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

ngio/images/_ome_zarr_container.py

@@ -2,9 +2,10 @@
 
 import warnings
 from collections.abc import Sequence
+from typing import Literal
 
 import numpy as np
-from zarr.types import DIMENSION_SEPARATOR
+from zarr.core.array import CompressorLike
 
 from ngio.images._create import create_empty_image_container
 from ngio.images._image import Image, ImagesContainer
@@ -409,10 +410,11 @@ class OmeZarrContainer:
         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,
         copy_labels: bool = False,
         copy_tables: bool = False,
+        ngff_version: NgffVersions | None = None,
         overwrite: bool = False,
     ) -> "OmeZarrContainer":
         """Create an empty OME-Zarr container from an existing image.
@@ -431,17 +433,18 @@ class OmeZarrContainer:
             dimension_separator (DIMENSION_SEPARATOR | None): The dimension
                 separator to use. If None, the dimension separator of the
                 reference image will be used.
-            compressor: The compressor to use. If None, the compressor of the
-                reference image will be used.
+            compressors (CompressorLike | None): The compressors to use. If None,
+                the compressors of the reference image will be used.
             copy_labels (bool): Whether to copy the labels from the reference image.
             copy_tables (bool): Whether to copy the tables from the reference image.
+            ngff_version (NgffVersions): The NGFF version to use.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
             OmeZarrContainer: The new image container.
 
         """
-        _ = self._images_container.derive(
+        new_container = self._images_container.derive(
             store=store,
             ref_path=ref_path,
             shape=shape,
@@ -452,16 +455,13 @@ class OmeZarrContainer:
             chunks=chunks,
             dtype=dtype,
             dimension_separator=dimension_separator,
-            compressor=compressor,
+            compressors=compressors,
+            ngff_version=ngff_version,
             overwrite=overwrite,
         )
 
-        handler = ZarrGroupHandler(
-            store, cache=self._group_handler.use_cache, mode=self._group_handler.mode
-        )
-
         new_ome_zarr = OmeZarrContainer(
-            group_handler=handler,
+            group_handler=new_container._group_handler,
             validate_paths=False,
         )
 
@@ -693,8 +693,8 @@ class OmeZarrContainer:
         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.
@@ -714,8 +714,8 @@ class OmeZarrContainer:
             dimension_separator (DIMENSION_SEPARATOR | None): The dimension
                 separator to use. If None, the dimension separator of the
                 reference image will be used.
-            compressor: The compressor to use. If None, the compressor of the
-                reference image will be used.
+            compressors (CompressorLike | None): The compressors to use. If None,
+                the compressors of the reference image will be used.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
@@ -733,7 +733,7 @@ class OmeZarrContainer:
             chunks=chunks,
             dtype=dtype,
             dimension_separator=dimension_separator,
-            compressor=compressor,
+            compressors=compressors,
             overwrite=overwrite,
         )
 
@@ -773,7 +773,7 @@ def open_image(
         mode (AccessModeLiteral): The
             access mode for the image. Defaults to "r+".
     """
-    group_handler = ZarrGroupHandler(store, cache, mode)
+    group_handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     images_container = ImagesContainer(group_handler)
     return images_container.get(
         path=path,
@@ -806,7 +806,7 @@ def open_label(
         mode (AccessModeLiteral): The access mode for the image. Defaults to "r+".
 
     """
-    group_handler = ZarrGroupHandler(store, cache, mode)
+    group_handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     if name is None:
         label_meta_handler = find_label_meta_handler(group_handler)
         path = label_meta_handler.meta.get_dataset(
@@ -836,10 +836,10 @@ def create_empty_ome_zarr(
     time_unit: TimeUnits = 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",
     channel_labels: list[str] | None = None,
     channel_wavelengths: list[str] | None = None,
     channel_colors: Sequence[str] | None = None,
@@ -874,7 +874,7 @@ def create_empty_ome_zarr(
         dtype (str, optional): The data type of the image. Defaults to "uint16".
         dimension_separator (DIMENSION_SEPARATOR): The dimension
             separator to use. Defaults to "/".
-        compressor: The compressor to use. Defaults to "default".
+        compressors (CompressorLike): The compressor to use. 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
@@ -904,7 +904,7 @@ def create_empty_ome_zarr(
         chunks=chunks,
         dtype=dtype,
         dimension_separator=dimension_separator,
-        compressor=compressor,
+        compressors=compressors,
         overwrite=overwrite,
         version=version,
     )
@@ -938,9 +938,9 @@ def create_ome_zarr_from_array(
     channel_colors: Sequence[str] | None = None,
     channel_active: Sequence[bool] | None = None,
     name: str | None = None,
-    chunks: Sequence[int] | None = None,
-    dimension_separator: DIMENSION_SEPARATOR = "/",
-    compressor: str = "default",
+    chunks: Sequence[int] | Literal["auto"] = "auto",
+    dimension_separator: Literal[".", "/"] = "/",
+    compressors: CompressorLike = "auto",
     overwrite: bool = False,
     version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
@@ -980,7 +980,7 @@ def create_ome_zarr_from_array(
             active. 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".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
         version (str, optional): The version of the OME-Zarr specification.
@@ -1003,7 +1003,7 @@ def create_ome_zarr_from_array(
         dtype=str(array.dtype),
         overwrite=overwrite,
         dimension_separator=dimension_separator,
-        compressor=compressor,
+        compressors=compressors,
         version=version,
     )
 

ngio/ome_zarr_meta/_meta_handlers.py

@@ -21,6 +21,16 @@ from ngio.ome_zarr_meta.v04 import (
     v04_to_ngio_plate_meta,
     v04_to_ngio_well_meta,
 )
+from ngio.ome_zarr_meta.v05 import (
+    ngio_to_v05_image_meta,
+    ngio_to_v05_label_meta,
+    ngio_to_v05_plate_meta,
+    ngio_to_v05_well_meta,
+    v05_to_ngio_image_meta,
+    v05_to_ngio_label_meta,
+    v05_to_ngio_plate_meta,
+    v05_to_ngio_well_meta,
+)
 from ngio.utils import (
     NgioValidationError,
     NgioValueError,
@@ -678,17 +688,36 @@ ImplementedMetaImporterExporter().register_image_ie(
     importer=v04_to_ngio_image_meta,
     exporter=ngio_to_v04_image_meta,
 )
+
+ImplementedMetaImporterExporter().register_label_ie(
+    version="0.5",
+    importer=v05_to_ngio_label_meta,
+    exporter=ngio_to_v05_label_meta,
+)
+
 ImplementedMetaImporterExporter().register_label_ie(
     version="0.4",
     importer=v04_to_ngio_label_meta,
     exporter=ngio_to_v04_label_meta,
 )
+ImplementedMetaImporterExporter().register_image_ie(
+    version="0.5",
+    importer=v05_to_ngio_image_meta,
+    exporter=ngio_to_v05_image_meta,
+)
+
 ImplementedMetaImporterExporter().register_well_ie(
     version="0.4", importer=v04_to_ngio_well_meta, exporter=ngio_to_v04_well_meta
 )
+ImplementedMetaImporterExporter().register_well_ie(
+    version="0.5", importer=v05_to_ngio_well_meta, exporter=ngio_to_v05_well_meta
+)
 ImplementedMetaImporterExporter().register_plate_ie(
     version="0.4", importer=v04_to_ngio_plate_meta, exporter=ngio_to_v04_plate_meta
 )
+ImplementedMetaImporterExporter().register_plate_ie(
+    version="0.5", importer=v05_to_ngio_plate_meta, exporter=ngio_to_v05_plate_meta
+)
 
 
 ###########################################################################

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -25,7 +25,7 @@ from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
 from ngio.utils import NgioValidationError, NgioValueError
 
 T = TypeVar("T")
-NgffVersions = Literal["0.4"]
+NgffVersions = Literal["0.4", "0.5"]
 DefaultNgffVersion: Literal["0.4"] = "0.4"
 
 
@@ -146,6 +146,17 @@ class AbstractNgioImageMeta:
         """Version of the OME-NFF metadata used to build the object."""
         return self._version  # type: ignore (version is a Literal type)
 
+    @property
+    def zarr_format(self) -> Literal[2, 3]:
+        """Zarr version used to store the data."""
+        match self.version:
+            case "0.4":
+                return 2
+            case "0.5":
+                return 3
+            case _:
+                raise NgioValueError(f"Unsupported NGFF version: {self.version}")
+
     @property
     def name(self) -> str | None:
         """Name of the image."""

ngio/ome_zarr_meta/v04/_v04_spec_utils.py

@@ -9,7 +9,6 @@ For Images and Labels implements the following functionalities:
 - A function to convert a ngio image metadata to a v04 image metadata.
 """
 
-from ome_zarr_models.common.multiscales import ValidTransform as ValidTransformV04
 from ome_zarr_models.v04.axes import Axis as AxisV04
 from ome_zarr_models.v04.coordinate_transformations import VectorScale as VectorScaleV04
 from ome_zarr_models.v04.coordinate_transformations import (
@@ -20,6 +19,7 @@ from ome_zarr_models.v04.image import ImageAttrs as ImageAttrsV04
 from ome_zarr_models.v04.image_label import ImageLabelAttrs as LabelAttrsV04
 from ome_zarr_models.v04.multiscales import Dataset as DatasetV04
 from ome_zarr_models.v04.multiscales import Multiscale as MultiscaleV04
+from ome_zarr_models.v04.multiscales import ValidTransform as ValidTransformV04
 from ome_zarr_models.v04.omero import Channel as ChannelV04
 from ome_zarr_models.v04.omero import Omero as OmeroV04
 from ome_zarr_models.v04.omero import Window as WindowV04
@@ -169,7 +169,7 @@ def _v04_to_ngio_datasets(
             unit = str(unit)
         axes.append(
             Axis(
-                name=v04_axis.name,
+                name=str(v04_axis.name),
                 axis_type=AxisType(v04_axis.type),
                 # (for some reason the type is a generic JsonValue,
                 # but it should be a string or None)

ngio/ome_zarr_meta/v05/__init__.py

@@ -0,0 +1,23 @@
+"""Utility to read/write OME-Zarr metadata v0.4."""
+
+from ngio.ome_zarr_meta.v05._v05_spec_utils import (
+    ngio_to_v05_image_meta,
+    ngio_to_v05_label_meta,
+    ngio_to_v05_plate_meta,
+    ngio_to_v05_well_meta,
+    v05_to_ngio_image_meta,
+    v05_to_ngio_label_meta,
+    v05_to_ngio_plate_meta,
+    v05_to_ngio_well_meta,
+)
+
+__all__ = [
+    "ngio_to_v05_image_meta",
+    "ngio_to_v05_label_meta",
+    "ngio_to_v05_plate_meta",
+    "ngio_to_v05_well_meta",
+    "v05_to_ngio_image_meta",
+    "v05_to_ngio_label_meta",
+    "v05_to_ngio_plate_meta",
+    "v05_to_ngio_well_meta",
+]

ngio/ome_zarr_meta/v05/_custom_models.py

@@ -0,0 +1,18 @@
+from typing import Annotated
+
+from ome_zarr_models.v05.well import WellAttrs as WellAttrs05
+from ome_zarr_models.v05.well_types import WellImage as WellImage05
+from ome_zarr_models.v05.well_types import WellMeta as WellMeta05
+from pydantic import SkipValidation
+
+
+class CustomWellImage(WellImage05):
+    path: Annotated[str, SkipValidation]
+
+
+class CustomWellMeta(WellMeta05):
+    images: list[CustomWellImage]  # type: ignore[valid-type]
+
+
+class CustomWellAttrs(WellAttrs05):
+    well: CustomWellMeta  # type: ignore[valid-type]