C++ matrix::size1方法代码示例

int reorderRows( ublas::matrix< double >& U, int start, int leftCol )
{
    int leftMostRow = start;
    int numReacs = U.size2() - U.size1();
    int newLeftCol = numReacs;
    for ( size_t i = start; i < U.size1(); ++i )
    {
        for ( int j = leftCol; j < numReacs; ++j )
        {
            if ( fabs( U(i,j )) > SteadyState::EPSILON )
            {
                if ( j < newLeftCol )
                {
                    newLeftCol = j;
                    leftMostRow = i;
                }
                break;
            }
        }
    }

    if ( leftMostRow != start )   // swap them.
        swapRows( U, start, leftMostRow );

    return newLeftCol;
}

void peel_n_mutations(const alphabet& a, const vector<int>& letters, const SequenceTree& T,
		      const ublas::matrix<B>& cost,ublas::matrix<B>& n_muts,
		      const vector<const_branchview>& branches)
{
  const int A = a.size();

  assert(letters.size() == T.n_leaves());
  assert(cost.size1() == A);
  assert(cost.size2() == A);

  // we need a scratch row in the matrix
  assert(n_muts.size1() == T.n_nodes());
  assert(n_muts.size2() == A);

  // compute the max cost -- is this approach a good idea?
  // Well... this apparently doesn't work.
  B max_cost = 0;
  for(int i=0;i<A;i++)
    for(int j=0;j<A;j++)
      max_cost = std::max(cost(i,j)+1, max_cost);
    
  // clear the length matrix.
  for(int i=0;i<n_muts.size1();i++)
    for(int j=0;j<n_muts.size2();j++)
      n_muts(i,j)=0;
  
  // set the leaf costs
  for(int s=0;s<T.n_leaves();s++)
  {
    int L = letters[s];

    if (a.is_letter_class(L))
      for(int l=0;l<A;l++)
	if (a.matches(l,L))
	  n_muts(s,l) = 0;
	else
	  n_muts(s,l) = max_cost;
  }


  // compute the costs for letters at each node
  for(int i=0;i<branches.size();i++)
  {
    int s = branches[i].source();
    int t = branches[i].target();

    // for each letter l of node target...
    for(int l=0;l<A;l++)
    {
      // compute minimum treelength for data behind source.
      B temp = n_muts(s,0)+cost(0,l);
      for(int k=1;k<A;k++)
	temp = min(temp, n_muts(s,k)+cost(k,l) );

      // add it to treelengths for data behind target
      n_muts(t,l) += temp;
    }
  }
}

	ublas::matrix<double> normalize_affinity(ublas::matrix<double> input) {
		ublas::vector<double> ones = ublas::scalar_vector<double>(input.size1(), 1);
		ublas::vector<double> diag(input.size1());
		
		for (int i = 0; i < input.size1(); i++)
			diag[i] = input(i, i);
		
		return ublas::outer_prod(diag, ones) + ublas::outer_prod(ublas::trans(ones), ublas::trans(diag)) - input - ublas::trans(input);
	}

void dispMatrix(const ublas::matrix<float>& inMat) {
    cout << "Matrix [" << inMat.size1() << ", " << inMat.size2() << "]" << endl << "(";
    for (int n = 0; n < (int) inMat.size1(); n++) {
        for (int m = 0; m < (int) inMat.size2(); m++) {
            cout << inMat(n,m) << " ";
        }
        cout << endl;
    }
    cout << "\b)" << endl;
}

/**
 * @brief Utility funtion to doing scans for steady states.
 *
 * @param tot
 * @param g
 * @param S
 */
void recalcTotal( vector< double >& tot, ublas::matrix<double>& g, const double* S )
{
    assert( g.size1() == tot.size() );
    for ( size_t i = 0; i < g.size1(); ++i ) 
    {
        double t = 0.0;
        for ( unsigned int j = 0; j < g.size2(); ++j )
            t += g( i, j ) * S[j];
        tot[ i ] = t;
    }
}

T cond2( ublas::matrix<T> const& M )
{
    gmm::dense_matrix<T> Q( M.size1(), M.size2() );

    for ( int_type i=0; i < M.size1(); ++i )
        for ( int_type j=0; j < M.size2(); ++j )
        {
            Q( i,j ) = M( i,j );
        }

    return gmm::condition_number( Q );
}

double fourSums(const ublas::matrix<long double>& A, ublas::matrix<long double>& sums)
{
	long double total = 0.0;
	sums = ublas::zero_matrix<long double>(A.size1(), A.size2()/4);
	for (size_t i = 0; i < A.size1(); ++i)
		for (size_t j = 0; j < A.size2(); ++j)
		{
			sums(i,j/4) += A(i,j);
			total += A(i,j);
		}
	
	return total;
}

  // ublas::matrix<T> matrix_sum(ublas::matrix<T>& m, int index) {
  ublas::vector<T> matrix_sum(const ublas::matrix<T>& m, int index) {
    using namespace boost::numeric::ublas;
    ublas::vector<T> result;
    if (index == 0) {
      result.resize(m.size2());
      for (size_t i=0; i<m.size2(); ++i)
	result(i) = sum(column(m, i));
    }
    else if (index == 1) {
      result.resize(m.size1());
      for (size_t i=0; i<m.size1(); ++i)
	result(i) = sum(row(m, i));
    }
    return result;
  }

ublas::vector<ublas::matrix<double> > wishart_rnd(const int df, ublas::matrix<double>& S, const int mc) {
  //! inverse Wishart random matrix
  //! does not correct for poorly conditioned matrix 
  size_t p = S.size1();
  ublas::vector<double> D(p);
  ublas::matrix<double> P(p, p);
  ublas::matrix<double> F(p, p);
  F = ublas::zero_matrix<double>(p, p);

  // make copy of S
  // ublas::matrix<double> SS(S);

  lapack::gesvd('A', 'A', S, D, P, F);
  // svd0(S, P, D, F);
  
  P = prod(trans(P), diagm(ublas::apply_to_all<functor::inv_sqrt<double> >(D)));
  // rprod does not seem any faster than diagonalizing D before multiplication
  // P = rprod(P, ublas::apply_to_all<functor::inv_sqrt<double> >(D));

  // generate mc samples
  ublas::vector<ublas::matrix<double> > K(mc);
  for (int i=0; i<mc; ++i)
    K(i) = wishart_1(df, P, p, p);
  return K;
}

long int asymmetric_pairs_distance(const ublas::matrix<int>& M1,const ublas::matrix<int>& M2,
				    const vector< vector<int> >& column_indices2)
{
  int mismatch=0;

  for(int column=0;column<M1.size1();column++) 
    for(int i=0;i<M1.size2();i++)
      for(int j=0;j<i;j++)
      {
	if (M1(column,i) == alphabet::unknown or M1(column,j) == alphabet::unknown)
	  continue;

	if (M1(column,i) != alphabet::gap or M1(column,j)!= alphabet::gap) {
	  if (not A_match(M1,column,i,j,M2,column_indices2)) 
          {
	    if (M1(column,i) != alphabet::gap)
	      mismatch++;
	    if (M1(column,j) != alphabet::gap)
	      mismatch++;
	  }
	}
      }

  return mismatch;
}

void initMatrix(ublas::matrix<T> &A, const T data[]) {
  for (unsigned int i = 0; i < A.size1(); i++) {
    for (unsigned int j = 0; j < A.size2(); j++) {
      A(i, j) = data[i * A.size2() + j];
    }
  }
}

ublas::vector<int> makeParityCheck(const ublas::vector<int> &dSource, const ublas::matrix<int> &H, const ublas::matrix<int> &L, const ublas::matrix<int> &U) {
  // Get matrix dimensions
  const unsigned int M = H.size1();
  const unsigned int N = H.size2();

  // Find B.dsource
  const ublas::vector<int> z(mod2(ublas::prod(ublas::subrange(H, 0, M, N - M, N), dSource)));

  //std::cout << "z=" << std::endl;
  //printVector<int>(z);

  //std::cout << "L=" << std::endl;
  //printMatrix<int>(L);

  //std::cout << "U=" << std::endl;
  //printMatrix<int>(U);

  // Parity check vector found by solving sparse LU
  const ublas::vector<int> x1(solve(L, z));
  //std::cout << "x1=" << std::endl;
  //printVector<int>(x1);

  const ublas::vector<int> x2(solve(U, x1));
  //std::cout << "x2=" << std::endl;
  //printVector<int>(x2);

  const ublas::vector<int> c(mod2(x2));

  return c;
}

void printMatrix(const ublas::matrix<T> &A) {
  for (unsigned int i = 0; i < A.size1(); i++) {
    for (unsigned int j = 0; j < A.size2(); j++) {
      std::cout << A(i, j);

      if (j + 1 < A.size2()) {
        std::cout << ", ";
      }
    }

    if (i + 1 < A.size1()) {
      std::cout << ";";
    }

    std::cout << std::endl;
  }
}

bool BenchmarkVienna<ScalarType>::is_equal(const ublas::matrix<ScalarType, orientation> &A,
                                           const ublas::matrix<ScalarType, orientation> &B) {
    for (std::size_t i = 0; i < A.size1(); ++i) {
        for (std::size_t j = 0; j < A.size2(); ++j) {
            if ( std::fabs(A(i,j) - B(i,j)) / B(i,j) > 1e-4 ) return false;
        }
    }
    return true;
}

int check_matrices(const ublas::matrix< ScalarType >& ref_mat, const ublas::matrix< ScalarType >& mat) {

  std::size_t size1, size2;
  ScalarType eps = 0.00001;
  size1 = ref_mat.size1(); size2 = ref_mat.size2();
  if( (size1 != mat.size1()) || (size2 != mat.size2()) )
    return EXIT_FAILURE;

  for (unsigned int i = 0; i < size1; i++)
    for (unsigned int j = 0; j < size2; j++)
      if ( abs(ref_mat(i,j) - mat(i,j)) > eps ) {
        std::cout << "!!Verification failed at " << i <<" : "<< j
                  << "(expected: " << ref_mat(i,j) << " get: " << mat(i,j) << " )" << std::endl;
        return EXIT_FAILURE;
      }

  std::cout << "Everything went well!" << std::endl;
  return EXIT_SUCCESS;
}