first check in

2007-12-01 03:44:07 +00:00
parent 7df1abb7cb
commit 74df495c66
2 changed files with 125 additions and 0 deletions
@@ -0,0 +1,67 @@
+/*
+ * =====================================================================================
+ * 
+ *       Filename:  kernel_pca.h
+ * 
+ *    Description:  
+ * 
+ *        Version:  1.0
+ *        Created:  11/30/2007 08:34:19 PM EST
+ *       Revision:  none
+ *       Compiler:  gcc
+ * 
+ *         Author:  Nikolaos Vasiloglou (NV), nvasil@ieee.org
+ *        Company:  Georgia Tech Fastlab-ESP Lab
+ * 
+ * =====================================================================================
+ */
+
+#ifndef KERNEL_PCA_H_
+#define KERNEL_PCA_H_
+#ifndef HAVING_CONFIG_H
+#define HAVE_CONFIG_H
+#endif
+#include <string>
+#include "fastlib/fastlib.h"
+#include "fastlib/la/matrix.h"
+#include "u/nvasil/binary_dataset.h"
+#include "Epetra_SerialDenseMatrix.h"
+#include "Epetra_SerialComm.h"
+#include "Epetra_Version.h"
+
+template<typename TREE, bool diagnostic>
+class KernelPCA {
+	typedef typename TREE::Precision_t   Precision_t;
+	typedef TREE                         Tree_t;
+	typdef enum OutputMode_t {Matrix_E=0, TexFile_E, BinaryFile_E};
+ public:
+	void Init();
+  void Destruct();
+	void ComputeAffinity(index_t knn);
+  template<typename DISTANCEKERNEL>		
+	void ComputeGeneralKernelPCA(DISTANCEKERNEL kernel, index_t num_of_eigenvalues);
+	void ComputeIsomap(index_t num_of_eigenvalues);
+	void ComputeLLE(index_t num_of_eigenvalues);
+	template<KERNEL>
+	void ComputeDiffusionMaps(KERNEL kernel, index_t num_of_eigenvalues);
+	void ComputeLaplacialnEigenmaps(index_t);
+	void ComputeSpectralRegression(std::string label_file);
+  Vector get_eigenvalues();
+	Matrix get_eigenvectors();
+	void SaveToTextFile(std::string file);
+	void SaveToBinaryFile(std::string file);
+  void set_output_mode(OutputMode_t mode) {
+	  output_mode_ = mode;
+	}
+	
+ private:
+  Tree_t tree_;
+  Epetra_SerialComm comm_;
+  Epetra_CrsMatrix kernel_matrix_;	
+  BinaryDataset<Precision_t> data_; 
+  OutputMode_t output_mode_;
+
+} ;
+
+#include "u/nvasil/kernel_pca/kernel_pca_impl.h"
+#endif
@@ -0,0 +1,58 @@
+/*
+ * =====================================================================================
+ * 
+ *       Filename:  kernel_pca_impl.h
+ * 
+ *    Description:  
+ * 
+ *        Version:  1.0
+ *        Created:  11/30/2007 09:03:12 PM EST
+ *       Revision:  none
+ *       Compiler:  gcc
+ * 
+ *         Author:  Nikolaos Vasiloglou (NV), nvasil@ieee.org
+ *        Company:  Georgia Tech Fastlab-ESP Lab
+ * 
+ * =====================================================================================
+ */
+
+#define TEMPLATE__           \
+template<typename TREE, bool diagnostic>
+#define KERNELPCA__ KernelPCA<TREE, diagnostic>
+
+TEMPLATE__
+void KERNELPCA::Init(std::string data_file, 
+		                 std::string index_file) {
+	if (index_file.empty()) {
+    data_.Init(data_file);
+	} else {
+	  data_.Init(data_file, index_file);
+	}
+	tree_.Init(&data_);
+}
+
+TEMPLATE__
+void KERNELPCA::Destruct() {
+  tree_.Destruct();
+  data_.Destruct();	
+}
+
+TEMPLATE__
+void KERNELPCA::ComputeAffinity(index_t knns) {
+    fx_timer_start(fx_root, "build_tree")
+	  test_tree.BuildDepthFirst();
+		fx_timer_start(fx_root, "duall_tree");	
+	  train_tree.AllNearestNeighbors(tree_.get_parent(), knns);
+	  fx_timer_stop(fx_root, "duall_tree");
+}
+
+TEMPLATE__
+template<typename DISTANCEKERNEL>
+void KERNELPCA::ComputeGeneralKernelPCA(DISTANCEKERNEL kernel, 
+		                                    index_t num_of_eigenvalues){
+
+
+}
+
+
+