Spatial Join between pyspark dataframe and polygons (geopandas)

Question

Problem :

I would like to make a spatial join between:

A big Spark Dataframe (500M rows) with points (eg. points on a road)
a small geojson (20000 shapes) with polygons (eg. regions boundaries).

Here is what I have so far, which I find to be slow (lot of scheduler delay, maybe due to the fact that communes is not broadcasted) :

@pandas_udf(schema_out, PandasUDFType.GROUPED_MAP)
def join_communes(traces):   
    geometry = gpd.points_from_xy(traces['longitude'], traces['latitude'])
    gdf_traces = gpd.GeoDataFrame(traces, geometry=geometry, crs = communes.crs)
    joined_df = gpd.sjoin(gdf_traces, communes, how='left', op='within')
    return joined_df[columns]

The pandas_udf takes in a bit of the points dataframe (traces) as a pandas dataframe, turns it into a GeoDataFrame with geopandas, and operates the spatial join with the polygons GeoDataFrame (therefore benefitting from the Rtree join of Geopandas)

Questions:

Is there a way to make it faster ? I understand that my communes geodataframe is in the Spark Driver’s memory and that each worker has to download it for each call to the udf, is this correct ?

However I do not know how I could make this GeoDataFrame available directly to the workers (as in a broadcast join)

Any ideas ?

Asked By: Luis Blanche

||

Source

Answer 1

A year after , here is what I ended up doing as @ndricca suggested, the trick is to broadcast the communes, but you can’t broadcast a GeoDataFrame directy so you have to load it as a Spark DataFrame, then convert it to JSON before broadcasting it. Then you rebuild the GeoDataFrame inside the UDF using shapely.wkt (Well Known Text : a way to encode geometric objects as text)

Another trick is to use a salt in the groupby to ensure equal repartition of the data across the cluster

import geopandas as gpd
from shapely import wkt
from pyspark.sql.functions import broadcast
communes = gpd.load_file('...communes.geojson')
# Use a previously created spark session
traces= spark_session.read_csv('trajectoires.csv')
communes_spark = spark.createDataFrame(communes[['insee_comm', 'wkt']])
communes_json = provinces_spark.toJSON().collect()
communes_bc = spark.sparkContext.broadcast(communes_json)

@pandas_udf(schema_out, PandasUDFType.GROUPED_MAP)
def join_communes_bc(traces):
    communes = pd.DataFrame.from_records([json.loads(c) for c in communes_bc.value])
    polygons = [wkt.loads(w) for w in communes['wkt']]
    gdf_communes = gpd.GeoDataFrame(communes, geometry=polygons, crs=crs )
    geometry = gpd.points_from_xy(traces['longitude'], traces['latitude'])
    gdf_traces = gpd.GeoDataFrame(traces , geometry=geometry, crs=crs)
    joined_df = gpd.sjoin(gdf_traces, gdf_communes, how='left', op='within')
    return joined_df[columns]
    

traces = traces.groupby(salt).apply(join_communes_bc)

Answered By: Luis Blanche

Answer 2

Can we use shapely geometry polygon/linestring in pyspark pandas-api??

Answered By: user19835589

Spatial Join between pyspark dataframe and polygons (geopandas)

Question:

Answers: