int main(int argc, char **argv) {
if(argc!=5){
printf("Usage: cubeNonMaxSup cube.nfo theta.nfo phi.nfo output\n");
exit(0);
}
Cube< float, double>* orig = new Cube<float, double>(argv[1]);
Cube< float, double>* theta = new Cube<float, double>(argv[2]);
Cube< float, double>* phi = new Cube<float, double>(argv[3]);
Cube< float, double>* output;
// Cube< float, double>* outputOrient;
string outputName = argv[4];
// string outputOrientName = argv[5];
if(fileExists(outputName)){
output = new Cube<float, double>(outputName);
} else {
output = orig->duplicate_clean(outputName);
}
// if(fileExists(outputOrientName)){
// outputOrient = new Cube<float, double>(outputOrientName);
// } else {
// outputOrient = orig->duplicate_clean(outputOrientName);
// }
// Loop for all the voxels of the cube. For now we will ignore the borders
printf("Performing non-maxima-supression[");
#pragma omp parallel for
for(int z = 1; z < orig->cubeDepth -1; z++){
int currOrient = 0;
bool isMax = false;
for(int y = 1; y < orig->cubeHeight -1; y++){
for(int x = 1; x < orig->cubeWidth -1; x++){
isMax = true;
currOrient = computeOrientation(theta->at(x,y,z), phi->at(x,y,z));
// outputOrient->put(x,y,z,currOrient);
for(int neigh = 0; neigh < 8; neigh++){
if(orig->at(x+nbrToIdx[perpNeigh[currOrient][neigh]][0],
y+nbrToIdx[perpNeigh[currOrient][neigh]][1],
z+nbrToIdx[perpNeigh[currOrient][neigh]][2])
> orig->at(x,y,z)){
isMax = false;
break;
}
} //Neighbors
if(isMax){
output->put(x,y,z, orig->at(x,y,z));
}
}
}
printf("#"); fflush(stdout);
}
printf("]\n");
}
int main(int argc, char **argv) {
if(argc!=7) {
printf("Usage: kMSTanalyzeDir directory kInit kEnd kStep groundTruth.nfo pp.asc\n");
exit(0);
}
//string directory = "/home/ggonzale/mount/bbpsg1scratch/n2/3d/tree/";
string directory = argv[1];
Cube<uchar, ulong>* mask = new Cube<uchar, ulong>(argv[5]);
Cube<uchar, ulong>* rendered = new Cube<uchar, ulong>(argv[5], false);
rendered->load_volume_data("", false);
//Cube<uchar, ulong>* rendered = mask->duplicate_clean("rendered");
int kInit = atoi(argv[2]);;
int kEnd = atoi(argv[3]);
int kStep = atoi(argv[4]);
Neuron* gtNeuron = new Neuron(argv[6]);
char nameGraph[2048];
vector< vector< double > > toSave;
//Counts all the negative points in the ground truth
int negativePoints = 0;
for(int z = 0; z < mask->cubeDepth; z++)
for(int y = 0; y < mask->cubeHeight; y++)
for(int x = 0; x < mask->cubeWidth; x++)
if(mask->at(x,y,z) == 255)
negativePoints++;
double tp = 0;
double fp = 0;
double fn = 0;
if(0){
Cube<uchar, ulong>* rendered = mask->duplicate_clean("rendered");
sprintf(nameGraph, "%s/tree/kmsts/kmst%iw.gr", directory.c_str(), 725);
printf("%s\n", nameGraph);
Graph< Point3Dw, EdgeW<Point3Dw> >* gr =
new Graph< Point3Dw, EdgeW<Point3Dw> >(nameGraph);
evaluateGraph(directory, mask, rendered, gtNeuron, gr, tp, fp, fn);
}
if(0){
for(int k = kInit; k <=kEnd; k+=kStep){
tp = 0; fp = 0; fn = 0;
sprintf(nameGraph, "%s/tree/kmsts/kmst%iw.gr", directory.c_str(), k);
printf("%s\n", nameGraph);
Graph< Point3Dw, EdgeW<Point3Dw> >* gr =
new Graph< Point3Dw, EdgeW<Point3Dw> >(nameGraph);
evaluateGraph(directory, mask, rendered, gtNeuron, gr, tp, fp, fn);
vector< double > it(5);
double tn = negativePoints - fp;
it[0] = k; it[1] = tp; it[2] = fp; it[3] = tn; it[4] = fn;
toSave.push_back(it);
}
saveMatrix(toSave, directory + "/tree/kmsts/evaluation.txt");
}
//Evaluatoin of the mst
if(1){
toSave.resize(0);
sprintf(nameGraph, "%s/tree/mstFromCptGraphw.gr", directory.c_str());
printf("Evaluating the graph: %s\n", nameGraph);
tp = 0; fp = 0; fn = 0;
Graph< Point3Dw, EdgeW<Point3Dw> >* gr =
new Graph< Point3Dw, EdgeW<Point3Dw> >(nameGraph);
printf("Loaded the graph: %s\n", nameGraph);
evaluateGraph(directory, mask, rendered, gtNeuron, gr, tp, fp, fn);
vector< double > it(5);
double tn = negativePoints - fp;
it[0] = 0; it[1] = tp; it[2] = fp; it[3] = tn; it[4] = fn;
toSave.push_back(it);
saveMatrix(toSave, directory + "/tree/mstFromCptGraphwE.txt");
}
if(0){
toSave.resize(0);
sprintf(nameGraph, "%s/tree/mst/mstFromCptGraphPrunedw.gr", directory.c_str());
printf("Evaluating the graph: %s\n", nameGraph);
tp = 0; fp = 0; fn = 0;
Graph< Point3Dw, EdgeW<Point3Dw> >* gr =
new Graph< Point3Dw, EdgeW<Point3Dw> >(nameGraph);
printf("Loaded the graph: %s\n", nameGraph);
evaluateGraph(directory, mask, rendered, gtNeuron, gr, tp, fp, fn);
vector< double > it(5);
double tn = negativePoints - fp;
it[0] = 0; it[1] = tp; it[2] = fp; it[3] = tn; it[4] = fn;
toSave.push_back(it);
saveMatrix(toSave, directory + "/tree/mst/mstFromCptGraphwPrunedE.txt");
}
}