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

ngio/io_pipes/_io_pipes_masked.py

@@ -0,0 +1,488 @@
+from collections.abc import Sequence
+
+import dask.array as da
+import numpy as np
+import zarr
+from dask.array import Array as DaskArray
+
+from ngio.common._dimensions import Dimensions
+from ngio.common._roi import Roi, RoiPixels
+from ngio.io_pipes._io_pipes import (
+    DaskGetter,
+    DaskSetter,
+    DataGetter,
+    DataSetter,
+    NumpyGetter,
+    NumpySetter,
+)
+from ngio.io_pipes._io_pipes_roi import roi_to_slicing_dict
+from ngio.io_pipes._match_shape import dask_match_shape, numpy_match_shape
+from ngio.io_pipes._ops_slices import SlicingInputType
+from ngio.io_pipes._ops_transforms import TransformProtocol
+from ngio.io_pipes._zoom_transform import BaseZoomTransform
+
+##############################################################
+#
+# Numpy Pipes
+#
+##############################################################
+
+
+def _numpy_label_to_bool_mask(
+    label_data: np.ndarray,
+    label: int | None,
+    data_shape: tuple[int, ...],
+    label_axes: tuple[str, ...],
+    data_axes: tuple[str, ...],
+    allow_rescaling: bool = True,
+) -> np.ndarray:
+    """Convert label data to a boolean mask."""
+    if label is not None:
+        bool_mask = label_data == label
+    else:
+        bool_mask = label_data != 0
+
+    bool_mask = numpy_match_shape(
+        array=bool_mask,
+        reference_shape=data_shape,
+        array_axes=label_axes,
+        reference_axes=data_axes,
+        allow_rescaling=allow_rescaling,
+    )
+    return bool_mask
+
+
+def _setup_numpy_getters(
+    zarr_array: zarr.Array,
+    dimensions: Dimensions,
+    label_zarr_array: zarr.Array,
+    label_dimensions: Dimensions,
+    roi: Roi | RoiPixels,
+    axes_order: Sequence[str] | None = None,
+    transforms: Sequence[TransformProtocol] | None = None,
+    label_transforms: Sequence[TransformProtocol] | None = None,
+    slicing_dict: dict[str, SlicingInputType] | None = None,
+    label_slicing_dict: dict[str, SlicingInputType] | None = None,
+    allow_rescaling: bool = True,
+    remove_channel_selection: bool = False,
+) -> tuple[NumpyGetter, NumpyGetter, dict[str, SlicingInputType]]:
+    """Prepare slice kwargs for getting a masked array."""
+    slicing_dict = roi_to_slicing_dict(
+        roi=roi,
+        pixel_size=dimensions.pixel_size,
+        slicing_dict=slicing_dict,
+    )
+
+    data_getter = NumpyGetter(
+        zarr_array=zarr_array,
+        dimensions=dimensions,
+        axes_order=axes_order,
+        transforms=transforms,
+        slicing_dict=slicing_dict,
+        remove_channel_selection=remove_channel_selection,
+    )
+
+    if allow_rescaling:
+        _zoom_transform = BaseZoomTransform(
+            input_dimensions=dimensions,
+            target_dimensions=label_dimensions,
+            order="nearest",
+        )
+        if label_transforms is None or len(label_transforms) == 0:
+            label_transforms = [_zoom_transform]
+        else:
+            label_transforms = [_zoom_transform, *label_transforms]
+
+    label_slicing_dict = roi_to_slicing_dict(
+        roi=roi,
+        pixel_size=label_dimensions.pixel_size,
+        slicing_dict=label_slicing_dict,
+    )
+    label_data_getter = NumpyGetter(
+        zarr_array=label_zarr_array,
+        dimensions=label_dimensions,
+        axes_order=axes_order,
+        transforms=label_transforms,
+        slicing_dict=label_slicing_dict,
+        remove_channel_selection=True,
+    )
+    return data_getter, label_data_getter, slicing_dict
+
+
+class NumpyGetterMasked(DataGetter[np.ndarray]):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        label_zarr_array: zarr.Array,
+        label_dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        label_transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        label_slicing_dict: dict[str, SlicingInputType] | None = None,
+        fill_value: int | float = 0,
+        allow_rescaling: bool = True,
+        remove_channel_selection: bool = False,
+    ):
+        """Prepare slice kwargs for getting a masked array."""
+        data_getter, label_data_getter, slicing_dict = _setup_numpy_getters(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            label_zarr_array=label_zarr_array,
+            label_dimensions=label_dimensions,
+            roi=roi,
+            axes_order=axes_order,
+            transforms=transforms,
+            label_transforms=label_transforms,
+            slicing_dict=slicing_dict,
+            label_slicing_dict=label_slicing_dict,
+            allow_rescaling=allow_rescaling,
+            remove_channel_selection=remove_channel_selection,
+        )
+        self._data_getter = data_getter
+        self._label_data_getter = label_data_getter
+
+        self._label_id = roi.label
+        self._fill_value = fill_value
+        self._allow_rescaling = allow_rescaling
+        super().__init__(
+            zarr_array=zarr_array,
+            slicing_ops=self._data_getter.slicing_ops,
+            axes_ops=self._data_getter.axes_ops,
+            transforms=self._data_getter.transforms,
+            roi=roi,
+        )
+
+    @property
+    def label_id(self) -> int | None:
+        return self._label_id
+
+    def get(self) -> np.ndarray:
+        """Get the masked data as a numpy array."""
+        data = self._data_getter()
+        label_data = self._label_data_getter()
+
+        bool_mask = _numpy_label_to_bool_mask(
+            label_data=label_data,
+            label=self.label_id,
+            data_shape=data.shape,
+            label_axes=self._label_data_getter.axes_ops.output_axes,
+            data_axes=self._data_getter.axes_ops.output_axes,
+            allow_rescaling=self._allow_rescaling,
+        )
+        if bool_mask.shape != data.shape:
+            bool_mask = np.broadcast_to(bool_mask, data.shape)
+        masked_data = np.where(bool_mask, data, self._fill_value)
+        return masked_data
+
+
+class NumpySetterMasked(DataSetter[np.ndarray]):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        label_zarr_array: zarr.Array,
+        label_dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        label_transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        label_slicing_dict: dict[str, SlicingInputType] | None = None,
+        allow_rescaling: bool = True,
+        remove_channel_selection: bool = False,
+    ):
+        """Prepare slice kwargs for setting a masked array."""
+        _data_getter, _label_data_getter, slicing_dict = _setup_numpy_getters(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            label_zarr_array=label_zarr_array,
+            label_dimensions=label_dimensions,
+            roi=roi,
+            axes_order=axes_order,
+            transforms=transforms,
+            label_transforms=label_transforms,
+            slicing_dict=slicing_dict,
+            label_slicing_dict=label_slicing_dict,
+            allow_rescaling=allow_rescaling,
+            remove_channel_selection=remove_channel_selection,
+        )
+        self._data_getter = _data_getter
+        self._label_data_getter = _label_data_getter
+        self._label_id = roi.label
+        self._allow_rescaling = allow_rescaling
+
+        self._data_setter = NumpySetter(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            axes_order=axes_order,
+            transforms=transforms,
+            slicing_dict=slicing_dict,
+            remove_channel_selection=remove_channel_selection,
+        )
+        super().__init__(
+            zarr_array=zarr_array,
+            slicing_ops=self._data_setter.slicing_ops,
+            axes_ops=self._data_setter.axes_ops,
+            transforms=self._data_setter.transforms,
+            roi=roi,
+        )
+
+    @property
+    def label_id(self) -> int | None:
+        return self._label_id
+
+    def set(self, patch: np.ndarray) -> None:
+        data = self._data_getter()
+        label_data = self._label_data_getter()
+
+        bool_mask = _numpy_label_to_bool_mask(
+            label_data=label_data,
+            label=self.label_id,
+            data_shape=data.shape,
+            label_axes=self._label_data_getter.axes_ops.output_axes,
+            data_axes=self._data_getter.axes_ops.output_axes,
+            allow_rescaling=self._allow_rescaling,
+        )
+        if bool_mask.shape != data.shape:
+            bool_mask = np.broadcast_to(bool_mask, data.shape)
+        masked_patch = np.where(bool_mask, patch, data)
+        self._data_setter(masked_patch)
+
+
+##############################################################
+#
+# Dask Pipes
+#
+##############################################################
+
+
+def _dask_label_to_bool_mask(
+    label_data: DaskArray,
+    label: int | None,
+    data_shape: tuple[int, ...],
+    label_axes: tuple[str, ...],
+    data_axes: tuple[str, ...],
+    allow_rescaling: bool = True,
+) -> DaskArray:
+    """Convert label data to a boolean mask."""
+    if label is not None:
+        bool_mask = label_data == label
+    else:
+        bool_mask = label_data != 0
+
+    bool_mask = dask_match_shape(
+        array=bool_mask,
+        reference_shape=data_shape,
+        array_axes=label_axes,
+        reference_axes=data_axes,
+        allow_rescaling=allow_rescaling,
+    )
+    return bool_mask
+
+
+def _setup_dask_getters(
+    zarr_array: zarr.Array,
+    dimensions: Dimensions,
+    label_zarr_array: zarr.Array,
+    label_dimensions: Dimensions,
+    roi: Roi | RoiPixels,
+    axes_order: Sequence[str] | None = None,
+    transforms: Sequence[TransformProtocol] | None = None,
+    label_transforms: Sequence[TransformProtocol] | None = None,
+    slicing_dict: dict[str, SlicingInputType] | None = None,
+    label_slicing_dict: dict[str, SlicingInputType] | None = None,
+    allow_rescaling: bool = True,
+    remove_channel_selection: bool = False,
+) -> tuple[DaskGetter, DaskGetter, dict[str, SlicingInputType]]:
+    """Prepare slice kwargs for getting a masked array."""
+    slicing_dict = roi_to_slicing_dict(
+        roi=roi,
+        pixel_size=dimensions.pixel_size,
+        slicing_dict=slicing_dict,
+    )
+
+    data_getter = DaskGetter(
+        zarr_array=zarr_array,
+        dimensions=dimensions,
+        axes_order=axes_order,
+        transforms=transforms,
+        slicing_dict=slicing_dict,
+        remove_channel_selection=remove_channel_selection,
+    )
+
+    if allow_rescaling:
+        _zoom_transform = BaseZoomTransform(
+            input_dimensions=dimensions,
+            target_dimensions=label_dimensions,
+            order="nearest",
+        )
+        if label_transforms is None or len(label_transforms) == 0:
+            label_transforms = [_zoom_transform]
+        else:
+            label_transforms = [_zoom_transform, *label_transforms]
+
+    label_slicing_dict = roi_to_slicing_dict(
+        roi=roi,
+        pixel_size=label_dimensions.pixel_size,
+        slicing_dict=label_slicing_dict,
+    )
+    label_data_getter = DaskGetter(
+        zarr_array=label_zarr_array,
+        dimensions=label_dimensions,
+        axes_order=axes_order,
+        transforms=label_transforms,
+        slicing_dict=label_slicing_dict,
+        remove_channel_selection=True,
+    )
+    return data_getter, label_data_getter, slicing_dict
+
+
+class DaskGetterMasked(DataGetter[DaskArray]):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        label_zarr_array: zarr.Array,
+        label_dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        label_transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        label_slicing_dict: dict[str, SlicingInputType] | None = None,
+        fill_value: int | float = 0,
+        allow_rescaling: bool = True,
+        remove_channel_selection: bool = False,
+    ):
+        """Prepare slice kwargs for getting a masked array."""
+        _data_getter, _label_data_getter, slicing_dict = _setup_dask_getters(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            label_zarr_array=label_zarr_array,
+            label_dimensions=label_dimensions,
+            roi=roi,
+            axes_order=axes_order,
+            transforms=transforms,
+            label_transforms=label_transforms,
+            slicing_dict=slicing_dict,
+            label_slicing_dict=label_slicing_dict,
+            allow_rescaling=allow_rescaling,
+            remove_channel_selection=remove_channel_selection,
+        )
+        self._data_getter = _data_getter
+        self._label_data_getter = _label_data_getter
+        self._label_id = roi.label
+        self._fill_value = fill_value
+        self._allow_rescaling = allow_rescaling
+        super().__init__(
+            zarr_array=zarr_array,
+            slicing_ops=self._data_getter.slicing_ops,
+            axes_ops=self._data_getter.axes_ops,
+            transforms=self._data_getter.transforms,
+            roi=roi,
+        )
+
+    @property
+    def label_id(self) -> int | None:
+        return self._label_id
+
+    def get(self) -> DaskArray:
+        data = self._data_getter()
+        label_data = self._label_data_getter()
+        data_shape = tuple(int(dim) for dim in data.shape)
+        bool_mask = _dask_label_to_bool_mask(
+            label_data=label_data,
+            label=self.label_id,
+            data_shape=data_shape,
+            label_axes=self._label_data_getter.axes_ops.output_axes,
+            data_axes=self._data_getter.axes_ops.output_axes,
+            allow_rescaling=self._allow_rescaling,
+        )
+        if bool_mask.shape != data.shape:
+            bool_mask = da.broadcast_to(bool_mask, data.shape)
+        masked_data = da.where(bool_mask, data, self._fill_value)
+        return masked_data
+
+
+class DaskSetterMasked(DataSetter[DaskArray]):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        label_zarr_array: zarr.Array,
+        label_dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        label_transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        label_slicing_dict: dict[str, SlicingInputType] | None = None,
+        allow_rescaling: bool = True,
+        remove_channel_selection: bool = False,
+    ):
+        """Prepare slice kwargs for setting a masked array."""
+        _data_getter, _label_data_getter, slicing_dict = _setup_dask_getters(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            label_zarr_array=label_zarr_array,
+            label_dimensions=label_dimensions,
+            roi=roi,
+            axes_order=axes_order,
+            transforms=transforms,
+            label_transforms=label_transforms,
+            slicing_dict=slicing_dict,
+            label_slicing_dict=label_slicing_dict,
+            allow_rescaling=allow_rescaling,
+            remove_channel_selection=remove_channel_selection,
+        )
+        self._data_getter = _data_getter
+        self._label_data_getter = _label_data_getter
+
+        self._label_id = roi.label
+        self._allow_rescaling = allow_rescaling
+
+        self._data_setter = DaskSetter(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            axes_order=axes_order,
+            transforms=transforms,
+            slicing_dict=slicing_dict,
+            remove_channel_selection=remove_channel_selection,
+        )
+
+        super().__init__(
+            zarr_array=zarr_array,
+            slicing_ops=self._data_setter.slicing_ops,
+            axes_ops=self._data_setter.axes_ops,
+            transforms=self._data_setter.transforms,
+            roi=roi,
+        )
+
+    @property
+    def label_id(self) -> int | None:
+        return self._label_id
+
+    def set(self, patch: DaskArray) -> None:
+        data = self._data_getter()
+        label_data = self._label_data_getter()
+        data_shape = tuple(int(dim) for dim in data.shape)
+
+        bool_mask = _dask_label_to_bool_mask(
+            label_data=label_data,
+            label=self.label_id,
+            data_shape=data_shape,
+            label_axes=self._label_data_getter.axes_ops.output_axes,
+            data_axes=self._data_getter.axes_ops.output_axes,
+            allow_rescaling=self._allow_rescaling,
+        )
+        if bool_mask.shape != data.shape:
+            bool_mask = da.broadcast_to(bool_mask, data.shape)
+        masked_patch = da.where(bool_mask, patch, data)
+        self._data_setter(masked_patch)

ngio/io_pipes/_io_pipes_roi.py

@@ -0,0 +1,152 @@
+from collections.abc import Sequence
+
+import zarr
+
+from ngio.common._dimensions import Dimensions
+from ngio.common._roi import Roi, RoiPixels
+from ngio.io_pipes._io_pipes import (
+    DaskGetter,
+    DaskSetter,
+    NumpyGetter,
+    NumpySetter,
+)
+from ngio.io_pipes._ops_slices import SlicingInputType
+from ngio.io_pipes._ops_transforms import TransformProtocol
+from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
+from ngio.utils import NgioValueError
+
+
+def roi_to_slicing_dict(
+    *,
+    roi: Roi | RoiPixels,
+    pixel_size: PixelSize | None = None,
+    slicing_dict: dict[str, SlicingInputType] | None = None,
+) -> dict[str, SlicingInputType]:
+    """Convert a ROI to a slicing dictionary."""
+    if isinstance(roi, Roi):
+        if pixel_size is None:
+            raise NgioValueError(
+                "pixel_size must be provided when converting a Roi to slice_kwargs."
+            )
+        roi = roi.to_roi_pixels(pixel_size=pixel_size)
+
+    roi_slicing_dict: dict[str, SlicingInputType] = roi.to_slicing_dict()  # type: ignore
+    if slicing_dict is None:
+        return roi_slicing_dict
+
+    # Additional slice kwargs can be provided
+    # and will override the ones from the ROI
+    roi_slicing_dict.update(slicing_dict)
+    return roi_slicing_dict
+
+
+class NumpyRoiGetter(NumpyGetter):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        remove_channel_selection: bool = False,
+    ) -> None:
+        input_slice_kwargs = roi_to_slicing_dict(
+            roi=roi,
+            pixel_size=dimensions.pixel_size,
+            slicing_dict=slicing_dict,
+        )
+        super().__init__(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            axes_order=axes_order,
+            transforms=transforms,
+            slicing_dict=input_slice_kwargs,
+            remove_channel_selection=remove_channel_selection,
+            roi=roi,
+        )
+
+
+class DaskRoiGetter(DaskGetter):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        remove_channel_selection: bool = False,
+    ) -> None:
+        input_slice_kwargs = roi_to_slicing_dict(
+            roi=roi,
+            pixel_size=dimensions.pixel_size,
+            slicing_dict=slicing_dict,
+        )
+        super().__init__(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            axes_order=axes_order,
+            transforms=transforms,
+            slicing_dict=input_slice_kwargs,
+            remove_channel_selection=remove_channel_selection,
+            roi=roi,
+        )
+
+
+class NumpyRoiSetter(NumpySetter):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        remove_channel_selection: bool = False,
+    ) -> None:
+        input_slice_kwargs = roi_to_slicing_dict(
+            roi=roi,
+            pixel_size=dimensions.pixel_size,
+            slicing_dict=slicing_dict,
+        )
+        super().__init__(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            axes_order=axes_order,
+            transforms=transforms,
+            slicing_dict=input_slice_kwargs,
+            remove_channel_selection=remove_channel_selection,
+            roi=roi,
+        )
+
+
+class DaskRoiSetter(DaskSetter):
+    def __init__(
+        self,
+        *,
+        zarr_array: zarr.Array,
+        dimensions: Dimensions,
+        roi: Roi | RoiPixels,
+        axes_order: Sequence[str] | None = None,
+        transforms: Sequence[TransformProtocol] | None = None,
+        slicing_dict: dict[str, SlicingInputType] | None = None,
+        remove_channel_selection: bool = False,
+    ) -> None:
+        input_slice_kwargs = roi_to_slicing_dict(
+            roi=roi,
+            pixel_size=dimensions.pixel_size,
+            slicing_dict=slicing_dict,
+        )
+        super().__init__(
+            zarr_array=zarr_array,
+            dimensions=dimensions,
+            axes_order=axes_order,
+            transforms=transforms,
+            slicing_dict=input_slice_kwargs,
+            remove_channel_selection=remove_channel_selection,
+            roi=roi,
+        )

ngio/io_pipes/_io_pipes_types.py

@@ -0,0 +1,56 @@
+from collections.abc import Sequence
+from typing import Protocol, TypeVar
+
+import zarr
+
+from ngio.common._roi import Roi, RoiPixels
+from ngio.io_pipes._ops_axes import AxesOps
+from ngio.io_pipes._ops_slices import SlicingOps
+from ngio.io_pipes._ops_transforms import TransformProtocol
+
+GetterDataType = TypeVar("GetterDataType", covariant=True)
+SetterDataType = TypeVar("SetterDataType", contravariant=True)
+
+
+class DataGetterProtocol(Protocol[GetterDataType]):
+    @property
+    def zarr_array(self) -> zarr.Array: ...
+
+    @property
+    def slicing_ops(self) -> SlicingOps: ...
+
+    @property
+    def axes_ops(self) -> AxesOps: ...
+
+    @property
+    def transforms(self) -> Sequence[TransformProtocol] | None: ...
+
+    @property
+    def roi(self) -> Roi | RoiPixels: ...
+
+    def __call__(self) -> GetterDataType:
+        return self.get()
+
+    def get(self) -> GetterDataType: ...
+
+
+class DataSetterProtocol(Protocol[SetterDataType]):
+    @property
+    def zarr_array(self) -> zarr.Array: ...
+
+    @property
+    def slicing_ops(self) -> SlicingOps: ...
+
+    @property
+    def axes_ops(self) -> AxesOps: ...
+
+    @property
+    def transforms(self) -> Sequence[TransformProtocol] | None: ...
+
+    @property
+    def roi(self) -> Roi | RoiPixels: ...
+
+    def __call__(self, patch: SetterDataType) -> None:
+        return self.set(patch)
+
+    def set(self, patch: SetterDataType) -> None: ...