string TrackedObject::getDataForUpdate(string inputVideoFile){
evaluateParameters();
stringstream outStream;
outStream << inputVideoFile << "," << firstFrame << "," << lastFrame << ",";
outStream << id << "," << speed << "," << intercept << "," << slope << "," << avgX << "," << avgY;
for (vector<int*>::iterator iter = positions.begin(); iter != positions.end(); ++iter){
outStream << "," << (*iter)[0] << "_" << (*iter)[1];
}
return outStream.str();
}
void RegionAnalysis::NelderMeadOptimization (std::vector<BasecallerRead> &dataAll, DPTreephaser& treephaser,
float *parameters, int numEvaluations, int numParameters)
{
int iEvaluation = 0;
//
// Step 1. Pick initial vertices, evaluate the function at vertices, and sort the vertices
//
float vertex[numParameters+1][numParameters];
float value[numParameters+1];
int order[numParameters+1];
for (int iVertex = 0; iVertex <= numParameters; iVertex++) {
for (int iParam = 0; iParam < numParameters; iParam++)
vertex[iVertex][iParam] = parameters[iParam];
switch (iVertex) {
case 0: // First vertex just matches the provided starting values
break;
case 1: // Second vertex has higher CF
vertex[iVertex][0] += 0.004;
break;
case 2: // Third vertex has higher IE
vertex[iVertex][1] += 0.004;
break;
case 3: // Fourth vertex has higher DR
vertex[iVertex][2] += 0.001;
break;
default: // Default for future parameters
vertex[iVertex][iVertex-1] *= 1.5;
break;
}
value[iVertex] = evaluateParameters(dataAll, treephaser, vertex[iVertex]);
iEvaluation++;
order[iVertex] = iVertex;
for (int xVertex = iVertex; xVertex > 0; xVertex--) {
if (value[order[xVertex]] < value[order[xVertex-1]]) {
int x = order[xVertex];
order[xVertex] = order[xVertex-1];
order[xVertex-1] = x;
}
}
}
// Main optimization loop
while (iEvaluation < numEvaluations) {
//
// Step 2. Attempt reflection (and possibly expansion)
//
float center[numParameters];
float reflection[numParameters];
int worst = order[numParameters];
int secondWorst = order[numParameters-1];
int best = order[0];
for (int iParam = 0; iParam < numParameters; iParam++) {
center[iParam] = 0;
for (int iVertex = 0; iVertex <= numParameters; iVertex++)
if (iVertex != worst)
center[iParam] += vertex[iVertex][iParam];
center[iParam] /= numParameters ;
reflection[iParam] = center[iParam] + NMalpha * (center[iParam] - vertex[worst][iParam]);
}
float reflectionValue = evaluateParameters(dataAll, treephaser, reflection);
iEvaluation++;
if (reflectionValue < value[best]) { // Consider expansion:
float expansion[numParameters];
for (int iParam = 0; iParam < numParameters; iParam++)
expansion[iParam] = center[iParam] + NMgamma * (center[iParam] - vertex[worst][iParam]);
float expansionValue = evaluateParameters(dataAll, treephaser, expansion);
iEvaluation++;
if (expansionValue < reflectionValue) { // Expansion indeed better than reflection
for (int iParam = 0; iParam < numParameters; iParam++)
reflection[iParam] = expansion[iParam];
reflectionValue = expansionValue;
}
}
if (reflectionValue < value[secondWorst]) { // Either reflection or expansion was successful
for (int iParam = 0; iParam < numParameters; iParam++)
vertex[worst][iParam] = reflection[iParam];
value[worst] = reflectionValue;
for (int xVertex = numParameters; xVertex > 0; xVertex--) {
if (value[order[xVertex]] < value[order[xVertex-1]]) {
int x = order[xVertex];
order[xVertex] = order[xVertex-1];
order[xVertex-1] = x;
}
}
continue;
}
//
// Step 3. Attempt contraction (reflection was unsuccessful)
//
float contraction[numParameters];
for (int iParam = 0; iParam < numParameters; iParam++)
contraction[iParam] = vertex[worst][iParam] + NMrho * (center[iParam] - vertex[worst][iParam]);
float contractionValue = evaluateParameters(dataAll, treephaser, contraction);
iEvaluation++;
if (contractionValue < value[worst]) { // Contraction was successful
for (int iParam = 0; iParam < numParameters; iParam++)
vertex[worst][iParam] = contraction[iParam];
value[worst] = contractionValue;
for (int xVertex = numParameters; xVertex > 0; xVertex--) {
if (value[order[xVertex]] < value[order[xVertex-1]]) {
int x = order[xVertex];
order[xVertex] = order[xVertex-1];
order[xVertex-1] = x;
}
}
continue;
}
//
// Step 4. Perform reduction (contraction was unsuccessful)
//
for (int iVertex = 1; iVertex <= numParameters; iVertex++) {
for (int iParam = 0; iParam < numParameters; iParam++)
vertex[order[iVertex]][iParam] = vertex[best][iParam] + NMsigma * (vertex[order[iVertex]][iParam] - vertex[best][iParam]);
value[order[iVertex]] = evaluateParameters(dataAll, treephaser, vertex[order[iVertex]]);
iEvaluation++;
for (int xVertex = iVertex; xVertex > 0; xVertex--) {
if (value[order[xVertex]] < value[order[xVertex-1]]) {
int x = order[xVertex];
order[xVertex] = order[xVertex-1];
order[xVertex-1] = x;
}
}
}
}
for (int iParam = 0; iParam < numParameters; iParam++)
parameters[iParam] = vertex[order[0]][iParam];
}
