float PhaseEstimator::EvaluateParameters(vector<BasecallerRead *>& useful_reads, DPTreephaser& treephaser, const float *parameters, const bool usePIDNorm)
{
float try_cf = parameters[0];
float try_ie = parameters[1];
float try_dr = parameters[2];
if (try_cf < 0 or try_ie < 0 or try_dr < 0 or try_cf > 0.04 or try_ie > 0.04 or try_dr > 0.01)
return 1e10;
treephaser.SetModelParameters(try_cf, try_ie, try_dr);
float metric = 0;
for (vector<BasecallerRead *>::iterator read = useful_reads.begin(); read != useful_reads.end(); ++read) {
treephaser.Simulate(**read, 120);
float normalizer = (usePIDNorm ? treephaser.PIDNormalize(**read, 8, 100) : treephaser.Normalize(**read, 20, 100));
for (unsigned int flow = 20; flow < 100 and flow < (*read)->raw_measurements.size(); flow++) {
if ((*read)->raw_measurements[flow] > 1.2)
continue;
float delta = (*read)->raw_measurements[flow] - (*read)->prediction[flow] * normalizer;
metric += delta * delta;
}
}
return isnan(metric) ? 1e10 : metric;
}
float PhaseEstimator::EvaluateParameters(vector<BasecallerRead *>& useful_reads, DPTreephaser& treephaser, const float *parameters)
{
float try_cf = parameters[0];
float try_ie = parameters[1];
float try_dr = parameters[2];
if (try_cf < 0 or try_ie < 0 or try_dr < 0 or try_cf > 0.04 or try_ie > 0.04 or try_dr > 0.01)
return 1e10;
treephaser.SetModelParameters(try_cf, try_ie, try_dr);
float metric = 0;
for (vector<BasecallerRead *>::iterator read = useful_reads.begin(); read != useful_reads.end(); ++read) {
// Simulate phasing parameter
treephaser.Simulate(**read, phasing_end_flow_+20);
// Optionally determine optimal normalization for this parameter set?
if (norm_during_param_eval_)
NormalizeBasecallerRead(treephaser, **read, phasing_start_flow_, phasing_end_flow_);
// Determine squared distance penalty for this parameter set
for (int flow = phasing_start_flow_; flow < phasing_end_flow_ and flow < (int)(*read)->raw_measurements.size(); ++flow) {
if ((*read)->raw_measurements[flow] > inclusion_threshold_)
continue;
// Keep key normalized raw measurements as a constant and normalize predictions towards key normalized values
float delta = ((*read)->normalized_measurements[flow] - (*read)->prediction[flow]) * (*read)->multiplicative_correction[flow];
metric += delta * delta;
}
}
return isnan(metric) ? 1e10 : metric;
}
float RegionAnalysis::evaluateParameters(std::vector<BasecallerRead> &dataAll, DPTreephaser& treephaser, float *parameters)
{
float metric = 0;
if (clo->cfe_control.libPhaseEstimator == "nel-mead-treephaser") {
if (parameters[0] < 0) // cf
metric = 1e10;
if (parameters[1] < 0) // ie
metric = 1e10;
if (parameters[2] < 0) // dr
metric = 1e10;
if (parameters[0] > 0.04) // cf
metric = 1e10;
if (parameters[1] > 0.04) // ie
metric = 1e10;
if (parameters[2] > 0.01) // dr
metric = 1e10;
if (metric == 0) {
treephaser.SetModelParameters(parameters[0], parameters[1], parameters[2]);
for (std::vector<BasecallerRead>::iterator data = dataAll.begin(); data != dataAll.end(); data++) {
treephaser.Simulate3(*data, 120);
data->Normalize(20, 100);
for (int iFlow = 20; iFlow < std::min(100, data->numFlows); iFlow++) {
if (data->measurements[iFlow] > 1.2)
continue;
float delta = data->measurements[iFlow] - data->prediction[iFlow] * data->miscNormalizer;
metric += delta * delta;
}
}
}
} else if (clo->cfe_control.libPhaseEstimator == "nel-mead-adaptive-treephaser") {
if (parameters[0] < 0) // cf
metric = 1e10;
if (parameters[1] < 0) // ie
metric = 1e10;
if (parameters[0] > 0.04) // cf
metric = 1e10;
if (parameters[1] > 0.04) // ie
metric = 1e10;
if (metric == 0) {
treephaser.SetModelParameters(parameters[0], parameters[1], 0);
for (std::vector<BasecallerRead>::iterator data = dataAll.begin(); data != dataAll.end(); data++) {
// treephaser.Simulate3(*data, 150);
// data->AdaptiveNormalizationOfPredictions(3, 50);
treephaser.Simulate3(*data, 200);
data->AdaptiveNormalizationOfPredictions(4, 50);
for (int iFlow = 25; iFlow < std::min(175, data->numFlows); iFlow++) {
if (data->measurements[iFlow] > 1.2)
continue;
float delta = data->measurements[iFlow] - data->prediction[iFlow];
metric += delta * delta;
}
}
}
}
// printf("CF = %1.2f%% IE = %1.2f%% DR = %1.2f%% V = %1.6f\n",
// 100*parameters[0], 100*parameters[1], 100*parameters[2], metric);
if (isnan(metric))
metric = 1e10;
return metric;
}
