ngio 0.2.0a3__py3-none-any.whl → 0.2.0b1__py3-none-any.whl

ngio-0.2.0b1.dist-info/RECORD

@@ -0,0 +1,54 @@
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+ngio-0.2.0b1.dist-info/RECORD,,

ngio/ome_zarr_meta/_generic_handlers.py

@@ -1,320 +0,0 @@
-"""Base class for handling OME-NGFF metadata in Zarr groups."""
-
-from typing import Generic, Protocol, TypeVar
-
-from pydantic import ValidationError
-
-from ngio.ome_zarr_meta.ngio_specs import AxesSetup, NgioImageMeta, NgioLabelMeta
-from ngio.utils import (
-    NgioValueError,
-    ZarrGroupHandler,
-)
-
-ConverterError = ValidationError | Exception | None
-
-
-class ImageMetaHandler(Protocol):
-    """Protocol for OME-Zarr image handlers."""
-
-    def __init__(
-        self,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        """Initialize the handler."""
-        ...
-
-    def safe_load_meta(self) -> NgioImageMeta | ConverterError:
-        """Load the metadata from the store."""
-        ...
-
-    @property
-    def meta(self) -> NgioImageMeta:
-        """Return the metadata."""
-        ...
-
-    def write_meta(self, meta: NgioImageMeta) -> None:
-        """Write the metadata to the store."""
-        ...
-
-
-class LabelMetaHandler(Protocol):
-    """Protocol for OME-Zarr label handlers."""
-
-    def __init__(
-        self,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        """Initialize the handler."""
-        ...
-
-    def safe_load_meta(self) -> NgioLabelMeta | ConverterError:
-        """Load the metadata from the store."""
-        ...
-
-    @property
-    def meta(self) -> NgioLabelMeta:
-        """Return the metadata."""
-        ...
-
-    def write_meta(self, meta: NgioLabelMeta) -> None:
-        """Write the metadata to the store."""
-        ...
-
-
-###########################################################################
-#
-# The code below implements a generic class for handling OME-Zarr metadata
-# in Zarr groups.
-#
-###########################################################################
-
-
-class ImageMetaImporter(Protocol):
-    @staticmethod
-    def __call__(
-        metadata: dict,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ) -> tuple[bool, NgioImageMeta | ConverterError]:
-        """Convert the metadata to a NgioImageMeta object.
-
-        Args:
-            metadata (dict): The metadata (typically from a Zarr group .attrs).
-            axes_setup (AxesSetup, optional): The axes setup.
-                This is used to map axes with non-canonical names.
-            allow_non_canonical_axes (bool, optional): Whether to allow non-canonical
-                axes.
-            strict_canonical_order (bool, optional): Whether to enforce a strict
-                canonical order.
-
-        Returns:
-            tuple[bool, NgioImageMeta | ConverterError]: A tuple with a boolean
-                indicating whether the conversion was successful and the
-                NgioImageMeta object or an error.
-
-        """
-        ...
-
-
-class ImageMetaExporter(Protocol):
-    def __call__(self, metadata: NgioImageMeta) -> dict: ...
-
-
-class LabelMetaImporter(Protocol):
-    @staticmethod
-    def __call__(
-        metadata: dict,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ) -> tuple[bool, NgioLabelMeta | ConverterError]:
-        """Convert the metadata to a NgioLabelMeta object.
-
-        Args:
-            metadata (dict): The metadata (typically from a Zarr group .attrs).
-            axes_setup (AxesSetup, optional): The axes setup.
-                This is used to map axes with non-canonical names.
-            allow_non_canonical_axes (bool, optional): Whether to allow non-canonical
-                axes.
-            strict_canonical_order (bool, optional): Whether to enforce a strict
-                canonical order.
-
-        Returns:
-            tuple[bool, NgioLabelMeta | ConverterError]: A tuple with a boolean
-                indicating whether the conversion was successful and the
-                NgioLabelMeta object or an error.
-
-        """
-        ...
-
-
-class LabelMetaExporter(Protocol):
-    def __call__(self, metadata: NgioLabelMeta) -> dict: ...
-
-
-_meta = TypeVar("_meta", NgioImageMeta, NgioLabelMeta)
-_meta_importer = TypeVar("_meta_importer", ImageMetaImporter, LabelMetaImporter)
-_meta_exporter = TypeVar("_meta_exporter", ImageMetaExporter, LabelMetaExporter)
-
-
-class GenericMetaHandler(Generic[_meta, _meta_importer, _meta_exporter]):
-    """Generic class for handling OME-Zarr metadata in Zarr groups."""
-
-    def __init__(
-        self,
-        meta_importer: _meta_importer,
-        meta_exporter: _meta_exporter,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        """Initialize the handler.
-
-        Args:
-            meta_importer (MetaImporter): The metadata importer.
-            meta_exporter (MetaExporter): The metadata exporter.
-            group_handler (ZarrGroupHandler): The Zarr group handler.
-            axes_setup (AxesSetup, optional): The axes setup.
-                This is used to map axes with non-canonical names.
-            allow_non_canonical_axes (bool, optional): Whether to allow non-canonical
-                axes.
-            strict_canonical_order (bool, optional): Whether to enforce a strict
-                canonical order.
-        """
-        self._group_handler = group_handler
-        self._meta_importer = meta_importer
-        self._meta_exporter = meta_exporter
-        self._axes_setup = axes_setup
-        self._allow_non_canonical_axes = allow_non_canonical_axes
-        self._strict_canonical_order = strict_canonical_order
-
-    def _load_meta(self, return_error: bool = False):
-        """Load the metadata from the store."""
-        attrs = self._group_handler.load_attrs()
-        is_valid, meta_or_error = self._meta_importer(
-            metadata=attrs,
-            axes_setup=self._axes_setup,
-            allow_non_canonical_axes=self._allow_non_canonical_axes,
-            strict_canonical_order=self._strict_canonical_order,
-        )
-        if is_valid:
-            return meta_or_error
-
-        if return_error:
-            return meta_or_error
-
-        raise NgioValueError(f"Could not load metadata: {meta_or_error}")
-
-    def safe_load_meta(self) -> _meta | ConverterError:
-        """Load the metadata from the store."""
-        return self._load_meta(return_error=True)
-
-    def _write_meta(self, meta) -> None:
-        """Write the metadata to the store."""
-        v04_meta = self._meta_exporter(metadata=meta)
-        self._group_handler.write_attrs(v04_meta)
-
-    def write_meta(self, meta: _meta) -> None:
-        """Write the metadata to the store."""
-        raise NotImplementedError
-
-    @property
-    def meta(self) -> _meta:
-        """Return the metadata."""
-        raise NotImplementedError
-
-
-class BaseImageMetaHandler(
-    GenericMetaHandler[NgioImageMeta, ImageMetaImporter, ImageMetaExporter]
-):
-    """Generic class for handling OME-Zarr metadata in Zarr groups."""
-
-    def __init__(
-        self,
-        meta_importer: ImageMetaImporter,
-        meta_exporter: ImageMetaExporter,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        """Initialize the handler.
-
-        Args:
-            meta_importer (ImageMetaImporter): The metadata importer.
-            meta_exporter (ImageMetaExporter): The metadata exporter.
-            group_handler (ZarrGroupHandler): The Zarr group handler.
-            axes_setup (AxesSetup, optional): The axes setup.
-                This is used to map axes with non-canonical names.
-            allow_non_canonical_axes (bool, optional): Whether to allow non-canonical
-                axes.
-            strict_canonical_order (bool, optional): Whether to enforce a strict
-                canonical order.
-        """
-        super().__init__(
-            meta_importer=meta_importer,
-            meta_exporter=meta_exporter,
-            group_handler=group_handler,
-            axes_setup=axes_setup,
-            allow_non_canonical_axes=allow_non_canonical_axes,
-            strict_canonical_order=strict_canonical_order,
-        )
-
-    def safe_load_meta(
-        self, return_error: bool = False
-    ) -> NgioImageMeta | ConverterError:
-        """Load the metadata from the store."""
-        return self._load_meta(return_error)
-
-    @property
-    def meta(self) -> NgioImageMeta:
-        """Load the metadata from the store."""
-        meta = self._load_meta()
-        if isinstance(meta, NgioImageMeta):
-            return meta
-        raise NgioValueError(f"Could not load metadata: {meta}")
-
-    def write_meta(self, meta: NgioImageMeta) -> None:
-        self._write_meta(meta)
-
-
-class BaseLabelMetaHandler(
-    GenericMetaHandler[NgioLabelMeta, LabelMetaImporter, LabelMetaExporter]
-):
-    """Generic class for handling OME-Zarr metadata in Zarr groups."""
-
-    def __init__(
-        self,
-        meta_importer: LabelMetaImporter,
-        meta_exporter: LabelMetaExporter,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        """Initialize the handler.
-
-        Args:
-            meta_importer (LabelMetaImporter): The metadata importer.
-            meta_exporter (LabelMetaExporter): The metadata exporter.
-            group_handler (ZarrGroupHandler): The Zarr group handler.
-            axes_setup (AxesSetup, optional): The axes setup.
-                This is used to map axes with non-canonical names.
-            allow_non_canonical_axes (bool, optional): Whether to allow non-canonical
-                axes.
-            strict_canonical_order (bool, optional): Whether to enforce a strict
-                canonical order.
-        """
-        super().__init__(
-            meta_importer=meta_importer,
-            meta_exporter=meta_exporter,
-            group_handler=group_handler,
-            axes_setup=axes_setup,
-            allow_non_canonical_axes=allow_non_canonical_axes,
-            strict_canonical_order=strict_canonical_order,
-        )
-
-    def safe_load_meta(
-        self, return_error: bool = False
-    ) -> NgioLabelMeta | ConverterError:
-        """Load the metadata from the store."""
-        return self._load_meta(return_error)
-
-    @property
-    def meta(self) -> NgioLabelMeta:
-        """Load the metadata from the store."""
-        meta = self._load_meta()
-        if isinstance(meta, NgioLabelMeta):
-            return meta
-        raise NgioValueError(f"Could not load metadata: {meta}")
-
-    def write_meta(self, meta: NgioLabelMeta) -> None:
-        self._write_meta(meta)

ngio/ome_zarr_meta/v04/_meta_handlers.py

@@ -1,54 +0,0 @@
-"""Concrete implementation of the OME-Zarr metadata handlers for version 0.4."""
-
-from ngio.ome_zarr_meta._generic_handlers import (
-    BaseImageMetaHandler,
-    BaseLabelMetaHandler,
-)
-from ngio.ome_zarr_meta.ngio_specs import AxesSetup
-from ngio.ome_zarr_meta.v04._v04_spec_utils import (
-    ngio_to_v04_image_meta,
-    ngio_to_v04_label_meta,
-    v04_to_ngio_image_meta,
-    v04_to_ngio_label_meta,
-)
-from ngio.utils import ZarrGroupHandler
-
-
-class V04ImageMetaHandler(BaseImageMetaHandler):
-    """Base class for handling OME-Zarr 0.4 metadata."""
-
-    def __init__(
-        self,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        super().__init__(
-            meta_importer=v04_to_ngio_image_meta,
-            meta_exporter=ngio_to_v04_image_meta,
-            group_handler=group_handler,
-            axes_setup=axes_setup,
-            allow_non_canonical_axes=allow_non_canonical_axes,
-            strict_canonical_order=strict_canonical_order,
-        )
-
-
-class V04LabelMetaHandler(BaseLabelMetaHandler):
-    """Base class for handling OME-Zarr 0.4 metadata."""
-
-    def __init__(
-        self,
-        group_handler: ZarrGroupHandler,
-        axes_setup: AxesSetup | None = None,
-        allow_non_canonical_axes: bool = False,
-        strict_canonical_order: bool = True,
-    ):
-        super().__init__(
-            meta_importer=v04_to_ngio_label_meta,
-            meta_exporter=ngio_to_v04_label_meta,
-            group_handler=group_handler,
-            axes_setup=axes_setup,
-            allow_non_canonical_axes=allow_non_canonical_axes,
-            strict_canonical_order=strict_canonical_order,
-        )

ngio/tables/v1/_masking_roi_table.py

@@ -1,175 +0,0 @@
-"""Implementation of the Masking ROI table class.
-
-This class follows the roi_table specification at:
-https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-"""
-
-from collections.abc import Iterable
-from typing import Literal
-
-from pydantic import BaseModel
-
-from ngio.common import WorldCooROI
-from ngio.tables._validators import validate_columns
-from ngio.tables.backends import ImplementedTableBackends
-from ngio.tables.v1._roi_table import (
-    OPTIONAL_COLUMNS,
-    REQUIRED_COLUMNS,
-    _dataframe_to_rois,
-    _rois_to_dataframe,
-)
-from ngio.utils import NgioValueError, ZarrGroupHandler
-
-
-class RegionMeta(BaseModel):
-    """Metadata for the region."""
-
-    path: str
-
-
-class MaskingROITableV1Meta(BaseModel):
-    """Metadata for the ROI table."""
-
-    fractal_table_version: Literal["1"] = "1"
-    type: Literal["masking_roi_table"] = "masking_roi_table"
-    backend: str | None = None
-    region: RegionMeta | None = None
-    instance_key: str = "label"
-
-
-class MaskingROITableV1:
-    """Class to handle fractal ROI tables.
-
-    To know more about the ROI table format, please refer to the
-    specification at:
-    https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-    """
-
-    def __init__(
-        self,
-        rois: Iterable[WorldCooROI] | None = None,
-        reference_label: str | None = None,
-    ) -> None:
-        """Create a new ROI table."""
-        if reference_label is None:
-            self._meta = MaskingROITableV1Meta()
-        else:
-            path = f"../labels/{reference_label}"
-            self._meta = MaskingROITableV1Meta(region=RegionMeta(path=path))
-        self._table_backend = None
-
-        self._rois = {}
-        if rois is not None:
-            self.add(rois)
-
-    @staticmethod
-    def type() -> Literal["masking_roi_table"]:
-        """Return the type of the table."""
-        return "masking_roi_table"
-
-    @staticmethod
-    def version() -> Literal["1"]:
-        """Return the version of the fractal table."""
-        return "1"
-
-    @property
-    def backend_name(self) -> str | None:
-        """Return the name of the backend."""
-        if self._table_backend is None:
-            return None
-        return self._table_backend.backend_name()
-
-    @classmethod
-    def _from_handler(
-        cls, handler: ZarrGroupHandler, backend_name: str | None = None
-    ) -> "MaskingROITableV1":
-        """Create a new ROI table from a Zarr store."""
-        meta = MaskingROITableV1Meta(**handler.load_attrs())
-
-        if backend_name is None:
-            backend = ImplementedTableBackends().get_backend(
-                backend_name=meta.backend,
-                group_handler=handler,
-                index_key="label",
-                index_type="int",
-            )
-        else:
-            backend = ImplementedTableBackends().get_backend(
-                backend_name=backend_name,
-                group_handler=handler,
-                index_key="label",
-                index_type="int",
-            )
-            meta.backend = backend_name
-
-        if not backend.implements_dataframe:
-            raise NgioValueError(
-                "The backend does not implement the dataframe protocol."
-            )
-
-        table = cls()
-        table._meta = meta
-        table._table_backend = backend
-
-        dataframe = backend.load_as_dataframe()
-        dataframe = validate_columns(
-            dataframe,
-            required_columns=REQUIRED_COLUMNS,
-            optional_columns=OPTIONAL_COLUMNS,
-        )
-        table._rois = _dataframe_to_rois(dataframe)
-        return table
-
-    def _set_backend(
-        self,
-        handler: ZarrGroupHandler,
-        backend_name: str | None = None,
-    ) -> None:
-        """Set the backend of the table."""
-        backend = ImplementedTableBackends().get_backend(
-            backend_name=backend_name,
-            group_handler=handler,
-            index_key="label",
-            index_type="int",
-        )
-        self._meta.backend = backend_name
-        self._table_backend = backend
-
-    def rois(self) -> list[WorldCooROI]:
-        """List all ROIs in the table."""
-        return list(self._rois.values())
-
-    def get(self, label: int) -> WorldCooROI:
-        """Get an ROI from the table."""
-        _label = str(label)
-        if _label not in self._rois:
-            raise KeyError(f"ROI {_label} not found in the table.")
-        return self._rois[_label]
-
-    def add(self, roi: WorldCooROI | Iterable[WorldCooROI]) -> None:
-        """Append ROIs to the current table."""
-        if isinstance(roi, WorldCooROI):
-            roi = [roi]
-
-        for _roi in roi:
-            if _roi.name in self._rois:
-                raise NgioValueError(f"ROI {_roi.name} already exists in the table.")
-            self._rois[_roi.name] = _roi
-
-    def consolidate(self) -> None:
-        """Write the current state of the table to the Zarr file."""
-        if self._table_backend is None:
-            raise NgioValueError(
-                "No backend set for the table. "
-                "Please add the table to a OME-Zarr Image before calling consolidate."
-            )
-
-        dataframe = _rois_to_dataframe(self._rois, index_key="label")
-        dataframe = validate_columns(
-            dataframe,
-            required_columns=REQUIRED_COLUMNS,
-            optional_columns=OPTIONAL_COLUMNS,
-        )
-        self._table_backend.write_from_dataframe(
-            dataframe, metadata=self._meta.model_dump(exclude_none=True)
-        )

ngio-0.2.0a3.dist-info/RECORD

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