void FibersFromPlanarFiguresFilter::GeneratePoints()
{
Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
randGen->SetSeed((unsigned int)0);
m_2DPoints.clear();
unsigned int count = 0;
while (count < m_Parameters.m_Density)
{
mitk::Vector2D p;
switch (m_Parameters.m_Distribution) {
case FiberGenerationParameters::DISTRIBUTE_GAUSSIAN:
p[0] = randGen->GetNormalVariate(0, m_Parameters.m_Variance);
p[1] = randGen->GetNormalVariate(0, m_Parameters.m_Variance);
break;
default:
p[0] = randGen->GetUniformVariate(-1, 1);
p[1] = randGen->GetUniformVariate(-1, 1);
}
if (sqrt(p[0]*p[0]+p[1]*p[1]) <= 1)
{
m_2DPoints.push_back(p);
count++;
}
}
}
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";
}
void GibbsTrackingFilter< ItkQBallImageType >::GenerateData()
{
TimeProbe preClock; preClock.Start();
// check if input is qball or tensor image and generate qball if necessary
if (m_QBallImage.IsNull() && m_TensorImage.IsNotNull())
{
TensorImageToQBallImageFilter<float,float>::Pointer filter = TensorImageToQBallImageFilter<float,float>::New();
filter->SetInput( m_TensorImage );
filter->Update();
m_QBallImage = filter->GetOutput();
}
else if (m_DuplicateImage) // generate local working copy of QBall image (if not disabled)
{
typedef itk::ImageDuplicator< ItkQBallImageType > DuplicateFilterType;
typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New();
duplicator->SetInputImage( m_QBallImage );
duplicator->Update();
m_QBallImage = duplicator->GetOutput();
}
// perform mean subtraction on odfs
typedef ImageRegionIterator< ItkQBallImageType > InputIteratorType;
InputIteratorType it(m_QBallImage, m_QBallImage->GetLargestPossibleRegion() );
it.GoToBegin();
while (!it.IsAtEnd())
{
itk::OrientationDistributionFunction<float, QBALL_ODFSIZE> odf(it.Get().GetDataPointer());
float mean = odf.GetMeanValue();
odf -= mean;
it.Set(odf.GetDataPointer());
++it;
}
// check if mask image is given if it needs resampling
PrepareMaskImage();
// load parameter file
LoadParameters();
// prepare parameters
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];
if(m_ParticleLength == 0)
m_ParticleLength = 1.5*minSpacing;
if(m_ParticleWidth == 0)
m_ParticleWidth = 0.5*minSpacing;
if(m_ParticleWeight == 0)
EstimateParticleWeight();
float alpha = log(m_EndTemperature/m_StartTemperature);
m_Steps = m_Iterations/10000;
if (m_Steps<10)
m_Steps = 10;
if (m_Steps>m_Iterations)
{
MITK_INFO << "GibbsTrackingFilter: not enough iterations!";
m_AbortTracking = true;
}
if (m_CurvatureThreshold < mitk::eps)
m_CurvatureThreshold = 0;
unsigned long singleIts = (unsigned long)((1.0*m_Iterations) / (1.0*m_Steps));
// seed random generators
Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
if (m_RandomSeed>-1)
randGen->SetSeed(m_RandomSeed);
else
randGen->SetSeed();
// load sphere interpolator to evaluate the ODFs
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.";
}
// initialize the actual tracking components (ParticleGrid, Metropolis Hastings Sampler and Energy Computer)
ParticleGrid* particleGrid;
GibbsEnergyComputer* encomp;
MetropolisHastingsSampler* sampler;
try{
particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity);
encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen);
encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential);
sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold);
}
catch(...)
{
MITK_ERROR << "Particle grid allocation failed. Not enough memory? Try to increase the particle length.";
m_IsInValidState = false;
m_AbortTracking = true;
m_BuildFibers = false;
return;
}
MITK_INFO << "----------------------------------------";
MITK_INFO << "Iterations: " << m_Iterations;
MITK_INFO << "Steps: " << m_Steps;
MITK_INFO << "Particle length: " << m_ParticleLength;
MITK_INFO << "Particle width: " << m_ParticleWidth;
MITK_INFO << "Particle weight: " << m_ParticleWeight;
MITK_INFO << "Start temperature: " << m_StartTemperature;
MITK_INFO << "End temperature: " << m_EndTemperature;
MITK_INFO << "In/Ex balance: " << m_InexBalance;
MITK_INFO << "Min. fiber length: " << m_MinFiberLength;
MITK_INFO << "Curvature threshold: " << m_CurvatureThreshold;
MITK_INFO << "Random seed: " << m_RandomSeed;
MITK_INFO << "----------------------------------------";
// main loop
preClock.Stop();
TimeProbe clock; clock.Start();
m_NumAcceptedFibers = 0;
unsigned long counter = 1;
boost::progress_display disp(m_Steps*singleIts);
if (!m_AbortTracking)
for( m_CurrentStep = 1; m_CurrentStep <= m_Steps; m_CurrentStep++ )
{
// update temperatur for simulated annealing process
float temperature = m_StartTemperature * exp(alpha*(((1.0)*m_CurrentStep)/((1.0)*m_Steps)));
sampler->SetTemperature(temperature);
for (unsigned long i=0; i<singleIts; i++)
{
++disp;
if (m_AbortTracking)
break;
sampler->MakeProposal();
if (m_BuildFibers || (i==singleIts-1 && m_CurrentStep==m_Steps))
{
m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter;
m_NumParticles = particleGrid->m_NumParticles;
m_NumConnections = particleGrid->m_NumConnections;
FiberBuilder fiberBuilder(particleGrid, m_MaskImage);
m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength);
m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines();
m_BuildFibers = false;
}
counter++;
}
m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter;
m_NumParticles = particleGrid->m_NumParticles;
m_NumConnections = particleGrid->m_NumConnections;
if (m_AbortTracking)
break;
}
if (m_AbortTracking)
{
FiberBuilder fiberBuilder(particleGrid, m_MaskImage);
m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength);
m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines();
}
clock.Stop();
delete sampler;
delete encomp;
delete interpolator;
delete particleGrid;
m_AbortTracking = true;
m_BuildFibers = false;
int h = clock.GetTotal()/3600;
int m = ((int)clock.GetTotal()%3600)/60;
int s = (int)clock.GetTotal()%60;
MITK_INFO << "GibbsTrackingFilter: finished gibbs tracking in " << h << "h, " << m << "m and " << s << "s";
m = (int)preClock.GetTotal()/60;
s = (int)preClock.GetTotal()%60;
MITK_INFO << "GibbsTrackingFilter: preparation of the data took " << m << "m and " << s << "s";
MITK_INFO << "GibbsTrackingFilter: " << m_NumAcceptedFibers << " fibers accepted";
// sampler->PrintProposalTimes();
SaveParameters();
}
