Add missing file

Author: sunfanyunn

MLGkernel/MLGkernel/swig/MLGK.cpp

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+#include "ThreadManager.hpp"
+#include "pMMFbase.hpp"
+#include "Vectorv.hpp"
+#include "Vectorl.hpp"
+#include "Vectorh.hpp"
+
+std::default_random_engine randomNumberGenerator;
+bool multithreading=true;
+ThreadManager threadManager(4);
+char strbuffer[255];
+mutex CoutLock::mx;

MLGkernel/MLGkernel/swig/MLGK.i

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+%module MLGK
+%include "std_string.i"
+%{
+ #define SWIG_FILE_WITH_INIT
+ #include "../params.hpp"
+ #include "../MLGdataset.hpp"
+ using namespace std;
+%}
+
+%include "numpy.i"
+%init
+%{
+import_array();
+%}
+
+%apply (double* INPLACE_ARRAY2, int DIM1, int DIM2) {(double *npmatrix, int rows, int cols)};
+%include "../params.hpp"
+%include "../MLGdataset.hpp"

MLGkernel/MLGkernel/swig/Makefile

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+# Adjust accordingly
+ROOTDIR=/home/hopan/MLGkernel
+include ../../Makefile.base
+
+
+CC=g++
+CFLAGS= -std=c++11 -I $(INCLUDEDIR) -I $(UTILITYDIR) -I $(FILETYPESDIR) -I $(MATRIXDIR) 
+
+MKLVARS+= -lmkl_rt
+MLGDIR=/home/hopan/MLGkernel/MLGkernel
+ALLOBJECTS= $(MATRIXDIR)/*.o $(MLGDIR)/*.o $(UTILITYDIR)/*.o
+
+# These need to be set according to your python location/distribution
+PYINCLUDE= -I/software/python-3.4-2015q1-el6-x86_64/include/python3.4m \
+-I/software/python-3.4-2015q1-el6-x86_64/lib/python3.4/site-packages/numpy/core/include
+PYLIBS= -L/Library/Frameworks/Python.framework/Versions/3.4/lib -ldl -framework CoreFoundation -lpython3.4m
+
+MLGK_wrap.cxx: MLGK.i $(MLGDIR)/*.hpp $(MATRIXDIR)/*.hpp $(UTILITYDIR)/*.hpp
+swig -python -shadow -c++ MLGK.i
+
+_MLGK.so: MLGK_wrap.cxx MLGK.cpp
+$(CC) -fPIC -shared MLGK_wrap.cxx MLGK.cpp \
+-o _MLGK.so $(CFLAGS) $(PYINCLUDE) $(ALLOBJECTS) -I $(INCLUDEDIR)
+
+all: MLGK_wrap.cxx _MLGK.so
+
+clean: 
+rm -f $(OBJECTS) MLGK_wrap.cxx _MLGK.so
+
+anew: clean all

MLGkernel/MLGkernel/swig/README.txt

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+Run 'make all' at the top level of the MLGkernel directory.
+Then in this directory("MLGkernel/MLGkernel/swig/"), run make all.
+This will create the _MLGK.so shared object file as well as
+the MLGK.py file.
+
+In python you should then be able to stuff like:
+import MLGK
+lvls = 2
+radius = 2
+m = MLGK.MLGdataset()
+m.loadGraphs("sampledata.txt")
+m.computeGram(lvls, radius)
+m.saveGram("savefile.txt")
+
+
+See test.py for further details.
+
+NOTE: You will have to change some of the macros in the Makefile here(to change
+the location of where the Python.h file is stored - it should probably be
+somewhere like /usr/include/python3.x/. Also, in the top level directory inside
+Makefile.options, you need to specify where the eigen library is located, as well
+as the C++ compiler(IE: clang/g++/etc).

MLGkernel/MLGkernel/swig/test.py

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+from MLGK import *
+import numpy as np
+import pdb
+import os.path as path
+import sys
+
+fname = path.abspath(path.join(__file__ ,"../../../data/MUTAG.txt"))
+save_name = "m.txt"
+num_graphs = 188
+eta = 0.01
+gamma= 0.001
+grow = True
+radius = 2
+levels = 2
+
+m = MLGdataset(fname, eta, gamma, grow)
+m.computeGram(levels, radius)
+m.saveGram(save_name)
+
+# fill a numpy matrix. Note: need to call compute gram
+# before calling fillGram
+gram = np.zeros((num_graphs, num_graphs))
+m.fillGram(gram)
+pdb.set_trace()