This tutorial demonstrates how to take advantage of Rtree for querying data that have a spatial component that can be modeled as bounding boxes.

Creating an index

The following section describes the basic instantiation and usage of Rtree.


After installing Rtree, you should be able to open up a Python prompt and issue the following:

>>> from rtree import index

rtree is organized as a Python package with a couple of modules and two major classes - rtree.index.Index and rtree.index.Property. Users manipulate these classes to interact with the index.

Construct an instance

After importing the index module, construct an index with the default construction:

>>> idx = index.Index()


While the default construction is useful in many cases, if you want to manipulate how the index is constructed you will need pass in a rtree.index.Property instance when creating the index.

Create a bounding box

After instantiating the index, create a bounding box that we can insert into the index:

>>> left, bottom, right, top = (0.0, 0.0, 1.0, 1.0)


The coordinate ordering for all functions are sensitive the the index’s interleaved data member. If interleaved is False, the coordinates must be in the form [xmin, xmax, ymin, ymax, …, …, kmin, kmax]. If interleaved is True, the coordinates must be in the form [xmin, ymin, …, kmin, xmax, ymax, …, kmax].

Insert records into the index

Insert an entry into the index:

>>> idx.insert(0, (left, bottom, right, top))


Entries that are inserted into the index are not unique in either the sense of the id or of the bounding box that is inserted with index entries. If you need to maintain uniqueness, you need to manage that before inserting entries into the Rtree.


Inserting a point, i.e. where left == right && top == bottom, will essentially insert a single point entry into the index instead of copying extra coordinates and inserting them. There is no shortcut to explicitly insert a single point, however.

Query the index

There are three primary methods for querying the index. rtree.index.Index.intersection() will return you index entries that cross or are contained within the given query window. rtree.index.Index.intersection()


Given a query window, return ids that are contained within the window:

>>> list(idx.intersection((1.0, 1.0, 2.0, 2.0)))

Given a query window that is beyond the bounds of data we have in the index:

>>> list(idx.intersection((1.0000001, 1.0000001, 2.0, 2.0)))

Nearest Neighbors

The following finds the 1 nearest item to the given bounds. If multiple items are of equal distance to the bounds, both are returned:

>>> idx.insert(1, (left, bottom, right, top))
>>> list(idx.nearest((1.0000001, 1.0000001, 2.0, 2.0), 1))
[0, 1]

Using Rtree as a cheapo spatial database

Rtree also supports inserting any object you can pickle into the index (called a clustered index in libspatialindex parlance). The following inserts the picklable object 42 into the index with the given id:

>>> idx.insert(id=id, coordinates=(left, bottom, right, top), obj=42)

You can then return a list of objects by giving the objects=True flag to intersection:

>>> [n.object for n in idx.intersection((left, bottom, right, top), objects=True)]
[None, None, 42]


libspatialindex’s clustered indexes were not designed to be a database. You get none of the data integrity protections that a database would purport to offer, but this behavior of Rtree can be useful nonetheless. Consider yourself warned. Now go do cool things with it.

Serializing your index to a file

One of Rtree’s most useful properties is the ability to serialize Rtree indexes to disk. These include the clustered indexes described here:

>>> file_idx = index.Rtree('rtree')
>>> file_idx.insert(1, (left, bottom, right, top))
>>> file_idx.insert(2, (left - 1.0, bottom - 1.0, right + 1.0, top + 1.0))
>>> [n for n in file_idx.intersection((left, bottom, right, top))]
[1, 2]


By default, if an index file with the given name rtree in the example above already exists on the file system, it will be opened in append mode and not be re-created. You can control this behavior with the rtree.index.Property.overwrite property of the index property that can be given to the rtree.index.Index constructor.

See also

Performance describes some parameters you can tune to make file-based indexes run a bit faster. The choices you make for the parameters is entirely dependent on your usage.

Modifying file names

Rtree uses the extensions dat and idx by default for the two index files that are created when serializing index data to disk. These file extensions are controllable using the rtree.index.Property.dat_extension and rtree.index.Property.idx_extension index properties.

>>> p = rtree.index.Property()
>>> p.dat_extension = 'data'
>>> p.idx_extension = 'index'
>>> file_idx = index.Index('rtree', properties = p)

3D indexes

As of Rtree version 0.5.0, you can create 3D (actually kD) indexes. The following is a 3D index that is to be stored on disk. Persisted indexes are stored on disk using two files – an index file (.idx) and a data (.dat) file. You can modify the extensions these files use by altering the properties of the index at instantiation time. The following creates a 3D index that is stored on disk as the files 3d_index.data and 3d_index.index:

>>> from rtree import index
>>> p = index.Property()
>>> p.dimension = 3
>>> p.dat_extension = 'data'
>>> p.idx_extension = 'index'
>>> idx3d = index.Index('3d_index',properties=p)
>>> idx3d.insert(1, (0, 60, 23.0, 0, 60, 42.0))
>>> idx3d.intersection( (-1, 62, 22, -1, 62, 43))

ZODB and Custom Storages

https://mail.zope.org/pipermail/zodb-dev/2010-June/013491.html contains a custom storage backend for ZODB and you can find example python code here. Note that the code was written in 2011, hasn’t been updated and was only an alpha version.