ngio 0.3.0a1__tar.gz → 0.3.1__tar.gz

{ngio-0.3.0a1 → ngio-0.3.1}/PKG-INFO

@@ -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-0.3.1/README.md

@@ -0,0 +1,74 @@
+# 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)
+[![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
+[![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 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 → ngio-0.3.1}/docs/index.md

@@ -1,4 +1,3 @@
-
 ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
 
 ## What is Ngio?
@@ -30,12 +29,14 @@ Refer to the [Getting Started](getting_started/0_quickstart.md) guide to integra
 For more advanced usage and API documentation, see our [API Reference](api/ngio.md).
 
 ## 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
 

{ngio-0.3.0a1 → ngio-0.3.1}/docs/table_specs/backend.md

@@ -14,7 +14,8 @@ AnnData is a widely used format in single-cell genomics, and can natively store
 The following normalization steps are applied to each table before saving it to the AnnData backend:
 
 - We separate the table in two parts: The floating point columns are casted to `float32` and stored as `X` in the AnnData object, while the categorical, boolean, and integer columns are stored as `obs`.
-- The index column is cast to a string, and the name and original type is stored in the zarr attributes.
+- The index column is cast to a string, and is stored in the `obs` index.
+- The index column name must match the `index_key` specified in the metadata.
 
 AnnData backend metadata:
 

{ngio-0.3.0a1 → ngio-0.3.1}/mkdocs.yml

@@ -104,6 +104,7 @@ nav:
     - "Overview": table_specs/overview.md
     - "Table Backends": table_specs/backend.md
     - "Table Types":
+      - "Generic Table": table_specs/table_types/generic_table.md 
       - "ROI Table": table_specs/table_types/roi_table.md
       - "Masking ROI Table": table_specs/table_types/masking_roi_table.md
       - "Feature Table": table_specs/table_types/feature_table.md

{ngio-0.3.0a1 → ngio-0.3.1}/src/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-0.3.0a1 → ngio-0.3.1}/src/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-0.3.0a1 → ngio-0.3.1}/src/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-0.3.0a1/src/ngio/hcs/plate.py → ngio-0.3.1/src/ngio/hcs/_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-0.3.0a1 → ngio-0.3.1}/src/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-0.3.0a1/src/ngio/images/image.py → ngio-0.3.1/src/ngio/images/_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-0.3.0a1/src/ngio/images/label.py → ngio-0.3.1/src/ngio/images/_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-0.3.0a1/src/ngio/images/masked_image.py → ngio-0.3.1/src/ngio/images/_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 (