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June 2011

98 participants
102 discussions

efficient computation of point cloud nearest neighbors
by Christian Jauvin June 1, 2011

June 1, 2011

Hi, I need to compute the k nearest neighbors of every point in a point cloud of at least a million points. I've been looking at the documentation for the scipy.spatial.KDTree and cKDTree classes, but it's not clear to me how I should use their query() method (and possibly their distance_upper_bound parameter) to optimize the computation. I've also been looking at the ANN and FLANN C++ libraries, but in both cases I've had trouble compiling/installing their Python bindings on my Ubuntu system. I'd appreciate some advice as to what would be the ideal strategy to solve this problem (either with Scipy or some other package that I wouldn't know about). Thanks in advance, Christian

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f2py on Windows with MSVC9
by Klonuo Umom June 1, 2011

June 1, 2011

I tried to make use of fortran code, and made trivial fortran code example. It runs fine with ifort compiler, FYI Then I declare CF2PY in and outs and hoping to see it work ===================================================================== f2py -c -m dummy dummy.f --------------------------------------------------------------------- which unfortunatelly throws error: ===================================================================== dummymodule.c(77) : error C2010: '.' : unexpected in macro formal parameter list --------------------------------------------------------------------- dummymodule.c(77) is this line: ===================================================================== #define size(var, dim...) f2py_size((PyArrayObject *)(capi_ ## var ## _tmp), ##dim, -1) --------------------------------------------------------------------- Any ideas what's wrong and if it's possible to do this under: Windows XP SP3 32 bit MSVC 2008 Intel Fortran Compiler 11.1 Python 2.6.6 NumPy 1.6 Thanks in advance Here is full log: running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "dummy" sources f2py options: [] f2py:> c:\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.c creating c:\temp\tmp\tmpgkb57o creating c:\temp\tmp\tmpgkb57o\src.win32-2.6 Reading fortran codes... Reading file 'dummy.f' (format:fix,strict) crackline: groupcounter=3 groupname={0: '', 1: 'module', 2: 'interface', 3: 'subroutine'} crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. crackline: groupcounter=2 groupname={0: '', 1: 'module', 2: 'interface', 3: 'subroutine'} crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. crackline: groupcounter=1 groupname={0: '', 1: 'module', 2: 'interface', 3: 'subroutine'} crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. Post-processing... Block: dummy Block: fhist Post-processing (stage 2)... Building modules... Building module "dummy"... Constructing wrapper function "fhist"... fhist(wavdata,[l]) Wrote C/API module "dummy" to file "c:\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.c" adding 'c:\temp\tmp\tmpgkb57o\src.win32-2.6\fortranobject.c' to sources. adding 'c:\temp\tmp\tmpgkb57o\src.win32-2.6' to include_dirs. copying C:\Python26\lib\site-packages\numpy\f2py\src\fortranobject.c -> c:\temp\tmp\tmpgkb57o\src.win32-2.6 copying C:\Python26\lib\site-packages\numpy\f2py\src\fortranobject.h -> c:\temp\tmp\tmpgkb57o\src.win32-2.6 build_src: building npy-pkg config files running build_ext No module named msvccompiler in numpy.distutils; trying from distutils customize MSVCCompiler customize MSVCCompiler using build_ext customize GnuFCompiler Could not locate executable g77 Could not locate executable f77 customize IntelVisualFCompiler Found executable C:\Program Files\Intel\Compiler\11.1\067\Bin\ia32\ifort.exe Found executable C:\Program Files\Intel\Compiler\11.1\067\Bin\ia32\ifort.exe customize IntelVisualFCompiler customize IntelVisualFCompiler using build_ext building 'dummy' extension compiling C sources creating c:\temp\tmp\tmpgkb57o\Release creating c:\temp\tmp\tmpgkb57o\Release\temp creating c:\temp\tmp\tmpgkb57o\Release\temp\tmp creating c:\temp\tmp\tmpgkb57o\Release\temp\tmp\tmpgkb57o creating c:\temp\tmp\tmpgkb57o\Release\temp\tmp\tmpgkb57o\src.win32-2.6 c:\Program Files\Microsoft Visual Studio 9.0\VC\BIN\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -Ic:\temp\tmp\tmpgkb57o\src.win32-2.6-IC:\Python26\lib\site-packages\numpy\core\include -IC:\Python26\include -IC:\Python26\PC /Tcc:\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.c /Foc:\temp\tmp\tmpgkb57o\Release\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.obj Found executable c:\Program Files\Microsoft Visual Studio 9.0\VC\BIN\cl.exe dummymodule.c c:\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.c(77) : error C2010: '.' : unexpected in macro formal parameter list error: Command "c:\Program Files\Microsoft Visual Studio 9.0\VC\BIN\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -Ic:\temp\tmp\tmpgkb57o\src.win32-2.6 -IC:\Python26\lib\site-packages\numpy\core\include -IC:\Python26\include -IC:\Python26\PC /Tcc:\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.c /Foc:\temp\tmp\tmpgkb57o\Release\temp\tmp\tmpgkb57o\src.win32-2.6\dummymodule.obj" failed with exit status 2

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