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;
}
void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType threadID )
{
typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) );
ImageRegionConstIterator< CoefficientImageType > cit(ShCoeffImage, outputRegionForThread );
OdfType odf;
while( !cit.IsAtEnd() )
{
typename CoefficientImageType::IndexType index = cit.GetIndex();
if (m_MaskImage->GetPixel(index)==0)
{
++cit;
continue;
}
CoefficientPixelType c = cit.Get();
// calculate ODF
double max = 0;
odf.Fill(0.0);
for (int i=0; i<NrOdfDirections; i++)
{
for (int j=0; j<m_NumCoeffs; j++)
odf[i] += c[j]*m_ShBasis(i,j);
if (odf[i]>max)
max = odf[i];
}
if (max<0.0001)
{
++cit;
continue;
}
std::vector< DirectionType > candidates, peaks, temp;
peaks.clear();
max *= m_PeakThreshold; // relative threshold
FindCandidatePeaks(odf, max, candidates); // find all local maxima
candidates = MeanShiftClustering(candidates); // cluster maxima
vnl_matrix< double > shBasis, sphCoords;
Cart2Sph(candidates, sphCoords); // convert candidate peaks to spherical angles
shBasis = CalcShBasis(sphCoords); // evaluate spherical harmonics at each peak
max = 0.0;
for (unsigned int i=0; i<candidates.size(); i++) // scale peaks according to ODF value
{
double val = 0;
for (int j=0; j<m_NumCoeffs; j++)
val += c[j]*shBasis(i,j);
if (val>max)
max = val;
peaks.push_back(candidates[i]*val);
}
std::sort( peaks.begin(), peaks.end(), CompareVectors ); // sort peaks
// kick out directions to close to a larger direction (too far away to cluster but too close to keep)
unsigned int m = peaks.size();
if ( m>m_DirectionImageContainer->Size() )
m = m_DirectionImageContainer->Size();
for (unsigned int i=0; i<m; i++)
{
DirectionType v1 = peaks.at(i);
double val = v1.magnitude();
if (val<max*m_PeakThreshold || val<m_AbsolutePeakThreshold)
break;
bool flag = true;
for (unsigned int j=0; j<peaks.size(); j++)
if (i!=j)
{
DirectionType v2 = peaks.at(j);
double val2 = v2.magnitude();
double angle = fabs(dot_product(v1,v2)/(val*val2));
if (angle>m_AngularThreshold && val<val2)
{
flag = false;
break;
}
}
if (flag)
temp.push_back(v1);
}
peaks = temp;
// fill output image
unsigned int num = peaks.size();
if ( num>m_DirectionImageContainer->Size() )
num = m_DirectionImageContainer->Size();
for (unsigned int i=0; i<num; i++)
{
vnl_vector<double> dir = peaks.at(i);
ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i);
switch (m_NormalizationMethod)
{
case NO_NORM:
break;
case SINGLE_VEC_NORM:
dir.normalize();
break;
case MAX_VEC_NORM:
dir /= max;
break;
}
dir = m_MaskImage->GetDirection()*dir;
itk::Vector< float, 3 > pixel;
pixel.SetElement(0, -dir[0]);
pixel.SetElement(1, dir[1]);
pixel.SetElement(2, dir[2]);
img->SetPixel(index, pixel);
}
m_NumDirectionsImage->SetPixel(index, num);
++cit;
}
MITK_INFO << "Thread " << threadID << " finished extraction";
}
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);
}
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;
}
