I'm having trouble understanding the use of spatial indexes with RTree.

Example: I have 300 buffered points, and I need to know each buffer's intersection area with a polygon shapefile. The polygon shapefile has >20,000 polygons. It was suggested I use spatial indices to speed up the process.

SO... If I create a spatial index for my polygon shapefile, will it be "attached" to the file in some way, or will the index stand alone? That is, after creating it can I just run my intersection function on the polygon file and get faster results? Will intersection "see" that there are spatial indices and know what to do? Or, do I need to run it on the index, then relate those results back to my original polygon file via FIDs or some such?

The RTree documentation is not helping me very much (probably because I'm just learning programming). They show how to create an index by reading in manually created points, and then querying it against other manually created points, which returns ids that are contained within the window. Makes sense. But, they don't explain how that would relate back to some original file that the index would have come from.

I'm thinking it must go something like this:

  1. Pull bboxes for each polygon feature from my polygon shapefile and place them in a spatial index, giving them an id that is the same as their id in the shapefile.
  2. Query that index to get the ids that intersect.
  3. Then re-run my intersection on only the features in my original shapefile that were identified by querying my index (not sure how I'd do this last part).

Do I have the right idea? Am I missing anything?

Right now I'm trying to get this code to work on one point shapefile that contains only one point feature, and one polygon shapefile that contains >20,000 polygon features.

I'm importing the shapefiles using Fiona, adding the spatial index using RTree, and trying to do the intersection using Shapely.

My test code looks like this:

#point shapefile representing location of desired focal statistic
traps = fiona.open('single_pt_speed_test.shp', 'r') 

#polygon shapefile representing land cover of interest 
gl = MultiPolygon([shape(pol['geometry']) for pol in fiona.open('class3_aa.shp', 'r')]) 

#search area
areaKM2 = 20

#create empty spatial index
idx = index.Index()

#set initial search radius for buffer
areaM2 = areaKM2 * 1000000
r = (math.sqrt(areaM2/math.pi))

#create spatial index from gl
for i, shape in enumerate(gl):
    idx.insert(i, shape.bounds)

#query index for ids that intersect with buffer (will eventually have multiple points)
for point in traps:
        pt_buffer = shape(point['geometry']).buffer(r)
        intersect_ids = pt_buffer.intersection(idx)

But I keep getting TypeError: 'Polygon' object is not callable

  • 1
    A spatial index is integral and transparent to the dataset (contained, not a single entity from the user perspective) The software that performs the intersections is aware of and will use spatial indices to create a short list to perform the real intersection with by quickly informing the software which features should be considered for closer inspection and which are clearly nowhere near intersecting. How you create one depends on your software and your data type... please provide more information on these points for more specific help. For a shape file it's the .shx file. Nov 5, 2014 at 1:07
  • 4
    .shx is not a spatial index. It's just the variable width record dynamic access offset file. .sbn/.sbx is the ArcGIS shapefile spatial index pair, though the specification for those was not released.
    – Vince
    Nov 5, 2014 at 2:31
  • 1
    Also .qix is the MapServer/GDAL/OGR/SpatiaLite quadtree index
    – Mike T
    Nov 5, 2014 at 4:48
  • Your idea is percfectly right for Spatialite which does not have a real spatial index. Most other formats, if they support spatial indexes at all, do it transparently.
    – user30184
    Nov 5, 2014 at 6:59
  • 2
    You keep getting TypeError: 'Polygon' object is not callable with your update example because you overwrite the shape function you imported from shapely with a Polygon object you create with this line: for i, shape in enumerate(gl):
    – user2856
    Oct 25, 2016 at 4:04

3 Answers 3


That's the gist of it. The R-tree allows you to make a very fast first pass and gives you a set of results that will have "false positives" (bounding boxes may intersect when the geometries precisely do not). Then you go over the set of candidates (fetching them from the shapefile by their index) and do a mathematically precise intersection test using, e.g., Shapely. This is the very same strategy that's employed in spatial databases like PostGIS.

  • 2
    Nice pun (GiST)! GiST is normally described as a B-Tree variant but Postgresql has an GiST implementation of R-Tree. Although wiki is not necessarily the best reference to cite it does have a nice diagram to explain bounding box searches. Nov 5, 2014 at 8:06
  • It can be worth learning a manual way for using the R-tree index as in your steps 2 and 3. This blog about OGC GeoPackage which does also support R-tree as separate database tables show some SQL and screen captures openjump.blogspot.fi/2014/02/….
    – user30184
    Nov 5, 2014 at 8:18

You've almost got it, but you've made a small error. You need to use the intersection method on the spatial index, rather than passing the index to the intersection method on the buffered point. Once you've found a list of features where the bounding boxes overlap, then you need to check if your buffered point actually intersects the geometries.

import fiona
from shapely.geometry import mapping
import rtree
import math

areaM2 = areaKM2 * 1000000
r = (math.sqrt(areaM2/math.pi))

# open both layers
with fiona.open('single_pt_speed_test.shp', 'r') as layer_pnt:
    with fiona.open('class3_aa.shp', 'r') as layer_land:

        # create an empty spatial index object
        index = rtree.index.Index()

        # populate the spatial index
        for fid, feature in layer_land.items():
            geometry = shape(feature['geometry'])
            idx.insert(fid, geometry.bounds)

        for feature in layer_pnt:
            # buffer the point
            geometry = shape(feature['geometry'])
            geometry_buffered = geometry.buffer(r)

            # get list of fids where bounding boxes intersect
            fids = [int(i) for i in index.intersection(geometry_buffered.bounds)]

            # access the features that those fids reference
            for fid in fids:
                feature_land = layer_land[fid]
                geometry_land = shape(feature_land['geometry'])

                # check the geometries intersect, not just their bboxs
                if geometry.intersects(geometry_land):
                    print('Found an intersection!')  # do something useful here

If you're interested in finding points that are within a minimum distance to your land class, you could use the distance method instead (swap out the appropriate section from previous).

for feature in layer_pnt:
    geometry = shape(feature['geometry'])

    # expand bounds by r in all directions
    bounds = [a+b*r for a,b in zip(geometry.bounds, [-1, -1, 1, 1])]

    # get list of fids where bounding boxes intersect
    fids = [int(i) for i in index.intersection(geometry_buffered.bounds)]

    for fid in fids:
        feature_land = layer_land[fid]
        geometry_land = shape(feature_land['geometry'])

        # check the geometries are within r metres
        if geometry.distance(geometry_land) <= r:
            print('Found a match!')

If it's taking a long time to build your spatial index and you're going to do this more than a few times, you should look into serialising the index to a file. The documentation describes how to do this: http://toblerity.org/rtree/tutorial.html#serializing-your-index-to-a-file

You could also look at bulk-loading the bounding boxes into the rtree using a generator, like this:

def gen(collection):
    for fid, feature in collection.items():
        geometry = shape(feature['geometry'])
        yield((fid, geometry.bounds, None))
index = rtree.index.Index(gen(layer_land))

Yes that is the idea. Here is an excerpt from this tutorial on using an r-tree spatial index in Python, using shapely, Fiona, and geopandas:

An r-tree represents individual objects and their bounding boxes (the “r” is for “rectangle”) as the lowest level of the spatial index. It then aggregates nearby objects and represents them with their aggregate bounding box in the next higher level of the index. At yet higher levels, the r-tree aggregates bounding boxes and represents them by their bounding box, iteratively, until everything is nested into one top-level bounding box. To search, the r-tree takes a query box and, starting at the top level, sees which (if any) bounding boxes intersect it. It then expands each intersecting bounding box and sees which of the child bounding boxes inside it intersect the query box. This proceeds recursively until all intersecting boxes are searched down to the lowest level, and returns the matching objects from the lowest level.

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