Q: geopandas spatial join extremely slow I am using the code below to find a country (and sometimes state) for millions of GPS points. The code currently takes about one second per point, which is incredibly slow. The shapefile is 6 MB.
I read that geopandas uses rtrees for spatial joins, making them incredibly efficient, but this does not seem to work here. What am I doing wrong? I was hoping for a thousand points per second or so.
The shapefile and csv can be downloaded here (5MB): https://www.dropbox.com/s/gdkxtpqupj0sidm/SpatialJoin.zip?dl=0
import pandas as pd
import geopandas as gpd
from geopandas import GeoDataFrame, read_file
from geopandas.tools import sjoin
from shapely.geometry import Point, mapping,shape
import time


#parameters
shapefile="K:/.../Shapefiles/Used/World.shp"
df=pd.read_csv("K:/.../output2.csv",index_col=None,nrows=20)# Limit to 20 rows for testing    

if __name__=="__main__":
    start=time.time()
    df['geometry'] = df.apply(lambda z: Point(z.Longitude, z.Latitude), axis=1)
    PointsGeodataframe = gpd.GeoDataFrame(df)
    PolygonsGeodataframe = gpd.GeoDataFrame.from_file(shapefile)
    PointsGeodataframe.crs = PolygonsGeodataframe.crs
    print time.time()-start
    merged=sjoin(PointsGeodataframe, PolygonsGeodataframe, how='left')
    print time.time()-start
    merged.to_csv("K:/01. Personal/04. Models/10. Location/output.csv",index=None)
    print time.time()-start


A: adding the argument predicate='within' in the sjoin function speeds up the point-in-polygon operation dramatically.
Default value is predicate='intersects', which I guess would also lead to correct result, but is 100 to 1000 times slower.

A: What's likely going on here is that only the dataframe on the right is fed into the rtree index:
https://github.com/geopandas/geopandas/blob/master/geopandas/tools/sjoin.py#L48-L55
Which for an predicate="intersects" run would mean the Polygon was fed into the index, so for every point, the corresponding polygon is found through the rtree index.
But for predicate="within", the geodataframes are flipped since the operation is actually the inverse of contains:
https://github.com/geopandas/geopandas/blob/master/geopandas/tools/sjoin.py#L41-L43
So what happened when you switched the predicate from predicate="intersects" to predicate="within" is that for every polygon, the corresponding points are found through the rtree index, which in your case sped up the query.

A: The question asks how to take advantage of r-tree in geopandas spatial joins, and another responder correctly points out that you should use 'within' instead of 'intersects'. However, you can also take advantage of an r-tree spatial index in geopandas while using intersects/intersection, as demonstrated in this geopandas r-tree tutorial:
spatial_index = gdf.sindex
possible_matches_index = list(spatial_index.intersection(polygon.bounds))
possible_matches = gdf.iloc[possible_matches_index]
precise_matches = possible_matches[possible_matches.intersects(polygon)]


A: Related to the issue in geopandas discussed in this answer and seen here in the latest release:
If you have two geodataframes and want to perform an intersects operation and you know which spatial index should be queried, you can join from small to large and use how="right" to force this index to be used:
small_gdf.sjoin(large_gdf, predicate="intersects", how="right")

