void Annotator::update_color(MeshBundle<DefaultMesh>::Ptr m,const arma::uvec& label)
{
assert(m->mesh_.n_vertices()==label.size());
uint32_t* c = (uint32_t*)m->custom_color_.vertex_colors();
#pragma omp parallel for
for(int i=0;i<label.size();++i)
{
assert( l2c_.find(int(label(i))) != l2c_.end() );
c[i] = l2c_[ int(label(i)) ];
}
}
/**
* Add a random local matrix and rhs spanning over given rows and columns.
*
*/
void add(arma::uvec rows, arma::uvec cols) {
arma::mat loc_mat=arma::randu<arma::mat>(rows.size(), cols.size());
arma::vec loc_rhs=arma::randu<arma::vec>(rows.size());
// apply to full system
full_matrix_.submat(rows, cols)+=loc_mat;
full_rhs_.elem(rows)+=loc_rhs;
// apply to fixture system
arma::vec row_sol=dirichlet_values_.elem(rows);
arma::vec col_sol=dirichlet_values_.elem(cols);
auto i_rows=arma::conv_to<std::vector<int> >::from(
arma::conv_to<arma::ivec>::from(rows)%dirichlet_.elem(rows));
auto i_cols=arma::conv_to<std::vector<int> >::from(
arma::conv_to<arma::ivec>::from(cols)%dirichlet_.elem(cols));
//cout << "i_rows\n" << arma::ivec(i_rows);
//cout << "i_cols\n" << arma::ivec(i_cols);
this->set_values(i_rows, i_cols, loc_mat, loc_rhs, row_sol, col_sol);
// check consistency
double eps=4*arma::datum::eps;
// zero dirichlet rows and cols
//cout << "Dirich rows:\n" << dirichlet_rows_;
//cout << "matrix_:\n" << matrix_;
EXPECT_TRUE( arma::norm(matrix_.submat(dirichlet_rows_, non_dirichlet_rows_), "inf") < eps);
EXPECT_TRUE( arma::norm(matrix_.submat(non_dirichlet_rows_, dirichlet_rows_), "inf") < eps);
auto dirich_submat = matrix_.submat(dirichlet_rows_, dirichlet_rows_);
EXPECT_TRUE( arma::norm( dirich_submat - arma::diagmat(dirich_submat), "inf") < eps );
/*
// full check
arma::mat reduced_matrix_=full_matrix_;
auto dirich_cols=reduced_matrix_.submat(arma::span::all, dirichlet_rows_);
arma::vec reduced_rhs_=full_rhs_ - dirich_cols *dirichlet_values_;
dirich_cols.zeros();
reduced_matrix_.submat(dirichlet_rows_, arma::span::all).zeros();
reduced_matrix_.submat(dirichlet_rows_, dirichlet_rows_) = dirich_submat;
reduced_rhs_.subvec(dirichlet_rows_)=dirich_submat*dirichlet_values_;
EXPECT_TRUE( arma::all( abs(matrix_ - reduced_matrix_)<eps ) );
EXPECT_TRUE( arma::all( abs(rhs_ - reduced_rhs_)<eps ) );
*/
}
void SVMConfiguration::setSparseData(
arma::uvec rowptr,
arma::uvec colind,
arma::vec values,
size_t nrow,
size_t ncol,
bool one_indexed
) {
// rowind and colptr are one-indexed -- we are sad
if (one_indexed) {
for (size_t i=0; i < rowptr.size(); ++i) {
rowptr[i] -= 1;
}
for (size_t i=0; i < colind.size(); ++i) {
colind[i] -= 1;
}
}
// THIS IS TRICKY:
// we are using fact that CSR format for A is CSC format for A^T
this->sparse_data = arma::sp_mat(colind, rowptr, values, ncol, nrow);
}
void InPatchGraphCut::applyToFrame(const arma::uvec& gc_label,const arma::uvec& label_indices)
{
MeshBundle<DefaultMesh>& mesh = *meshes_[current_frame_];
arma::uvec& label = labels_[current_frame_];
arma::uvec patch_label;
current_patch_graph_->sv2pix(gc_label,patch_label);
if(patch_label.size()!=label_indices.size())std::logic_error("gc_label.size()!=label_indices.size()");
arma::uvec new_patch_indices = arma::find( patch_label==0 );
arma::uvec new_patch_value = label(label_indices);
new_patch_value(new_patch_indices).fill(0);
label(label_indices) = new_patch_value;
mesh.custom_color_.fromlabel(label);
}
/* Metropolis-Hastings updates of mu
* Updates are implemented simulateaneously for all biological genes
*/
arma::mat muUpdateNoSpikes(
arma::vec const& mu0,
arma::vec const& prop_var,
arma::mat const& Counts,
arma::vec const& invdelta,
arma::vec const& nu,
arma::vec const& sum_bycell_all,
double const& s2_mu,
int const& q0,
int const& n,
arma::vec & mu1,
arma::vec & u,
arma::vec & ind,
double const& Constrain,
int const& RefGene,
arma::uvec const& ConstrainGene,
arma::uvec const& NotConstrainGene,
int const& ConstrainType)
{
using arma::span;
int nConstrainGene = ConstrainGene.size();
int nNotConstrainGene = NotConstrainGene.size();
// PROPOSAL STEP
mu1 = exp(arma::randn(q0) % sqrt(prop_var) + log(mu0));
u = arma::randu(q0);
// INITIALIZE MU
double aux; double iAux;
double sumAux = sum(log(mu0.elem(ConstrainGene))) - log(mu0(RefGene));
// ACCEPT/REJECT STEP
// Step 1: Computing the likelihood contribution of the acceptance rate
// Calculated in the same way for all genes,
// but the reference one (no need to be sequential)
arma::vec log_aux = (log(mu1) - log(mu0)) % sum_bycell_all;
for (int i=0; i < q0; i++) {
if(i != RefGene) {
for (int j=0; j < n; j++) {
log_aux(i) -= ( Counts(i,j) + invdelta(i) ) *
log( ( nu(j)*mu1(i) + invdelta(i) ) /
( nu(j)*mu0(i) + invdelta(i) ));
}
}
}
// Step 2: Computing prior component of the acceptance rate
// Step 2.1: For genes that are under the constrain (excluding the reference one)
for (int i=0; i < nConstrainGene; i++) {
iAux = ConstrainGene(i);
if(iAux != RefGene) {
aux = 0.5 * (ConstrainGene.size() * Constrain - (sumAux - log(mu0(iAux))));
log_aux(iAux) -= (0.5 * 2 /s2_mu) * (pow(log(mu1(iAux)) - aux,2));
log_aux(iAux) += (0.5 * 2 /s2_mu) * (pow(log(mu0(iAux)) - aux,2));
// ACCEPT REJECT
if((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > 1e-3)) {
ind(iAux) = 1; sumAux += log(mu1(iAux)) - log(mu0(iAux));
}
else{ind(iAux) = 0; mu1(iAux) = mu0(iAux); }
}
}
// Step 2.2: For the reference gene
ind(RefGene) = 1;
mu1(RefGene) = exp(ConstrainGene.size() * Constrain - sumAux);
// Step 2.3: For genes that are *not* under the constrain
// Only relevant for a trimmed constrain
if(ConstrainType == 2) {
for (int i=0; i < nNotConstrainGene; i++) {
iAux = NotConstrainGene(i);
log_aux(iAux) -= (0.5/s2_mu) * (pow(log(mu1(iAux)),2) - pow(log(mu0(iAux)),2));
// ACCEPT REJECT
if((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > 1e-3)) { ind(iAux) = 1; }
else{ind(iAux) = 0; mu1(iAux) = mu0(iAux);}
}
}
// OUTPUT
return join_rows(mu1, ind);
}