add support for director kernel

shogun-toolbox · Mar 26, 2012 · dfbb2fd · dfbb2fd
1 parent 97e8e21
commit dfbb2fd
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Showing 9 changed files with 185 additions and 4 deletions.
diff --git a/examples/undocumented/python_modular/kernel_director_modular.py b/examples/undocumented/python_modular/kernel_director_modular.py
@@ -0,0 +1,65 @@
+#import numpy
+#from _modshogun import DirectorKernel,Labels,CombinedKernel
+#
+#class MyKernel(DirectorKernel):
+#	def init(self, f1,f2):
+#		print "hallo"
+#		return true
+#
+#	def compute(self, i,j):
+#		print i+j
+#		return i+j
+#
+#
+#
+#from tools.load import LoadMatrix
+#lm=LoadMatrix()
+##
+##traindat = lm.load_numbers('../data/fm_train_real.dat')
+##testdat = lm.load_numbers('../data/fm_test_real.dat')
+#label_traindat = lm.load_labels('../data/label_train_twoclass.dat')
+##
+##parameter_list = [[traindat,testdat,label_traindat,2.1,1,1e-5],[traindat,testdat,label_traindat,2.2,1,1e-5]]
+##
+##def classifier_libsvm_modular (fm_train_real=traindat,fm_test_real=testdat,label_train_twoclass=label_traindat,width=2.1,C=1,epsilon=1e-5):
+##	from shogun.Features import RealFeatures, Labels
+##	from shogun.Kernel import GaussianKernel
+##	from shogun.Classifier import LibSVM
+##
+##	feats_train=RealFeatures(fm_train_real)
+##	feats_train.parallel.set_num_threads(1)
+##	feats_test=RealFeatures(fm_test_real)
+##	
+##	kernel=MyKernel()
+##	labels=Labels(label_train_twoclass)
+##
+##	svm=LibSVM(C, kernel, labels)
+##	svm.set_epsilon(epsilon)
+##	svm.train()
+##
+##	kernel.init(feats_train, feats_test)
+##	labels = svm.apply().get_labels()
+##	supportvectors = sv_idx=svm.get_support_vectors()
+##	alphas=svm.get_alphas()
+##	predictions = svm.apply()
+##	return predictions, svm, predictions.get_labels()
+##
+##if __name__=='__main__':
+##	print 'LibSVM'
+##	classifier_libsvm_modular(*parameter_list[0])
+#
+#labels=Labels(label_traindat)
+##kernel=DirectorKernel()
+#kernel=MyKernel()
+#print kernel.get_cache_size()
+#print kernel.get_name()
+#k=CombinedKernel()
+#k.io.set_loglevel(0)
+#k.append_kernel(kernel)
+##
+#k.list_kernels()
+##
+##svm=LibSVM(0.1, kernel, labels)
+##svm.train()
+##print kernel.compute(0,0)
+#
diff --git a/src/interfaces/modular/Kernel.i b/src/interfaces/modular/Kernel.i
@@ -14,6 +14,13 @@
 
 %ignore CWeightedDegreePositionStringKernel::set_position_weights(float64_t*);
 
+%feature("director") shogun::CDirectorKernel;
+%feature("director:except") {
+    if ($error != NULL) {
+        throw Swig::DirectorMethodException();
+    }
+}
+
 /* Remove C Prefix */
 %rename(Kernel) CKernel;
 %rename(KernelNormalizer) CKernelNormalizer;
@@ -40,6 +47,7 @@
 %rename(DistanceKernel) CDistanceKernel;
 %rename(FixedDegreeStringKernel) CFixedDegreeStringKernel;
 %rename(GaussianKernel) CGaussianKernel;
+%rename(DirectorKernel) CDirectorKernel;
 %rename(WaveletKernel) CWaveletKernel;
 %rename(GaussianShiftKernel) CGaussianShiftKernel;
 %rename(GaussianShortRealKernel) CGaussianShortRealKernel;
@@ -155,6 +163,7 @@ namespace shogun
 %include <shogun/kernel/ExponentialKernel.h>
 %include <shogun/kernel/FixedDegreeStringKernel.h>
 %include <shogun/kernel/GaussianKernel.h>
+%include <shogun/kernel/DirectorKernel.h>
 %include <shogun/kernel/GaussianShiftKernel.h>
 %include <shogun/kernel/GaussianShortRealKernel.h>
 %include <shogun/kernel/HistogramIntersectionKernel.h>

diff --git a/src/interfaces/modular/Kernel_includes.i b/src/interfaces/modular/Kernel_includes.i
@@ -24,6 +24,7 @@
 #include <shogun/kernel/DistanceKernel.h>
 #include <shogun/kernel/FixedDegreeStringKernel.h>
 #include <shogun/kernel/GaussianKernel.h>
+#include <shogun/kernel/DirectorKernel.h>
 #include <shogun/kernel/GaussianShiftKernel.h>
 #include <shogun/kernel/GaussianShortRealKernel.h>
 #include <shogun/kernel/HistogramIntersectionKernel.h>

diff --git a/src/interfaces/modular/SGBase.i b/src/interfaces/modular/SGBase.i
@@ -228,6 +228,12 @@ public void readExternal(java.io.ObjectInput in) throws java.io.IOException, jav
     {
         $action
     }
+#ifdef SWIGPYTHON
+    catch (Swig::DirectorException &e)
+    {
+        SWIG_fail;
+    }
+#endif
     catch (std::bad_alloc)
     {
         SWIG_exception(SWIG_MemoryError, const_cast<char*>("Out of memory error.\n"));

diff --git a/src/interfaces/modular/modshogun.i b/src/interfaces/modular/modshogun.i
@@ -11,7 +11,7 @@
 "The `modshogun` module gathers all modules available in the SHOGUN toolkit."
 %enddef
 
-%module(docstring=DOCSTR) modshogun
+%module(directors="1", docstring=DOCSTR) modshogun
 #undef DOCSTR
 
 %include "modshogun_ignores.i"

diff --git a/src/shogun/kernel/DirectorKernel.h b/src/shogun/kernel/DirectorKernel.h
@@ -0,0 +1,99 @@
+/*
+ * 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.
+ *
+ * Written (W) 2011 Soeren Sonnenburg
+ * Copyright (C) 2011 Soeren Sonnenburg
+ */
+
+#ifndef _DIRECTORKERNEL_H___
+#define _DIRECTORKERNEL_H___
+
+#include <shogun/lib/common.h>
+#include <shogun/kernel/Kernel.h>
+
+namespace shogun
+{
+class CDirectorKernel: public CKernel
+{
+	public:
+		/** default constructor
+		 *
+		 */
+		CDirectorKernel() : CKernel()
+		{
+		}
+
+		/** constructor
+		 *
+		 */
+		CDirectorKernel(int32_t size) : CKernel(size)
+		{
+		}
+
+		/** default constructor
+		 *
+		 */
+		virtual ~CDirectorKernel()
+		{
+			cleanup();
+		}
+
+		/** initialize kernel
+		 *
+		 * @param l features of left-hand side
+		 * @param r features of right-hand side
+		 * @return if initializing was successful
+		 */
+		virtual bool init(CFeatures* l, CFeatures* r)
+		{
+		}
+
+		/** clean up kernel */
+		virtual void cleanup()
+		{
+		}
+
+		/** return what type of kernel we are
+		 *
+		 * @return kernel type DIRECTOR
+		 */
+		virtual EKernelType get_kernel_type() { return K_DIRECTOR; }
+
+		 /** return what type of features kernel can deal with
+		  *
+		  * @return feature type ANY
+		  */
+		virtual EFeatureType get_feature_type() { return F_ANY; }
+
+		 /** return what class of features kernel can deal with
+		  *
+		  * @return feature class ANY
+		  */
+		virtual EFeatureClass get_feature_class() { return C_ANY; }
+
+		/** return the kernel's name
+		 *
+		 * @return name Director
+		 */
+		inline virtual const char* get_name() const { return "DirectorKernel"; }
+
+	protected:
+		/** compute kernel function for features a and b
+		 * idx_{a,b} denote the index of the feature vectors
+		 * in the corresponding feature object
+		 *
+		 * @param idx_a index a
+		 * @param idx_b index b
+		 * @return computed kernel function at indices a,b
+		 */
+		virtual float64_t compute(int32_t idx_a, int32_t idx_b)
+		{
+			SG_ERROR("Compute method of Director Kernel needs to be overridden.\n");
+			return 0;
+		}
+};
+}
+#endif /* _GAUSSIANKERNEL_H__ */
diff --git a/src/shogun/kernel/Kernel.cpp b/src/shogun/kernel/Kernel.cpp
@@ -752,6 +752,7 @@ void CKernel::list_kernel()
 		ENUM_CASE(K_DISTANTSEGMENTS)
 		ENUM_CASE(K_BESSEL)
 		ENUM_CASE(K_JENSENSHANNON)
+		ENUM_CASE(K_DIRECTOR)
 	}
 
 	switch (get_feature_class())

diff --git a/src/shogun/kernel/Kernel.h b/src/shogun/kernel/Kernel.h
@@ -24,8 +24,6 @@
 #include <shogun/features/Features.h>
 #include <shogun/kernel/KernelNormalizer.h>
 
-#include <vector>
-
 namespace shogun
 {
 	class CFile;
@@ -107,7 +105,8 @@ enum EKernelType
 	K_INVERSEMULTIQUADRIC = 440,
 	K_DISTANTSEGMENTS = 450,
 	K_BESSEL = 460,
-	K_JENSENSHANNON = 470
+	K_JENSENSHANNON = 470,
+	K_DIRECTOR = 480
 };
 
 /** kernel property */

diff --git a/src/shogun/kernel/SpectrumMismatchRBFKernel.h b/src/shogun/kernel/SpectrumMismatchRBFKernel.h
@@ -21,6 +21,7 @@
 #include <shogun/lib/Array.h>
 #include <shogun/lib/Array2.h>
 #include <string>
+#include <vector>
 
 namespace shogun
 {