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ContextualCountEmbedder

Bases: CountEmbedder

ContextualCountEmbedder.

Source code in srai/embedders/contextual_count_embedder.py 
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class ContextualCountEmbedder(CountEmbedder):
    """ContextualCountEmbedder."""

    def __init__(
        self,
        neighbourhood: Neighbourhood[IndexType],
        neighbourhood_distance: int,
        concatenate_vectors: bool = False,
        expected_output_features: Optional[
            Union[List[str], OsmTagsFilter, GroupedOsmTagsFilter]
        ] = None,
        count_subcategories: bool = False,
    ) -> None:
        """
        Init ContextualCountEmbedder.

        Args:
            neighbourhood (Neighbourhood[T]): Neighbourhood object used to get neighbours for
                the contextualization.
            neighbourhood_distance (int): How many neighbours levels should be included in
                the embedding.
            concatenate_vectors (bool, optional): Whether to sum all neighbours into a single vector
                with the same width as `CountEmbedder`, or to concatenate them to the wide format
                and keep all neighbour levels separate. Defaults to False.
            expected_output_features
                (Union[List[str], OsmTagsFilter, GroupedOsmTagsFilter], optional):
                The features that are expected to be found in the resulting embedding.
                If not None, the missing features are added and filled with 0.
                The unexpected features are removed. The resulting columns are sorted accordingly.
                Defaults to None.
            count_subcategories (bool, optional): Whether to count all subcategories individually
                or count features only on the highest level based on features column name.
                Defaults to False.

        Raises:
            ValueError: If `neighbourhood_distance` is negative.
        """
        super().__init__(expected_output_features, count_subcategories)

        self.neighbourhood = neighbourhood
        self.neighbourhood_distance = neighbourhood_distance
        self.concatenate_vectors = concatenate_vectors

        if self.neighbourhood_distance < 0:
            raise ValueError("Neighbourhood distance must be positive.")

    def transform(
        self,
        regions_gdf: gpd.GeoDataFrame,
        features_gdf: gpd.GeoDataFrame,
        joint_gdf: gpd.GeoDataFrame,
    ) -> pd.DataFrame:
        """
        Embed a given GeoDataFrame.

        Creates region embeddings by counting the frequencies of each feature value and applying
        a contextualization based on neighbours of regions. For each region, features will be
        altered based on the neighbours either by adding averaged values dimished based on distance,
        or by adding new separate columns with neighbour distance postfix.
        Expects features_gdf to be in wide format with each column being a separate type of
        feature (e.g. amenity, leisure) and rows to hold values of these features for each object.
        The rows will hold numbers of this type of feature in each region. Numbers can be
        fractional because neighbourhoods are averaged to represent a single value from
        all neighbours on a given level.

        Args:
            regions_gdf (gpd.GeoDataFrame): Region indexes and geometries.
            features_gdf (gpd.GeoDataFrame): Feature indexes, geometries and feature values.
            joint_gdf (gpd.GeoDataFrame): Joiner result with region-feature multi-index.

        Returns:
            pd.DataFrame: Embedding for each region in regions_gdf.

        Raises:
            ValueError: If features_gdf is empty and self.expected_output_features is not set.
            ValueError: If any of the gdfs index names is None.
            ValueError: If joint_gdf.index is not of type pd.MultiIndex or doesn't have 2 levels.
            ValueError: If index levels in gdfs don't overlap correctly.
        """
        counts_df = super().transform(regions_gdf, features_gdf, joint_gdf)

        result_df: pd.DataFrame
        if self.concatenate_vectors:
            result_df = self._get_concatenated_embeddings(counts_df)
        else:
            result_df = self._get_squashed_embeddings(counts_df)

        return result_df

    def _get_squashed_embeddings(self, counts_df: pd.DataFrame) -> pd.DataFrame:
        """
        Generate embeddings for regions by summing all neighbourhood levels.

        Creates embedding by getting an average of a neighbourhood at a given distance and adding it
        to the base values with weight equal to 1 / (distance + 1) squared. This way, farther
        neighbourhoods have lower impact on feature values.

        Args:
            counts_df (pd.DataFrame): Calculated features from CountEmbedder.

        Returns:
            pd.DataFrame: Embedding for each region in regions_gdf with number of features equal to
                the same as returned by the CountEmbedder.
        """
        base_columns = list(counts_df.columns)

        result_array = counts_df.values.astype(float)

        for distance, averaged_values in self._get_averaged_values_for_distances(counts_df):
            result_array += averaged_values / ((distance + 1) ** 2)

        return pd.DataFrame(data=result_array, index=counts_df.index, columns=base_columns)

    def _get_concatenated_embeddings(self, counts_df: pd.DataFrame) -> pd.DataFrame:
        """
        Generate embeddings for regions by concatenating different neighbourhood levels.

        Creates embedding by getting an average of a neighbourhood at a given distance and adding
        those features as separate columns with a postfix added to feature name. This way,
        all neighbourhoods can be analyzed separately, but number of columns grows linearly with
        a distance.

        Args:
            counts_df (pd.DataFrame): Calculated features from CountEmbedder.

        Returns:
            pd.DataFrame: Embedding for each region in regions_gdf with number of features equal to
                a number of features returned by the CountEmbedder multiplied
                by (neighbourhood distance + 1).
        """
        base_columns = list(counts_df.columns)
        number_of_base_columns = len(base_columns)
        columns = [
            f"{column}_{distance}"
            for distance in range(self.neighbourhood_distance + 1)
            for column in base_columns
        ]

        result_array = np.zeros(shape=(len(counts_df.index), len(columns)))
        result_array[:, 0:number_of_base_columns] = counts_df.values

        for distance, averaged_values in self._get_averaged_values_for_distances(counts_df):
            result_array[
                :, number_of_base_columns * distance : number_of_base_columns * (distance + 1)
            ] = averaged_values

        return pd.DataFrame(data=result_array, index=counts_df.index, columns=columns)

    def _get_averaged_values_for_distances(
        self, counts_df: pd.DataFrame
    ) -> Iterator[Tuple[int, npt.NDArray[np.float32]]]:
        """
        Generate averaged values for neighbours at given distances.

        Function will yield tuples of distances and averaged values arrays
        calculated based on neighbours at a given distance.

        Distance 0 is skipped.
        If embedder has `neighbourhood_distance` set to 0, nothing will be returned.

        Args:
            counts_df (pd.DataFrame): Calculated features from CountEmbedder.

        Yields:
            Iterator[Tuple[int, npt.NDArray[np.float32]]]: Iterator of distances and values.
        """
        if self.neighbourhood_distance == 0:
            return

        number_of_base_columns = len(counts_df.columns)

        for distance in range(1, self.neighbourhood_distance + 1):
            neighbours_series = counts_df.index.map(
                lambda region_id, neighbour_distance=distance: counts_df.index.intersection(
                    self.neighbourhood.get_neighbours_at_distance(
                        region_id, neighbour_distance, include_center=False
                    )
                ).values
            )
            if len(neighbours_series) == 0:
                continue

            averaged_values_stacked = np.stack(
                neighbours_series.map(
                    lambda region_ids: (
                        np.nan_to_num(np.nanmean(counts_df.loc[region_ids].values, axis=0))
                        if len(region_ids) > 0
                        else np.zeros((number_of_base_columns,))
                    )
                ).values
            )

            yield distance, averaged_values_stacked

__init__ 

__init__(neighbourhood: Neighbourhood[IndexType], neighbourhood_distance: int, concatenate_vectors: bool = False, expected_output_features: Optional[Union[List[str], OsmTagsFilter, GroupedOsmTagsFilter]] = None, count_subcategories: bool = False) -> None

Init ContextualCountEmbedder.

PARAMETER DESCRIPTION
neighbourhood

Neighbourhood object used to get neighbours for the contextualization.

TYPE: Neighbourhood[T]

neighbourhood_distance

How many neighbours levels should be included in the embedding.

TYPE: int

concatenate_vectors

Whether to sum all neighbours into a single vector with the same width as CountEmbedder, or to concatenate them to the wide format and keep all neighbour levels separate. Defaults to False.

TYPE: bool DEFAULT: False

count_subcategories

Whether to count all subcategories individually or count features only on the highest level based on features column name. Defaults to False.

TYPE: bool DEFAULT: False

RAISES DESCRIPTION
ValueError

If neighbourhood_distance is negative.
Source code in srai/embedders/contextual_count_embedder.py 
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def __init__(
    self,
    neighbourhood: Neighbourhood[IndexType],
    neighbourhood_distance: int,
    concatenate_vectors: bool = False,
    expected_output_features: Optional[
        Union[List[str], OsmTagsFilter, GroupedOsmTagsFilter]
    ] = None,
    count_subcategories: bool = False,
) -> None:
    """
    Init ContextualCountEmbedder.

    Args:
        neighbourhood (Neighbourhood[T]): Neighbourhood object used to get neighbours for
            the contextualization.
        neighbourhood_distance (int): How many neighbours levels should be included in
            the embedding.
        concatenate_vectors (bool, optional): Whether to sum all neighbours into a single vector
            with the same width as `CountEmbedder`, or to concatenate them to the wide format
            and keep all neighbour levels separate. Defaults to False.
        expected_output_features
            (Union[List[str], OsmTagsFilter, GroupedOsmTagsFilter], optional):
            The features that are expected to be found in the resulting embedding.
            If not None, the missing features are added and filled with 0.
            The unexpected features are removed. The resulting columns are sorted accordingly.
            Defaults to None.
        count_subcategories (bool, optional): Whether to count all subcategories individually
            or count features only on the highest level based on features column name.
            Defaults to False.

    Raises:
        ValueError: If `neighbourhood_distance` is negative.
    """
    super().__init__(expected_output_features, count_subcategories)

    self.neighbourhood = neighbourhood
    self.neighbourhood_distance = neighbourhood_distance
    self.concatenate_vectors = concatenate_vectors

    if self.neighbourhood_distance < 0:
        raise ValueError("Neighbourhood distance must be positive.")

transform 

transform(regions_gdf: gpd.GeoDataFrame, features_gdf: gpd.GeoDataFrame, joint_gdf: gpd.GeoDataFrame) -> pd.DataFrame

Embed a given GeoDataFrame.

Creates region embeddings by counting the frequencies of each feature value and applying a contextualization based on neighbours of regions. For each region, features will be altered based on the neighbours either by adding averaged values dimished based on distance, or by adding new separate columns with neighbour distance postfix. Expects features_gdf to be in wide format with each column being a separate type of feature (e.g. amenity, leisure) and rows to hold values of these features for each object. The rows will hold numbers of this type of feature in each region. Numbers can be fractional because neighbourhoods are averaged to represent a single value from all neighbours on a given level.

PARAMETER DESCRIPTION
regions_gdf

Region indexes and geometries.

TYPE: gpd.GeoDataFrame

features_gdf

Feature indexes, geometries and feature values.

TYPE: gpd.GeoDataFrame

joint_gdf

Joiner result with region-feature multi-index.

TYPE: gpd.GeoDataFrame

RETURNS DESCRIPTION
pd.DataFrame

pd.DataFrame: Embedding for each region in regions_gdf.
RAISES DESCRIPTION
ValueError

If features_gdf is empty and self.expected_output_features is not set.
ValueError

If any of the gdfs index names is None.
ValueError

If joint_gdf.index is not of type pd.MultiIndex or doesn't have 2 levels.
ValueError

If index levels in gdfs don't overlap correctly.
Source code in srai/embedders/contextual_count_embedder.py 
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def transform(
    self,
    regions_gdf: gpd.GeoDataFrame,
    features_gdf: gpd.GeoDataFrame,
    joint_gdf: gpd.GeoDataFrame,
) -> pd.DataFrame:
    """
    Embed a given GeoDataFrame.

    Creates region embeddings by counting the frequencies of each feature value and applying
    a contextualization based on neighbours of regions. For each region, features will be
    altered based on the neighbours either by adding averaged values dimished based on distance,
    or by adding new separate columns with neighbour distance postfix.
    Expects features_gdf to be in wide format with each column being a separate type of
    feature (e.g. amenity, leisure) and rows to hold values of these features for each object.
    The rows will hold numbers of this type of feature in each region. Numbers can be
    fractional because neighbourhoods are averaged to represent a single value from
    all neighbours on a given level.

    Args:
        regions_gdf (gpd.GeoDataFrame): Region indexes and geometries.
        features_gdf (gpd.GeoDataFrame): Feature indexes, geometries and feature values.
        joint_gdf (gpd.GeoDataFrame): Joiner result with region-feature multi-index.

    Returns:
        pd.DataFrame: Embedding for each region in regions_gdf.

    Raises:
        ValueError: If features_gdf is empty and self.expected_output_features is not set.
        ValueError: If any of the gdfs index names is None.
        ValueError: If joint_gdf.index is not of type pd.MultiIndex or doesn't have 2 levels.
        ValueError: If index levels in gdfs don't overlap correctly.
    """
    counts_df = super().transform(regions_gdf, features_gdf, joint_gdf)

    result_df: pd.DataFrame
    if self.concatenate_vectors:
        result_df = self._get_concatenated_embeddings(counts_df)
    else:
        result_df = self._get_squashed_embeddings(counts_df)

    return result_df