I posted this question on stackoverflow here, but it seems that gis.stackexchange is the more appropriate platform.

I am trying to merge two geodataframes in geopandas (want to see which polygon each point is in).

The following code gets me an error ("RTreeError: Coordinates must not have minimums more than maximums").

I cannot find any explanation as to what this means and how to solve it. Any ideas?

import geopandas as gpd
from shapely.geometry import Point, mapping,shape
from geopandas import GeoDataFrame, read_file
#from geopandas.tools import overlay
from geopandas.tools import sjoin

print('Reading points...')
points['geometry'] = points.apply(lambda z: Point(z.Latitude, z.Longitude), axis=1)
PointsGeodataframe = gpd.GeoDataFrame(points)
print PointsGeodataframe.head()
print('Reading polygons...')
PolygonsGeodataframe = gpd.GeoDataFrame.from_file(china_shapefile+".shp")
print PolygonsGeodataframe.head()
print('Merging GeoDataframes...')
merged=sjoin(PointsGeodataframe, PolygonsGeodataframe, how='left', op='intersects')

#merged = PointsGeodataframe.merge(PolygonsGeodataframe, left_on='iso_alpha2', right_on='ISO2', how='left')

Link to data for reproduction: Shapefile, GPS points

3 Answers 3


For the benefit of anyone else searching for this error message, one thing that can cause it is attempting to do a spatial join where the point coordinates contain nulls.

  • 2
    Thank you for this comment! Saved me a some debugging time.
    – n3utrino
    Commented Aug 7, 2018 at 20:59
  • 1
    That also saved me some debugging time.
    – MKJ
    Commented Jan 5, 2019 at 19:05
  • I came back here twice in as many weeks because of this. Shapely will allow Point(nan,nan) without complaints; make sure you check for / drop any such values and avoid this issue. Commented Jul 14, 2020 at 13:47
  • Hero saved me some debugging time.
    – JG_RS_GIS
    Commented Nov 6, 2020 at 14:03
  • Just adding to the list of comments saying that you saved me some debugging time
    – Ric S
    Commented Jan 18, 2021 at 16:08

There are many problems in your data (sample_map_data.csv) and in your script.

1) the sample_map_data.csv file contains 6 valid lines and 730 lines with ''

import pandas as pd  
points = pd.read_csv("sample_map_data.csv")
(735, 3)

Resulting in the error "RTreeError: Coordinates must not have minimums more than maximums"

The right result should be .

points = pd.read_csv("sample_map_data.csv",nrows= 5)
(5, 3)
Latitude   Longitude  Heat
0  23.124700  113.282776   100
1  22.618574  113.999634    80
2  23.694332  113.049316    70
3  23.809973  114.735718    90
4  21.815098  110.961914    80)

2) In Shapely, a Point is defined by Point(x,y) and not Point(y,x) so

from shapely.geometry import Point
points['geometry'] = points.apply(lambda z: Point(z.Longitude, z.Latitude), axis=1)
import geopandas as gpd
PointsGeodataframe = gpd.GeoDataFrame(points)
Latitude      Longitude    Heat         geometry
0  23.124700  113.282776   100  POINT (113.282776 23.1247)
1  22.618574  113.999634    80  POINT (113.999634 22.618574)
2  23.694332  113.049316    70  POINT (113.049316 23.694332)
3  23.809973  114.735718    90  POINT (114.735718 23.809973)
4  21.815098  110.961914    80  POINT (110.961914 21.815098)

3) For Points in Polygons, look at More Efficient Spatial join in Python without QGIS, ArcGIS, PostGIS, etc): no need of op='intersects'

PolygonsGeodataframe = gpd.GeoDataFrame.from_file("CHN_adm1.shp")
PointsGeodataframe.crs = PolygonsGeodataframe.crs #same crs for the two layers
from geopandas.tools import sjoin
pointInPolys = sjoin(PointsGeodataframe, PolygonsGeodataframe, how='left') 

and it works.


To check if there are Point(nan, nan):


To clean them up:

gdf = gdf[gdf.is_valid]

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