B row_min(const ublas::matrix<B>& M,int row)
{
B min=M(row,0);
for(int i=1;i<M.size2();i++)
min = std::min(min,M(row,i));
return min;
}
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 writeMatrix(const ublas::matrix<T> &A, const char *fileName) {
std::ofstream fout(fileName, std::ofstream::out);
for (unsigned int i = 0; i < A.size1(); i++) {
for (unsigned int j = 0; j < A.size2(); j++) {
fout << A(i, j);
if (j + 1 < A.size2()) {
fout << ",";
}
}
fout << std::endl;
}
fout.close();
}
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;
}
}
double compute_tv_21(int y,const ublas::matrix<double>& count1,const ublas::matrix<double>& count2)
{
y++;
double D=0;
assert(count1.size1() == count2.size1());
assert(count1.size2() == count2.size2());
for(int x=0;x<count1.size1();x++)
D += std::abs(count1(x,y)-count2(x,y));
D /= 2.0;
assert(D <= 1.0);
return D;
}
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;
}
/// Extract column @c from the index-matrix @M
vector<int> get_column(const ublas::matrix<int>& M, int c)
{
vector<int> column(M.size2(),-1);
for(int i=0;i<column.size();i++)
if (M(c,i) >= 0)
column[i] = M(c,i);
return column;
}
long int homologies_total(const ublas::matrix<int>& M1)
{
long int total=0;
for(int column=0;column<M1.size1();column++)
for(int i=0;i<M1.size2();i++)
if (M1(column,i) != alphabet::gap and M1(column,i) != alphabet::unknown)
total++;
return total;
}
/**
* @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;
}
}
int score(const ublas::matrix<int>& M1, const ublas::matrix<int>& M2, int c1, int c2)
{
assert(M1.size2() == M2.size2());
const int N = M1.size2();
int total = 0;
for(int i=0;i<N;i++)
{
if (M1(c1,i) == alphabet::unknown or M2(c2,i) == alphabet::unknown)
continue;
if (M1(c1,i) == alphabet::unknown or M2(c2,i) == alphabet::gap)
continue;
if (M1(c1,i) == M2(c2,i))
total++;
}
return total;
}
int check_matrices(const ublas::matrix< ScalarType >& ref_mat, const ublas::matrix< ScalarType >& mat, ScalarType eps) {
std::size_t size1, size2;
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++)
{
ScalarType rel_error = std::abs(ref_mat(i,j) - mat(i,j)) / std::max(std::abs(ref_mat(i,j)), std::abs(mat(i,j)));
if ( rel_error > eps ) {
std::cout << "ERROR: Verification failed at (" << i <<", "<< j << "): "
<< " Expected: " << ref_mat(i,j) << ", got: " << mat(i,j) << " (relative error: " << rel_error << ")" << std::endl;
return EXIT_FAILURE;
}
}
std::cout << "Everything went well!" << std::endl;
return EXIT_SUCCESS;
}
void ublas_to_vector(const ublas::matrix<float> &mat, std::vector<double> &vec)
{
vec.clear();
for (size_t i=0; i < mat.size1(); i++)
{
for (size_t j=0; j < mat.size2(); j++)
{
vec.push_back(mat(i,j));
}
}
}
long int homologies_preserved(const ublas::matrix<int>& M1,const ublas::matrix<int>& M2,
const vector< vector<int> >& column_indices2)
{
long int match=0;
long int mismatch=0;
for(int column=0;column<M1.size1();column++)
for(int i=0;i<M1.size2();i++)
if (M1(column,i) != alphabet::gap and M1(column,i) != alphabet::unknown)
for(int j=0;j<M1.size2();j++)
if (j != i) {
if (A_match(M1,column,i,j,M2,column_indices2))
match++;
else
mismatch++;
}
assert(homologies_total(M1) == homologies_total(M2));
assert(homologies_total(M1) == match + mismatch);
return match;
}
ublas::vector<double> mvnormpdf(const ublas::matrix<double>& x, const ublas::vector<double>& mu, const ublas::matrix<double>& Omega) {
//! Multivariate normal density
size_t p = x.size1();
size_t n = x.size2();
double f = sqrt(det(Omega))/pow(2.0*PI, p/2.0);
// cout << "O: " << Omega << "\n";
// cout << "f: " << f << "\n";
ublas::matrix<double> e(p, n);
e.assign(x - outer_prod(mu, ublas::scalar_vector<double>(n, 1)));
e = element_prod(e, prod(Omega, e));
return ublas::apply_to_all<functor::exp<double> > (-(ublas::matrix_sum(e, 0))/2.0)*f;
}
void reorderHMatrix(ublas::matrix<int> &H, ublas::matrix<int> &L, ublas::matrix<int> &U) {
// Get matrix dimensions
const unsigned int M = H.size1();
const unsigned int N = H.size2();
// Set a new matrix F for LU decomposition
ublas::matrix<int> F(H);
// Re-order the M x (N - M) submatrix
for (unsigned int i = 0; i < M; i++) {
int chosenCol = 0;
// Create diagonally structured matrix using 'First' strategy
for (unsigned int j = i; j < N; j++) {
if (F(i, j) != 0) {
chosenCol = j;
break;
}
}
//std::cout << "chosenCol=" << chosenCol << std::endl;
//printMatrix<int>(H);
// Re-ordering columns of F
const ublas::vector<int> tmp1(ublas::column(F, i));
ublas::column(F, i) = ublas::column(F, chosenCol);
ublas::column(F, chosenCol) = tmp1;
// Re-ordering columns of H
const ublas::vector<int> tmp2(ublas::column(H, i));
ublas::column(H, i) = ublas::column(H, chosenCol);
ublas::column(H, chosenCol) = tmp2;
// Fill the LU matrices column by column
ublas::subrange(L, i, M, i, i + 1) = ublas::subrange(F, i, M, i, i + 1);
ublas::subrange(U, 0, i + 1, i, i + 1) = ublas::subrange(F, 0, i + 1, i, i + 1);
// There will be no rows operation at the last row
if (i < M - 1) {
// Find the later rows with non-zero elements in column i
for (unsigned int k = i + 1; k < M; k++) {
if (F(k, i) != 0) {
// Add current row to the later rows which have a 1 in column i
ublas::row(F, k) = mod2(ublas::row(F, k) + ublas::row(F, i));
}
}
}
}
}
unsigned int rankUsingBoost( ublas::matrix<double>& U )
{
int numMols = U.size1();
int numReacs = U.size2() - numMols;
int i;
// Start out with a nonzero entry at 0,0
int leftCol = reorderRows( U, 0, 0 );
for ( i = 0; i < numMols - 1; ++i )
{
eliminateRowsBelow( U, i, leftCol );
leftCol = reorderRows( U, i + 1, leftCol );
if ( leftCol == numReacs )
break;
}
return i + 1;
}
bool UniGridApprox::WriteMatrix(ublas::matrix<double> M)
{
int row = M.size1();
int col = M.size2();
for (int i=0; i<row; ++i)
{
for (int j=0; j<col; ++j)
{
cout << M(i,j) << ", ";
}
cout << endl;
}
return true;
}
void PrintMatlab( const ublas::matrix<T> & M )
{
ofstream str( "Data/Mat.m" );
str << "function M = Mat()\n";
str << "% Create the matrix Mat in order to manipulate it in Matlab\n";
str << "M = [ ... \n";
for ( int_type i=0; i < M.size1() ; ++i )
{
for ( int_type j=0; j < M.size2() ; ++j )
str << M( i,j ) << " ";
str << "\n";
}
str <<"];\n";
str <<"\n return";
}
void eliminateRowsBelow( ublas::matrix< double >& U, int start, int leftCol )
{
int numMols = U.size1();
double pivot = U( start, leftCol );
assert( fabs( pivot ) > SteadyState::EPSILON );
for ( int i = start + 1; i < numMols; ++i )
{
double factor = U(i, leftCol);
if( fabs ( factor ) > SteadyState::EPSILON )
{
factor = factor / pivot;
for ( size_t j = leftCol + 1; j < U.size2(); ++j )
{
double x = U(i,j);
double y = U( start, j );
x -= y * factor;
if ( fabs( x ) < SteadyState::EPSILON )
x = 0.0;
U( i, j ) = x;
}
}
U(i, leftCol) = 0.0;
}
}
// ----------------------------------------------------------------------------
boost::numeric::ublas::vector<double>
LOGP(
const ublas::matrix<double> &A,
const ublas::matrix<double> &Xi_tmp,
const boost::numeric::ublas::vector<double> &y,
double weight,
const int iter)
{
ublas::matrix<double> Xi = Xi_tmp;
boost::numeric::ublas::vector<double> yA = prod(trans(A), y );
std::vector<unsigned int> foreach_array;
boost::numeric::ublas::vector<double> x( A.size2() ); // ret value
for(unsigned int i = 0; i != x.size(); ++i){
foreach_array.push_back( i );
x(i) = 0;
}
// -------------------------------------------------------
const auto compute_m = [&](
const unsigned int j,
const ublas::matrix<double> &A,
const ublas::matrix<double> &Xi,
const boost::numeric::ublas::vector<double> &y,
const boost::numeric::ublas::vector<double> &x
) -> double
{
double Xix = 0;
for(unsigned int i = 0; i != Xi.size2(); ++i)
if(i != j)
Xix += Xi(i,j) * x(i);
return (yA(j) - Xix) / Xi(j,j);
};
// -------------------------------------------------------
const auto compute_Delta = [&](
const double m_k,
const unsigned int k
) -> double
{
double Xix = 0;
for(unsigned int i = 0; i != Xi.size2(); ++i)
if(i != k)
Xix += Xi(i,k) * x(i);
const double logp = logPenalty( m_k );
return ((2 * yA(k) * m_k) + (Xi(k, k) * m_k * m_k) - (2 * m_k * Xix))/2 - weight * logp;
};
// -------------------------------------------------------
for(int it = 0; it != iter; ++it){
random_shuffle( foreach_array.begin(), foreach_array.end() );
for(auto ind = foreach_array.begin(); ind != foreach_array.end(); ++ind)
{
unsigned int j = *ind;
const double m = compute_m(j, A, Xi, y, x);
const double D = m * m - 4 * weight / Xi(j,j);
if(D < 0){
x(j) = 0;
}else{
const double tmp = m - weight / Xi(j,j)/ m;
const double delta = compute_Delta(tmp, j);
if(delta > 0){
x(j) = tmp;
}else{
x(j) = 0;
}
}
}
}
return x;
}
void ones(ublas::matrix<long double>& A)
{
for (size_t i = 0; i < A.size1(); ++i)
for (size_t j = 0; j < A.size2(); ++j)
A(i,j) = 1;
}
ublas::vector<int> decodeLogDomainSimple(const ublas::vector<double> &rx, const ublas::matrix<int> &H, const unsigned int iterations) {
// Get matrix dimensions
const unsigned int M = H.size1();
const unsigned int N = H.size2();
// Prior hard-decision
ublas::vector<double> Lci(rx.size());
for (unsigned int i = 0; i < rx.size(); i++) {
Lci(i) = -rx(i);
}
// Initialization
ublas::matrix<double> Lrji(ublas::zero_matrix<double>(M, N));
ublas::matrix<double> Pibetaij(ublas::zero_matrix<double>(M, N));
// Associate the L(ci) matrix with non-zero elements of H
ublas::matrix<double> Lqij(M, N);
for (unsigned int i = 0; i < M; i++) {
ublas::row(Lqij, i) = ublas::element_prod(ublas::row(H, i), Lci);
}
ublas::vector<int> vHat(N);
// Iteration
for (unsigned int n = 0; n < iterations; n++) {
//std::cout << "Iteration : " << n << std::endl;
// Get the sign and magnitude of L(qij)
ublas::matrix<int> alphaij(M, N);
ublas::matrix<double> betaij(M, N);
for (unsigned int i = 0; i < M; i++) {
for (unsigned int j = 0; j < N; j++) {
alphaij(i, j) = sign(Lqij(i, j));
betaij(i, j) = std::abs(Lqij(i, j));
}
}
// Horizontal step
for (unsigned int i = 0; i < M; i++) {
int prodOfalphaij = 1;
for (unsigned int j = 0; j < N; j++) {
if (H(i, j) != 0) {
prodOfalphaij *= alphaij(i, j);
}
}
// Get the minimum of betaij
for (unsigned int j = 0; j < N; j++) {
if (H(i, j) != 0) {
// Minimum of betaij
double minOfBetaij = std::numeric_limits<double>::max();
for (unsigned int k = 0; k < N; k++) {
if (j != k && H(i, k) != 0) {
if (betaij(i, k) < minOfBetaij) {
minOfBetaij = betaij(i, k);
}
}
}
// Multiplication alphaij
// Update L(rji)
Lrji(i, j) = prodOfalphaij * alphaij(i, j) * minOfBetaij;
}
}
}
// Vertical step
for (unsigned int j = 0; j < N; j++) {
double sumOfLrji = 0.0;
for (unsigned int i = 0; i < M; i++) {
if (H(i, j) != 0) {
sumOfLrji += Lrji(i, j);
}
}
for (unsigned int i = 0; i < M; i++) {
if (H(i, j) != 0) {
// Update L(qij) by summation of L(rij)
Lqij(i, j) = Lci(j) + sumOfLrji - Lrji(i, j);
}
}
// Get L(Qij)
double LQi = Lci(j) + sumOfLrji;
// Decode L(Qi)
if (LQi < 0) {
vHat(j) = 1;
} else {
vHat(j) = 0;
}
}
}
return vHat;
}
ublas::vector<int> decodeBitFlipping(const ublas::vector<double> &rx, const ublas::matrix<int> &H, const unsigned int iterations) {
// Get matrix dimensions
const unsigned int M = H.size1();
const unsigned int N = H.size2();
// Prior hard-decision
ublas::vector<int> ci(rx.size());
for (unsigned int i = 0; i < rx.size(); i++) {
ci(i) = 0.5 * (sign(rx(i)) + 1);
}
//std::cout << "ci=" << std::endl;
//printVector<int>(ci);
// Initialization
ublas::matrix<int> rji(ublas::zero_matrix<int>(M, N));
// Associate the ci matrix with non-zero elements of H
ublas::matrix<int> qij(M, N);
for (unsigned int i = 0; i < M; i++) {
ublas::row(qij, i) = ublas::element_prod(ublas::row(H, i), ci);
}
//std::cout << "qij=" << std::endl;
//printMatrix<int>(qij);
ublas::vector<int> vHat(N);
// Iteration
for (unsigned int n = 0; n < iterations; n++) {
//std::cout << "Iteration : " << n << std::endl;
// Horizontal step
for (unsigned int i = 0; i < M; i++) {
int qijSum = 0;
for (unsigned int j = 0; j < N; j++) {
if (H(i, j) != 0) {
qijSum += qij(i, j);
}
}
for (unsigned int j = 0; j < N; j++) {
if (H(i, j) != 0) {
rji(i, j) = (qijSum + qij(i, j)) % 2;
}
}
}
// Vertical step
for (unsigned int j = 0; j < N; j++) {
int rjiNumberOfOnes = 0;
for (unsigned int i = 0; i < M; i++) {
if (rji(i, j) != 0) {
rjiNumberOfOnes++;
}
}
int hNumberOfOnes = 0;
for (unsigned int i = 0; i < M; i++) {
if (H(i, j) != 0) {
hNumberOfOnes++;
}
}
for (unsigned int i = 0; i < M; i++) {
if (H(i, j) != 0) {
// Update qij, set '1' for majority of 1s else '0', excluding i
if (rjiNumberOfOnes + ci(j) >= hNumberOfOnes - rjiNumberOfOnes + rji(i, j)) {
qij(i, j) = 1;
} else {
qij(i, j) = 0;
}
}
}
// Bit decoding
if (rjiNumberOfOnes + ci(j) >= hNumberOfOnes - rjiNumberOfOnes) {
vHat(j) = 1;
} else {
vHat(j) = 0;
}
}
}
return vHat;
}