Fast kd-tree implementation with OpenMP-enabled queries

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  • License: GNU Lesser General Public License v3 (LGPLv3)
  • Author: Esben S. Nielsen
  • Requires: Python >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*
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pykdtree

Objective

pykdtree is a kd-tree implementation for fast nearest neighbour search in Python. The aim is to be the fastest implementation around for common use cases (low dimensions and low number of neighbours) for both tree construction and queries.

The implementation is based on scipy.spatial.cKDTree and libANN by combining the best features from both and focus on implementation efficiency.

The interface is similar to that of scipy.spatial.cKDTree except only Euclidean distance measure is supported.

Queries are optionally multithreaded using OpenMP.

Installation

By default pykdtree is built with OpenMP enabled queries using libgomp except on OSX systems using the clang compiler (conda environments use a separate compiler).

$ cd <pykdtree_dir>
$ python setup.py install

If it fails with undefined compiler flags or you want to use another OpenMP implementation please modify setup.py at the indicated point to match your system.

Building without OpenMP support is controlled by the USE_OMP environment variable

$ cd <pykdtree_dir>
$ export USE_OMP=0
$ python setup.py install

Note evironment variables are by default not exported when using sudo so in this case do

$ USE_OMP=0 sudo -E python setup.py install

Pykdtree can also be installed with conda via the conda-forge channel:

$ conda install -c conda-forge pykdtree

Usage

The usage of pykdtree is similar to scipy.spatial.cKDTree so for now refer to its documentation

>>> from pykdtree.kdtree import KDTree
>>> kd_tree = KDTree(data_pts)
>>> dist, idx = kd_tree.query(query_pts, k=8)

The number of threads to be used in OpenMP enabled queries can be controlled with the standard OpenMP environment variable OMP_NUM_THREADS.

The leafsize argument (number of data points per leaf) for the tree creation can be used to control the memory overhead of the kd-tree. pykdtree uses a default leafsize=16. Increasing leafsize will reduce the memory overhead and construction time but increase query time.

pykdtree accepts data in double precision (numpy.float64) or single precision (numpy.float32) floating point. If data of another type is used an internal copy in double precision is made resulting in a memory overhead. If the kd-tree is constructed on single precision data the query points must be single precision as well.

Benchmarks

Comparison with scipy.spatial.cKDTree and libANN. This benchmark is on geospatial 3D data with 10053632 data points and 4276224 query points. The results are indexed relative to the construction time of scipy.spatial.cKDTree. A leafsize of 10 (scipy.spatial.cKDTree default) is used.

Note: libANN is not thread safe. In this benchmark libANN is compiled with “-O3 -funroll-loops -ffast-math -fprefetch-loop-arrays” in order to achieve optimum performance.

Operation

scipy.spatial.cKDTree

libANN

pykdtree

pykdtree 4 threads

Construction

100

304

96

96

query 1 neighbour

1267

294

223

70

Total 1 neighbour

1367

598

319

166

query 8 neighbours

2193

625

449

143

Total 8 neighbours

2293

929

545

293

Looking at the combined construction and query this gives the following performance improvement relative to scipy.spatial.cKDTree

Neighbours

libANN

pykdtree

pykdtree 4 threads

1

129%

329%

723%

8

147%

320%

682%

Note: mileage will vary with the dataset at hand and computer architecture.

Test

Run the unit tests using nosetest

$ cd <pykdtree_dir>
$ python setup.py nosetests

Installing on AppVeyor

Pykdtree requires the “stdint.h” header file which is not available on certain versions of Windows or certain Windows compilers including those on the continuous integration platform AppVeyor. To get around this the header file(s) can be downloaded and placed in the correct “include” directory. This can be done by adding the anaconda/missing-headers.ps1 script to your repository and running it the install step of appveyor.yml:

# install missing headers that aren’t included with MSVC 2008 # https://github.com/omnia-md/conda-recipes/pull/524 - “powershell ./appveyor/missing-headers.ps1”

In addition to this, AppVeyor does not support OpenMP so this feature must be turned off by adding the following to appveyor.yml in the environment section:

environment:
global:

# Don’t build with openmp because it isn’t supported in appveyor’s compilers USE_OMP: “0”

Changelog

v1.3.3 : Add compatibility to python 3.9

v1.3.2 : Change OSX installation to not use OpenMP without conda interpreter

v1.3.1 : Fix masking in the “query” method introduced in 1.3.0

v1.3.0 : Keyword argument “mask” added to “query” method. OpenMP compilation now works for MS Visual Studio compiler

v1.2.2 : Build process fixes

v1.2.1 : Fixed OpenMP thread safety issue introduced in v1.2.0

v1.2.0 : 64 and 32 bit MSVC Windows support added

v1.1.1 : Same as v1.1 release due to incorrect pypi release

v1.1 : Build process improvements. Add data attribute to kdtree class for scipy interface compatibility

v1.0 : Switched license from GPLv3 to LGPLv3

v0.3 : Avoid zipping of installed egg

v0.2 : Reduced memory footprint. Can now handle single precision data internally avoiding copy conversion to double precision. Default leafsize changed from 10 to 16 as this reduces the memory footprint and makes it a cache line multiplum (negligible if any query performance observed in benchmarks). Reduced memory allocation for leaf nodes. Applied patch for building on OS X.

v0.1 : Initial version.

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  • Author: Esben S. Nielsen
  • Requires: Python >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*
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