int main(int argc, char **argv) {
if(argc!=3){
printf("graphFindLeaves graph.gr leaves.cl\n");
exit(0);
}
Graph<Point3D, EdgeW<Point3D> >* gr =
new Graph<Point3D, EdgeW<Point3D> >(argv[1]);
Cloud<Point3D>* cl = new Cloud<Point3D>();
vector<int> pointsToAdd = gr->findLeaves();
for(int i = 0; i < pointsToAdd.size(); i++){
cl->addPoint(gr->cloud->points[pointsToAdd[i]]->coords[0],
gr->cloud->points[pointsToAdd[i]]->coords[1],
gr->cloud->points[pointsToAdd[i]]->coords[2]);
}
//Leaves are green
cl->v_r = 0;
cl->v_g = 1;
cl->v_b = 0;
cl->v_radius = 0.8;
cl->saveToFile(argv[2]);
}
int main(int argc, char **argv) {
vector<int> idxs(3);
vector<float> microm(3);
char buff[1024];
// For the color
const gsl_rng_type * T2;
gsl_rng * r;
gsl_rng_env_setup();
T2 = gsl_rng_default;
r = gsl_rng_alloc (T2);
// Cube<uchar, ulong>* cube = new Cube<uchar, ulong>("/media/neurons/cut2/cut2.nfo");
// Cloud_P* decimatedCloud = CloudFactory::load("/media/neurons/cut2/decimated.cl");
Cube<float, double>* cube = new Cube<float, double>
("/media/neurons/steerableFilters3D/tmp/cut/cut.nfo");
Cloud_P* decimatedCloud = CloudFactory::load
("/media/neurons/steerableFilters3D/tmp/cut/dense.cl");
Cloud<Point3D>* seedPointsSelected = new Cloud<Point3D>();
DistanceDijkstraColorNegatedEuclidean* djkc
= new DistanceDijkstraColorNegatedEuclidean(cube);
CubeLiveWire* cubeLiveWire = new CubeLiveWire(cube, djkc);;
vector<int> origIdxs(3);
origIdxs[0] = 151;
origIdxs[1] = 152;
origIdxs[2] = 9;
if(fileExists("/media/neurons/steerableFilters3D/tmp/cut/parents.nfo") &&
fileExists("/media/neurons/steerableFilters3D/tmp/cut/distances.nfo")){
printf("Loading the distances .... ");fflush(stdout);
cubeLiveWire->loadParents("/media/neurons/steerableFilters3D/tmp/cut/parents.nfo");
cubeLiveWire->loadDistances("/media/neurons/steerableFilters3D/tmp/cut/distances.nfo");
} else{
printf("Computing the distances .... ");fflush(stdout);
cubeLiveWire->computeDistances(origIdxs[0],origIdxs[1],origIdxs[2]);
cubeLiveWire->saveParents("parents");
cubeLiveWire->saveDistances("distances");
}
printf(" distances done \n");
multimap<float, Graph<Point3D, EdgeW<Point3D> >*> paths;
Cloud< Point3D>* cloud = new Cloud<Point3D>();
cube->indexesToMicrometers(origIdxs,microm);
cloud->addPoint(microm[0],microm[1],microm[2]);
cloud->v_g = 1.0;
cloud->v_radius = 2.0;
cloud->saveToFile("/media/neurons/steerableFilters3D/tmp/cut/original.cl");
float cost;
printf("Finding the shortest paths from all points to the soma[");fflush(stdout);
for(int i = 0; i < decimatedCloud->points.size(); i++){
cube->micrometersToIndexes3(decimatedCloud->points[i]->coords[0],
decimatedCloud->points[i]->coords[1],
decimatedCloud->points[i]->coords[2],
idxs[0],idxs[1],idxs[2]);
Graph<Point3D, EdgeW<Point3D> >* shortestPath =
cubeLiveWire->findShortestPathG(origIdxs[0],origIdxs[1],origIdxs[2],
idxs[0],idxs[1],idxs[2]
);
cost = shortestPath->cloud->points.size() -
cube->integralOverCloud(shortestPath->cloud);
paths.insert(pair<float, Graph<Point3D, EdgeW<Point3D> >*>
( exp(cost/(shortestPath->cloud->points.size())), shortestPath));
if(i%100 == 0) printf("%02f]\r",
float(i*100)/decimatedCloud->points.size());fflush(stdout);
}
printf("\n");
// Saves the paths according to the minimum mean distance
if(1){
int nGraphSaved = 0;
for(multimap< float, Graph<Point3D, EdgeW<Point3D> >*>::iterator
iter = paths.begin();
iter != paths.end();
iter++){
Graph<Point3D, EdgeW<Point3D> >* gr = (*iter).second;
sprintf(buff, "/media/neurons/steerableFilters3D/tmp/cut/opath%04i.gr",
nGraphSaved++);
gr->v_r = gsl_rng_uniform(r);
gr->v_g = gsl_rng_uniform(r);
gr->v_b = gsl_rng_uniform(r);
gr->v_radius = 0.3;
gr->cloud->v_r = gsl_rng_uniform(r);
gr->cloud->v_g = gsl_rng_uniform(r);
gr->cloud->v_b = gsl_rng_uniform(r);
gr->cloud->v_radius = 0.3;
gr->saveToFile(buff);
if(nGraphSaved%100 == 0)
printf("Saving the %i path with size %i\n", nGraphSaved, gr->cloud->points.size());
}
}
// Getting the first 100 paths
multimap< float, Graph<Point3D, EdgeW<Point3D> >*>::iterator
iter = paths.begin();
int cubeLength = cube->cubeDepth*cube->cubeHeight*cube->cubeWidth;
int* visited_orig = (int*) malloc(cubeLength*sizeof(int));
int*** visited;
visited = (int***) malloc(cube->cubeDepth*sizeof(int**));
for(int z = 0; z < cube->cubeDepth; z++){
visited [z] = (int**) malloc(cube->cubeHeight*sizeof(int*));
for(int j = 0; j < cube->cubeHeight; j++){
visited[z][j] =(int*) &visited_orig [(z*cube->cubeHeight + j)*cube->cubeWidth];
}
}
for(int i = 0; i < cubeLength; i++)
visited_orig[i] = 0;
int limitEnd = decimatedCloud->points.size()-1;
// int limitEnd = 500 ;
int nGraphsAdded = 0;
int nGraphsRejected = 0;
while(nGraphsAdded < limitEnd){
iter = paths.begin();
Graph<Point3D, EdgeW<Point3D> >* gr = (*iter).second;
int nPoint = 0;
bool alreadyVisited = false;
//Check if there is a visited part of the path
for(nPoint = 0; nPoint < gr->cloud->points.size(); nPoint++){
microm[0] = gr->cloud->points[nPoint]->coords[0];
microm[1] = gr->cloud->points[nPoint]->coords[1];
microm[2] = gr->cloud->points[nPoint]->coords[2];
cube->micrometersToIndexes(microm, idxs);
if(visited[idxs[2]][idxs[1]][idxs[0]] == true){
alreadyVisited = true;
break; // we reached a visited voxel
}
}
//If the path has been already visited, we better forget of the visited part
// and add a new graph to the list
if(alreadyVisited){
Graph<Point3D, EdgeW<Point3D> >* toAdd = gr->subGraphToPoint(nPoint);
cost = toAdd->cloud->points.size() -
cube->integralOverCloud(toAdd->cloud);
if(nGraphsRejected%100 == 0)
printf("Rejected %i paths\n", nGraphsRejected++);
fflush(stdout);
nGraphsRejected++;
paths.erase(paths.begin());
paths.insert(pair<float, Graph<Point3D, EdgeW<Point3D> >*>
(exp(cost/(toAdd->cloud->points.size())), toAdd));
} else {
for(int i = 0; i < gr->cloud->points.size(); i++){
microm[0] = gr->cloud->points[i]->coords[0];
microm[1] = gr->cloud->points[i]->coords[1];
microm[2] = gr->cloud->points[i]->coords[2];
if( (i==0) ||
((i == gr->cloud->points.size()-1)&&(i>0))
)
seedPointsSelected->points.push_back
(new Point3D(microm[0],microm[1],microm[2]));
cube->micrometersToIndexes(microm, idxs);
visited[idxs[2]][idxs[1]][idxs[0]] = true;
visited[origIdxs[2]][origIdxs[1]][origIdxs[0]] = false;
}
gr->v_r = gsl_rng_uniform(r);
gr->v_g = gsl_rng_uniform(r);
gr->v_b = gsl_rng_uniform(r);
gr->v_radius = 0.3;
gr->cloud->v_r = gsl_rng_uniform(r);
gr->cloud->v_g = gsl_rng_uniform(r);
gr->cloud->v_b = gsl_rng_uniform(r);
gr->cloud->v_radius = 0.3;
// cost = cube->integralOverCloud(gr->cloud)/gr->cloud->points.size();
sprintf(buff, "/media/neurons/steerableFilters3D/tmp/cut/path%04i.gr",nGraphsAdded);
nGraphsAdded++;
gr->saveToFile(buff);
if(nGraphsAdded%100 == 0)
printf("Adding the %i path with size %i\n", nGraphsAdded, gr->cloud->points.size());
paths.erase(paths.begin());
}
}//while
seedPointsSelected->v_r = 1;
seedPointsSelected->v_g = 0;
seedPointsSelected->v_b = 1;
seedPointsSelected->v_radius = 0.7;
seedPointsSelected->saveToFile("/media/neurons/steerableFilters3D/tmp/cut/seedPointsSelected.cl");
// Saves the visited points into a cube
Cube<int, long>* visitedC =
new Cube<int, long>(cube->cubeWidth, cube->cubeHeight, cube->cubeDepth,
cube->directory + "visited",
cube->voxelWidth, cube->voxelHeight, cube->voxelDepth);
for(int x = 0; x < cube->cubeWidth; x++)
for(int y = 0; y < cube->cubeHeight; y++)
for(int z = 0; z < cube->cubeDepth; z++){
visitedC->put(x,y,z, visited[z][y][x]);
}
}//main
