ngio 0.2.0a2__py3-none-any.whl → 0.5.0b4__py3-none-any.whl

ngio-0.5.0b4.dist-info/METADATA

@@ -0,0 +1,147 @@
+Metadata-Version: 2.4
+Name: ngio
+Version: 0.5.0b4
+Summary: Next Generation file format IO
+Project-URL: homepage, https://github.com/BioVisionCenter/ngio
+Project-URL: repository, https://github.com/BioVisionCenter/ngio
+Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Typing :: Typed
+Requires-Python: <3.14,>=3.11
+Requires-Dist: aiohttp
+Requires-Dist: anndata
+Requires-Dist: dask[array]<2025.11.0
+Requires-Dist: dask[distributed]<2025.11.0
+Requires-Dist: filelock
+Requires-Dist: numpy
+Requires-Dist: ome-zarr-models
+Requires-Dist: pandas>=1.2.0
+Requires-Dist: pillow
+Requires-Dist: polars
+Requires-Dist: pooch
+Requires-Dist: pyarrow
+Requires-Dist: pydantic
+Requires-Dist: requests
+Requires-Dist: zarr>3
+Provides-Extra: dev
+Requires-Dist: matplotlib; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: napari; extra == 'dev'
+Requires-Dist: notebook; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pympler; extra == 'dev'
+Requires-Dist: pyqt5; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: scikit-image; extra == 'dev'
+Requires-Dist: zarrs; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: griffe-typingdoc; extra == 'docs'
+Requires-Dist: markdown-exec[ansi]; extra == 'docs'
+Requires-Dist: matplotlib; extra == 'docs'
+Requires-Dist: mike; extra == 'docs'
+Requires-Dist: mkdocs; extra == 'docs'
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+Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
+Requires-Dist: mkdocs-git-revision-date-localized-plugin; extra == 'docs'
+Requires-Dist: mkdocs-include-markdown-plugin; extra == 'docs'
+Requires-Dist: mkdocs-jupyter; extra == 'docs'
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocstrings[python]; extra == 'docs'
+Requires-Dist: rich; extra == 'docs'
+Requires-Dist: scikit-image; extra == 'docs'
+Requires-Dist: tabulate; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: boto; extra == 'test'
+Requires-Dist: devtools; extra == 'test'
+Requires-Dist: moto[server]; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-httpserver; extra == 'test'
+Requires-Dist: s3fs; extra == 'test'
+Requires-Dist: scikit-image; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Ngio - Next Generation file format IO
+
+[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/BioVisionCenter/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/BioVisionCenter/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/BioVisionCenter/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/BioVisionCenter/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
+
+- Tight integration with [tabular data](https://biovisioncenter.github.io/ngio/stable/table_specs/overview/)
+- Extract and analyze specific regions of interest
+- Store measurements and other metadata in the OME-Zarr container
+- Extensible & modular allowing users to define custom table schemas and on disk serialization
+
+### 🔄 Scalable Data Processing
+
+- Powerful iterators for building scalable and generalizable image processing pipelines
+- Extensible mapping mechanism for custom parallelization strategies
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://BioVisionCenter.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
+
+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
+- ✅ Image processing iterators
+- ✅ Streaming from remote sources
+- ✅ Documentation and examples
+
+### Upcoming Features
+
+- Support for OME-Zarr v0.5 and Zarr v3 (via `zarr-python` v3)
+- Enhanced performance optimizations (parallel iterators, optimized io strategies)
+
+## 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/BioVisionCenter/ngio/blob/main/LICENSE) for details.

ngio-0.5.0b4.dist-info/RECORD

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{ngio-0.2.0a2.dist-info → ngio-0.5.0b4.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

ngio/common/_array_pipe.py

@@ -1,160 +0,0 @@
-from collections.abc import Collection, Iterable
-from typing import Literal
-
-import dask
-import dask.delayed
-import numpy as np
-import zarr
-
-from ngio.common._axes_transforms import transform_dask_array, transform_numpy_array
-from ngio.common._common_types import ArrayLike
-from ngio.common._dimensions import Dimensions
-from ngio.common._slicer import (
-    SliceTransform,
-    compute_and_slices,
-    dask_get_slice,
-    dask_set_slice,
-    numpy_get_slice,
-    numpy_set_slice,
-)
-from ngio.ome_zarr_meta.ngio_specs import AxesTransformation
-from ngio.utils import NgioValueError
-
-
-def _compute_from_disk_transforms(
-    *,
-    dimensions: Dimensions,
-    axes_order: Collection[str] | None = None,
-    **slice_kwargs: slice | int | Iterable[int],
-) -> tuple[SliceTransform, tuple[AxesTransformation, ...]]:
-    slices = compute_and_slices(dimensions=dimensions, **slice_kwargs)
-
-    if axes_order is None:
-        return slices, ()
-
-    additional_transformations = dimensions._axes_mapper.to_order(axes_order)
-    return slices, additional_transformations
-
-
-def _compute_to_disk_transforms(
-    *,
-    dimensions: Dimensions,
-    axes_order: Collection[str] | None = None,
-    **slice_kwargs: slice | int | Iterable[int],
-) -> tuple[SliceTransform, tuple[AxesTransformation, ...]]:
-    slices = compute_and_slices(dimensions=dimensions, **slice_kwargs)
-    if axes_order is None:
-        return slices, ()
-
-    additional_transformations = dimensions._axes_mapper.from_order(axes_order)
-    return slices, additional_transformations
-
-
-def _numpy_get_pipe(
-    array: zarr.Array,
-    slices: SliceTransform,
-    transformations: tuple[AxesTransformation, ...],
-) -> np.ndarray:
-    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)
-
-
-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)
-
-
-def _numpy_set_pipe(
-    array: zarr.Array,
-    patch: np.ndarray,
-    slices: SliceTransform,
-    transformations: tuple[AxesTransformation, ...],
-) -> None:
-    patch = transform_numpy_array(patch, transformations)
-    numpy_set_slice(array, patch, slices)
-
-
-def _dask_set_pipe(
-    array: zarr.Array,
-    patch: np.ndarray,
-    slices: SliceTransform,
-    transformations: tuple[AxesTransformation, ...],
-) -> None:
-    patch = transform_dask_array(patch, transformations)
-    dask_set_slice(array, patch, slices)
-
-
-def _delayed_numpy_set_pipe(
-    array: zarr.Array,
-    patch: np.ndarray,
-    slices: SliceTransform,
-    transformations: tuple[AxesTransformation, ...],
-) -> dask.delayed:
-    patch = dask.delayed(transform_numpy_array)(patch, transformations)
-    return dask.delayed(numpy_set_slice)(array, patch, slices)
-
-
-def get_pipe(
-    array: zarr.Array,
-    *,
-    dimensions: Dimensions,
-    axes_order: Collection[str] | None = None,
-    mode: Literal["numpy", "dask", "delayed"] = "numpy",
-    **slice_kwargs: slice | int | Iterable[int],
-):
-    slices, transformations = _compute_from_disk_transforms(
-        dimensions=dimensions, axes_order=axes_order, **slice_kwargs
-    )
-    match mode:
-        case "numpy":
-            return _numpy_get_pipe(array, slices, transformations)
-        case "dask":
-            return _dask_get_pipe(array, slices, transformations)
-
-        case "delayed_numpy":
-            return _delayed_numpy_get_pipe(array, slices, transformations)
-
-        case _:
-            raise NgioValueError(
-                f"Unknown get pipe mode {mode}, expected 'numpy', 'dask' or 'delayed'."
-            )
-
-
-def set_pipe(
-    array: zarr.Array,
-    patch: ArrayLike,
-    *,
-    dimensions: Dimensions,
-    axes_order: Collection[str] | None = None,
-    **slice_kwargs: slice | int | Iterable[int],
-):
-    slices, transformations = _compute_to_disk_transforms(
-        dimensions=dimensions, axes_order=axes_order, **slice_kwargs
-    )
-    if isinstance(patch, dask.array.Array):
-        _dask_set_pipe(
-            array=array, patch=patch, slices=slices, transformations=transformations
-        )
-    elif isinstance(patch, np.ndarray):
-        _numpy_set_pipe(
-            array=array, patch=patch, slices=slices, transformations=transformations
-        )
-    elif isinstance(patch, dask.delayed.Delayed):
-        _delayed_numpy_set_pipe(
-            array=array, patch=patch, slices=slices, transformations=transformations
-        )
-    else:
-        raise NgioValueError("Unknown patch type, expected numpy, dask or delayed.")

ngio/common/_axes_transforms.py

@@ -1,63 +0,0 @@
-from typing import TypeVar
-
-import dask.array as da
-import numpy as np
-
-from ngio.ome_zarr_meta.ngio_specs._axes import (
-    AxesExpand,
-    AxesSqueeze,
-    AxesTransformation,
-    AxesTranspose,
-)
-
-T = TypeVar("T")
-
-
-def transform_list(
-    input_list: list[T], default: T, operations: tuple[AxesTransformation, ...]
-) -> list[T]:
-    if isinstance(input_list, tuple):
-        input_list = list(input_list)
-
-    for operation in operations:
-        if isinstance(operation, AxesTranspose):
-            input_list = [input_list[i] for i in operation.axes]
-
-        if isinstance(operation, AxesExpand):
-            for ax in operation.axes:
-                input_list.insert(ax, default)
-        elif isinstance(operation, AxesSqueeze):
-            for offset, ax in enumerate(operation.axes):
-                input_list.pop(ax - offset)
-
-    return input_list
-
-
-def transform_numpy_array(
-    array: np.ndarray, operations: tuple[AxesTransformation, ...]
-) -> np.ndarray:
-    for operation in operations:
-        if isinstance(operation, AxesTranspose):
-            array = np.transpose(array, operation.axes)
-        elif isinstance(operation, AxesExpand):
-            array = np.expand_dims(array, axis=operation.axes)
-        elif isinstance(operation, AxesSqueeze):
-            array = np.squeeze(array, axis=operation.axes)
-        else:
-            raise ValueError(f"Unknown operation {operation}")
-    return array
-
-
-def transform_dask_array(
-    array: da.Array, operations: tuple[AxesTransformation, ...]
-) -> da.Array:
-    for operation in operations:
-        if isinstance(operation, AxesTranspose):
-            array = da.transpose(array, axes=operation.axes)
-        elif isinstance(operation, AxesExpand):
-            array = da.expand_dims(array, axis=operation.axes)
-        elif isinstance(operation, AxesSqueeze):
-            array = da.squeeze(array, axis=operation.axes)
-        else:
-            raise ValueError(f"Unknown operation {operation}")
-    return array

ngio/common/_common_types.py

@@ -1,5 +0,0 @@
-import numpy as np
-import zarr
-from dask import array as da
-
-ArrayLike = np.ndarray | da.core.Array | zarr.Array  # type: ignore

ngio/common/_slicer.py

@@ -1,97 +0,0 @@
-# %%
-from collections.abc import Iterable
-
-import dask.array as da
-import numpy as np
-import zarr
-
-from ngio.common._dimensions import Dimensions
-from ngio.ome_zarr_meta.ngio_specs import AxesTransformation
-from ngio.utils import NgioValueError
-
-
-def _validate_int(value: int, shape: int) -> int:
-    if not isinstance(value, int):
-        raise NgioValueError(f"Invalid value {value} of type {type(value)}")
-    if value < 0 or value >= shape:
-        raise NgioValueError(
-            f"Invalid value {value}. Index out of bounds for axis of shape {shape}"
-        )
-    return value
-
-
-def _validate_iter_of_ints(value: Iterable[int], shape: int) -> list[int]:
-    if not isinstance(value, list):
-        raise NgioValueError(f"Invalid value {value} of type {type(value)}")
-    value = [_validate_int(v, shape=shape) for v in value]
-    return value
-
-
-def _validate_slice(value: slice, shape: int) -> slice:
-    start = value.start if value.start is not None else 0
-    start = max(start, 0)
-    stop = value.stop if value.stop is not None else shape
-    return slice(start, stop)
-
-
-class SliceTransform(AxesTransformation):
-    slices: tuple[slice | tuple[int, ...], ...]
-
-
-def compute_and_slices(
-    *,
-    dimensions: Dimensions,
-    **slice_kwargs: slice | int | Iterable[int],
-) -> SliceTransform:
-    _slices = {}
-    axes_names = dimensions._axes_mapper.on_disk_axes_names
-    for axis_name, slice_ in slice_kwargs.items():
-        axis = dimensions._axes_mapper.get_axis(axis_name)
-        if axis is None:
-            raise NgioValueError(
-                f"Invalid axis {axis_name}. "
-                f"Not found on the on-disk axes {axes_names}. "
-                "If you want to get/set a singletorn value include "
-                "it in the axes_order parameter."
-            )
-
-        shape = dimensions.get(axis.on_disk_name)
-
-        if isinstance(slice_, int):
-            slice_ = _validate_int(slice_, shape)
-            slice_ = slice(slice_, slice_ + 1)
-
-        elif isinstance(slice_, Iterable):
-            slice_ = _validate_iter_of_ints(slice_, shape)
-            slice_ = tuple(slice_)
-
-        elif isinstance(slice_, slice):
-            slice_ = _validate_slice(slice_, shape)
-
-        elif not isinstance(slice_, slice):
-            raise ValueError(
-                f"Invalid slice definition {slice_} of type {type(slice_)}"
-            )
-        _slices[axis.on_disk_name] = slice_
-
-    slices = tuple(_slices.get(axis, slice(None)) for axis in axes_names)
-    return SliceTransform(slices=slices)
-
-
-def numpy_get_slice(array: zarr.Array, slices: SliceTransform) -> np.ndarray:
-    return array[slices.slices]
-
-
-def dask_get_slice(array: zarr.Array, slices: SliceTransform) -> da.Array:
-    da_array = da.from_zarr(array)
-    return da_array[slices.slices]
-
-
-def numpy_set_slice(
-    array: zarr.Array, patch: np.ndarray, slices: SliceTransform
-) -> None:
-    array[slices.slices] = patch
-
-
-def dask_set_slice(array: zarr.Array, patch: da.Array, slices: SliceTransform) -> None:
-    da.to_zarr(arr=patch, url=array, region=slices.slices)