void MLBSTrackingFilter< NumImageFeatures >::ThreadedGenerateData(const InputImageRegionType ®ionForThread, ThreadIdType threadId)
{
m_Mutex.Lock();
m_Threads++;
m_Mutex.Unlock();
typedef ImageRegionConstIterator< ItkUcharImgType > MaskIteratorType;
MaskIteratorType sit(m_SeedImage, regionForThread );
MaskIteratorType mit(m_MaskImage, regionForThread );
sit.GoToBegin();
mit.GoToBegin();
itk::Point<double> worldPos;
while( !sit.IsAtEnd() )
{
if (sit.Value()==0 || mit.Value()==0)
{
++sit;
++mit;
continue;
}
for (int s=0; s<m_SeedsPerVoxel; s++)
{
FiberType fib;
double tractLength = 0;
typename FeatureImageType::IndexType index = sit.GetIndex();
itk::ContinuousIndex<double, 3> start;
unsigned int counter = 0;
if (m_SeedsPerVoxel>1)
{
start[0] = index[0]+GetRandDouble(-0.5, 0.5);
start[1] = index[1]+GetRandDouble(-0.5, 0.5);
start[2] = index[2]+GetRandDouble(-0.5, 0.5);
}
else
{
start[0] = index[0];
start[1] = index[1];
start[2] = index[2];
}
// get staring position
m_SeedImage->TransformContinuousIndexToPhysicalPoint( start, worldPos );
// get starting direction
int candidates = 0;
double prob = 0;
vnl_vector_fixed<double,3> dirOld; dirOld.fill(0.0);
vnl_vector_fixed<double,3> dir = Classify(worldPos, candidates, dirOld, 0, prob);
if (dir.magnitude()<0.0001)
continue;
// forward tracking
tractLength = FollowStreamline(threadId, worldPos, dir, &fib, 0, false);
fib.push_front(worldPos);
if (m_RemoveWmEndFibers)
{
itk::Point<double> check = fib.back();
dirOld.fill(0.0);
vnl_vector_fixed<double,3> check2 = GetNewDirection(check, dirOld);
if (check2.magnitude()>0.001)
{
MITK_INFO << "Detected WM ending. Discarding fiber.";
continue;
}
}
// backward tracking
tractLength = FollowStreamline(threadId, worldPos, -dir, &fib, tractLength, true);
counter = fib.size();
if (m_RemoveWmEndFibers)
{
itk::Point<double> check = fib.front();
dirOld.fill(0.0);
vnl_vector_fixed<double,3> check2 = GetNewDirection(check, dirOld);
if (check2.magnitude()>0.001)
{
MITK_INFO << "Detected WM ending. Discarding fiber.";
continue;
}
}
if (tractLength<m_MinTractLength || counter<2)
continue;
m_Mutex.Lock();
m_Tractogram.push_back(fib);
m_Mutex.Unlock();
if (m_AbortTracking)
break;
}
if (m_AbortTracking)
break;
++sit;
++mit;
}
m_Threads--;
std::cout << "Thread " << threadId << " finished tracking" << std::endl;
}
vnl_vector_fixed<double,3> MLBSTrackingFilter< ShOrder, NumImageFeatures >::GetNewDirection(itk::Point<double, 3> &pos, vnl_vector_fixed<double, 3>& olddir)
{
if (m_DemoMode)
{
m_SamplingPointset->Clear();
m_AlternativePointset->Clear();
}
vnl_vector_fixed<double,3> direction; direction.fill(0);
ItkUcharImgType::IndexType idx;
m_StoppingRegions->TransformPhysicalPointToIndex(pos, idx);
if (m_StoppingRegions->GetLargestPossibleRegion().IsInside(idx) && m_StoppingRegions->GetPixel(idx)>0)
return direction;
if (m_MaskImage.IsNotNull() && ((m_MaskImage->GetLargestPossibleRegion().IsInside(idx) && m_MaskImage->GetPixel(idx)<=0) || !m_MaskImage->GetLargestPossibleRegion().IsInside(idx)) )
return direction;
if (olddir.magnitude()>0)
olddir.normalize();
int candidates = 0; // number of directions with probability > 0
double w = 0; // weight of the direction predicted at each sampling point
if (IsValidPosition(pos))
{
direction = m_ForestHandler.Classify(pos, candidates, olddir, m_AngularThreshold, w, m_MaskImage); // get direction proposal at current streamline position
direction *= w; // HERE WE ARE WEIGHTING AGAIN EVEN THOUGH THE OUTPUT DIRECTIONS ARE ALREADY WEIGHTED!!! THE EFFECT OF THIS HAS YET TO BE EVALUATED.
}
itk::OrientationDistributionFunction< double, 50 > probeVecs;
itk::Point<double, 3> sample_pos;
int alternatives = 1;
for (int i=0; i<m_NumberOfSamples; i++)
{
vnl_vector_fixed<double,3> d;
if (m_RandomSampling)
{
d[0] = GetRandDouble();
d[1] = GetRandDouble();
d[2] = GetRandDouble();
d.normalize();
d *= GetRandDouble(0,m_SamplingDistance);
}
else
{
d = probeVecs.GetDirection(i)*m_SamplingDistance;
}
sample_pos[0] = pos[0] + d[0];
sample_pos[1] = pos[1] + d[1];
sample_pos[2] = pos[2] + d[2];
if(m_DemoMode)
m_SamplingPointset->InsertPoint(i, sample_pos);
candidates = 0;
vnl_vector_fixed<double,3> tempDir; tempDir.fill(0.0);
if (IsValidPosition(sample_pos))
tempDir = m_ForestHandler.Classify(sample_pos, candidates, olddir, m_AngularThreshold, w, m_MaskImage); // sample neighborhood
if (candidates>0 && tempDir.magnitude()>0.001)
{
direction += tempDir*w;
}
else if (m_AvoidStop && candidates==0 && olddir.magnitude()>0) // out of white matter
{
double dot = dot_product(d, olddir);
if (dot >= 0.0) // in front of plane defined by pos and olddir
d = -d + 2*dot*olddir; // reflect
else
d = -d; // invert
// look a bit further into the other direction
sample_pos[0] = pos[0] + d[0];
sample_pos[1] = pos[1] + d[1];
sample_pos[2] = pos[2] + d[2];
if(m_DemoMode)
m_AlternativePointset->InsertPoint(alternatives, sample_pos);
alternatives++;
candidates = 0;
vnl_vector_fixed<double,3> tempDir; tempDir.fill(0.0);
if (IsValidPosition(sample_pos))
tempDir = m_ForestHandler.Classify(sample_pos, candidates, olddir, m_AngularThreshold, w, m_MaskImage); // sample neighborhood
if (candidates>0 && tempDir.magnitude()>0.001) // are we back in the white matter?
{
direction += d; // go into the direction of the white matter
direction += tempDir*w; // go into the direction of the white matter direction at this location
}
}
}
if (direction.magnitude()>0.001)
{
direction.normalize();
olddir[0] = direction[0];
olddir[1] = direction[1];
olddir[2] = direction[2];
}
else
direction.fill(0);
return direction;
}
