int uimon_out(const char *buffer)
{
const char *c;
for(c = buffer; *c; c++) {
if(*c == '\n') {
write_to_terminal(&fixed, "\r", 1);
}
write_to_terminal(&fixed, c, 1);
}
return 0;
}
void Verify::apply()
{
print_pre_info();
if(!_valid || _c == NULL)
{
std::cerr << "Verify not valid. Exiting" << std::endl;
return;
}
int steps = _strides;
int samples = _samples;
int N = _size;
if(_exp){
nr_links = stat::make_exponential_points_array( N, steps, START_POINT );
}else{
nr_links = stat::make_linear_points_array( N, steps, START_POINT );
}
link_mean = (nr_links.segment(0, steps) + nr_links.segment(1, steps)) / 2;
set_theoretical_values();
Eigen::ArrayXXd binned_chain = Eigen::ArrayXXd::Zero(steps,3*samples);
std::vector< std::vector<PFloat> > w = std::vector< std::vector<PFloat> >(steps);
for(int i = 0; i < steps; i++)
{
w[i] = std::vector<PFloat>(samples);
}
Eigen::ArrayXXd Rg_tmp = Eigen::ArrayXXd::Zero(steps,samples);
for(int i = 0; i < samples; i++)
{
_c->build(N);
// Vector containing the weight for each individual link
Eigen::VectorXd w_tmp = _c->weights();
// bin values
for(int j = 0; j<steps; j++)
{
Eigen::ArrayXXd sub_chain = _c->as_array( nr_links(j), nr_links(j+1)-nr_links(j) ).transpose();
binned_chain(j,3*i+0) = sub_chain.col(0).mean();
binned_chain(j,3*i+1) = sub_chain.col(1).mean();
binned_chain(j,3*i+2) = sub_chain.col(2).mean();
Rg_tmp(j,i) = _c->Rg(0,floor(link_mean(j)));
w[j][i] = mult_weights( w_tmp.segment(0, nr_links(j+1)) );
}
if(verbose)
{
write_to_terminal(N,i,steps);
}
}
Eigen::ArrayXXd R_tmp = Eigen::ArrayXXd::Zero(steps,samples);
R = Eigen::ArrayXd::Zero(steps);
R_var = Eigen::ArrayXd::Zero(steps);
Rg = Eigen::ArrayXd::Zero(steps);
Rg_var = Eigen::ArrayXd::Zero(steps);
for(int i = 0; i < steps; i++)
{
for(int j = 0; j < samples; j++)
{
Eigen::Vector3d pos = binned_chain.block(i,3*j,1,3).transpose();
R_tmp(i,j) = pos.norm();
}
}
for(int i = 0; i<steps; i++)
{
Eigen::Vector2d mv = stat::get_mean_and_variance(R_tmp.row(i), w[i]);
R(i) = mv(0);
R_var(i) = mv(1);
mv = stat::get_mean_and_variance(Rg_tmp.row(i), w[i]);
Rg(i) = mv(0);
Rg_var(i) = mv(1);
}
write_to_file();
print_post_info();
}