ngio 0.5.0b6__py3-none-any.whl

ngio/tables/v1/_feature_table.py

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+"""Implementation of the FeatureTableV1 class.
+
+This class follows the roi_table specification at:
+https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
+"""
+
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+from ngio.tables._abstract_table import AbstractBaseTable
+from ngio.tables.backends import BackendMeta, TableBackend, TabularData
+from ngio.utils import NgioValueError
+from ngio.utils._zarr_utils import ZarrGroupHandler
+
+
+class RegionMeta(BaseModel):
+    """Metadata for the region."""
+
+    path: str
+
+
+class FeatureTableMeta(BackendMeta):
+    """Metadata for the ROI table."""
+
+    table_version: Literal["1"] = "1"
+    type: Literal["feature_table"] = "feature_table"
+    region: RegionMeta | None = None
+    instance_key: str = "label"  # Legacy field, kept for compatibility
+    # Backend metadata
+    index_key: str | None = "label"
+    index_type: Literal["int", "str"] | None = "int"
+    # Columns optional types
+    categorical_columns: list[str] = Field(default_factory=list)
+    measurement_columns: list[str] = Field(default_factory=list)
+    metadata_columns: list[str] = Field(default_factory=list)
+
+
+class FeatureTableV1(AbstractBaseTable):
+    def __init__(
+        self,
+        table_data: TabularData | None = None,
+        *,
+        reference_label: str | None = None,
+        meta: FeatureTableMeta | None = None,
+    ) -> None:
+        """Initialize the GenericTable."""
+        if meta is None:
+            meta = FeatureTableMeta()
+
+        if reference_label is not None:
+            path = f"../labels/{reference_label}"
+            meta = FeatureTableMeta(region=RegionMeta(path=path))
+
+        if table_data is not None and not isinstance(table_data, TabularData):
+            raise NgioValueError(
+                f"The table is not of type SupportedTables. Got {type(table_data)}"
+            )
+
+        if meta.index_key is None:
+            meta.index_key = "label"
+
+        if meta.index_type is None:
+            meta.index_type = "int"
+
+        meta.instance_key = meta.index_key
+
+        super().__init__(
+            table_data=table_data,
+            meta=meta,
+        )
+
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        num_rows = len(self.dataframe) if self.dataframe is not None else 0
+        num_columns = len(self.dataframe.columns) if self.dataframe is not None else 0
+        properties = f"num_rows={num_rows}, num_columns={num_columns}"
+        if self.reference_label is not None:
+            properties += f", reference_label={self.reference_label}"
+        return f"FeatureTableV1({properties})"
+
+    @classmethod
+    def from_handler(
+        cls,
+        handler: ZarrGroupHandler,
+        backend: TableBackend | None = None,
+    ) -> "FeatureTableV1":
+        return cls._from_handler(
+            handler=handler,
+            backend=backend,
+            meta_model=FeatureTableMeta,
+        )
+
+    @property
+    def meta(self) -> FeatureTableMeta:
+        """Return the metadata of the table."""
+        if not isinstance(self._meta, FeatureTableMeta):
+            raise NgioValueError(
+                "The metadata of the table is not of type FeatureTableMeta."
+            )
+        return self._meta
+
+    @staticmethod
+    def table_type() -> str:
+        """Return the type of the table."""
+        return "feature_table"
+
+    @staticmethod
+    def version() -> str:
+        """The generic table does not have a version.
+
+        Since does not follow a specific schema.
+        """
+        return "1"
+
+    @property
+    def reference_label(self) -> str | None:
+        """Return the reference label."""
+        path = self.meta.region
+        if path is None:
+            return None
+
+        path = path.path
+        path = path.split("/")[-1]
+        return path

ngio/tables/v1/_generic_table.py

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+"""Implementation of a generic table class."""
+
+from ngio.tables._abstract_table import AbstractBaseTable
+from ngio.tables.backends import BackendMeta, TableBackend
+from ngio.utils import ZarrGroupHandler
+
+
+class GenericTableMeta(BackendMeta):
+    """Metadata for the generic table.
+
+    This is used to store metadata for a generic table.
+    It does not have a specific definition.
+    """
+
+    table_version: str | None = "1"
+    type: str | None = "generic_table"
+
+
+class GenericTable(AbstractBaseTable):
+    """Class to a non-specific table.
+
+    This can be used to load any table that does not have
+    a specific definition.
+    """
+
+    @staticmethod
+    def table_type() -> str:
+        """Return the type of the table."""
+        return "generic_table"
+
+    @staticmethod
+    def version() -> str:
+        """The generic table does not have a version.
+
+        Since does not follow a specific schema.
+        """
+        return "1"
+
+    @classmethod
+    def from_handler(
+        cls,
+        handler: ZarrGroupHandler,
+        backend: TableBackend | None = None,
+    ) -> "GenericTable":
+        return cls._from_handler(
+            handler=handler,
+            backend=backend,
+            meta_model=BackendMeta,
+        )