/** Function get_seeds()
*
* Produce seeds: rID-> (s0, s1, s2...) for each fragment given two
* fq files f and f2
*/
void get_seeds (ii64vec_t& list_seeds, const std::string& f,
const std::string& f2, int seed_len, int batch, bool silent) {
std::ifstream fh, fh2;
xny::openfile<std::ifstream>(fh, f);
xny::openfile<std::ifstream>(fh2, f2);
bio::fastq_input_iterator<> fq(fh), end, fq2(fh2);
int total_read_pairs = 0;
strvec_t pairs;
while (fq != end && fq2 != end) {
add_fq_reads_only (pairs, batch/2, fq, end);
add_fq_reads_only (pairs, batch/2, fq2, end);
generate_seeds (list_seeds, pairs, seed_len);
total_read_pairs += pairs.size()/2;
pairs.clear();
} // while
if (!silent) {
std::cout << "\t\ttotal frags: " << total_read_pairs << "\n";
}
xny::closefile(fh);
xny::closefile(fh2);
} // get_seeds
void
Optimization::optimize()
{
tt.tic();
current_iteration = 0;
start_dist = 0.1;
current_dist = start_dist;
_current_seeds = 0;
while (max_iterations>current_iteration&&min_dist<dist_update) {
//emit emit_progress(0);
std::vector<Method_Coefficients> seeds = generate_seeds(this->coefficients_end);
for(std::vector<Method_Coefficients>::iterator kit = seeds.begin(); kit < seeds.end(); kit++)
{
Method_Coefficients seed = *kit;
make_coefficients_positive(seed);
WorkerSphereFollowing * worker = new WorkerSphereFollowing(1);
// worker->set_control(this->controller);
worker->setOptimize(shared_from_this());
worker->set_coefficients(seed);
worker->setA(coefficients_end.a);
worker->setB(coefficients_end.b);
worker->setFac(coefficients_end.fact);
worker->setMinRad(coefficients_end.minRad);
worker->setCloudPtr(_cloud_ptr);
worker->setTreeID(treeID);
worker->setIsStem(isStem);
this->start(worker);
}
current_iteration ++;
this->waitForDone();
end_dist = current_dist;
start_dist = end_dist;
update_sd();
coefficients_start = coefficients_end;
}
std::vector<float>
minRadii;
minRadii.push_back(0.015);
minRadii.push_back(0.02);
minRadii.push_back(0.025);
minRadii.push_back(0.03);
minRadii.push_back(0.035);
minRadii.push_back(0.04);
minRadii.push_back(0.045);
if(!qFuzzyCompare(coefficients_start.minRad,0.0025f))
{
for(std::vector<float>::iterator f_it = minRadii.begin(); f_it < minRadii.end(); f_it++)
{
float radius = *f_it;
WorkerSphereFollowing * worker = new WorkerSphereFollowing(1);
// worker->set_control(this->controller);
worker->setOptimize(shared_from_this());
worker->set_coefficients(coefficients_start);
worker->setA(coefficients_end.a);
worker->setB(coefficients_end.b);
worker->setFac(coefficients_end.fact);
worker->setMinRad(radius);
worker->setCloudPtr(_cloud_ptr);
worker->setTreeID(treeID);
worker->setIsStem(isStem);
this->start(worker);
}
}
this->waitForDone();
end_dist = current_dist;
start_dist = end_dist;
update_sd();
coefficients_start = coefficients_end;
}
