ngio 0.4.8__py3-none-any.whl → 0.5.0a1__py3-none-any.whl

ngio/common/_pyramid.py

@@ -2,12 +2,12 @@ import math
 from collections.abc import Callable, Sequence
 from typing import Literal
 
-import dask
 import dask.array as da
 import numpy as np
 import zarr
-from zarr.types import DIMENSION_SEPARATOR
+from zarr.core.array import CompressorLike
 
+# from zarr.types import DIMENSION_SEPARATOR
 from ngio.common._zoom import (
     InterpolationOrder,
     _zoom_inputs_check,
@@ -27,7 +27,10 @@ def _on_disk_numpy_zoom(
     target: zarr.Array,
     order: InterpolationOrder,
 ) -> None:
-    target[...] = numpy_zoom(source[...], target_shape=target.shape, order=order)
+    source_array = source[...]
+    if not isinstance(source_array, np.ndarray):
+        raise NgioValueError("source zarr array could not be read as a numpy array")
+    target[...] = numpy_zoom(source_array, target_shape=target.shape, order=order)
 
 
 def _on_disk_dask_zoom(
@@ -37,17 +40,9 @@ def _on_disk_dask_zoom(
 ) -> None:
     source_array = da.from_zarr(source)
     target_array = dask_zoom(source_array, target_shape=target.shape, order=order)
-    # This is a potential fix for Dask 2025.11
-    # chunk_size_bytes = np.prod(target.chunks) * target_array.dtype.itemsize
-    # current_chunk_size = dask.config.get("array.chunk-size", 0)
-    #
-    #if current_chunk_size < chunk_size_bytes:
-    #    # Increase the chunk size to avoid dask potentially creating 
-    #    # corrupted chunks when writing chunks that are not multiple of the
-    #    # target chunk size
-    #    dask.config.set({"array.chunk-size": f"{chunk_size_bytes}B"})
-    target_array = target_array.rechunk(target.chunks)
-    target_array = target_array.compute_chunk_sizes()
+
+    target_array = target_array.rechunk(target.chunks)  # type: ignore
+    target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
 
 
@@ -208,20 +203,24 @@ def init_empty_pyramid(
     paths: list[str],
     ref_shape: Sequence[int],
     scaling_factors: Sequence[float],
-    chunks: Sequence[int] | None = None,
+    axes: Sequence[str],
+    chunks: Sequence[int] | Literal["auto"] = "auto",
     dtype: str = "uint16",
     mode: AccessModeLiteral = "a",
-    dimension_separator: DIMENSION_SEPARATOR = "/",
-    compressor="default",
+    dimension_separator: Literal[".", "/"] = "/",
+    compressors: CompressorLike = "auto",
+    zarr_format: Literal[2, 3] = 2,
 ) -> None:
     # Return the an Image object
-    if chunks is not None and len(chunks) != len(ref_shape):
+    if chunks != "auto" and len(chunks) != len(ref_shape):
         raise NgioValueError(
             "The shape and chunks must have the same number of dimensions."
         )
 
-    if chunks is not None:
-        chunks = [min(c, s) for c, s in zip(chunks, ref_shape, strict=True)]
+    if chunks != "auto":
+        chunks = tuple(min(c, s) for c, s in zip(chunks, ref_shape, strict=True))
+    else:
+        chunks = "auto"
 
     if len(ref_shape) != len(scaling_factors):
         raise NgioValueError(
@@ -232,7 +231,25 @@ def init_empty_pyramid(
     # To reduce the risk of floating point issues
     scaling_factors = [_maybe_int(s) for s in scaling_factors]
 
-    root_group = open_group_wrapper(store, mode=mode)
+    root_group = open_group_wrapper(store, mode=mode, zarr_format=zarr_format)
+
+    array_static_kwargs = {
+        "dtype": dtype,
+        "overwrite": True,
+        "compressors": compressors,
+    }
+
+    if zarr_format == 2:
+        array_static_kwargs["chunk_key_encoding"] = {
+            "name": "v2",
+            "separator": dimension_separator,
+        }
+    else:
+        array_static_kwargs["chunk_key_encoding"] = {
+            "name": "default",
+            "separator": dimension_separator,
+        }
+        array_static_kwargs["dimension_names"] = axes
 
     for path in paths:
         if any(s < 1 for s in ref_shape):
@@ -240,14 +257,11 @@ def init_empty_pyramid(
                 "Level shape must be at least 1 on all dimensions. "
                 f"Calculated shape: {ref_shape} at level {path}."
             )
-        new_arr = root_group.zeros(
+        new_arr = root_group.create_array(
             name=path,
-            shape=ref_shape,
-            dtype=dtype,
+            shape=tuple(ref_shape),
             chunks=chunks,
-            dimension_separator=dimension_separator,
-            overwrite=True,
-            compressor=compressor,
+            **array_static_kwargs,
         )
 
         ref_shape = [
@@ -256,5 +270,4 @@ def init_empty_pyramid(
         chunks = tuple(
             min(c, s) for c, s in zip(new_arr.chunks, ref_shape, strict=True)
         )
-
     return None

ngio/images/_create.py

@@ -1,9 +1,9 @@
 """Utility functions for working with OME-Zarr images."""
 
 from collections.abc import Sequence
-from typing import TypeVar
+from typing import Literal, TypeVar
 
-from zarr.types import DIMENSION_SEPARATOR
+from zarr.core.array import CompressorLike
 
 from ngio.common._pyramid import init_empty_pyramid
 from ngio.ome_zarr_meta import (
@@ -93,10 +93,10 @@ def create_empty_label_container(
     time_unit: TimeUnits | str | None = DefaultTimeUnit,
     axes_names: Sequence[str] | None = None,
     name: str | None = None,
-    chunks: Sequence[int] | None = None,
+    chunks: Sequence[int] | Literal["auto"] = "auto",
     dtype: str = "uint32",
-    dimension_separator: DIMENSION_SEPARATOR = "/",
-    compressor="default",
+    dimension_separator: Literal[".", "/"] = "/",
+    compressors: CompressorLike = "auto",
     overwrite: bool = False,
     version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
@@ -122,11 +122,11 @@ def create_empty_label_container(
         axes_names (Sequence[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 (Sequence[int] | None, optional): The chunk shape. If None the shape
+        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
             is used. Defaults to None.
         dimension_separator (DIMENSION_SEPARATOR): The separator to use for
             dimensions. Defaults to "/".
-        compressor: The compressor to use. Defaults to "default".
+        compressors (CompressorLike): The compressors to use. Defaults to "auto".
         dtype (str, optional): The data type of the image. Defaults to "uint16".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
@@ -159,7 +159,9 @@ def create_empty_label_container(
     )
 
     mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(store=store, mode=mode, cache=False)
+    group_handler = ZarrGroupHandler(
+        store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
+    )
     image_handler = get_label_meta_handler(version=version, group_handler=group_handler)
     image_handler.write_meta(meta)
 
@@ -169,10 +171,11 @@ def create_empty_label_container(
         scaling_factors=scaling_factors,
         ref_shape=shape,
         chunks=chunks,
+        axes=axes_names,
         dtype=dtype,
         mode="a",
         dimension_separator=dimension_separator,
-        compressor=compressor,
+        compressors=compressors,
     )
     group_handler._mode = "r+"
     return group_handler
@@ -191,10 +194,10 @@ def create_empty_image_container(
     time_unit: TimeUnits | str | None = DefaultTimeUnit,
     axes_names: Sequence[str] | None = None,
     name: str | None = None,
-    chunks: Sequence[int] | None = None,
+    chunks: Sequence[int] | Literal["auto"] = "auto",
     dtype: str = "uint16",
-    dimension_separator: DIMENSION_SEPARATOR = "/",
-    compressor="default",
+    dimension_separator: Literal[".", "/"] = "/",
+    compressors: CompressorLike = "auto",
     overwrite: bool = False,
     version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
@@ -220,12 +223,12 @@ def create_empty_image_container(
         axes_names (Sequence[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 (Sequence[int] | None, optional): The chunk shape. If None the shape
+        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
             is used. Defaults to None.
         dtype (str, optional): The data type of the image. Defaults to "uint16".
         dimension_separator (DIMENSION_SEPARATOR): The separator to use for
             dimensions. Defaults to "/".
-        compressor: The compressor to use. Defaults to "default".
+        compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
         version (str, optional): The version of the OME-Zarr specification.
@@ -256,7 +259,9 @@ def create_empty_image_container(
         version=version,
     )
     mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(store=store, mode=mode, cache=False)
+    group_handler = ZarrGroupHandler(
+        store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
+    )
     image_handler = get_image_meta_handler(version=version, group_handler=group_handler)
     image_handler.write_meta(meta)
 
@@ -266,10 +271,12 @@ def create_empty_image_container(
         scaling_factors=scaling_factors,
         ref_shape=shape,
         chunks=chunks,
+        axes=axes_names,
         dtype=dtype,
         mode="a",
         dimension_separator=dimension_separator,
-        compressor=compressor,
+        compressors=compressors,
+        zarr_format=meta.zarr_format,
     )
 
     group_handler._mode = "r+"

ngio/images/_create_synt_container.py

@@ -1,10 +1,11 @@
 """Abstract class for handling OME-NGFF images."""
 
 from collections.abc import Sequence
+from typing import Literal
 
 import numpy as np
 import PIL.Image
-from zarr.types import DIMENSION_SEPARATOR
+from zarr.core.array import CompressorLike
 
 from ngio.common._synt_images_utils import fit_to_shape
 from ngio.images._ome_zarr_container import OmeZarrContainer, create_ome_zarr_from_array
@@ -30,14 +31,14 @@ def create_synthetic_ome_zarr(
     xy_scaling_factor: float = 2,
     z_scaling_factor: float = 1.0,
     axes_names: Sequence[str] | None = None,
-    chunks: Sequence[int] | None = None,
+    chunks: Sequence[int] | Literal["auto"] = "auto",
     channel_labels: list[str] | None = None,
     channel_wavelengths: list[str] | None = None,
     channel_colors: Sequence[str] | None = None,
     channel_active: Sequence[bool] | None = None,
     table_backend: TableBackend = DefaultTableBackend,
-    dimension_separator: DIMENSION_SEPARATOR = "/",
-    compressor="default",
+    dimension_separator: Literal[".", "/"] = "/",
+    compressors: CompressorLike = "auto",
     overwrite: bool = False,
     version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
@@ -55,8 +56,8 @@ def create_synthetic_ome_zarr(
             Defaults to 1.0.
         axes_names (Sequence[str] | None, optional): The names of the axes.
             If None the canonical names are used. Defaults to None.
-        chunks (Sequence[int] | None, optional): The chunk shape. If None the shape
-            is used. Defaults to None.
+        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
+            is used. Defaults to "auto".
         channel_labels (list[str] | None, optional): The labels of the channels.
             Defaults to None.
         channel_wavelengths (list[str] | None, optional): The wavelengths of the
@@ -68,7 +69,7 @@ def create_synthetic_ome_zarr(
         table_backend (TableBackend): Table backend to be used to store tables
         dimension_separator (DIMENSION_SEPARATOR): The separator to use for
             dimensions. Defaults to "/".
-        compressor: The compressor to use. Defaults to "default".
+        compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
         version (NgffVersion, optional): The version of the OME-Zarr specification.
@@ -103,7 +104,7 @@ def create_synthetic_ome_zarr(
         chunks=chunks,
         overwrite=overwrite,
         dimension_separator=dimension_separator,
-        compressor=compressor,
+        compressors=compressors,
         version=version,
     )
 

ngio/images/_image.py

@@ -6,7 +6,7 @@ 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 zarr.core.array import CompressorLike
 
 from ngio.common import (
     Dimensions,
@@ -32,6 +32,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ChannelVisualisation,
     DefaultSpaceUnit,
     DefaultTimeUnit,
+    NgffVersions,
     SpaceUnits,
     TimeUnits,
 )
@@ -40,6 +41,7 @@ from ngio.utils import (
     StoreOrGroup,
     ZarrGroupHandler,
 )
+from ngio.utils._zarr_utils import find_dimension_separator
 
 
 class ChannelSelectionModel(BaseModel):
@@ -604,8 +606,9 @@ 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,
+        dimension_separator: Literal[".", "/"] | None = None,
+        compressors: CompressorLike | None = None,
+        ngff_version: NgffVersions | None = None,
         overwrite: bool = False,
     ) -> "ImagesContainer":
         """Create an empty OME-Zarr image from an existing image.
@@ -619,12 +622,13 @@ class ImagesContainer:
             pixel_size (PixelSize | None): The pixel size of the new image.
             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.
+            chunks (Sequence[int] | Literal["auto"]): 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
+            compressors: 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.
+            ngff_version (NgffVersions): The NGFF version to use.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
@@ -642,7 +646,8 @@ class ImagesContainer:
             chunks=chunks,
             dtype=dtype,
             dimension_separator=dimension_separator,
-            compressor=compressor,
+            compressors=compressors,
+            ngff_version=ngff_version,
             overwrite=overwrite,
         )
 
@@ -725,8 +730,9 @@ 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,
+    dimension_separator: Literal[".", "/"] | None = None,
+    compressors: CompressorLike | None = None,
+    ngff_version: NgffVersions | None = None,
     overwrite: bool = False,
 ) -> ImagesContainer:
     """Create an empty OME-Zarr image from an existing image.
@@ -743,8 +749,9 @@ def derive_image_container(
         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
+        compressors (CompressorLike | None): The compressors to use. If None it will use
             the same as the reference image.
+        ngff_version (NgffVersions): The NGFF version to use.
         dtype (str | None): The data type of the new image.
         overwrite (bool): Whether to overwrite an existing image.
 
@@ -790,10 +797,13 @@ def derive_image_container(
         dtype = ref_image.dtype
 
     if dimension_separator is None:
-        dimension_separator = ref_image.zarr_array._dimension_separator  # type: ignore
+        dimension_separator = find_dimension_separator(ref_image.zarr_array)
 
-    if compressor is None:
-        compressor = ref_image.zarr_array.compressor  # type: ignore
+    if compressors is None:
+        compressors = ref_image.zarr_array.compressors  # type: ignore
+
+    if ngff_version is None:
+        ngff_version = ref_meta.version
 
     handler = create_empty_image_container(
         store=store,
@@ -810,10 +820,10 @@ def derive_image_container(
         name=name,
         chunks=chunks,
         dtype=dtype,
-        dimension_separator=dimension_separator,  # type: ignore
-        compressor=compressor,  # type: ignore
+        dimension_separator=dimension_separator,
+        compressors=compressors,
         overwrite=overwrite,
-        version=ref_meta.version,
+        version=ngff_version,
     )
     image_container = ImagesContainer(handler)
 
@@ -875,7 +885,7 @@ def _parse_str_or_model(
             )
         elif channel_selection.mode == "wavelength_id":
             return image.get_channel_idx(
-                wavelength_id=str(channel_selection.identifier)
+                channel_label=str(channel_selection.identifier)
             )
         elif channel_selection.mode == "index":
             return int(channel_selection.identifier)

ngio/images/_label.py

@@ -3,7 +3,7 @@
 from collections.abc import Sequence
 from typing import Literal
 
-from zarr.types import DIMENSION_SEPARATOR
+from zarr.core.array import CompressorLike
 
 from ngio.common import compute_masking_roi
 from ngio.images._abstract_image import AbstractImage
@@ -28,6 +28,7 @@ from ngio.utils import (
     StoreOrGroup,
     ZarrGroupHandler,
 )
+from ngio.utils._zarr_utils import find_dimension_separator
 
 
 class Label(AbstractImage[LabelMetaHandler]):
@@ -107,7 +108,6 @@ class LabelsContainer:
     def __init__(self, group_handler: ZarrGroupHandler) -> None:
         """Initialize the LabelGroupHandler."""
         self._group_handler = group_handler
-
         # Validate the group
         # Either contains a labels attribute or is empty
         attrs = self._group_handler.load_attrs()
@@ -169,8 +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,
+        dimension_separator: Literal[".", "/"] | None = None,
+        compressors: CompressorLike | None = None,
         overwrite: bool = False,
     ) -> "Label":
         """Create an empty OME-Zarr label from a reference image.
@@ -190,8 +190,8 @@ class LabelsContainer:
             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.
+            compressors (CompressorLike | None): The compressors to use. If None it will
+                use the same as the reference image.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
@@ -217,7 +217,7 @@ class LabelsContainer:
             chunks=chunks,
             dtype=dtype,
             dimension_separator=dimension_separator,
-            compressor=compressor,
+            compressors=compressors,
             overwrite=overwrite,
         )
 
@@ -236,8 +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,
+    dimension_separator: Literal[".", "/"] | None = None,
+    compressors: CompressorLike | None = None,
     dtype: str = "uint32",
     overwrite: bool = False,
 ) -> None:
@@ -256,7 +256,7 @@ def derive_label(
         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
+        compressors (CompressorLike | None): The compressor to use. If None it will use
             the same as the reference image.
         overwrite (bool): Whether to overwrite an existing image.
 
@@ -308,9 +308,9 @@ def derive_label(
         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
+        dimension_separator = find_dimension_separator(ref_image.zarr_array)
+    if compressors is None:
+        compressors = ref_image.zarr_array.compressors  # type: ignore
 
     _ = create_empty_label_container(
         store=store,
@@ -326,8 +326,8 @@ def derive_label(
         axes_names=axes_names,
         chunks=chunks,
         dtype=dtype,
-        dimension_separator=dimension_separator,  # type: ignore
-        compressor=compressor,  # type: ignore
+        dimension_separator=dimension_separator,
+        compressors=compressors,
         overwrite=overwrite,
         version=ref_meta.version,
         name=name,