ngio 0.3.5__py3-none-any.whl → 0.4.0a1__py3-none-any.whl

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

ngio/common/_slicer.py

@@ -1,96 +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 NgioValueError(
-                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)

ngio-0.3.5.dist-info/RECORD

@@ -1,61 +0,0 @@
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