ngio 0.3.4__py3-none-any.whl → 0.4.0__py3-none-any.whl

ngio/utils/_zarr_utils.py

@@ -1,6 +1,5 @@
 """Common utilities for working with Zarr groups in consistent ways."""
 
-# %%
 from pathlib import Path
 from typing import Literal
 
@@ -9,6 +8,7 @@ import zarr
 from filelock import BaseFileLock, FileLock
 from zarr.errors import ContainsGroupError, GroupNotFoundError
 from zarr.storage import DirectoryStore, FSStore, MemoryStore, Store, StoreLike
+from zarr.types import DIMENSION_SEPARATOR
 
 from ngio.utils import NgioFileExistsError, NgioFileNotFoundError, NgioValueError
 from ngio.utils._errors import NgioError
@@ -164,7 +164,7 @@ class ZarrGroupHandler:
     @property
     def mode(self) -> AccessModeLiteral:
         """Return the mode of the group."""
-        return self._mode  # type: ignore
+        return self._mode  # type: ignore (return type is Literal)
 
     @property
     def lock(self) -> BaseFileLock:
@@ -343,6 +343,8 @@ class ZarrGroupHandler:
         shape: tuple[int, ...],
         dtype: str,
         chunks: tuple[int, ...] | None = None,
+        dimension_separator: DIMENSION_SEPARATOR = "/",
+        compressor: str = "default",
         overwrite: bool = False,
     ) -> zarr.Array:
         if self.mode == "r":
@@ -354,7 +356,8 @@ class ZarrGroupHandler:
                 shape=shape,
                 dtype=dtype,
                 chunks=chunks,
-                dimension_separator="/",
+                dimension_separator=dimension_separator,
+                compressor=compressor,
                 overwrite=overwrite,
             )
         except ContainsGroupError as e:
@@ -410,6 +413,3 @@ class ZarrGroupHandler:
                 f"Error copying group to {handler.full_url}, "
                 f"#{n_skipped} files where skipped."
             )
-
-
-# %%

{ngio-0.3.4.dist-info → ngio-0.4.0.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.4
+Version: 0.4.0
 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
+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
@@ -16,7 +16,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
-Requires-Dist: anndata>=0.8.0
+Requires-Dist: anndata<0.11.4,>=0.8.0
 Requires-Dist: dask[array]
 Requires-Dist: dask[distributed]
 Requires-Dist: filelock
@@ -28,7 +28,6 @@ Requires-Dist: pooch
 Requires-Dist: pyarrow
 Requires-Dist: pydantic
 Requires-Dist: requests
-Requires-Dist: xarray
 Requires-Dist: zarr<3
 Provides-Extra: dev
 Requires-Dist: devtools; extra == 'dev'
@@ -38,11 +37,13 @@ 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'
 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'
@@ -65,11 +66,11 @@ 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/lorenzocerrone/ngio/raw/main/LICENSE)
+[![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/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)
+[![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.
 
@@ -81,20 +82,22 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 
 ## Key Features
 
-### 📊 Simple Object-Based API
+### 🔍 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
+### 📊 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
-- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+- 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 (Coming Soon)
+### 🔄 Scalable Data Processing
 
-- Powerful iterators for processing data at scale
-- Efficient memory management for large datasets
+- Powerful iterators for building scalable and generalizable image processing pipelines
+- Extensible mapping mechanism for custom parallelization strategies
 
 ## Installation
 
@@ -104,7 +107,7 @@ You can install ngio via pip:
 pip install ngio
 ```
 
-To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+To get started check out the [Quickstart Guide](https://BioVisionCenter.github.io/ngio/stable/getting_started/0_quickstart/).
 
 ## Supported OME-Zarr versions
 
@@ -112,23 +115,22 @@ Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher
 
 ## 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.
+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
 
-- Advanced image processing iterators
-- Parallel processing capabilities
-- Support for OME-Zarr v0.5 and Zarr v3
+- Support for OME-Zarr v0.5 and Zarr v3 (via `zarr-python` v3)
+- Enhanced performance optimizations (parallel iterators, optimized io strategies)
 
 ## Contributors
 
@@ -136,4 +138,4 @@ Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en
 
 ## 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 is released under the BSD-3-Clause License. See [LICENSE](https://github.com/BioVisionCenter/ngio/blob/main/LICENSE) for details.

ngio-0.4.0.dist-info/RECORD

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ngio/common/_array_pipe.py

@@ -1,288 +0,0 @@
-from collections.abc import Collection, Iterable
-from typing import Literal
-
-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
-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, ...],
-) -> 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, ...],
-) -> DaskArray:
-    _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: DaskArray,
-    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 | Delayed,
-    slices: SliceTransform,
-    transformations: tuple[AxesTransformation, ...],
-) -> Delayed:
-    _patch = delayed(transform_numpy_array)(patch, transformations)
-    return 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":
-            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, DaskArray):
-        _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, Delayed):
-        _delayed_numpy_set_pipe(
-            array=array, patch=patch, slices=slices, transformations=transformations
-        )
-    else:
-        raise NgioValueError("Unknown patch type, expected numpy, dask or delayed.")
-
-
-def _mask_pipe_common(
-    array: zarr.Array,
-    label_array: zarr.Array,
-    label: int,
-    *,
-    dimensions_array: Dimensions,
-    dimensions_label: Dimensions,
-    axes_order: Collection[str] | None = None,
-    mode: Literal["numpy", "dask", "delayed"] = "numpy",
-    **slice_kwargs: slice | int | Iterable[int],
-):
-    array_patch = get_pipe(
-        array,
-        dimensions=dimensions_array,
-        axes_order=axes_order,
-        mode=mode,
-        **slice_kwargs,
-    )
-
-    if not dimensions_label.has_axis("c"):
-        # Remove the 'c' from the slice_kwargs
-        # This will not work if the query uses non-default
-        # axes names for channel
-        slice_kwargs = {k: v for k, v in slice_kwargs.items() if k != "c"}
-
-    label_patch = get_pipe(
-        label_array,
-        dimensions=dimensions_label,
-        axes_order=axes_order,
-        mode=mode,
-        **slice_kwargs,
-    )
-
-    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, DaskArray) and isinstance(label_patch, DaskArray):
-        label_patch = da.broadcast_to(label_patch, array_patch.shape)
-    else:
-        raise NgioValueError(
-            "Incompatible types for array and label: "
-            f"{type(array_patch)} and {type(label_patch)}"
-        )
-
-    mask = label_patch == label
-    return array_patch, mask
-
-
-def get_masked_pipe(
-    array: zarr.Array,
-    label_array: zarr.Array,
-    label: int,
-    *,
-    dimensions_array: Dimensions,
-    dimensions_label: Dimensions,
-    axes_order: Collection[str] | None = None,
-    mode: Literal["numpy", "dask", "delayed"] = "numpy",
-    **slice_kwargs: slice | int | Iterable[int],
-):
-    array_patch, mask = _mask_pipe_common(
-        array=array,
-        label_array=label_array,
-        label=label,
-        dimensions_array=dimensions_array,
-        dimensions_label=dimensions_label,
-        axes_order=axes_order,
-        mode=mode,
-        **slice_kwargs,
-    )
-    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
-
-
-def set_masked_pipe(
-    array: zarr.Array,
-    label_array: zarr.Array,
-    label: int,
-    patch: ArrayLike,
-    *,
-    dimensions_array: Dimensions,
-    dimensions_label: Dimensions,
-    axes_order: Collection[str] | None = None,
-    **slice_kwargs: slice | int | Iterable[int],
-):
-    if isinstance(patch, DaskArray):
-        mode = "dask"
-    elif isinstance(patch, np.ndarray):
-        mode = "numpy"
-    else:
-        raise NgioValueError(
-            "Mode not yet supported for masked array. Expected a numpy or dask array."
-        )
-
-    array_patch, mask = _mask_pipe_common(
-        array=array,
-        label_array=label_array,
-        label=label,
-        dimensions_array=dimensions_array,
-        dimensions_label=dimensions_label,
-        axes_order=axes_order,
-        mode=mode,
-        **slice_kwargs,
-    )
-    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,
-    )

ngio/common/_axes_transforms.py

@@ -1,64 +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,
-)
-from ngio.utils import NgioValueError
-
-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 NgioValueError(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 NgioValueError(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