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

ngio/tables/v1/roi_tables.py

@@ -1,285 +0,0 @@
-"""Implementation of the 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 functools import partial
-from typing import Literal
-
-import pandas as pd
-import zarr
-from pydantic import BaseModel
-
-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 ROITableV1Meta(BaseModel):
-    """Metadata for the ROI table."""
-
-    fractal_table_version: Literal["1"] = "1"
-    type: Literal["roi_table"] = "roi_table"
-
-
-ORIGIN_COLUMNS = [
-    "x_micrometer_original",
-    "y_micrometer_original",
-]
-TRANSLATION_COLUMNS = ["translation_x", "translation_y", "translation_z"]
-OPTIONAL_COLUMNS = ORIGIN_COLUMNS + TRANSLATION_COLUMNS
-
-
-def create_empty_roi_table(
-    include_origin: bool = False, include_translation: bool = False
-) -> pd.DataFrame:
-    """Create an empty ROI table."""
-    origin_columns = ORIGIN_COLUMNS if include_origin else []
-    translation_columns = TRANSLATION_COLUMNS if include_translation else []
-
-    columns = [
-        *REQUIRED_COLUMNS,
-        *origin_columns,
-        *translation_columns,
-    ]
-    table = pd.DataFrame(
-        index=pd.Index([], name="FieldIndex", dtype="str"), columns=columns
-    )
-
-    return table
-
-
-class ROITableV1:
-    """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,
-        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 = ROITableV1Meta(**group.attrs)
-        else:
-            self._meta = ROITableV1Meta.model_construct(**group.attrs)
-
-        # Validate the table is not implemented for the ROI table
-        validators = [
-            partial(
-                validate_columns,
-                required_columns=REQUIRED_COLUMNS,
-                optional_columns=OPTIONAL_COLUMNS,
-            )
-        ]
-        validators = validators if validate_table else None
-
-        index_key = "FieldIndex" if index_key is None else index_key
-
-        self._table_handler = BaseTable(
-            group=group, index_key=index_key, index_type="str", validators=validators
-        )
-        self._name = name
-
-    @classmethod
-    def _new(
-        cls,
-        parent_group: zarr.Group,
-        name: str,
-        include_origin: bool = False,
-        include_translation: bool = False,
-        overwrite: bool = False,
-    ) -> "ROITableV1":
-        """Create a new 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.
-            table (DataFrame): The ROI table as a DataFrame.
-            include_origin (bool): Whether to include the origin columns in the table.
-            include_translation (bool): Whether to include the translation columns
-                in the table.
-            overwrite (bool): Whether to overwrite the table if it already exists.
-        """
-        group = parent_group.create_group(name, overwrite=overwrite)
-
-        table = create_empty_roi_table(
-            include_origin=include_origin, include_translation=include_translation
-        )
-
-        meta = ROITableV1Meta()
-        write_table_ad(
-            group=group,
-            table=table,
-            index_key="FieldIndex",
-            index_type="str",
-            meta=meta,
-        )
-        return cls(group=group, name=name)
-
-    def __repr__(self) -> str:
-        """Return the string representation of the ROI table."""
-        name = "ROITableV1("
-        len_name = len(name)
-        return (
-            f"{name}"
-            f"group_path={self.group_path}, \n"
-            f"{' ':>{len_name}}name={self.name},\n"
-            f"{' ':>{len_name}}num_rois={self.num_rois}, \n"
-            ")"
-        )
-
-    @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) -> ROITableV1Meta:
-        """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 set_table(self, table: pd.DataFrame) -> None:
-        """Set the feature table."""
-        self._table_handler.set_table(table)
-
-    @property
-    def field_indexes(self) -> list[str]:
-        """Return a list of all field indexes in the table."""
-        return self.table.index.tolist()
-
-    @property
-    def num_rois(self) -> int:
-        """Return the number of ROIs in the table."""
-        return len(self.field_indexes)
-
-    def set_rois(
-        self,
-        rois: Iterable[WorldCooROI] | WorldCooROI,
-        overwrite: bool = False,
-    ) -> None:
-        """Append ROIs to the current table.
-
-        Args:
-            rois (Iterable[WorldCooROI] | WorldCooROI): The ROIs to append.
-            overwrite (bool): Whether to overwrite the ROIs if they already exist.
-                If False, the ROIs will be appended. If True, the ROIs will be
-                overwritten.
-        """
-        if isinstance(rois, WorldCooROI):
-            rois = [rois]
-
-        rois_dict = {}
-        for roi in rois:
-            field_index = roi.infos.get("FieldIndex", None)
-            if field_index is None:
-                raise ValueError("Field index is required in the ROI infos.")
-
-            rois_dict[field_index] = {
-                "x_micrometer": roi.x,
-                "y_micrometer": roi.y,
-                "z_micrometer": roi.z,
-                "len_x_micrometer": roi.x_length,
-                "len_y_micrometer": roi.y_length,
-                "len_z_micrometer": roi.z_length,
-            }
-
-            for column in OPTIONAL_COLUMNS:
-                if column in roi.infos:
-                    rois_dict[field_index][column] = roi.infos[column]
-
-        table_df = self.table
-        new_table_df = pd.DataFrame.from_dict(rois_dict, orient="index")
-
-        if overwrite or table_df.empty:
-            table_df = new_table_df
-        else:
-            table_df = pd.concat([table_df, new_table_df], axis=0)
-
-        table_df.index.name = "FieldIndex"
-        table_df.index = table_df.index.astype(str)
-        self.set_table(table_df)
-
-    def _gater_optional_columns(self, series: pd.Series) -> dict:
-        """Gather the optional columns from a series."""
-        optional_dict = {}
-        for column in OPTIONAL_COLUMNS:
-            if column in series.index:
-                optional_dict[column] = series[column]
-        return optional_dict
-
-    def get_roi(self, field_index: str) -> WorldCooROI:
-        """Get an ROI from the table."""
-        if field_index not in self.field_indexes:
-            raise ValueError(f"Field index {field_index} is not in the table")
-
-        table_df = self.table.loc[field_index]
-        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={"FieldIndex": field_index, **self._gater_optional_columns(table_df)},
-        )
-        return roi
-
-    @property
-    def rois(self) -> list[WorldCooROI]:
-        """List all ROIs in the table."""
-        return [self.get_roi(field_index) for field_index in self.field_indexes]
-
-    def consolidate(self) -> None:
-        """Write the crrent state of the table to the Zarr file."""
-        self._table_handler.consolidate(self.meta)

ngio/utils/_common_types.py

@@ -1,5 +0,0 @@
-import numpy as np
-import zarr
-from dask import array as da
-
-ArrayLike = np.ndarray | da.core.Array | zarr.Array

ngio/utils/_pydantic_utils.py

@@ -1,52 +0,0 @@
-"""Utility functions for Pydantic models."""
-
-import os
-from collections import namedtuple
-from typing import Any, NamedTuple, TypeVar
-
-from pydantic import BaseModel, Field, model_serializer, model_validator
-
-# Debugging flag to skip validation of the metadata (for testing purposes only)
-# check if this is an environment variable
-SKIP_NGFF_VALIDATION = bool(os.getenv("SKIP_NGFF_VALIDATION", False))
-
-
-class BaseWithExtraFields(BaseModel):
-    """Base class for all Fractal spec models.
-
-    Every field that is not defined in the model will
-        be stored in the `extra_fields` attribute.
-    """
-
-    extra_fields: dict = Field(default_factory=dict)
-
-    @model_validator(mode="before")
-    def _collect_extra_fields(cls, values: dict[str, Any]) -> dict[str, Any]:
-        extra = {k: v for k, v in values.items() if k not in cls.model_fields}
-        values["extra_fields"] = extra
-        return values
-
-    @model_serializer(mode="wrap")
-    def _custom_serializer(self, handler: Any) -> dict[str, Any]:
-        basic_dict = handler(self)
-        extra = basic_dict.pop("extra_fields")
-        return {**basic_dict, **extra}
-
-
-T = TypeVar("T")
-
-
-def unique_items_validator(values: list[T]) -> list[T]:
-    """Validate that all items in the list are unique."""
-    if SKIP_NGFF_VALIDATION:
-        return values
-
-    for ind, value in enumerate(values, start=1):
-        if value in values[ind:]:
-            raise ValueError(f"Non-unique values in {values}.")
-    return values
-
-
-def named_tuple_from_pydantic_model(model: BaseModel) -> NamedTuple:
-    """Create a namedtuple from a Pydantic model."""
-    return namedtuple(name=model.__name__, field_names=model.model_fields.keys())  # type: ignore

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