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gdf_to_file

cellseg_gsontools.gdf_to_file(gdf, out_fn, format='.feather')

Write a geojson/feather/parquet file from a gdf.

This is wrapper around geopandas.GeoDataFrame I/O methods that adds some extra functionality.

Parameters:

Name Type Description Default
gdf GeoDataFrame

The input gdf.

 required
out_fn Union[str, Path]

The output filename.

 required
format str

The output format. One of ".feather", ".parquet", ".geojson".

 '.feather'

Raises:

Type Description
ValueError

If format is not one of ".feather", ".geojson", ".parquet".
ValueError

If the input gdf does not have a "class_name" column.

Examples:

Write a geojson file.

>>> from cellseg_gsontools import gdf_to_file
>>> gdf_to_file(gdf, "out.geojson")
Source code in cellseg_gsontools/merging/save_utils.py 
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def gdf_to_file(
    gdf: gpd.GeoDataFrame,
    out_fn: Union[str, Path],
    format: str = ".feather",
) -> None:
    """Write a geojson/feather/parquet file from a gdf.

    This is wrapper around `geopandas.GeoDataFrame` I/O methods
    that adds some extra functionality.

    Parameters:
        gdf (gpd.GeoDataFrame):
            The input gdf.
        out_fn (Union[str, Path]):
            The output filename.
        format (str):
            The output format. One of ".feather", ".parquet", ".geojson".

    Raises:
        ValueError: If `format` is not one of ".feather", ".geojson", ".parquet".
        ValueError: If the input gdf does not have a "class_name" column.

    Examples:
        Write a geojson file.
        >>> from cellseg_gsontools import gdf_to_file
        >>> gdf_to_file(gdf, "out.geojson")
    """
    out_fn = Path(out_fn)
    if format not in (".feather", ".parquet", ".geojson", None):
        raise ValueError(
            f"Invalid format. Got: {format}. Allowed: .feather, .parquet, .geojson"
        )

    if "class_name" not in gdf.columns:
        raise ValueError("The input gdf needs to have a 'class_name' column.")

    # add objectType col (QuPath)
    if "objectType" not in gdf.columns:
        gdf["objectType"] = "annotation"

    # add classification col (QuPath)
    if "classification" not in gdf.columns:
        gdf["classification"] = gdf_apply(
            gdf, _add_qupath_classification, axis=1, columns=["class_name"]
        )

    if format == ".feather":
        gdf.to_feather(out_fn.with_suffix(".feather"))
    elif format == ".parquet":
        gdf.to_parquet(out_fn.with_suffix(".parquet"))
    elif format == ".geojson":
        gdf.to_file(out_fn.with_suffix(".geojson"), driver="GeoJSON", index=False)