TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths)
{
DirectionContainerType::Pointer outDirs = DirectionContainerType::New();
if (inDirs->size()<2)
{
if (inDirs->size()==1)
inDirs->SetElement(0, inDirs->at(0)*lengths.at(0));
return inDirs;
}
DirectionType oldMean, currentMean;
std::vector< int > touched;
// initialize
touched.resize(inDirs->size(), 0);
bool free = true;
currentMean = inDirs->at(0); // initialize first seed
currentMean.normalize();
double length = lengths.at(0);
touched[0] = 1;
std::vector< double > newLengths;
bool meanChanged = false;
double max = 0;
while (free)
{
oldMean.fill(0.0);
// start mean-shift clustering
double angle = 0;
while (fabs(dot_product(currentMean, oldMean))<0.99)
{
oldMean = currentMean;
currentMean.fill(0.0);
for (unsigned int i=0; i<inDirs->size(); i++)
{
angle = dot_product(oldMean, inDirs->at(i));
if (angle>=m_AngularThreshold)
{
currentMean += inDirs->at(i);
if (meanChanged)
length += lengths.at(i);
touched[i] = 1;
meanChanged = true;
}
else if (-angle>=m_AngularThreshold)
{
currentMean -= inDirs->at(i);
if (meanChanged)
length += lengths.at(i);
touched[i] = 1;
meanChanged = true;
}
}
if(!meanChanged)
currentMean = oldMean;
else
currentMean.normalize();
}
// found stable mean
outDirs->push_back(currentMean);
newLengths.push_back(length);
if (length>max)
max = length;
// find next unused seed
free = false;
for (unsigned int i=0; i<touched.size(); i++)
if (touched[i]==0)
{
currentMean = inDirs->at(i);
free = true;
meanChanged = false;
length = lengths.at(i);
touched[i] = 1;
break;
}
}
if (inDirs->size()==outDirs->size())
{
if (max>0)
{
for (unsigned int i=0; i<outDirs->size(); i++)
outDirs->SetElement(i, outDirs->at(i)*newLengths.at(i));
}
return outDirs;
}
else
return FastClustering(outDirs, newLengths);
}
void TractsToVectorImageFilter< PixelType >::GenerateData()
{
mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry();
// calculate new image parameters
itk::Vector<double> spacing3;
itk::Point<double> origin3;
itk::Matrix<double, 3, 3> direction3;
ImageRegion<3> imageRegion3;
if (!m_MaskImage.IsNull())
{
spacing3 = m_MaskImage->GetSpacing();
imageRegion3 = m_MaskImage->GetLargestPossibleRegion();
origin3 = m_MaskImage->GetOrigin();
direction3 = m_MaskImage->GetDirection();
}
else
{
spacing3 = geometry->GetSpacing();
origin3 = geometry->GetOrigin();
mitk::BaseGeometry::BoundsArrayType bounds = geometry->GetBounds();
origin3[0] += bounds.GetElement(0);
origin3[1] += bounds.GetElement(2);
origin3[2] += bounds.GetElement(4);
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
direction3[j][i] = geometry->GetMatrixColumn(i)[j];
imageRegion3.SetSize(0, geometry->GetExtent(0)+1);
imageRegion3.SetSize(1, geometry->GetExtent(1)+1);
imageRegion3.SetSize(2, geometry->GetExtent(2)+1);
m_MaskImage = ItkUcharImgType::New();
m_MaskImage->SetSpacing( spacing3 );
m_MaskImage->SetOrigin( origin3 );
m_MaskImage->SetDirection( direction3 );
m_MaskImage->SetRegions( imageRegion3 );
m_MaskImage->Allocate();
m_MaskImage->FillBuffer(1);
}
OutputImageType::RegionType::SizeType outImageSize = imageRegion3.GetSize();
m_OutImageSpacing = m_MaskImage->GetSpacing();
m_ClusteredDirectionsContainer = ContainerType::New();
// initialize num directions image
m_NumDirectionsImage = ItkUcharImgType::New();
m_NumDirectionsImage->SetSpacing( spacing3 );
m_NumDirectionsImage->SetOrigin( origin3 );
m_NumDirectionsImage->SetDirection( direction3 );
m_NumDirectionsImage->SetRegions( imageRegion3 );
m_NumDirectionsImage->Allocate();
m_NumDirectionsImage->FillBuffer(0);
itk::Vector<double, 4> spacing4;
itk::Point<float, 4> origin4;
itk::Matrix<double, 4, 4> direction4;
itk::ImageRegion<4> imageRegion4;
spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin3[3] = 0;
for (int r=0; r<3; r++)
for (int c=0; c<3; c++)
direction4[r][c] = direction3[r][c];
direction4[3][3] = 1;
imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
imageRegion4.SetSize(3, m_MaxNumDirections*3);
m_DirectionImage = ItkDirectionImageType::New();
m_DirectionImage->SetSpacing( spacing4 );
m_DirectionImage->SetOrigin( origin4 );
m_DirectionImage->SetDirection( direction4 );
m_DirectionImage->SetRegions( imageRegion4 );
m_DirectionImage->Allocate();
m_DirectionImage->FillBuffer(0.0);
// iterate over all fibers
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
int numFibers = m_FiberBundle->GetNumFibers();
m_DirectionsContainer = ContainerType::New();
VectorContainer< unsigned int, std::vector< double > >::Pointer peakLengths = VectorContainer< unsigned int, std::vector< double > >::New();
MITK_INFO << "Generating directions from tractogram";
boost::progress_display disp(numFibers);
for( int i=0; i<numFibers; i++ )
{
++disp;
vtkCell* cell = fiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (numPoints<2)
continue;
vnl_vector_fixed<double, 3> dir;
vnl_vector<double> v;
float fiberWeight = m_FiberBundle->GetFiberWeight(i);
for( int j=0; j<numPoints-1; j++)
{
itk::Point<float, 3> startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
itk::Index<3> startIndex;
itk::ContinuousIndex<float, 3> startIndexCont;
m_MaskImage->TransformPhysicalPointToIndex(startVertex, startIndex);
m_MaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
itk::Point<float, 3> endVertex = mitk::imv::GetItkPoint(points->GetPoint(j + 1));
itk::Index<3> endIndex;
itk::ContinuousIndex<float, 3> endIndexCont;
m_MaskImage->TransformPhysicalPointToIndex(endVertex, endIndex);
m_MaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
dir[0] = endVertex[0]-startVertex[0];
dir[1] = endVertex[1]-startVertex[1];
dir[2] = endVertex[2]-startVertex[2];
if (dir.is_zero())
continue;
dir.normalize();
std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing3, startIndex, endIndex, startIndexCont, endIndexCont);
for (std::pair< itk::Index<3>, double > segment : segments)
{
if (!m_MaskImage->GetLargestPossibleRegion().IsInside(segment.first) || (!m_OnlyUseMaskGeometry && m_MaskImage->GetPixel(segment.first)==0))
continue;
// add direction to container
unsigned int idx = segment.first[0] + outImageSize[0]*(segment.first[1] + outImageSize[1]*segment.first[2]);
DirectionContainerType::Pointer dirCont;
if (m_DirectionsContainer->IndexExists(idx))
{
peakLengths->ElementAt(idx).push_back(fiberWeight*segment.second);
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->push_back(dir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->push_back(dir);
}
else
{
dirCont = DirectionContainerType::New();
dirCont->push_back(dir);
m_DirectionsContainer->InsertElement(idx, dirCont);
std::vector< double > lengths; lengths.push_back(fiberWeight*segment.second);
peakLengths->InsertElement(idx, lengths);
}
}
}
}
itk::ImageRegionIterator<ItkUcharImgType> dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion());
MITK_INFO << "Clustering directions";
float max_dir_mag = 0;
boost::progress_display disp2(outImageSize[0]*outImageSize[1]*outImageSize[2]);
while(!dirIt.IsAtEnd())
{
++disp2;
OutputImageType::IndexType idx3 = dirIt.GetIndex();
int idx_lin = idx3[0]+(idx3[1]+idx3[2]*outImageSize[1])*outImageSize[0];
itk::Index<4> idx4; idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2];
if (!m_DirectionsContainer->IndexExists(idx_lin))
{
++dirIt;
continue;
}
DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx_lin);
if (dirCont.IsNull() || dirCont->empty())
{
++dirIt;
continue;
}
DirectionContainerType::Pointer directions;
if (m_MaxNumDirections>0)
{
directions = FastClustering(dirCont, peakLengths->GetElement(idx_lin));
std::sort( directions->begin(), directions->end(), CompareVectorLengths );
}
else
directions = dirCont;
unsigned int numDir = directions->size();
if (m_MaxNumDirections>0 && numDir>m_MaxNumDirections)
numDir = m_MaxNumDirections;
float voxel_max_mag = 0;
for (unsigned int i=0; i<numDir; i++)
{
DirectionType dir = directions->at(i);
float mag = dir.magnitude();
if (mag>voxel_max_mag)
voxel_max_mag = mag;
if (mag>max_dir_mag)
max_dir_mag = mag;
}
int count = 0;
for (unsigned int i=0; i<numDir; i++)
{
DirectionType dir = directions->at(i);
count++;
float mag = dir.magnitude();
if (m_NormalizationMethod==MAX_VEC_NORM && voxel_max_mag>mitk::eps)
dir /= voxel_max_mag;
else if (m_NormalizationMethod==SINGLE_VEC_NORM && mag>mitk::eps)
dir.normalize();
for (unsigned int j = 0; j<3; j++)
{
idx4[3] = i*3 + j;
m_DirectionImage->SetPixel(idx4, dir[j]);
}
}
dirIt.Set(count);
++dirIt;
}
if (m_NormalizationMethod==GLOBAL_MAX && max_dir_mag>0)
{
itk::ImageRegionIterator<ItkDirectionImageType> dirImgIt(m_DirectionImage, m_DirectionImage->GetLargestPossibleRegion());
while(!dirImgIt.IsAtEnd())
{
dirImgIt.Set(dirImgIt.Get()/max_dir_mag);
++dirImgIt;
}
}
}
void TractsToVectorImageFilter< PixelType >::GenerateData()
{
mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry();
// calculate new image parameters
itk::Vector<double> spacing;
itk::Point<double> origin;
itk::Matrix<double, 3, 3> direction;
ImageRegion<3> imageRegion;
if (!m_MaskImage.IsNull())
{
spacing = m_MaskImage->GetSpacing();
imageRegion = m_MaskImage->GetLargestPossibleRegion();
origin = m_MaskImage->GetOrigin();
direction = m_MaskImage->GetDirection();
}
else
{
spacing = geometry->GetSpacing();
origin = geometry->GetOrigin();
mitk::BaseGeometry::BoundsArrayType bounds = geometry->GetBounds();
origin[0] += bounds.GetElement(0);
origin[1] += bounds.GetElement(2);
origin[2] += bounds.GetElement(4);
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
direction[j][i] = geometry->GetMatrixColumn(i)[j];
imageRegion.SetSize(0, geometry->GetExtent(0));
imageRegion.SetSize(1, geometry->GetExtent(1));
imageRegion.SetSize(2, geometry->GetExtent(2));
m_MaskImage = ItkUcharImgType::New();
m_MaskImage->SetSpacing( spacing );
m_MaskImage->SetOrigin( origin );
m_MaskImage->SetDirection( direction );
m_MaskImage->SetRegions( imageRegion );
m_MaskImage->Allocate();
m_MaskImage->FillBuffer(1);
}
OutputImageType::RegionType::SizeType outImageSize = imageRegion.GetSize();
m_OutImageSpacing = m_MaskImage->GetSpacing();
m_ClusteredDirectionsContainer = ContainerType::New();
// initialize num directions image
m_NumDirectionsImage = ItkUcharImgType::New();
m_NumDirectionsImage->SetSpacing( spacing );
m_NumDirectionsImage->SetOrigin( origin );
m_NumDirectionsImage->SetDirection( direction );
m_NumDirectionsImage->SetRegions( imageRegion );
m_NumDirectionsImage->Allocate();
m_NumDirectionsImage->FillBuffer(0);
// initialize direction images
m_DirectionImageContainer = DirectionImageContainerType::New();
// resample fiber bundle
double minSpacing = 1;
if(m_OutImageSpacing[0]<m_OutImageSpacing[1] && m_OutImageSpacing[0]<m_OutImageSpacing[2])
minSpacing = m_OutImageSpacing[0];
else if (m_OutImageSpacing[1] < m_OutImageSpacing[2])
minSpacing = m_OutImageSpacing[1];
else
minSpacing = m_OutImageSpacing[2];
if (m_UseWorkingCopy)
m_FiberBundle = m_FiberBundle->GetDeepCopy();
// resample fiber bundle for sufficient voxel coverage
m_FiberBundle->ResampleSpline(minSpacing/10);
// iterate over all fibers
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
int numFibers = m_FiberBundle->GetNumFibers();
m_DirectionsContainer = ContainerType::New();
VectorContainer< unsigned int, std::vector< double > >::Pointer peakLengths = VectorContainer< unsigned int, std::vector< double > >::New();
MITK_INFO << "Generating directions from tractogram";
boost::progress_display disp(numFibers);
for( int i=0; i<numFibers; i++ )
{
++disp;
vtkCell* cell = fiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (numPoints<2)
continue;
vnl_vector_fixed<double, 3> dir;
itk::Point<double, 3> worldPos;
vnl_vector<double> v;
float fiberWeight = m_FiberBundle->GetFiberWeight(i);
for( int j=0; j<numPoints-1; j++)
{
// get current position along fiber in world coordinates
double* temp = points->GetPoint(j);
worldPos = GetItkPoint(temp);
itk::Index<3> index;
m_MaskImage->TransformPhysicalPointToIndex(worldPos, index);
if (!m_MaskImage->GetLargestPossibleRegion().IsInside(index) || m_MaskImage->GetPixel(index)==0)
continue;
// get fiber tangent direction at this position
v = GetVnlVector(temp);
dir = GetVnlVector(points->GetPoint(j+1))-v;
if (dir.is_zero())
continue;
dir.normalize();
// add direction to container
unsigned int idx = index[0] + outImageSize[0]*(index[1] + outImageSize[1]*index[2]);
DirectionContainerType::Pointer dirCont;
if (m_DirectionsContainer->IndexExists(idx))
{
peakLengths->ElementAt(idx).push_back(fiberWeight);
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->push_back(dir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->push_back(dir);
}
else
{
dirCont = DirectionContainerType::New();
dirCont->push_back(dir);
m_DirectionsContainer->InsertElement(idx, dirCont);
std::vector< double > lengths; lengths.push_back(fiberWeight);
peakLengths->InsertElement(idx, lengths);
}
}
}
vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
itk::ImageRegionIterator<ItkUcharImgType> dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion());
MITK_INFO << "Clustering directions";
boost::progress_display disp2(outImageSize[0]*outImageSize[1]*outImageSize[2]);
while(!dirIt.IsAtEnd())
{
++disp2;
OutputImageType::IndexType index = dirIt.GetIndex();
int idx = index[0]+(index[1]+index[2]*outImageSize[1])*outImageSize[0];
if (!m_DirectionsContainer->IndexExists(idx))
{
++dirIt;
continue;
}
DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull() || dirCont->empty())
{
++dirIt;
continue;
}
// std::vector< double > lengths; lengths.resize(dirCont->size(), 1); // all peaks have size 1
DirectionContainerType::Pointer directions;
if (m_MaxNumDirections>0)
{
directions = FastClustering(dirCont, peakLengths->GetElement(idx));
std::sort( directions->begin(), directions->end(), CompareVectorLengths );
}
else
directions = dirCont;
unsigned int numDir = directions->size();
if (m_MaxNumDirections>0 && numDir>m_MaxNumDirections)
numDir = m_MaxNumDirections;
int count = 0;
for (unsigned int i=0; i<numDir; i++)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
itk::ContinuousIndex<double, 3> center;
center[0] = index[0];
center[1] = index[1];
center[2] = index[2];
itk::Point<double> worldCenter;
m_MaskImage->TransformContinuousIndexToPhysicalPoint( center, worldCenter );
DirectionType dir = directions->at(i);
if (dir.magnitude()<m_SizeThreshold)
continue;
if (m_NormalizeVectors)
dir.normalize();
count++;
if (m_CreateDirectionImages && i<10)
{
if (i==m_DirectionImageContainer->size())
{
ItkDirectionImageType::Pointer directionImage = ItkDirectionImageType::New();
directionImage->SetSpacing( spacing );
directionImage->SetOrigin( origin );
directionImage->SetDirection( direction );
directionImage->SetRegions( imageRegion );
directionImage->Allocate();
Vector< float, 3 > nullVec; nullVec.Fill(0.0);
directionImage->FillBuffer(nullVec);
m_DirectionImageContainer->InsertElement(i, directionImage);
}
// set direction image pixel
ItkDirectionImageType::Pointer directionImage = m_DirectionImageContainer->GetElement(i);
Vector< float, 3 > pixel;
pixel.SetElement(0, dir[0]);
pixel.SetElement(1, dir[1]);
pixel.SetElement(2, dir[2]);
directionImage->SetPixel(index, pixel);
}
// add direction to vector field (with spacing compensation)
itk::Point<double> worldStart;
worldStart[0] = worldCenter[0]-dir[0]/2*minSpacing;
worldStart[1] = worldCenter[1]-dir[1]/2*minSpacing;
worldStart[2] = worldCenter[2]-dir[2]/2*minSpacing;
vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
itk::Point<double> worldEnd;
worldEnd[0] = worldCenter[0]+dir[0]/2*minSpacing;
worldEnd[1] = worldCenter[1]+dir[1]/2*minSpacing;
worldEnd[2] = worldCenter[2]+dir[2]/2*minSpacing;
id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
m_VtkCellArray->InsertNextCell(container);
}
dirIt.Set(count);
++dirIt;
}
vtkSmartPointer<vtkPolyData> directionsPolyData = vtkSmartPointer<vtkPolyData>::New();
directionsPolyData->SetPoints(m_VtkPoints);
directionsPolyData->SetLines(m_VtkCellArray);
m_OutputFiberBundle = mitk::FiberBundle::New(directionsPolyData);
}