Moved isomap_distance to .cpp

src/shogun/preprocessor/Isomap.cpp

@@ -0,0 +1,95 @@
+/*
+ * 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 Sergey Lisitsyn
+ * Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society
+ */
+
+#include <shogun/preprocessor/Isomap.h>
+#ifdef HAVE_LAPACK
+#include <shogun/lib/common.h>
+#include <shogun/distance/CustomDistance.h>
+#include <shogun/mathematics/Math.h>
+#include <shogun/io/SGIO.h>
+#include <shogun/lib/Signal.h>
+
+using namespace shogun;
+
+CCustomDistance* CIsomap::isomap_distance(CDistance* distance)
+{
+	int32_t N,k,i,j;
+	SGMatrix<float64_t> D_matrix=distance->get_distance_matrix();
+	N=D_matrix.num_cols;
+
+	if (m_type==EISOMAP)
+	{
+		// just replace distances >e with infty
+		for (i=0; i<N*N; i++)
+		{
+			if (D_matrix.matrix[i]>m_epsilon)
+				D_matrix.matrix[i] = CMath::ALMOST_INFTY;
+		}
+	}
+	if (m_type==KISOMAP)
+	{
+		// cut by k-nearest neighbors
+
+		float64_t* col = new float64_t[N];
+		int32_t* col_idx = new int32_t[N];
+
+		// -> INFTY edges connecting NOT neighbors
+		for (i=0; i<N; i++)
+		{
+			for (j=0; j<N; j++)
+			{
+				col[j] = D_matrix.matrix[j*N+i];
+				col_idx[j] = j;
+			}
+
+			CMath::qsort_index(col,col_idx,N);
+
+			for (j=m_k+1; j<N; j++)
+			{
+				D_matrix.matrix[col_idx[j]*N+i] = CMath::ALMOST_INFTY;
+			}
+		}
+
+		// symmetrize matrix
+		for (i=0; i<N; i++)
+		{
+			for (j=0; j<N; j++)
+				if (D_matrix.matrix[j*N+i] >= CMath::ALMOST_INFTY)
+					D_matrix.matrix[i*N+j] = D_matrix.matrix[j*N+i];
+		}			
+
+		delete[] col;
+		delete[] col_idx;
+	}
+
+	// Floyd-Warshall on distance matrix
+	// TODO replace by dijkstra
+	for (k=0; k<N; k++)
+	{
+		for (i=0; i<N; i++)
+		{
+			for (j=0; j<N; j++)
+			{
+				D_matrix.matrix[i*N+j] =
+						CMath::min(D_matrix.matrix[i*N+j],
+								   D_matrix.matrix[i*N+k] + D_matrix.matrix[k*N+j]);
+			}
+		}
+	}
+
+	CCustomDistance* geodesic_distance = new CCustomDistance(D_matrix.matrix,N,N);
+
+	// should be removed if custom distance doesn't copy the matrix
+	delete[] D_matrix.matrix;
+
+	return geodesic_distance;
+}
+
+#endif /* HAVE_LAPACK */

src/shogun/preprocessor/Isomap.h

@@ -180,84 +180,11 @@ class CIsomap: public CDimensionReductionPreprocessor
 	 * @param distance
 	 * @return custom distance with approximate geodesic distance matrix
 	 */
-	CCustomDistance* isomap_distance(CDistance* distance)
-	{
-		int32_t N,k,i,j;
-		SGMatrix<float64_t> D_matrix=distance->get_distance_matrix();
-		N=D_matrix.num_cols;
-
-		if (m_type==EISOMAP)
-		{
-			// just replace distances >e with infty
-
-			for (i=0; i<N*N; i++)
-			{
-				if (D_matrix.matrix[i]>m_epsilon)
-					D_matrix.matrix[i] = CMath::ALMOST_INFTY;
-			}
-		}
-		if (m_type==KISOMAP)
-		{
-			// cut by k-nearest neighbors
-
-			float64_t* col = new float64_t[N];
-			int32_t* col_idx = new int32_t[N];
-
-			// -> INFTY edges connecting NOT neighbors
-			for (i=0; i<N; i++)
-			{
-				for (j=0; j<N; j++)
-				{
-					col[j] = D_matrix.matrix[j*N+i];
-					col_idx[j] = j;
-				}
-
-				CMath::qsort_index(col,col_idx,N);
-
-				for (j=m_k+1; j<N; j++)
-				{
-					D_matrix.matrix[col_idx[j]*N+i] = CMath::ALMOST_INFTY;
-				}
-			}
-
-			// symmetrize matrix
-			for (i=0; i<N; i++)
-			{
-				for (j=0; j<N; j++)
-					if (D_matrix.matrix[j*N+i] >= CMath::ALMOST_INFTY)
-						D_matrix.matrix[i*N+j] = D_matrix.matrix[j*N+i];
-			}			
-
-			delete[] col;
-			delete[] col_idx;
-		}
-
-		// Floyd-Warshall on distance matrix
-		// TODO replace by dijkstra
-		for (k=0; k<N; k++)
-		{
-			for (i=0; i<N; i++)
-			{
-				for (j=0; j<N; j++)
-				{
-					D_matrix.matrix[i*N+j] =
-							CMath::min(D_matrix.matrix[i*N+j],
-									   D_matrix.matrix[i*N+k] + D_matrix.matrix[k*N+j]);
-				}
-			}
-		}
-
-		CCustomDistance* geodesic_distance = new CCustomDistance(D_matrix.matrix,N,N);
-
-		// should be removed if custom distance doesn't copy the matrix
-		delete[] D_matrix.matrix;
-
-		return geodesic_distance;
-	}
+	CCustomDistance* isomap_distance(CDistance* distance);
 
 	/** mds embedding 
 	 * @param distance
-	 * @return new feature representing given distance
+	 * @return new feature matrix representing given distance
 	 */
 	virtual SGMatrix<float64_t> mds_embed(CDistance* distance) = 0;