I'm very new to using QGIS, what I have is a points shapefile and a polygon shapefile. I would like to select all the polygons which have at least one point in them. The problem I'm running into is how long this takes. I have 1 million points and about 320,000 polygons, so using spatial query takes far too long. I've heard that I'd need to write a python script with spatial indexing to get a feasibly quick result, but I have no idea how to approach this.

I don't mind if it's a little inaccurate, if it runs significantly quicker.

What I've tried to cobble together from other stack overflow questions is:

pointProvider = self.pointLayer.dataProvider()
all_point = pointProvider.getFeatures()
delta = 0.1

for point in all_point:

    searchRectangle = QgsRectangle(point.x() - delta, point.y()  - delta, point.x() + delta, point.y() + delta)

    candidateIDs = line_index.intesects(searchRectangle)

    for candidateID in candidateIDs:
        candFeature == rotateProvider.getFeatures(QgsFeatureRequest(candidateID)).next()
        if candFeature.geometry().contains(point):


This throws up a NameError: name 'self' is not defined

  • 1
    Welcome to GIS:SE @JoshuaKidd! Remove self, you don't really need this in a script. Also take a look at Using a QGIS spatial index to speed up your code which may be helpful :) – Joseph Jan 18 '17 at 11:42
  • Thank you! If what I've written works, what should I replace self with? I can see in the example you posted that he finds if features in a single vector layer touch another. I'm guessing if I try and adapt what he's written I'll have to find a way to see if a point from one layer overlaps a vector in another. – Joshua Kidd Jan 18 '17 at 12:01
  • If you have acces to GeoPandas Python module, it could be very straightforward to do that with 'sjoin' method and 'intersects' option (see my answer). – xunilk Jan 18 '17 at 12:10
  • @JoshuaKidd -No need to replace self, just remove it. In terms of the example link I posted, you could replace touches with intersects. – Joseph Jan 18 '17 at 12:20

EDIT I have taken a rollback according to the needs of @Joshua Kidd, which was looking for the fastest (and not the most correct) solution. The code posted in the following will select a polygon feature when its bounding box contains at least one point. Instead, the most correct solution (i.e. the selection of a polygon feature when its real geometry contains at least one point) is reported at this previous revision of my answer.

The fastest solution I could apply in PyQGIS would be this one:

##Points=vector point
##Polygons=vector polygon

from qgis.core import *
import processing

layer1 = processing.getObject(Points)
layer2 = processing.getObject(Polygons)

index = QgsSpatialIndex() # Spatial index
for ft in layer1.getFeatures():

selection = [] # This list stores the features which contains at least one point
for feat in layer2.getFeatures():
    inGeom = feat.geometry()
    idsList = index.intersects(inGeom.boundingBox())
    if idsList:

# Select all the polygon features which contains at least one point
layer2.setSelectedFeatures([k.id() for k in selection])

Starting from this sample layers:

enter image description here

and running the above code, I obtain this output:

enter image description here

  • I'm getting an error saying processing not defined. – Joshua Kidd Jan 18 '17 at 13:26
  • That's weird.. Try typing import processing at the top of the code. However, I need to edit it because at this moment it selects all the polygons for which the bounding box contains a point (it's a minor fix, I'll edit the answer as soon as possible, sorry) – mgri Jan 18 '17 at 13:31
  • I just added 'import processing' and it's running now :) – Joshua Kidd Jan 18 '17 at 13:33
  • WOW, that ran in 40 seconds as opposed to my previous best 16 min! – Joshua Kidd Jan 18 '17 at 13:37
  • Well! I edited the code, now it should work as expected! Please, let me know if it works for you! =) – mgri Jan 18 '17 at 13:37

If you have acces to GeoPandas Python module, it could be very straightforward to do that with 'sjoin' method and 'intersects' option. I tried out my approach with next situation:

enter image description here

The code was:

from geopandas import gpd 

points = gpd.GeoDataFrame.from_file('/home/zeito/pyqgis_data/random_points.shp')  
polys = gpd.GeoDataFrame.from_file('/home/zeito/pyqgis_data/polygon8.shp') 
polyWithPoints = gpd.sjoin(polys, points, op='intersects') 


After running the code at the Python Console of QGIS, I loaded resulting shapefile (polyWithPoints.shp) and it was as expected: all the polygons (blue color) which have at least one point in them:

enter image description here

  • Alright, I'll give this a try. I'm just installing geopandas now. My main problem isn't that I can't get it to select the features, it's that I'm looking for the quickest way to do it. Does this method use spatial indexing, or something similar? – Joshua Kidd Jan 18 '17 at 12:23
  • Yes, it does. So, you also need Rtree python module (in my case installed with easy_install) and libspatialindex library (from my Debian Linux repository). If you are Windows user see: gis.stackexchange.com/questions/120527/… – xunilk Jan 18 '17 at 12:27
  • hmmm, this geopandas install is more involved than I thought. I'm using spyder through anaconda – Joshua Kidd Jan 18 '17 at 12:39
  • I use GNU/Debian Linux where installation of these libraries are much easier. – xunilk Jan 18 '17 at 12:45
  • Ok, i got it working, and it ran for 16 minutes which is good. A problem though, is that it creates entries for each point in a poly. – Joshua Kidd Jan 18 '17 at 13:20

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