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get_interfaces

Get the interfaces b/w the polygons defined in a areas and buffer_area.

Note

Identifies the interface regions between polygons in area1 and in area2 by buffering the area2 polygons and finding their intersections with area1. The width of the interface is controlled by the buffer_dist parameter.

Parameters:

Name Type Description Default
area1 GeoDataFrame

The area or region of interest that is buffered on top of polygons in area2.

 required
area2 GeoDataFrame

A geodataframe containing polygons (tissue areas) that might intersect. with the buffer_area.

 required
buffer_dist int

The radius (in pixels) of the buffer.

 200
symmetric_buffer bool

Whether to use a symmetric buffering to both directions. This doubles the buffer size.

 False

Returns:

Type Description
GeoDataFrame

gpd.GeoDataFrame: A geodataframe containing the intersecting polygons including the buffer.

Examples:

>>> from histolytics.spatial_ops import get_interfaces
>>> from histolytics.data import cervix_tissue
>>> # load the tissue data
>>> tis = cervix_tissue()
>>>
>>> # get the stromal and CIN tissue
>>> stroma = tis[tis["class_name"] == "stroma"]
>>> cin_tissue = tis[tis["class_name"] == "cin"]
>>>
>>> # get the interface between cin lesion and stroma
>>> interface = get_interfaces(cin_tissue, stroma, buffer_dist=300)
>>> print(interface.head(3))
    class_name                                           geometry
0     stroma  POLYGON ((1588.71 4829.03, 1591.18 4828.83, 15...
1     stroma  POLYGON ((743.07 5587.48, 743.63 5589, 744.07 ...
2     stroma  POLYGON ((1151 7566, 1150 7567, 1148.2 7568.2,...
>>> # plot the tissue and the interface
>>> ax = tis.plot(column="class_name", figsize=(5, 5), aspect=1, alpha=0.5)
>>> interface.plot(ax=ax, color="blue", lw=1, alpha=0.3)
>>> ax.set_axis_off()

out

Source code in src/histolytics/spatial_ops/ops.py 
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def get_interfaces(
    area1: gpd.GeoDataFrame,
    area2: gpd.GeoDataFrame,
    buffer_dist: int = 200,
    symmetric_buffer: bool = False,
) -> gpd.GeoDataFrame:
    """Get the interfaces b/w the polygons defined in a `areas` and `buffer_area`.

    Note:
        Identifies the interface regions between polygons in `area1` and in `area2`
        by buffering the `area2` polygons and finding their intersections with `area1`.
        The width of the interface is controlled by the `buffer_dist` parameter.

    Parameters:
        area1 (gpd.GeoDataFrame):
            The area or region of interest that is buffered on top of polygons in area2.
        area2 (gpd.GeoDataFrame):
            A geodataframe containing polygons (tissue areas) that might intersect.
            with the `buffer_area`.
        buffer_dist (int):
            The radius (in pixels) of the buffer.
        symmetric_buffer (bool):
            Whether to use a symmetric buffering to both directions. This doubles the
            buffer size.

    Returns:
        gpd.GeoDataFrame:
            A geodataframe containing the intersecting polygons including the buffer.

    Examples:
        >>> from histolytics.spatial_ops import get_interfaces
        >>> from histolytics.data import cervix_tissue
        >>> # load the tissue data
        >>> tis = cervix_tissue()
        >>>
        >>> # get the stromal and CIN tissue
        >>> stroma = tis[tis["class_name"] == "stroma"]
        >>> cin_tissue = tis[tis["class_name"] == "cin"]
        >>>
        >>> # get the interface between cin lesion and stroma
        >>> interface = get_interfaces(cin_tissue, stroma, buffer_dist=300)
        >>> print(interface.head(3))
            class_name                                           geometry
        0     stroma  POLYGON ((1588.71 4829.03, 1591.18 4828.83, 15...
        1     stroma  POLYGON ((743.07 5587.48, 743.63 5589, 744.07 ...
        2     stroma  POLYGON ((1151 7566, 1150 7567, 1148.2 7568.2,...
        >>> # plot the tissue and the interface
        >>> ax = tis.plot(column="class_name", figsize=(5, 5), aspect=1, alpha=0.5)
        >>> interface.plot(ax=ax, color="blue", lw=1, alpha=0.3)
        >>> ax.set_axis_off()
    ![out](../../img/interfaces.png)
    """
    area1 = set_crs(area1)
    area2 = set_crs(area2)

    buffer_zone = gpd.GeoDataFrame(
        {"geometry": list(area1.buffer(buffer_dist))},
        crs=area1.crs,
    )
    inter = area2.overlay(buffer_zone, how="intersection")

    if symmetric_buffer:
        buffer_zone2 = gpd.GeoDataFrame(
            {"geometry": list(area2.buffer(buffer_dist))},
            crs=area2.crs,
        )
        inter = buffer_zone.overlay(buffer_zone2, how="intersection")

    # if the intersecting area is covered totally by any polygon in the `areas` gdf
    # take the difference of the intresecting area and the orig roi to discard
    # the roi from the interface 'sheet'
    if not inter.empty:
        if area2.covers(inter.geometry.loc[0]).any():  # len(inter) == 1
            inter = inter.overlay(area1, how="difference", keep_geom_type=True)

    return inter.dissolve().explode().reset_index(drop=True)