vnl_matrix<double> FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
::CalcShBasis(vnl_matrix<double>& sphCoords)
{
int M = sphCoords.rows();
int j, m; double mag, plm;
vnl_matrix<double> shBasis;
shBasis.set_size(M, m_NumCoeffs);
for (int p=0; p<M; p++)
{
j=0;
for (int l=0; l<=ShOrder; l=l+2)
for (m=-l; m<=l; m++)
{
switch (m_Toolkit)
{
case FSL:
plm = legendre_p<double>(l,abs(m),cos(sphCoords(p,0)));
mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial<double>(l-abs(m))/factorial<double>(l+abs(m)))*plm;
if (m<0)
shBasis(p,j) = sqrt(2.0)*mag*cos(fabs((double)m)*sphCoords(p,1));
else if (m==0)
shBasis(p,j) = mag;
else
shBasis(p,j) = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*sphCoords(p,1));
break;
case MRTRIX:
plm = legendre_p<double>(l,abs(m),-cos(sphCoords(p,0)));
mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial<double>(l-abs(m))/factorial<double>(l+abs(m)))*plm;
if (m>0)
shBasis(p,j) = mag*cos(m*sphCoords(p,1));
else if (m==0)
shBasis(p,j) = mag;
else
shBasis(p,j) = mag*sin(-m*sphCoords(p,1));
break;
}
j++;
}
}
return shBasis;
}
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 idx3 = cit.GetIndex();
if (m_MaskImage->GetPixel(idx3)==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> sphCoords;
CreateDirMatrix(candidates, sphCoords); // convert candidate peaks to spherical angles
vnl_matrix< float > shBasis;
if (m_Toolkit==Toolkit::MRTRIX)
shBasis = mitk::sh::CalcShBasisForDirections(ShOrder, sphCoords);
else
shBasis = mitk::sh::CalcShBasisForDirections(ShOrder, sphCoords, false);
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_MaxNumPeaks )
m = m_MaxNumPeaks;
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;
itk::Index<4> idx4; idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2];
// fill output image
unsigned int num = peaks.size();
if ( num>m_MaxNumPeaks )
num = m_MaxNumPeaks;
for (unsigned int i=0; i<num; i++)
{
DirectionType dir = peaks.at(i);
switch (m_NormalizationMethod)
{
case NO_NORM:
break;
case SINGLE_VEC_NORM:
dir.normalize();
break;
case MAX_VEC_NORM:
dir /= max;
break;
}
if (m_ApplyDirectionMatrix)
dir = m_MaskImage->GetDirection()*dir;
if (m_FlipX)
dir[0] = -dir[0];
if (m_FlipY)
dir[1] = -dir[1];
if (m_FlipZ)
dir[2] = -dir[2];
for (unsigned int j = 0; j<3; j++)
{
idx4[3] = i*3 + j;
m_PeakImage->SetPixel(idx4, dir[j]);
}
}
m_NumDirectionsImage->SetPixel(idx3, num);
++cit;
}
MITK_INFO << "Thread " << threadID << " finished extraction";
}
