ngio 0.1.6__py3-none-any.whl → 0.2.0a2__py3-none-any.whl

ngio/tables/v1/feature_tables.py

@@ -1,182 +0,0 @@
-"""Implementation of the FeatureTableV1 class.
-
-This class follows the feature_table specification at:
-https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-"""
-
-from typing import Literal
-
-import pandas as pd
-import zarr
-from pydantic import BaseModel
-
-from ngio.tables.v1._generic_table import BaseTable, write_table_ad
-
-
-class FeatureTableV1Meta(BaseModel):
-    """Metadata for the ROI table."""
-
-    region: dict[Literal["path"], str] | None = None
-    instance_key: str = "label"
-    fractal_table_version: Literal["1"] = "1"
-    type: Literal["feature_table"] = "feature_table"
-
-
-class FeatureTableV1:
-    """Class to handle fractal Feature tables.
-
-    To know more about the Feature table format, please refer to the
-    https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-    """
-
-    def __init__(
-        self,
-        group: zarr.Group,
-        name: str,
-        validate_metadata: bool = True,
-        validate_table: bool = True,
-        index_key: str | None = None,
-    ):
-        """Initialize the class from an existing group.
-
-        Args:
-            group (zarr.Group): The group containing the
-                ROI table.
-            name (str): The name of the ROI table.
-            validate_metadata (bool): If True, the metadata is validated.
-            validate_table (bool): If True, the table is validated.
-            index_key (str): The column name to use as the index of the DataFrame.
-        """
-        if validate_metadata:
-            self._meta = FeatureTableV1Meta(**group.attrs)
-        else:
-            self._meta = FeatureTableV1Meta.model_construct(**group.attrs)
-
-        # Validate the table is not implemented for the Feature table
-        validators = None
-        validators = validators if validate_table else None
-
-        index_key = index_key if index_key is not None else self._meta.instance_key
-        self._table_handler = BaseTable(
-            group=group,
-            index_key=index_key,
-            index_type="int",
-            validators=validators,
-        )
-
-        self._name = name
-
-    def __repr__(self) -> str:
-        """Return the string representation of the class."""
-        name = "FeatureTableV1("
-        len_name = len(name)
-        return (
-            f"{name}"
-            f"group_path={self.group_path}, \n"
-            f"{' ':>{len_name}}name={self.name},\n"
-            f"{' ':>{len_name}}features={self.table.columns.to_list()}, \n"
-            f"{' ':>{len_name}}source_label={self.source_label()}, \n"
-            f"{' ':>{len_name}}num_labels={len(self.table.index)}), \n"
-            ")"
-        )
-
-    @classmethod
-    def _new(
-        cls,
-        parent_group: zarr.Group,
-        name: str,
-        label_image: str | None = None,
-        instance_key: str = "label",
-        overwrite: bool = False,
-    ) -> None:
-        """Create a new Feature table.
-
-        Args:
-            parent_group (zarr.Group): The parent group where the ROI table
-                will be created.
-            name (str): The name of the ROI table.
-            label_image (str | None): The relative path to the label image used to
-                create the feature table.
-            instance_key (str): The column name to use as the index of the DataFrame.
-                Default is 'label'.
-            overwrite (bool): If True, the table will be overwritten if it exists.
-                Default is False.
-        """
-        group = parent_group.create_group(name, overwrite=overwrite)
-        table = pd.DataFrame(index=pd.Index([], name=instance_key, dtype="int"))
-
-        label_image = label_image if label_image is not None else "None"
-        meta = FeatureTableV1Meta(
-            region={"path": label_image}, instance_key=instance_key
-        )
-        write_table_ad(
-            group=group,
-            table=table,
-            index_key=instance_key,
-            index_type="int",
-            meta=meta,
-        )
-        return cls(group=group, name=name)
-
-    @property
-    def name(self) -> str:
-        """Return the name of the feature table."""
-        return self._name
-
-    @property
-    def root_path(self) -> str:
-        """Return the path of the root group."""
-        return self._table_handler.root_path
-
-    @property
-    def group_path(self) -> str:
-        """Return the path of the group."""
-        return self._table_handler.group_path
-
-    @property
-    def meta(self) -> FeatureTableV1Meta:
-        """Return the metadata of the feature table."""
-        return self._meta
-
-    @property
-    def table_handler(self) -> BaseTable:
-        """Return the table handler."""
-        return self._table_handler
-
-    @property
-    def table(self) -> pd.DataFrame:
-        """Return the feature table as a DataFrame."""
-        return self._table_handler.table
-
-    @table.setter
-    def table(self, table: pd.DataFrame) -> None:
-        """Set the feature table."""
-        raise NotImplementedError(
-            "Setting the table is not implemented. Please use the 'set_table' method."
-        )
-
-    def set_table(self, table: pd.DataFrame) -> None:
-        """Set the feature table."""
-        self._table_handler.set_table(table)
-
-    def source_label(self, get_full_path: bool = False) -> str | None:
-        """Return the name of the label image.
-
-        The name is assumed to be after the last '/' in the path.
-        Since this might fails, get_full_path is True, the full path is returned.
-
-        Args:
-            get_full_path (bool): If True, the full path is returned.
-        """
-        region = self.meta.region
-        if region is None:
-            return None
-        path = region["path"]
-
-        if get_full_path:
-            return path
-        return path.split("/")[-1]
-
-    def consolidate(self) -> None:
-        """Write the table to the group."""
-        self._table_handler.consolidate(meta=self.meta)

ngio/tables/v1/masking_roi_tables.py

@@ -1,243 +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 functools import partial
-from typing import Literal
-
-import pandas as pd
-import zarr
-from pydantic import BaseModel
-
-from ngio.core.label_handler import Label
-from ngio.core.roi import SpaceUnits, WorldCooROI
-from ngio.tables._utils import validate_columns
-from ngio.tables.v1._generic_table import REQUIRED_COLUMNS, BaseTable, write_table_ad
-
-
-class MaskingROITableV1Meta(BaseModel):
-    """Metadata for the ROI table."""
-
-    fractal_table_version: Literal["1"] = "1"
-    type: Literal["masking_roi_table"] = "masking_roi_table"
-    region: dict[Literal["path"], str]
-    instance_key: str = "label"
-
-
-def create_empty_roi_table() -> pd.DataFrame:
-    """Create an empty ROI table."""
-    table = pd.DataFrame(
-        index=pd.Index([], name="label", dtype="str"), columns=REQUIRED_COLUMNS
-    )
-
-    return table
-
-
-class MaskingROITableV1:
-    """Class to handle fractal Masking ROI tables.
-
-    To know more about the Masking ROI table format, please refer to the
-    specification at:
-    https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-    """
-
-    def __init__(
-        self,
-        group: zarr.Group,
-        name: str,
-        validate_metadata: bool = True,
-        validate_table: bool = True,
-        index_key: str | None = None,
-    ):
-        """Initialize the class from an existing group.
-
-        Args:
-            group (zarr.Group): The group containing the
-                ROI table.
-            name (str): The name of the ROI table.
-            validate_metadata (bool): If True, the metadata is validated.
-            validate_table (bool): If True, the table is validated.
-            index_key (str): The column name to use as the index of the DataFrame.
-        """
-        if validate_metadata:
-            self._meta = MaskingROITableV1Meta(**group.attrs)
-        else:
-            self._meta = MaskingROITableV1Meta.model_construct(**group.attrs)
-
-        # Validate the table is not implemented for the Masking ROI table
-        validators = [partial(validate_columns, required_columns=REQUIRED_COLUMNS)]
-        validators = validators if validate_table else None
-
-        index_key = index_key if index_key is not None else self._meta.instance_key
-        self._table_handler = BaseTable(
-            group=group,
-            index_key=index_key,
-            index_type="int",
-            validators=validators,
-        )
-        self._name = name
-
-    def __repr__(self) -> str:
-        """Return the string representation of the class."""
-        name = "MaskingROITableV1("
-        len_name = len(name)
-        return (
-            f"{name}"
-            f"group_path={self.group_path}, \n"
-            f"{' ':>{len_name}}name={self.name},\n"
-            f"{' ':>{len_name}}source_label={self.source_label()}, \n"
-            f"{' ':>{len_name}}num_labels={len(self.table.index)}), \n"
-            ")"
-        )
-
-    @classmethod
-    def _new(
-        cls,
-        parent_group: zarr.Group,
-        name: str,
-        label_image: str,
-        instance_key: str = "label",
-        overwrite: bool = False,
-    ) -> "MaskingROITableV1":
-        """Create a new Masking ROI table.
-
-        Note this method is not meant to be called directly.
-        But should be called from the TablesHandler class.
-
-        Args:
-            parent_group (zarr.Group): The parent group where the ROI table
-                will be created.
-            name (str): The name of the ROI table.
-            label_image (str): Name of the label image.
-            instance_key (str): The column name to use as the index of the DataFrame.
-                Default is 'label'.
-            overwrite (bool): Whether to overwrite the table if it already exists.
-        """
-        group = parent_group.create_group(name, overwrite=overwrite)
-
-        table = pd.DataFrame(
-            index=pd.Index([], name=instance_key, dtype="int"), columns=REQUIRED_COLUMNS
-        )
-
-        meta = MaskingROITableV1Meta(
-            region={"path": label_image}, instance_key=instance_key
-        )
-        write_table_ad(
-            group=group,
-            table=table,
-            index_key=instance_key,
-            index_type="int",
-            meta=meta,
-        )
-        return cls(group=group, name=name)
-
-    @property
-    def name(self) -> str:
-        """Return the name of the ROI table."""
-        return self._name
-
-    @property
-    def root_path(self) -> str:
-        """Return the path of the root group."""
-        return self._table_handler.root_path
-
-    @property
-    def group_path(self) -> str:
-        """Return the path of the group."""
-        return self._table_handler.group_path
-
-    @property
-    def meta(self) -> MaskingROITableV1Meta:
-        """Return the metadata of the ROI table."""
-        return self._meta
-
-    @property
-    def table_handler(self) -> BaseTable:
-        """Return the table handler."""
-        return self._table_handler
-
-    @property
-    def table(self) -> pd.DataFrame:
-        """Return the ROI table as a DataFrame."""
-        return self._table_handler.table
-
-    @table.setter
-    def table(self, table: pd.DataFrame) -> None:
-        """Set the feature table."""
-        raise NotImplementedError(
-            "Setting the table is not implemented. Please use the 'set_table' method."
-        )
-
-    def source_label(self, get_full_path: bool = False) -> str | None:
-        """Return the name of the label image.
-
-        The name is assumed to be after the last '/' in the path.
-        Since this might fails, get_full_path is True, the full path is returned.
-
-        Args:
-            get_full_path (bool): If True, the full path is returned.
-        """
-        region = self.meta.region
-        if region is None:
-            return None
-        path = region["path"]
-
-        if get_full_path:
-            return path
-        return path.split("/")[-1]
-
-    def set_table(self, table: pd.DataFrame) -> None:
-        """Set the feature table."""
-        self._table_handler.set_table(table)
-
-    @property
-    def list_labels(self) -> list[int]:
-        """Return a list of all field indexes in the table."""
-        return self.table.index.tolist()
-
-    def from_label(self, label: Label, overwrite: bool = False) -> None:
-        """Create a new ROI table from a label.
-
-        Args:
-            label (Label): The label to create the ROI table from.
-            overwrite (bool): Whether to overwrite the elements in the table.
-        """
-        if not overwrite and self.table.empty:
-            raise ValueError(
-                "The table is not empty. Set overwrite to True to proceed."
-            )
-        raise NotImplementedError("Method not implemented yet.")
-
-    def get_roi(self, label: int) -> WorldCooROI:
-        """Get an ROI from the table."""
-        if label not in self.list_labels:
-            raise ValueError(f"Label {label} not found in the table.")
-
-        table_df = self.table.loc[label]
-
-        roi = WorldCooROI(
-            x=table_df.loc["x_micrometer"],
-            y=table_df.loc["y_micrometer"],
-            z=table_df.loc["z_micrometer"],
-            x_length=table_df.loc["len_x_micrometer"],
-            y_length=table_df.loc["len_y_micrometer"],
-            z_length=table_df.loc["len_z_micrometer"],
-            unit=SpaceUnits.micrometer,
-            infos={
-                "label": label,
-                "source_label_path": self.source_label(get_full_path=True),
-                "source_label": self.source_label(),
-            },
-        )
-        return roi
-
-    @property
-    def rois(self) -> list[WorldCooROI]:
-        """List all ROIs in the table."""
-        return [self.get_roi(label) for label in self.list_labels]
-
-    def consolidate(self) -> None:
-        """Write the crrent state of the table to the Zarr file."""
-        self._table_handler.consolidate(self.meta)