ngio 0.5.0b6__py3-none-any.whl

ngio/ome_zarr_meta/_meta_handlers.py

@@ -0,0 +1,536 @@
+"""Base class for handling OME-NGFF metadata in Zarr groups."""
+
+from collections.abc import Callable
+from typing import TypeVar
+
+from ngio.ome_zarr_meta.ngio_specs import (
+    AxesSetup,
+    NgioImageMeta,
+    NgioLabelMeta,
+    NgioLabelsGroupMeta,
+    NgioPlateMeta,
+    NgioWellMeta,
+)
+from ngio.ome_zarr_meta.ngio_specs._ngio_image import NgffVersions
+from ngio.ome_zarr_meta.v04 import (
+    ngio_to_v04_image_meta,
+    ngio_to_v04_label_meta,
+    ngio_to_v04_labels_group_meta,
+    ngio_to_v04_plate_meta,
+    ngio_to_v04_well_meta,
+    v04_to_ngio_image_meta,
+    v04_to_ngio_label_meta,
+    v04_to_ngio_labels_group_meta,
+    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_labels_group_meta,
+    ngio_to_v05_plate_meta,
+    ngio_to_v05_well_meta,
+    v05_to_ngio_image_meta,
+    v05_to_ngio_label_meta,
+    v05_to_ngio_labels_group_meta,
+    v05_to_ngio_plate_meta,
+    v05_to_ngio_well_meta,
+)
+from ngio.utils import (
+    NgioValidationError,
+    NgioValueError,
+    ZarrGroupHandler,
+)
+
+# This could be replaced with a more dynamic registry if needed in the future
+_image_encoder_registry = {"0.4": ngio_to_v04_image_meta, "0.5": ngio_to_v05_image_meta}
+_image_decoder_registry = {"0.4": v04_to_ngio_image_meta, "0.5": v05_to_ngio_image_meta}
+_label_encoder_registry = {"0.4": ngio_to_v04_label_meta, "0.5": ngio_to_v05_label_meta}
+_label_decoder_registry = {"0.4": v04_to_ngio_label_meta, "0.5": v05_to_ngio_label_meta}
+_plate_encoder_registry = {"0.4": ngio_to_v04_plate_meta, "0.5": ngio_to_v05_plate_meta}
+_plate_decoder_registry = {"0.4": v04_to_ngio_plate_meta, "0.5": v05_to_ngio_plate_meta}
+_well_encoder_registry = {"0.4": ngio_to_v04_well_meta, "0.5": ngio_to_v05_well_meta}
+_well_decoder_registry = {"0.4": v04_to_ngio_well_meta, "0.5": v05_to_ngio_well_meta}
+_labels_group_encoder_registry = {
+    "0.4": ngio_to_v04_labels_group_meta,
+    "0.5": ngio_to_v05_labels_group_meta,
+}
+_labels_group_decoder_registry = {
+    "0.4": v04_to_ngio_labels_group_meta,
+    "0.5": v05_to_ngio_labels_group_meta,
+}
+
+_meta_type = TypeVar(
+    "_meta_type",
+    NgioImageMeta,
+    NgioLabelMeta,
+    NgioLabelsGroupMeta,
+    NgioPlateMeta,
+    NgioWellMeta,
+)
+
+
+def _find_encoder_registry(
+    ngio_meta: _meta_type,
+) -> dict[str, Callable]:
+    if isinstance(ngio_meta, NgioImageMeta):
+        return _image_encoder_registry
+    elif isinstance(ngio_meta, NgioLabelMeta):
+        return _label_encoder_registry
+    elif isinstance(ngio_meta, NgioPlateMeta):
+        return _plate_encoder_registry
+    elif isinstance(ngio_meta, NgioWellMeta):
+        return _well_encoder_registry
+    elif isinstance(ngio_meta, NgioLabelsGroupMeta):
+        return _labels_group_encoder_registry
+    else:
+        raise NgioValueError(f"Unsupported NGIO metadata type: {type(ngio_meta)}")
+
+
+def update_ngio_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: _meta_type,
+) -> None:
+    """Update the metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (_meta_type): The new NGIO metadata.
+
+    """
+    registry = _find_encoder_registry(ngio_meta)
+    exporter = registry.get(ngio_meta.version)
+    if exporter is None:
+        raise NgioValueError(f"Unsupported NGFF version: {ngio_meta.version}")
+
+    zarr_meta = exporter(ngio_meta)
+    group_handler.write_attrs(zarr_meta)
+
+
+def _find_decoder_registry(
+    meta_type: type[_meta_type],
+) -> dict[str, Callable]:
+    if meta_type is NgioImageMeta:
+        return _image_decoder_registry
+    elif meta_type is NgioLabelMeta:
+        return _label_decoder_registry
+    elif meta_type is NgioPlateMeta:
+        return _plate_decoder_registry
+    elif meta_type is NgioWellMeta:
+        return _well_decoder_registry
+    elif meta_type is NgioLabelsGroupMeta:
+        return _labels_group_decoder_registry
+    else:
+        raise NgioValueError(f"Unsupported NGIO metadata type: {meta_type}")
+
+
+def get_ngio_meta(
+    group_handler: ZarrGroupHandler,
+    meta_type: type[_meta_type],
+    version: str | None = None,
+    **kwargs,
+) -> _meta_type:
+    """Retrieve the NGIO metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        meta_type (type[_meta_type]): The type of NGIO metadata to retrieve.
+        version (str | None): Optional NGFF version to use for decoding.
+        **kwargs: Additional arguments to pass to the decoder.
+
+    Returns:
+        _meta_type: The NGIO metadata.
+    """
+    registry = _find_decoder_registry(meta_type)
+    if version is not None:
+        decoder = registry.get(version)
+        if decoder is None:
+            raise NgioValueError(f"Unsupported NGFF version: {version}")
+        versions_to_try = {version: decoder}
+    else:
+        versions_to_try = registry
+
+    attrs = group_handler.load_attrs()
+    all_errors = []
+    for version, decoder in versions_to_try.items():
+        try:
+            ngio_meta = decoder(attrs, **kwargs)
+            return ngio_meta
+        except Exception as e:
+            all_errors.append(f"Version {version}: {e}")
+    error_message = (
+        f"Failed to decode NGIO {meta_type.__name__} metadata:\n"
+        + "\n".join(all_errors)
+    )
+    raise NgioValidationError(error_message)
+
+
+##################################################
+#
+# Concrete implementations for NGIO metadata types
+#
+##################################################
+
+
+def get_ngio_image_meta(
+    group_handler: ZarrGroupHandler,
+    version: str | None = None,
+    axes_setup: AxesSetup | None = None,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
+) -> NgioImageMeta:
+    """Retrieve the NGIO image metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        version (str | None): Optional NGFF version to use for decoding.
+        axes_setup (AxesSetup | None): Optional axes setup for validation.
+        allow_non_canonical_axes (bool): Whether to allow non-canonical axes.
+        strict_canonical_order (bool): Whether to enforce strict canonical order.
+
+    Returns:
+        NgioImageMeta: The NGIO image metadata.
+    """
+    return get_ngio_meta(
+        group_handler=group_handler,
+        meta_type=NgioImageMeta,
+        version=version,
+        axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
+    )
+
+
+def update_ngio_image_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: NgioImageMeta,
+) -> None:
+    """Update the NGIO image metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (NgioImageMeta): The new NGIO image metadata.
+
+    """
+    update_ngio_meta(
+        group_handler=group_handler,
+        ngio_meta=ngio_meta,
+    )
+
+
+class ImageMetaHandler:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        version: str | None = None,
+        axes_setup: AxesSetup | None = None,
+        allow_non_canonical_axes: bool = False,
+        strict_canonical_order: bool = True,
+    ):
+        self._group_handler = group_handler
+        self._version = version
+        self._axes_setup = axes_setup
+        self._allow_non_canonical_axes = allow_non_canonical_axes
+        self._strict_canonical_order = strict_canonical_order
+
+        # Validate metadata
+        meta = self.get_meta()
+        # Store the resolved version
+        self._version = meta.version
+
+    def get_meta(self) -> NgioImageMeta:
+        """Retrieve the NGIO image metadata."""
+        return get_ngio_image_meta(
+            group_handler=self._group_handler,
+            version=self._version,
+            axes_setup=self._axes_setup,
+            allow_non_canonical_axes=self._allow_non_canonical_axes,
+            strict_canonical_order=self._strict_canonical_order,
+        )
+
+    def update_meta(self, ngio_meta: NgioImageMeta) -> None:
+        """Update the NGIO image metadata."""
+        update_ngio_meta(
+            group_handler=self._group_handler,
+            ngio_meta=ngio_meta,
+        )
+
+
+def get_ngio_label_meta(
+    group_handler: ZarrGroupHandler,
+    version: str | None = None,
+    axes_setup: AxesSetup | None = None,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
+) -> NgioLabelMeta:
+    """Retrieve the NGIO label metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        version (str | None): Optional NGFF version to use for decoding.
+        axes_setup (AxesSetup | None): Optional axes setup for validation.
+        allow_non_canonical_axes (bool): Whether to allow non-canonical axes.
+        strict_canonical_order (bool): Whether to enforce strict canonical order.
+
+    Returns:
+        NgioLabelMeta: The NGIO label metadata.
+    """
+    return get_ngio_meta(
+        group_handler=group_handler,
+        meta_type=NgioLabelMeta,
+        version=version,
+        axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
+    )
+
+
+def update_ngio_label_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: NgioLabelMeta,
+) -> None:
+    """Update the NGIO label metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (NgioLabelMeta): The new NGIO label metadata.
+
+    """
+    update_ngio_meta(
+        group_handler=group_handler,
+        ngio_meta=ngio_meta,
+    )
+
+
+class LabelMetaHandler:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        version: str | None = None,
+        axes_setup: AxesSetup | None = None,
+        allow_non_canonical_axes: bool = False,
+        strict_canonical_order: bool = True,
+    ):
+        self._group_handler = group_handler
+        self._version = version
+        self._axes_setup = axes_setup
+        self._allow_non_canonical_axes = allow_non_canonical_axes
+        self._strict_canonical_order = strict_canonical_order
+
+        # Validate metadata
+        meta = self.get_meta()
+        # Store the resolved version
+        self._version = meta.version
+
+    def get_meta(self) -> NgioLabelMeta:
+        """Retrieve the NGIO label metadata."""
+        return get_ngio_label_meta(
+            group_handler=self._group_handler,
+            version=self._version,
+            axes_setup=self._axes_setup,
+            allow_non_canonical_axes=self._allow_non_canonical_axes,
+            strict_canonical_order=self._strict_canonical_order,
+        )
+
+    def update_meta(self, ngio_meta: NgioLabelMeta) -> None:
+        """Update the NGIO label metadata."""
+        update_ngio_meta(
+            group_handler=self._group_handler,
+            ngio_meta=ngio_meta,
+        )
+
+
+def get_ngio_plate_meta(
+    group_handler: ZarrGroupHandler,
+    version: str | None = None,
+) -> NgioPlateMeta:
+    """Retrieve the NGIO plate metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        version (str | None): Optional NGFF version to use for decoding.
+
+    Returns:
+        NgioPlateMeta: The NGIO plate metadata.
+    """
+    return get_ngio_meta(
+        group_handler=group_handler,
+        meta_type=NgioPlateMeta,
+        version=version,
+    )
+
+
+def update_ngio_plate_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: NgioPlateMeta,
+) -> None:
+    """Update the NGIO plate metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (NgioPlateMeta): The new NGIO plate metadata.
+
+    """
+    update_ngio_meta(
+        group_handler=group_handler,
+        ngio_meta=ngio_meta,
+    )
+
+
+class PlateMetaHandler:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        version: str | None = None,
+    ):
+        self._group_handler = group_handler
+        self._version = version
+
+        # Validate metadata
+        _ = self.get_meta()
+        # Store the resolved version
+        # self._version = meta.version
+
+    def get_meta(self) -> NgioPlateMeta:
+        """Retrieve the NGIO plate metadata."""
+        return get_ngio_plate_meta(
+            group_handler=self._group_handler,
+            version=self._version,
+        )
+
+    def update_meta(self, ngio_meta: NgioPlateMeta) -> None:
+        """Update the NGIO plate metadata."""
+        update_ngio_meta(
+            group_handler=self._group_handler,
+            ngio_meta=ngio_meta,
+        )
+
+
+def get_ngio_well_meta(
+    group_handler: ZarrGroupHandler,
+    version: str | None = None,
+) -> NgioWellMeta:
+    """Retrieve the NGIO well metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        version (str | None): Optional NGFF version to use for decoding.
+
+    Returns:
+        NgioWellMeta: The NGIO well metadata.
+    """
+    return get_ngio_meta(
+        group_handler=group_handler,
+        meta_type=NgioWellMeta,
+        version=version,
+    )
+
+
+def update_ngio_well_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: NgioWellMeta,
+) -> None:
+    """Update the NGIO well metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (NgioWellMeta): The new NGIO well metadata.
+
+    """
+    update_ngio_meta(
+        group_handler=group_handler,
+        ngio_meta=ngio_meta,
+    )
+
+
+class WellMetaHandler:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        version: str | None = None,
+    ):
+        self._group_handler = group_handler
+        self._version = version
+
+        # Validate metadata
+        _ = self.get_meta()
+        # Store the resolved version
+        # self._version = meta.version
+
+    def get_meta(self) -> NgioWellMeta:
+        """Retrieve the NGIO well metadata."""
+        return get_ngio_well_meta(
+            group_handler=self._group_handler,
+            version=self._version,
+        )
+
+    def update_meta(self, ngio_meta: NgioWellMeta) -> None:
+        """Update the NGIO well metadata."""
+        update_ngio_meta(
+            group_handler=self._group_handler,
+            ngio_meta=ngio_meta,
+        )
+
+
+def get_ngio_labels_group_meta(
+    group_handler: ZarrGroupHandler,
+    version: str | None = None,
+) -> NgioLabelsGroupMeta:
+    """Retrieve the NGIO labels group metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        version (str | None): Optional NGFF version to use for decoding.
+
+    Returns:
+        NgioLabelsGroupMeta: The NGIO labels group metadata.
+    """
+    return get_ngio_meta(
+        group_handler=group_handler,
+        meta_type=NgioLabelsGroupMeta,
+        version=version,
+    )
+
+
+def update_ngio_labels_group_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: NgioLabelsGroupMeta,
+) -> None:
+    """Update the NGIO labels group metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (NgioLabelsGroupMeta): The new NGIO labels group metadata.
+
+    """
+    update_ngio_meta(
+        group_handler=group_handler,
+        ngio_meta=ngio_meta,
+    )
+
+
+class LabelsGroupMetaHandler:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        version: NgffVersions | None = None,
+    ):
+        self._group_handler = group_handler
+        self._version = version
+
+        meta = self.get_meta()
+        self._version = meta.version
+
+    def get_meta(self) -> NgioLabelsGroupMeta:
+        """Retrieve the NGIO labels group metadata."""
+        return get_ngio_labels_group_meta(
+            group_handler=self._group_handler,
+            version=self._version,
+        )
+
+    def update_meta(self, ngio_meta: NgioLabelsGroupMeta) -> None:
+        """Update the NGIO labels group metadata."""
+        update_ngio_labels_group_meta(
+            group_handler=self._group_handler,
+            ngio_meta=ngio_meta,
+        )

ngio/ome_zarr_meta/ngio_specs/__init__.py

@@ -0,0 +1,77 @@
+"""ngio internal specs module.
+
+Since the OME-Zarr specification are still evolving, this module provides a
+set of classes to internally handle the metadata.
+
+This models can be tr
+"""
+
+from ngio.ome_zarr_meta.ngio_specs._axes import (
+    AxesHandler,
+    AxesSetup,
+    Axis,
+    AxisType,
+    DefaultSpaceUnit,
+    DefaultTimeUnit,
+    SpaceUnits,
+    TimeUnits,
+    build_canonical_axes_handler,
+    canonical_axes_order,
+    canonical_label_axes_order,
+)
+from ngio.ome_zarr_meta.ngio_specs._channels import (
+    Channel,
+    ChannelsMeta,
+    ChannelVisualisation,
+    NgioColors,
+    default_channel_name,
+)
+from ngio.ome_zarr_meta.ngio_specs._dataset import Dataset
+from ngio.ome_zarr_meta.ngio_specs._ngio_hcs import (
+    ImageInWellPath,
+    NgioPlateMeta,
+    NgioWellMeta,
+    path_in_well_validation,
+)
+from ngio.ome_zarr_meta.ngio_specs._ngio_image import (
+    DefaultNgffVersion,
+    ImageLabelSource,
+    NgffVersions,
+    NgioImageLabelMeta,
+    NgioImageMeta,
+    NgioLabelMeta,
+    NgioLabelsGroupMeta,
+)
+from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
+
+__all__ = [
+    "AxesHandler",
+    "AxesSetup",
+    "Axis",
+    "AxisType",
+    "Channel",
+    "ChannelVisualisation",
+    "ChannelsMeta",
+    "Dataset",
+    "DefaultNgffVersion",
+    "DefaultSpaceUnit",
+    "DefaultTimeUnit",
+    "ImageInWellPath",
+    "ImageLabelSource",
+    "NgffVersions",
+    "NgioColors",
+    "NgioImageLabelMeta",
+    "NgioImageMeta",
+    "NgioLabelMeta",
+    "NgioLabelsGroupMeta",
+    "NgioPlateMeta",
+    "NgioWellMeta",
+    "PixelSize",
+    "SpaceUnits",
+    "TimeUnits",
+    "build_canonical_axes_handler",
+    "canonical_axes_order",
+    "canonical_label_axes_order",
+    "default_channel_name",
+    "path_in_well_validation",
+]