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) {
struct arguments arguments;
/* Default values. */
arguments.verbose = 0;
arguments.outputFile = "out.cl";
arguments.cloudName = "";
arguments.volumeX = "";
arguments.volumeY = "";
arguments.volumeZ = "";
argp_parse (&argp, argc, argv, 0, 0, &arguments);
printf ("Cloud = %s\n OutputFile = %s\n",
arguments.cloudName.c_str(), arguments.outputFile.c_str());
//Code starts here
Cloud<Point3D>* cl = new Cloud<Point3D>(arguments.cloudName);
Cloud<Point3Do>* out = new Cloud<Point3Do>(arguments.outputFile);
Cube< float, double>* vx = new Cube<float, double>(arguments.volumeX);
Cube< float, double>* vy = new Cube<float, double>(arguments.volumeY);
Cube< float, double>* vz = new Cube<float, double>(arguments.volumeZ);
vector< int > idx(3);
vector< float > micr(3);
float theta, phi, r;
for(int i = 0; i < cl->points.size(); i++){
micr[0] = cl->points[i]->coords[0];
micr[1] = cl->points[i]->coords[1];
micr[2] = cl->points[i]->coords[2];
vx->micrometersToIndexes(micr, idx);
r = sqrt( vx->at(idx[0],idx[1],idx[2])*vx->at(idx[0],idx[1],idx[2]) +
vy->at(idx[0],idx[1],idx[2])*vy->at(idx[0],idx[1],idx[2]) +
vz->at(idx[0],idx[1],idx[2])*vz->at(idx[0],idx[1],idx[2]) );
theta = atan2(vy->at(idx[0],idx[1],idx[2]), vx->at(idx[0],idx[1],idx[2]));
phi = acos(vz->at(idx[0],idx[1],idx[2])/r);
Point3Do* pt = new Point3Do(micr[0], micr[1], micr[2],
theta, phi);
out->points.push_back(pt);
}
out->saveToFile(arguments.outputFile);
}
int main(int argc, char **argv) {
if(argc!=5)
{
printf("Usage: cubeAt volume_name x y z\n");
exit(0);
}
string volume_str = argv[1];
Cube<uchar,ulong>* cube_test = new Cube<uchar,ulong>(volume_str,false);
if(cube_test->type == "uchar"){
Cube<uchar,ulong>* cube = new Cube<uchar,ulong>(volume_str);
printf("%s ->at(%i, %i,%i) = %u\n", argv[1], atoi(argv[2]), atoi(argv[3]), atoi(argv[4]),
cube->at(atoi(argv[2]), atoi(argv[3]), atoi(argv[4])));
}
if(cube_test->type == "float"){
Cube<float,double>* cube = new Cube<float,double>(volume_str);
printf("%s ->at(%i, %i,%i) = %f\n", argv[1], atoi(argv[2]), atoi(argv[3]), atoi(argv[4]),
cube->at(atoi(argv[2]), atoi(argv[3]), atoi(argv[4])));
}
}
arma_inline elem_type at (const u32 row, const u32 col, const u32 slice) const { return Q.at(row, col, slice); }
inline
void
op_mean::apply_noalias_unwrap(Cube<typename T1::elem_type>& out, const ProxyCube<T1>& P, const uword dim)
{
arma_extra_debug_sigprint();
typedef typename T1::elem_type eT;
typedef typename get_pod_type<eT>::result T;
typedef typename ProxyCube<T1>::stored_type P_stored_type;
const unwrap_cube<P_stored_type> U(P.Q);
const Cube<eT>& X = U.M;
const uword X_n_rows = X.n_rows;
const uword X_n_cols = X.n_cols;
const uword X_n_slices = X.n_slices;
if(dim == 0)
{
out.set_size((X_n_rows > 0) ? 1 : 0, X_n_cols, X_n_slices);
if(X_n_rows == 0) { return; }
for(uword slice=0; slice < X_n_slices; ++slice)
{
eT* out_mem = out.slice_memptr(slice);
for(uword col=0; col < X_n_cols; ++col)
{
out_mem[col] = op_mean::direct_mean( X.slice_colptr(slice,col), X_n_rows );
}
}
}
else
if(dim == 1)
{
out.zeros(X_n_rows, (X_n_cols > 0) ? 1 : 0, X_n_slices);
if(X_n_cols == 0) { return; }
for(uword slice=0; slice < X_n_slices; ++slice)
{
eT* out_mem = out.slice_memptr(slice);
for(uword col=0; col < X_n_cols; ++col)
{
const eT* col_mem = X.slice_colptr(slice,col);
for(uword row=0; row < X_n_rows; ++row)
{
out_mem[row] += col_mem[row];
}
}
const Mat<eT> tmp('j', X.slice_memptr(slice), X_n_rows, X_n_cols);
for(uword row=0; row < X_n_rows; ++row)
{
out_mem[row] /= T(X_n_cols);
if(arma_isfinite(out_mem[row]) == false)
{
out_mem[row] = op_mean::direct_mean_robust( tmp, row );
}
}
}
}
else
if(dim == 2)
{
out.zeros(X_n_rows, X_n_cols, (X_n_slices > 0) ? 1 : 0);
if(X_n_slices == 0) { return; }
eT* out_mem = out.memptr();
for(uword slice=0; slice < X_n_slices; ++slice)
{
arrayops::inplace_plus(out_mem, X.slice_memptr(slice), X.n_elem_slice );
}
out /= T(X_n_slices);
podarray<eT> tmp(X_n_slices);
for(uword col=0; col < X_n_cols; ++col)
for(uword row=0; row < X_n_rows; ++row)
{
if(arma_isfinite(out.at(row,col,0)) == false)
{
for(uword slice=0; slice < X_n_slices; ++slice)
{
tmp[slice] = X.at(row,col,slice);
}
out.at(row,col,0) = op_mean::direct_mean_robust(tmp.memptr(), X_n_slices);
}
}
}
}
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");
}
}