Added embed kernel to DiffusionMaps

shogun-toolbox · Oct 23, 2011 · 4bd8b18 · 4bd8b18
1 parent ae5401a
commit 4bd8b18
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Showing 2 changed files with 24 additions and 25 deletions.
diff --git a/src/shogun/converter/DiffusionMaps.cpp b/src/shogun/converter/DiffusionMaps.cpp
@@ -9,11 +9,10 @@
  */
 
 #include <shogun/converter/DiffusionMaps.h>
+#include <shogun/converter/EmbeddingConverter.h>
 #include <shogun/lib/config.h>
 #ifdef HAVE_LAPACK
-#include <shogun/converter/EmbeddingConverter.h>
 #include <shogun/mathematics/lapack.h>
-#include <shogun/mathematics/arpack_d.h>
 #include <shogun/mathematics/Math.h>
 #include <shogun/io/SGIO.h>
 #include <shogun/kernel/Kernel.h>
@@ -57,28 +56,24 @@ const char* CDiffusionMaps::get_name() const
 CFeatures* CDiffusionMaps::apply(CFeatures* features)
 {
 	ASSERT(features);
-	if (!(features->get_feature_class()==C_SIMPLE &&
-	      features->get_feature_type()==F_DREAL))
-	{
-		SG_ERROR("Given features are not of SimpleRealFeatures type.\n");
-	}
 	// shorthand for simplefeatures
-	CSimpleFeatures<float64_t>* simple_features = (CSimpleFeatures<float64_t>*) features;
 	SG_REF(features);
-
-	// get dimensionality and number of vectors of data
-	int32_t N = simple_features->get_num_vectors();
-	int32_t dim = simple_features->get_num_features();
-
-	// loop variables
-	int32_t i,j;
-
 	// compute distance matrix
 	ASSERT(m_kernel);
-	m_kernel->init(simple_features,simple_features);
-	SGMatrix<float64_t> kernel_matrix = m_kernel->get_kernel_matrix();
+	m_kernel->init(features,features);
+	CSimpleFeatures<float64_t>* embedding = embed_kernel(m_kernel);
 	m_kernel->cleanup();
-
+	SG_UNREF(features);
+	return (CFeatures*)embedding;
+}
+
+CSimpleFeatures<float64_t>* CDiffusionMaps::embed_kernel(CKernel* kernel)
+{
+	int32_t i,j;
+	SGMatrix<float64_t> kernel_matrix = kernel->get_kernel_matrix();
+	ASSERT(kernel_matrix.num_rows==kernel_matrix.num_cols);
+	int32_t N = kernel_matrix.num_rows;
+
 	float64_t* p_vector = SG_CALLOC(float64_t, N);
 	for (i=0; i<N; i++)
 	{
@@ -142,12 +137,10 @@ CFeatures* CDiffusionMaps::apply(CFeatures* features)
 	for (i=0; i<m_target_dim; i++)
 	{
 		for (j=0; j<N; j++)
-			new_feature_matrix[j*m_target_dim+i] = kernel_matrix.matrix[(m_target_dim-i-1)*N+j]/kernel_matrix.matrix[(m_target_dim)*N+j];
+			new_feature_matrix[j*m_target_dim+i] = kernel_matrix.matrix[(m_target_dim-i-1)*N+j];///kernel_matrix.matrix[(m_target_dim)*N+j];
 	}
 	kernel_matrix.destroy_matrix();
 
-	SG_UNREF(features);
-	return (CFeatures*)(new CSimpleFeatures<float64_t>(new_feature_matrix));
+	return new CSimpleFeatures<float64_t>(new_feature_matrix);
 }
-
 #endif /* HAVE_LAPACK */
diff --git a/src/shogun/converter/DiffusionMaps.h b/src/shogun/converter/DiffusionMaps.h
@@ -11,10 +11,10 @@
 #ifndef DIFFUSIONMAPS_H_
 #define DIFFUSIONMAPS_H_
 #include <shogun/lib/config.h>
-#ifdef HAVE_LAPACK
 #include <shogun/converter/EmbeddingConverter.h>
+#ifdef HAVE_LAPACK
 #include <shogun/features/Features.h>
-#include <shogun/distance/Distance.h>
+#include <shogun/kernel/Kernel.h>
 
 namespace shogun
 {
@@ -40,6 +40,12 @@ class CDiffusionMaps: public CEmbeddingConverter
 	 */
 	virtual CFeatures* apply(CFeatures* features);
 
+	/** embed kernel
+	 * @param kernel to use for embedding
+	 * @return embedding simple features
+	 */
+	virtual CSimpleFeatures<float64_t>* embed_kernel(CKernel* kernel);
+
 	/** setter for t parameter
 	 * @param t t value
 	 */