ngio 0.4.0a3__py3-none-any.whl → 0.4.0b1__py3-none-any.whl

ngio/images/_image.py

@@ -6,17 +6,20 @@ from typing import Literal
 import dask.array as da
 import numpy as np
 from pydantic import BaseModel, model_validator
+from zarr.types import DIMENSION_SEPARATOR
 
 from ngio.common import (
-    ArrayLike,
     Dimensions,
+    InterpolationOrder,
     Roi,
     RoiPixels,
-    SlicingInputType,
-    TransformProtocol,
 )
 from ngio.images._abstract_image import AbstractImage
 from ngio.images._create import create_empty_image_container
+from ngio.io_pipes import (
+    SlicingInputType,
+    TransformProtocol,
+)
 from ngio.ome_zarr_meta import (
     ImageMetaHandler,
     NgioImageMeta,
@@ -269,7 +272,7 @@ class Image(AbstractImage[ImageMetaHandler]):
         transforms: Sequence[TransformProtocol] | None = None,
         mode: Literal["numpy", "dask"] = "numpy",
         **slicing_kwargs: SlicingInputType,
-    ) -> ArrayLike:
+    ) -> np.ndarray | da.Array:
         """Get the image as a zarr array.
 
         Args:
@@ -299,7 +302,7 @@ class Image(AbstractImage[ImageMetaHandler]):
         transforms: Sequence[TransformProtocol] | None = None,
         mode: Literal["numpy", "dask"] = "numpy",
         **slicing_kwargs: SlicingInputType,
-    ) -> ArrayLike:
+    ) -> np.ndarray | da.Array:
         """Get the image as a zarr array for a region of interest.
 
         Args:
@@ -328,7 +331,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
     def set_array(
         self,
-        patch: ArrayLike,
+        patch: np.ndarray | da.Array,
         channel_selection: ChannelSlicingInputType = None,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
@@ -354,7 +357,7 @@ class Image(AbstractImage[ImageMetaHandler]):
     def set_roi(
         self,
         roi: Roi | RoiPixels,
-        patch: ArrayLike,
+        patch: np.ndarray | da.Array,
         channel_selection: ChannelSlicingInputType = None,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
@@ -383,7 +386,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
     def consolidate(
         self,
-        order: Literal[0, 1, 2] = 1,
+        order: InterpolationOrder = "linear",
         mode: Literal["dask", "numpy", "coarsen"] = "dask",
     ) -> None:
         """Consolidate the label on disk."""
@@ -601,6 +604,8 @@ class ImagesContainer:
         name: str | None = None,
         chunks: Sequence[int] | None = None,
         dtype: str | None = None,
+        dimension_separator: DIMENSION_SEPARATOR | None = None,
+        compressor: str | None = None,
         overwrite: bool = False,
     ) -> "ImagesContainer":
         """Create an empty OME-Zarr image from an existing image.
@@ -615,6 +620,10 @@ class ImagesContainer:
             axes_names (Sequence[str] | None): The axes names of the new image.
             name (str | None): The name of the new image.
             chunks (Sequence[int] | None): The chunk shape of the new image.
+            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+                dimensions. If None it will use the same as the reference image.
+            compressor (str | None): The compressor to use. If None it will use
+                the same as the reference image.
             dtype (str | None): The data type of the new image.
             overwrite (bool): Whether to overwrite an existing image.
 
@@ -632,6 +641,8 @@ class ImagesContainer:
             name=name,
             chunks=chunks,
             dtype=dtype,
+            dimension_separator=dimension_separator,
+            compressor=compressor,
             overwrite=overwrite,
         )
 
@@ -714,6 +725,8 @@ def derive_image_container(
     name: str | None = None,
     chunks: Sequence[int] | None = None,
     dtype: str | None = None,
+    dimension_separator: DIMENSION_SEPARATOR | None = None,
+    compressor=None,
     overwrite: bool = False,
 ) -> ImagesContainer:
     """Create an empty OME-Zarr image from an existing image.
@@ -728,6 +741,10 @@ def derive_image_container(
         axes_names (Sequence[str] | None): The axes names of the new image.
         name (str | None): The name of the new image.
         chunks (Sequence[int] | None): The chunk shape of the new image.
+        dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+            dimensions. If None it will use the same as the reference image.
+        compressor: The compressor to use. If None it will use
+            the same as the reference image.
         dtype (str | None): The data type of the new image.
         overwrite (bool): Whether to overwrite an existing image.
 
@@ -749,7 +766,7 @@ def derive_image_container(
         pixel_size = ref_image.pixel_size
 
     if axes_names is None:
-        axes_names = ref_meta.axes_mapper.axes_names
+        axes_names = ref_meta.axes_handler.axes_names
 
     if len(axes_names) != len(shape):
         raise NgioValidationError(
@@ -771,6 +788,13 @@ def derive_image_container(
 
     if dtype is None:
         dtype = ref_image.dtype
+
+    if dimension_separator is None:
+        dimension_separator = ref_image.zarr_array._dimension_separator  # type: ignore
+
+    if compressor is None:
+        compressor = ref_image.zarr_array.compressor  # type: ignore
+
     handler = create_empty_image_container(
         store=store,
         shape=shape,
@@ -786,6 +810,8 @@ def derive_image_container(
         name=name,
         chunks=chunks,
         dtype=dtype,
+        dimension_separator=dimension_separator,  # type: ignore
+        compressor=compressor,  # type: ignore
         overwrite=overwrite,
         version=ref_meta.version,
     )

ngio/images/_label.py

@@ -3,6 +3,8 @@
 from collections.abc import Sequence
 from typing import Literal
 
+from zarr.types import DIMENSION_SEPARATOR
+
 from ngio.common import compute_masking_roi
 from ngio.images._abstract_image import AbstractImage
 from ngio.images._create import create_empty_label_container
@@ -94,7 +96,7 @@ class Label(AbstractImage[LabelMetaHandler]):
     ) -> None:
         """Consolidate the label on disk."""
         self._consolidate(
-            order=0,
+            order="nearest",
             mode=mode,
         )
 
@@ -167,6 +169,8 @@ class LabelsContainer:
         axes_names: Sequence[str] | None = None,
         chunks: Sequence[int] | None = None,
         dtype: str = "uint32",
+        dimension_separator: DIMENSION_SEPARATOR | None = None,
+        compressor=None,
         overwrite: bool = False,
     ) -> "Label":
         """Create an empty OME-Zarr label from a reference image.
@@ -184,6 +188,10 @@ class LabelsContainer:
                 For labels, the channel axis is not allowed.
             chunks (Sequence[int] | None): The chunk shape of the new image.
             dtype (str): The data type of the new label.
+            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+                dimensions. If None it will use the same as the reference image.
+            compressor: The compressor to use. If None it will use
+                the same as the reference image.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
@@ -208,6 +216,8 @@ class LabelsContainer:
             axes_names=axes_names,
             chunks=chunks,
             dtype=dtype,
+            dimension_separator=dimension_separator,
+            compressor=compressor,
             overwrite=overwrite,
         )
 
@@ -226,6 +236,8 @@ def derive_label(
     pixel_size: PixelSize | None = None,
     axes_names: Sequence[str] | None = None,
     chunks: Sequence[int] | None = None,
+    dimension_separator: DIMENSION_SEPARATOR | None = None,
+    compressor=None,
     dtype: str = "uint32",
     overwrite: bool = False,
 ) -> None:
@@ -242,6 +254,10 @@ def derive_label(
             For labels, the channel axis is not allowed.
         chunks (Sequence[int] | None): The chunk shape of the new image.
         dtype (str): The data type of the new label.
+        dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+            dimensions. If None it will use the same as the reference image.
+        compressor: The compressor to use. If None it will use
+            the same as the reference image.
         overwrite (bool): Whether to overwrite an existing image.
 
     Returns:
@@ -257,8 +273,8 @@ def derive_label(
         pixel_size = ref_image.pixel_size
 
     if axes_names is None:
-        axes_names = ref_meta.axes_mapper.axes_names
-        c_axis = ref_meta.axes_mapper.get_index("c")
+        axes_names = ref_meta.axes_handler.axes_names
+        c_axis = ref_meta.axes_handler.get_index("c")
     else:
         if "c" in axes_names:
             raise NgioValidationError(
@@ -291,6 +307,11 @@ def derive_label(
         axes_names = list(axes_names)
         axes_names = axes_names[:c_axis] + axes_names[c_axis + 1 :]
 
+    if dimension_separator is None:
+        dimension_separator = ref_image.zarr_array._dimension_separator  # type: ignore
+    if compressor is None:
+        compressor = ref_image.zarr_array.compressor  # type: ignore
+
     _ = create_empty_label_container(
         store=store,
         shape=shape,
@@ -305,6 +326,8 @@ def derive_label(
         axes_names=axes_names,
         chunks=chunks,
         dtype=dtype,
+        dimension_separator=dimension_separator,  # type: ignore
+        compressor=compressor,  # type: ignore
         overwrite=overwrite,
         version=ref_meta.version,
         name=name,

ngio/images/_masked_image.py

@@ -6,14 +6,6 @@ from typing import Literal
 import dask.array as da
 import numpy as np
 
-from ngio.common import (
-    ArrayLike,
-    TransformProtocol,
-    build_roi_masked_dask_getter,
-    build_roi_masked_dask_setter,
-    build_roi_masked_numpy_getter,
-    build_roi_masked_numpy_setter,
-)
 from ngio.images._image import (
     ChannelSlicingInputType,
     Image,
@@ -21,6 +13,13 @@ from ngio.images._image import (
     add_channel_selection_to_slicing_dict,
 )
 from ngio.images._label import Label
+from ngio.io_pipes import (
+    DaskGetterMasked,
+    DaskSetterMasked,
+    NumpyGetterMasked,
+    NumpySetterMasked,
+    TransformProtocol,
+)
 from ngio.ome_zarr_meta import ImageMetaHandler, LabelMetaHandler
 from ngio.tables import MaskingRoiTable
 from ngio.utils import (
@@ -70,7 +69,7 @@ class MaskedImage(Image):
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         **slicing_kwargs: slice | int | Sequence[int],
-    ) -> ArrayLike:
+    ) -> np.ndarray:
         """Return the array for a given ROI."""
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
@@ -111,7 +110,7 @@ class MaskedImage(Image):
         transforms: Sequence[TransformProtocol] | None = None,
         mode: Literal["numpy", "dask"] = "numpy",
         **slicing_kwargs: slice | int | Sequence[int],
-    ) -> ArrayLike:
+    ) -> np.ndarray | da.Array:
         """Return the array for a given ROI."""
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
@@ -127,7 +126,7 @@ class MaskedImage(Image):
     def set_roi(  # type: ignore (this ignore the method override issue)
         self,
         label: int,
-        patch: ArrayLike,
+        patch: np.ndarray | da.Array,
         zoom_factor: float = 1.0,
         channel_selection: ChannelSlicingInputType | None = None,
         axes_order: Sequence[str] | None = None,
@@ -153,7 +152,7 @@ class MaskedImage(Image):
         zoom_factor: float = 1.0,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
     ) -> np.ndarray:
         """Return the masked array for a given label as a NumPy array."""
@@ -163,18 +162,16 @@ class MaskedImage(Image):
 
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
-        masked_getter = build_roi_masked_numpy_getter(
+        masked_getter = NumpyGetterMasked(
             roi=roi,
             zarr_array=self.zarr_array,
             label_zarr_array=self._label.zarr_array,
             dimensions=self.dimensions,
-            pixel_size=self.pixel_size,
             label_dimensions=self._label.dimensions,
-            label_pixel_size=self._label.pixel_size,
             axes_order=axes_order,
             transforms=transforms,
             slicing_dict=slicing_kwargs,
-            allow_scaling=allow_scaling,
+            allow_rescaling=allow_rescaling,
         )
         return masked_getter()
 
@@ -185,7 +182,7 @@ class MaskedImage(Image):
         zoom_factor: float = 1.0,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
     ) -> da.Array:
         """Return the masked array for a given label as a Dask array."""
@@ -195,18 +192,16 @@ class MaskedImage(Image):
 
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
-        masked_getter = build_roi_masked_dask_getter(
+        masked_getter = DaskGetterMasked(
             roi=roi,
             zarr_array=self.zarr_array,
             label_zarr_array=self._label.zarr_array,
             dimensions=self.dimensions,
-            pixel_size=self.pixel_size,
             label_dimensions=self._label.dimensions,
-            label_pixel_size=self._label.pixel_size,
             axes_order=axes_order,
             transforms=transforms,
             slicing_dict=slicing_kwargs,
-            allow_scaling=allow_scaling,
+            allow_rescaling=allow_rescaling,
         )
         return masked_getter()
 
@@ -218,9 +213,9 @@ class MaskedImage(Image):
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         mode: Literal["numpy", "dask"] = "numpy",
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
-    ) -> ArrayLike:
+    ) -> np.ndarray | da.Array:
         """Return the masked array for a given label."""
         if mode == "numpy":
             return self.get_roi_masked_as_numpy(
@@ -229,9 +224,10 @@ class MaskedImage(Image):
                 zoom_factor=zoom_factor,
                 axes_order=axes_order,
                 transforms=transforms,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
                 **slicing_kwargs,
             )
+
         elif mode == "dask":
             return self.get_roi_masked_as_dask(
                 label=label,
@@ -239,7 +235,7 @@ class MaskedImage(Image):
                 zoom_factor=zoom_factor,
                 axes_order=axes_order,
                 transforms=transforms,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
                 **slicing_kwargs,
             )
         else:
@@ -248,12 +244,12 @@ class MaskedImage(Image):
     def set_roi_masked(
         self,
         label: int,
-        patch: ArrayLike,
+        patch: np.ndarray | da.Array,
         channel_selection: ChannelSlicingInputType | None = None,
         axes_order: Sequence[str] | None = None,
         zoom_factor: float = 1.0,
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
     ) -> None:
         """Set the masked array for a given label."""
@@ -264,33 +260,29 @@ class MaskedImage(Image):
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
         if isinstance(patch, da.Array):
-            path_setter = build_roi_masked_dask_setter(
+            path_setter = DaskSetterMasked(
                 roi=roi,
                 zarr_array=self.zarr_array,
                 label_zarr_array=self._label.zarr_array,
                 dimensions=self.dimensions,
-                pixel_size=self.pixel_size,
                 label_dimensions=self._label.dimensions,
-                label_pixel_size=self._label.pixel_size,
                 axes_order=axes_order,
                 transforms=transforms,
                 slicing_dict=slicing_kwargs,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
             )
             path_setter(patch)
         elif isinstance(patch, np.ndarray):
-            path_setter = build_roi_masked_numpy_setter(
+            path_setter = NumpySetterMasked(
                 roi=roi,
                 zarr_array=self.zarr_array,
                 label_zarr_array=self._label.zarr_array,
                 dimensions=self.dimensions,
-                pixel_size=self.pixel_size,
                 label_dimensions=self._label.dimensions,
-                label_pixel_size=self._label.pixel_size,
                 axes_order=axes_order,
                 transforms=transforms,
                 slicing_dict=slicing_kwargs,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
             )
             path_setter(patch)
         else:
@@ -378,7 +370,7 @@ class MaskedLabel(Label):
         mode: Literal["numpy", "dask"] = "numpy",
         transforms: Sequence[TransformProtocol] | None = None,
         **slicing_kwargs: slice | int | Sequence[int],
-    ) -> ArrayLike:
+    ) -> np.ndarray | da.Array:
         """Return the array for a given ROI."""
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
@@ -393,7 +385,7 @@ class MaskedLabel(Label):
     def set_roi(
         self,
         label: int,
-        patch: ArrayLike,
+        patch: np.ndarray | da.Array,
         zoom_factor: float = 1.0,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
@@ -416,24 +408,22 @@ class MaskedLabel(Label):
         zoom_factor: float = 1.0,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
     ) -> np.ndarray:
         """Return the masked array for a given label as a NumPy array."""
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
-        masked_getter = build_roi_masked_numpy_getter(
+        masked_getter = NumpyGetterMasked(
             roi=roi,
             zarr_array=self.zarr_array,
             label_zarr_array=self._label.zarr_array,
             dimensions=self.dimensions,
-            pixel_size=self.pixel_size,
             label_dimensions=self._label.dimensions,
-            label_pixel_size=self._label.pixel_size,
             axes_order=axes_order,
             transforms=transforms,
             slicing_dict=slicing_kwargs,
-            allow_scaling=allow_scaling,
+            allow_rescaling=allow_rescaling,
         )
         return masked_getter()
 
@@ -443,24 +433,22 @@ class MaskedLabel(Label):
         zoom_factor: float = 1.0,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
     ) -> da.Array:
         """Return the masked array for a given label as a Dask array."""
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
-        masked_getter = build_roi_masked_dask_getter(
+        masked_getter = DaskGetterMasked(
             roi=roi,
             zarr_array=self.zarr_array,
             label_zarr_array=self._label.zarr_array,
             dimensions=self.dimensions,
-            pixel_size=self.pixel_size,
             label_dimensions=self._label.dimensions,
-            label_pixel_size=self._label.pixel_size,
             axes_order=axes_order,
             transforms=transforms,
             slicing_dict=slicing_kwargs,
-            allow_scaling=allow_scaling,
+            allow_rescaling=allow_rescaling,
         )
         return masked_getter()
 
@@ -471,9 +459,9 @@ class MaskedLabel(Label):
         axes_order: Sequence[str] | None = None,
         mode: Literal["numpy", "dask"] = "numpy",
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
-    ) -> ArrayLike:
+    ) -> np.ndarray | da.Array:
         """Return the masked array for a given label."""
         if mode == "numpy":
             return self.get_roi_masked_as_numpy(
@@ -481,7 +469,7 @@ class MaskedLabel(Label):
                 zoom_factor=zoom_factor,
                 axes_order=axes_order,
                 transforms=transforms,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
                 **slicing_kwargs,
             )
 
@@ -491,7 +479,7 @@ class MaskedLabel(Label):
                 zoom_factor=zoom_factor,
                 axes_order=axes_order,
                 transforms=transforms,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
                 **slicing_kwargs,
             )
         else:
@@ -500,44 +488,40 @@ class MaskedLabel(Label):
     def set_roi_masked(
         self,
         label: int,
-        patch: ArrayLike,
+        patch: np.ndarray | da.Array,
         axes_order: Sequence[str] | None = None,
         zoom_factor: float = 1.0,
         transforms: Sequence[TransformProtocol] | None = None,
-        allow_scaling: bool = True,
+        allow_rescaling: bool = True,
         **slicing_kwargs: SlicingInputType,
     ) -> None:
         """Set the masked array for a given label."""
         roi = self._masking_roi_table.get_label(label)
         roi = roi.zoom(zoom_factor)
         if isinstance(patch, da.Array):
-            path_setter = build_roi_masked_dask_setter(
+            path_setter = DaskSetterMasked(
                 roi=roi,
                 zarr_array=self.zarr_array,
                 label_zarr_array=self._label.zarr_array,
                 dimensions=self.dimensions,
-                pixel_size=self.pixel_size,
                 label_dimensions=self._label.dimensions,
-                label_pixel_size=self._label.pixel_size,
                 axes_order=axes_order,
                 transforms=transforms,
                 slicing_dict=slicing_kwargs,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
             )
             path_setter(patch)
         elif isinstance(patch, np.ndarray):
-            path_setter = build_roi_masked_numpy_setter(
+            path_setter = NumpySetterMasked(
                 roi=roi,
                 zarr_array=self.zarr_array,
                 label_zarr_array=self._label.zarr_array,
                 dimensions=self.dimensions,
-                pixel_size=self.pixel_size,
                 label_dimensions=self._label.dimensions,
-                label_pixel_size=self._label.pixel_size,
                 axes_order=axes_order,
                 transforms=transforms,
                 slicing_dict=slicing_kwargs,
-                allow_scaling=allow_scaling,
+                allow_rescaling=allow_rescaling,
             )
             path_setter(patch)
         else: