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

ngio/images/abstract_image.py

@@ -1,240 +0,0 @@
-"""Generic class to handle Image-like data in a OME-NGFF file."""
-
-from collections.abc import Collection, Iterable
-from typing import Generic, Literal, TypeVar
-
-import zarr
-
-from ngio.common import (
-    ArrayLike,
-    Dimensions,
-    WorldCooROI,
-    consolidate_pyramid,
-    get_pipe,
-    set_pipe,
-)
-from ngio.ome_zarr_meta import (
-    Dataset,
-    ImageMetaHandler,
-    LabelMetaHandler,
-    PixelSize,
-)
-from ngio.utils import (
-    NgioFileExistsError,
-    ZarrGroupHandler,
-)
-
-_image_handler = TypeVar("_image_handler", ImageMetaHandler, LabelMetaHandler)
-
-
-class AbstractImage(Generic[_image_handler]):
-    """A class to handle a single image (or level) in an OME-Zarr image.
-
-    This class is meant to be subclassed by specific image types.
-    """
-
-    def __init__(
-        self,
-        group_handler: ZarrGroupHandler,
-        path: str,
-        meta_handler: _image_handler,
-    ) -> None:
-        """Initialize the Image at a single level.
-
-        Args:
-            group_handler: The Zarr group handler.
-            path: The path to the image in the omezarr file.
-            meta_handler: The image metadata handler.
-
-        """
-        self._path = path
-        self._group_handler = group_handler
-        self._meta_handler = meta_handler
-
-        self._dataset = self._meta_handler.meta.get_dataset(path=path)
-        self._pixel_size = self._dataset.pixel_size
-
-        try:
-            self._zarr_array = self._group_handler.get_array(self._dataset.path)
-        except NgioFileExistsError as e:
-            raise NgioFileExistsError(f"Could not find the dataset at {path}.") from e
-
-        self._dimensions = Dimensions(
-            shape=self._zarr_array.shape, axes_mapper=self._dataset.axes_mapper
-        )
-
-        self._axer_mapper = self._dataset.axes_mapper
-
-    def __repr__(self) -> str:
-        """Return a string representation of the image."""
-        return f"Image(path={self.path}, {self.dimensions})"
-
-    @property
-    def meta_handler(self) -> _image_handler:
-        """Return the metadata."""
-        return self._meta_handler
-
-    @property
-    def zarr_array(self) -> zarr.Array:
-        """Return the Zarr array."""
-        return self._zarr_array
-
-    @property
-    def shape(self) -> tuple[int, ...]:
-        """Return the shape of the image."""
-        return self.zarr_array.shape
-
-    @property
-    def dtype(self) -> str:
-        """Return the dtype of the image."""
-        return str(self.zarr_array.dtype)
-
-    @property
-    def chunks(self) -> tuple[int, ...]:
-        """Return the chunks of the image."""
-        return self.zarr_array.chunks
-
-    @property
-    def dimensions(self) -> Dimensions:
-        """Return the dimensions of the image."""
-        return self._dimensions
-
-    @property
-    def pixel_size(self) -> PixelSize:
-        """Return the pixel size of the image."""
-        return self._pixel_size
-
-    @property
-    def dataset(self) -> Dataset:
-        """Return the dataset of the image."""
-        return self._dataset
-
-    @property
-    def path(self) -> str:
-        """Return the path of the image."""
-        return self._dataset.path
-
-    def get_array(
-        self,
-        axes_order: Collection[str] | None = None,
-        mode: Literal["numpy", "dask", "delayed"] = "numpy",
-        **slice_kwargs: slice | int | Iterable[int],
-    ) -> ArrayLike:
-        """Get a slice of the image.
-
-        Args:
-            axes_order: The order of the axes to return the array.
-            mode: The mode to return the array.
-            **slice_kwargs: The slices to get the array.
-
-        Returns:
-            The array of the region of interest.
-        """
-        return get_pipe(
-            array=self.zarr_array,
-            dimensions=self.dimensions,
-            axes_order=axes_order,
-            mode=mode,
-            **slice_kwargs,
-        )
-
-    def get_roi(
-        self,
-        roi: WorldCooROI,
-        axes_order: Collection[str] | None = None,
-        mode: Literal["numpy", "dask", "delayed"] = "numpy",
-        **slice_kwargs: slice | int | Iterable[int],
-    ) -> ArrayLike:
-        """Get a slice of the image.
-
-        Args:
-            roi: The region of interest to get the array.
-            axes_order: The order of the axes to return the array.
-            mode: The mode to return the array.
-            **slice_kwargs: The slices to get the array.
-
-        Returns:
-            The array of the region of interest.
-        """
-        raster_roi = roi.to_raster_coo(
-            pixel_size=self.pixel_size, dimensions=self.dimensions
-        ).to_slices()
-
-        for key in slice_kwargs.keys():
-            if key in raster_roi:
-                raise ValueError(
-                    f"Key {key} is already in the slice_kwargs. "
-                    "Ambiguous which one to use: "
-                    f"{key}={slice_kwargs[key]} or roi_{key}={raster_roi[key]}"
-                )
-        return self.get_array(
-            axes_order=axes_order, mode=mode, **raster_roi, **slice_kwargs
-        )
-
-    def set_array(
-        self,
-        patch: ArrayLike,
-        axes_order: Collection[str] | None = None,
-        **slice_kwargs: slice | int | Iterable[int],
-    ) -> None:
-        """Set a slice of the image.
-
-        Args:
-            patch: The patch to set.
-            axes_order: The order of the axes to set the patch.
-            **slice_kwargs: The slices to set the patch.
-
-        """
-        set_pipe(
-            array=self.zarr_array,
-            patch=patch,
-            dimensions=self.dimensions,
-            axes_order=axes_order,
-            **slice_kwargs,
-        )
-
-    def set_roi(
-        self,
-        roi: WorldCooROI,
-        patch: ArrayLike,
-        axes_order: Collection[str] | None = None,
-        **slice_kwargs: slice | int | Iterable[int],
-    ) -> None:
-        """Set a slice of the image.
-
-        Args:
-            roi: The region of interest to set the patch.
-            patch: The patch to set.
-            axes_order: The order of the axes to set the patch.
-            **slice_kwargs: The slices to set the patch.
-
-        """
-        raster_roi = roi.to_raster_coo(
-            pixel_size=self.pixel_size, dimensions=self.dimensions
-        ).to_slices()
-
-        for key in slice_kwargs.keys():
-            if key in raster_roi:
-                raise ValueError(
-                    f"Key {key} is already in the slice_kwargs. "
-                    "Ambiguous which one to use: "
-                    f"{key}={slice_kwargs[key]} or roi_{key}={raster_roi[key]}"
-                )
-        self.set_array(patch=patch, axes_order=axes_order, **raster_roi, **slice_kwargs)
-
-
-def consolidate_image(
-    image: AbstractImage,
-    order: Literal[0, 1, 2] = 1,
-    mode: Literal["dask", "numpy", "coarsen"] = "dask",
-) -> None:
-    """Consolidate the image on disk."""
-    target_paths = image._meta_handler.meta.paths
-    targets = [
-        image._group_handler.get_array(path)
-        for path in target_paths
-        if path != image.path
-    ]
-    consolidate_pyramid(
-        source=image.zarr_array, targets=targets, order=order, mode=mode
-    )

ngio/images/create.py

@@ -1,251 +0,0 @@
-"""Utility functions for working with OME-Zarr images."""
-
-from collections.abc import Collection
-from typing import TypeVar
-
-from ngio.common._pyramid import init_empty_pyramid
-from ngio.ome_zarr_meta import (
-    ImplementedImageMetaHandlers,
-    ImplementedLabelMetaHandlers,
-    NgioImageMeta,
-    NgioLabelMeta,
-    PixelSize,
-)
-from ngio.ome_zarr_meta.ngio_specs import (
-    SpaceUnits,
-    TimeUnits,
-    canonical_axes_order,
-    canonical_label_axes_order,
-)
-from ngio.utils import StoreOrGroup, ZarrGroupHandler
-
-_image_or_label_meta = TypeVar("_image_or_label_meta", NgioImageMeta, NgioLabelMeta)
-
-
-def _init_generic_meta(
-    meta_type: type[_image_or_label_meta],
-    xy_pixelsize: float,
-    axes_names: Collection[str],
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    xy_scaling_factor: float = 2.0,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = None,
-    time_unit: TimeUnits | str | None = None,
-    name: str | None = None,
-    version: str = "0.4",
-) -> tuple[_image_or_label_meta, list[float]]:
-    """Initialize the metadata for an image or label."""
-    scaling_factors = []
-    for ax in axes_names:
-        if ax == "z":
-            scaling_factors.append(z_scaling_factor)
-        elif ax in ["x", "y"]:
-            scaling_factors.append(xy_scaling_factor)
-        else:
-            scaling_factors.append(1.0)
-
-    if space_unit is None:
-        space_unit = SpaceUnits.micrometer
-    elif isinstance(space_unit, str):
-        space_unit = SpaceUnits(space_unit)
-    elif not isinstance(space_unit, SpaceUnits):
-        raise ValueError(f"space_unit can not be {type(space_unit)}.")
-
-    if time_unit is None:
-        time_unit = TimeUnits.seconds
-    elif isinstance(time_unit, str):
-        time_unit = TimeUnits(time_unit)
-    elif not isinstance(time_unit, TimeUnits):
-        raise ValueError(f"time_units can not be {type(time_unit)}.")
-
-    pixel_sizes = PixelSize(
-        x=xy_pixelsize,
-        y=xy_pixelsize,
-        z=z_spacing,
-        t=time_spacing,
-        space_unit=space_unit,
-        time_unit=time_unit,
-    )
-
-    meta = meta_type.default_init(
-        name=name,
-        levels=levels,
-        axes_names=axes_names,
-        pixel_size=pixel_sizes,
-        scaling_factors=scaling_factors,
-        version=version,
-    )
-    return meta, scaling_factors
-
-
-def _create_empty_label(
-    store: StoreOrGroup,
-    shape: Collection[int],
-    xy_pixelsize: float,
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    xy_scaling_factor: float = 2.0,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = None,
-    time_unit: TimeUnits | str | None = None,
-    axes_names: Collection[str] | None = None,
-    name: str | None = None,
-    chunks: Collection[int] | None = None,
-    dtype: str = "uint16",
-    overwrite: bool = False,
-    version: str = "0.4",
-) -> ZarrGroupHandler:
-    """Create an empty label with the given shape and metadata.
-
-    Args:
-        store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Collection[int]): The shape of the image.
-        xy_pixelsize (float): The pixel size in x and y dimensions.
-        z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
-        time_spacing (float, optional): The spacing between time points.
-            Defaults to 1.0.
-        levels (int | list[str], optional): The number of levels in the pyramid or a
-            list of level names. Defaults to 5.
-        xy_scaling_factor (float, optional): The down-scaling factor in x and y
-            dimensions. Defaults to 2.0.
-        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
-            Defaults to 1.0.
-        space_unit (SpaceUnits | str | None, optional): The unit of space. Defaults to
-            None.
-        time_unit (TimeUnits | str | None, optional): The unit of time. Defaults to
-            None.
-        axes_names (Collection[str] | None, optional): The names of the axes.
-            If None the canonical names are used. Defaults to None.
-        name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Collection[int] | None, optional): The chunk shape. If None the shape
-            is used. Defaults to None.
-        dtype (str, optional): The data type of the image. Defaults to "uint16".
-        overwrite (bool, optional): Whether to overwrite an existing image.
-            Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
-            Defaults to "0.4".
-
-    """
-    if axes_names is None:
-        axes_names = canonical_label_axes_order()[-len(shape) :]
-
-    meta, scaling_factors = _init_generic_meta(
-        meta_type=NgioLabelMeta,
-        xy_pixelsize=xy_pixelsize,
-        z_spacing=z_spacing,
-        time_spacing=time_spacing,
-        levels=levels,
-        xy_scaling_factor=xy_scaling_factor,
-        z_scaling_factor=z_scaling_factor,
-        space_unit=space_unit,
-        time_unit=time_unit,
-        axes_names=axes_names,
-        name=name,
-        version=version,
-    )
-
-    mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(store=store, mode=mode, cache=False)
-    image_handler = ImplementedLabelMetaHandlers().get_handler(
-        version=version, group_handler=group_handler
-    )
-    image_handler.write_meta(meta)
-
-    init_empty_pyramid(
-        store=store,
-        paths=meta.paths,
-        scaling_factors=scaling_factors,
-        ref_shape=shape,
-        chunks=chunks,
-        dtype=dtype,
-        mode="a",
-    )
-    return group_handler
-
-
-def _create_empty_image(
-    store: StoreOrGroup,
-    shape: Collection[int],
-    xy_pixelsize: float,
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    xy_scaling_factor: float = 2,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = None,
-    time_unit: TimeUnits | str | None = None,
-    axes_names: Collection[str] | None = None,
-    name: str | None = None,
-    chunks: Collection[int] | None = None,
-    dtype: str = "uint16",
-    overwrite: bool = False,
-    version: str = "0.4",
-) -> ZarrGroupHandler:
-    """Create an empty OME-Zarr image with the given shape and metadata.
-
-    Args:
-        store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Collection[int]): The shape of the image.
-        xy_pixelsize (float): The pixel size in x and y dimensions.
-        z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
-        time_spacing (float, optional): The spacing between time points.
-            Defaults to 1.0.
-        levels (int | list[str], optional): The number of levels in the pyramid or a
-            list of level names. Defaults to 5.
-        xy_scaling_factor (float, optional): The down-scaling factor in x and y
-            dimensions. Defaults to 2.0.
-        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
-            Defaults to 1.0.
-        space_unit (SpaceUnits | str | None, optional): The unit of space. Defaults to
-            None.
-        time_unit (TimeUnits | str | None, optional): The unit of time. Defaults to
-            None.
-        axes_names (Collection[str] | None, optional): The names of the axes.
-            If None the canonical names are used. Defaults to None.
-        name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Collection[int] | None, optional): The chunk shape. If None the shape
-            is used. Defaults to None.
-        dtype (str, optional): The data type of the image. Defaults to "uint16".
-        overwrite (bool, optional): Whether to overwrite an existing image.
-            Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
-            Defaults to "0.4".
-
-    """
-    if axes_names is None:
-        axes_names = canonical_axes_order()[-len(shape) :]
-
-    meta, scaling_factors = _init_generic_meta(
-        meta_type=NgioImageMeta,
-        xy_pixelsize=xy_pixelsize,
-        z_spacing=z_spacing,
-        time_spacing=time_spacing,
-        levels=levels,
-        xy_scaling_factor=xy_scaling_factor,
-        z_scaling_factor=z_scaling_factor,
-        space_unit=space_unit,
-        time_unit=time_unit,
-        axes_names=axes_names,
-        name=name,
-        version=version,
-    )
-    mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(store=store, mode=mode, cache=False)
-    image_handler = ImplementedImageMetaHandlers().get_handler(
-        version=version, group_handler=group_handler
-    )
-    image_handler.write_meta(meta)
-
-    init_empty_pyramid(
-        store=store,
-        paths=meta.paths,
-        scaling_factors=scaling_factors,
-        ref_shape=shape,
-        chunks=chunks,
-        dtype=dtype,
-        mode="a",
-    )
-    return group_handler