void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
::AfterThreadedGenerateData()
{
MITK_INFO << "Generating vector field";
vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) );
ImageRegionConstIterator< CoefficientImageType > cit(ShCoeffImage, ShCoeffImage->GetLargestPossibleRegion() );
mitk::Vector3D spacing = ShCoeffImage->GetSpacing();
double minSpacing = spacing[0];
if (spacing[1]<minSpacing)
minSpacing = spacing[1];
if (spacing[2]<minSpacing)
minSpacing = spacing[2];
int maxProgress = ShCoeffImage->GetLargestPossibleRegion().GetSize()[0]*ShCoeffImage->GetLargestPossibleRegion().GetSize()[1]*ShCoeffImage->GetLargestPossibleRegion().GetSize()[2];
boost::progress_display disp(maxProgress);
while( !cit.IsAtEnd() )
{
++disp;
typename CoefficientImageType::IndexType index = cit.GetIndex();
if (m_MaskImage->GetPixel(index)==0)
{
++cit;
continue;
}
for (unsigned int i=0; i<m_DirectionImageContainer->Size(); i++)
{
ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i);
itk::Vector< float, 3 > pixel = img->GetPixel(index);
DirectionType dir; dir[0] = pixel[0]; dir[1] = pixel[1]; dir[2] = pixel[2];
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 );
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);
}
++cit;
}
vtkSmartPointer<vtkPolyData> directionsPolyData = vtkSmartPointer<vtkPolyData>::New();
directionsPolyData->SetPoints(m_VtkPoints);
directionsPolyData->SetLines(m_VtkCellArray);
m_OutputFiberBundle = mitk::FiberBundle::New(directionsPolyData);
for (unsigned int i=0; i<m_DirectionImageContainer->Size(); i++)
{
ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i);
this->SetNthOutput(i, img);
}
}
void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
::BeforeThreadedGenerateData()
{
typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) );
itk::Vector<double,3> spacing = ShCoeffImage->GetSpacing();
double minSpacing = spacing[0];
if (spacing[1]<minSpacing)
minSpacing = spacing[1];
if (spacing[2]<minSpacing)
minSpacing = spacing[2];
mitk::Point3D origin = ShCoeffImage->GetOrigin();
itk::Matrix<double, 3, 3> direction = ShCoeffImage->GetDirection();
ImageRegion<3> imageRegion = ShCoeffImage->GetLargestPossibleRegion();
if (m_MaskImage.IsNotNull())
{
origin = m_MaskImage->GetOrigin();
direction = m_MaskImage->GetDirection();
imageRegion = m_MaskImage->GetLargestPossibleRegion();
}
itk::Vector<double, 3> spacing3 = ShCoeffImage->GetSpacing();
itk::Point<float, 3> origin3 = ShCoeffImage->GetOrigin();
itk::Matrix<double, 3, 3> direction3 = ShCoeffImage->GetDirection();
itk::ImageRegion<3> imageRegion3 = ShCoeffImage->GetLargestPossibleRegion();
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]; origin4[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_MaxNumPeaks*3);
m_PeakImage = PeakImageType::New();
m_PeakImage->SetSpacing( spacing4 );
m_PeakImage->SetOrigin( origin4 );
m_PeakImage->SetDirection( direction4 );
m_PeakImage->SetRegions( imageRegion4 );
m_PeakImage->Allocate();
m_PeakImage->FillBuffer(0.0);
if (m_MaskImage.IsNull())
{
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);
}
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);
// calculate SH basis
OdfType odf;
vnl_matrix< double > sphCoords;
std::vector< DirectionType > dirs;
for (int i=0; i<NrOdfDirections; i++)
{
DirectionType odf_dir;
odf_dir[0] = odf.GetDirection(i)[0];
odf_dir[1] = odf.GetDirection(i)[1];
odf_dir[2] = odf.GetDirection(i)[2];
dirs.push_back(odf_dir);
}
CreateDirMatrix(dirs, sphCoords); // convert candidate peaks to spherical angles
if (m_Toolkit==Toolkit::MRTRIX)
m_ShBasis = mitk::sh::CalcShBasisForDirections(ShOrder, sphCoords);
else
m_ShBasis = mitk::sh::CalcShBasisForDirections(ShOrder, sphCoords, false);
MITK_INFO << "Starting finite differences maximum extraction";
MITK_INFO << "ODF sampling points: " << NrOdfDirections;
MITK_INFO << "SH order: " << ShOrder;
MITK_INFO << "Maximum peaks: " << m_MaxNumPeaks;
MITK_INFO << "Relative threshold: " << m_PeakThreshold;
MITK_INFO << "Absolute threshold: " << m_AbsolutePeakThreshold;
MITK_INFO << "Clustering threshold: " << m_ClusteringThreshold;
MITK_INFO << "Angular threshold: " << m_AngularThreshold;
}
void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
::BeforeThreadedGenerateData()
{
typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) );
itk::Vector<double,3> spacing = ShCoeffImage->GetSpacing();
double minSpacing = spacing[0];
if (spacing[1]<minSpacing)
minSpacing = spacing[1];
if (spacing[2]<minSpacing)
minSpacing = spacing[2];
mitk::Point3D origin = ShCoeffImage->GetOrigin();
itk::Matrix<double, 3, 3> direction = ShCoeffImage->GetDirection();
ImageRegion<3> imageRegion = ShCoeffImage->GetLargestPossibleRegion();
if (m_MaskImage.IsNotNull())
{
origin = m_MaskImage->GetOrigin();
direction = m_MaskImage->GetDirection();
imageRegion = m_MaskImage->GetLargestPossibleRegion();
}
m_DirectionImageContainer = ItkDirectionImageContainer::New();
for (unsigned int i=0; i<m_MaxNumPeaks; i++)
{
itk::Vector< float, 3 > nullVec; nullVec.Fill(0.0);
ItkDirectionImage::Pointer img = ItkDirectionImage::New();
img->SetSpacing( spacing );
img->SetOrigin( origin );
img->SetDirection( direction );
img->SetRegions( imageRegion );
img->Allocate();
img->FillBuffer(nullVec);
m_DirectionImageContainer->InsertElement(m_DirectionImageContainer->Size(), img);
}
if (m_MaskImage.IsNull())
{
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);
}
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);
this->SetNumberOfIndexedOutputs(m_MaxNumPeaks);
// calculate SH basis
OdfType odf;
vnl_matrix_fixed<double, 3, NrOdfDirections>* directions = odf.GetDirections();
vnl_matrix< double > sphCoords;
std::vector< DirectionType > dirs;
for (int i=0; i<NrOdfDirections; i++)
dirs.push_back(directions->get_column(i));
Cart2Sph(dirs, sphCoords); // convert candidate peaks to spherical angles
m_ShBasis = CalcShBasis(sphCoords); // evaluate spherical harmonics at each peak
MITK_INFO << "Starting finite differences maximum extraction";
MITK_INFO << "ODF sampling points: " << NrOdfDirections;
MITK_INFO << "SH order: " << ShOrder;
MITK_INFO << "Maximum peaks: " << m_MaxNumPeaks;
MITK_INFO << "Relative threshold: " << m_PeakThreshold;
MITK_INFO << "Absolute threshold: " << m_AbsolutePeakThreshold;
MITK_INFO << "Clustering threshold: " << m_ClusteringThreshold;
MITK_INFO << "Angular threshold: " << m_AngularThreshold;
}
