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It's necessary to write '\x00'==0 to get something that's true only with -std. */ int osf4_cc_array ['\x00' == 0 ? 1 : -1]; /* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters inside strings and character constants. */ #define FOO(x) 'x' int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); int argc; char **argv; int main () { return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; ; return 0; } _ACEOF for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_c89=$ac_arg fi rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c89" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c89" { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac if test "x$ac_cv_prog_cc_c89" != xno; then : fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu OPENMP_CFLAGS= # Check whether --enable-openmp was given. if test "${enable_openmp+set}" = set; then : enableval=$enable_openmp; fi if test "$enable_openmp" != no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5 $as_echo_n "checking for $CC option to support OpenMP... 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Compiler: ${CXX} ${CXXFLAGS} ${MPI_INC} ${MPI_LIBDIR} ${MPI_LIBS} Package features: OpenMP enabled: ${openmp_enabled} MPI enabled: ${mpi_enabled} CUDA enabled: ${cuda_enabled} Now type 'make []' where the optional is: all - build all binaries install - install everything --------------------------------------------------" somoclu-1.4.1/CHANGES0000644000175000001440000000370612462121043013420 0ustar wittekusersVersion 1.4.1: 2015-01-28 - Better support for ICC. - Faster code when compiling with GCC. - Building instructions and documentation improved. - Bug fixes: portability for R, using native R random number generator. Version 1.4: 2014-09-05 - Better Windows support. - Completed CUDA support for Python and R interfaces. - Faster compilation by removing unnecessary flags for nvcc and support for CUDA 6.5. - Bug fixes: R version no longer needs separate code. Version 1.3.1: 2014-04-10 - Better I/O separation for the Python, R, and MATLAB interfaces. - Initial Windows support through GCC on Windows. - Bug fixes: major MPI initialization bug fixed. Version 1.3: 2014-03-31 - Learning rate parameter included. - Linear and exponential cooling strategies added for radius and learning rate. - CLI interface made more user-friendly. - Default radius depends on both X and Y of the map. - Bug fixes: CUDA build without MPI, best matching unit passing without MPI, coordinate order in best matching unit file. - Python, R, and MATLAB interfaces added. Version 1.2: 2013-12-17 - Massive improvements in OpenMP parallelization. - MPI libraries are no longer mandatory. - Best matching units are saved. - Option for specifying an initial codebook for the map. - ESOM .lrn input format added. - Parsing of white-space characters corrected. - Long-named command line switches for specifying SOM dimensions. - Fine-grained control of which interim files to save across epochs - Option in Makefile for building shared library. Version 1.1.2: 2013-11-28 - Toroid maps were added. - Initial radius is exposed as a parameter via the command line interface. - Formats of codebook and U-matrix export are compatible with Databionic ESOM Tools for advanced visualisation. - Bug fixes: codebook update with a compact support was removed, NaN entry no longer appears in U-matrices. Version 1.0: 2013-05-14 - Initial release. somoclu-1.4.1/README.md0000644000175000001440000002557012462120712013711 0ustar wittekusersSomoclu === Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs, it is able to rely on MPI for distributing the workload in a cluster, and it can be accelerated by CUDA. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes. The topology of the grid of neurons is rectangular. Key features: * Fast execution by parallelization: OpenMP, MPI, and CUDA are supported. * Multi-platform: Linux, OS X, and Windows are supported. * Planar and toroid maps. * Both dense and sparse input data are supported. * Large maps of several hundred thousand neurons are feasible. * Integration with [Databionic ESOM Tools](http://databionic-esom.sourceforge.net/). * Python, R, and MATLAB interfaces for the dense CPU and GPU kernels. For more information, refer to the following paper: Peter Wittek (2013). Somoclu: An Efficient Distributed Library for Self-Organizing Maps. [arXiv:1305.1422](http://arxiv.org/abs/1305.1422). Usage === Basic Command Line Use --- Somoclu takes a plain text input file -- either dense or sparse data. Example files are included. $ [mpirun -np NPROC] somoclu [OPTIONs] INPUT_FILE OUTPUT_PREFIX Arguments: -c FILENAME Specify an initial codebook for the map. -e NUMBER Maximum number of epochs -k NUMBER Kernel type 0: Dense CPU 1: Dense GPU 2: Sparse CPU -m TYPE Map type: planar or toroid (default: planar) -t STRATEGY Radius cooling strategy: linear or exponential (default: linear) -r NUMBER Start radius (default: half of the map in direction min(x,y)) -R NUMBER End radius (default: 1) -T STRATEGY Learning rate cooling strategy: linear or exponential (default: linear) -l NUMBER Starting learning rate (default: 0.1) -L NUMBER Finishing learning rate (default: 0.01) -s NUMBER Save interim files (default: 0): 0: Do not save interim files 1: Save U-matrix only 2: Also save codebook and best matching -x, --columns NUMBER Number of columns in map (size of SOM in direction x) -y, --rows NUMBER Number of rows in map (size of SOM in direction y) Examples: $ somoclu data/rgbs.txt data/rgbs $ mpirun -np 4 somoclu -k 0 --rows 20 --columns 20 data/rgbs.txt data/rgbs Efficient Parallel Execution --- The CPU kernels use OpenMP to load multicore processors. On a single node, this is more efficient than launching tasks with MPI to match the number of cores. The MPI tasks replicated the codebook, which is especially inefficient for large maps. For instance, given a single node with eight cores, the following execution will use 1/8th of the memory, and will run 10-20% faster: $ somoclu -x 200 -y 200 data/rgbs.txt data/rgbs Or, equivalently: $ OMP_NUM_THREADS=8 somoclu -x 200 -y 200 data/rgbs.txt data/rgbs Avoid the following on a single node: $ OMP_NUM_THREADS=1 mpirun -np 8 somoclu -x 200 -y 200 data/rgbs.txt data/rgbs The same caveats apply for the sparse CPU kernel. Visualisation --- The primary purpose of generating a map is visualisation. Somoclu does not come with its own functions for visualisation, since there are numerous generic tools that are capable of plotting high-quality figures. The output formats of the U-matrix and the codebook are compatible with [Databionic ESOM Tools](http://databionic-esom.sourceforge.net/) for more advanced visualisation. Input File Formats === One sparse and two dense data formats are supported. All of them are plain text files. The entries can be separated by any white-space character. One row represents one data instance across all formats. Comment lines starting with a hash mark are ignored. The sparse format follows the [libsvm](http://www.csie.ntu.edu.tw/~cjlin/libsvm/) guidelines. The first feature is zero-indexed. For instance, the vector [ 1.2 0 0 3.4] is represented as the following line in the file: 0:1.2 3:3.4. The file is parsed twice: once to get the number of instances and features, and the second time to read the data in the individual threads. The basic dense format includes the coordinates of the data vectors, separated by a white-space. Just like the sparse format, this file is parsed twice to get the basic dimensions right. The .lrn file of [Databionic ESOM Tools](http://databionic-esom.sourceforge.net/) is also accepted and it is parsed only once. The format is described as follows: % n % m % s1 s2 .. sm % var_name1 var_name2 .. var_namem x11 x12 .. x1m x21 x22 .. x2m . . . . . . . . xn1 xn2 .. xnm Here n is the number of rows in the file, that is, the number of data instances. Parameter m defines the number of columns in the file. The next row defines the column mask: the value 1 for a column means the column should be used in the training. Note that the first column in this format is always a unique key, so this should have the value 9 in the column mask. The row with the variable names is ignore by Somoclu. The elements of the matrix follow -- from here, the file is identical to the basic dense format, with the addition of the first column as the unique key. If the input file is sparse, but a dense kernel is invoked, Somoclu will execute and results will be incorrect. Invoking a sparse kernel on a dense input file is likely to lead to a segmentation fault. Interfaces === Python, R, and MATLAB interfaces are available for the dense CPU kernel. MPI, CUDA, and the sparse kernel are not support through the interfaces. The connection to the C++ library is seamless, data structures are not duplicated. For respective examples, see the folders in src. The Python version is also available in PyPI. You can install it with $ sudo pip install somoclu The R version is available on CRAN. You can install it with install.packages("Rsomoclu") For using the MATLAB toolbox, define the location of the mex compiler in MEX_BIN. Then invoke makeMex.sh in the src/MATLAB folder. For more information on the respective interfaces, including building with GPU support, refer to the subfolders in `src` ([R](https://github.com/peterwittek/somoclu/tree/master/src/Rscript), [Python](https://github.com/peterwittek/somoclu/tree/master/src/Python), [MATLAB](https://github.com/peterwittek/somoclu/tree/master/src/MATLAB)). Compilation & Installation === These are the instructions for compiling the core library and the command line interface. The only dependency is a C++ compiler chain -- GCC, ICC, and VC were tested. Multicore execution is supported through OpenMP -- the compiler must support this. Distributed systems are supported through MPI. The package was tested with OpenMPI. It should also work with other MPI flavours. CUDA support is optional. Linux or Mac OS X --- From GIT repository first run $ ./autogen.sh Then follow the standard POSIX procedure: $ ./configure [options] $ make $ make install Options for configure --prefix=PATH Set directory prefix for installation By default Somoclu is installed into /usr/local. If you prefer a different location, use this option to select an installation directory. --without-mpi Disregard any MPI installation found. --with-mpi=MPIROOT Use MPI root directory. --with-mpi-compilers=DIR or --with-mpi-compilers=yes use MPI compiler (mpicxx) found in directory DIR, or in your PATH if =yes --with-mpi-libs="LIBS" MPI libraries [default "-lmpi"] --with-mpi-incdir=DIR MPI include directory [default MPIROOT/include] --with-mpi-libdir=DIR MPI library directory [default MPIROOT/lib] The above flags allow the identification of the correct MPI library the user wishes to use. The flags are especially useful if MPI is installed in a non-standard location, or when multiple MPI libraries are available. --with-cuda=/path/to/cuda Set path for CUDA Somoclu looks for CUDA in /usr/local/cuda. If your installation is not there, then specify the path with this parameter. If you do not want CUDA enabled, set the parameter to ```--without-cuda```. Windows --- Use the `somoclu.sln` under `src/Windows/somoclu` as an example Visual Studio 2013 solution. Modify the CUDA version or VC compiler version according to your needs. The default solution enables all of OpenMP, MPI, and CUDA. The default MPI installation path is `C:\Program Files\Microsoft MPI`, modify the settings if yours is in a different path. The configuration default CUDA version is 6.5. Disable MPI by removing `HAVE_MPI` macro in the project properties (`Properties -> Configuration Properties -> C/C++ -> Preprocessor`). Disable CUDA by removing `CUDA` macro in the solution properties. The usage is identical to the Linux version through command line (see the relevant section). When using the Somoclu Python interface on Windows, if you encounter errors like: ImportError: DLL load failed: The specified module could not be found You may need to find the right version (32/64bit) of `vcomp90.dll, msvcp90.dll, msvcr90.dll` and put to `C:\Windows\System32` or `C:\Windows\SysWOW64`. Instructions on building Python extension with CUDA support on Windows is at [here](https://github.com/peterwittek/somoclu/tree/master/src/Python). Known Issues === The MATLAB CUDA interface crashes with unknown reasons. R interface with CUDA support on Windows cannot be properly built. The CUDA code that requires VC to compile, whereas Rcpp requires GCC to compile, and linking cannot be done without error. Though the linking completes, a function call results in wrong/inaccessible values and crashes the R session. The maps generated by the GPU and the CPU kernels are likely to be different. For computational efficiency, Somoclu uses single-precision floats. This occasionally results in identical distances between a data instance and the neurons. The CPU version will pick the best matching unit with the lowest coordinate values. Such sequentiality cannot be guaranteed in the reduction kernel of the GPU variant. This is not a bug, but it is better to be aware of it. Version 1.4.1 reintroduced the noncompactly supported distance function as default behaviour. This results in higher quality maps in general. There is no command line option or a parameter in the interfaces to control this behaviour and change it to a compactly supported distance function. If the change is necessary, line 53 in `mapDistanceFunctions.cpp` has to be modified to `if (false) {`. Acknowledgment === This work was supported by the European Commission Seventh Framework Programme under Grant Agreement Number FP7-601138 PERICLES and by the AWS in Education Machine Learning Grant award. somoclu-1.4.1/autogen.sh0000755000175000001440000000007012433136714014426 0ustar wittekusersautoreconf -i automake --add-missing --copy &>/dev/null somoclu-1.4.1/m4/0000755000175000001440000000000012433136714012750 5ustar wittekuserssomoclu-1.4.1/m4/ax_mpi_options.m40000644000175000001440000000531312433136714016244 0ustar wittekusersAC_DEFUN([AX_MPI_OPTIONS],[ dnl dnl Command-line options for setting up MPI dnl MPI_CXX=none ### AC_ARG_WITH(mpi-compilers, AS_HELP_STRING([--with-mpi-compilers=DIR or --with-mpi-compilers=yes], [use MPI compiler (mpicxx) found in directory DIR, or in your PATH if =yes]), [ if test "X${withval}" = "Xyes"; then # Look for MPI C++ compile script/program in user's path, set # MPI_CXX to name of program found, else set it to "none". Could # add more paths to check as 4th argument if you wanted to. # Calls AC_SUBST for MPI_CXX, etc. if test "X${MPI_CXX}" = "Xnone" ; then echo "Looking for an MPI C++ compiler in your path" AC_CHECK_PROGS([MY_CXX], [mpic++ mpicxx mpiCC mpiicpc], [none],) MPI_CXX=${MY_CXX} fi else foundCompiler=no if test "X${MPI_CXX}" = "Xnone" ; then AC_MSG_CHECKING(MPI C++ compiler in ${withval}) if test -f ${withval}/mpic++ ; then MPI_CXX=${withval}/mpic++ fi if test "X${MPI_CXX}" = "Xnone" && test -f ${withval}/mpicxx ; then MPI_CXX=${withval}/mpicxx fi if test "X${MPI_CXX}" = "Xnone" && test -f ${withval}/mpiCC ; then MPI_CXX=${withval}/mpiCC fi if test "X${MPI_CXX}" = "Xnone" && test -f ${withval}/mpiicpc ; then MPI_CXX=${withval}/mpiicpc fi AC_MSG_RESULT([${MPI_CXX}]) fi fi if test "X${MPI_CXX}" = "Xnone" ; then AC_MSG_ERROR([MPI C++ compiler script/program not found.]) fi ] ) if test "X${MPI_CXX}" = "Xnone" ; then echo "Looking for an MPI C++ compiler in your path" AC_CHECK_PROGS([MY_CXX], [mpic++ mpicxx mpiCC mpiicpc], [none],) MPI_CXX=${MY_CXX} fi AC_ARG_WITH(mpi, AS_HELP_STRING([--with-mpi=MPIROOT],[use MPI root directory.]), [ if test "X${withval}" = "Xno"; then :; else MPI_DIR=${withval} AC_MSG_CHECKING(MPI directory) AC_MSG_RESULT([${MPI_DIR}]) fi ] ) AC_ARG_WITH(mpi-libs, AS_HELP_STRING([--with-mpi-libs="LIBS"],[MPI libraries @<:@default "-lmpi"@:>@]), [ if test "X${withval}" = "Xno"; then :; else MPI_LIBS=${withval} AC_MSG_CHECKING(user-defined MPI libraries) AC_MSG_RESULT([${MPI_LIBS}]) fi ] ) AC_ARG_WITH(mpi-incdir, AS_HELP_STRING([--with-mpi-incdir=DIR],[MPI include directory @<:@default MPIROOT/include@:>@]), [ if test "X${withval}" = "Xno"; then :; else MPI_INC="-I${withval}" AC_MSG_CHECKING(user-defined MPI includes) AC_MSG_RESULT([${MPI_INC}]) fi ] ) AC_ARG_WITH(mpi-libdir, AS_HELP_STRING([--with-mpi-libdir=DIR],[MPI library directory @<:@default MPIROOT/lib@:>@]), [ if test "X${withval}" = "Xno"; then :; else MPI_LIBDIR="-L${withval}" AC_MSG_CHECKING(user-defined MPI library directory) AC_MSG_RESULT([${MPI_LIBDIR}]) fi ] ) ]) somoclu-1.4.1/m4/ax_mpi_tests.m40000644000175000001440000000372412433136714015717 0ustar wittekusersdnl MPI tests dnl dnl AX_MPI_TESTS(subpackage) AC_DEFUN([AX_MPI_TESTS],[ dnl dnl Test to see if MPI compilers work properly dnl if test -n "${MPI_DIR}" && test -z "${MPI_INC}"; then MPI_INC="-I${MPI_DIR}/include" fi if test -z "${MPI_INC}"; then AC_LANG([C++]) AC_MSG_CHECKING(whether we can preprocess mpi.h) AC_PREPROC_IFELSE( [AC_LANG_SOURCE([[#include "mpi.h"]])], [ AC_MSG_RESULT(yes) ],[ AC_MSG_RESULT(no) echo "---" echo "Cannot find header file mpi.h." echo "View the mpi options with \"configure --help\", and provide a valid MPI." echo "---" AC_MSG_ERROR(cannot find mpi.h) ]) AC_MSG_CHECKING(whether we can compile mpi.h) AC_COMPILE_IFELSE( [AC_LANG_SOURCE([[#include "mpi.h"]],[[int c; char** v; MPI_Init(&c,&v);]])], [ AC_MSG_RESULT(yes) AC_DEFINE(HAVE_MPI,,[define that mpi is being used]) ],[ AC_MSG_RESULT(no) echo "---" echo "mpi.h has compile errors" echo "View the mpi options with \"configure --help\", and provide a valid MPI." echo "---" AC_MSG_ERROR(invalid mpi.h) ]) fi AC_SUBST([MPI_INC]) if test -n "${MPI_DIR}" && test -z "${MPI_LIBDIR}"; then MPI_LIBDIR="-L${MPI_DIR}/lib" fi AC_SUBST([MPI_LIBDIR]) if test -z "${MPI_LIBS}" && test -n "${MPI_LIBDIR}"; then MPI_LIBS="-lmpi" fi AC_SUBST([MPI_LIBS]) AC_LANG([C++]) AC_MSG_CHECKING(whether special compile flag for MPICH is required) AC_RUN_IFELSE( [AC_LANG_PROGRAM( [[#define MPICH_IGNORE_CXX_SEEK] [#include ]], [[#ifdef MPICH_NAME return 0; #endif return 1;]])], [AC_MSG_RESULT(yes) CXXFLAGS="${CXXFLAGS} -DMPICH_IGNORE_CXX_SEEK" echo "-----" echo "Adding -DMPICH_IGNORE_CXX_SEEK to MPICH compilations" echo "-----"], [AC_MSG_RESULT(no)], [AC_MSG_RESULT(cross compiling) CXXFLAGS="${CXXFLAGS} -DMPICH_IGNORE_CXX_SEEK" echo "-----" echo "Adding -DMPICH_IGNORE_CXX_SEEK because we can't determine whether or not it is required" echo "-----"] ) ]) somoclu-1.4.1/LICENSE0000644000175000001440000010575512433136714013452 0ustar wittekusers GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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But first, please read . somoclu-1.4.1/TODO0000644000175000001440000000040312462151234013111 0ustar wittekusers - Integration with data structures of SOM libraries in Python and R. - Implement hexagonal grid. - Reimplement GPU kernels in CUDA to replace Thrust (testing is currently in cuda_opt branch). - MATLAB extension building on Windows - Python 3 supportsomoclu-1.4.1/aclocal.m40000644000175000001440000000437412462151402014271 0ustar wittekusers# generated automatically by aclocal 1.15 -*- Autoconf -*- # Copyright (C) 1996-2014 Free Software Foundation, Inc. # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. m4_ifndef([AC_CONFIG_MACRO_DIRS], [m4_defun([_AM_CONFIG_MACRO_DIRS], [])m4_defun([AC_CONFIG_MACRO_DIRS], [_AM_CONFIG_MACRO_DIRS($@)])]) # AM_CONDITIONAL -*- Autoconf -*- # Copyright (C) 1997-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # AM_CONDITIONAL(NAME, SHELL-CONDITION) # ------------------------------------- # Define a conditional. AC_DEFUN([AM_CONDITIONAL], [AC_PREREQ([2.52])dnl m4_if([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])], [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl AC_SUBST([$1_TRUE])dnl AC_SUBST([$1_FALSE])dnl _AM_SUBST_NOTMAKE([$1_TRUE])dnl _AM_SUBST_NOTMAKE([$1_FALSE])dnl m4_define([_AM_COND_VALUE_$1], [$2])dnl if $2; then $1_TRUE= $1_FALSE='#' else $1_TRUE='#' $1_FALSE= fi AC_CONFIG_COMMANDS_PRE( [if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then AC_MSG_ERROR([[conditional "$1" was never defined. Usually this means the macro was only invoked conditionally.]]) fi])]) # Copyright (C) 2006-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # _AM_SUBST_NOTMAKE(VARIABLE) # --------------------------- # Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in. # This macro is traced by Automake. AC_DEFUN([_AM_SUBST_NOTMAKE]) # AM_SUBST_NOTMAKE(VARIABLE) # -------------------------- # Public sister of _AM_SUBST_NOTMAKE. AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)]) somoclu-1.4.1/src/0000755000175000001440000000000012462117220013210 5ustar wittekuserssomoclu-1.4.1/src/denseCpuKernels.cpp0000644000175000001440000001441212445351346017022 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include "somoclu.h" #ifdef HAVE_R #include #endif /** Distance b/w a feature vector and a weight vector * = Euclidean * @param som_y * @param som_x * @param r - row number in the input feature file */ float get_distance(float* codebook, float* data, unsigned int som_y, unsigned int som_x, unsigned int nSomX, unsigned int nDimensions, unsigned int r) { float distance = 0.0f; for (unsigned int d = 0; d < nDimensions; d++) distance += (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] - *(data + r*nDimensions + d)) * (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] - *(data + r*nDimensions + d)); return distance; } /** Get node coords for the best matching unit (BMU) * @param coords - BMU coords * @param n - row num in the input feature file */ void get_bmu_coord(float* codebook, float* data, unsigned int nSomY, unsigned int nSomX, unsigned int nDimensions, unsigned int* coords, unsigned int n) { float mindist = 9999.99; float dist = 0.0f; /// Check nSomX * nSomY nodes one by one and compute the distance /// D(W_K, Fvec) and get the mindist and get the coords for the BMU. /// for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { dist = get_distance(codebook, data, som_y, som_x, nSomX, nDimensions, n); if (dist < mindist) { mindist = dist; coords[0] = som_x; coords[1] = som_y; } } } } void trainOneEpochDenseCPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus) { unsigned int p1[2] = {0, 0}; unsigned int *bmus = new unsigned int[nVectorsPerRank*2]; #ifdef _OPENMP #pragma omp parallel default(shared) private(p1) #endif { #ifdef _OPENMP #pragma omp for #endif #ifdef _WIN32 for (int n = 0; n < nVectorsPerRank; n++) { #else for (unsigned int n = 0; n < nVectorsPerRank; n++) { #endif if (itask*nVectorsPerRank+n #include #include using namespace std; void trainWrapper(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename, float *codebook, int codebook_size, int *globalBmus, int globalBmus_size, float *uMatrix, int uMatrix_size) { /// /// Codebook /// int itask = 0; svm_node ** sparseData = NULL; core_data coreData; coreData.codebook_size = nSomY*nSomX*nDimensions; coreData.codebook = new float[coreData.codebook_size]; coreData.globalBmus = NULL; coreData.uMatrix = NULL; unsigned int nVectorsPerRank = nVectors; coreData.globalBmus_size = nVectorsPerRank*int(ceil(nVectors/(double)nVectorsPerRank))*2; if (itask == 0) { coreData.globalBmus = new int[coreData.globalBmus_size]; if (initialCodebookFilename.empty()){ initializeCodebook(0, coreData.codebook, nSomX, nSomY, nDimensions); } else { unsigned int nSomXY = 0; unsigned int tmpNDimensions = 0; delete [] coreData.codebook; coreData.codebook = readMatrix(initialCodebookFilename, nSomXY, tmpNDimensions); if (tmpNDimensions != nDimensions) { cerr << "Dimension of initial codebook does not match data!\n"; // my_abort(5); } else if (nSomXY / nSomY != nSomX) { cerr << "Dimension of initial codebook does not match specified SOM grid!\n"; // my_abort(6); } cout << "Read initial codebook: " << initialCodebookFilename << "\n"; } } #ifdef CUDA if(kernelType==DENSE_GPU){ int rank = 0; int nProcs = 1; setDevice(rank, nProcs); initializeGpu(data, nVectorsPerRank, nDimensions, nSomX, nSomY); } #endif /// /// Parameters for SOM /// if (radius0 == 0) { radius0 = nSomX / 2.0f; /// init radius for updating neighbors } if (radiusN == 0) { radiusN = 1; } if (scale0 == 0) { scale0 = 1.0; } unsigned int currentEpoch = 0; /// 0...nEpoch-1 /// /// Training /// while ( currentEpoch < nEpoch ) { coreData = trainOneEpoch(itask, data, sparseData, coreData, nEpoch, currentEpoch, snapshots > 0, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, kernelType, mapType); currentEpoch++; } if (itask == 0) { /// /// Save U-mat /// coreData.uMatrix = calculateUMatrix(coreData.codebook, nSomX, nSomY, nDimensions, mapType); coreData.uMatrix_size = nSomX * nSomY; } #ifdef CUDA if (kernelType == DENSE_GPU) { freeGpu(); } #endif if(coreData.codebook != NULL){ memcpy(codebook, coreData.codebook, sizeof(float) * codebook_size); delete [] coreData.codebook; } if(coreData.globalBmus != NULL){ memcpy(globalBmus, coreData.globalBmus, sizeof(int) * globalBmus_size); delete [] coreData.globalBmus; } if(coreData.uMatrix != NULL){ memcpy(uMatrix, coreData.uMatrix, sizeof(float) * uMatrix_size); delete [] coreData.uMatrix; } } somoclu-1.4.1/src/mapDistanceFunctions.cpp0000644000175000001440000000457412462117146020056 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #include "somoclu.h" float euclideanDistanceOnToroidMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y, const unsigned int nSomX, const unsigned int nSomY) { unsigned int x1 = std::min(som_x, x); unsigned int y1 = std::min(som_y, y); unsigned int x2 = std::max(som_x, x); unsigned int y2 = std::max(som_y, y); unsigned int xdist = std::min(x2-x1, x1+nSomX-x2); unsigned int ydist = std::min(y2-y1, y1+nSomY-y2); //unsigned int xdist = std::min(std::abs(x1-x2), std::abs(x1+nSomX-x2)); //unsigned int ydist = std::min(std::abs(y1-y2), std::abs(y1+nSomY-y2)); return sqrt(float(xdist*xdist+ydist*ydist)); } float euclideanDistanceOnPlanarMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y) { unsigned int x1 = std::min(som_x, x); unsigned int y1 = std::min(som_y, y); unsigned int x2 = std::max(som_x, x); unsigned int y2 = std::max(som_y, y); unsigned int xdist = x2-x1; unsigned int ydist = y2-y1; return sqrt(float(xdist*xdist+ydist*ydist)); } float gaussianNeighborhood(float distance, float radius, float stddevs) { float norm = (2 * (radius + 1)*(radius + 1)) / (stddevs*stddevs); return exp((-(float) distance * distance) / norm); } float getWeight(float distance, float radius, float scaling) { if (true) { return scaling * gaussianNeighborhood(distance, radius, 2); } else { if (distance <= radius){ return scaling * gaussianNeighborhood(distance, radius, 2); } else { return 0.0; } } } somoclu-1.4.1/src/Makefile.in0000644000175000001440000000354612433136714015274 0ustar wittekusers# @configure_input@ # Package-related substitution variables package = @PACKAGE_NAME@ version = @PACKAGE_VERSION@ tarname = @PACKAGE_TARNAME@ distdir = $(tarname)-$(version) # Prefix-related substitution variables prefix = @prefix@ exec_prefix = @exec_prefix@ bindir = @bindir@ libdir = @libdir@ # Tool-related substitution variables CXX = @CXX@ CXXFLAGS = @CXXFLAGS@ LIBS = @LIBS@ DEFS = @DEFS@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM= @INSTALL_PROGRAM@ INSTALL_SCRIPT = @INSTALL_SCRIPT@ CUDA_CFLAGS = @CUDA_CFLAGS@ CUDA_LIBS = @CUDA_LIBS@ CUDA_LDFLAGS = @CUDA_LDFLAGS@ NVCC = @NVCC@ MPI_INC = @MPI_INC@ MPI_LIBDIR = @MPI_LIBDIR@ MPI_LIBS = @MPI_LIBS@ # VPATH-related substitution variables srcdir = @srcdir@ VPATH = @srcdir@ LIBOBJS=sparseCpuKernels.o io.o denseCpuKernels.o mapDistanceFunctions.o training.o uMatrix.o trainOneEpoch.o ifdef CUDA_LIBS LIBOBJS+=denseGpuKernels.cu.co endif OBJS=$(LIBOBJS) somoclu.o all: somoclu lib: $(LIBOBJS) $(CXX) $(DEFS) $(CXXFLAGS) $(CUDA_LDFLAGS) ${MPI_LIBDIR} -shared -o libsomoclu.so $^ $(LIBS) $(CUDA_LIBS) ${MPI_LIBS} somoclu: $(OBJS) $(CXX) $(DEFS) $(CXXFLAGS) $(CUDA_LDFLAGS) ${MPI_LIBDIR} -o $@ $^ $(LIBS) $(CUDA_LIBS) ${MPI_LIBS} %.o: %.cpp $(CXX) $(DEFS) $(CXXFLAGS) ${MPI_INC} -I$(srcdir) -I.. -o $@ -c $(srcdir)/$< %.cu.co: %.cu $(NVCC) $(DEFS) $(CUDA_CFLAGS) ${MPI_INC} -I$(srcdir) -I.. -o $@ -c $(srcdir)/$< clean: -rm -f somoclu libsomoclu.so $(OBJS) 1>/dev/null install: $(INSTALL) -d $(DESTDIR)$(bindir) $(INSTALL_PROGRAM) -m 0755 somoclu \ $(DESTDIR)$(bindir) uninstall: -rm $(DESTDIR)$(bindir)/somoclu &>/dev/null Makefile: Makefile.in ../config.status cd .. && ./config.status $@ ../config.status: ../configure cd .. && ./config.status --recheck .PHONY: all clean install uninstall somoclu-1.4.1/src/trainOneEpoch.cpp0000644000175000001440000001332412445351346016467 0ustar wittekusers#include"somoclu.h" #include #include #ifdef HAVE_R #include #endif float linearCooling(float start, float end, float nEpoch, float epoch) { float diff = (start - end) / (nEpoch-1); return start - (epoch * diff); } float exponentialCooling(float start, float end, float nEpoch, float epoch) { float diff = 0; if (end == 0.0) { diff = -log(0.1) / nEpoch; } else { diff = -log(end / start) / nEpoch; } return start * exp(-epoch * diff); } /** Initialize SOM codebook with random values * @param seed - random seed * @param codebook - the codebook to fill in * @param nSomX - dimensions of SOM map in the currentEpoch direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ void initializeCodebook(unsigned int seed, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions) { /// /// Fill initial random weights /// #ifdef HAVE_R GetRNGstate(); #else srand(seed); #endif for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { for (unsigned int d = 0; d < nDimensions; d++) { #ifdef HAVE_R int w = 0xFFF & (int) (RAND_MAX*unif_rand()); #else int w = 0xFFF & rand(); #endif w -= 0x800; codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] = (float)w / 4096.0f; } } } #ifdef HAVE_R PutRNGstate(); #endif } core_data trainOneEpoch(int itask, float *data, svm_node **sparseData, core_data coreData, unsigned int nEpoch, unsigned int currentEpoch, bool enableCalculatingUMatrix, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int kernelType, string mapType){ float N = (float)nEpoch; float *numerator; float *denominator; float scale = scale0; float radius = radius0; if (itask == 0) { numerator = new float[nSomY*nSomX*nDimensions]; denominator = new float[nSomY*nSomX]; for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { denominator[som_y*nSomX + som_x] = 0.0; for (unsigned int d = 0; d < nDimensions; d++) { numerator[som_y*nSomX*nDimensions + som_x*nDimensions + d] = 0.0; } } } if (radiusCooling == "linear") { radius = linearCooling(float(radius0), radiusN, N, currentEpoch); } else { radius = exponentialCooling(radius0, radiusN, N, currentEpoch); } if (scaleCooling == "linear") { scale = linearCooling(scale0, scaleN, N, currentEpoch); } else { scale = exponentialCooling(scale0, scaleN, N, currentEpoch); } // cout << "Epoch: " << currentEpoch << " Radius: " << radius << endl; } #ifdef HAVE_MPI MPI_Bcast(&radius, 1, MPI_FLOAT, 0, MPI_COMM_WORLD); MPI_Bcast(&scale, 1, MPI_FLOAT, 0, MPI_COMM_WORLD); MPI_Bcast(coreData.codebook, nSomY*nSomX*nDimensions, MPI_FLOAT, 0, MPI_COMM_WORLD); #endif /// 1. Each task fills localNumerator and localDenominator /// 2. MPI_reduce sums up each tasks localNumerator and localDenominator to the root's /// numerator and denominator. switch (kernelType) { default: case DENSE_CPU: trainOneEpochDenseCPU(itask, data, numerator, denominator, coreData.codebook, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius, scale, mapType, coreData.globalBmus); break; #ifdef CUDA case DENSE_GPU: trainOneEpochDenseGPU(itask, data, numerator, denominator, coreData.codebook, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius, scale, mapType, coreData.globalBmus); break; #endif case SPARSE_CPU: trainOneEpochSparseCPU(itask, sparseData, numerator, denominator, coreData.codebook, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius, scale, mapType, coreData.globalBmus); break; } /// 3. Update codebook using numerator and denominator #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); #endif if (itask == 0) { #pragma omp parallel for #ifdef _WIN32 for (int som_y = 0; som_y < nSomY; som_y++) { #else for (unsigned int som_y = 0; som_y < nSomY; som_y++) { #endif for (unsigned int som_x = 0; som_x < nSomX; som_x++) { float denom = denominator[som_y*nSomX + som_x]; for (unsigned int d = 0; d < nDimensions; d++) { float newWeight = numerator[som_y*nSomX*nDimensions + som_x*nDimensions + d] / denom; if (newWeight > 0.0) { coreData.codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] = newWeight; } } } } } if (enableCalculatingUMatrix) { coreData.uMatrix = calculateUMatrix(coreData.codebook, nSomX, nSomY, nDimensions, mapType); } if (itask == 0) { delete [] numerator; delete [] denominator; } return coreData; } somoclu-1.4.1/src/sparseCpuKernels.cpp0000644000175000001440000001522112445351346017220 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include "somoclu.h" #ifdef HAVE_R #include #endif /** Distance b/w a feature vector and a weight vector * = Euclidean * @param som_y * @param som_x * @param r - row number in the input feature file */ float get_distance(float* codebook, svm_node **sparseData, unsigned int som_y, unsigned int som_x, unsigned int nSomX, unsigned int nDimensions, unsigned int r) { float distance = 0.0f; unsigned int j=0; for ( unsigned int d=0; d < nDimensions; d++ ) { if ( (int) d == sparseData[r][j].index ) { distance += (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]- sparseData[r][j].value) * (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]- sparseData[r][j].value); ++j; } else { distance += codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]* codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]; } } return distance; } /** Get node coords for the best matching unit (BMU) * @param coords - BMU coords * @param n - row num in the input feature file */ void get_bmu_coord(float* codebook, svm_node **sparseData, unsigned int nSomY, unsigned int nSomX, unsigned int nDimensions, int* coords, unsigned int n) { float mindist = 9999.99; float dist = 0.0f; /// Check nSomX * nSomY nodes one by one and compute the distance /// D(W_K, Fvec) and get the mindist and get the coords for the BMU. /// for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { dist = get_distance(codebook, sparseData, som_y, som_x, nSomX, nDimensions, n); if (dist < mindist) { mindist = dist; coords[0] = som_x; coords[1] = som_y; } } } } void trainOneEpochSparseCPU(int itask, svm_node **sparseData, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus) { int p1[2] = {0, 0}; int *bmus = new int[nVectorsPerRank*2]; #ifdef _OPENMP #pragma omp parallel default(shared) private(p1) #endif { #ifdef _OPENMP #pragma omp for #endif #ifdef _WIN32 for (int n = 0; n < nVectorsPerRank; n++) { #else for (unsigned int n = 0; n < nVectorsPerRank; n++) { #endif if (itask*nVectorsPerRank+n {4FC737F1-C7A5-4376-A066-2A32D752A2FF} cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx {93995380-89BD-4b04-88EB-625FBE52EBFB} h;hh;hpp;hxx;hm;inl;inc;xsd {67DA6AB6-F800-4c08-8B7A-83BB121AAD01} rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav;mfcribbon-ms Header Files Header Files Header Files Header Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files somoclu-1.4.1/src/Windows/somoclu/somoclu.sln0000644000175000001440000000240512433136714020532 0ustar wittekusers Microsoft Visual Studio Solution File, Format Version 12.00 # Visual Studio 2013 VisualStudioVersion = 12.0.30501.0 MinimumVisualStudioVersion = 10.0.40219.1 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "somoclu", "somoclu.vcxproj", "{278ED25D-49D8-4A54-8FCC-00954022746F}" EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Win32 = Debug|Win32 Debug|x64 = Debug|x64 Release|Win32 = Release|Win32 Release|x64 = Release|x64 EndGlobalSection GlobalSection(ProjectConfigurationPlatforms) = postSolution {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|Win32.ActiveCfg = Debug|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|Win32.Build.0 = Debug|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|x64.ActiveCfg = Debug|x64 {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|x64.Build.0 = Debug|x64 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|Win32.ActiveCfg = Release|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|Win32.Build.0 = Release|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|x64.ActiveCfg = Release|x64 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|x64.Build.0 = Release|x64 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE EndGlobalSection EndGlobal somoclu-1.4.1/src/Windows/somoclu/somoclu.vcxproj0000644000175000001440000002514412433136714021436 0ustar wittekusers Debug Win32 Debug x64 Release Win32 Release x64 {278ED25D-49D8-4A54-8FCC-00954022746F} Win32Proj somoclu Application true v120 Unicode Application true v120 Unicode Application false v120 true Unicode Application false v120 true Unicode true $(CUDA_INC_PATH);$(IncludePath) true $(CUDA_INC_PATH);$(IncludePath) false $(CUDA_INC_PATH);$(IncludePath) false $(CUDA_INC_PATH);$(IncludePath) Level3 Disabled CUDA;HAVE_MPI;WIN32;_DEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) true C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) Console true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\;C:\Program Files\Microsoft MPI\Lib\i386;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) Level3 Disabled CUDA;HAVE_MPI;WIN32;_DEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) true C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) Console true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\amd64;C:\Program Files\Microsoft MPI\Lib\;C:\Program Files\Microsoft MPI\Lib\i386;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) Level3 MaxSpeed true true CUDA;HAVE_MPI;WIN32;NDEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) true Console true true true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\i386;C:\Program Files\Microsoft MPI\Lib\;C:\Program Files\Microsoft MPI\Lib\amd64;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) Level3 MaxSpeed true true CUDA;HAVE_MPI;WIN32;NDEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) true Console true true true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\amd64;C:\Program Files\Microsoft MPI\Lib\;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) somoclu-1.4.1/src/Windows/getopt.h0000644000175000001440000000600612433136714016326 0ustar wittekusers#ifndef __GETOPT_H__ /** * DISCLAIMER * This file has no copyright assigned and is placed in the Public Domain. * This file is a part of the w64 mingw-runtime package. * * The w64 mingw-runtime package and its code is distributed in the hope that it * will be useful but WITHOUT ANY WARRANTY. ALL WARRANTIES, EXPRESSED OR * IMPLIED ARE HEREBY DISCLAIMED. This includes but is not limited to * warranties of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. */ #define __GETOPT_H__ /* All the headers include this file. */ #include #ifdef __cplusplus extern "C" { #endif extern int optind; /* index of first non-option in argv */ extern int optopt; /* single option character, as parsed */ extern int opterr; /* flag to enable built-in diagnostics... */ /* (user may set to zero, to suppress) */ extern char *optarg; /* pointer to argument of current option */ extern int getopt(int nargc, char * const *nargv, const char *options); #ifdef _BSD_SOURCE /* * BSD adds the non-standard `optreset' feature, for reinitialisation * of `getopt' parsing. We support this feature, for applications which * proclaim their BSD heritage, before including this header; however, * to maintain portability, developers are advised to avoid it. */ # define optreset __mingw_optreset extern int optreset; #endif #ifdef __cplusplus } #endif /* * POSIX requires the `getopt' API to be specified in `unistd.h'; * thus, `unistd.h' includes this header. However, we do not want * to expose the `getopt_long' or `getopt_long_only' APIs, when * included in this manner. Thus, close the standard __GETOPT_H__ * declarations block, and open an additional __GETOPT_LONG_H__ * specific block, only when *not* __UNISTD_H_SOURCED__, in which * to declare the extended API. */ #endif /* !defined(__GETOPT_H__) */ #if !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__) #define __GETOPT_LONG_H__ #ifdef __cplusplus extern "C" { #endif struct option /* specification for a long form option... */ { const char *name; /* option name, without leading hyphens */ int has_arg; /* does it take an argument? */ int *flag; /* where to save its status, or NULL */ int val; /* its associated status value */ }; enum /* permitted values for its `has_arg' field... */ { no_argument = 0, /* option never takes an argument */ required_argument, /* option always requires an argument */ optional_argument /* option may take an argument */ }; extern int getopt_long(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx); extern int getopt_long_only(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx); /* * Previous MinGW implementation had... */ #ifndef HAVE_DECL_GETOPT /* * ...for the long form API only; keep this for compatibility. */ # define HAVE_DECL_GETOPT 1 #endif #ifdef __cplusplus } #endif #endif /* !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__) */ somoclu-1.4.1/src/Windows/getopt.c0000644000175000001440000003634612433136714016333 0ustar wittekusers/* $OpenBSD: getopt_long.c,v 1.23 2007/10/31 12:34:57 chl Exp $ */ /* $NetBSD: getopt_long.c,v 1.15 2002/01/31 22:43:40 tv Exp $ */ /* * Copyright (c) 2002 Todd C. Miller * * Permission to use, copy, modify, and distribute this software for any * purpose with or without fee is hereby granted, provided that the above * copyright notice and this permission notice appear in all copies. * * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. * * Sponsored in part by the Defense Advanced Research Projects * Agency (DARPA) and Air Force Research Laboratory, Air Force * Materiel Command, USAF, under agreement number F39502-99-1-0512. */ /*- * Copyright (c) 2000 The NetBSD Foundation, Inc. * All rights reserved. * * This code is derived from software contributed to The NetBSD Foundation * by Dieter Baron and Thomas Klausner. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE * POSSIBILITY OF SUCH DAMAGE. */ #include #include #include #include "getopt.h" #include #include #include #define REPLACE_GETOPT /* use this getopt as the system getopt(3) */ #ifdef REPLACE_GETOPT int opterr = 1; /* if error message should be printed */ int optind = 1; /* index into parent argv vector */ int optopt = '?'; /* character checked for validity */ #undef optreset /* see getopt.h */ #define optreset __mingw_optreset int optreset; /* reset getopt */ char *optarg; /* argument associated with option */ #endif #define PRINT_ERROR ((opterr) && (*options != ':')) #define FLAG_PERMUTE 0x01 /* permute non-options to the end of argv */ #define FLAG_ALLARGS 0x02 /* treat non-options as args to option "-1" */ #define FLAG_LONGONLY 0x04 /* operate as getopt_long_only */ /* return values */ #define BADCH (int)'?' #define BADARG ((*options == ':') ? (int)':' : (int)'?') #define INORDER (int)1 #ifndef __CYGWIN__ #define __progname __argv[0] #else extern char __declspec(dllimport) *__progname; #endif #ifdef __CYGWIN__ static char EMSG[] = ""; #else #define EMSG "" #endif static int getopt_internal(int, char * const *, const char *, const struct option *, int *, int); static int parse_long_options(char * const *, const char *, const struct option *, int *, int); static int gcd(int, int); static void permute_args(int, int, int, char * const *); static char *place = EMSG; /* option letter processing */ /* XXX: set optreset to 1 rather than these two */ static int nonopt_start = -1; /* first non option argument (for permute) */ static int nonopt_end = -1; /* first option after non options (for permute) */ /* Error messages */ static const char recargchar[] = "option requires an argument -- %c"; static const char recargstring[] = "option requires an argument -- %s"; static const char ambig[] = "ambiguous option -- %.*s"; static const char noarg[] = "option doesn't take an argument -- %.*s"; static const char illoptchar[] = "unknown option -- %c"; static const char illoptstring[] = "unknown option -- %s"; static void _vwarnx(const char *fmt,va_list ap) { (void)fprintf(stderr,"%s: ",__progname); if (fmt != NULL) (void)vfprintf(stderr,fmt,ap); (void)fprintf(stderr,"\n"); } static void warnx(const char *fmt,...) { va_list ap; va_start(ap,fmt); _vwarnx(fmt,ap); va_end(ap); } /* * Compute the greatest common divisor of a and b. */ static int gcd(int a, int b) { int c; c = a % b; while (c != 0) { a = b; b = c; c = a % b; } return (b); } /* * Exchange the block from nonopt_start to nonopt_end with the block * from nonopt_end to opt_end (keeping the same order of arguments * in each block). */ static void permute_args(int panonopt_start, int panonopt_end, int opt_end, char * const *nargv) { int cstart, cyclelen, i, j, ncycle, nnonopts, nopts, pos; char *swap; /* * compute lengths of blocks and number and size of cycles */ nnonopts = panonopt_end - panonopt_start; nopts = opt_end - panonopt_end; ncycle = gcd(nnonopts, nopts); cyclelen = (opt_end - panonopt_start) / ncycle; for (i = 0; i < ncycle; i++) { cstart = panonopt_end+i; pos = cstart; for (j = 0; j < cyclelen; j++) { if (pos >= panonopt_end) pos -= nnonopts; else pos += nopts; swap = nargv[pos]; /* LINTED const cast */ ((char **) nargv)[pos] = nargv[cstart]; /* LINTED const cast */ ((char **)nargv)[cstart] = swap; } } } /* * parse_long_options -- * Parse long options in argc/argv argument vector. * Returns -1 if short_too is set and the option does not match long_options. */ static int parse_long_options(char * const *nargv, const char *options, const struct option *long_options, int *idx, int short_too) { char *current_argv, *has_equal; size_t current_argv_len; int i, ambiguous, match; #define IDENTICAL_INTERPRETATION(_x, _y) \ (long_options[(_x)].has_arg == long_options[(_y)].has_arg && \ long_options[(_x)].flag == long_options[(_y)].flag && \ long_options[(_x)].val == long_options[(_y)].val) current_argv = place; match = -1; ambiguous = 0; optind++; if ((has_equal = strchr(current_argv, '=')) != NULL) { /* argument found (--option=arg) */ current_argv_len = has_equal - current_argv; has_equal++; } else current_argv_len = strlen(current_argv); for (i = 0; long_options[i].name; i++) { /* find matching long option */ if (strncmp(current_argv, long_options[i].name, current_argv_len)) continue; if (strlen(long_options[i].name) == current_argv_len) { /* exact match */ match = i; ambiguous = 0; break; } /* * If this is a known short option, don't allow * a partial match of a single character. */ if (short_too && current_argv_len == 1) continue; if (match == -1) /* partial match */ match = i; else if (!IDENTICAL_INTERPRETATION(i, match)) ambiguous = 1; } if (ambiguous) { /* ambiguous abbreviation */ if (PRINT_ERROR) warnx(ambig, (int)current_argv_len, current_argv); optopt = 0; return (BADCH); } if (match != -1) { /* option found */ if (long_options[match].has_arg == no_argument && has_equal) { if (PRINT_ERROR) warnx(noarg, (int)current_argv_len, current_argv); /* * XXX: GNU sets optopt to val regardless of flag */ if (long_options[match].flag == NULL) optopt = long_options[match].val; else optopt = 0; return (BADARG); } if (long_options[match].has_arg == required_argument || long_options[match].has_arg == optional_argument) { if (has_equal) optarg = has_equal; else if (long_options[match].has_arg == required_argument) { /* * optional argument doesn't use next nargv */ optarg = nargv[optind++]; } } if ((long_options[match].has_arg == required_argument) && (optarg == NULL)) { /* * Missing argument; leading ':' indicates no error * should be generated. */ if (PRINT_ERROR) warnx(recargstring, current_argv); /* * XXX: GNU sets optopt to val regardless of flag */ if (long_options[match].flag == NULL) optopt = long_options[match].val; else optopt = 0; --optind; return (BADARG); } } else { /* unknown option */ if (short_too) { --optind; return (-1); } if (PRINT_ERROR) warnx(illoptstring, current_argv); optopt = 0; return (BADCH); } if (idx) *idx = match; if (long_options[match].flag) { *long_options[match].flag = long_options[match].val; return (0); } else return (long_options[match].val); #undef IDENTICAL_INTERPRETATION } /* * getopt_internal -- * Parse argc/argv argument vector. Called by user level routines. */ static int getopt_internal(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx, int flags) { char *oli; /* option letter list index */ int optchar, short_too; static int posixly_correct = -1; if (options == NULL) return (-1); /* * XXX Some GNU programs (like cvs) set optind to 0 instead of * XXX using optreset. Work around this braindamage. */ if (optind == 0) optind = optreset = 1; /* * Disable GNU extensions if POSIXLY_CORRECT is set or options * string begins with a '+'. * * CV, 2009-12-14: Check POSIXLY_CORRECT anew if optind == 0 or * optreset != 0 for GNU compatibility. */ if (posixly_correct == -1 || optreset != 0) posixly_correct = (getenv("POSIXLY_CORRECT") != NULL); if (*options == '-') flags |= FLAG_ALLARGS; else if (posixly_correct || *options == '+') flags &= ~FLAG_PERMUTE; if (*options == '+' || *options == '-') options++; optarg = NULL; if (optreset) nonopt_start = nonopt_end = -1; start: if (optreset || !*place) { /* update scanning pointer */ optreset = 0; if (optind >= nargc) { /* end of argument vector */ place = EMSG; if (nonopt_end != -1) { /* do permutation, if we have to */ permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } else if (nonopt_start != -1) { /* * If we skipped non-options, set optind * to the first of them. */ optind = nonopt_start; } nonopt_start = nonopt_end = -1; return (-1); } if (*(place = nargv[optind]) != '-' || (place[1] == '\0' && strchr(options, '-') == NULL)) { place = EMSG; /* found non-option */ if (flags & FLAG_ALLARGS) { /* * GNU extension: * return non-option as argument to option 1 */ optarg = nargv[optind++]; return (INORDER); } if (!(flags & FLAG_PERMUTE)) { /* * If no permutation wanted, stop parsing * at first non-option. */ return (-1); } /* do permutation */ if (nonopt_start == -1) nonopt_start = optind; else if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); nonopt_start = optind - (nonopt_end - nonopt_start); nonopt_end = -1; } optind++; /* process next argument */ goto start; } if (nonopt_start != -1 && nonopt_end == -1) nonopt_end = optind; /* * If we have "-" do nothing, if "--" we are done. */ if (place[1] != '\0' && *++place == '-' && place[1] == '\0') { optind++; place = EMSG; /* * We found an option (--), so if we skipped * non-options, we have to permute. */ if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } nonopt_start = nonopt_end = -1; return (-1); } } /* * Check long options if: * 1) we were passed some * 2) the arg is not just "-" * 3) either the arg starts with -- we are getopt_long_only() */ if (long_options != NULL && place != nargv[optind] && (*place == '-' || (flags & FLAG_LONGONLY))) { short_too = 0; if (*place == '-') place++; /* --foo long option */ else if (*place != ':' && strchr(options, *place) != NULL) short_too = 1; /* could be short option too */ optchar = parse_long_options(nargv, options, long_options, idx, short_too); if (optchar != -1) { place = EMSG; return (optchar); } } if ((optchar = (int)*place++) == (int)':' || (optchar == (int)'-' && *place != '\0') || (oli = strchr(options, optchar)) == NULL) { /* * If the user specified "-" and '-' isn't listed in * options, return -1 (non-option) as per POSIX. * Otherwise, it is an unknown option character (or ':'). */ if (optchar == (int)'-' && *place == '\0') return (-1); if (!*place) ++optind; if (PRINT_ERROR) warnx(illoptchar, optchar); optopt = optchar; return (BADCH); } if (long_options != NULL && optchar == 'W' && oli[1] == ';') { /* -W long-option */ if (*place) /* no space */ /* NOTHING */; else if (++optind >= nargc) { /* no arg */ place = EMSG; if (PRINT_ERROR) warnx(recargchar, optchar); optopt = optchar; return (BADARG); } else /* white space */ place = nargv[optind]; optchar = parse_long_options(nargv, options, long_options, idx, 0); place = EMSG; return (optchar); } if (*++oli != ':') { /* doesn't take argument */ if (!*place) ++optind; } else { /* takes (optional) argument */ optarg = NULL; if (*place) /* no white space */ optarg = place; else if (oli[1] != ':') { /* arg not optional */ if (++optind >= nargc) { /* no arg */ place = EMSG; if (PRINT_ERROR) warnx(recargchar, optchar); optopt = optchar; return (BADARG); } else optarg = nargv[optind]; } place = EMSG; ++optind; } /* dump back option letter */ return (optchar); } #ifdef REPLACE_GETOPT /* * getopt -- * Parse argc/argv argument vector. * * [eventually this will replace the BSD getopt] */ int getopt(int nargc, char * const *nargv, const char *options) { /* * We don't pass FLAG_PERMUTE to getopt_internal() since * the BSD getopt(3) (unlike GNU) has never done this. * * Furthermore, since many privileged programs call getopt() * before dropping privileges it makes sense to keep things * as simple (and bug-free) as possible. */ return (getopt_internal(nargc, nargv, options, NULL, NULL, 0)); } #endif /* REPLACE_GETOPT */ /* * getopt_long -- * Parse argc/argv argument vector. */ int getopt_long(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx) { return (getopt_internal(nargc, nargv, options, long_options, idx, FLAG_PERMUTE)); } /* * getopt_long_only -- * Parse argc/argv argument vector. */ int getopt_long_only(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx) { return (getopt_internal(nargc, nargv, options, long_options, idx, FLAG_PERMUTE|FLAG_LONGONLY)); } somoclu-1.4.1/src/Windows/unistd.h0000644000175000001440000000323012433136714016326 0ustar wittekusers#ifndef _UNISTD_H #define _UNISTD_H 1 /* This file intended to serve as a drop-in replacement for * unistd.h on Windows * Please add functionality as neeeded */ #include #include #include "getopt.h" /* getopt at: https://gist.github.com/ashelly/7776712 */ #include /* for getpid() and the exec..() family */ #include /* for _getcwd() and _chdir() */ #define srandom srand #define random rand /* Values for the second argument to access. These may be OR'd together. */ #define R_OK 4 /* Test for read permission. */ #define W_OK 2 /* Test for write permission. */ //#define X_OK 1 /* execute permission - unsupported in windows*/ #define F_OK 0 /* Test for existence. */ #define access _access #define dup2 _dup2 #define execve _execve #define ftruncate _chsize #define unlink _unlink #define fileno _fileno #define getcwd _getcwd #define chdir _chdir #define isatty _isatty #define lseek _lseek /* read, write, and close are NOT being #defined here, because while there are file handle specific versions for Windows, they probably don't work for sockets. You need to look at your app and consider whether to call e.g. closesocket(). */ #define ssize_t int #define STDIN_FILENO 0 #define STDOUT_FILENO 1 #define STDERR_FILENO 2 /* should be in some equivalent to */ typedef __int8 int8_t; typedef __int16 int16_t; typedef __int32 int32_t; typedef __int64 int64_t; typedef unsigned __int8 uint8_t; typedef unsigned __int16 uint16_t; typedef unsigned __int32 uint32_t; typedef unsigned __int64 uint64_t; #endif /* unistd.h */somoclu-1.4.1/src/somoclu.cpp0000644000175000001440000003346612445351346015423 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #ifdef _WIN32 #include "Windows/unistd.h" #include "Windows/getopt.h" #else #include #include #endif #include "somoclu.h" using namespace std; /// For synchronized timing #ifndef MPI_WTIME_IS_GLOBAL #define MPI_WTIME_IS_GLOBAL 1 #endif // Default parameters #define N_EPOCH 10 #define N_SOM_X 50 #define N_SOM_Y 50 #define KERNEL_TYPE 0 #define SNAPSHOTS 0 void processCommandLine(int argc, char** argv, string *inFilename, string* outPrefix, unsigned int *nEpoch, unsigned int *radius0, unsigned int *radiusN, string *radiusCooling, float *scale0, float *scaleN, string *scaleCooling, unsigned int *nSomX, unsigned int *nSomY, unsigned int *kernelType, string *mapType, unsigned int *snapshots, string *initialCodebookFilename); /* -------------------------------------------------------------------------- */ int main(int argc, char** argv) /* -------------------------------------------------------------------------- */ { int rank = 0; int nProcs = 1; #ifdef HAVE_MPI /// /// MPI init /// MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &nProcs); MPI_Barrier(MPI_COMM_WORLD); #endif unsigned int nEpoch = 0; unsigned int nSomX = 0; unsigned int nSomY = 0; unsigned int kernelType = 0; string mapType; unsigned int radius0 = 0; unsigned int radiusN = 0; string radiusCooling; float scale0 = 0.0; float scaleN = 0.0; string scaleCooling; unsigned int snapshots = 0; string inFilename; string initialCodebookFilename; string outPrefix; if (rank==0) { processCommandLine(argc, argv, &inFilename, &outPrefix, &nEpoch, &radius0, &radiusN, &radiusCooling, &scale0, &scaleN, &scaleCooling, &nSomX, &nSomY, &kernelType, &mapType, &snapshots, &initialCodebookFilename); #ifndef CUDA if (kernelType == DENSE_GPU) { cerr << "Somoclu was compile without GPU support!\n"; my_abort(1); } #endif } #ifdef HAVE_MPI MPI_Bcast(&nEpoch, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&radius0, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&nSomX, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&nSomY, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&kernelType, 1, MPI_INT, 0, MPI_COMM_WORLD); char *inFilenameCStr = new char[255]; if (rank == 0) { strcpy(inFilenameCStr,inFilename.c_str()); } MPI_Bcast(inFilenameCStr, 255, MPI_CHAR, 0, MPI_COMM_WORLD); inFilename = inFilenameCStr; char *mapTypeCStr = new char[255]; if (rank == 0) { strcpy(mapTypeCStr,mapType.c_str()); } MPI_Bcast(mapTypeCStr, 255, MPI_CHAR, 0, MPI_COMM_WORLD); mapType = mapTypeCStr; double profile_time = MPI_Wtime(); #endif float * dataRoot = NULL; unsigned int nDimensions = 0; unsigned int nVectors = 0; if(rank == 0 ) { if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { dataRoot = readMatrix(inFilename, nVectors, nDimensions); } else { readSparseMatrixDimensions(inFilename, nVectors, nDimensions); } } #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); MPI_Bcast(&nVectors, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&nDimensions, 1, MPI_INT, 0, MPI_COMM_WORLD); #endif unsigned int nVectorsPerRank = ceil(nVectors / (1.0*nProcs)); // Allocate a buffer on each node float* data = NULL; svm_node **sparseData; sparseData = NULL; if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { #ifdef HAVE_MPI // Dispatch a portion of the input data to each node data = new float[nVectorsPerRank*nDimensions]; MPI_Scatter(dataRoot, nVectorsPerRank*nDimensions, MPI_FLOAT, data, nVectorsPerRank*nDimensions, MPI_FLOAT, 0, MPI_COMM_WORLD); #else data = dataRoot; #endif } else { int currentRankProcessed = 0; while (currentRankProcessed < nProcs) { if (rank == currentRankProcessed) { sparseData=readSparseMatrixChunk(inFilename, nVectors, nVectorsPerRank, rank*nVectorsPerRank); } currentRankProcessed++; #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); #endif } } if(rank == 0) { // No need for root data any more if compiled with MPI #ifdef HAVE_MPI if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { delete [] dataRoot; } #endif cout << "nVectors: " << nVectors << " "; cout << "nVectorsPerRank: " << nVectorsPerRank << " "; cout << "nDimensions: " << nDimensions << " "; cout << endl; } #ifdef CUDA if (kernelType == DENSE_GPU) { setDevice(rank, nProcs); initializeGpu(data, nVectorsPerRank, nDimensions, nSomX, nSomY); } #endif #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); #endif // TRAINING train(rank, data, sparseData, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, nEpoch, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, outPrefix, snapshots, kernelType, mapType, initialCodebookFilename); if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { delete [] data; } else { delete [] sparseData; } #ifdef HAVE_MPI profile_time = MPI_Wtime() - profile_time; if (rank == 0) { cerr << "Total Execution Time: " << profile_time << endl; } #endif #ifdef CUDA if (kernelType == DENSE_GPU) { freeGpu(); } #endif #ifdef HAVE_MPI MPI_Finalize(); #endif return 0; } void printUsage() { cout << "Usage:\n" \ " [mpirun -np NPROC] somoclu [OPTIONs] INPUT_FILE OUTPUT_PREFIX\n" \ "Arguments:\n" \ " -c FILENAME Specify an initial codebook for the map.\n" \ " -e NUMBER Maximum number of epochs (default: " << N_EPOCH << ")\n" \ " -k NUMBER Kernel type (default: " << KERNEL_TYPE << "): \n" \ " 0: Dense CPU\n" \ " 1: Dense GPU\n" \ " 2: Sparse CPU\n" \ " -m TYPE Map type: planar or toroid (default: planar) \n" \ " -t STRATEGY Radius cooling strategy: linear or exponential (default: linear)\n" \ " -r NUMBER Start radius (default: half of the map in direction min(x,y))\n" \ " -R NUMBER End radius (default: 1)\n" \ " -T STRATEGY Learning rate cooling strategy: linear or exponential (default: linear)\n" \ " -l NUMBER Starting learning rate (default: 0.1)\n" \ " -L NUMBER Finishing learning rate (default: 0.01)\n" \ " -s NUMBER Save interim files (default: 0):\n" \ " 0: Do not save interim files\n" \ " 1: Save U-matrix only\n" \ " 2: Also save codebook and best matching neurons\n" \ " -x, --columns NUMBER Number of columns in map (size of SOM in direction x) (default: " << N_SOM_X << ")\n" \ " -y, --rows NUMBER Number of rows in map (size of SOM in direction y) (default: " << N_SOM_Y << ")\n" \ "Examples:\n" \ " somoclu data/rgbs.txt data/rgbs\n" " mpirun -np 4 somoclu -k 0 -x 20 -y 20 data/rgbs.txt data/rgbs\n"; } void processCommandLine(int argc, char** argv, string *inFilename, string* outPrefix, unsigned int *nEpoch, unsigned int *radius0, unsigned int *radiusN, string *radiusCooling, float *scale0, float *scaleN, string *scaleCooling, unsigned int *nSomX, unsigned int *nSomY, unsigned int *kernelType, string *mapType, unsigned int *snapshots, string *initialCodebookFilename) { // Setting default values *nEpoch = N_EPOCH; *nSomX = N_SOM_X; *nSomY = N_SOM_Y; *kernelType = KERNEL_TYPE; *snapshots = SNAPSHOTS; *mapType = "planar"; *radius0 = 0; *radiusN = 0; *radiusCooling = "linear"; *scale0 = 0.0; *scaleN = 0.01; *scaleCooling = "linear"; static struct option long_options[] = { {"rows", required_argument, 0, 'y'}, {"columns", required_argument, 0, 'x'}, {0, 0, 0, 0} }; int c; extern int optind, optopt; int option_index = 0; while ((c = getopt_long (argc, argv, "hx:y:e:k:l:m:r:s:t:c:L:R:T:", long_options, &option_index)) != -1) { switch (c) { case 'c': *initialCodebookFilename = optarg; break; case 'e': *nEpoch = atoi(optarg); if (*nEpoch<=0) { cerr << "The argument of option -e should be a positive integer.\n"; my_abort(1); } break; case 'h': printUsage(); my_abort(0); break; case 'k': *kernelType = atoi(optarg); if (*kernelType>SPARSE_CPU) { cerr << "The argument of option -k should be a valid kernel.\n"; my_abort(1); } break; case 'm': *mapType = optarg; if (*mapType!="planar"&&*mapType!="toroid") { cerr << "The argument of option -m should be either planar or toroid.\n"; my_abort(1); } break; case 'r': *radius0 = atoi(optarg); if (*radius0<=0) { cerr << "The argument of option -r should be a positive integer.\n"; my_abort(1); } break; case 'R': *radiusN = atoi(optarg); if (*radiusN<=0) { cerr << "The argument of option -R should be a positive integer.\n"; my_abort(1); } break; case 't': *radiusCooling = optarg; if (*radiusCooling!="linear"&&*radiusCooling!="exponential") { cerr << "The argument of option -t should be linear or exponential.\n"; my_abort(1); } break; case 'l': *scale0 = atof(optarg); if (*scale0<=0) { cerr << "The argument of option -l should be a positive float.\n"; my_abort(1); } break; case 'L': *scaleN = atof(optarg); if (*scaleN<=0) { cerr << "The argument of option -L should be a positive float.\n"; my_abort(1); } break; case 'T': *scaleCooling = optarg; if (*scaleCooling!="linear"&&*scaleCooling!="exponential") { cerr << "The argument of option -T should be linear or exponential.\n"; my_abort(1); } break; case 's': *snapshots = atoi(optarg); if (*snapshots>2) { cerr << "The argument of option -s should be 0, 1, or 2.\n"; my_abort(1); } break; case 'x': *nSomX = atoi(optarg); if (*nSomX<=0) { cerr << "The argument of option -x should be a positive integer.\n"; my_abort(1); } break; case 'y': *nSomY = atoi(optarg); if (*nSomY<=0) { cerr << "The argument of option -y should be a positive integer.\n"; my_abort(1); } break; case '?': if (optopt == 'e' || optopt == 'k' || optopt == 's' || optopt == 'x' || optopt == 'y') { cerr << "Option -" << optopt << " requires an argument.\n"; printUsage(); my_abort(1); } else if (isprint (optopt)) { cerr << "Unknown option `-" << optopt << "'.\n"; printUsage(); my_abort(1); } else { cerr << "Unknown option character `\\x" << optopt << "'.\n"; printUsage(); my_abort(1); } default: abort (); } } if (argc-optind!=2) { cerr << "Incorrect number of mandatory parameters\n"; printUsage(); my_abort(1); } *inFilename = argv[optind++]; *outPrefix = argv[optind++]; } /// EOF somoclu-1.4.1/src/R/0000755000175000001440000000000012462116543013420 5ustar wittekuserssomoclu-1.4.1/src/R/R/0000755000175000001440000000000012433136714013621 5ustar wittekuserssomoclu-1.4.1/src/R/R/Rsomoclu.R0000644000175000001440000000104012433136714015542 0ustar wittekusers#require(Rcpp) .onLoad <- function(lib, pkg){ library.dynam("Rsomoclu", pkg, lib) } Rsomoclu.train <- function(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType ) { res <- .Call("Rtrain", input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) res } somoclu-1.4.1/src/R/DESCRIPTION0000644000175000001440000000165012462116543015130 0ustar wittekusersPackage: Rsomoclu Version: 1.4.1 Date: 2015-01-28 Title: R package for somoclu Depends: Rcpp Imports: Suggests: Authors@R: c(person(given = "Peter", family = "Wittek", role = c("aut"), email = ""), person(given = "Shichao", family = "Gao", role = c("cre"), email = "xgdgsc@gmail.com")) Description: Somoclu is a cluster-oriented implementation of self-organizing maps. It relies on MPI for distributing the workload, and it can be accelerated by CUDA on a GPU cluster. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes. URL: http://peterwittek.github.io/somoclu/ BugReports: https://github.com/peterwittek/somoclu/issues License: GPL-3 Packaged: 2014-03-16 16:55:16 UTC; Author: Peter Wittek [aut], Shichao Gao [cre] Maintainer: Shichao Gao NeedsCompilation: yes Repository: CRAN SystemRequirements: GNU make somoclu-1.4.1/src/R/man/0000755000175000001440000000000012433136714014173 5ustar wittekuserssomoclu-1.4.1/src/R/man/Rsomoclu.train.Rd0000644000175000001440000000445512433136714017411 0ustar wittekusers\name{Rsomoclu.train} \alias{Rsomoclu.train} \title{Train function for somoclu} \description{ A function call to somoclu to train the Self Organizing Map. } \usage{ Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType ) } \arguments{ \item{input_data}{input data, matrix format} \item{nEpoch}{Maximum number of epochs} \item{nSomX}{Number of columns in map (size of SOM in direction x)} \item{nSomY}{Number of rows in map (size of SOM in direction y)} \item{radius0}{Start radius (default: half of the map in direction min(x,y))} \item{radiusN}{End radius (default: 1)} \item{radiusCooling}{Radius cooling strategy: linear or exponential (default: linear)} \item{scale0}{Starting learning rate (default: 1.0)} \item{scaleN}{Finishing learning rate (default: 0.01)} \item{scaleCooling}{Learning rate cooling strategy: linear or exponential (default: linear)} \item{snapshots}{Save interim files (default: 0): 0: Do not save interim files 1: Save U-matrix only 2: Also save codebook and best matching} \item{kernelType}{Kernel type 0: Dense CPU 1: Dense GPU 2: Sparse CPU} \item{mapType}{Map type: planar or toroid (default: planar)} %% \item{initialCodebookFilename}{Specify an initial codebook for the map} } \references{Peter Wittek (2013). Somoclu: An Efficient Distributed Library for Self-Organizing Maps. arXiv:1305.1422.} \author{Peter Wittek, Shichao Gao} \examples{ library('Rsomoclu') data_file <- system.file("data", "rgbs.txt.gz", package = 'Rsomoclu') input_data <- read.table(data_file) input_data <- data.matrix(input_data) nSomX <- 50 nSomY <- 50 nEpoch <- 10 radius0 <- 0 radiusN <- 0 radiusCooling <- "linear" scale0 <- 0 scaleN <- 0.01 scaleCooling <- "linear" kernelType <- 0 mapType <- "planar" snapshots <- 0 res <- Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) res$codebook res$globalBmus res$uMatrix }somoclu-1.4.1/src/R/man/rgbs.Rd0000644000175000001440000000025612433136714015422 0ustar wittekusers\name{rgbs} \docType{data} \alias{rgbs} \title{tiny rgbs data} \description{ tiny rgbs data for testing } \usage{rgbs} \format{matrix in plain text form} \keyword{datasets}somoclu-1.4.1/src/R/NAMESPACE0000644000175000001440000000007012433136714014634 0ustar wittekusersuseDynLib(Rsomoclu) export(Rsomoclu.train) import(Rcpp) somoclu-1.4.1/src/R/src/0000755000175000001440000000000012433136714014207 5ustar wittekuserssomoclu-1.4.1/src/R/src/Makevars0000644000175000001440000000026212433136714015703 0ustar wittekusersPKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) PKG_CXXFLAGS = `$(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()"` $(SHLIB_OPENMP_CXXFLAGS) -DHAVE_R somoclu-1.4.1/src/R/src/Makevars.win0000644000175000001440000000026312433136714016500 0ustar wittekusersPKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) PKG_CXXFLAGS = `$(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()"` $(SHLIB_OPENMP_CXXFLAGS) -DHAVE_R somoclu-1.4.1/src/R/src/Rsomoclu.cpp0000644000175000001440000001407512433136714016525 0ustar wittekusers #include //#include using namespace std; using namespace Rcpp; #include"somocluWrap.h" void trainWrapperR(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, // string initialCodebookFilename, float *codebook, int codebook_size, int *globalBmus, int globalBmus_size, float *uMatrix, int uMatrix_size) { /// /// Codebook /// int itask = 0; svm_node ** sparseData = NULL; core_data coreData; coreData.codebook_size = nSomY*nSomX*nDimensions; coreData.codebook = new float[coreData.codebook_size]; coreData.globalBmus = NULL; coreData.uMatrix = NULL; unsigned int nVectorsPerRank = nVectors; coreData.globalBmus_size = nVectorsPerRank*int(ceil(nVectors/(double)nVectorsPerRank))*2; if (itask == 0) { coreData.globalBmus = new int[coreData.globalBmus_size]; initializeCodebook(0, coreData.codebook, nSomX, nSomY, nDimensions); } #ifdef CUDA if(kernelType==DENSE_GPU){ int rank = 0; int nProcs = 1; setDevice(rank, nProcs); initializeGpu(data, nVectorsPerRank, nDimensions, nSomX, nSomY); } #endif /// /// Parameters for SOM /// if (radius0 == 0) { radius0 = nSomX / 2.0f; /// init radius for updating neighbors } if (radiusN == 0) { radiusN = 1; } if (scale0 == 0) { scale0 = 1.0; } unsigned int currentEpoch = 0; /// 0...nEpoch-1 /// /// Training /// while ( currentEpoch < nEpoch ) { coreData = trainOneEpoch(itask, data, sparseData, coreData, nEpoch, currentEpoch, snapshots > 0, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, kernelType, mapType); currentEpoch++; } if (itask == 0) { /// /// Save U-mat /// coreData.uMatrix = calculateUMatrix(coreData.codebook, nSomX, nSomY, nDimensions, mapType); coreData.uMatrix_size = nSomX * nSomY; } #ifdef CUDA if (kernelType == DENSE_GPU) { freeGpu(); } #endif if(coreData.codebook != NULL){ memcpy(codebook, coreData.codebook, sizeof(float) * codebook_size); delete [] coreData.codebook; } if(coreData.globalBmus != NULL){ memcpy(globalBmus, coreData.globalBmus, sizeof(int) * globalBmus_size); delete [] coreData.globalBmus; } if(coreData.uMatrix != NULL){ memcpy(uMatrix, coreData.uMatrix, sizeof(float) * uMatrix_size); delete [] coreData.uMatrix; } } RcppExport SEXP Rtrain(SEXP data_p, SEXP nEpoch_p, SEXP nSomX_p, SEXP nSomY_p, SEXP radius0_p, SEXP radiusN_p, SEXP radiusCooling_p, SEXP scale0_p, SEXP scaleN_p, SEXP scaleCooling_p, SEXP snapshots_p, SEXP kernelType_p, SEXP mapType_p) { Rcpp::NumericMatrix dataMatrix(data_p); int nVectors = dataMatrix.rows(); int nDimensions = dataMatrix.cols(); int nEpoch = as(nEpoch_p); unsigned int nSomX = (unsigned int) as (nSomX_p); unsigned int nSomY = (unsigned int) as (nSomY_p); unsigned int radius0 = (unsigned int) as (radius0_p); unsigned int radiusN = (unsigned int) as (radiusN_p); string radiusCooling = as(radiusCooling_p); unsigned int scale0 = (unsigned int) as (scale0_p); unsigned int scaleN = (unsigned int) as (scaleN_p); string scaleCooling = as (scaleCooling_p); unsigned int snapshots = (unsigned int) as(snapshots_p); unsigned int kernelType = (unsigned int) as(kernelType_p); string mapType = as(mapType_p); int data_length = nVectors * nDimensions; float* data = new float[data_length]; // convert matrix to data c float array for(int i = 0; i < nVectors; i++){ for(int j = 0; j < nDimensions; j++){ data[i * nDimensions + j] = (float) dataMatrix(i,j); } } int codebook_size = nSomY * nSomX * nDimensions; int globalBmus_size = nVectors * 2; int uMatrix_size = nSomX * nSomY; float* codebook = new float[codebook_size]; int* globalBmus = new int[globalBmus_size]; float* uMatrix = new float[uMatrix_size]; trainWrapperR(data, data_length, nEpoch, nSomX, nSomY, nDimensions, nVectors, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType, codebook, codebook_size, globalBmus, globalBmus_size, uMatrix, uMatrix_size); Rcpp::NumericVector codebook_vec(codebook_size); Rcpp::NumericVector globalBmus_vec(globalBmus_size); Rcpp::NumericVector uMatrix_vec(uMatrix_size); if(codebook != NULL){ for(int i = 0; i < codebook_size; i++){ codebook_vec(i) = codebook[i]; } } if(globalBmus != NULL){ for(int i = 0; i < globalBmus_size; i++){ globalBmus_vec(i) = globalBmus[i]; } } if(uMatrix != NULL){ for(int i = 0; i < uMatrix_size; i++){ uMatrix_vec(i) = uMatrix[i]; } } delete[] codebook; delete[] globalBmus; delete[] uMatrix; return Rcpp::List::create(Rcpp::Named("codebook") = codebook_vec, Rcpp::Named("globalBmus") = globalBmus_vec, Rcpp::Named("uMatrix") = uMatrix_vec);; } RCPP_MODULE(Rsomoclu){ Rcpp::function("Rtrain", &Rtrain); } somoclu-1.4.1/src/R/tests/0000755000175000001440000000000012433136714014562 5ustar wittekuserssomoclu-1.4.1/src/R/tests/R_interface_test.R0000644000175000001440000000117412433136714020170 0ustar wittekuserslibrary('Rsomoclu') data_file <- system.file("data", "rgbs.txt.gz", package = 'Rsomoclu') input_data <- read.table(data_file) input_data <- data.matrix(input_data) nSomX <- 50 nSomY <- 50 nEpoch <- 10 radius0 <- 0 radiusN <- 0 radiusCooling <- "linear" scale0 <- 0 scaleN <- 0.01 scaleCooling <- "linear" kernelType <- 0 mapType <- "planar" snapshots <- 0 res <- Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) res$codebook res$globalBmus res$uMatrix somoclu-1.4.1/src/training.cpp0000644000175000001440000001367112433136714015546 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #include #include #include "somoclu.h" using namespace std; /** Main training loop * @param itask - number of work items * @param kv * @param ptr */ void train(int itask, float *data, svm_node **sparseData, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int nEpoch, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, string outPrefix, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename) { /// /// Codebook /// core_data coreData; coreData.codebook = new float[nSomY*nSomX*nDimensions]; coreData.globalBmus = NULL; coreData.uMatrix = NULL; if (itask == 0) { coreData.globalBmus = new int[nVectorsPerRank*int(ceil(nVectors/(double)nVectorsPerRank))*2]; if (initialCodebookFilename.empty()){ initializeCodebook(0, coreData.codebook, nSomX, nSomY, nDimensions); } else { unsigned int nSomXY = 0; unsigned int tmpNDimensions = 0; delete [] coreData.codebook; coreData.codebook = readMatrix(initialCodebookFilename, nSomXY, tmpNDimensions); if (tmpNDimensions != nDimensions) { cerr << "Dimension of initial codebook does not match data!\n"; my_abort(5); } else if (nSomXY / nSomY != nSomX) { cerr << "Dimension of initial codebook does not match specified SOM grid!\n"; my_abort(6); } cout << "Read initial codebook: " << initialCodebookFilename << "\n"; } } /// /// Parameters for SOM /// if (radius0 == 0) { unsigned int minDim = min(nSomX, nSomY); radius0 = minDim / 2.0f; /// init radius for updating neighbors } if (radiusN == 0) { radiusN = 1; } if (scale0 == 0) { scale0 = 0.1; } unsigned int currentEpoch = 0; /// 0...nEpoch-1 /// /// Training /// #ifdef HAVE_MPI double training_time = MPI_Wtime(); #endif while ( currentEpoch < nEpoch ) { #ifdef HAVE_MPI double epoch_time = MPI_Wtime(); #endif coreData = trainOneEpoch(itask, data, sparseData, coreData, nEpoch, currentEpoch, snapshots > 0, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, kernelType, mapType); if (snapshots > 0 && itask == 0) { cout << "Saving interim U-Matrix..." << endl; stringstream sstm; sstm << outPrefix << "." << currentEpoch + 1; saveUMatrix(sstm.str() + string(".umx"), coreData.uMatrix, nSomX, nSomY); if (snapshots == 2){ saveBmus(sstm.str() + string(".bm"), coreData.globalBmus, nSomX, nSomY, nVectors); saveCodebook(sstm.str() + string(".wts"), coreData.codebook, nSomX, nSomY, nDimensions); } } currentEpoch++; #ifdef HAVE_MPI if (itask == 0) { epoch_time = MPI_Wtime() - epoch_time; cerr << "Epoch Time: " << epoch_time << endl; if ( (currentEpoch != nEpoch) && (currentEpoch % (nEpoch/100+1) != 0) ){} else{ float ratio = currentEpoch/(float)nEpoch; int c = ratio * 50 + 1; cout << std::setw(7) << (int)(ratio*100) << "% ["; for (int x=0; x nrhs) mexErrMsgIdAndTxt( "MATLAB:mexfunction:inputOutputMismatch", "Cannot specify more outputs than inputs.\n"); plhs[0] = mxCreateDoubleMatrix(codebook_size, 1, mxREAL); double* codebook_p = mxGetPr(plhs[0]); for(int i = 0; i < codebook_size; i++){ codebook_p[i] = (double) codebook[i]; } if(globalBmus!=NULL){ plhs[1] = mxCreateDoubleMatrix(globalBmus_size, 1, mxREAL); double* globalBmus_p = mxGetPr(plhs[1]); for(int i = 0; i < globalBmus_size; i++){ globalBmus_p[i] = (double) globalBmus[i]; } } else{ plhs[1] = mxCreateDoubleMatrix(1, 1, mxREAL); *mxGetPr(plhs[1]) = 1; } plhs[2] = mxCreateDoubleMatrix(uMatrix_size, 1, mxREAL); double* uMatrix_p = mxGetPr(plhs[2]); for(int i = 0; i < uMatrix_size; i++){ uMatrix_p[i] = (double) uMatrix[i]; } delete[] codebook; delete[] globalBmus; delete[] uMatrix; } somoclu-1.4.1/src/MATLAB/mex_interface_test.m0000644000175000001440000000104712433136714020207 0ustar wittekusersdata = importdata('../../data/rgbs.txt'); nSomX = 50; nSomY = 50; dataSize = size(data); nVectors = dataSize(1); nDimensions = dataSize(2); nEpoch = 10; radius0 = 0; radiusN = 0; radiusCooling = 'linear'; scale0 = 0; scaleN = 0.01; scaleCooling = 'linear'; kernelType = 0; mapType = 'planar'; snapshots = 0; initialCodebookFilename = ''; [codebook, globalBmus, uMatrix] = MexSomoclu(data, nEpoch, nSomX, nSomY, ... radius0, radiusN, ... radiusCooling, scale0, scaleN, ... scaleCooling, snapshots, ... kernelType, mapType, ... initialCodebookFilename);somoclu-1.4.1/src/MATLAB/README.rst0000644000175000001440000000445512462116543015656 0ustar wittekusersVersion: 1.4.1 Maintainer: ShichaoGao URL: http://peterwittek.github.io/somoclu/ BugReports: https://github.com/peterwittek/somoclu/issues License: GPL-3 OS_type: unix Somoclu MATLAB Extension Build Guide: ================================ 1. Follow the instructions to build Somoclu itself at: https://github.com/peterwittek/somoclu **(OS X users see the Note below first)** 2. Build MATLAB Extension by running: :: MEX_BIN="/usr/local/MATLAB/R2013a/bin/mex" ./makeMex.sh where ``MEX_BIN`` is the path to the MATLAB installation mex binary. 3. Then ``MexSomoclu.mexa64`` or ``MexSomoclu.mexa32`` is generated for use, you can test by running the ``mex_interface_test.m``. Note for Mac OS X users: ================================ As of OS X 10.9, gcc is just symlink to clang. To build somoclu and this extension correctly, it is recommended to install gcc using something like: :: $ brew install gcc48 and set environment using: :: export CC=/usr/local/bin/gcc export CXX=/usr/local/bin/g++ export CPP=/usr/local/bin/cpp export LD=/usr/local/bin/gcc alias c++=/usr/local/bin/c++ alias g++=/usr/local/bin/g++ alias gcc=/usr/local/bin/gcc alias cpp=/usr/local/bin/cpp alias ld=/usr/local/bin/gcc alias cc=/usr/local/bin/gcc Then follow the instructions at https://github.com/peterwittek/somoclu to build somoclu itself. Building Mex Extension on OS X: =============================== To build the extension on OS X, we need to make mex use gcc instead of the default clang compiler. So we need to copy ``MATLAB_ROOT/bin/mexopts.sh`` to ``~/.matlab/VERSION/mexopts.sh`` , replace ``MATLAB_ROOT`` with your installation path of MATLAB and replace ``VERSION`` with your MATLAB version in that folder. Example: :: cp /Applications/MATLAB_R2013a.app/bin/mexopts.sh ~/.matlab/R2013a/mexopts.sh Then modify ``~/.matlab/VERSION/mexopts.sh`` to use gcc as follows: 1. change ``CC='gcc'`` and comment out all ``CC=`` statements after that. 2. change ``CXX='g++'`` and comment out all ``CXX=`` statements after that. 3. change ``MACOSX_DEPLOYMENT_TARGET='10.9'`` where ``10.9`` is your OS X version number. an example is given at https://gist.github.com/xgdgsc/9832340, then you can follow the instruction step 2 at the top to build the extension and test. somoclu-1.4.1/src/MATLAB/makeMex-GPU.sh0000755000175000001440000000057012433136714016540 0ustar wittekusers#!/bin/sh if [ -z "$MEX_BIN" ] then MEX_BIN="/usr/local/MATLAB/R2013a/bin/mex" fi CUDA_LIB="/opt/cuda/lib64" $MEX_BIN -I../ MexSomoclu.cpp -DCUDA ../somocluWrap.cpp ../somoclu.o ../denseCpuKernels.o ../io.o ../sparseCpuKernels.o ../training.o ../mapDistanceFunctions.o ../trainOneEpoch.o ../uMatrix.o ../denseGpuKernels.cu.co -lgomp -L$CUDA_LIB -lcudart -lcublas -lnvblas somoclu-1.4.1/src/MATLAB/makeMex.sh0000755000175000001440000000042612433136714016107 0ustar wittekusers#!/bin/sh if [ -z "$MEX_BIN" ] then MEX_BIN="/usr/local/MATLAB/R2013a/bin/mex" fi $MEX_BIN -I../ MexSomoclu.cpp ../somocluWrap.cpp ../somoclu.o ../denseCpuKernels.o ../io.o ../sparseCpuKernels.o ../training.o ../mapDistanceFunctions.o ../trainOneEpoch.o ../uMatrix.o -lgomp somoclu-1.4.1/src/denseGpuKernels.cu0000644000175000001440000003610012433136714016646 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #undef _GLIBCXX_ATOMIC_BUILTINS #undef _GLIBCXX_USE_INT128 #include #include #include #include #include #include #include #include #include #include "somoclu.h" #ifdef _WIN32 #define popen _popen #define pclose _pclose #endif // Error handling macro #define CUDA_CHECK(call) \ if((call) != cudaSuccess) { \ cudaError_t err = cudaGetLastError(); \ cerr << "CUDA error calling \""#call"\", code is " << err << endl; \ my_abort(err); } //Globals cublasHandle_t handle; thrust::device_vector deviceData; thrust::device_vector deviceDataNorms; thrust::device_vector deviceCodebook; thrust::device_vector deviceCodebookNorms; // convert a linear index to a row index template struct linear_index_to_row_index : public thrust::unary_function { T C; // number of columns __host__ __device__ linear_index_to_row_index(T C) : C(C) {} __host__ __device__ T operator()(T i) { return i / C; } }; // note: functor inherits from unary_function template struct square : public thrust::unary_function { __host__ __device__ T operator()(T x) const { return x*x; } }; typedef thrust::tuple argMinType; struct argMin : public thrust::binary_function { __host__ __device__ argMinType operator()(const argMinType& a, const argMinType& b) const { if (thrust::get<1>(a) < thrust::get<1>(b)) { return a; } else { return b; } } }; template thrust::device_vector normsOfRowSpace(thrust::device_vector A, int nRows, int nColumns) { // allocate storage for row sums and indices thrust::device_vector row_sums(nRows); thrust::device_vector row_indices(nRows); // compute row sums by summing values with equal row indices thrust::reduce_by_key (thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)), thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)) + (nRows*nColumns), thrust::make_transform_iterator(A.begin(), square()), row_indices.begin(), row_sums.begin(), thrust::equal_to(), thrust::plus()); return row_sums; } thrust::device_vector minsOfRowSpace(thrust::device_vector A, int nRows, int nColumns) { // allocate storage for row sums and indices thrust::device_vector row_sums(nRows); thrust::device_vector row_indices(nRows); // compute row sums by summing values with equal row indices thrust::reduce_by_key (thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)), thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)) + (nRows*nColumns), thrust::make_zip_iterator(thrust::make_tuple(thrust::counting_iterator(0),A.begin())), row_indices.begin(), row_sums.begin(), thrust::equal_to(), argMin()); return row_sums; } template __global__ void euclidean(float *anorm2, float *bnorm2, float *M, int height, int width) { unsigned int xIndex = blockIdx.x * BLOCK_DIM + threadIdx.x; unsigned int yStartIndex = blockIdx.y * BLOCK_DIM; if (xIndex < width) { float bNormForX = bnorm2[xIndex]; unsigned int yEndIndex=(yStartIndex+BLOCK_DIM < height ? yStartIndex+BLOCK_DIM : height); for (unsigned int yIndex=yStartIndex; yIndex void printMatrix(thrust::device_vector A, int nRows, int nColumns) { for (size_t i = 0; i < nRows; i++) { for (size_t j = 0; j < nColumns; j++) { std::cout << A[i*nColumns+j] << " "; } std::cout << "\n"; } std::cout << "\n"; } /** Clear the device memory and shut down CUBLAS * */ void freeGpu() { deviceData.clear(); deviceDataNorms.clear(); deviceCodebook.clear(); deviceCodebookNorms.clear(); thrust::device_vector().swap(deviceData); thrust::device_vector().swap(deviceDataNorms); thrust::device_vector().swap(deviceCodebook); thrust::device_vector().swap(deviceCodebookNorms); cublasStatus_t status = cublasDestroy(handle); if (status != CUBLAS_STATUS_SUCCESS) { cerr << "!!!! shutdown error (A)\n"; my_abort(-1); } } /** Find the best matching units -- called from the map function * @param bmus - array of best matching units * @param codebook - the codebook to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance * @param nVectorsPerRank - the number of data points assigned to this GPU */ void getBmusOnGpu(int *bmus, float *codebook, int nSomX, int nSomY, int nDimensions, int nVectorsPerRank) { deviceCodebook = thrust::device_vector(codebook, codebook+nSomX*nSomY*nDimensions); deviceCodebookNorms = normsOfRowSpace(deviceCodebook, nSomX*nSomY, nDimensions); thrust::device_vector deviceGramMatrix(nSomX*nSomY*nVectorsPerRank, 0); //Calculate the inner products of the data vectors and the weight vectors float alpha = 1.0f; float beta = 0.0f; cublasStatus_t status = cublasSgemm(handle, CUBLAS_OP_T, CUBLAS_OP_N, nSomX*nSomY, nVectorsPerRank, nDimensions, &alpha, thrust::raw_pointer_cast(&deviceCodebook[0]), nDimensions, thrust::raw_pointer_cast(&deviceData[0]), nDimensions, &beta, thrust::raw_pointer_cast(&deviceGramMatrix[0]), nSomX*nSomY); if (status != CUBLAS_STATUS_SUCCESS) { cerr << "!!!! kernel execution error.\n"; my_abort(-1); } //All components of the vectorized Euclidean distance are available // 32 is a magic number, this is the block size that works best on Tesla C2050 int BLOCK_DIM=32; dim3 grid((nSomX*nSomY+BLOCK_DIM-1)/BLOCK_DIM, (nVectorsPerRank+BLOCK_DIM-1)/BLOCK_DIM,1); dim3 threads(BLOCK_DIM,1,1); if (BLOCK_DIM==32) { euclidean<32><<>>(thrust::raw_pointer_cast(&deviceDataNorms[0]), thrust::raw_pointer_cast(&deviceCodebookNorms[0]), thrust::raw_pointer_cast(&deviceGramMatrix[0]), nVectorsPerRank, nSomX*nSomY); } //Finding minimums thrust::host_vector minsOfA=minsOfRowSpace(deviceGramMatrix, nVectorsPerRank, nSomX*nSomY); CUDA_CHECK(cudaDeviceSynchronize()); //Getting back SOM coordinates from minimums for (int i=0; i(tmp) % (nSomX*nSomY); bmus[i*2] = somCoordinate % nSomX; bmus[i*2+1] = somCoordinate / nSomX; } } /** Initialize CUBLAS and device data * @param hostData - the data in the main memory * @param height - number of data points assigned to this GPU * @param width - dimensions of a data instance */ void initializeGpu(float *hostData, int nVectorsPerRank, int nDimensions, int nSomX, int nSomY) { /* Initialize CUBLAS */ cublasStatus_t status = cublasCreate(&handle); if (status != CUBLAS_STATUS_SUCCESS) { cerr << "!!!! CUBLAS initialization error\n"; my_abort(-1); } deviceData = thrust::device_vector(hostData, hostData+nVectorsPerRank*nDimensions); deviceDataNorms = normsOfRowSpace(deviceData, nVectorsPerRank, nDimensions); deviceCodebook = thrust::device_vector(nSomX*nSomY*nDimensions,0); deviceCodebookNorms = thrust::device_vector(nSomX*nSomY,0); } /** Check and initialize a device attached to a node * @param commRank - the MPI rank of this process * @param commSize - the size of MPI comm world */ /// Note that this function was lifted from http://code.google.com/p/gpmr/ void setDevice(int commRank, int commSize) { int devCount; int deviceNum=0; CUDA_CHECK(cudaGetDeviceCount(&devCount)); #ifdef HAVE_MPI #ifdef _WIN32 FILE * fp = popen("hostname.exe", "r"); #else FILE * fp = popen("/bin/hostname", "r"); #endif char buf[1024]; if (fgets(buf, 1023, fp) == NULL) strcpy(buf, "localhost"); pclose(fp); string host = buf; host = host.substr(0, host.size() - 1); strcpy(buf, host.c_str()); if (commRank == 0) { map > hosts; map devCounts; hosts[buf].push_back(0); devCounts[buf] = devCount; MPI_Status stat; MPI_Request req; for (int i = 1; i < commSize; ++i) { MPI_Recv(buf, 1024, MPI_CHAR, i, 0, MPI_COMM_WORLD, &stat); MPI_Recv(&devCount, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &stat); // check to make sure each process on each node reports the same number of devices. hosts[buf].push_back(i); if (devCounts.find(buf) != devCounts.end()) { if (devCounts[buf] != devCount) { printf("Error, device count mismatch %d != %d on %s\n", devCounts[buf], devCount, buf); fflush(stdout); } } else devCounts[buf] = devCount; } // check to make sure that we don't have more jobs on a node than we have GPUs. for (map >::iterator it = hosts.begin(); it != hosts.end(); ++it) { if (it->second.size() > static_cast(devCounts[it->first])) { printf("Error, more jobs running on '%s' than devices - %d jobs > %d devices.\n", it->first.c_str(), static_cast(it->second.size()), devCounts[it->first]); fflush(stdout); my_abort(1); } } // send out the device number for each process to use. MPI_Irecv(&deviceNum, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &req); for (map >::iterator it = hosts.begin(); it != hosts.end(); ++it) { for (unsigned int i = 0; i < it->second.size(); ++i) { int devID = i; MPI_Send(&devID, 1, MPI_INT, it->second[i], 0, MPI_COMM_WORLD); } } MPI_Wait(&req, &stat); } else { // send out the hostname and device count for your local node, then get back the device number you should use. MPI_Status stat; MPI_Send(buf, strlen(buf) + 1, MPI_CHAR, 0, 0, MPI_COMM_WORLD); MPI_Send(&devCount, 1, MPI_INT, 0, 0, MPI_COMM_WORLD); MPI_Recv(&deviceNum, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &stat); } MPI_Barrier(MPI_COMM_WORLD); #endif CUDA_CHECK(cudaSetDevice(deviceNum)); } /** One epoch on the GPU, dense variant */ void trainOneEpochDenseGPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus) { #ifdef _WIN32 int* bmus = (int *)alloca(sizeof(int) * nVectorsPerRank * 2); #else int bmus[nVectorsPerRank*2]; #endif getBmusOnGpu(bmus, codebook, nSomX, nSomY, nDimensions, nVectorsPerRank); float *localNumerator = new float[nSomY*nSomX*nDimensions]; float *localDenominator = new float[nSomY*nSomX]; #pragma omp parallel default(shared) { #pragma omp for for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { localDenominator[som_y*nSomX + som_x] = 0.0; for (unsigned int d = 0; d < nDimensions; d++) localNumerator[som_y*nSomX*nDimensions + som_x*nDimensions + d] = 0.0; } } /// Accumulate denoms and numers #pragma omp for for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { for (unsigned int n = 0; n < nVectorsPerRank; n++) { if (itask*nVectorsPerRank+n using namespace std; void trainWrapper(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename, float* codebook, int codebook_size, int* globalBmus, int globalBmus_size, float* uMatrix, int uMatrix_size); void trainWrapperR(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, float *codebook, int codebook_size, int *globalBmus, int globalBmus_size, float *uMatrix, int uMatrix_size); #endif // SOMOCLUWRAP_H somoclu-1.4.1/src/uMatrix.cpp0000644000175000001440000000610412433136714015355 0ustar wittekusers #include"somoclu.h" #include /** Get weight vector from a codebook using x, y index * @param codebook - the codebook to save * @param som_y - y coordinate of a node in the map * @param som_x - x coordinate of a node in the map * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance * @return the weight vector */ float* get_wvec(float *codebook, unsigned int som_y, unsigned int som_x, unsigned int nSomX, unsigned int nDimensions) { float* wvec = new float[nDimensions]; for (unsigned int d = 0; d < nDimensions; d++) wvec[d] = codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]; /// CAUTION: (y,x) order return wvec; } /** Euclidean distance between vec1 and vec2 * @param vec1 * @param vec2 * @param nDimensions * @return distance */ float get_distance(const float* vec1, const float* vec2, unsigned int nDimensions) { float distance = 0.0f; float x1 = 0.0f; float x2 = 0.0f; for (unsigned int d = 0; d < nDimensions; d++) { x1 = std::min(vec1[d], vec2[d]); x2 = std::max(vec1[d], vec2[d]); distance += std::abs(x1-x2)*std::abs(x1-x2); } return sqrt(distance); } /** Calculate U-matrix * @param codebook - the codebook * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ float *calculateUMatrix(float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, string mapType) { float *uMatrix = new float[nSomX*nSomY]; float min_dist = 1.5f; for (unsigned int som_y1 = 0; som_y1 < nSomY; som_y1++) { for (unsigned int som_x1 = 0; som_x1 < nSomX; som_x1++) { float dist = 0.0f; unsigned int nodes_number = 0; for (unsigned int som_y2 = 0; som_y2 < nSomY; som_y2++) { for (unsigned int som_x2 = 0; som_x2 < nSomX; som_x2++) { if (som_x1 == som_x2 && som_y1 == som_y2) continue; float tmp = 0.0f; if (mapType == "planar") { tmp = euclideanDistanceOnPlanarMap(som_x1, som_y1, som_x2, som_y2); } else if (mapType == "toroid") { tmp = euclideanDistanceOnToroidMap(som_x1, som_y1, som_x2, som_y2, nSomX, nSomY); } if (tmp <= min_dist) { nodes_number++; float* vec1 = get_wvec(codebook, som_y1, som_x1, nSomX, nDimensions); float* vec2 = get_wvec(codebook, som_y2, som_x2, nSomX, nDimensions); dist += get_distance(vec1, vec2, nDimensions); delete [] vec1; delete [] vec2; } } } dist /= (float)nodes_number; uMatrix[som_y1*nSomX+som_x1] = dist; } } return uMatrix; } somoclu-1.4.1/src/somoclu.h0000644000175000001440000001267012433136714015057 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include using namespace std; #ifndef SOMOCLU_H #define SOMOCLU_H #if HAVE_CONFIG_H #include #endif #ifdef HAVE_MPI #include #endif #define DENSE_CPU 0 #define DENSE_GPU 1 #define SPARSE_CPU 2 /// The neighbor_fuct value below which we consider /// the impact zero for a given node in the map #define NEIGHBOR_THRESHOLD 0.05 /// Sparse structures and routines struct svm_node { int index; float value; }; /// Core data structures struct core_data { float *codebook; int *globalBmus; float *uMatrix; int codebook_size; int globalBmus_size; int uMatrix_size; }; float euclideanDistanceOnToroidMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y, const unsigned int nSomX, const unsigned int nSomY); float euclideanDistanceOnPlanarMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y); float getWeight(float distance, float radius, float scaling); int saveCodebook(string cbFileName, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions); float *calculateUMatrix(float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, string mapType); int saveUMatrix(string fname, float *uMatrix, unsigned int nSomX, unsigned int nSomY); int saveBmus(string filename, int *bmus, unsigned int nSomX, unsigned int nSomY, unsigned int nVectors); //void printMatrix(float *A, int nRows, int nCols); float *readMatrix(const string inFilename, unsigned int &nRows, unsigned int &nCols); void readSparseMatrixDimensions(const string filename, unsigned int &nRows, unsigned int &nColumns); svm_node** readSparseMatrixChunk(const string filename, unsigned int nRows, unsigned int nRowsToRead, unsigned int rowOffset); core_data trainOneEpoch(int itask, float *data, svm_node **sparseData, core_data coreData, unsigned int nEpoch, unsigned int currentEpoch, bool enableCalculatingUMatrix, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int kernelType, string mapType); void train(int itask, float *data, svm_node **sparseData, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int nEpoch, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, string outPrefix, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename); void trainOneEpochDenseCPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus); void trainOneEpochSparseCPU(int itask, svm_node **sparseData, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus); void initializeCodebook(unsigned int seed, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions); extern "C" { #ifdef CUDA void setDevice(int commRank, int commSize); void freeGpu(); void initializeGpu(float *hostData, int nVectorsPerRank, int nDimensions, int nSomX, int nSomY); void trainOneEpochDenseGPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus); #endif void my_abort(int err); } #endif somoclu-1.4.1/src/io.cpp0000644000175000001440000002424512433136714014341 0ustar wittekusers/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #include #include #include #include "somoclu.h" using namespace std; /** Save a SOM codebook * @param cbFileName - name of the file to save * @param codebook - the codebook to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ int saveCodebook(string cbFilename, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions) { FILE* file = fopen(cbFilename.c_str(), "wt"); cout << " Saving Codebook " << cbFilename << endl; fprintf(file, "%%%d %d\n", nSomY, nSomX); fprintf(file, "%%%d\n", nDimensions); if (file!=0) { for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { for (unsigned int d = 0; d < nDimensions; d++) { fprintf(file, "%0.10f ", codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]); } fprintf(file, "\n"); } } fclose(file); return 0; } else { return 1; } } /** Save best matching units * @param filename - name of the file to save * @param bmus - the best matching units to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nVectors - the number of vectors */ int saveBmus(string filename, int *bmus, unsigned int nSomX, unsigned int nSomY, unsigned int nVectors) { FILE* file = fopen(filename.c_str(), "wt"); cout << " Saving best matching units " << filename << endl; fprintf(file, "%%%d %d\n", nSomY, nSomX); fprintf(file, "%%%d\n", nVectors); if (file!=0) { for (unsigned int i = 0; i < nVectors; ++i) { // ESOM Tools swaps x and y! fprintf(file, "%d %d %d\n", i, bmus[2*i+1], bmus[2*i]); } fclose(file); return 0; } else { return 1; } } /** Save u-matrix * @param fname * @param codebook - the codebook to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ int saveUMatrix(string fname, float *uMatrix, unsigned int nSomX, unsigned int nSomY) { FILE* fp = fopen(fname.c_str(), "wt"); fprintf(fp, "%%"); fprintf(fp, "%d %d", nSomY, nSomX); fprintf(fp, "\n"); if (fp != 0) { for (unsigned int som_y1 = 0; som_y1 < nSomY; som_y1++) { for (unsigned int som_x1 = 0; som_x1 < nSomX; som_x1++) { fprintf(fp, " %f", uMatrix[som_y1*nSomX+som_x1]); } fprintf(fp, "\n"); } fclose(fp); return 0; } else return -2; } void getMatrixDimensions(string inFilename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(inFilename.c_str()); if (file.is_open()) { string line; float tmp; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } std::istringstream iss(line); if (nRows == 0) { while (iss >> tmp) { nColumns++; } } nRows++; } file.close(); } else { std::cerr << "Input file could not be opened!\n"; my_abort(-1); } } unsigned int *readLrnHeader(string inFilename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(inFilename.c_str()); string line; unsigned int currentColumn = 0; unsigned int nAllColumns = 0; unsigned int *columnMap = NULL; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } if (line.substr(0,1) == "%") { std::istringstream iss(line.substr(1,line.length())); if (nRows == 0) { iss >> nRows; } else if (nAllColumns == 0) { iss >> nAllColumns; } else if (columnMap == NULL) { columnMap = new unsigned int[nAllColumns]; unsigned int itmp = 0; currentColumn = 0; while (iss >> itmp) { columnMap[currentColumn++] = itmp; if (itmp == 1) { ++nColumns; } } } else { break; } } } file.close(); return columnMap; } unsigned int *readWtsHeader(string inFilename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(inFilename.c_str()); string line; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } if (line.substr(0,1) == "%") { std::istringstream iss(line.substr(1,line.length())); if (nRows == 0) { iss >> nRows; unsigned int nSomY = 0; iss >> nSomY; nRows = nRows*nSomY; } else if (nColumns == 0) { iss >> nColumns; } else { break; } } } file.close(); unsigned int *columnMap = new unsigned int[nColumns]; for (unsigned int i = 0; i < nColumns; ++i) { columnMap[i] = 1; } return columnMap; } /** Reads a matrix * @param inFilename * @param nRows - returns the number of rows * @param nColumns - returns the number of columns * @return the matrix */ float *readMatrix(string inFilename, unsigned int &nRows, unsigned int &nColumns) { float *data = NULL; unsigned int *columnMap = NULL; if (inFilename.compare(inFilename.size()-3, 3, "lrn") == 0) { columnMap = readLrnHeader(inFilename, nRows, nColumns); } else if (inFilename.compare(inFilename.size()-3, 3, "wts") == 0) { columnMap = readWtsHeader(inFilename, nRows, nColumns); } else { getMatrixDimensions(inFilename, nRows, nColumns); columnMap = new unsigned int[nColumns]; for (unsigned int i = 0; i < nColumns; ++i) { columnMap[i] = 1; } } ifstream file; file.open(inFilename.c_str()); string line; float tmp; unsigned int j = 0; unsigned int currentColumn = 0; while(getline(file,line)) { if ( (line.substr(0,1) == "#") | (line.substr(0,1) == "%") ) { continue; } if (data == NULL) { data = new float[nRows*nColumns]; } std::istringstream iss(line); currentColumn = 0; while (iss >> tmp) { if (columnMap[currentColumn++] != 1) { continue; } data[j++] = tmp; } } file.close(); delete [] columnMap; return data; } void readSparseMatrixDimensions(string filename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(filename.c_str()); if (file.is_open()) { string line; int max_index=-1; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } stringstream linestream(line); string value; int dummy_index; while(getline(linestream,value,' ')) { int separator=value.find(":"); istringstream myStream(value.substr(0,separator)); myStream >> dummy_index; if(dummy_index > max_index) { max_index = dummy_index; } } ++nRows; } nColumns=max_index+1; file.close(); } else { std::cerr << "Input file could not be opened!\n"; my_abort(-1); } } svm_node** readSparseMatrixChunk(string filename, unsigned int nRows, unsigned int nRowsToRead, unsigned int rowOffset) { ifstream file; file.open(filename.c_str()); string line; for (unsigned int i=0; i= nRows) { nRowsToRead = nRows-rowOffset; } svm_node **x_matrix = new svm_node *[nRowsToRead]; for(unsigned int i=0; i> x_matrix[i][j].index; istringstream myStream2(value.substr(separator+1)); myStream2 >> x_matrix[i][j].value; j++; } x_matrix[i][j].index = -1; } file.close(); return x_matrix; } /** Shut down MPI cleanly if something goes wrong * @param err - error code to print */ void my_abort(int err) { cerr << "Aborted\n"; #ifdef HAVE_MPI MPI_Abort(MPI_COMM_WORLD, err); #else exit(err); #endif } somoclu-1.4.1/src/Python/0000755000175000001440000000000012462151234014474 5ustar wittekuserssomoclu-1.4.1/src/Python/setup.py0000644000175000001440000000326612462151234016215 0ustar wittekusers#!/usr/bin/env python2 """ setup.py file for SWIG example """ from setuptools import setup, Extension from setuptools.command.install import install from subprocess import call import numpy import os import sys try: numpy_include = numpy.get_include() except AttributeError: numpy_include = numpy.get_numpy_include() sources_files=[ 'src/src/somocluWrap.cpp', 'src/src/denseCpuKernels.cpp', 'src/src/io.cpp', 'src/src/sparseCpuKernels.cpp', 'src/src/training.cpp', 'src/src/mapDistanceFunctions.cpp', 'src/src/trainOneEpoch.cpp', 'src/src/uMatrix.cpp', 'somoclu_wrap.cxx'] if sys.platform.startswith('win'): extra_compile_args = ['-openmp'] extra_link_args = [] else: extra_compile_args = ['-fopenmp'] extra_link_args = [ '-lgomp' ] somoclu_module = Extension('_somoclu', sources=sources_files, include_dirs=[numpy_include, 'src/src'], extra_compile_args=extra_compile_args, extra_link_args=extra_link_args ) setup(name='somoclu', version='1.4.1', license='GPL3', author="peterwittek", author_email="", maintainer="shichaogao", maintainer_email="xgdgsc@gmail.com", url="http://peterwittek.github.io/somoclu/", platforms=["unix", "windows"], description="a massively parallel implementation of " "self-organizing maps", ext_modules=[somoclu_module], py_modules=["somoclu"], install_requires=['numpy'] ) somoclu-1.4.1/src/Python/somoclu.i0000644000175000001440000000333412433136714016336 0ustar wittekusers%module somoclu %include "std_string.i" %{ #define SWIG_FILE_WITH_INIT #include "src/src/somocluWrap.h" %} %include "numpy.i" %init %{ import_array(); %} %apply (float* INPLACE_ARRAY1, int DIM1) {(float* data, int data_length)} %apply (float* INPLACE_ARRAY1, int DIM1) {(float* codebook, int codebook_size)} %apply (int* INPLACE_ARRAY1, int DIM1) {(int* globalBmus, int globalBmus_size)} %apply (float* INPLACE_ARRAY1, int DIM1) {(float* uMatrix, int uMatrix_size)} /* %typemap (in,numinputs=0) core_data * (core_data temp) { */ /* $1 = &temp; */ /* } */ /* %typemap (argout) core_data * { */ /* /\* codebook *\/ */ /* { */ /* npy_intp dims[1] = { $1->codebook_size }; */ /* PyObject * array = PyArray_SimpleNewFromData(1, dims, NPY_FLOAT32, (void*)($1->codebook)); */ /* if (!array) SWIG_fail; */ /* $result = SWIG_Python_AppendOutput($result,array); */ /* } */ /* /\* globalBmus *\/ */ /* { */ /* npy_intp dims[1] = { $1->globalBmus_size }; */ /* PyObject * array = PyArray_SimpleNewFromData(1, dims, NPY_INT32, (void*)($1->globalBmus)); */ /* if (!array) SWIG_fail; */ /* $result = SWIG_Python_AppendOutput($result,array); */ /* } */ /* /\* uMatrix *\/ */ /* { */ /* npy_intp dims[1] = { $1->uMatrix_size }; */ /* PyObject * array = PyArray_SimpleNewFromData(1, dims, NPY_FLOAT32, (void*)($1->uMatrix)); */ /* if (!array) SWIG_fail; */ /* $result = SWIG_Python_AppendOutput($result,array); */ /* } */ /* } */ /* %ignore core_data; */ /* struct core_data */ /* { */ /* float *codebook; */ /* int *globalBmus; */ /* float *uMatrix; */ /* int codebook_size; */ /* int globalBmus_size; */ /* int uMatrix_size; */ /* }; */ %include "src/src/somocluWrap.h" somoclu-1.4.1/src/Python/setup_with_CUDA.py0000644000175000001440000000451712462116543020050 0ustar wittekusers#!/usr/bin/env python2 """ setup.py file for CUDA use sudo python2 setup_with_CUDA.py install to install """ from setuptools import setup, Extension from setuptools.command.install import install from subprocess import call import numpy import os try: numpy_include = numpy.get_include() except AttributeError: numpy_include = numpy.get_numpy_include() class MyInstall(install): def run(self): #call(["src/autogen.sh"]) call(["pwd"]) os.chdir('src') call(["bash", "autogen.sh"]) ## CUDA PATH here: call(["./configure", "--without-mpi","--with-cuda=/opt/cuda/"]) call(["make"]) os.chdir('../') install.run(self) somoclu_module = Extension('_somoclu', sources=['somoclu_wrap.cxx', 'src/src/somocluWrap.cpp'], extra_objects=['src/src/somoclu.o', 'src/src/denseCpuKernels.o', 'src/src/io.o', 'src/src/sparseCpuKernels.o', 'src/src/training.o', 'src/src/mapDistanceFunctions.o', 'src/src/trainOneEpoch.o', 'src/src/uMatrix.o', 'src/src/denseGpuKernels.cu.co'], define_macros=[('CUDA', None)], #PATH to CUDA library here, 64 for 64 bit library_dirs=['/opt/cuda/lib64'], libraries=['gomp','cudart','cublas'], include_dirs=[numpy_include] ) setup(name='somoclu', version='1.4.1', license='GPL3', author="peterwittek", author_email="", maintainer="shichaogao", maintainer_email="xgdgsc@gmail.com", url="http://peterwittek.github.io/somoclu/", platforms="unix", description="a cluster-oriented implementation of self-organizing maps", ext_modules=[somoclu_module], py_modules=["somoclu"], install_requires=['numpy'], # test_suite="tests", cmdclass={'install': MyInstall} # , 'build_ext': MyBuildExt ) somoclu-1.4.1/src/Python/somoclu.py0000644000175000001440000000432412433136714016536 0ustar wittekusers# This file was automatically generated by SWIG (http://www.swig.org). # Version 2.0.12 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead. from sys import version_info if version_info >= (2,6,0): def swig_import_helper(): from os.path import dirname import imp fp = None try: fp, pathname, description = imp.find_module('_somoclu', [dirname(__file__)]) except ImportError: import _somoclu return _somoclu if fp is not None: try: _mod = imp.load_module('_somoclu', fp, pathname, description) finally: fp.close() return _mod _somoclu = swig_import_helper() del swig_import_helper else: import _somoclu del version_info try: _swig_property = property except NameError: pass # Python < 2.2 doesn't have 'property'. def _swig_setattr_nondynamic(self,class_type,name,value,static=1): if (name == "thisown"): return self.this.own(value) if (name == "this"): if type(value).__name__ == 'SwigPyObject': self.__dict__[name] = value return method = class_type.__swig_setmethods__.get(name,None) if method: return method(self,value) if (not static): self.__dict__[name] = value else: raise AttributeError("You cannot add attributes to %s" % self) def _swig_setattr(self,class_type,name,value): return _swig_setattr_nondynamic(self,class_type,name,value,0) def _swig_getattr(self,class_type,name): if (name == "thisown"): return self.this.own() method = class_type.__swig_getmethods__.get(name,None) if method: return method(self) raise AttributeError(name) def _swig_repr(self): try: strthis = "proxy of " + self.this.__repr__() except: strthis = "" return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,) try: _object = object _newclass = 1 except AttributeError: class _object : pass _newclass = 0 def trainWrapper(*args): return _somoclu.trainWrapper(*args) trainWrapper = _somoclu.trainWrapper # This file is compatible with both classic and new-style classes. somoclu-1.4.1/src/Python/makepy.sh0000644000175000001440000000103212445351346016321 0ustar wittekusers#!/bin/sh # rm _somoclu.so # rm somoclu.pyc # swig -c++ -python -module somoclu somoclu.i # ./setup.py clean # ./setup.py build_ext --inplace rm -rf ./src rm -rf ./dist rm -rf ./build mkdir src mkdir src/src mkdir src/src/Windows cp ../../autogen.sh ./src cp -r ../../m4 ./src cp ../../configure.ac ./src cp ../../Makefile.in ./src cp ../../src/*.h ./src/src cp ../../src/*.cpp ./src/src cp ../../src/*.cu ./src/src cp ../../src/Makefile.in ./src/src cp ../../data/rgbs.txt tests/ python2 setup.py sdist #sudo python2 setup.py install somoclu-1.4.1/src/Python/somoclu_wrap.cxx0000644000175000001440000042276212433136714017753 0ustar wittekusers/* ---------------------------------------------------------------------------- * This file was automatically generated by SWIG (http://www.swig.org). * Version 2.0.12 * * This file is not intended to be easily readable and contains a number of * coding conventions designed to improve portability and efficiency. Do not make * changes to this file unless you know what you are doing--modify the SWIG * interface file instead. * ----------------------------------------------------------------------------- */ #define SWIGPYTHON #define SWIG_PYTHON_DIRECTOR_NO_VTABLE #ifdef __cplusplus /* SwigValueWrapper is described in swig.swg */ template class SwigValueWrapper { struct SwigMovePointer { T *ptr; SwigMovePointer(T *p) : ptr(p) { } ~SwigMovePointer() { delete ptr; } SwigMovePointer& operator=(SwigMovePointer& rhs) { T* oldptr = ptr; ptr = 0; delete oldptr; ptr = rhs.ptr; rhs.ptr = 0; return *this; } } pointer; SwigValueWrapper& operator=(const SwigValueWrapper& rhs); SwigValueWrapper(const SwigValueWrapper& rhs); public: SwigValueWrapper() : pointer(0) { } SwigValueWrapper& operator=(const T& t) { SwigMovePointer tmp(new T(t)); pointer = tmp; return *this; } operator T&() const { return *pointer.ptr; } T *operator&() { return pointer.ptr; } }; template T SwigValueInit() { return T(); } #endif /* ----------------------------------------------------------------------------- * This section contains generic SWIG labels for method/variable * declarations/attributes, and other compiler dependent labels. * ----------------------------------------------------------------------------- */ /* template workaround for compilers that cannot correctly implement the C++ standard */ #ifndef SWIGTEMPLATEDISAMBIGUATOR # if defined(__SUNPRO_CC) && (__SUNPRO_CC <= 0x560) # define SWIGTEMPLATEDISAMBIGUATOR template # elif defined(__HP_aCC) /* Needed even with `aCC -AA' when `aCC -V' reports HP ANSI C++ B3910B A.03.55 */ /* If we find a maximum version that requires this, the test would be __HP_aCC <= 35500 for A.03.55 */ # define SWIGTEMPLATEDISAMBIGUATOR template # else # define SWIGTEMPLATEDISAMBIGUATOR # endif #endif /* inline attribute */ #ifndef SWIGINLINE # if defined(__cplusplus) || (defined(__GNUC__) && !defined(__STRICT_ANSI__)) # define SWIGINLINE inline # else # define SWIGINLINE # endif #endif /* attribute recognised by some compilers to avoid 'unused' warnings */ #ifndef SWIGUNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define SWIGUNUSED __attribute__ ((__unused__)) # else # define SWIGUNUSED # endif # elif defined(__ICC) # define SWIGUNUSED __attribute__ ((__unused__)) # else # define SWIGUNUSED # endif #endif #ifndef SWIG_MSC_UNSUPPRESS_4505 # if defined(_MSC_VER) # pragma warning(disable : 4505) /* unreferenced local function has been removed */ # endif #endif #ifndef SWIGUNUSEDPARM # ifdef __cplusplus # define SWIGUNUSEDPARM(p) # else # define SWIGUNUSEDPARM(p) p SWIGUNUSED # endif #endif /* internal SWIG method */ #ifndef SWIGINTERN # define SWIGINTERN static SWIGUNUSED #endif /* internal inline SWIG method */ #ifndef SWIGINTERNINLINE # define SWIGINTERNINLINE SWIGINTERN SWIGINLINE #endif /* exporting methods */ #if (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) # ifndef GCC_HASCLASSVISIBILITY # define GCC_HASCLASSVISIBILITY # endif #endif #ifndef SWIGEXPORT # if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) # if defined(STATIC_LINKED) # define SWIGEXPORT # else # define SWIGEXPORT __declspec(dllexport) # endif # else # if defined(__GNUC__) && defined(GCC_HASCLASSVISIBILITY) # define SWIGEXPORT __attribute__ ((visibility("default"))) # else # define SWIGEXPORT # endif # endif #endif /* calling conventions for Windows */ #ifndef SWIGSTDCALL # if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) # define SWIGSTDCALL __stdcall # else # define SWIGSTDCALL # endif #endif /* Deal with Microsoft's attempt at deprecating C standard runtime functions */ #if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_CRT_SECURE_NO_DEPRECATE) # define _CRT_SECURE_NO_DEPRECATE #endif /* Deal with Microsoft's attempt at deprecating methods in the standard C++ library */ #if !defined(SWIG_NO_SCL_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_SCL_SECURE_NO_DEPRECATE) # define _SCL_SECURE_NO_DEPRECATE #endif #if defined(_DEBUG) && defined(SWIG_PYTHON_INTERPRETER_NO_DEBUG) /* Use debug wrappers with the Python release dll */ # undef _DEBUG # include # define _DEBUG #else # include #endif /* ----------------------------------------------------------------------------- * swigrun.swg * * This file contains generic C API SWIG runtime support for pointer * type checking. * ----------------------------------------------------------------------------- */ /* This should only be incremented when either the layout of swig_type_info changes, or for whatever reason, the runtime changes incompatibly */ #define SWIG_RUNTIME_VERSION "4" /* define SWIG_TYPE_TABLE_NAME as "SWIG_TYPE_TABLE" */ #ifdef SWIG_TYPE_TABLE # define SWIG_QUOTE_STRING(x) #x # define SWIG_EXPAND_AND_QUOTE_STRING(x) SWIG_QUOTE_STRING(x) # define SWIG_TYPE_TABLE_NAME SWIG_EXPAND_AND_QUOTE_STRING(SWIG_TYPE_TABLE) #else # define SWIG_TYPE_TABLE_NAME #endif /* You can use the SWIGRUNTIME and SWIGRUNTIMEINLINE macros for creating a static or dynamic library from the SWIG runtime code. In 99.9% of the cases, SWIG just needs to declare them as 'static'. But only do this if strictly necessary, ie, if you have problems with your compiler or suchlike. */ #ifndef SWIGRUNTIME # define SWIGRUNTIME SWIGINTERN #endif #ifndef SWIGRUNTIMEINLINE # define SWIGRUNTIMEINLINE SWIGRUNTIME SWIGINLINE #endif /* Generic buffer size */ #ifndef SWIG_BUFFER_SIZE # define SWIG_BUFFER_SIZE 1024 #endif /* Flags for pointer conversions */ #define SWIG_POINTER_DISOWN 0x1 #define SWIG_CAST_NEW_MEMORY 0x2 /* Flags for new pointer objects */ #define SWIG_POINTER_OWN 0x1 /* Flags/methods for returning states. The SWIG conversion methods, as ConvertPtr, return an integer that tells if the conversion was successful or not. And if not, an error code can be returned (see swigerrors.swg for the codes). Use the following macros/flags to set or process the returning states. In old versions of SWIG, code such as the following was usually written: if (SWIG_ConvertPtr(obj,vptr,ty.flags) != -1) { // success code } else { //fail code } Now you can be more explicit: int res = SWIG_ConvertPtr(obj,vptr,ty.flags); if (SWIG_IsOK(res)) { // success code } else { // fail code } which is the same really, but now you can also do Type *ptr; int res = SWIG_ConvertPtr(obj,(void **)(&ptr),ty.flags); if (SWIG_IsOK(res)) { // success code if (SWIG_IsNewObj(res) { ... delete *ptr; } else { ... } } else { // fail code } I.e., now SWIG_ConvertPtr can return new objects and you can identify the case and take care of the deallocation. Of course that also requires SWIG_ConvertPtr to return new result values, such as int SWIG_ConvertPtr(obj, ptr,...) { if () { if () { *ptr = ; return SWIG_NEWOBJ; } else { *ptr = ; return SWIG_OLDOBJ; } } else { return SWIG_BADOBJ; } } Of course, returning the plain '0(success)/-1(fail)' still works, but you can be more explicit by returning SWIG_BADOBJ, SWIG_ERROR or any of the SWIG errors code. Finally, if the SWIG_CASTRANK_MODE is enabled, the result code allows to return the 'cast rank', for example, if you have this int food(double) int fooi(int); and you call food(1) // cast rank '1' (1 -> 1.0) fooi(1) // cast rank '0' just use the SWIG_AddCast()/SWIG_CheckState() */ #define SWIG_OK (0) #define SWIG_ERROR (-1) #define SWIG_IsOK(r) (r >= 0) #define SWIG_ArgError(r) ((r != SWIG_ERROR) ? r : SWIG_TypeError) /* The CastRankLimit says how many bits are used for the cast rank */ #define SWIG_CASTRANKLIMIT (1 << 8) /* The NewMask denotes the object was created (using new/malloc) */ #define SWIG_NEWOBJMASK (SWIG_CASTRANKLIMIT << 1) /* The TmpMask is for in/out typemaps that use temporal objects */ #define SWIG_TMPOBJMASK (SWIG_NEWOBJMASK << 1) /* Simple returning values */ #define SWIG_BADOBJ (SWIG_ERROR) #define SWIG_OLDOBJ (SWIG_OK) #define SWIG_NEWOBJ (SWIG_OK | SWIG_NEWOBJMASK) #define SWIG_TMPOBJ (SWIG_OK | SWIG_TMPOBJMASK) /* Check, add and del mask methods */ #define SWIG_AddNewMask(r) (SWIG_IsOK(r) ? (r | SWIG_NEWOBJMASK) : r) #define SWIG_DelNewMask(r) (SWIG_IsOK(r) ? (r & ~SWIG_NEWOBJMASK) : r) #define SWIG_IsNewObj(r) (SWIG_IsOK(r) && (r & SWIG_NEWOBJMASK)) #define SWIG_AddTmpMask(r) (SWIG_IsOK(r) ? (r | SWIG_TMPOBJMASK) : r) #define SWIG_DelTmpMask(r) (SWIG_IsOK(r) ? (r & ~SWIG_TMPOBJMASK) : r) #define SWIG_IsTmpObj(r) (SWIG_IsOK(r) && (r & SWIG_TMPOBJMASK)) /* Cast-Rank Mode */ #if defined(SWIG_CASTRANK_MODE) # ifndef SWIG_TypeRank # define SWIG_TypeRank unsigned long # endif # ifndef SWIG_MAXCASTRANK /* Default cast allowed */ # define SWIG_MAXCASTRANK (2) # endif # define SWIG_CASTRANKMASK ((SWIG_CASTRANKLIMIT) -1) # define SWIG_CastRank(r) (r & SWIG_CASTRANKMASK) SWIGINTERNINLINE int SWIG_AddCast(int r) { return SWIG_IsOK(r) ? ((SWIG_CastRank(r) < SWIG_MAXCASTRANK) ? (r + 1) : SWIG_ERROR) : r; } SWIGINTERNINLINE int SWIG_CheckState(int r) { return SWIG_IsOK(r) ? SWIG_CastRank(r) + 1 : 0; } #else /* no cast-rank mode */ # define SWIG_AddCast(r) (r) # define SWIG_CheckState(r) (SWIG_IsOK(r) ? 1 : 0) #endif #include #ifdef __cplusplus extern "C" { #endif typedef void *(*swig_converter_func)(void *, int *); typedef struct swig_type_info *(*swig_dycast_func)(void **); /* Structure to store information on one type */ typedef struct swig_type_info { const char *name; /* mangled name of this type */ const char *str; /* human readable name of this type */ swig_dycast_func dcast; /* dynamic cast function down a hierarchy */ struct swig_cast_info *cast; /* linked list of types that can cast into this type */ void *clientdata; /* language specific type data */ int owndata; /* flag if the structure owns the clientdata */ } swig_type_info; /* Structure to store a type and conversion function used for casting */ typedef struct swig_cast_info { swig_type_info *type; /* pointer to type that is equivalent to this type */ swig_converter_func converter; /* function to cast the void pointers */ struct swig_cast_info *next; /* pointer to next cast in linked list */ struct swig_cast_info *prev; /* pointer to the previous cast */ } swig_cast_info; /* Structure used to store module information * Each module generates one structure like this, and the runtime collects * all of these structures and stores them in a circularly linked list.*/ typedef struct swig_module_info { swig_type_info **types; /* Array of pointers to swig_type_info structures that are in this module */ size_t size; /* Number of types in this module */ struct swig_module_info *next; /* Pointer to next element in circularly linked list */ swig_type_info **type_initial; /* Array of initially generated type structures */ swig_cast_info **cast_initial; /* Array of initially generated casting structures */ void *clientdata; /* Language specific module data */ } swig_module_info; /* Compare two type names skipping the space characters, therefore "char*" == "char *" and "Class" == "Class", etc. Return 0 when the two name types are equivalent, as in strncmp, but skipping ' '. */ SWIGRUNTIME int SWIG_TypeNameComp(const char *f1, const char *l1, const char *f2, const char *l2) { for (;(f1 != l1) && (f2 != l2); ++f1, ++f2) { while ((*f1 == ' ') && (f1 != l1)) ++f1; while ((*f2 == ' ') && (f2 != l2)) ++f2; if (*f1 != *f2) return (*f1 > *f2) ? 1 : -1; } return (int)((l1 - f1) - (l2 - f2)); } /* Check type equivalence in a name list like ||... Return 0 if equal, -1 if nb < tb, 1 if nb > tb */ SWIGRUNTIME int SWIG_TypeCmp(const char *nb, const char *tb) { int equiv = 1; const char* te = tb + strlen(tb); const char* ne = nb; while (equiv != 0 && *ne) { for (nb = ne; *ne; ++ne) { if (*ne == '|') break; } equiv = SWIG_TypeNameComp(nb, ne, tb, te); if (*ne) ++ne; } return equiv; } /* Check type equivalence in a name list like ||... Return 0 if not equal, 1 if equal */ SWIGRUNTIME int SWIG_TypeEquiv(const char *nb, const char *tb) { return SWIG_TypeCmp(nb, tb) == 0 ? 1 : 0; } /* Check the typename */ SWIGRUNTIME swig_cast_info * SWIG_TypeCheck(const char *c, swig_type_info *ty) { if (ty) { swig_cast_info *iter = ty->cast; while (iter) { if (strcmp(iter->type->name, c) == 0) { if (iter == ty->cast) return iter; /* Move iter to the top of the linked list */ iter->prev->next = iter->next; if (iter->next) iter->next->prev = iter->prev; iter->next = ty->cast; iter->prev = 0; if (ty->cast) ty->cast->prev = iter; ty->cast = iter; return iter; } iter = iter->next; } } return 0; } /* Identical to SWIG_TypeCheck, except strcmp is replaced with a pointer comparison */ SWIGRUNTIME swig_cast_info * SWIG_TypeCheckStruct(swig_type_info *from, swig_type_info *ty) { if (ty) { swig_cast_info *iter = ty->cast; while (iter) { if (iter->type == from) { if (iter == ty->cast) return iter; /* Move iter to the top of the linked list */ iter->prev->next = iter->next; if (iter->next) iter->next->prev = iter->prev; iter->next = ty->cast; iter->prev = 0; if (ty->cast) ty->cast->prev = iter; ty->cast = iter; return iter; } iter = iter->next; } } return 0; } /* Cast a pointer up an inheritance hierarchy */ SWIGRUNTIMEINLINE void * SWIG_TypeCast(swig_cast_info *ty, void *ptr, int *newmemory) { return ((!ty) || (!ty->converter)) ? ptr : (*ty->converter)(ptr, newmemory); } /* Dynamic pointer casting. Down an inheritance hierarchy */ SWIGRUNTIME swig_type_info * SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) { swig_type_info *lastty = ty; if (!ty || !ty->dcast) return ty; while (ty && (ty->dcast)) { ty = (*ty->dcast)(ptr); if (ty) lastty = ty; } return lastty; } /* Return the name associated with this type */ SWIGRUNTIMEINLINE const char * SWIG_TypeName(const swig_type_info *ty) { return ty->name; } /* Return the pretty name associated with this type, that is an unmangled type name in a form presentable to the user. */ SWIGRUNTIME const char * SWIG_TypePrettyName(const swig_type_info *type) { /* The "str" field contains the equivalent pretty names of the type, separated by vertical-bar characters. We choose to print the last name, as it is often (?) the most specific. */ if (!type) return NULL; if (type->str != NULL) { const char *last_name = type->str; const char *s; for (s = type->str; *s; s++) if (*s == '|') last_name = s+1; return last_name; } else return type->name; } /* Set the clientdata field for a type */ SWIGRUNTIME void SWIG_TypeClientData(swig_type_info *ti, void *clientdata) { swig_cast_info *cast = ti->cast; /* if (ti->clientdata == clientdata) return; */ ti->clientdata = clientdata; while (cast) { if (!cast->converter) { swig_type_info *tc = cast->type; if (!tc->clientdata) { SWIG_TypeClientData(tc, clientdata); } } cast = cast->next; } } SWIGRUNTIME void SWIG_TypeNewClientData(swig_type_info *ti, void *clientdata) { SWIG_TypeClientData(ti, clientdata); ti->owndata = 1; } /* Search for a swig_type_info structure only by mangled name Search is a O(log #types) We start searching at module start, and finish searching when start == end. Note: if start == end at the beginning of the function, we go all the way around the circular list. */ SWIGRUNTIME swig_type_info * SWIG_MangledTypeQueryModule(swig_module_info *start, swig_module_info *end, const char *name) { swig_module_info *iter = start; do { if (iter->size) { register size_t l = 0; register size_t r = iter->size - 1; do { /* since l+r >= 0, we can (>> 1) instead (/ 2) */ register size_t i = (l + r) >> 1; const char *iname = iter->types[i]->name; if (iname) { register int compare = strcmp(name, iname); if (compare == 0) { return iter->types[i]; } else if (compare < 0) { if (i) { r = i - 1; } else { break; } } else if (compare > 0) { l = i + 1; } } else { break; /* should never happen */ } } while (l <= r); } iter = iter->next; } while (iter != end); return 0; } /* Search for a swig_type_info structure for either a mangled name or a human readable name. It first searches the mangled names of the types, which is a O(log #types) If a type is not found it then searches the human readable names, which is O(#types). We start searching at module start, and finish searching when start == end. Note: if start == end at the beginning of the function, we go all the way around the circular list. */ SWIGRUNTIME swig_type_info * SWIG_TypeQueryModule(swig_module_info *start, swig_module_info *end, const char *name) { /* STEP 1: Search the name field using binary search */ swig_type_info *ret = SWIG_MangledTypeQueryModule(start, end, name); if (ret) { return ret; } else { /* STEP 2: If the type hasn't been found, do a complete search of the str field (the human readable name) */ swig_module_info *iter = start; do { register size_t i = 0; for (; i < iter->size; ++i) { if (iter->types[i]->str && (SWIG_TypeEquiv(iter->types[i]->str, name))) return iter->types[i]; } iter = iter->next; } while (iter != end); } /* neither found a match */ return 0; } /* Pack binary data into a string */ SWIGRUNTIME char * SWIG_PackData(char *c, void *ptr, size_t sz) { static const char hex[17] = "0123456789abcdef"; register const unsigned char *u = (unsigned char *) ptr; register const unsigned char *eu = u + sz; for (; u != eu; ++u) { register unsigned char uu = *u; *(c++) = hex[(uu & 0xf0) >> 4]; *(c++) = hex[uu & 0xf]; } return c; } /* Unpack binary data from a string */ SWIGRUNTIME const char * SWIG_UnpackData(const char *c, void *ptr, size_t sz) { register unsigned char *u = (unsigned char *) ptr; register const unsigned char *eu = u + sz; for (; u != eu; ++u) { register char d = *(c++); register unsigned char uu; if ((d >= '0') && (d <= '9')) uu = ((d - '0') << 4); else if ((d >= 'a') && (d <= 'f')) uu = ((d - ('a'-10)) << 4); else return (char *) 0; d = *(c++); if ((d >= '0') && (d <= '9')) uu |= (d - '0'); else if ((d >= 'a') && (d <= 'f')) uu |= (d - ('a'-10)); else return (char *) 0; *u = uu; } return c; } /* Pack 'void *' into a string buffer. */ SWIGRUNTIME char * SWIG_PackVoidPtr(char *buff, void *ptr, const char *name, size_t bsz) { char *r = buff; if ((2*sizeof(void *) + 2) > bsz) return 0; *(r++) = '_'; r = SWIG_PackData(r,&ptr,sizeof(void *)); if (strlen(name) + 1 > (bsz - (r - buff))) return 0; strcpy(r,name); return buff; } SWIGRUNTIME const char * SWIG_UnpackVoidPtr(const char *c, void **ptr, const char *name) { if (*c != '_') { if (strcmp(c,"NULL") == 0) { *ptr = (void *) 0; return name; } else { return 0; } } return SWIG_UnpackData(++c,ptr,sizeof(void *)); } SWIGRUNTIME char * SWIG_PackDataName(char *buff, void *ptr, size_t sz, const char *name, size_t bsz) { char *r = buff; size_t lname = (name ? strlen(name) : 0); if ((2*sz + 2 + lname) > bsz) return 0; *(r++) = '_'; r = SWIG_PackData(r,ptr,sz); if (lname) { strncpy(r,name,lname+1); } else { *r = 0; } return buff; } SWIGRUNTIME const char * SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) { if (*c != '_') { if (strcmp(c,"NULL") == 0) { memset(ptr,0,sz); return name; } else { return 0; } } return SWIG_UnpackData(++c,ptr,sz); } #ifdef __cplusplus } #endif /* Errors in SWIG */ #define SWIG_UnknownError -1 #define SWIG_IOError -2 #define SWIG_RuntimeError -3 #define SWIG_IndexError -4 #define SWIG_TypeError -5 #define SWIG_DivisionByZero -6 #define SWIG_OverflowError -7 #define SWIG_SyntaxError -8 #define SWIG_ValueError -9 #define SWIG_SystemError -10 #define SWIG_AttributeError -11 #define SWIG_MemoryError -12 #define SWIG_NullReferenceError -13 /* Compatibility macros for Python 3 */ #if PY_VERSION_HEX >= 0x03000000 #define PyClass_Check(obj) PyObject_IsInstance(obj, (PyObject *)&PyType_Type) #define PyInt_Check(x) PyLong_Check(x) #define PyInt_AsLong(x) PyLong_AsLong(x) #define PyInt_FromLong(x) PyLong_FromLong(x) #define PyInt_FromSize_t(x) PyLong_FromSize_t(x) #define PyString_Check(name) PyBytes_Check(name) #define PyString_FromString(x) PyUnicode_FromString(x) #define PyString_Format(fmt, args) PyUnicode_Format(fmt, args) #define PyString_AsString(str) PyBytes_AsString(str) #define PyString_Size(str) PyBytes_Size(str) #define PyString_InternFromString(key) PyUnicode_InternFromString(key) #define Py_TPFLAGS_HAVE_CLASS Py_TPFLAGS_BASETYPE #define PyString_AS_STRING(x) PyUnicode_AS_STRING(x) #define _PyLong_FromSsize_t(x) PyLong_FromSsize_t(x) #endif #ifndef Py_TYPE # define Py_TYPE(op) ((op)->ob_type) #endif /* SWIG APIs for compatibility of both Python 2 & 3 */ #if PY_VERSION_HEX >= 0x03000000 # define SWIG_Python_str_FromFormat PyUnicode_FromFormat #else # define SWIG_Python_str_FromFormat PyString_FromFormat #endif /* Warning: This function will allocate a new string in Python 3, * so please call SWIG_Python_str_DelForPy3(x) to free the space. */ SWIGINTERN char* SWIG_Python_str_AsChar(PyObject *str) { #if PY_VERSION_HEX >= 0x03000000 char *cstr; char *newstr; Py_ssize_t len; str = PyUnicode_AsUTF8String(str); PyBytes_AsStringAndSize(str, &cstr, &len); newstr = (char *) malloc(len+1); memcpy(newstr, cstr, len+1); Py_XDECREF(str); return newstr; #else return PyString_AsString(str); #endif } #if PY_VERSION_HEX >= 0x03000000 # define SWIG_Python_str_DelForPy3(x) free( (void*) (x) ) #else # define SWIG_Python_str_DelForPy3(x) #endif SWIGINTERN PyObject* SWIG_Python_str_FromChar(const char *c) { #if PY_VERSION_HEX >= 0x03000000 return PyUnicode_FromString(c); #else return PyString_FromString(c); #endif } /* Add PyOS_snprintf for old Pythons */ #if PY_VERSION_HEX < 0x02020000 # if defined(_MSC_VER) || defined(__BORLANDC__) || defined(_WATCOM) # define PyOS_snprintf _snprintf # else # define PyOS_snprintf snprintf # endif #endif /* A crude PyString_FromFormat implementation for old Pythons */ #if PY_VERSION_HEX < 0x02020000 #ifndef SWIG_PYBUFFER_SIZE # define SWIG_PYBUFFER_SIZE 1024 #endif static PyObject * PyString_FromFormat(const char *fmt, ...) { va_list ap; char buf[SWIG_PYBUFFER_SIZE * 2]; int res; va_start(ap, fmt); res = vsnprintf(buf, sizeof(buf), fmt, ap); va_end(ap); return (res < 0 || res >= (int)sizeof(buf)) ? 0 : PyString_FromString(buf); } #endif /* Add PyObject_Del for old Pythons */ #if PY_VERSION_HEX < 0x01060000 # define PyObject_Del(op) PyMem_DEL((op)) #endif #ifndef PyObject_DEL # define PyObject_DEL PyObject_Del #endif /* A crude PyExc_StopIteration exception for old Pythons */ #if PY_VERSION_HEX < 0x02020000 # ifndef PyExc_StopIteration # define PyExc_StopIteration PyExc_RuntimeError # endif # ifndef PyObject_GenericGetAttr # define PyObject_GenericGetAttr 0 # endif #endif /* Py_NotImplemented is defined in 2.1 and up. */ #if PY_VERSION_HEX < 0x02010000 # ifndef Py_NotImplemented # define Py_NotImplemented PyExc_RuntimeError # endif #endif /* A crude PyString_AsStringAndSize implementation for old Pythons */ #if PY_VERSION_HEX < 0x02010000 # ifndef PyString_AsStringAndSize # define PyString_AsStringAndSize(obj, s, len) {*s = PyString_AsString(obj); *len = *s ? strlen(*s) : 0;} # endif #endif /* PySequence_Size for old Pythons */ #if PY_VERSION_HEX < 0x02000000 # ifndef PySequence_Size # define PySequence_Size PySequence_Length # endif #endif /* PyBool_FromLong for old Pythons */ #if PY_VERSION_HEX < 0x02030000 static PyObject *PyBool_FromLong(long ok) { PyObject *result = ok ? Py_True : Py_False; Py_INCREF(result); return result; } #endif /* Py_ssize_t for old Pythons */ /* This code is as recommended by: */ /* http://www.python.org/dev/peps/pep-0353/#conversion-guidelines */ #if PY_VERSION_HEX < 0x02050000 && !defined(PY_SSIZE_T_MIN) typedef int Py_ssize_t; # define PY_SSIZE_T_MAX INT_MAX # define PY_SSIZE_T_MIN INT_MIN typedef inquiry lenfunc; typedef intargfunc ssizeargfunc; typedef intintargfunc ssizessizeargfunc; typedef intobjargproc ssizeobjargproc; typedef intintobjargproc ssizessizeobjargproc; typedef getreadbufferproc readbufferproc; typedef getwritebufferproc writebufferproc; typedef getsegcountproc segcountproc; typedef getcharbufferproc charbufferproc; static long PyNumber_AsSsize_t (PyObject *x, void *SWIGUNUSEDPARM(exc)) { long result = 0; PyObject *i = PyNumber_Int(x); if (i) { result = PyInt_AsLong(i); Py_DECREF(i); } return result; } #endif #if PY_VERSION_HEX < 0x02050000 #define PyInt_FromSize_t(x) PyInt_FromLong((long)x) #endif #if PY_VERSION_HEX < 0x02040000 #define Py_VISIT(op) \ do { \ if (op) { \ int vret = visit((op), arg); \ if (vret) \ return vret; \ } \ } while (0) #endif #if PY_VERSION_HEX < 0x02030000 typedef struct { PyTypeObject type; PyNumberMethods as_number; PyMappingMethods as_mapping; PySequenceMethods as_sequence; PyBufferProcs as_buffer; PyObject *name, *slots; } PyHeapTypeObject; #endif #if PY_VERSION_HEX < 0x02030000 typedef destructor freefunc; #endif #if ((PY_MAJOR_VERSION == 2 && PY_MINOR_VERSION > 6) || \ (PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION > 0) || \ (PY_MAJOR_VERSION > 3)) # define SWIGPY_USE_CAPSULE # define SWIGPY_CAPSULE_NAME ((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION ".type_pointer_capsule" SWIG_TYPE_TABLE_NAME) #endif #if PY_VERSION_HEX < 0x03020000 #define PyDescr_TYPE(x) (((PyDescrObject *)(x))->d_type) #define PyDescr_NAME(x) (((PyDescrObject *)(x))->d_name) #endif /* ----------------------------------------------------------------------------- * error manipulation * ----------------------------------------------------------------------------- */ SWIGRUNTIME PyObject* SWIG_Python_ErrorType(int code) { PyObject* type = 0; switch(code) { case SWIG_MemoryError: type = PyExc_MemoryError; break; case SWIG_IOError: type = PyExc_IOError; break; case SWIG_RuntimeError: type = PyExc_RuntimeError; break; case SWIG_IndexError: type = PyExc_IndexError; break; case SWIG_TypeError: type = PyExc_TypeError; break; case SWIG_DivisionByZero: type = PyExc_ZeroDivisionError; break; case SWIG_OverflowError: type = PyExc_OverflowError; break; case SWIG_SyntaxError: type = PyExc_SyntaxError; break; case SWIG_ValueError: type = PyExc_ValueError; break; case SWIG_SystemError: type = PyExc_SystemError; break; case SWIG_AttributeError: type = PyExc_AttributeError; break; default: type = PyExc_RuntimeError; } return type; } SWIGRUNTIME void SWIG_Python_AddErrorMsg(const char* mesg) { PyObject *type = 0; PyObject *value = 0; PyObject *traceback = 0; if (PyErr_Occurred()) PyErr_Fetch(&type, &value, &traceback); if (value) { char *tmp; PyObject *old_str = PyObject_Str(value); PyErr_Clear(); Py_XINCREF(type); PyErr_Format(type, "%s %s", tmp = SWIG_Python_str_AsChar(old_str), mesg); SWIG_Python_str_DelForPy3(tmp); Py_DECREF(old_str); Py_DECREF(value); } else { PyErr_SetString(PyExc_RuntimeError, mesg); } } #if defined(SWIG_PYTHON_NO_THREADS) # if defined(SWIG_PYTHON_THREADS) # undef SWIG_PYTHON_THREADS # endif #endif #if defined(SWIG_PYTHON_THREADS) /* Threading support is enabled */ # if !defined(SWIG_PYTHON_USE_GIL) && !defined(SWIG_PYTHON_NO_USE_GIL) # if (PY_VERSION_HEX >= 0x02030000) /* For 2.3 or later, use the PyGILState calls */ # define SWIG_PYTHON_USE_GIL # endif # endif # if defined(SWIG_PYTHON_USE_GIL) /* Use PyGILState threads calls */ # ifndef SWIG_PYTHON_INITIALIZE_THREADS # define SWIG_PYTHON_INITIALIZE_THREADS PyEval_InitThreads() # endif # ifdef __cplusplus /* C++ code */ class SWIG_Python_Thread_Block { bool status; PyGILState_STATE state; public: void end() { if (status) { PyGILState_Release(state); status = false;} } SWIG_Python_Thread_Block() : status(true), state(PyGILState_Ensure()) {} ~SWIG_Python_Thread_Block() { end(); } }; class SWIG_Python_Thread_Allow { bool status; PyThreadState *save; public: void end() { if (status) { PyEval_RestoreThread(save); status = false; }} SWIG_Python_Thread_Allow() : status(true), save(PyEval_SaveThread()) {} ~SWIG_Python_Thread_Allow() { end(); } }; # define SWIG_PYTHON_THREAD_BEGIN_BLOCK SWIG_Python_Thread_Block _swig_thread_block # define SWIG_PYTHON_THREAD_END_BLOCK _swig_thread_block.end() # define SWIG_PYTHON_THREAD_BEGIN_ALLOW SWIG_Python_Thread_Allow _swig_thread_allow # define SWIG_PYTHON_THREAD_END_ALLOW _swig_thread_allow.end() # else /* C code */ # define SWIG_PYTHON_THREAD_BEGIN_BLOCK PyGILState_STATE _swig_thread_block = PyGILState_Ensure() # define SWIG_PYTHON_THREAD_END_BLOCK PyGILState_Release(_swig_thread_block) # define SWIG_PYTHON_THREAD_BEGIN_ALLOW PyThreadState *_swig_thread_allow = PyEval_SaveThread() # define SWIG_PYTHON_THREAD_END_ALLOW PyEval_RestoreThread(_swig_thread_allow) # endif # else /* Old thread way, not implemented, user must provide it */ # if !defined(SWIG_PYTHON_INITIALIZE_THREADS) # define SWIG_PYTHON_INITIALIZE_THREADS # endif # if !defined(SWIG_PYTHON_THREAD_BEGIN_BLOCK) # define SWIG_PYTHON_THREAD_BEGIN_BLOCK # endif # if !defined(SWIG_PYTHON_THREAD_END_BLOCK) # define SWIG_PYTHON_THREAD_END_BLOCK # endif # if !defined(SWIG_PYTHON_THREAD_BEGIN_ALLOW) # define SWIG_PYTHON_THREAD_BEGIN_ALLOW # endif # if !defined(SWIG_PYTHON_THREAD_END_ALLOW) # define SWIG_PYTHON_THREAD_END_ALLOW # endif # endif #else /* No thread support */ # define SWIG_PYTHON_INITIALIZE_THREADS # define SWIG_PYTHON_THREAD_BEGIN_BLOCK # define SWIG_PYTHON_THREAD_END_BLOCK # define SWIG_PYTHON_THREAD_BEGIN_ALLOW # define SWIG_PYTHON_THREAD_END_ALLOW #endif /* ----------------------------------------------------------------------------- * Python API portion that goes into the runtime * ----------------------------------------------------------------------------- */ #ifdef __cplusplus extern "C" { #endif /* ----------------------------------------------------------------------------- * Constant declarations * ----------------------------------------------------------------------------- */ /* Constant Types */ #define SWIG_PY_POINTER 4 #define SWIG_PY_BINARY 5 /* Constant information structure */ typedef struct swig_const_info { int type; char *name; long lvalue; double dvalue; void *pvalue; swig_type_info **ptype; } swig_const_info; /* ----------------------------------------------------------------------------- * Wrapper of PyInstanceMethod_New() used in Python 3 * It is exported to the generated module, used for -fastproxy * ----------------------------------------------------------------------------- */ #if PY_VERSION_HEX >= 0x03000000 SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self), PyObject *func) { return PyInstanceMethod_New(func); } #else SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self), PyObject *SWIGUNUSEDPARM(func)) { return NULL; } #endif #ifdef __cplusplus } #endif /* ----------------------------------------------------------------------------- * pyrun.swg * * This file contains the runtime support for Python modules * and includes code for managing global variables and pointer * type checking. * * ----------------------------------------------------------------------------- */ /* Common SWIG API */ /* for raw pointers */ #define SWIG_Python_ConvertPtr(obj, pptr, type, flags) SWIG_Python_ConvertPtrAndOwn(obj, pptr, type, flags, 0) #define SWIG_ConvertPtr(obj, pptr, type, flags) SWIG_Python_ConvertPtr(obj, pptr, type, flags) #define SWIG_ConvertPtrAndOwn(obj,pptr,type,flags,own) SWIG_Python_ConvertPtrAndOwn(obj, pptr, type, flags, own) #ifdef SWIGPYTHON_BUILTIN #define SWIG_NewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(self, ptr, type, flags) #else #define SWIG_NewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags) #endif #define SWIG_InternalNewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags) #define SWIG_CheckImplicit(ty) SWIG_Python_CheckImplicit(ty) #define SWIG_AcquirePtr(ptr, src) SWIG_Python_AcquirePtr(ptr, src) #define swig_owntype int /* for raw packed data */ #define SWIG_ConvertPacked(obj, ptr, sz, ty) SWIG_Python_ConvertPacked(obj, ptr, sz, ty) #define SWIG_NewPackedObj(ptr, sz, type) SWIG_Python_NewPackedObj(ptr, sz, type) /* for class or struct pointers */ #define SWIG_ConvertInstance(obj, pptr, type, flags) SWIG_ConvertPtr(obj, pptr, type, flags) #define SWIG_NewInstanceObj(ptr, type, flags) SWIG_NewPointerObj(ptr, type, flags) /* for C or C++ function pointers */ #define SWIG_ConvertFunctionPtr(obj, pptr, type) SWIG_Python_ConvertFunctionPtr(obj, pptr, type) #define SWIG_NewFunctionPtrObj(ptr, type) SWIG_Python_NewPointerObj(NULL, ptr, type, 0) /* for C++ member pointers, ie, member methods */ #define SWIG_ConvertMember(obj, ptr, sz, ty) SWIG_Python_ConvertPacked(obj, ptr, sz, ty) #define SWIG_NewMemberObj(ptr, sz, type) SWIG_Python_NewPackedObj(ptr, sz, type) /* Runtime API */ #define SWIG_GetModule(clientdata) SWIG_Python_GetModule(clientdata) #define SWIG_SetModule(clientdata, pointer) SWIG_Python_SetModule(pointer) #define SWIG_NewClientData(obj) SwigPyClientData_New(obj) #define SWIG_SetErrorObj SWIG_Python_SetErrorObj #define SWIG_SetErrorMsg SWIG_Python_SetErrorMsg #define SWIG_ErrorType(code) SWIG_Python_ErrorType(code) #define SWIG_Error(code, msg) SWIG_Python_SetErrorMsg(SWIG_ErrorType(code), msg) #define SWIG_fail goto fail /* Runtime API implementation */ /* Error manipulation */ SWIGINTERN void SWIG_Python_SetErrorObj(PyObject *errtype, PyObject *obj) { SWIG_PYTHON_THREAD_BEGIN_BLOCK; PyErr_SetObject(errtype, obj); Py_DECREF(obj); SWIG_PYTHON_THREAD_END_BLOCK; } SWIGINTERN void SWIG_Python_SetErrorMsg(PyObject *errtype, const char *msg) { SWIG_PYTHON_THREAD_BEGIN_BLOCK; PyErr_SetString(errtype, msg); SWIG_PYTHON_THREAD_END_BLOCK; } #define SWIG_Python_Raise(obj, type, desc) SWIG_Python_SetErrorObj(SWIG_Python_ExceptionType(desc), obj) /* Set a constant value */ #if defined(SWIGPYTHON_BUILTIN) SWIGINTERN void SwigPyBuiltin_AddPublicSymbol(PyObject *seq, const char *key) { PyObject *s = PyString_InternFromString(key); PyList_Append(seq, s); Py_DECREF(s); } SWIGINTERN void SWIG_Python_SetConstant(PyObject *d, PyObject *public_interface, const char *name, PyObject *obj) { #if PY_VERSION_HEX < 0x02030000 PyDict_SetItemString(d, (char *)name, obj); #else PyDict_SetItemString(d, name, obj); #endif Py_DECREF(obj); if (public_interface) SwigPyBuiltin_AddPublicSymbol(public_interface, name); } #else SWIGINTERN void SWIG_Python_SetConstant(PyObject *d, const char *name, PyObject *obj) { #if PY_VERSION_HEX < 0x02030000 PyDict_SetItemString(d, (char *)name, obj); #else PyDict_SetItemString(d, name, obj); #endif Py_DECREF(obj); } #endif /* Append a value to the result obj */ SWIGINTERN PyObject* SWIG_Python_AppendOutput(PyObject* result, PyObject* obj) { #if !defined(SWIG_PYTHON_OUTPUT_TUPLE) if (!result) { result = obj; } else if (result == Py_None) { Py_DECREF(result); result = obj; } else { if (!PyList_Check(result)) { PyObject *o2 = result; result = PyList_New(1); PyList_SetItem(result, 0, o2); } PyList_Append(result,obj); Py_DECREF(obj); } return result; #else PyObject* o2; PyObject* o3; if (!result) { result = obj; } else if (result == Py_None) { Py_DECREF(result); result = obj; } else { if (!PyTuple_Check(result)) { o2 = result; result = PyTuple_New(1); PyTuple_SET_ITEM(result, 0, o2); } o3 = PyTuple_New(1); PyTuple_SET_ITEM(o3, 0, obj); o2 = result; result = PySequence_Concat(o2, o3); Py_DECREF(o2); Py_DECREF(o3); } return result; #endif } /* Unpack the argument tuple */ SWIGINTERN int SWIG_Python_UnpackTuple(PyObject *args, const char *name, Py_ssize_t min, Py_ssize_t max, PyObject **objs) { if (!args) { if (!min && !max) { return 1; } else { PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got none", name, (min == max ? "" : "at least "), (int)min); return 0; } } if (!PyTuple_Check(args)) { if (min <= 1 && max >= 1) { register int i; objs[0] = args; for (i = 1; i < max; ++i) { objs[i] = 0; } return 2; } PyErr_SetString(PyExc_SystemError, "UnpackTuple() argument list is not a tuple"); return 0; } else { register Py_ssize_t l = PyTuple_GET_SIZE(args); if (l < min) { PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d", name, (min == max ? "" : "at least "), (int)min, (int)l); return 0; } else if (l > max) { PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d", name, (min == max ? "" : "at most "), (int)max, (int)l); return 0; } else { register int i; for (i = 0; i < l; ++i) { objs[i] = PyTuple_GET_ITEM(args, i); } for (; l < max; ++l) { objs[l] = 0; } return i + 1; } } } /* A functor is a function object with one single object argument */ #if PY_VERSION_HEX >= 0x02020000 #define SWIG_Python_CallFunctor(functor, obj) PyObject_CallFunctionObjArgs(functor, obj, NULL); #else #define SWIG_Python_CallFunctor(functor, obj) PyObject_CallFunction(functor, "O", obj); #endif /* Helper for static pointer initialization for both C and C++ code, for example static PyObject *SWIG_STATIC_POINTER(MyVar) = NewSomething(...); */ #ifdef __cplusplus #define SWIG_STATIC_POINTER(var) var #else #define SWIG_STATIC_POINTER(var) var = 0; if (!var) var #endif /* ----------------------------------------------------------------------------- * Pointer declarations * ----------------------------------------------------------------------------- */ /* Flags for new pointer objects */ #define SWIG_POINTER_NOSHADOW (SWIG_POINTER_OWN << 1) #define SWIG_POINTER_NEW (SWIG_POINTER_NOSHADOW | SWIG_POINTER_OWN) #define SWIG_POINTER_IMPLICIT_CONV (SWIG_POINTER_DISOWN << 1) #define SWIG_BUILTIN_TP_INIT (SWIG_POINTER_OWN << 2) #define SWIG_BUILTIN_INIT (SWIG_BUILTIN_TP_INIT | SWIG_POINTER_OWN) #ifdef __cplusplus extern "C" { #endif /* How to access Py_None */ #if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) # ifndef SWIG_PYTHON_NO_BUILD_NONE # ifndef SWIG_PYTHON_BUILD_NONE # define SWIG_PYTHON_BUILD_NONE # endif # endif #endif #ifdef SWIG_PYTHON_BUILD_NONE # ifdef Py_None # undef Py_None # define Py_None SWIG_Py_None() # endif SWIGRUNTIMEINLINE PyObject * _SWIG_Py_None(void) { PyObject *none = Py_BuildValue((char*)""); Py_DECREF(none); return none; } SWIGRUNTIME PyObject * SWIG_Py_None(void) { static PyObject *SWIG_STATIC_POINTER(none) = _SWIG_Py_None(); return none; } #endif /* The python void return value */ SWIGRUNTIMEINLINE PyObject * SWIG_Py_Void(void) { PyObject *none = Py_None; Py_INCREF(none); return none; } /* SwigPyClientData */ typedef struct { PyObject *klass; PyObject *newraw; PyObject *newargs; PyObject *destroy; int delargs; int implicitconv; PyTypeObject *pytype; } SwigPyClientData; SWIGRUNTIMEINLINE int SWIG_Python_CheckImplicit(swig_type_info *ty) { SwigPyClientData *data = (SwigPyClientData *)ty->clientdata; return data ? data->implicitconv : 0; } SWIGRUNTIMEINLINE PyObject * SWIG_Python_ExceptionType(swig_type_info *desc) { SwigPyClientData *data = desc ? (SwigPyClientData *) desc->clientdata : 0; PyObject *klass = data ? data->klass : 0; return (klass ? klass : PyExc_RuntimeError); } SWIGRUNTIME SwigPyClientData * SwigPyClientData_New(PyObject* obj) { if (!obj) { return 0; } else { SwigPyClientData *data = (SwigPyClientData *)malloc(sizeof(SwigPyClientData)); /* the klass element */ data->klass = obj; Py_INCREF(data->klass); /* the newraw method and newargs arguments used to create a new raw instance */ if (PyClass_Check(obj)) { data->newraw = 0; data->newargs = obj; Py_INCREF(obj); } else { #if (PY_VERSION_HEX < 0x02020000) data->newraw = 0; #else data->newraw = PyObject_GetAttrString(data->klass, (char *)"__new__"); #endif if (data->newraw) { Py_INCREF(data->newraw); data->newargs = PyTuple_New(1); PyTuple_SetItem(data->newargs, 0, obj); } else { data->newargs = obj; } Py_INCREF(data->newargs); } /* the destroy method, aka as the C++ delete method */ data->destroy = PyObject_GetAttrString(data->klass, (char *)"__swig_destroy__"); if (PyErr_Occurred()) { PyErr_Clear(); data->destroy = 0; } if (data->destroy) { int flags; Py_INCREF(data->destroy); flags = PyCFunction_GET_FLAGS(data->destroy); #ifdef METH_O data->delargs = !(flags & (METH_O)); #else data->delargs = 0; #endif } else { data->delargs = 0; } data->implicitconv = 0; data->pytype = 0; return data; } } SWIGRUNTIME void SwigPyClientData_Del(SwigPyClientData *data) { Py_XDECREF(data->newraw); Py_XDECREF(data->newargs); Py_XDECREF(data->destroy); } /* =============== SwigPyObject =====================*/ typedef struct { PyObject_HEAD void *ptr; swig_type_info *ty; int own; PyObject *next; #ifdef SWIGPYTHON_BUILTIN PyObject *dict; #endif } SwigPyObject; SWIGRUNTIME PyObject * SwigPyObject_long(SwigPyObject *v) { return PyLong_FromVoidPtr(v->ptr); } SWIGRUNTIME PyObject * SwigPyObject_format(const char* fmt, SwigPyObject *v) { PyObject *res = NULL; PyObject *args = PyTuple_New(1); if (args) { if (PyTuple_SetItem(args, 0, SwigPyObject_long(v)) == 0) { PyObject *ofmt = SWIG_Python_str_FromChar(fmt); if (ofmt) { #if PY_VERSION_HEX >= 0x03000000 res = PyUnicode_Format(ofmt,args); #else res = PyString_Format(ofmt,args); #endif Py_DECREF(ofmt); } Py_DECREF(args); } } return res; } SWIGRUNTIME PyObject * SwigPyObject_oct(SwigPyObject *v) { return SwigPyObject_format("%o",v); } SWIGRUNTIME PyObject * SwigPyObject_hex(SwigPyObject *v) { return SwigPyObject_format("%x",v); } SWIGRUNTIME PyObject * #ifdef METH_NOARGS SwigPyObject_repr(SwigPyObject *v) #else SwigPyObject_repr(SwigPyObject *v, PyObject *args) #endif { const char *name = SWIG_TypePrettyName(v->ty); PyObject *repr = SWIG_Python_str_FromFormat("", (name ? name : "unknown"), (void *)v); if (v->next) { # ifdef METH_NOARGS PyObject *nrep = SwigPyObject_repr((SwigPyObject *)v->next); # else PyObject *nrep = SwigPyObject_repr((SwigPyObject *)v->next, args); # endif # if PY_VERSION_HEX >= 0x03000000 PyObject *joined = PyUnicode_Concat(repr, nrep); Py_DecRef(repr); Py_DecRef(nrep); repr = joined; # else PyString_ConcatAndDel(&repr,nrep); # endif } return repr; } SWIGRUNTIME int SwigPyObject_compare(SwigPyObject *v, SwigPyObject *w) { void *i = v->ptr; void *j = w->ptr; return (i < j) ? -1 : ((i > j) ? 1 : 0); } /* Added for Python 3.x, would it also be useful for Python 2.x? */ SWIGRUNTIME PyObject* SwigPyObject_richcompare(SwigPyObject *v, SwigPyObject *w, int op) { PyObject* res; if( op != Py_EQ && op != Py_NE ) { Py_INCREF(Py_NotImplemented); return Py_NotImplemented; } res = PyBool_FromLong( (SwigPyObject_compare(v, w)==0) == (op == Py_EQ) ? 1 : 0); return res; } SWIGRUNTIME PyTypeObject* SwigPyObject_TypeOnce(void); #ifdef SWIGPYTHON_BUILTIN static swig_type_info *SwigPyObject_stype = 0; SWIGRUNTIME PyTypeObject* SwigPyObject_type(void) { SwigPyClientData *cd; assert(SwigPyObject_stype); cd = (SwigPyClientData*) SwigPyObject_stype->clientdata; assert(cd); assert(cd->pytype); return cd->pytype; } #else SWIGRUNTIME PyTypeObject* SwigPyObject_type(void) { static PyTypeObject *SWIG_STATIC_POINTER(type) = SwigPyObject_TypeOnce(); return type; } #endif SWIGRUNTIMEINLINE int SwigPyObject_Check(PyObject *op) { #ifdef SWIGPYTHON_BUILTIN PyTypeObject *target_tp = SwigPyObject_type(); if (PyType_IsSubtype(op->ob_type, target_tp)) return 1; return (strcmp(op->ob_type->tp_name, "SwigPyObject") == 0); #else return (Py_TYPE(op) == SwigPyObject_type()) || (strcmp(Py_TYPE(op)->tp_name,"SwigPyObject") == 0); #endif } SWIGRUNTIME PyObject * SwigPyObject_New(void *ptr, swig_type_info *ty, int own); SWIGRUNTIME void SwigPyObject_dealloc(PyObject *v) { SwigPyObject *sobj = (SwigPyObject *) v; PyObject *next = sobj->next; if (sobj->own == SWIG_POINTER_OWN) { swig_type_info *ty = sobj->ty; SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0; PyObject *destroy = data ? data->destroy : 0; if (destroy) { /* destroy is always a VARARGS method */ PyObject *res; if (data->delargs) { /* we need to create a temporary object to carry the destroy operation */ PyObject *tmp = SwigPyObject_New(sobj->ptr, ty, 0); res = SWIG_Python_CallFunctor(destroy, tmp); Py_DECREF(tmp); } else { PyCFunction meth = PyCFunction_GET_FUNCTION(destroy); PyObject *mself = PyCFunction_GET_SELF(destroy); res = ((*meth)(mself, v)); } Py_XDECREF(res); } #if !defined(SWIG_PYTHON_SILENT_MEMLEAK) else { const char *name = SWIG_TypePrettyName(ty); printf("swig/python detected a memory leak of type '%s', no destructor found.\n", (name ? name : "unknown")); } #endif } Py_XDECREF(next); PyObject_DEL(v); } SWIGRUNTIME PyObject* SwigPyObject_append(PyObject* v, PyObject* next) { SwigPyObject *sobj = (SwigPyObject *) v; #ifndef METH_O PyObject *tmp = 0; if (!PyArg_ParseTuple(next,(char *)"O:append", &tmp)) return NULL; next = tmp; #endif if (!SwigPyObject_Check(next)) { return NULL; } sobj->next = next; Py_INCREF(next); return SWIG_Py_Void(); } SWIGRUNTIME PyObject* #ifdef METH_NOARGS SwigPyObject_next(PyObject* v) #else SwigPyObject_next(PyObject* v, PyObject *SWIGUNUSEDPARM(args)) #endif { SwigPyObject *sobj = (SwigPyObject *) v; if (sobj->next) { Py_INCREF(sobj->next); return sobj->next; } else { return SWIG_Py_Void(); } } SWIGINTERN PyObject* #ifdef METH_NOARGS SwigPyObject_disown(PyObject *v) #else SwigPyObject_disown(PyObject* v, PyObject *SWIGUNUSEDPARM(args)) #endif { SwigPyObject *sobj = (SwigPyObject *)v; sobj->own = 0; return SWIG_Py_Void(); } SWIGINTERN PyObject* #ifdef METH_NOARGS SwigPyObject_acquire(PyObject *v) #else SwigPyObject_acquire(PyObject* v, PyObject *SWIGUNUSEDPARM(args)) #endif { SwigPyObject *sobj = (SwigPyObject *)v; sobj->own = SWIG_POINTER_OWN; return SWIG_Py_Void(); } SWIGINTERN PyObject* SwigPyObject_own(PyObject *v, PyObject *args) { PyObject *val = 0; #if (PY_VERSION_HEX < 0x02020000) if (!PyArg_ParseTuple(args,(char *)"|O:own",&val)) #elif (PY_VERSION_HEX < 0x02050000) if (!PyArg_UnpackTuple(args, (char *)"own", 0, 1, &val)) #else if (!PyArg_UnpackTuple(args, "own", 0, 1, &val)) #endif { return NULL; } else { SwigPyObject *sobj = (SwigPyObject *)v; PyObject *obj = PyBool_FromLong(sobj->own); if (val) { #ifdef METH_NOARGS if (PyObject_IsTrue(val)) { SwigPyObject_acquire(v); } else { SwigPyObject_disown(v); } #else if (PyObject_IsTrue(val)) { SwigPyObject_acquire(v,args); } else { SwigPyObject_disown(v,args); } #endif } return obj; } } #ifdef METH_O static PyMethodDef swigobject_methods[] = { {(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_NOARGS, (char *)"releases ownership of the pointer"}, {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_NOARGS, (char *)"acquires ownership of the pointer"}, {(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"}, {(char *)"append", (PyCFunction)SwigPyObject_append, METH_O, (char *)"appends another 'this' object"}, {(char *)"next", (PyCFunction)SwigPyObject_next, METH_NOARGS, (char *)"returns the next 'this' object"}, {(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_NOARGS, (char *)"returns object representation"}, {0, 0, 0, 0} }; #else static PyMethodDef swigobject_methods[] = { {(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_VARARGS, (char *)"releases ownership of the pointer"}, {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_VARARGS, (char *)"aquires ownership of the pointer"}, {(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"}, {(char *)"append", (PyCFunction)SwigPyObject_append, METH_VARARGS, (char *)"appends another 'this' object"}, {(char *)"next", (PyCFunction)SwigPyObject_next, METH_VARARGS, (char *)"returns the next 'this' object"}, {(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_VARARGS, (char *)"returns object representation"}, {0, 0, 0, 0} }; #endif #if PY_VERSION_HEX < 0x02020000 SWIGINTERN PyObject * SwigPyObject_getattr(SwigPyObject *sobj,char *name) { return Py_FindMethod(swigobject_methods, (PyObject *)sobj, name); } #endif SWIGRUNTIME PyTypeObject* SwigPyObject_TypeOnce(void) { static char swigobject_doc[] = "Swig object carries a C/C++ instance pointer"; static PyNumberMethods SwigPyObject_as_number = { (binaryfunc)0, /*nb_add*/ (binaryfunc)0, /*nb_subtract*/ (binaryfunc)0, /*nb_multiply*/ /* nb_divide removed in Python 3 */ #if PY_VERSION_HEX < 0x03000000 (binaryfunc)0, /*nb_divide*/ #endif (binaryfunc)0, /*nb_remainder*/ (binaryfunc)0, /*nb_divmod*/ (ternaryfunc)0,/*nb_power*/ (unaryfunc)0, /*nb_negative*/ (unaryfunc)0, /*nb_positive*/ (unaryfunc)0, /*nb_absolute*/ (inquiry)0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_VERSION_HEX < 0x03000000 0, /*nb_coerce*/ #endif (unaryfunc)SwigPyObject_long, /*nb_int*/ #if PY_VERSION_HEX < 0x03000000 (unaryfunc)SwigPyObject_long, /*nb_long*/ #else 0, /*nb_reserved*/ #endif (unaryfunc)0, /*nb_float*/ #if PY_VERSION_HEX < 0x03000000 (unaryfunc)SwigPyObject_oct, /*nb_oct*/ (unaryfunc)SwigPyObject_hex, /*nb_hex*/ #endif #if PY_VERSION_HEX >= 0x03000000 /* 3.0 */ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index, nb_inplace_divide removed */ #elif PY_VERSION_HEX >= 0x02050000 /* 2.5.0 */ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index */ #elif PY_VERSION_HEX >= 0x02020000 /* 2.2.0 */ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_true_divide */ #elif PY_VERSION_HEX >= 0x02000000 /* 2.0.0 */ 0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_or */ #endif }; static PyTypeObject swigpyobject_type; static int type_init = 0; if (!type_init) { const PyTypeObject tmp = { /* PyObject header changed in Python 3 */ #if PY_VERSION_HEX >= 0x03000000 PyVarObject_HEAD_INIT(NULL, 0) #else PyObject_HEAD_INIT(NULL) 0, /* ob_size */ #endif (char *)"SwigPyObject", /* tp_name */ sizeof(SwigPyObject), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor)SwigPyObject_dealloc, /* tp_dealloc */ 0, /* tp_print */ #if PY_VERSION_HEX < 0x02020000 (getattrfunc)SwigPyObject_getattr, /* tp_getattr */ #else (getattrfunc)0, /* tp_getattr */ #endif (setattrfunc)0, /* tp_setattr */ #if PY_VERSION_HEX >= 0x03000000 0, /* tp_reserved in 3.0.1, tp_compare in 3.0.0 but not used */ #else (cmpfunc)SwigPyObject_compare, /* tp_compare */ #endif (reprfunc)SwigPyObject_repr, /* tp_repr */ &SwigPyObject_as_number, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ (hashfunc)0, /* tp_hash */ (ternaryfunc)0, /* tp_call */ 0, /* tp_str */ PyObject_GenericGetAttr, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT, /* tp_flags */ swigobject_doc, /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ (richcmpfunc)SwigPyObject_richcompare,/* tp_richcompare */ 0, /* tp_weaklistoffset */ #if PY_VERSION_HEX >= 0x02020000 0, /* tp_iter */ 0, /* tp_iternext */ swigobject_methods, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ 0, /* tp_init */ 0, /* tp_alloc */ 0, /* tp_new */ 0, /* tp_free */ 0, /* tp_is_gc */ 0, /* tp_bases */ 0, /* tp_mro */ 0, /* tp_cache */ 0, /* tp_subclasses */ 0, /* tp_weaklist */ #endif #if PY_VERSION_HEX >= 0x02030000 0, /* tp_del */ #endif #if PY_VERSION_HEX >= 0x02060000 0, /* tp_version */ #endif #ifdef COUNT_ALLOCS 0,0,0,0 /* tp_alloc -> tp_next */ #endif }; swigpyobject_type = tmp; type_init = 1; #if PY_VERSION_HEX < 0x02020000 swigpyobject_type.ob_type = &PyType_Type; #else if (PyType_Ready(&swigpyobject_type) < 0) return NULL; #endif } return &swigpyobject_type; } SWIGRUNTIME PyObject * SwigPyObject_New(void *ptr, swig_type_info *ty, int own) { SwigPyObject *sobj = PyObject_NEW(SwigPyObject, SwigPyObject_type()); if (sobj) { sobj->ptr = ptr; sobj->ty = ty; sobj->own = own; sobj->next = 0; } return (PyObject *)sobj; } /* ----------------------------------------------------------------------------- * Implements a simple Swig Packed type, and use it instead of string * ----------------------------------------------------------------------------- */ typedef struct { PyObject_HEAD void *pack; swig_type_info *ty; size_t size; } SwigPyPacked; SWIGRUNTIME int SwigPyPacked_print(SwigPyPacked *v, FILE *fp, int SWIGUNUSEDPARM(flags)) { char result[SWIG_BUFFER_SIZE]; fputs("pack, v->size, 0, sizeof(result))) { fputs("at ", fp); fputs(result, fp); } fputs(v->ty->name,fp); fputs(">", fp); return 0; } SWIGRUNTIME PyObject * SwigPyPacked_repr(SwigPyPacked *v) { char result[SWIG_BUFFER_SIZE]; if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))) { return SWIG_Python_str_FromFormat("", result, v->ty->name); } else { return SWIG_Python_str_FromFormat("", v->ty->name); } } SWIGRUNTIME PyObject * SwigPyPacked_str(SwigPyPacked *v) { char result[SWIG_BUFFER_SIZE]; if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))){ return SWIG_Python_str_FromFormat("%s%s", result, v->ty->name); } else { return SWIG_Python_str_FromChar(v->ty->name); } } SWIGRUNTIME int SwigPyPacked_compare(SwigPyPacked *v, SwigPyPacked *w) { size_t i = v->size; size_t j = w->size; int s = (i < j) ? -1 : ((i > j) ? 1 : 0); return s ? s : strncmp((char *)v->pack, (char *)w->pack, 2*v->size); } SWIGRUNTIME PyTypeObject* SwigPyPacked_TypeOnce(void); SWIGRUNTIME PyTypeObject* SwigPyPacked_type(void) { static PyTypeObject *SWIG_STATIC_POINTER(type) = SwigPyPacked_TypeOnce(); return type; } SWIGRUNTIMEINLINE int SwigPyPacked_Check(PyObject *op) { return ((op)->ob_type == SwigPyPacked_TypeOnce()) || (strcmp((op)->ob_type->tp_name,"SwigPyPacked") == 0); } SWIGRUNTIME void SwigPyPacked_dealloc(PyObject *v) { if (SwigPyPacked_Check(v)) { SwigPyPacked *sobj = (SwigPyPacked *) v; free(sobj->pack); } PyObject_DEL(v); } SWIGRUNTIME PyTypeObject* SwigPyPacked_TypeOnce(void) { static char swigpacked_doc[] = "Swig object carries a C/C++ instance pointer"; static PyTypeObject swigpypacked_type; static int type_init = 0; if (!type_init) { const PyTypeObject tmp = { /* PyObject header changed in Python 3 */ #if PY_VERSION_HEX>=0x03000000 PyVarObject_HEAD_INIT(NULL, 0) #else PyObject_HEAD_INIT(NULL) 0, /* ob_size */ #endif (char *)"SwigPyPacked", /* tp_name */ sizeof(SwigPyPacked), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor)SwigPyPacked_dealloc, /* tp_dealloc */ (printfunc)SwigPyPacked_print, /* tp_print */ (getattrfunc)0, /* tp_getattr */ (setattrfunc)0, /* tp_setattr */ #if PY_VERSION_HEX>=0x03000000 0, /* tp_reserved in 3.0.1 */ #else (cmpfunc)SwigPyPacked_compare, /* tp_compare */ #endif (reprfunc)SwigPyPacked_repr, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ (hashfunc)0, /* tp_hash */ (ternaryfunc)0, /* tp_call */ (reprfunc)SwigPyPacked_str, /* tp_str */ PyObject_GenericGetAttr, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT, /* tp_flags */ swigpacked_doc, /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ #if PY_VERSION_HEX >= 0x02020000 0, /* tp_iter */ 0, /* tp_iternext */ 0, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ 0, /* tp_init */ 0, /* tp_alloc */ 0, /* tp_new */ 0, /* tp_free */ 0, /* tp_is_gc */ 0, /* tp_bases */ 0, /* tp_mro */ 0, /* tp_cache */ 0, /* tp_subclasses */ 0, /* tp_weaklist */ #endif #if PY_VERSION_HEX >= 0x02030000 0, /* tp_del */ #endif #if PY_VERSION_HEX >= 0x02060000 0, /* tp_version */ #endif #ifdef COUNT_ALLOCS 0,0,0,0 /* tp_alloc -> tp_next */ #endif }; swigpypacked_type = tmp; type_init = 1; #if PY_VERSION_HEX < 0x02020000 swigpypacked_type.ob_type = &PyType_Type; #else if (PyType_Ready(&swigpypacked_type) < 0) return NULL; #endif } return &swigpypacked_type; } SWIGRUNTIME PyObject * SwigPyPacked_New(void *ptr, size_t size, swig_type_info *ty) { SwigPyPacked *sobj = PyObject_NEW(SwigPyPacked, SwigPyPacked_type()); if (sobj) { void *pack = malloc(size); if (pack) { memcpy(pack, ptr, size); sobj->pack = pack; sobj->ty = ty; sobj->size = size; } else { PyObject_DEL((PyObject *) sobj); sobj = 0; } } return (PyObject *) sobj; } SWIGRUNTIME swig_type_info * SwigPyPacked_UnpackData(PyObject *obj, void *ptr, size_t size) { if (SwigPyPacked_Check(obj)) { SwigPyPacked *sobj = (SwigPyPacked *)obj; if (sobj->size != size) return 0; memcpy(ptr, sobj->pack, size); return sobj->ty; } else { return 0; } } /* ----------------------------------------------------------------------------- * pointers/data manipulation * ----------------------------------------------------------------------------- */ SWIGRUNTIMEINLINE PyObject * _SWIG_This(void) { return SWIG_Python_str_FromChar("this"); } static PyObject *swig_this = NULL; SWIGRUNTIME PyObject * SWIG_This(void) { if (swig_this == NULL) swig_this = _SWIG_This(); return swig_this; } /* #define SWIG_PYTHON_SLOW_GETSET_THIS */ /* TODO: I don't know how to implement the fast getset in Python 3 right now */ #if PY_VERSION_HEX>=0x03000000 #define SWIG_PYTHON_SLOW_GETSET_THIS #endif SWIGRUNTIME SwigPyObject * SWIG_Python_GetSwigThis(PyObject *pyobj) { PyObject *obj; if (SwigPyObject_Check(pyobj)) return (SwigPyObject *) pyobj; #ifdef SWIGPYTHON_BUILTIN (void)obj; # ifdef PyWeakref_CheckProxy if (PyWeakref_CheckProxy(pyobj)) { pyobj = PyWeakref_GET_OBJECT(pyobj); if (pyobj && SwigPyObject_Check(pyobj)) return (SwigPyObject*) pyobj; } # endif return NULL; #else obj = 0; #if (!defined(SWIG_PYTHON_SLOW_GETSET_THIS) && (PY_VERSION_HEX >= 0x02030000)) if (PyInstance_Check(pyobj)) { obj = _PyInstance_Lookup(pyobj, SWIG_This()); } else { PyObject **dictptr = _PyObject_GetDictPtr(pyobj); if (dictptr != NULL) { PyObject *dict = *dictptr; obj = dict ? PyDict_GetItem(dict, SWIG_This()) : 0; } else { #ifdef PyWeakref_CheckProxy if (PyWeakref_CheckProxy(pyobj)) { PyObject *wobj = PyWeakref_GET_OBJECT(pyobj); return wobj ? SWIG_Python_GetSwigThis(wobj) : 0; } #endif obj = PyObject_GetAttr(pyobj,SWIG_This()); if (obj) { Py_DECREF(obj); } else { if (PyErr_Occurred()) PyErr_Clear(); return 0; } } } #else obj = PyObject_GetAttr(pyobj,SWIG_This()); if (obj) { Py_DECREF(obj); } else { if (PyErr_Occurred()) PyErr_Clear(); return 0; } #endif if (obj && !SwigPyObject_Check(obj)) { /* a PyObject is called 'this', try to get the 'real this' SwigPyObject from it */ return SWIG_Python_GetSwigThis(obj); } return (SwigPyObject *)obj; #endif } /* Acquire a pointer value */ SWIGRUNTIME int SWIG_Python_AcquirePtr(PyObject *obj, int own) { if (own == SWIG_POINTER_OWN) { SwigPyObject *sobj = SWIG_Python_GetSwigThis(obj); if (sobj) { int oldown = sobj->own; sobj->own = own; return oldown; } } return 0; } /* Convert a pointer value */ SWIGRUNTIME int SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int flags, int *own) { int res; SwigPyObject *sobj; int implicit_conv = (flags & SWIG_POINTER_IMPLICIT_CONV) != 0; if (!obj) return SWIG_ERROR; if (obj == Py_None && !implicit_conv) { if (ptr) *ptr = 0; return SWIG_OK; } res = SWIG_ERROR; sobj = SWIG_Python_GetSwigThis(obj); if (own) *own = 0; while (sobj) { void *vptr = sobj->ptr; if (ty) { swig_type_info *to = sobj->ty; if (to == ty) { /* no type cast needed */ if (ptr) *ptr = vptr; break; } else { swig_cast_info *tc = SWIG_TypeCheck(to->name,ty); if (!tc) { sobj = (SwigPyObject *)sobj->next; } else { if (ptr) { int newmemory = 0; *ptr = SWIG_TypeCast(tc,vptr,&newmemory); if (newmemory == SWIG_CAST_NEW_MEMORY) { assert(own); /* badly formed typemap which will lead to a memory leak - it must set and use own to delete *ptr */ if (own) *own = *own | SWIG_CAST_NEW_MEMORY; } } break; } } } else { if (ptr) *ptr = vptr; break; } } if (sobj) { if (own) *own = *own | sobj->own; if (flags & SWIG_POINTER_DISOWN) { sobj->own = 0; } res = SWIG_OK; } else { if (implicit_conv) { SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0; if (data && !data->implicitconv) { PyObject *klass = data->klass; if (klass) { PyObject *impconv; data->implicitconv = 1; /* avoid recursion and call 'explicit' constructors*/ impconv = SWIG_Python_CallFunctor(klass, obj); data->implicitconv = 0; if (PyErr_Occurred()) { PyErr_Clear(); impconv = 0; } if (impconv) { SwigPyObject *iobj = SWIG_Python_GetSwigThis(impconv); if (iobj) { void *vptr; res = SWIG_Python_ConvertPtrAndOwn((PyObject*)iobj, &vptr, ty, 0, 0); if (SWIG_IsOK(res)) { if (ptr) { *ptr = vptr; /* transfer the ownership to 'ptr' */ iobj->own = 0; res = SWIG_AddCast(res); res = SWIG_AddNewMask(res); } else { res = SWIG_AddCast(res); } } } Py_DECREF(impconv); } } } } if (!SWIG_IsOK(res) && obj == Py_None) { if (ptr) *ptr = 0; if (PyErr_Occurred()) PyErr_Clear(); res = SWIG_OK; } } return res; } /* Convert a function ptr value */ SWIGRUNTIME int SWIG_Python_ConvertFunctionPtr(PyObject *obj, void **ptr, swig_type_info *ty) { if (!PyCFunction_Check(obj)) { return SWIG_ConvertPtr(obj, ptr, ty, 0); } else { void *vptr = 0; /* here we get the method pointer for callbacks */ const char *doc = (((PyCFunctionObject *)obj) -> m_ml -> ml_doc); const char *desc = doc ? strstr(doc, "swig_ptr: ") : 0; if (desc) desc = ty ? SWIG_UnpackVoidPtr(desc + 10, &vptr, ty->name) : 0; if (!desc) return SWIG_ERROR; if (ty) { swig_cast_info *tc = SWIG_TypeCheck(desc,ty); if (tc) { int newmemory = 0; *ptr = SWIG_TypeCast(tc,vptr,&newmemory); assert(!newmemory); /* newmemory handling not yet implemented */ } else { return SWIG_ERROR; } } else { *ptr = vptr; } return SWIG_OK; } } /* Convert a packed value value */ SWIGRUNTIME int SWIG_Python_ConvertPacked(PyObject *obj, void *ptr, size_t sz, swig_type_info *ty) { swig_type_info *to = SwigPyPacked_UnpackData(obj, ptr, sz); if (!to) return SWIG_ERROR; if (ty) { if (to != ty) { /* check type cast? */ swig_cast_info *tc = SWIG_TypeCheck(to->name,ty); if (!tc) return SWIG_ERROR; } } return SWIG_OK; } /* ----------------------------------------------------------------------------- * Create a new pointer object * ----------------------------------------------------------------------------- */ /* Create a new instance object, without calling __init__, and set the 'this' attribute. */ SWIGRUNTIME PyObject* SWIG_Python_NewShadowInstance(SwigPyClientData *data, PyObject *swig_this) { #if (PY_VERSION_HEX >= 0x02020000) PyObject *inst = 0; PyObject *newraw = data->newraw; if (newraw) { inst = PyObject_Call(newraw, data->newargs, NULL); if (inst) { #if !defined(SWIG_PYTHON_SLOW_GETSET_THIS) PyObject **dictptr = _PyObject_GetDictPtr(inst); if (dictptr != NULL) { PyObject *dict = *dictptr; if (dict == NULL) { dict = PyDict_New(); *dictptr = dict; PyDict_SetItem(dict, SWIG_This(), swig_this); } } #else PyObject *key = SWIG_This(); PyObject_SetAttr(inst, key, swig_this); #endif } } else { #if PY_VERSION_HEX >= 0x03000000 inst = PyBaseObject_Type.tp_new((PyTypeObject*) data->newargs, Py_None, Py_None); if (inst) { PyObject_SetAttr(inst, SWIG_This(), swig_this); Py_TYPE(inst)->tp_flags &= ~Py_TPFLAGS_VALID_VERSION_TAG; } #else PyObject *dict = PyDict_New(); if (dict) { PyDict_SetItem(dict, SWIG_This(), swig_this); inst = PyInstance_NewRaw(data->newargs, dict); Py_DECREF(dict); } #endif } return inst; #else #if (PY_VERSION_HEX >= 0x02010000) PyObject *inst = 0; PyObject *dict = PyDict_New(); if (dict) { PyDict_SetItem(dict, SWIG_This(), swig_this); inst = PyInstance_NewRaw(data->newargs, dict); Py_DECREF(dict); } return (PyObject *) inst; #else PyInstanceObject *inst = PyObject_NEW(PyInstanceObject, &PyInstance_Type); if (inst == NULL) { return NULL; } inst->in_class = (PyClassObject *)data->newargs; Py_INCREF(inst->in_class); inst->in_dict = PyDict_New(); if (inst->in_dict == NULL) { Py_DECREF(inst); return NULL; } #ifdef Py_TPFLAGS_HAVE_WEAKREFS inst->in_weakreflist = NULL; #endif #ifdef Py_TPFLAGS_GC PyObject_GC_Init(inst); #endif PyDict_SetItem(inst->in_dict, SWIG_This(), swig_this); return (PyObject *) inst; #endif #endif } SWIGRUNTIME void SWIG_Python_SetSwigThis(PyObject *inst, PyObject *swig_this) { PyObject *dict; #if (PY_VERSION_HEX >= 0x02020000) && !defined(SWIG_PYTHON_SLOW_GETSET_THIS) PyObject **dictptr = _PyObject_GetDictPtr(inst); if (dictptr != NULL) { dict = *dictptr; if (dict == NULL) { dict = PyDict_New(); *dictptr = dict; } PyDict_SetItem(dict, SWIG_This(), swig_this); return; } #endif dict = PyObject_GetAttrString(inst, (char*)"__dict__"); PyDict_SetItem(dict, SWIG_This(), swig_this); Py_DECREF(dict); } SWIGINTERN PyObject * SWIG_Python_InitShadowInstance(PyObject *args) { PyObject *obj[2]; if (!SWIG_Python_UnpackTuple(args, "swiginit", 2, 2, obj)) { return NULL; } else { SwigPyObject *sthis = SWIG_Python_GetSwigThis(obj[0]); if (sthis) { SwigPyObject_append((PyObject*) sthis, obj[1]); } else { SWIG_Python_SetSwigThis(obj[0], obj[1]); } return SWIG_Py_Void(); } } /* Create a new pointer object */ SWIGRUNTIME PyObject * SWIG_Python_NewPointerObj(PyObject *self, void *ptr, swig_type_info *type, int flags) { SwigPyClientData *clientdata; PyObject * robj; int own; if (!ptr) return SWIG_Py_Void(); clientdata = type ? (SwigPyClientData *)(type->clientdata) : 0; own = (flags & SWIG_POINTER_OWN) ? SWIG_POINTER_OWN : 0; if (clientdata && clientdata->pytype) { SwigPyObject *newobj; if (flags & SWIG_BUILTIN_TP_INIT) { newobj = (SwigPyObject*) self; if (newobj->ptr) { PyObject *next_self = clientdata->pytype->tp_alloc(clientdata->pytype, 0); while (newobj->next) newobj = (SwigPyObject *) newobj->next; newobj->next = next_self; newobj = (SwigPyObject *)next_self; } } else { newobj = PyObject_New(SwigPyObject, clientdata->pytype); } if (newobj) { newobj->ptr = ptr; newobj->ty = type; newobj->own = own; newobj->next = 0; #ifdef SWIGPYTHON_BUILTIN newobj->dict = 0; #endif return (PyObject*) newobj; } return SWIG_Py_Void(); } assert(!(flags & SWIG_BUILTIN_TP_INIT)); robj = SwigPyObject_New(ptr, type, own); if (robj && clientdata && !(flags & SWIG_POINTER_NOSHADOW)) { PyObject *inst = SWIG_Python_NewShadowInstance(clientdata, robj); Py_DECREF(robj); robj = inst; } return robj; } /* Create a new packed object */ SWIGRUNTIMEINLINE PyObject * SWIG_Python_NewPackedObj(void *ptr, size_t sz, swig_type_info *type) { return ptr ? SwigPyPacked_New((void *) ptr, sz, type) : SWIG_Py_Void(); } /* -----------------------------------------------------------------------------* * Get type list * -----------------------------------------------------------------------------*/ #ifdef SWIG_LINK_RUNTIME void *SWIG_ReturnGlobalTypeList(void *); #endif SWIGRUNTIME swig_module_info * SWIG_Python_GetModule(void *SWIGUNUSEDPARM(clientdata)) { static void *type_pointer = (void *)0; /* first check if module already created */ if (!type_pointer) { #ifdef SWIG_LINK_RUNTIME type_pointer = SWIG_ReturnGlobalTypeList((void *)0); #else # ifdef SWIGPY_USE_CAPSULE type_pointer = PyCapsule_Import(SWIGPY_CAPSULE_NAME, 0); # else type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME); # endif if (PyErr_Occurred()) { PyErr_Clear(); type_pointer = (void *)0; } #endif } return (swig_module_info *) type_pointer; } #if PY_MAJOR_VERSION < 2 /* PyModule_AddObject function was introduced in Python 2.0. The following function is copied out of Python/modsupport.c in python version 2.3.4 */ SWIGINTERN int PyModule_AddObject(PyObject *m, char *name, PyObject *o) { PyObject *dict; if (!PyModule_Check(m)) { PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs module as first arg"); return SWIG_ERROR; } if (!o) { PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs non-NULL value"); return SWIG_ERROR; } dict = PyModule_GetDict(m); if (dict == NULL) { /* Internal error -- modules must have a dict! */ PyErr_Format(PyExc_SystemError, "module '%s' has no __dict__", PyModule_GetName(m)); return SWIG_ERROR; } if (PyDict_SetItemString(dict, name, o)) return SWIG_ERROR; Py_DECREF(o); return SWIG_OK; } #endif SWIGRUNTIME void #ifdef SWIGPY_USE_CAPSULE SWIG_Python_DestroyModule(PyObject *obj) #else SWIG_Python_DestroyModule(void *vptr) #endif { #ifdef SWIGPY_USE_CAPSULE swig_module_info *swig_module = (swig_module_info *) PyCapsule_GetPointer(obj, SWIGPY_CAPSULE_NAME); #else swig_module_info *swig_module = (swig_module_info *) vptr; #endif swig_type_info **types = swig_module->types; size_t i; for (i =0; i < swig_module->size; ++i) { swig_type_info *ty = types[i]; if (ty->owndata) { SwigPyClientData *data = (SwigPyClientData *) ty->clientdata; if (data) SwigPyClientData_Del(data); } } Py_DECREF(SWIG_This()); swig_this = NULL; } SWIGRUNTIME void SWIG_Python_SetModule(swig_module_info *swig_module) { #if PY_VERSION_HEX >= 0x03000000 /* Add a dummy module object into sys.modules */ PyObject *module = PyImport_AddModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION); #else static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} }; /* Sentinel */ PyObject *module = Py_InitModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION, swig_empty_runtime_method_table); #endif #ifdef SWIGPY_USE_CAPSULE PyObject *pointer = PyCapsule_New((void *) swig_module, SWIGPY_CAPSULE_NAME, SWIG_Python_DestroyModule); if (pointer && module) { PyModule_AddObject(module, (char*)"type_pointer_capsule" SWIG_TYPE_TABLE_NAME, pointer); } else { Py_XDECREF(pointer); } #else PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule); if (pointer && module) { PyModule_AddObject(module, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME, pointer); } else { Py_XDECREF(pointer); } #endif } /* The python cached type query */ SWIGRUNTIME PyObject * SWIG_Python_TypeCache(void) { static PyObject *SWIG_STATIC_POINTER(cache) = PyDict_New(); return cache; } SWIGRUNTIME swig_type_info * SWIG_Python_TypeQuery(const char *type) { PyObject *cache = SWIG_Python_TypeCache(); PyObject *key = SWIG_Python_str_FromChar(type); PyObject *obj = PyDict_GetItem(cache, key); swig_type_info *descriptor; if (obj) { #ifdef SWIGPY_USE_CAPSULE descriptor = (swig_type_info *) PyCapsule_GetPointer(obj, NULL); #else descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj); #endif } else { swig_module_info *swig_module = SWIG_GetModule(0); descriptor = SWIG_TypeQueryModule(swig_module, swig_module, type); if (descriptor) { #ifdef SWIGPY_USE_CAPSULE obj = PyCapsule_New((void*) descriptor, NULL, NULL); #else obj = PyCObject_FromVoidPtr(descriptor, NULL); #endif PyDict_SetItem(cache, key, obj); Py_DECREF(obj); } } Py_DECREF(key); return descriptor; } /* For backward compatibility only */ #define SWIG_POINTER_EXCEPTION 0 #define SWIG_arg_fail(arg) SWIG_Python_ArgFail(arg) #define SWIG_MustGetPtr(p, type, argnum, flags) SWIG_Python_MustGetPtr(p, type, argnum, flags) SWIGRUNTIME int SWIG_Python_AddErrMesg(const char* mesg, int infront) { if (PyErr_Occurred()) { PyObject *type = 0; PyObject *value = 0; PyObject *traceback = 0; PyErr_Fetch(&type, &value, &traceback); if (value) { char *tmp; PyObject *old_str = PyObject_Str(value); Py_XINCREF(type); PyErr_Clear(); if (infront) { PyErr_Format(type, "%s %s", mesg, tmp = SWIG_Python_str_AsChar(old_str)); } else { PyErr_Format(type, "%s %s", tmp = SWIG_Python_str_AsChar(old_str), mesg); } SWIG_Python_str_DelForPy3(tmp); Py_DECREF(old_str); } return 1; } else { return 0; } } SWIGRUNTIME int SWIG_Python_ArgFail(int argnum) { if (PyErr_Occurred()) { /* add information about failing argument */ char mesg[256]; PyOS_snprintf(mesg, sizeof(mesg), "argument number %d:", argnum); return SWIG_Python_AddErrMesg(mesg, 1); } else { return 0; } } SWIGRUNTIMEINLINE const char * SwigPyObject_GetDesc(PyObject *self) { SwigPyObject *v = (SwigPyObject *)self; swig_type_info *ty = v ? v->ty : 0; return ty ? ty->str : ""; } SWIGRUNTIME void SWIG_Python_TypeError(const char *type, PyObject *obj) { if (type) { #if defined(SWIG_COBJECT_TYPES) if (obj && SwigPyObject_Check(obj)) { const char *otype = (const char *) SwigPyObject_GetDesc(obj); if (otype) { PyErr_Format(PyExc_TypeError, "a '%s' is expected, 'SwigPyObject(%s)' is received", type, otype); return; } } else #endif { const char *otype = (obj ? obj->ob_type->tp_name : 0); if (otype) { PyObject *str = PyObject_Str(obj); const char *cstr = str ? SWIG_Python_str_AsChar(str) : 0; if (cstr) { PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s(%s)' is received", type, otype, cstr); SWIG_Python_str_DelForPy3(cstr); } else { PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s' is received", type, otype); } Py_XDECREF(str); return; } } PyErr_Format(PyExc_TypeError, "a '%s' is expected", type); } else { PyErr_Format(PyExc_TypeError, "unexpected type is received"); } } /* Convert a pointer value, signal an exception on a type mismatch */ SWIGRUNTIME void * SWIG_Python_MustGetPtr(PyObject *obj, swig_type_info *ty, int SWIGUNUSEDPARM(argnum), int flags) { void *result; if (SWIG_Python_ConvertPtr(obj, &result, ty, flags) == -1) { PyErr_Clear(); #if SWIG_POINTER_EXCEPTION if (flags) { SWIG_Python_TypeError(SWIG_TypePrettyName(ty), obj); SWIG_Python_ArgFail(argnum); } #endif } return result; } #ifdef SWIGPYTHON_BUILTIN SWIGRUNTIME int SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) { PyTypeObject *tp = obj->ob_type; PyObject *descr; PyObject *encoded_name; descrsetfunc f; int res = -1; # ifdef Py_USING_UNICODE if (PyString_Check(name)) { name = PyUnicode_Decode(PyString_AsString(name), PyString_Size(name), NULL, NULL); if (!name) return -1; } else if (!PyUnicode_Check(name)) # else if (!PyString_Check(name)) # endif { PyErr_Format(PyExc_TypeError, "attribute name must be string, not '%.200s'", name->ob_type->tp_name); return -1; } else { Py_INCREF(name); } if (!tp->tp_dict) { if (PyType_Ready(tp) < 0) goto done; } descr = _PyType_Lookup(tp, name); f = NULL; if (descr != NULL) f = descr->ob_type->tp_descr_set; if (!f) { if (PyString_Check(name)) { encoded_name = name; Py_INCREF(name); } else { encoded_name = PyUnicode_AsUTF8String(name); } PyErr_Format(PyExc_AttributeError, "'%.100s' object has no attribute '%.200s'", tp->tp_name, PyString_AsString(encoded_name)); Py_DECREF(encoded_name); } else { res = f(descr, obj, value); } done: Py_DECREF(name); return res; } #endif #ifdef __cplusplus } #endif #define SWIG_exception_fail(code, msg) do { SWIG_Error(code, msg); SWIG_fail; } while(0) #define SWIG_contract_assert(expr, msg) if (!(expr)) { SWIG_Error(SWIG_RuntimeError, msg); SWIG_fail; } else /* -------- TYPES TABLE (BEGIN) -------- */ #define SWIGTYPE_p_char swig_types[0] static swig_type_info *swig_types[2]; static swig_module_info swig_module = {swig_types, 1, 0, 0, 0, 0}; #define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name) #define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name) /* -------- TYPES TABLE (END) -------- */ #if (PY_VERSION_HEX <= 0x02000000) # if !defined(SWIG_PYTHON_CLASSIC) # error "This python version requires swig to be run with the '-classic' option" # endif #endif /*----------------------------------------------- @(target):= _somoclu.so ------------------------------------------------*/ #if PY_VERSION_HEX >= 0x03000000 # define SWIG_init PyInit__somoclu #else # define SWIG_init init_somoclu #endif #define SWIG_name "_somoclu" #define SWIGVERSION 0x020012 #define SWIG_VERSION SWIGVERSION #define SWIG_as_voidptr(a) const_cast< void * >(static_cast< const void * >(a)) #define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),reinterpret_cast< void** >(a)) #include namespace swig { class SwigPtr_PyObject { protected: PyObject *_obj; public: SwigPtr_PyObject() :_obj(0) { } SwigPtr_PyObject(const SwigPtr_PyObject& item) : _obj(item._obj) { Py_XINCREF(_obj); } SwigPtr_PyObject(PyObject *obj, bool initial_ref = true) :_obj(obj) { if (initial_ref) { Py_XINCREF(_obj); } } SwigPtr_PyObject & operator=(const SwigPtr_PyObject& item) { Py_XINCREF(item._obj); Py_XDECREF(_obj); _obj = item._obj; return *this; } ~SwigPtr_PyObject() { Py_XDECREF(_obj); } operator PyObject *() const { return _obj; } PyObject *operator->() const { return _obj; } }; } namespace swig { struct SwigVar_PyObject : SwigPtr_PyObject { SwigVar_PyObject(PyObject* obj = 0) : SwigPtr_PyObject(obj, false) { } SwigVar_PyObject & operator = (PyObject* obj) { Py_XDECREF(_obj); _obj = obj; return *this; } }; } #include #define SWIG_FILE_WITH_INIT #include "src/src/somocluWrap.h" #ifndef SWIG_FILE_WITH_INIT #define NO_IMPORT_ARRAY #endif #include "stdio.h" #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION #include #if NPY_API_VERSION < 0x00000007 #define NPY_ARRAY_DEFAULT NPY_DEFAULT #define NPY_ARRAY_FARRAY NPY_FARRAY #define NPY_FORTRANORDER NPY_FORTRAN #endif /* Macros to extract array attributes. */ #if NPY_API_VERSION < 0x00000007 #define is_array(a) ((a) && PyArray_Check((PyArrayObject*)a)) #define array_type(a) (int)(PyArray_TYPE((PyArrayObject*)a)) #define array_numdims(a) (((PyArrayObject*)a)->nd) #define array_dimensions(a) (((PyArrayObject*)a)->dimensions) #define array_size(a,i) (((PyArrayObject*)a)->dimensions[i]) #define array_strides(a) (((PyArrayObject*)a)->strides) #define array_stride(a,i) (((PyArrayObject*)a)->strides[i]) #define array_data(a) (((PyArrayObject*)a)->data) #define array_descr(a) (((PyArrayObject*)a)->descr) #define array_flags(a) (((PyArrayObject*)a)->flags) #define array_enableflags(a,f) (((PyArrayObject*)a)->flags) = f #else #define is_array(a) ((a) && PyArray_Check(a)) #define array_type(a) PyArray_TYPE((PyArrayObject*)a) #define array_numdims(a) PyArray_NDIM((PyArrayObject*)a) #define array_dimensions(a) PyArray_DIMS((PyArrayObject*)a) #define array_strides(a) PyArray_STRIDES((PyArrayObject*)a) #define array_stride(a,i) PyArray_STRIDE((PyArrayObject*)a,i) #define array_size(a,i) PyArray_DIM((PyArrayObject*)a,i) #define array_data(a) PyArray_DATA((PyArrayObject*)a) #define array_descr(a) PyArray_DESCR((PyArrayObject*)a) #define array_flags(a) PyArray_FLAGS((PyArrayObject*)a) #define array_enableflags(a,f) PyArray_ENABLEFLAGS((PyArrayObject*)a,f) #endif #define array_is_contiguous(a) (PyArray_ISCONTIGUOUS((PyArrayObject*)a)) #define array_is_native(a) (PyArray_ISNOTSWAPPED((PyArrayObject*)a)) #define array_is_fortran(a) (PyArray_ISFORTRAN((PyArrayObject*)a)) /* Given a PyObject, return a string describing its type. */ const char* pytype_string(PyObject* py_obj) { if (py_obj == NULL ) return "C NULL value"; if (py_obj == Py_None ) return "Python None" ; if (PyCallable_Check(py_obj)) return "callable" ; if (PyString_Check( py_obj)) return "string" ; if (PyInt_Check( py_obj)) return "int" ; if (PyFloat_Check( py_obj)) return "float" ; if (PyDict_Check( py_obj)) return "dict" ; if (PyList_Check( py_obj)) return "list" ; if (PyTuple_Check( py_obj)) return "tuple" ; #if PY_MAJOR_VERSION < 3 if (PyFile_Check( py_obj)) return "file" ; if (PyModule_Check( py_obj)) return "module" ; if (PyInstance_Check(py_obj)) return "instance" ; #endif return "unkown type"; } /* Given a NumPy typecode, return a string describing the type. */ const char* typecode_string(int typecode) { static const char* type_names[25] = {"bool", "byte", "unsigned byte", "short", "unsigned short", "int", "unsigned int", "long", "unsigned long", "long long", "unsigned long long", "float", "double", "long double", "complex float", "complex double", "complex long double", "object", "string", "unicode", "void", "ntypes", "notype", "char", "unknown"}; return typecode < 24 ? type_names[typecode] : type_names[24]; } /* Make sure input has correct numpy type. This now just calls PyArray_EquivTypenums(). */ int type_match(int actual_type, int desired_type) { return PyArray_EquivTypenums(actual_type, desired_type); } #ifdef SWIGPY_USE_CAPSULE void free_cap(PyObject * cap) { void* array = (void*) PyCapsule_GetPointer(cap,SWIGPY_CAPSULE_NAME); if (array != NULL) free(array); } #endif /* Given a PyObject pointer, cast it to a PyArrayObject pointer if * legal. If not, set the python error string appropriately and * return NULL. */ PyArrayObject* obj_to_array_no_conversion(PyObject* input, int typecode) { PyArrayObject* ary = NULL; if (is_array(input) && (typecode == NPY_NOTYPE || PyArray_EquivTypenums(array_type(input), typecode))) { ary = (PyArrayObject*) input; } else if is_array(input) { const char* desired_type = typecode_string(typecode); const char* actual_type = typecode_string(array_type(input)); PyErr_Format(PyExc_TypeError, "Array of type '%s' required. Array of type '%s' given", desired_type, actual_type); ary = NULL; } else { const char* desired_type = typecode_string(typecode); const char* actual_type = pytype_string(input); PyErr_Format(PyExc_TypeError, "Array of type '%s' required. A '%s' was given", desired_type, actual_type); ary = NULL; } return ary; } /* Convert the given PyObject to a NumPy array with the given * typecode. On success, return a valid PyArrayObject* with the * correct type. On failure, the python error string will be set and * the routine returns NULL. */ PyArrayObject* obj_to_array_allow_conversion(PyObject* input, int typecode, int* is_new_object) { PyArrayObject* ary = NULL; PyObject* py_obj; if (is_array(input) && (typecode == NPY_NOTYPE || PyArray_EquivTypenums(array_type(input),typecode))) { ary = (PyArrayObject*) input; *is_new_object = 0; } else { py_obj = PyArray_FROMANY(input, typecode, 0, 0, NPY_ARRAY_DEFAULT); /* If NULL, PyArray_FromObject will have set python error value.*/ ary = (PyArrayObject*) py_obj; *is_new_object = 1; } return ary; } /* Given a PyArrayObject, check to see if it is contiguous. If so, * return the input pointer and flag it as not a new object. If it is * not contiguous, create a new PyArrayObject using the original data, * flag it as a new object and return the pointer. */ PyArrayObject* make_contiguous(PyArrayObject* ary, int* is_new_object, int min_dims, int max_dims) { PyArrayObject* result; if (array_is_contiguous(ary)) { result = ary; *is_new_object = 0; } else { result = (PyArrayObject*) PyArray_ContiguousFromObject((PyObject*)ary, array_type(ary), min_dims, max_dims); *is_new_object = 1; } return result; } /* Given a PyArrayObject, check to see if it is Fortran-contiguous. * If so, return the input pointer, but do not flag it as not a new * object. If it is not Fortran-contiguous, create a new * PyArrayObject using the original data, flag it as a new object * and return the pointer. */ PyArrayObject* make_fortran(PyArrayObject* ary, int* is_new_object) { PyArrayObject* result; if (array_is_fortran(ary)) { result = ary; *is_new_object = 0; } else { Py_INCREF(array_descr(ary)); result = (PyArrayObject*) PyArray_FromArray(ary, array_descr(ary), NPY_FORTRANORDER); *is_new_object = 1; } return result; } /* Convert a given PyObject to a contiguous PyArrayObject of the * specified type. If the input object is not a contiguous * PyArrayObject, a new one will be created and the new object flag * will be set. */ PyArrayObject* obj_to_array_contiguous_allow_conversion(PyObject* input, int typecode, int* is_new_object) { int is_new1 = 0; int is_new2 = 0; PyArrayObject* ary2; PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode, &is_new1); if (ary1) { ary2 = make_contiguous(ary1, &is_new2, 0, 0); if ( is_new1 && is_new2) { Py_DECREF(ary1); } ary1 = ary2; } *is_new_object = is_new1 || is_new2; return ary1; } /* Convert a given PyObject to a Fortran-ordered PyArrayObject of the * specified type. If the input object is not a Fortran-ordered * PyArrayObject, a new one will be created and the new object flag * will be set. */ PyArrayObject* obj_to_array_fortran_allow_conversion(PyObject* input, int typecode, int* is_new_object) { int is_new1 = 0; int is_new2 = 0; PyArrayObject* ary2; PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode, &is_new1); if (ary1) { ary2 = make_fortran(ary1, &is_new2); if (is_new1 && is_new2) { Py_DECREF(ary1); } ary1 = ary2; } *is_new_object = is_new1 || is_new2; return ary1; } /* Test whether a python object is contiguous. If array is * contiguous, return 1. Otherwise, set the python error string and * return 0. */ int require_contiguous(PyArrayObject* ary) { int contiguous = 1; if (!array_is_contiguous(ary)) { PyErr_SetString(PyExc_TypeError, "Array must be contiguous. A non-contiguous array was given"); contiguous = 0; } return contiguous; } /* Require that a numpy array is not byte-swapped. If the array is * not byte-swapped, return 1. Otherwise, set the python error string * and return 0. */ int require_native(PyArrayObject* ary) { int native = 1; if (!array_is_native(ary)) { PyErr_SetString(PyExc_TypeError, "Array must have native byteorder. " "A byte-swapped array was given"); native = 0; } return native; } /* Require the given PyArrayObject to have a specified number of * dimensions. If the array has the specified number of dimensions, * return 1. Otherwise, set the python error string and return 0. */ int require_dimensions(PyArrayObject* ary, int exact_dimensions) { int success = 1; if (array_numdims(ary) != exact_dimensions) { PyErr_Format(PyExc_TypeError, "Array must have %d dimensions. Given array has %d dimensions", exact_dimensions, array_numdims(ary)); success = 0; } return success; } /* Require the given PyArrayObject to have one of a list of specified * number of dimensions. If the array has one of the specified number * of dimensions, return 1. Otherwise, set the python error string * and return 0. */ int require_dimensions_n(PyArrayObject* ary, int* exact_dimensions, int n) { int success = 0; int i; char dims_str[255] = ""; char s[255]; for (i = 0; i < n && !success; i++) { if (array_numdims(ary) == exact_dimensions[i]) { success = 1; } } if (!success) { for (i = 0; i < n-1; i++) { sprintf(s, "%d, ", exact_dimensions[i]); strcat(dims_str,s); } sprintf(s, " or %d", exact_dimensions[n-1]); strcat(dims_str,s); PyErr_Format(PyExc_TypeError, "Array must have %s dimensions. Given array has %d dimensions", dims_str, array_numdims(ary)); } return success; } /* Require the given PyArrayObject to have a specified shape. If the * array has the specified shape, return 1. Otherwise, set the python * error string and return 0. */ int require_size(PyArrayObject* ary, npy_intp* size, int n) { int i; int success = 1; int len; char desired_dims[255] = "["; char s[255]; char actual_dims[255] = "["; for(i=0; i < n;i++) { if (size[i] != -1 && size[i] != array_size(ary,i)) { success = 0; } } if (!success) { for (i = 0; i < n; i++) { if (size[i] == -1) { sprintf(s, "*,"); } else { sprintf(s, "%ld,", (long int)size[i]); } strcat(desired_dims,s); } len = strlen(desired_dims); desired_dims[len-1] = ']'; for (i = 0; i < n; i++) { sprintf(s, "%ld,", (long int)array_size(ary,i)); strcat(actual_dims,s); } len = strlen(actual_dims); actual_dims[len-1] = ']'; PyErr_Format(PyExc_TypeError, "Array must have shape of %s. Given array has shape of %s", desired_dims, actual_dims); } return success; } /* Require the given PyArrayObject to to be Fortran ordered. If the * the PyArrayObject is already Fortran ordered, do nothing. Else, * set the Fortran ordering flag and recompute the strides. */ int require_fortran(PyArrayObject* ary) { int success = 1; int nd = array_numdims(ary); int i; npy_intp * strides = array_strides(ary); if (array_is_fortran(ary)) return success; /* Set the Fortran ordered flag */ array_enableflags(ary,NPY_ARRAY_FARRAY); /* Recompute the strides */ strides[0] = strides[nd-1]; for (i=1; i < nd; ++i) strides[i] = strides[i-1] * array_size(ary,i-1); return success; } #include #if !defined(SWIG_NO_LLONG_MAX) # if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__) # define LLONG_MAX __LONG_LONG_MAX__ # define LLONG_MIN (-LLONG_MAX - 1LL) # define ULLONG_MAX (LLONG_MAX * 2ULL + 1ULL) # endif #endif SWIGINTERN int SWIG_AsVal_double (PyObject *obj, double *val) { int res = SWIG_TypeError; if (PyFloat_Check(obj)) { if (val) *val = PyFloat_AsDouble(obj); return SWIG_OK; } else if (PyInt_Check(obj)) { if (val) *val = PyInt_AsLong(obj); return SWIG_OK; } else if (PyLong_Check(obj)) { double v = PyLong_AsDouble(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_OK; } else { PyErr_Clear(); } } #ifdef SWIG_PYTHON_CAST_MODE { int dispatch = 0; double d = PyFloat_AsDouble(obj); if (!PyErr_Occurred()) { if (val) *val = d; return SWIG_AddCast(SWIG_OK); } else { PyErr_Clear(); } if (!dispatch) { long v = PyLong_AsLong(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_AddCast(SWIG_AddCast(SWIG_OK)); } else { PyErr_Clear(); } } } #endif return res; } #include #include SWIGINTERNINLINE int SWIG_CanCastAsInteger(double *d, double min, double max) { double x = *d; if ((min <= x && x <= max)) { double fx = floor(x); double cx = ceil(x); double rd = ((x - fx) < 0.5) ? fx : cx; /* simple rint */ if ((errno == EDOM) || (errno == ERANGE)) { errno = 0; } else { double summ, reps, diff; if (rd < x) { diff = x - rd; } else if (rd > x) { diff = rd - x; } else { return 1; } summ = rd + x; reps = diff/summ; if (reps < 8*DBL_EPSILON) { *d = rd; return 1; } } } return 0; } SWIGINTERN int SWIG_AsVal_unsigned_SS_long (PyObject *obj, unsigned long *val) { #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(obj)) { long v = PyInt_AsLong(obj); if (v >= 0) { if (val) *val = v; return SWIG_OK; } else { return SWIG_OverflowError; } } else #endif if (PyLong_Check(obj)) { unsigned long v = PyLong_AsUnsignedLong(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_OK; } else { PyErr_Clear(); #if PY_VERSION_HEX >= 0x03000000 { long v = PyLong_AsLong(obj); if (!PyErr_Occurred()) { if (v < 0) { return SWIG_OverflowError; } } else { PyErr_Clear(); } } #endif } } #ifdef SWIG_PYTHON_CAST_MODE { int dispatch = 0; unsigned long v = PyLong_AsUnsignedLong(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_AddCast(SWIG_OK); } else { PyErr_Clear(); } if (!dispatch) { double d; int res = SWIG_AddCast(SWIG_AsVal_double (obj,&d)); if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, 0, ULONG_MAX)) { if (val) *val = (unsigned long)(d); return res; } } } #endif return SWIG_TypeError; } SWIGINTERN int SWIG_AsVal_unsigned_SS_int (PyObject * obj, unsigned int *val) { unsigned long v; int res = SWIG_AsVal_unsigned_SS_long (obj, &v); if (SWIG_IsOK(res)) { if ((v > UINT_MAX)) { return SWIG_OverflowError; } else { if (val) *val = static_cast< unsigned int >(v); } } return res; } SWIGINTERN swig_type_info* SWIG_pchar_descriptor(void) { static int init = 0; static swig_type_info* info = 0; if (!init) { info = SWIG_TypeQuery("_p_char"); init = 1; } return info; } SWIGINTERN int SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc) { #if PY_VERSION_HEX>=0x03000000 if (PyUnicode_Check(obj)) #else if (PyString_Check(obj)) #endif { char *cstr; Py_ssize_t len; #if PY_VERSION_HEX>=0x03000000 if (!alloc && cptr) { /* We can't allow converting without allocation, since the internal representation of string in Python 3 is UCS-2/UCS-4 but we require a UTF-8 representation. TODO(bhy) More detailed explanation */ return SWIG_RuntimeError; } obj = PyUnicode_AsUTF8String(obj); PyBytes_AsStringAndSize(obj, &cstr, &len); if(alloc) *alloc = SWIG_NEWOBJ; #else PyString_AsStringAndSize(obj, &cstr, &len); #endif if (cptr) { if (alloc) { /* In python the user should not be able to modify the inner string representation. To warranty that, if you define SWIG_PYTHON_SAFE_CSTRINGS, a new/copy of the python string buffer is always returned. The default behavior is just to return the pointer value, so, be careful. */ #if defined(SWIG_PYTHON_SAFE_CSTRINGS) if (*alloc != SWIG_OLDOBJ) #else if (*alloc == SWIG_NEWOBJ) #endif { *cptr = reinterpret_cast< char* >(memcpy((new char[len + 1]), cstr, sizeof(char)*(len + 1))); *alloc = SWIG_NEWOBJ; } else { *cptr = cstr; *alloc = SWIG_OLDOBJ; } } else { #if PY_VERSION_HEX>=0x03000000 assert(0); /* Should never reach here in Python 3 */ #endif *cptr = SWIG_Python_str_AsChar(obj); } } if (psize) *psize = len + 1; #if PY_VERSION_HEX>=0x03000000 Py_XDECREF(obj); #endif return SWIG_OK; } else { swig_type_info* pchar_descriptor = SWIG_pchar_descriptor(); if (pchar_descriptor) { void* vptr = 0; if (SWIG_ConvertPtr(obj, &vptr, pchar_descriptor, 0) == SWIG_OK) { if (cptr) *cptr = (char *) vptr; if (psize) *psize = vptr ? (strlen((char *)vptr) + 1) : 0; if (alloc) *alloc = SWIG_OLDOBJ; return SWIG_OK; } } } return SWIG_TypeError; } SWIGINTERN int SWIG_AsPtr_std_string (PyObject * obj, std::string **val) { char* buf = 0 ; size_t size = 0; int alloc = SWIG_OLDOBJ; if (SWIG_IsOK((SWIG_AsCharPtrAndSize(obj, &buf, &size, &alloc)))) { if (buf) { if (val) *val = new std::string(buf, size - 1); if (alloc == SWIG_NEWOBJ) delete[] buf; return SWIG_NEWOBJ; } else { if (val) *val = 0; return SWIG_OLDOBJ; } } else { static int init = 0; static swig_type_info* descriptor = 0; if (!init) { descriptor = SWIG_TypeQuery("std::string" " *"); init = 1; } if (descriptor) { std::string *vptr; int res = SWIG_ConvertPtr(obj, (void**)&vptr, descriptor, 0); if (SWIG_IsOK(res) && val) *val = vptr; return res; } } return SWIG_ERROR; } /* Getting isfinite working pre C99 across multiple platforms is non-trivial. Users can provide SWIG_isfinite on older platforms. */ #ifndef SWIG_isfinite # if defined(isfinite) # define SWIG_isfinite(X) (isfinite(X)) # elif defined(_MSC_VER) # define SWIG_isfinite(X) (_finite(X)) # elif defined(__sun) && defined(__SVR4) # include # define SWIG_isfinite(X) (finite(X)) # endif #endif /* Accept infinite as a valid float value unless we are unable to check if a value is finite */ #ifdef SWIG_isfinite # define SWIG_Float_Overflow_Check(X) ((X < -FLT_MAX || X > FLT_MAX) && SWIG_isfinite(X)) #else # define SWIG_Float_Overflow_Check(X) ((X < -FLT_MAX || X > FLT_MAX)) #endif SWIGINTERN int SWIG_AsVal_float (PyObject * obj, float *val) { double v; int res = SWIG_AsVal_double (obj, &v); if (SWIG_IsOK(res)) { if (SWIG_Float_Overflow_Check(v)) { return SWIG_OverflowError; } else { if (val) *val = static_cast< float >(v); } } return res; } #ifdef __cplusplus extern "C" { #endif SWIGINTERN PyObject *_wrap_trainWrapper(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0; float *arg1 = (float *) 0 ; int arg2 ; unsigned int arg3 ; unsigned int arg4 ; unsigned int arg5 ; unsigned int arg6 ; unsigned int arg7 ; unsigned int arg8 ; unsigned int arg9 ; std::string arg10 ; float arg11 ; float arg12 ; std::string arg13 ; unsigned int arg14 ; unsigned int arg15 ; std::string arg16 ; std::string arg17 ; float *arg18 = (float *) 0 ; int arg19 ; int *arg20 = (int *) 0 ; int arg21 ; float *arg22 = (float *) 0 ; int arg23 ; PyArrayObject *array1 = NULL ; int i1 = 1 ; unsigned int val3 ; int ecode3 = 0 ; unsigned int val4 ; int ecode4 = 0 ; unsigned int val5 ; int ecode5 = 0 ; unsigned int val6 ; int ecode6 = 0 ; unsigned int val7 ; int ecode7 = 0 ; unsigned int val8 ; int ecode8 = 0 ; unsigned int val9 ; int ecode9 = 0 ; float val11 ; int ecode11 = 0 ; float val12 ; int ecode12 = 0 ; unsigned int val14 ; int ecode14 = 0 ; unsigned int val15 ; int ecode15 = 0 ; PyArrayObject *array18 = NULL ; int i18 = 1 ; PyArrayObject *array20 = NULL ; int i20 = 1 ; PyArrayObject *array22 = NULL ; int i22 = 1 ; PyObject * obj0 = 0 ; PyObject * obj1 = 0 ; PyObject * obj2 = 0 ; PyObject * obj3 = 0 ; PyObject * obj4 = 0 ; PyObject * obj5 = 0 ; PyObject * obj6 = 0 ; PyObject * obj7 = 0 ; PyObject * obj8 = 0 ; PyObject * obj9 = 0 ; PyObject * obj10 = 0 ; PyObject * obj11 = 0 ; PyObject * obj12 = 0 ; PyObject * obj13 = 0 ; PyObject * obj14 = 0 ; PyObject * obj15 = 0 ; PyObject * obj16 = 0 ; PyObject * obj17 = 0 ; PyObject * obj18 = 0 ; if (!PyArg_ParseTuple(args,(char *)"OOOOOOOOOOOOOOOOOOO:trainWrapper",&obj0,&obj1,&obj2,&obj3,&obj4,&obj5,&obj6,&obj7,&obj8,&obj9,&obj10,&obj11,&obj12,&obj13,&obj14,&obj15,&obj16,&obj17,&obj18)) SWIG_fail; { array1 = obj_to_array_no_conversion(obj0, NPY_FLOAT); if (!array1 || !require_dimensions(array1,1) || !require_contiguous(array1) || !require_native(array1)) SWIG_fail; arg1 = (float*) array_data(array1); arg2 = 1; for (i1=0; i1 < array_numdims(array1); ++i1) arg2 *= array_size(array1,i1); } ecode3 = SWIG_AsVal_unsigned_SS_int(obj1, &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "trainWrapper" "', argument " "3"" of type '" "unsigned int""'"); } arg3 = static_cast< unsigned int >(val3); ecode4 = SWIG_AsVal_unsigned_SS_int(obj2, &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "trainWrapper" "', argument " "4"" of type '" "unsigned int""'"); } arg4 = static_cast< unsigned int >(val4); ecode5 = SWIG_AsVal_unsigned_SS_int(obj3, &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "trainWrapper" "', argument " "5"" of type '" "unsigned int""'"); } arg5 = static_cast< unsigned int >(val5); ecode6 = SWIG_AsVal_unsigned_SS_int(obj4, &val6); if (!SWIG_IsOK(ecode6)) { SWIG_exception_fail(SWIG_ArgError(ecode6), "in method '" "trainWrapper" "', argument " "6"" of type '" "unsigned int""'"); } arg6 = static_cast< unsigned int >(val6); ecode7 = SWIG_AsVal_unsigned_SS_int(obj5, &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "trainWrapper" "', argument " "7"" of type '" "unsigned int""'"); } arg7 = static_cast< unsigned int >(val7); ecode8 = SWIG_AsVal_unsigned_SS_int(obj6, &val8); if (!SWIG_IsOK(ecode8)) { SWIG_exception_fail(SWIG_ArgError(ecode8), "in method '" "trainWrapper" "', argument " "8"" of type '" "unsigned int""'"); } arg8 = static_cast< unsigned int >(val8); ecode9 = SWIG_AsVal_unsigned_SS_int(obj7, &val9); if (!SWIG_IsOK(ecode9)) { SWIG_exception_fail(SWIG_ArgError(ecode9), "in method '" "trainWrapper" "', argument " "9"" of type '" "unsigned int""'"); } arg9 = static_cast< unsigned int >(val9); { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj8, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "10"" of type '" "std::string""'"); } arg10 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } ecode11 = SWIG_AsVal_float(obj9, &val11); if (!SWIG_IsOK(ecode11)) { SWIG_exception_fail(SWIG_ArgError(ecode11), "in method '" "trainWrapper" "', argument " "11"" of type '" "float""'"); } arg11 = static_cast< float >(val11); ecode12 = SWIG_AsVal_float(obj10, &val12); if (!SWIG_IsOK(ecode12)) { SWIG_exception_fail(SWIG_ArgError(ecode12), "in method '" "trainWrapper" "', argument " "12"" of type '" "float""'"); } arg12 = static_cast< float >(val12); { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj11, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "13"" of type '" "std::string""'"); } arg13 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } ecode14 = SWIG_AsVal_unsigned_SS_int(obj12, &val14); if (!SWIG_IsOK(ecode14)) { SWIG_exception_fail(SWIG_ArgError(ecode14), "in method '" "trainWrapper" "', argument " "14"" of type '" "unsigned int""'"); } arg14 = static_cast< unsigned int >(val14); ecode15 = SWIG_AsVal_unsigned_SS_int(obj13, &val15); if (!SWIG_IsOK(ecode15)) { SWIG_exception_fail(SWIG_ArgError(ecode15), "in method '" "trainWrapper" "', argument " "15"" of type '" "unsigned int""'"); } arg15 = static_cast< unsigned int >(val15); { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj14, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "16"" of type '" "std::string""'"); } arg16 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj15, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "17"" of type '" "std::string""'"); } arg17 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } { array18 = obj_to_array_no_conversion(obj16, NPY_FLOAT); if (!array18 || !require_dimensions(array18,1) || !require_contiguous(array18) || !require_native(array18)) SWIG_fail; arg18 = (float*) array_data(array18); arg19 = 1; for (i18=0; i18 < array_numdims(array18); ++i18) arg19 *= array_size(array18,i18); } { array20 = obj_to_array_no_conversion(obj17, NPY_INT); if (!array20 || !require_dimensions(array20,1) || !require_contiguous(array20) || !require_native(array20)) SWIG_fail; arg20 = (int*) array_data(array20); arg21 = 1; for (i20=0; i20 < array_numdims(array20); ++i20) arg21 *= array_size(array20,i20); } { array22 = obj_to_array_no_conversion(obj18, NPY_FLOAT); if (!array22 || !require_dimensions(array22,1) || !require_contiguous(array22) || !require_native(array22)) SWIG_fail; arg22 = (float*) array_data(array22); arg23 = 1; for (i22=0; i22 < array_numdims(array22); ++i22) arg23 *= array_size(array22,i22); } trainWrapper(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23); resultobj = SWIG_Py_Void(); return resultobj; fail: return NULL; } static PyMethodDef SwigMethods[] = { { (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL}, { (char *)"trainWrapper", _wrap_trainWrapper, METH_VARARGS, NULL}, { NULL, NULL, 0, NULL } }; /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0}; static swig_type_info *swig_type_initial[] = { &_swigt__p_char, }; static swig_cast_info _swigc__p_char[] = { {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info *swig_cast_initial[] = { _swigc__p_char, }; /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */ static swig_const_info swig_const_table[] = { {0, 0, 0, 0.0, 0, 0}}; #ifdef __cplusplus } #endif /* ----------------------------------------------------------------------------- * Type initialization: * This problem is tough by the requirement that no dynamic * memory is used. Also, since swig_type_info structures store pointers to * swig_cast_info structures and swig_cast_info structures store pointers back * to swig_type_info structures, we need some lookup code at initialization. * The idea is that swig generates all the structures that are needed. * The runtime then collects these partially filled structures. * The SWIG_InitializeModule function takes these initial arrays out of * swig_module, and does all the lookup, filling in the swig_module.types * array with the correct data and linking the correct swig_cast_info * structures together. * * The generated swig_type_info structures are assigned staticly to an initial * array. We just loop through that array, and handle each type individually. * First we lookup if this type has been already loaded, and if so, use the * loaded structure instead of the generated one. Then we have to fill in the * cast linked list. The cast data is initially stored in something like a * two-dimensional array. Each row corresponds to a type (there are the same * number of rows as there are in the swig_type_initial array). Each entry in * a column is one of the swig_cast_info structures for that type. * The cast_initial array is actually an array of arrays, because each row has * a variable number of columns. So to actually build the cast linked list, * we find the array of casts associated with the type, and loop through it * adding the casts to the list. The one last trick we need to do is making * sure the type pointer in the swig_cast_info struct is correct. * * First off, we lookup the cast->type name to see if it is already loaded. * There are three cases to handle: * 1) If the cast->type has already been loaded AND the type we are adding * casting info to has not been loaded (it is in this module), THEN we * replace the cast->type pointer with the type pointer that has already * been loaded. * 2) If BOTH types (the one we are adding casting info to, and the * cast->type) are loaded, THEN the cast info has already been loaded by * the previous module so we just ignore it. * 3) Finally, if cast->type has not already been loaded, then we add that * swig_cast_info to the linked list (because the cast->type) pointer will * be correct. * ----------------------------------------------------------------------------- */ #ifdef __cplusplus extern "C" { #if 0 } /* c-mode */ #endif #endif #if 0 #define SWIGRUNTIME_DEBUG #endif SWIGRUNTIME void SWIG_InitializeModule(void *clientdata) { size_t i; swig_module_info *module_head, *iter; int found, init; /* check to see if the circular list has been setup, if not, set it up */ if (swig_module.next==0) { /* Initialize the swig_module */ swig_module.type_initial = swig_type_initial; swig_module.cast_initial = swig_cast_initial; swig_module.next = &swig_module; init = 1; } else { init = 0; } /* Try and load any already created modules */ module_head = SWIG_GetModule(clientdata); if (!module_head) { /* This is the first module loaded for this interpreter */ /* so set the swig module into the interpreter */ SWIG_SetModule(clientdata, &swig_module); module_head = &swig_module; } else { /* the interpreter has loaded a SWIG module, but has it loaded this one? */ found=0; iter=module_head; do { if (iter==&swig_module) { found=1; break; } iter=iter->next; } while (iter!= module_head); /* if the is found in the list, then all is done and we may leave */ if (found) return; /* otherwise we must add out module into the list */ swig_module.next = module_head->next; module_head->next = &swig_module; } /* When multiple interpreters are used, a module could have already been initialized in a different interpreter, but not yet have a pointer in this interpreter. In this case, we do not want to continue adding types... everything should be set up already */ if (init == 0) return; /* Now work on filling in swig_module.types */ #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: size %d\n", swig_module.size); #endif for (i = 0; i < swig_module.size; ++i) { swig_type_info *type = 0; swig_type_info *ret; swig_cast_info *cast; #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name); #endif /* if there is another module already loaded */ if (swig_module.next != &swig_module) { type = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, swig_module.type_initial[i]->name); } if (type) { /* Overwrite clientdata field */ #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: found type %s\n", type->name); #endif if (swig_module.type_initial[i]->clientdata) { type->clientdata = swig_module.type_initial[i]->clientdata; #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: found and overwrite type %s \n", type->name); #endif } } else { type = swig_module.type_initial[i]; } /* Insert casting types */ cast = swig_module.cast_initial[i]; while (cast->type) { /* Don't need to add information already in the list */ ret = 0; #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: look cast %s\n", cast->type->name); #endif if (swig_module.next != &swig_module) { ret = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, cast->type->name); #ifdef SWIGRUNTIME_DEBUG if (ret) printf("SWIG_InitializeModule: found cast %s\n", ret->name); #endif } if (ret) { if (type == swig_module.type_initial[i]) { #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: skip old type %s\n", ret->name); #endif cast->type = ret; ret = 0; } else { /* Check for casting already in the list */ swig_cast_info *ocast = SWIG_TypeCheck(ret->name, type); #ifdef SWIGRUNTIME_DEBUG if (ocast) printf("SWIG_InitializeModule: skip old cast %s\n", ret->name); #endif if (!ocast) ret = 0; } } if (!ret) { #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: adding cast %s\n", cast->type->name); #endif if (type->cast) { type->cast->prev = cast; cast->next = type->cast; } type->cast = cast; } cast++; } /* Set entry in modules->types array equal to the type */ swig_module.types[i] = type; } swig_module.types[i] = 0; #ifdef SWIGRUNTIME_DEBUG printf("**** SWIG_InitializeModule: Cast List ******\n"); for (i = 0; i < swig_module.size; ++i) { int j = 0; swig_cast_info *cast = swig_module.cast_initial[i]; printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name); while (cast->type) { printf("SWIG_InitializeModule: cast type %s\n", cast->type->name); cast++; ++j; } printf("---- Total casts: %d\n",j); } printf("**** SWIG_InitializeModule: Cast List ******\n"); #endif } /* This function will propagate the clientdata field of type to * any new swig_type_info structures that have been added into the list * of equivalent types. It is like calling * SWIG_TypeClientData(type, clientdata) a second time. */ SWIGRUNTIME void SWIG_PropagateClientData(void) { size_t i; swig_cast_info *equiv; static int init_run = 0; if (init_run) return; init_run = 1; for (i = 0; i < swig_module.size; i++) { if (swig_module.types[i]->clientdata) { equiv = swig_module.types[i]->cast; while (equiv) { if (!equiv->converter) { if (equiv->type && !equiv->type->clientdata) SWIG_TypeClientData(equiv->type, swig_module.types[i]->clientdata); } equiv = equiv->next; } } } } #ifdef __cplusplus #if 0 { /* c-mode */ #endif } #endif #ifdef __cplusplus extern "C" { #endif /* Python-specific SWIG API */ #define SWIG_newvarlink() SWIG_Python_newvarlink() #define SWIG_addvarlink(p, name, get_attr, set_attr) SWIG_Python_addvarlink(p, name, get_attr, set_attr) #define SWIG_InstallConstants(d, constants) SWIG_Python_InstallConstants(d, constants) /* ----------------------------------------------------------------------------- * global variable support code. * ----------------------------------------------------------------------------- */ typedef struct swig_globalvar { char *name; /* Name of global variable */ PyObject *(*get_attr)(void); /* Return the current value */ int (*set_attr)(PyObject *); /* Set the value */ struct swig_globalvar *next; } swig_globalvar; typedef struct swig_varlinkobject { PyObject_HEAD swig_globalvar *vars; } swig_varlinkobject; SWIGINTERN PyObject * swig_varlink_repr(swig_varlinkobject *SWIGUNUSEDPARM(v)) { #if PY_VERSION_HEX >= 0x03000000 return PyUnicode_InternFromString(""); #else return PyString_FromString(""); #endif } SWIGINTERN PyObject * swig_varlink_str(swig_varlinkobject *v) { #if PY_VERSION_HEX >= 0x03000000 PyObject *str = PyUnicode_InternFromString("("); PyObject *tail; PyObject *joined; swig_globalvar *var; for (var = v->vars; var; var=var->next) { tail = PyUnicode_FromString(var->name); joined = PyUnicode_Concat(str, tail); Py_DecRef(str); Py_DecRef(tail); str = joined; if (var->next) { tail = PyUnicode_InternFromString(", "); joined = PyUnicode_Concat(str, tail); Py_DecRef(str); Py_DecRef(tail); str = joined; } } tail = PyUnicode_InternFromString(")"); joined = PyUnicode_Concat(str, tail); Py_DecRef(str); Py_DecRef(tail); str = joined; #else PyObject *str = PyString_FromString("("); swig_globalvar *var; for (var = v->vars; var; var=var->next) { PyString_ConcatAndDel(&str,PyString_FromString(var->name)); if (var->next) PyString_ConcatAndDel(&str,PyString_FromString(", ")); } PyString_ConcatAndDel(&str,PyString_FromString(")")); #endif return str; } SWIGINTERN int swig_varlink_print(swig_varlinkobject *v, FILE *fp, int SWIGUNUSEDPARM(flags)) { char *tmp; PyObject *str = swig_varlink_str(v); fprintf(fp,"Swig global variables "); fprintf(fp,"%s\n", tmp = SWIG_Python_str_AsChar(str)); SWIG_Python_str_DelForPy3(tmp); Py_DECREF(str); return 0; } SWIGINTERN void swig_varlink_dealloc(swig_varlinkobject *v) { swig_globalvar *var = v->vars; while (var) { swig_globalvar *n = var->next; free(var->name); free(var); var = n; } } SWIGINTERN PyObject * swig_varlink_getattr(swig_varlinkobject *v, char *n) { PyObject *res = NULL; swig_globalvar *var = v->vars; while (var) { if (strcmp(var->name,n) == 0) { res = (*var->get_attr)(); break; } var = var->next; } if (res == NULL && !PyErr_Occurred()) { PyErr_SetString(PyExc_NameError,"Unknown C global variable"); } return res; } SWIGINTERN int swig_varlink_setattr(swig_varlinkobject *v, char *n, PyObject *p) { int res = 1; swig_globalvar *var = v->vars; while (var) { if (strcmp(var->name,n) == 0) { res = (*var->set_attr)(p); break; } var = var->next; } if (res == 1 && !PyErr_Occurred()) { PyErr_SetString(PyExc_NameError,"Unknown C global variable"); } return res; } SWIGINTERN PyTypeObject* swig_varlink_type(void) { static char varlink__doc__[] = "Swig var link object"; static PyTypeObject varlink_type; static int type_init = 0; if (!type_init) { const PyTypeObject tmp = { /* PyObject header changed in Python 3 */ #if PY_VERSION_HEX >= 0x03000000 PyVarObject_HEAD_INIT(NULL, 0) #else PyObject_HEAD_INIT(NULL) 0, /* ob_size */ #endif (char *)"swigvarlink", /* tp_name */ sizeof(swig_varlinkobject), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor) swig_varlink_dealloc, /* tp_dealloc */ (printfunc) swig_varlink_print, /* tp_print */ (getattrfunc) swig_varlink_getattr, /* tp_getattr */ (setattrfunc) swig_varlink_setattr, /* tp_setattr */ 0, /* tp_compare */ (reprfunc) swig_varlink_repr, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ (reprfunc) swig_varlink_str, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ 0, /* tp_flags */ varlink__doc__, /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ #if PY_VERSION_HEX >= 0x02020000 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, /* tp_iter -> tp_weaklist */ #endif #if PY_VERSION_HEX >= 0x02030000 0, /* tp_del */ #endif #if PY_VERSION_HEX >= 0x02060000 0, /* tp_version */ #endif #ifdef COUNT_ALLOCS 0,0,0,0 /* tp_alloc -> tp_next */ #endif }; varlink_type = tmp; type_init = 1; #if PY_VERSION_HEX < 0x02020000 varlink_type.ob_type = &PyType_Type; #else if (PyType_Ready(&varlink_type) < 0) return NULL; #endif } return &varlink_type; } /* Create a variable linking object for use later */ SWIGINTERN PyObject * SWIG_Python_newvarlink(void) { swig_varlinkobject *result = PyObject_NEW(swig_varlinkobject, swig_varlink_type()); if (result) { result->vars = 0; } return ((PyObject*) result); } SWIGINTERN void SWIG_Python_addvarlink(PyObject *p, char *name, PyObject *(*get_attr)(void), int (*set_attr)(PyObject *p)) { swig_varlinkobject *v = (swig_varlinkobject *) p; swig_globalvar *gv = (swig_globalvar *) malloc(sizeof(swig_globalvar)); if (gv) { size_t size = strlen(name)+1; gv->name = (char *)malloc(size); if (gv->name) { strncpy(gv->name,name,size); gv->get_attr = get_attr; gv->set_attr = set_attr; gv->next = v->vars; } } v->vars = gv; } SWIGINTERN PyObject * SWIG_globals(void) { static PyObject *_SWIG_globals = 0; if (!_SWIG_globals) _SWIG_globals = SWIG_newvarlink(); return _SWIG_globals; } /* ----------------------------------------------------------------------------- * constants/methods manipulation * ----------------------------------------------------------------------------- */ /* Install Constants */ SWIGINTERN void SWIG_Python_InstallConstants(PyObject *d, swig_const_info constants[]) { PyObject *obj = 0; size_t i; for (i = 0; constants[i].type; ++i) { switch(constants[i].type) { case SWIG_PY_POINTER: obj = SWIG_InternalNewPointerObj(constants[i].pvalue, *(constants[i]).ptype,0); break; case SWIG_PY_BINARY: obj = SWIG_NewPackedObj(constants[i].pvalue, constants[i].lvalue, *(constants[i].ptype)); break; default: obj = 0; break; } if (obj) { PyDict_SetItemString(d, constants[i].name, obj); Py_DECREF(obj); } } } /* -----------------------------------------------------------------------------*/ /* Fix SwigMethods to carry the callback ptrs when needed */ /* -----------------------------------------------------------------------------*/ SWIGINTERN void SWIG_Python_FixMethods(PyMethodDef *methods, swig_const_info *const_table, swig_type_info **types, swig_type_info **types_initial) { size_t i; for (i = 0; methods[i].ml_name; ++i) { const char *c = methods[i].ml_doc; if (c && (c = strstr(c, "swig_ptr: "))) { int j; swig_const_info *ci = 0; const char *name = c + 10; for (j = 0; const_table[j].type; ++j) { if (strncmp(const_table[j].name, name, strlen(const_table[j].name)) == 0) { ci = &(const_table[j]); break; } } if (ci) { void *ptr = (ci->type == SWIG_PY_POINTER) ? ci->pvalue : 0; if (ptr) { size_t shift = (ci->ptype) - types; swig_type_info *ty = types_initial[shift]; size_t ldoc = (c - methods[i].ml_doc); size_t lptr = strlen(ty->name)+2*sizeof(void*)+2; char *ndoc = (char*)malloc(ldoc + lptr + 10); if (ndoc) { char *buff = ndoc; strncpy(buff, methods[i].ml_doc, ldoc); buff += ldoc; strncpy(buff, "swig_ptr: ", 10); buff += 10; SWIG_PackVoidPtr(buff, ptr, ty->name, lptr); methods[i].ml_doc = ndoc; } } } } } } #ifdef __cplusplus } #endif /* -----------------------------------------------------------------------------* * Partial Init method * -----------------------------------------------------------------------------*/ #ifdef __cplusplus extern "C" #endif SWIGEXPORT #if PY_VERSION_HEX >= 0x03000000 PyObject* #else void #endif SWIG_init(void) { PyObject *m, *d, *md; #if PY_VERSION_HEX >= 0x03000000 static struct PyModuleDef SWIG_module = { # if PY_VERSION_HEX >= 0x03020000 PyModuleDef_HEAD_INIT, # else { PyObject_HEAD_INIT(NULL) NULL, /* m_init */ 0, /* m_index */ NULL, /* m_copy */ }, # endif (char *) SWIG_name, NULL, -1, SwigMethods, NULL, NULL, NULL, NULL }; #endif #if defined(SWIGPYTHON_BUILTIN) static SwigPyClientData SwigPyObject_clientdata = { 0, 0, 0, 0, 0, 0, 0 }; static PyGetSetDef this_getset_def = { (char *)"this", &SwigPyBuiltin_ThisClosure, NULL, NULL, NULL }; static SwigPyGetSet thisown_getset_closure = { (PyCFunction) SwigPyObject_own, (PyCFunction) SwigPyObject_own }; static PyGetSetDef thisown_getset_def = { (char *)"thisown", SwigPyBuiltin_GetterClosure, SwigPyBuiltin_SetterClosure, NULL, &thisown_getset_closure }; PyObject *metatype_args; PyTypeObject *builtin_pytype; int builtin_base_count; swig_type_info *builtin_basetype; PyObject *tuple; PyGetSetDescrObject *static_getset; PyTypeObject *metatype; SwigPyClientData *cd; PyObject *public_interface, *public_symbol; PyObject *this_descr; PyObject *thisown_descr; int i; (void)builtin_pytype; (void)builtin_base_count; (void)builtin_basetype; (void)tuple; (void)static_getset; /* metatype is used to implement static member variables. */ metatype_args = Py_BuildValue("(s(O){})", "SwigPyObjectType", &PyType_Type); assert(metatype_args); metatype = (PyTypeObject *) PyType_Type.tp_call((PyObject *) &PyType_Type, metatype_args, NULL); assert(metatype); Py_DECREF(metatype_args); metatype->tp_setattro = (setattrofunc) &SwigPyObjectType_setattro; assert(PyType_Ready(metatype) >= 0); #endif /* Fix SwigMethods to carry the callback ptrs when needed */ SWIG_Python_FixMethods(SwigMethods, swig_const_table, swig_types, swig_type_initial); #if PY_VERSION_HEX >= 0x03000000 m = PyModule_Create(&SWIG_module); #else m = Py_InitModule((char *) SWIG_name, SwigMethods); #endif md = d = PyModule_GetDict(m); (void)md; SWIG_InitializeModule(0); #ifdef SWIGPYTHON_BUILTIN SwigPyObject_stype = SWIG_MangledTypeQuery("_p_SwigPyObject"); assert(SwigPyObject_stype); cd = (SwigPyClientData*) SwigPyObject_stype->clientdata; if (!cd) { SwigPyObject_stype->clientdata = &SwigPyObject_clientdata; SwigPyObject_clientdata.pytype = SwigPyObject_TypeOnce(); } else if (SwigPyObject_TypeOnce()->tp_basicsize != cd->pytype->tp_basicsize) { PyErr_SetString(PyExc_RuntimeError, "Import error: attempted to load two incompatible swig-generated modules."); # if PY_VERSION_HEX >= 0x03000000 return NULL; # else return; # endif } /* All objects have a 'this' attribute */ this_descr = PyDescr_NewGetSet(SwigPyObject_type(), &this_getset_def); (void)this_descr; /* All objects have a 'thisown' attribute */ thisown_descr = PyDescr_NewGetSet(SwigPyObject_type(), &thisown_getset_def); (void)thisown_descr; public_interface = PyList_New(0); public_symbol = 0; (void)public_symbol; PyDict_SetItemString(md, "__all__", public_interface); Py_DECREF(public_interface); for (i = 0; SwigMethods[i].ml_name != NULL; ++i) SwigPyBuiltin_AddPublicSymbol(public_interface, SwigMethods[i].ml_name); for (i = 0; swig_const_table[i].name != 0; ++i) SwigPyBuiltin_AddPublicSymbol(public_interface, swig_const_table[i].name); #endif SWIG_InstallConstants(d,swig_const_table); import_array(); #if PY_VERSION_HEX >= 0x03000000 return m; #else return; #endif } somoclu-1.4.1/src/Python/README.rst0000644000175000001440000001170312462121457016171 0ustar wittekusersSomoclu - Python Interface ================================ Somoclu is a massively parallel implementation of self-organizing maps. It relies on OpenMP for multicore execution, MPI for distributing the workload, and it can be accelerated by CUDA on a GPU cluster. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes. The topology of the grid is rectangular. Currently a subset of the command line version is supported with this package. Key features of the Python interface: * Fast execution by parallelization: OpenMP and CUDA are supported. * Multi-platform: Linux, OS X, and Windows are supported. * Planar and toroid maps. * Both dense and sparse input data are supported. * Large maps of several hundred thousand neurons are feasible. Usage ------ The following file uses rgbs.txt, which can be found at https://github.com/peterwittek/somoclu/tree/master/data .. code-block:: python #!/usr/bin/env python2 # -*- coding: utf-8 -*- import somoclu import numpy as np data = np.loadtxt('rgbs.txt') print(data) data = np.float32(data) nSomX = 50 nSomY = 50 nVectors = data.shape[0] nDimensions = data.shape[1] data1D = np.ndarray.flatten(data) nEpoch = 10 radius0 = 0 radiusN = 0 radiusCooling = "linear" scale0 = 0 scaleN = 0.01 scaleCooling = "linear" kernelType = 0 mapType = "planar" snapshots = 0 initialCodebookFilename = '' codebook_size = nSomY * nSomX * nDimensions codebook = np.zeros(codebook_size, dtype=np.float32) globalBmus_size = int(nVectors * int(np.ceil(nVectors/nVectors))*2) globalBmus = np.zeros(globalBmus_size, dtype=np.intc) uMatrix_size = nSomX * nSomY uMatrix = np.zeros(uMatrix_size, dtype=np.float32) somoclu.trainWrapper(data1D, nEpoch, nSomX, nSomY, nDimensions, nVectors, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType, initialCodebookFilename, codebook, globalBmus, uMatrix) print codebook print globalBmus print uMatrix Installation ------------ The code is available on PyPI, hence it can be installed by :: $ sudo pip install somoclu If you want the latest git version, follow the standard procedure for installing Python modules: :: $ sudo python setup.py install Build on Mac OS X -------------------- Before installing using pip, gcc should be installed first. As of OS X 10.9, gcc is just symlink to clang. To build somoclu and this extension correctly, it is recommended to install gcc using something like: :: $ brew install gcc48 and set environment using: :: export CC=/usr/local/bin/gcc export CXX=/usr/local/bin/g++ export CPP=/usr/local/bin/cpp export LD=/usr/local/bin/gcc alias c++=/usr/local/bin/c++ alias g++=/usr/local/bin/g++ alias gcc=/usr/local/bin/gcc alias cpp=/usr/local/bin/cpp alias ld=/usr/local/bin/gcc alias cc=/usr/local/bin/gcc Then you can issue :: $ sudo pip install somoclu Build with CUDA support on Linux and OS X: ------------------------------------------ You need to clone the GitHub repo or download the latest release tarball, and use the following script: :: $ cd src/Python $ bash makepy.sh Then if your CUDA installation is located at /opt/cuda and 64bit, you can do the following to install: :: $ sudo python2 setup_with_CUDA.py install Otherwise, you should modify the setup_with_CUDA.py , change the path to CUDA installation accordingly: :: call(["./configure", "--without-mpi","--with-cuda=/opt/cuda/"]) and :: library_dirs=['/opt/cuda/lib64'] Then run the install command :: $ sudo python2 setup_with_CUDA.py install Then you can use the python interface like before, with CUDA support. Build with CUDA support on Windows: -------------------------------------- You should first follow the instructions to build the windows binary at https://github.com/peterwittek/somoclu with MPI disabled with the same version Visual Studio as your Python is built.(Since currently Python is built by VS2008 by default and CUDA v6.5 removed VS2008 support, you may use CUDA 6.0 with VS2008 or find a Python prebuilt with VS2010. And remember to install VS2010 or Windows SDK7.1 to get the option in Platform Toolset if you use VS2013.) Then you should copy the .obj files generated in the release build path to the Python/src/src folder. Then modify the library_dirs in setup_with_CUDA_Win.py to your CUDA path. Then run the install command :: $ sudo python2 setup_with_CUDA_Win.py install Then it should be able to build and install the extension. somoclu-1.4.1/src/Python/setup_with_CUDA_Win.py0000644000175000001440000000374012462116543020662 0ustar wittekusers#!/usr/bin/env python2 """ setup.py file for CUDA use sudo python2 setup_with_CUDA.py install to install """ from setuptools import setup, Extension from setuptools.command.install import install from subprocess import call import numpy import os try: numpy_include = numpy.get_include() except AttributeError: numpy_include = numpy.get_numpy_include() somoclu_module = Extension('_somoclu', sources=['somoclu_wrap.cxx', 'src/src/somocluWrap.cpp'], # extra_objects=['src/src/somoclu.obj', extra_objects=[ 'src/src/denseCpuKernels.obj', 'src/src/io.obj', 'src/src/sparseCpuKernels.obj', 'src/src/training.obj', 'src/src/mapDistanceFunctions.obj', 'src/src/trainOneEpoch.obj', 'src/src/uMatrix.obj', 'src/src/denseGpuKernels.cu.obj'], define_macros=[('CUDA', None)], #PATH to CUDA library here, 64 for 64 bit library_dirs=["C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib/x64"], libraries=['cudart','cublas'], include_dirs=[numpy_include] ) setup(name='somoclu', version='1.4.1', license='GPL3', author="peterwittek", author_email="", maintainer="shichaogao", maintainer_email="xgdgsc@gmail.com", url="http://peterwittek.github.io/somoclu/", platforms="unix", description="a cluster-oriented implementation of self-organizing maps", ext_modules=[somoclu_module], py_modules=["somoclu"], install_requires=['numpy'] ) somoclu-1.4.1/src/Python/MANIFEST.in0000644000175000001440000000035112433136714016235 0ustar wittekusersinclude src/autogen.sh include src/configure.ac include src/Makefile.in include src/m4/* include src/src/*.h include src/src/*.cpp include src/src/*.cu include src/src/Makefile.in include tests/rgbs.txt include tests/somoclu_test.py somoclu-1.4.1/src/Python/tests/0000755000175000001440000000000012433136714015642 5ustar wittekuserssomoclu-1.4.1/src/Python/tests/rgbs.txt0000644000175000001440000000067012433136714017343 0ustar wittekusers0.01 1.00 0.0 0.0 0.97 0.01 0.0 0.99 0.02 0.01 0.94 0.03 0.0 0.91 0.01 0.01 1.00 0.0 0.0 0.98 0.02 1.00 0.01 0.0 0.97 0.01 0.0 0.97 0.02 0.0 0.99 0.02 0.0 0.94 0.03 0.01 0.91 0.0 0.01 1.00 0.01 0.01 0.98 0.02 0.01 0.97 0.01 0.02 0.92 0.03 0.01 0.01 0.0 1.00 0.01 0.0 0.97 0.02 0.0 0.97 0.02 0.0 0.99 0.03 0.01 0.94 0.0 0.01 0.91 0.01 0.01 1.00 0.02 0.01 0.98 0.01 0.02 0.97 0.03 0.01 0.92 0.01 0.02 0.97 somoclu-1.4.1/src/Python/tests/somoclu_test.py0000755000175000001440000000310612433136714020737 0ustar wittekusers#!/usr/bin/env python2 # -*- coding: utf-8 -*- import somoclu import numpy as np #import argparse if __name__ == "__main__": #parser = argparse.ArgumentParser("Somoclu python example") #parser.add_argument('-i', '--input_file', help='Input data file path', # required=True) #args = parser.parse_args() #data = np.loadtxt(args.input_file) data = np.loadtxt('rgbs.txt') #print(data) data = np.float32(data) nSomX = 50 nSomY = 50 nVectors = data.shape[0] nDimensions = data.shape[1] data1D = np.ndarray.flatten(data) nEpoch = 10 radius0 = 0 radiusN = 0 radiusCooling = "linear" scale0 = 0 scaleN = 0.01 scaleCooling = "linear" kernelType = 0 mapType = "planar" snapshots = 0 initialCodebookFilename = '' codebook_size = nSomY * nSomX * nDimensions codebook = np.zeros(codebook_size, dtype=np.float32) globalBmus_size = int(nVectors * int(np.ceil(nVectors/nVectors))*2) globalBmus = np.zeros(globalBmus_size, dtype=np.intc) uMatrix_size = nSomX * nSomY uMatrix = np.zeros(uMatrix_size, dtype=np.float32) somoclu.trainWrapper(data1D, nEpoch, nSomX, nSomY, nDimensions, nVectors, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType, initialCodebookFilename, codebook, globalBmus, uMatrix) #print codebook #print globalBmus #print uMatrix somoclu-1.4.1/src/Rscript/0000755000175000001440000000000012433136714014645 5ustar wittekuserssomoclu-1.4.1/src/Rscript/clean.sh0000755000175000001440000000012312433136714016262 0ustar wittekusers#!/bin/bash cd ../R/src/ shopt -s extglob rm !(Makevars|Makevars.win|Rsomoclu.cpp) somoclu-1.4.1/src/Rscript/configure0000755000175000001440000000153312433136714016556 0ustar wittekusers#!/bin/bash cd src bash autogen.sh HAS_CUDA=FALSE if test -z "${CUDA_HOME}"; then echo "could not determine CUDA_HOME. Please see the README file for installation requirements" exit 1 else HAS_CUDA=TRUE fi ARCH=$(uname -m) # replace these five lines with # CUDA_LIB := if [ ${ARCH} = 'i386' ] ; then CUDA_LIB=${CUDA_HOME}/lib else CUDA_LIB=${CUDA_HOME}/lib64 fi ./configure --with-cuda=${CUDA_HOME} --without-mpi make export PKG_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"` export PKG_CXXFLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"`" -DHAVE_R -DCUDA" cd src ${R_HOME}/bin/R CMD SHLIB $PKG_CXXFLAGS Rsomoclu.cpp denseCpuKernels.o sparseCpuKernels.o mapDistanceFunctions.o trainOneEpoch.o uMatrix.o denseGpuKernels.cu.co io.o -lgomp -L${CUDA_LIB} -lcudart -lcublas rm somoclu cp Rsomoclu.so ../ somoclu-1.4.1/src/Rscript/makeR-CUDA.sh0000755000175000001440000000101612433136714016753 0ustar wittekusers#!/bin/sh rm -rf ../R-CUDA cp -r ../R ../R-CUDA cp configure ../R-CUDA cp tests/R_interface_test_CUDA.R ../R-CUDA/tests cd ../R-CUDA mkdir data cp -r ../../m4/ ./src/ cp ../../autogen.sh ./src/ cp ../../configure.ac ./src/ cp ../../Makefile.in ./src/ mkdir ./src/src cp ../../src/*.cpp ./src/src cp ../../src/*.h ./src/src cp ../../src/*.cu ./src/src cp ../../src/Makefile.in ./src/src cp ../../data/rgbs.txt ./data/ gzip -f ./data/rgbs.txt cd src mv Rsomoclu.cpp src rm *.cpp rm *.h rm Makevars* cd ../../ R CMD build R-CUDA somoclu-1.4.1/src/Rscript/README.md0000644000175000001440000000111412433136714016121 0ustar wittekusersInstructions for building the R package with CUDA support on Linux == First after unzip the tarball, you can cd to the directory that contains the script to help you build the package with CUDA support: $ cd src/Rscript Then export the variable `CUDA_HOME` which indicates your installation: $ export CUDA_HOME=/opt/cuda or like: $ export CUDA_HOME=/usr/local/cuda then run the script to build: $ ./makeR-CUDA.sh If there isn' t error. You will then find the package `Rsomoclu_VERION.tar.gz` at the upper src folder. Install it with: $ R CMD INSTALL Rsomoclu_VERION.tar.gz somoclu-1.4.1/src/Rscript/tests/0000755000175000001440000000000012433136714016007 5ustar wittekuserssomoclu-1.4.1/src/Rscript/tests/R_interface_test_CUDA.R0000644000175000001440000000130612433136714022206 0ustar wittekuserslibrary('Rsomoclu') data_file <- system.file("data", "rgbs.txt.gz", package = 'Rsomoclu') input_data <- read.table(data_file) input_data <- data.matrix(input_data) nSomX <- 50 nSomY <- 50 nEpoch <- 10 radius0 <- 0 radiusN <- 0 radiusCooling <- "linear" scale0 <- 0 scaleN <- 0.01 scaleCooling <- "linear" kernelType <- 1 mapType <- "planar" snapshots <- 0 # initialCodebookFilename <- '' res <- Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) # initialCodebookFilename) res$codebook res$globalBmus res$uMatrix somoclu-1.4.1/src/Rscript/makeR.sh0000755000175000001440000000050312433136714016241 0ustar wittekusers#!/bin/sh cd ../R mkdir data cp ../../src/*.h ./src/ cp ../../src/mapDistanceFunctions.cpp ./src/ cp ../../src/trainOneEpoch.cpp ./src/ cp ../../src/uMatrix.cpp ./src/ cp ../../src/denseCpuKernels.cpp ./src/ cp ../../src/sparseCpuKernels.cpp ./src/ cp ../../data/rgbs.txt ./data/ gzip ./data/rgbs.txt cd ../ R CMD build R somoclu-1.4.1/configure.ac0000644000175000001440000000557112462116562014727 0ustar wittekusers# -*- Autoconf -*- # Process this file with autoconf to produce a configure script. AC_PREREQ([2.61]) AC_INIT([Somoclu], [1.4.1]) m4_include([m4/ax_mpi_options.m4]) m4_include([m4/ax_mpi_tests.m4]) AC_CONFIG_SRCDIR([src/somoclu.cpp]) AC_CONFIG_HEADERS([config.h]) # Checks for programs. CXXFLAGS="-fPIC" AC_PROG_CXX AC_PROG_INSTALL AC_OPENMP openmp_enabled=no if test x"$OPENMP_CFLAGS" != x"" ; then openmp_enabled=yes fi CXXFLAGS="${CXXFLAGS} ${OPENMP_CFLAGS}" string=`$CXX --version` if [[[ $string == *"ICC"* ]]] then CXXFLAGS="${CXXFLAGS} -fast" else AS_IF([test "x$GXX" = "xyes"],[CXXFLAGS="${CXXFLAGS} -Ofast -march=native"]) fi #find out what version we are running ARCH=`uname -m` if [[ $ARCH == "x86_64" ]]; then SUFFIX="64" else SUFFIX="" fi # Setup CUDA paths # ------------------------------------------------------------------------------ CUDA_PATH=/usr/local/cuda AC_ARG_WITH([cuda], [ --with-cuda=PATH prefix where cuda is installed [default=/usr/local/cuda]]) if test x"$with_cuda" != x"no" ; then if test -n "$with_cuda" then CUDA_PATH=$with_cuda fi AC_CHECK_PROG(NVCC_CHECK,nvcc,yes,no,$CUDA_PATH/bin) if test x"$NVCC_CHECK" = x"yes" ; then cuda_enabled=yes CUDA_CFLAGS="-I$CUDA_PATH/include -use_fast_math -Xcompiler \"${CXXFLAGS}\"" CUDA_LIBS="-lcudart -lcublas" CUDA_LDFLAGS="-L$CUDA_PATH/lib$SUFFIX" NVCC="$CUDA_PATH/bin/nvcc" AC_SUBST(CUDA_CFLAGS) AC_SUBST(CUDA_LIBS) AC_SUBST(CUDA_LDFLAGS) AC_SUBST(NVCC) AC_DEFINE([CUDA], 1, [cuda enabled]) elif test -n "$with_cuda" ; then echo "---------------------------------------" echo "Unable to find CUDA in $with_cuda." echo "Building a version without CUDA. " echo "---------------------------------------" cuda_enabled=no else cuda_enabled=no fi else cuda_enabled=no fi AM_CONDITIONAL([HAVE_CUDA], [test x"$cuda_enabled" = x"yes"]) #Setup MPI Paths # ------------------------------------------------------------------------------ AC_ARG_WITH([mpi], [ --with-mpi=PATH prefix where MPI is installed]) mpi_enabled=no if test x"$with_mpi" != x"no" ; then AX_MPI_OPTIONS if test x"$MPI_CXX" != x"none"; then AX_MPI_TESTS CXX=$MPI_CXX mpi_enabled=yes fi fi AC_CONFIG_FILES([Makefile src/Makefile]) AC_OUTPUT echo \ "------------------------------------------------- ${PACKAGE_NAME} Version ${PACKAGE_VERSION} Prefix: ${prefix}. Compiler: ${CXX} ${CXXFLAGS} ${MPI_INC} ${MPI_LIBDIR} ${MPI_LIBS} Package features: OpenMP enabled: ${openmp_enabled} MPI enabled: ${mpi_enabled} CUDA enabled: ${cuda_enabled} Now type 'make @<:@@:>@' where the optional is: all - build all binaries install - install everything --------------------------------------------------" somoclu-1.4.1/install-sh0000755000175000001440000003452312462151403014435 0ustar wittekusers#!/bin/sh # install - install a program, script, or datafile scriptversion=2013-12-25.23; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # 'make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. tab=' ' nl=' ' IFS=" $tab$nl" # Set DOITPROG to "echo" to test this script. doit=${DOITPROG-} doit_exec=${doit:-exec} # Put in absolute file names if you don't have them in your path; # or use environment vars. chgrpprog=${CHGRPPROG-chgrp} chmodprog=${CHMODPROG-chmod} chownprog=${CHOWNPROG-chown} cmpprog=${CMPPROG-cmp} cpprog=${CPPROG-cp} mkdirprog=${MKDIRPROG-mkdir} mvprog=${MVPROG-mv} rmprog=${RMPROG-rm} stripprog=${STRIPPROG-strip} posix_mkdir= # Desired mode of installed file. mode=0755 chgrpcmd= chmodcmd=$chmodprog chowncmd= mvcmd=$mvprog rmcmd="$rmprog -f" stripcmd= src= dst= dir_arg= dst_arg= copy_on_change=false is_target_a_directory=possibly usage="\ Usage: $0 [OPTION]... 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(umask $mkdir_umask && eval "\$doit_exec \$mkdirprog $prefixes") || test -d "$dstdir" || exit 1 obsolete_mkdir_used=true fi fi fi if test -n "$dir_arg"; then { test -z "$chowncmd" || $doit $chowncmd "$dst"; } && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } && { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false || test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1 else # Make a couple of temp file names in the proper directory. dsttmp=$dstdir/_inst.$$_ rmtmp=$dstdir/_rm.$$_ # Trap to clean up those temp files at exit. trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0 # Copy the file name to the temp name. (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") && # and set any options; do chmod last to preserve setuid bits. # # If any of these fail, we abort the whole thing. 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In this case, the final cleanup might fail but the new # file should still install successfully. { test ! -f "$dst" || $doit $rmcmd -f "$dst" 2>/dev/null || { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null && { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; } } || { echo "$0: cannot unlink or rename $dst" >&2 (exit 1); exit 1 } } && # Now rename the file to the real destination. $doit $mvcmd "$dsttmp" "$dst" } fi || exit 1 trap '' 0 fi done # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: somoclu-1.4.1/config.h.in0000644000175000001440000000116012462151403014443 0ustar wittekusers/* config.h.in. Generated from configure.ac by autoheader. */ /* cuda enabled */ #undef CUDA /* define that mpi is being used */ #undef HAVE_MPI /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION