www.pudn.com > libpmk.rar > kernel-matrix.cc, change:2007-05-27,size:3442b


// Copyright 2007, Massachusetts Institute of Technology.
// The use of this code is permitted for research only. There is
// absolutely no warranty for this software.
//
// Author: John Lee (jjl@mit.edu)
//

#include <math.h>
#include <assert.h>
#include <iostream>
#include <fstream>
#include "kernel/kernel-matrix.h"

namespace libpmk_util {

KernelMatrix::KernelMatrix(int size) : matrix_(size) {
   for (int ii = 0; ii < size; ++ii) {
      matrix_[ii].resize(ii+1);
      matrix_[ii][ii] = 1;
   }
}

void KernelMatrix::Resize(int new_size) {
   int old_size = GetSize();
   if (new_size > old_size) {
      matrix_.resize(new_size);
      for (int ii = old_size; ii < new_size; ++ii) {
         matrix_[ii].resize(ii+1);
         matrix_[ii][ii] = 1;
      }
   } else if (new_size < old_size) {
      matrix_.resize(new_size);
   }
}

int KernelMatrix::GetSize() const {
   return matrix_.size();
}

void KernelMatrix::Normalize() {
   int size = GetSize();
   vector<double> diag(size);
   for (int ii = 0; ii < size; ++ii) {
      diag[ii] = matrix_[ii][ii];
      assert(diag[ii] != 0);
   }

   double normval;
   for (int ii = 0; ii < size; ++ii) {
      for (int jj = 0; jj <= ii; ++jj) {
         normval = matrix_[ii][jj] / sqrt(diag[ii] * diag[jj]);
         matrix_[ii][jj] = normval;
      }
   }
}

void KernelMatrix::NormalizeByMinCardinality(const vector<int>& cards) {
   int size = GetSize();
   assert((int)cards.size() == size);
   for (int ii = 0; ii < size; ++ii) {
      for (int jj = 0; jj <= ii; ++jj) {
         double min_card = cards[ii] < cards[jj] ? cards[ii] : cards[jj];
         matrix_[ii][jj] /= min_card;
      }
   }
}

double& KernelMatrix::at(int row, int col) {
   assert(row < GetSize());
   assert(col < GetSize());
   // The matrix is a triangle, so the first index must always be at least
   // the second index.
   if (col <= row) {
      return matrix_[row][col];
   } else {
      return matrix_[col][row];
   }
}

double KernelMatrix::at(int row, int col) const {
   assert(row < GetSize());
   assert(col < GetSize());
   // The matrix is a triangle, so the first index must always be at least
   // the second index.
   if (col <= row) {
      return matrix_[row][col];
   } else {
      return matrix_[col][row];
   }
}

// File format:
// (int32_t) size
// (double) row 0
// (double*2) row 1
// ...
// (double*n) row n-1
void KernelMatrix::WriteToStream(ostream& output_stream) const {
   int32_t size = GetSize();
   output_stream.write((char *)&size, sizeof(int32_t));
   for (int ii = 0; ii < size; ++ii) {
      assert((int)matrix_[ii].size() == ii+1);
      for (int jj = 0; jj < ii+1; ++jj) {
         output_stream.write((char *)&matrix_[ii][jj], sizeof(double));
      }
   }
}

void KernelMatrix::WriteToFile(const char* filename) const {
   ofstream output_stream(filename, ios::binary | ios::trunc);
   WriteToStream(output_stream);
   output_stream.close();
}

void KernelMatrix::ReadFromStream(istream& input_stream) {
   int32_t size = 0;
   input_stream.read((char *)&size, sizeof(int32_t));

   Resize(size);
   for (int ii = 0; ii < size; ++ii) {
      for (int jj = 0; jj <= ii; ++jj) {
         input_stream.read((char *)&matrix_[ii][jj], sizeof(double));
      }
   }
}

void KernelMatrix::ReadFromFile(const char* filename) {
   ifstream input_stream(filename, ios::binary);
   ReadFromStream(input_stream);
   input_stream.close();
}
}  // namespace libpmk_util