| Base Documentation | ✅ | End-September | API Documentation and Examples |
-| Beta Ready Testing | ✅ | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
-| Streaming from Fractal | Ongoing | December | Ngio can stream OME-Zarr from fractal |
-| Mask Iterators | Ongoing | Early 2025 | Iterators over Masked Tables |
-| Advanced Iterators | Not started | mid-2025 | Iterators for advanced access patterns |
-| 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 is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
+
+## What is Ngio?
+
+Ngio is built for the [OME-Zarr](https://ngff.openmicroscopy.org/) file format, a modern, cloud-optimized format for biological imaging data. OME-Zarr stores large, multi-dimensional microscopy images and metadata in an efficient and scalable way.
+
+Ngio's mission is to streamline working with OME-Zarr files by providing a simple, object-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates. It also offers comprehensive support for labels, tables and regions of interest (ROIs), making it easy to extract and analyze specific regions in your data.
+
+## Key Features
+
+### 📊 Simple Object-Based API
+
+- Easily open, explore, and manipulate OME-Zarr images and HCS plates
+- Create and derive new images and labels with minimal boilerplate code
+
+### 🔍 Rich Tables and Regions of Interest (ROI) Support
+
+- Extract and analyze specific regions of interest
+- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+
+### 🔄 Scalable Data Processing (Coming Soon)
+
+- Powerful iterators for processing data at scale
+- Efficient memory management for large datasets
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+
+## Supported OME-Zarr versions
+
+Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher is planned for future releases.
+
+## Development Status
+
+!!! warning
+    Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
+    We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
+
+### Available Features
+
+- ✅ OME-Zarr metadata handling and validation
+- ✅ Image and label access across pyramid levels
+- ✅ ROI and table support
+- ✅ Streaming from remote sources
+- ✅ Documentation and examples
+
+### Upcoming Features
+
+- Advanced image processing iterators
+- Parallel processing capabilities
+- Support for OME-Zarr v0.5 and Zarr v3
+
+## Contributors
+
+Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html), University of Zurich, by [@lorenzocerrone](https://github.com/lorenzocerrone) and [@jluethi](https://github.com/jluethi).
+
+## License
+
+Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.

{ngio-0.3.0a1.dist-info → ngio-0.3.1.dist-info}/RECORD

@@ -1,6 +1,6 @@
 ngio/__init__.py,sha256=zce-RIfRhkiFyfKwO6s7A1-9ZCD3n6RuVuW3GeRj_VA,1309
 ngio/common/__init__.py,sha256=BttXCAV2ks6_oXVDfapk1Lvlxp4J0ffX7-FXR3LL1BM,1834
-ngio/common/_array_pipe.py,sha256=we3gZLhgUsiPQwPQqg_XVkyG_9EpQ2xoe0L_nOALDho,7828
+ngio/common/_array_pipe.py,sha256=mvBsOtNSow9S6bSPMJ0288gCqQFYffGnaTTLyuB2XHw,8641
 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
@@ -8,22 +8,22 @@ ngio/common/_masking_roi.py,sha256=-o6meGP17iTXEbkO9aGh1VX2drkc2laIcRJvCy_pRRM,4
 ngio/common/_pyramid.py,sha256=SJzPauuduuqcm9B7nFCJhMTzIg6Knjsnp4CY4lN61Is,7411
 ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
 ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
-ngio/common/_table_ops.py,sha256=oTjCcecBOG_GJoLgJLgag6yl_nznThOKBKANQJow0h8,15493
+ngio/common/_table_ops.py,sha256=ToNR7F053l1dubVv-gvBD-523T10HnE2UzqeU2BuNy8,15494
 ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
-ngio/hcs/__init__.py,sha256=5oAYT_454WGhms97kxo8gS4_rKHtFf_x-9uu8M_VeVM,356
-ngio/hcs/plate.py,sha256=Y_d-ZuV9FmYsSHqwZfcnm_Y024jfdiMd7WlaeNJy73k,43696
-ngio/images/__init__.py,sha256=DYbXAdBgPxyjBRdJrWvU0UnBRI0gUMmx9KaJ-Bucvz4,533
-ngio/images/abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
-ngio/images/create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
-ngio/images/image.py,sha256=mKLIR2DGQUWtQbf3my2fh0bEPkbbsabUoge_XJPhfWE,17824
-ngio/images/label.py,sha256=qgbBHFPGYpUR2fHf1OiXZh4sn0FgCeeWwH1F4SrOM1c,10460
-ngio/images/masked_image.py,sha256=IBo8x2jHyXBXn7ORo8fSiwBPjV_1JOTb_vatjKNxbJ0,8531
-ngio/images/ome_zarr_container.py,sha256=jOodimQzAnaLUSYG1OnBsWqtHeL8_V4wkg_4RSXbwcM,30003
+ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
+ngio/hcs/_plate.py,sha256=Z8M3slG5t16MYvPwvAzj-e9O4yAswWZp7_EDBlAxiHc,44225
+ngio/images/__init__.py,sha256=PlYvbHOMvZLDgn_PeGrytOEU3e_-AO8GWpRjEqoX_Gw,536
+ngio/images/_abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
+ngio/images/_create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
+ngio/images/_image.py,sha256=B9MTk3Cei-FBR4jbhSujTSNcKM_ySape28yXR_JlY0A,17980
+ngio/images/_label.py,sha256=Q1vPrXDcjJ7Gdd0wDz6NCVYQLNe1Ae6YDI4iK0oq31s,10557
+ngio/images/_masked_image.py,sha256=sd6aQetNVwtDkwUvKX-lssQyHzt5m-CYZL8ZFkwDSn8,8533
+ngio/images/_ome_zarr_container.py,sha256=hRx_8CPtFpxQUcprTT4_k5L5pjMUJ6t4wJaYr1tyljw,31181
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=ctknNDT8jxwyvxQf9on5gW31H1tRRsnneO38GT2UXoE,25880
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
-ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=Kqe9T7LWa_9o3UWS5uzALyyNluIhXxWhDGxWY4-GIo8,16707
-ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=2L-HM9K1Xu4qRI2MiXPqgCuHdCBRydEW1StThcqEuvY,15120
+ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=tHtx6NfBgDcCgDk9CosjIjw1KZJ2qi0i_eoLgrdiEWw,16681
+ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=Jwys1yYC8q6_gIaJ52KcKcTP7hzqVjBE-VlVQvJurCs,15394
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=hY8ogPPxvCgVg6k02t3zUr24lasYrvnxBd1iPEigdG4,5892
 ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=uh345KQmEQtslIyMmLK9sB-NbjPYxi0Y9FuYIFhd3Rc,17465
 ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=8E38Mgw-l0Ff1nkmCJIzo64G_paAVhM8xktUS_V5egY,17960
@@ -31,9 +31,9 @@ ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg
 ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=05tEr2eEP_XVIfBMOAWLT7lzJV4KS5eYrpK8l94tn3w,15876
-ngio/tables/__init__.py,sha256=np-XWjUY_HkwMfSy_bIRxh5t5SFZJ9yHEtvtbuaaSgg,824
-ngio/tables/abstract_table.py,sha256=naAeDsPTVjDUOnAxj_57UWXApg_nyWCsWdZ0f7bm740,8169
-ngio/tables/tables_container.py,sha256=c7YnzLy2aaDc0jCH8ih8FTAKpAX8dIAu743nF7EjNTY,11871
+ngio/tables/__init__.py,sha256=rJGcyQUlHQb_ZbeMM9ICD8_mhTE2X9H5nKp0J-z9tMM,825
+ngio/tables/_abstract_table.py,sha256=naAeDsPTVjDUOnAxj_57UWXApg_nyWCsWdZ0f7bm740,8169
+ngio/tables/_tables_container.py,sha256=a2NNExiP1HqFVJ6HPLn0nEkYHLdf2LONVz5OxoH7OkY,12118
 ngio/tables/backends/__init__.py,sha256=tx97ZkK5kF_sAGU2kf_ZI9JxbOXn8GVjE0rUUq9h-QM,1525
 ngio/tables/backends/_abstract_backend.py,sha256=jtai3AqcLNZyxYyK0rernbMtcwxWhWAahCS0fPlMNls,7454
 ngio/tables/backends/_anndata.py,sha256=8RX2NO15CLxys3p6gw54Nd-_0WATU4WBlNndX06wvzI,2587
@@ -42,20 +42,20 @@ ngio/tables/backends/_csv.py,sha256=Ev61D-AUKo4LIhXRmWPJgYbHI7eQdxiajQR574DevEM,
 ngio/tables/backends/_json.py,sha256=1ZsEuXDJm1rOZV_KjFm8CB0qhv7L1W7L2EGWPf4q_p0,3137
 ngio/tables/backends/_non_zarr_backends.py,sha256=SvPPhT6n5TrKUOyV1mNcdHQK49huZ5lwR8EVe9MdydM,7254
 ngio/tables/backends/_parquet.py,sha256=ic-p86h8lce8q9luBJGRzy6vxlWyJvA0-2l5cUD6OqY,1398
-ngio/tables/backends/_table_backends.py,sha256=9bAwiB93gR8E7NdpH9WMMQhjn34Iz6oW9i_H4upYbW4,6567
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