vector<Cross> createCrossingList()
{
vector<Cross> crosslist;
ParticleGrid<Particle>::GridArray *g = pcontainer.getVoxelGridArray();
for (int i = 0;i < g->gridsize;i++)
{
if (g->occnt[i] > 0)
{
for (int k = 0; k < g->occnt[i]; k++)
{
Particle *p1 = g->grid[g->csize*i+ k];
for (int j = k+1; j < g->occnt[i]; j++)
{
Particle *p2 = g->grid[g->csize*i+ j];
Cross x;
x.i = p1->label;
x.j = p2->label;
x.wi = p1->w;
x.wj = p2->w;
crosslist.push_back(x);
}
}
}
}
return crosslist;
}
// write out to MATLAB
void writeout(REAL *npoints)
{
for (int k = 0; k < pcontainer.pcnt; k++)
{
Particle *p = &(pcontainer.particles[k]);
npoints[attrcnt*k] = p->R.x;
npoints[attrcnt*k+1] = p->R.y;
npoints[attrcnt*k+2] = p->R.z;
npoints[attrcnt*k+3] = p->N.x;
npoints[attrcnt*k+4] = p->N.y;
npoints[attrcnt*k+5] = p->N.z;
npoints[attrcnt*k+6] = p->label;
npoints[attrcnt*k+7] = p->len;
npoints[attrcnt*k+8] = pcontainer.ID_2_index(p->mID);
npoints[attrcnt*k+9] = pcontainer.ID_2_index(p->pID);
npoints[attrcnt*k+10] = p->Di;
npoints[attrcnt*k+11] = p->Da;
npoints[attrcnt*k+12] = p->Dp;
npoints[attrcnt*k+13] = p->w;
npoints[attrcnt*k+14] = p->q;
}
}
void WriteOutParticles(float *npoints)
{
for (int k = 0; k < m_ParticleGrid.pcnt; k++)
{
Particle *p = &(m_ParticleGrid.particles[k]);
npoints[m_NumAttributes*k] = p->R.GetX();
npoints[m_NumAttributes*k+1] = p->R.GetY();
npoints[m_NumAttributes*k+2] = p->R.GetZ();
npoints[m_NumAttributes*k+3] = p->N.GetX();
npoints[m_NumAttributes*k+4] = p->N.GetY();
npoints[m_NumAttributes*k+5] = p->N.GetZ();
npoints[m_NumAttributes*k+6] = p->cap;
npoints[m_NumAttributes*k+7] = p->len;
npoints[m_NumAttributes*k+8] = m_ParticleGrid.ID_2_index(p->mID);
npoints[m_NumAttributes*k+9] = m_ParticleGrid.ID_2_index(p->pID);
}
}
void
GibbsTrackingFilter< ItkQBallImageType >
::EstimateParticleWeight()
{
MITK_INFO << "GibbsTrackingFilter: estimating particle weight";
float minSpacing;
if(m_QBallImage->GetSpacing()[0]<m_QBallImage->GetSpacing()[1] && m_QBallImage->GetSpacing()[0]<m_QBallImage->GetSpacing()[2])
minSpacing = m_QBallImage->GetSpacing()[0];
else if (m_QBallImage->GetSpacing()[1] < m_QBallImage->GetSpacing()[2])
minSpacing = m_QBallImage->GetSpacing()[1];
else
minSpacing = m_QBallImage->GetSpacing()[2];
float m_ParticleLength = 1.5*minSpacing;
float m_ParticleWidth = 0.5*minSpacing;
// seed random generators
Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
if (m_RandomSeed>-1)
randGen->SetSeed(m_RandomSeed);
else
randGen->SetSeed();
// instantiate all necessary components
SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath);
// handle lookup table not found cases
if( !interpolator->IsInValidState() )
{
m_IsInValidState = false;
m_AbortTracking = true;
m_BuildFibers = false;
mitkThrow() << "Unable to load lookup tables.";
}
ParticleGrid* particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity);
GibbsEnergyComputer* encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen);
// EnergyComputer* encomp = new EnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen);
MetropolisHastingsSampler* sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold);
float alpha = log(m_EndTemperature/m_StartTemperature);
m_ParticleWeight = 0.01;
int ppv = 0;
// main loop
int neededParts = 3000;
while (ppv<neededParts)
{
if (ppv<1000)
m_ParticleWeight /= 2;
else
m_ParticleWeight = ppv*m_ParticleWeight/neededParts;
encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential);
for( int step = 0; step < 10; step++ )
{
// update temperatur for simulated annealing process
float temperature = m_StartTemperature * exp(alpha*(((1.0)*step)/((1.0)*10)));
sampler->SetTemperature(temperature);
for (unsigned long i=0; i<10000; i++)
sampler->MakeProposal();
}
ppv = particleGrid->m_NumParticles;
particleGrid->ResetGrid();
}
delete sampler;
delete encomp;
delete particleGrid;
delete interpolator;
MITK_INFO << "GibbsTrackingFilter: finished estimating particle weight";
}
RJMCMCBase(float *points,int numPoints, float *dimg, const int *dsz, double *voxsize, double cellsize)
: m_QBallImageData(dimg)
, datasz(dsz)
, enc(0)
, width(dsz[1]*voxsize[0])
, height(dsz[2]*voxsize[1])
, depth(dsz[3]*voxsize[2])
, voxsize(voxsize)
, m_NumAttributes(0)
, m_AcceptedProposals(0)
{
fprintf(stderr,"Data dimensions (mm) : %f x %f x %f\n",width,height,depth);
fprintf(stderr,"Data dimensions (voxel) : %i x %i x %i\n",datasz[1],datasz[2],datasz[3]);
fprintf(stderr,"voxel size (mm) : %lf x %lf x %lf\n",voxsize[0],voxsize[1],voxsize[2]);
float cellcnt_x = (int)((float)width/cellsize) +1;
float cellcnt_y = (int)((float)height/cellsize) +1;
float cellcnt_z = (int)((float)depth/cellsize) +1;
//int cell_capacity = 2048;
//int cell_capacity = 64;
int cell_capacity = 512;
fprintf(stderr,"grid dimensions : %f x %f x %f\n",cellcnt_x,cellcnt_y,cellcnt_z);
fprintf(stderr,"grid cell size (mm) : %f^3\n",cellsize);
fprintf(stderr,"cell capacity : %i\n",cell_capacity);
fprintf(stderr,"#cells*cellcap : %.1f K\n",cell_capacity*cellcnt_x*cellcnt_y*cellcnt_z/1000);
int minsize = 1000000;
int err = m_ParticleGrid.allocate(((numPoints>minsize)? (numPoints+100000) : minsize), cellcnt_x, cellcnt_y, cellcnt_z, cellsize, cell_capacity);
if (err == -1)
{
fprintf(stderr,"RJMCMCBase: out of Memory!\n");
return;
}
m_NumAttributes = 10;
for (int k = 0; k < numPoints; k++)
{
Particle *p = m_ParticleGrid.newParticle(pVector(points[m_NumAttributes*k], points[m_NumAttributes*k+1],points[m_NumAttributes*k+2]));
if (p!=0)
{
p->N = pVector(points[m_NumAttributes*k+3],points[m_NumAttributes*k+4],points[m_NumAttributes*k+5]);
p->cap = points[m_NumAttributes*k+6];
p->len = points[m_NumAttributes*k+7];
p->mID = (int) points[m_NumAttributes*k+8];
p->pID = (int) points[m_NumAttributes*k+9];
if (p->mID != -1)
m_ParticleGrid.concnt++;
if (p->pID != -1)
m_ParticleGrid.concnt++;
p->label = 0;
}
else
{
fprintf(stderr,"error: cannot allocate particle, con. indices will be wrong! \n");
}
}
m_ParticleGrid.concnt /= 2;
m_Iterations = 0;
m_AcceptedProposals = 0;
}
RJMCMCBase(REAL *points,int numPoints, REAL *vfmap, REAL *dimg, const int *dsz, double *voxsize, double cellsize, REAL *cellsize2, REAL len, int numcores)
{
dataimg = dimg;
datasz = dsz;
this->vfmap = vfmap;
width = datasz[2]*voxsize[0];
height = datasz[3]*voxsize[1];
depth = datasz[4]*voxsize[2];
this->voxsize = voxsize;
this->numcores = numcores;
fprintf(stderr,"Data dimensions (mm) : %f x %f x %f\n",width,height,depth);
fprintf(stderr,"Data dimensions (voxel) : %i x %i x %i\n",datasz[2],datasz[3],datasz[4]);
fprintf(stderr,"Data directions (sizeLUT * dirs) : %i * %i\n",datasz[0],datasz[1]);
fprintf(stderr,"voxel size (mm) : %f x %f x %f\n",voxsize[0],voxsize[1],voxsize[2]);
////// dimensions of the particle grid
// the one to find connection partners
REAL cellcnt_x = (int)((REAL)width/cellsize) +2;
REAL cellcnt_y = (int)((REAL)height/cellsize) +2;
REAL cellcnt_z = (int)((REAL)depth/cellsize) +2;
int cell_capacity = 2048;
// for finding partners whithn the same voxel
REAL cellcnt_x2 = (int)((REAL)width/cellsize2[0]) +2;
REAL cellcnt_y2 = (int)((REAL)height/cellsize2[1]) +2;
REAL cellcnt_z2 = (int)((REAL)depth/cellsize2[2]) +2;
int cell_capacity2 = 20;
fprintf(stderr,"grid dimensions : %f x %f x %f\n",cellcnt_x,cellcnt_y,cellcnt_z);
fprintf(stderr,"grid cell size (mm) : %f^3\n",cellsize);
fprintf(stderr,"grid2 dimensions : %f x %f x %f\n",cellcnt_x2,cellcnt_y2,cellcnt_z2);
fprintf(stderr,"grid2 cell size (mm) : %fx%fx%f\n",cellsize2[0],cellsize2[1],cellsize2[2]);
fprintf(stderr,"cell capacity : %i\n",cell_capacity);
fprintf(stderr,"#cells*cellcap : %.1f K\n",cell_capacity*cellcnt_x*cellcnt_y*cellcnt_z/1000);
#ifdef PARALLEL_OPENMP
fprintf(stderr,"#threads : %i/%i\n",numcores,omp_get_max_threads());
#endif
// allocate the particle grid
int minsize = 100000;
int err = pcontainer.allocate(((numPoints>minsize)? (numPoints+100000) : minsize),
cellcnt_x, cellcnt_y, cellcnt_z, cellsize,cell_capacity,
cellcnt_x2, cellcnt_y2, cellcnt_z2, cellsize2,cell_capacity2,len);
if (err == -1)
{
fprintf(stderr,"RJMCMCBase: out of Memory!\n");
return;
}
// read the data from MATLAB into our structure
attrcnt = 15;
for (int k = 0; k < numPoints; k++)
{
Particle *p = pcontainer.newParticle(pVector(points[attrcnt*k ], points[attrcnt*k+1],points[attrcnt*k+2]),
pVector(points[attrcnt*k+3], points[attrcnt*k+4],points[attrcnt*k+5]));
if (p!=0)
{
p->N = pVector(points[attrcnt*k+3],points[attrcnt*k+4],points[attrcnt*k+5]);
p->len = points[attrcnt*k+7];
p->mID = (int) points[attrcnt*k+8];
p->pID = (int) points[attrcnt*k+9];
p->Di = points[attrcnt*k+10];
p->Da = points[attrcnt*k+11];
p->Dp = points[attrcnt*k+12];
p->w = points[attrcnt*k+13];
p->q = points[attrcnt*k+14];
p->label = 0;
p->active = true;
if (p->mID != -1)
{
pcontainer.removeFromGrid(1,p);
pcontainer.concnt++;
}
if (p->pID != -1)
{
pcontainer.removeFromGrid(0,p);
pcontainer.concnt++;
}
}
else
{
fprintf(stderr,"error: cannot allocate particle, con. indices will be wrong! \n");
}
}
pcontainer.concnt /= 2;
itmax = 0;
accepted = 0;
}
/////////////////////////////// the MAIN LOOP
void iterate(double handle)
{
#ifdef TIMING
tic(&total_time);
#endif
int frq = 500000; // number iteration between MATLAB calls of 'drawnow'
int numits;
int outer = 0;
REAL updownratio_break;
bool adaptiveschedule = false;
numits = (int) itmax;
if (frq > numits)
{
frq = numits;
outer = 1;
}
else
{
outer = numits/frq;
}
if (gammaDE != 0) // then we have an adative temp-schedule
{
REAL itmax_d = gammaDE;
stats.lam_deltaE = itmax_d;
birthstats.lam_deltaE = itmax_d;
deathstats.lam_deltaE = itmax_d;
shiftstats.lam_deltaE = itmax_d;
capstats.lam_deltaE = itmax_d;
vfstats.lam_deltaE = itmax_d;
connstats.lam_deltaE = itmax_d;
adaptiveschedule = true;
}
else
{
adaptiveschedule = false;
}
#ifdef PARALLEL_OPENMP
omp_set_dynamic(0); // Explicitly disable dynamic teams
omp_set_num_threads(numcores); // Use n threads for all consecutive parallel regions
#endif
#ifdef LINUX_MACHINE
static struct timeval timeS;
#endif
long time =0;
int f;
for (f = 0; f < outer;f++)
{
stats.clear();
birthstats.clear();
deathstats.clear();
connstats.clear();
shiftstats.clear();
capstats.clear();
vfstats.clear();
//fprintf(stderr,"parain\n"); fflush(stderr);
time = 0;
#ifdef LINUX_MACHINE
gettimeofday( &timeS, NULL);
time -= (timeS.tv_sec*1000000 + timeS.tv_usec);
#endif
#ifdef PARALLEL_OPENMP
#pragma omp parallel for
#endif
for (int it = 0; it < frq;it++)
{
if (!pcontainer.needs_reallocation)
iterate_onestep();
}
if (pcontainer.needs_reallocation)
{
if (pcontainer.reallocate() == -1)
{
fprintf(stderr,"out of Memory!!\n");
return;
}
}
#ifdef LINUX_MACHINE
gettimeofday( &timeS, NULL);
time += (timeS.tv_sec*1000000 + timeS.tv_usec);
#endif
fprintf(stderr,"#freeslots: %i pcnt:%i #particles:%i\n",
(int) pcontainer.freeslots.size(),(int) pcontainer.pcnt,(int)(pcontainer.pcnt-pcontainer.freeslots.size()));
pcontainer.defrag();
fprintf(stderr,"#it: %ik #p: %i #c: %i time: %.2fs \n", frq*(f+1)/1000, pcontainer.pcnt,pcontainer.concnt,double(time)/1000000);
stats.report_movetype(" total:");
char buf[256];
sprintf(buf,"birth (%.3f):",p_birth);
birthstats.report_movetype(buf);
sprintf(buf,"death (%.3f):",p_death);
deathstats.report_movetype(buf);
sprintf(buf,"shift (%.3f):",p_shift);
shiftstats.report_movetype(buf);
sprintf(buf,"model (%.3f):",p_Dmod);
capstats.report_movetype(buf);
sprintf(buf,"volfr (%.3f):",p_vfmod);
vfstats.report_movetype(buf);
sprintf(buf,"track (%.3f):",p_conprob);
connstats.report_movetype(buf);
REAL cr = (REAL) pcontainer.celloverflows;
if (cr > 0.01)
fprintf(stderr,"warning: celloverflows : %.2f \n",cr);
if (handle != 0)
{
mexEvalString("drawnow");
if (mexGet(handle,"Tag") == 0)
{
fprintf(stderr,"Termination by User.\n\n");
break;
}
}
accepted = 0;
if (adaptiveschedule && stats.deltaE < 0)
{
fprintf(stderr,"equilibrium threshold reached, breaking\n");
break;
}
}
iterations_done = (f+1)*frq; //it;
}
