Package: pykdtree
pykdtreeObjectivepykdtree 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.InstallationPykdtree can be installed via pip:pipinstallpykdtreeOr, if in a conda-based environment, with conda from the conda-forge channel:condainstall-cconda-forgepykdtreeNote that by default these packages (the binary wheels on PyPI and the binary
package on conda-forge) are only built with OpenMP for linux platforms.
To attempt to build from source with OpenMP support do:exportUSE_OMP="probe"pipinstall--no-binarypykdtreepykdtreeThis may not work on some systems that don’t have OpenMP installed. See the below development
instructions for more guidance. Disabling OpenMP can be accomplished by settingUSE_OMPto"0"in the above commands.Development InstallationIf you wish to contribute to pykdtree then it is a good idea to install from source
so you can quickly see the effects of your changes.
By default pykdtree is built with OpenMP enabled queries on unix-like systems.
On linux this is done using libgomp. On OSX systems OpenMP is provided using the
clang compiler (conda environments use a separate compiler).$cd<pykdtree_dir>$pipinstall-e.This installs pykdtree in an “editable” mode where changes to the Python files
are automatically reflected when running a new python interpreter instance
(ex. running a python script that uses pykdtree). It does not automatically rebuild
or recompile the.makotemplates and.pyxCython code in pykdtree. Editing
these files requires running thepykdtree/render_template.pyscript and then
rerunning the pip command above to recompile the Cython files.If installation fails with undefined compiler flags or you want to use another OpenMP
implementation you may need to modify setup.py or specify additional pip command line
flags to match the library locations on your system.Building without OpenMP support is controlled by the USE_OMP environment variable$cd<pykdtree_dir>$exportUSE_OMP=0$pipinstall-e.Note evironment variables are by default not exported when using sudo so in this case do$USE_OMP=0sudo-Epipinstall-e.Control OpenMP usageTheUSE_OMPvariable can be set to one of a couple different options. If
set to"probe", the installation process (setup.py) will attempt to
determine what variant of OpenMP is available based on the compiler being used,
the platform being run on, and the Python environment being run with. It will
then use the flags specified by one of the otherUSE_OMPmodes. Note that
in the case of MacOS, it will also try to identify if OpenMP is available from
macports or homebrew and include the necessary include and library paths.If set to"gcc"or"gomp"then compiler and linking flags will be set
appropriately for “GNU OpenMP” (gomp) library. If set to"clang"or"omp"then the flags will be set to support the “omp” library. If set to"msvc"then flags will be set for the Microsoft Visual C++ compiler’s
OpenMP variant. For backwards compatibility the previous"1"has the same
behavior as"probe". As mentioned above"0"can be used to disable
any detection of OpenMP or attempt to compile with it.UsageThe 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.Theleafsizeargument (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 defaultleafsize=16.
Increasingleafsizewill 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.BenchmarksComparison 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 isnotthread safe. In this benchmark libANN is compiled with “-O3 -funroll-loops -ffast-math -fprefetch-loop-arrays” in order to achieve optimum performance.Operationscipy.spatial.cKDTreelibANNpykdtreepykdtree 4 threadsConstruction1003049696query 1 neighbour126729422370Total 1 neighbour1367598319166query 8 neighbours2193625449143Total 8 neighbours2293929545293Looking at the combined construction and query this gives the following performance improvement relative to scipy.spatial.cKDTreeNeighbourslibANNpykdtreepykdtree 4 threads1129%329%723%8147%320%682%Note: mileage will vary with the dataset at hand and computer architecture.TestRun the unit tests using pytest$cd<pykdtree_dir>$pytestInstalling on AppVeyorPykdtree 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 theanaconda/missing-headers.ps1script to your repository
and running it the install step ofappveyor.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 toappveyor.ymlin theenvironmentsection:environment:global:# Don’t build with openmp because it isn’t supported in appveyor’s compilers
USE_OMP: “0”