//Add masses before first isotope
void addPreisotopeWeights(const std::vector<double>& firstIsotopeMasses,
std::vector<std::pair<double, double> >& isotopeSpec, // output
UInt nrpeaks, double preIsotopePeaksWeight, // weight of pre isotope peaks
double mannmass, double charge)
{
for (std::size_t i = 0; i < firstIsotopeMasses.size(); ++i)
{
double mul = 1.;
for (UInt j = 0; j < nrpeaks; ++j, ++mul)
{
isotopeSpec.push_back(
std::make_pair(firstIsotopeMasses[i] - (mul * mannmass) / charge,
preIsotopePeaksWeight));
}
}
sortByFirst(isotopeSpec);
}
vector<pair<int,svlObject2d> > CallButtonEnhancer::clusterCandidateObjects(svlObject2dFrame &objects)
{
svlObject2dFrame detect_centroids;;
int numObjects = objects.size();
for (int i=0; i<numObjects; i++) {
detect_centroids.push_back(objects[i]);
}
double numRemoved = removeOverlappingObjects(detect_centroids, CLUSTER_OVERLAP);
cout << "Removed overlapping objects: " << numRemoved << " objects." << endl;
int numClusters = detect_centroids.size();
cout << "Number remaining: " << detect_centroids.size() << endl;
cout << "Number of clusters to use for Kmeans: " << numClusters << endl;
cout << "Number of objects passed to Kmeans: " << numObjects << endl;
// Find cluster centroids using Kmeans.
svlKMeansT<svlPoint2d> kmeans;
// Initialize point and centroid svlPoint2d vectors
vector<svlPoint2d> points;
vector<svlPoint2d> centroids;
double h_mean=0;
double w_mean=0;
for (int i=0; i<numObjects; i++) {
cout << "OBJECT " << i << "x = " << objects[i].x << " y = " << objects[i].y << " w = " << objects[i].w <<endl;
points.push_back(svlPoint2d(objects[i].x,objects[i].y));
w_mean += objects[i].w;
h_mean += objects[i].h;
}
h_mean = h_mean/numObjects;
w_mean = w_mean/numObjects;
double l_mean = (h_mean+w_mean)/2;
for (int i=0; i<numClusters; i++) {
centroids.push_back(svlPoint2d(detect_centroids[i].x,detect_centroids[i].y));
}
vector<int> cluster_idx;
kmeans.do_kmeans(points,centroids,&cluster_idx,numClusters,-1);
cout << "kmeans successful" << endl;
vector<pair<int,svlObject2d> > clusterCentroids;
for (int i=0; i<numClusters; i++) {
pair<int,svlObject2d> p;
p = make_pair(0,svlObject2d(centroids[i].x,centroids[i].y,l_mean,l_mean,0));
clusterCentroids.push_back(p);
}
for (int i=0; i<numClusters; i++) {
cout << "CENTROID " << i << "x = " << clusterCentroids[i].second.x << " y = " << clusterCentroids[i].second.y << " w = " << clusterCentroids[i].second.h <<endl;
for (int j=0; j<numObjects; j++) {
if(abs((objects[j].x + objects[j].w* 0.4 ) - (clusterCentroids[i].second.x + clusterCentroids[i].second.w* 0.4 )) < clusterCentroids[i].second.w * 0.4
&& abs((objects[j].y + objects[j].h* 0.4 ) - (clusterCentroids[i].second.y + clusterCentroids[i].second.w* 0.4 )) < clusterCentroids[i].second.h* 0.4 ){
clusterCentroids[i].first++;
}
if(abs((objects[j].x + objects[j].w* 0.4 ) - (clusterCentroids[i].second.x + clusterCentroids[i].second.w* 0.4 )) > clusterCentroids[i].second.w * 0.4
&& abs((objects[j].y + objects[j].h* 0.4 ) - (clusterCentroids[i].second.y + clusterCentroids[i].second.h* 0.4 )) < clusterCentroids[i].second.h* 0.4 ){
clusterCentroids[i].first-=2;
}
}
}
bool isAligned = false;
for (int i=0; i<numClusters; i++) {
isAligned=false;
for (int j=0; j<numClusters; j++) {
if(i!=j && abs(clusterCentroids[i].second.x - clusterCentroids[j].second.x) < clusterCentroids[i].second.w*0.4 &&
abs(clusterCentroids[i].second.y - clusterCentroids[j].second.y) < clusterCentroids[i].second.h*1.9 &&
abs(clusterCentroids[i].second.y - clusterCentroids[j].second.y) >= clusterCentroids[i].second.h*0.4){
isAligned = true;
break;
}
}
if(isAligned){
clusterCentroids[i].first+=5;
}
}
sortByFirst(clusterCentroids);
/*
for (int i=0; i<objects.size(); i++) {
clusterCentroids[cluster_idx[i]].second.x += objects[i].x;
clusterCentroids[cluster_idx[i]].second.y += objects[i].y;
clusterCentroids[cluster_idx[i]].second.w += objects[i].w;
clusterCentroids[cluster_idx[i]].second.h += objects[i].h;
clusterCentroids[cluster_idx[i]].second.pr += objects[i].pr;
clusterCentroids[cluster_idx[i]].first--;
//cout << objects[i].x << " " << objects[i].y << " " << cluster_idx[i] << endl;
}
for (int i=0; i<numClusters; i++) {
clusterCentroids[i].second.x /= -clusterCentroids[i].first;
clusterCentroids[i].second.y /= -clusterCentroids[i].first;
clusterCentroids[i].second.w /= -clusterCentroids[i].first;
clusterCentroids[i].second.h /= -clusterCentroids[i].first;
clusterCentroids[i].second.pr /= -clusterCentroids[i].first;
}
// sort cluster centroids in decreasing order by number of points in cluster.
// Change cluster count to positive numbers.
for (int i=0; i<numClusters; i++) {
clusterCentroids[i].first = -clusterCentroids[i].first;
//cout << clusterCentroids[i].x << " " << clusterCentroids[i].y << " "
// << clusterCentroids[i].w << " " << clusterCentroids[i].h << " "
// << clusterCentroids[i].pr << " " << clusterCentroids[i].n << endl;
}
*/
return clusterCentroids;
}
