sane refactor and thaw frozen base model

src/ome_zarr_models/base.py

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+import pydantic
+
+
+class Base(pydantic.BaseModel):
+    """
+    The base pydantic model for all metadata classes 
+    """

src/ome_zarr_models/tmp/v04/bikeshed.py

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+"""
+Pydantic models related to OME-NGFF 0.4 specs, as implemented in
+fractal-tasks-core.
+"""
+import logging
+from typing import Optional
+from typing import TypeVar
+from typing import Union
+
+from pydantic import Field
+from pydantic import field_validator
+
+from ome_zarr_models.base import Base
+from ome_zarr_models.utils import unique_items_validator
+from ome_zarr_models.zarr_models.v04.multiscales import Dataset
+
+
+logger = logging.getLogger(__name__)
+
+
+T = TypeVar("T")
+
+class Axis(Base):
+    """
+    Model for an element of `Multiscale.axes`.
+
+    See https://ngff.openmicroscopy.org/0.4/#axes-md.
+    """
+
+    name: str
+    type: str | None = None
+    unit: str | None = None
+
+
+class ImageInWell(Base):
+    """
+    Model for an element of `Well.images`.
+
+    **Note 1:** The NGFF image is defined in a different model
+    (`NgffImageMeta`), while the `Image` model only refere to an item of
+    `Well.images`.
+
+    **Note 2:** We deviate from NGFF specs, since we allow `path` to be an
+    arbitrary string.
+    TODO: include a check like `constr(regex=r'^[A-Za-z0-9]+$')`, through a
+    Pydantic validator.
+
+    See https://ngff.openmicroscopy.org/0.4/#well-md.
+    """
+
+    acquisition: int | None = Field(
+        None, description="A unique identifier within the context of the plate"
+    )
+    path: str = Field(
+        ..., description="The path for this field of view subgroup"
+    )
+
+
+class Well(Base):
+    """
+    Model for `NgffWellMeta.well`.
+
+    See https://ngff.openmicroscopy.org/0.4/#well-md.
+    """
+
+    images: list[ImageInWell] = Field(
+        ..., description="The images included in this well", min_length=1
+    )
+    version: str | None = Field(
+        None, description="The version of the specification"
+    )
+    _check_unique = field_validator("images")(unique_items_validator)
+
+
+class NgffWellMeta(Base):
+    """
+    Model for the metadata of a NGFF well.
+
+    See https://ngff.openmicroscopy.org/0.4/#well-md.
+    """
+
+    well: Well | None = None
+
+    def get_acquisition_paths(self) -> dict[int, list[str]]:
+        """
+        Create mapping from acquisition indices to corresponding paths.
+
+        Runs on the well zarr attributes and loads the relative paths in the
+        well.
+
+        Returns:
+            Dictionary with `(acquisition index: [image_path])` key/value
+            pairs.
+
+        Raises:
+            ValueError:
+                If an element of `self.well.images` has no `acquisition`
+                    attribute.
+        """
+        acquisition_dict = {}
+        for image in self.well.images:
+            if image.acquisition is None:
+                raise ValueError(
+                    "Cannot get acquisition paths for Zarr files without "
+                    "'acquisition' metadata at the well level"
+                )
+            if image.acquisition not in acquisition_dict:
+                acquisition_dict[image.acquisition] = []
+            acquisition_dict[image.acquisition].append(image.path)
+        return acquisition_dict
+
+
+######################
+# Plate models
+######################
+
+
+class AcquisitionInPlate(Base):
+    """
+    Model for an element of `Plate.acquisitions`.
+
+    See https://ngff.openmicroscopy.org/0.4/#plate-md.
+    """
+
+    id: int = Field(
+        description="A unique identifier within the context of the plate"
+    )
+    maximumfieldcount: int | None = Field(
+        None,
+        description=(
+            "Int indicating the maximum number of fields of view for the "
+            "acquisition"
+        ),
+    )
+    name: str | None = Field(
+        None, description="a string identifying the name of the acquisition"
+    )
+    description: str | None = Field(
+        None,
+        description="The description of the acquisition",
+    )
+    # TODO: Add starttime & endtime
+    # starttime: str | None = Field()
+    # endtime: str | None = Field()
+
+
+class WellInPlate(Base):
+    """
+    Model for an element of `Plate.wells`.
+
+    See https://ngff.openmicroscopy.org/0.4/#plate-md.
+    """
+
+    path: str
+    rowIndex: int
+    columnIndex: int
+
+
+class ColumnInPlate(Base):
+    """
+    Model for an element of `Plate.columns`.
+
+    See https://ngff.openmicroscopy.org/0.4/#plate-md.
+    """
+
+    name: str
+
+
+class RowInPlate(Base):
+    """
+    Model for an element of `Plate.rows`.
+
+    See https://ngff.openmicroscopy.org/0.4/#plate-md.
+    """
+
+    name: str
+
+
+class Plate(Base):
+    """
+    Model for `NgffPlateMeta.plate`.
+
+    See https://ngff.openmicroscopy.org/0.4/#plate-md.
+    """
+
+    acquisitions: list[AcquisitionInPlate] | None = None
+    columns: list[ColumnInPlate]
+    field_count: int | None = None
+    name: str | None = None
+    rows: list[RowInPlate]
+    # version will become required in 0.5
+    version: str | None = Field(
+        None, description="The version of the specification"
+    )
+    wells: list[WellInPlate]
+
+
+class NgffPlateMeta(Base):
+    """
+    Model for the metadata of a NGFF plate.
+
+    See https://ngff.openmicroscopy.org/0.4/#plate-md.
+    """
+
+    plate: Plate

src/ome_zarr_models/tmp/v04/coordinate_transformations.py

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+from ome_zarr_models.base import Base
+
+
+from pydantic import Field
+
+
+from typing import Literal
+
+class Identity(Base):
+    """
+    Model for an identity transformation.
+
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md    
+    """
+    type: Literal["identity"]
+
+class VectorScale(Base):
+    """
+    Model for a scale transformation parametrized by a vector of numbers.
+
+    This corresponds to scale-type elements of
+    `Dataset.coordinateTransformations` or
+    `Multiscale.coordinateTransformations`.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["scale"]
+    scale: list[float] = Field(..., min_length=2)
+
+class PathScale(Base):
+    """
+    Model for a scale transformation parametrized by a path.
+
+    This corresponds to scale-type elements of
+    `Dataset.coordinateTransformations` or
+    `Multiscale.coordinateTransformations`.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["scale"]
+    path: str
+
+class VectorTranslation(Base):
+    """
+    Model for a translation transformation parametrized by a vector of numbers.
+
+    This corresponds to translation-type elements of
+    `Dataset.coordinateTransformations` or
+    `Multiscale.coordinateTransformations`.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["translation"]
+    translation: list[float] = Field(..., min_length=2)
+
+class PathTranslation(Base):
+    """
+    Model for a translation transformation parametrized by a path.
+
+    This corresponds to translation-type elements of
+    `Dataset.coordinateTransformations` or
+    `Multiscale.coordinateTransformations`.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["translation"]
+    translation: str

src/ome_zarr_models/tmp/v04/multiscales.py

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+from ome_zarr_models.base import Base
+from ome_zarr_models.utils import unique_items_validator
+from ome_zarr_models.zarr_models.v04.bikeshed import Axis
+from ome_zarr_models.zarr_models.v04.coordinate_transformations import PathScale, PathTranslation, VectorScale, VectorTranslation
+
+
+from pydantic import Field, field_validator
+
+from ome_zarr_models.zarr_models.v04.omero import Omero
+
+
+class Dataset(Base):
+    """
+    Model for an element of `Multiscale.datasets`.
+
+    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    """
+    # TODO: validate that path resolves to an actual zarr array 
+    path: str
+    # TODO: validate that transforms are consistent w.r.t dimensionality
+    coordinateTransformations: tuple[VectorScale | PathScale] | tuple[VectorScale | PathScale, VectorTranslation | PathTranslation]
+
+
+class Multiscale(Base):
+    """
+    Model for an element of `NgffImageMeta.multiscales`.
+
+    See https://ngff.openmicroscopy.org/0.4/#multiscale-md.
+    """
+
+    name: str | None = None
+    datasets: list[Dataset] = Field(..., min_length=1)
+    version: str | None = None
+    axes: list[Axis] = Field(..., max_length=5, min_length=2)
+    coordinateTransformations: Optional[
+        list[
+            Union[
+                PathScale,
+                VectorTranslation,
+            ]
+        ]
+    ] = None
+    _check_unique = field_validator("axes")(unique_items_validator)
+
+    @field_validator("coordinateTransformations", mode="after")
+    @classmethod
+    def _no_global_coordinateTransformations(
+        cls, v: list | None
+    ) -> list | None:
+        """
+        Fail if Multiscale has a (global) coordinateTransformations attribute.
+        """
+        if v is None:
+            return v
+        else:
+            raise NotImplementedError(
+                "Global coordinateTransformations at the multiscales "
+                "level are not currently supported in the fractal-tasks-core "
+                "model for the NGFF multiscale."
+            )
+
+
+class MultiscaleGroupAttrs(Base):
+    """
+    Model for the metadata of a NGFF image.
+
+    See https://ngff.openmicroscopy.org/0.4/#image-layout.
+    """
+
+    multiscales: list[Multiscale] = Field(
+        ...,
+        description="The multiscale datasets for this image",
+        min_length=1,
+    )
+    omero: Omero | None = None
+    _check_unique = field_validator("multiscales")(unique_items_validator)