void TractsToDWIImageFilter::GenerateParticleGrid()
{
MITK_INFO << "Generating particle grid from fiber bundle";
m_ParticleGrid = mitk::ParticleGrid::New();
float* bounds = m_FiberBundle->GetBounds();
int size[] = {(int)bounds[0],(int)bounds[1],(int)bounds[2]};
m_ParticleGrid->SetSize(size);
typedef itk::Point<float,3> ContainerPointType; //no need to init, is no smartpointer
typedef itk::VectorContainer<unsigned int, ContainerPointType> ContainerTractType;
typedef itk::VectorContainer< unsigned int, ContainerTractType::Pointer > ContainerType; //init via smartpointer
ContainerType::Pointer tractContainer = m_FiberBundle->GetTractContainer();
for (int i=0; i<tractContainer->Size(); i++)
{
ContainerTractType::Pointer tract = tractContainer->GetElement(i);
for (int j=0; j<tract->Size(); j++)
{
vnl_vector_fixed<float,3> pos = tract->GetElement(j).GetVnlVector();
vnl_vector_fixed<float,3> next;
vnl_vector_fixed<float,3> dir;
if (j<tract->Size()-1)
next = tract->GetElement(j+1).GetVnlVector();
else
next = tract->GetElement(j-1).GetVnlVector();
dir = next-pos;
dir.normalize();
mitk::Particle* p = new mitk::Particle();
p->SetPosition(pos);
p->SetDirection(dir);
m_ParticleGrid->AddParticle(p);
}
}
}
void TractsToFiberEndingsImageFilter< TInputImage, TOutputPixelType >
::GenerateData()
{
MITK_INFO << "Generating 2D fiber endings image";
if(&typeid(TOutputPixelType) != &typeid(unsigned char))
{
MITK_INFO << "Only 'unsigned char' and 'itk::RGBAPixel<unsigned char> supported as OutputPixelType";
return;
}
mitk::Geometry3D::Pointer geometry = m_FiberBundle->GetGeometry();
typename OutputImageType::Pointer outImage =
static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
outImage->SetSpacing( geometry->GetSpacing()/m_UpsamplingFactor ); // Set the image spacing
mitk::Point3D origin = geometry->GetOrigin();
mitk::Point3D indexOrigin;
geometry->WorldToIndex(origin, indexOrigin);
indexOrigin[0] = indexOrigin[0] - .5 * (1.0-1.0/m_UpsamplingFactor);
indexOrigin[1] = indexOrigin[1] - .5 * (1.0-1.0/m_UpsamplingFactor);
indexOrigin[2] = indexOrigin[2] - .5 * (1.0-1.0/m_UpsamplingFactor);
mitk::Point3D newOrigin;
geometry->IndexToWorld(indexOrigin, newOrigin);
outImage->SetOrigin( newOrigin ); // Set the image origin
itk::Matrix<double, 3, 3> matrix;
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
matrix[j][i] = geometry->GetMatrixColumn(i)[j]/geometry->GetSpacing().GetElement(i);
outImage->SetDirection( matrix ); // Set the image direction
float* bounds = m_FiberBundle->GetBounds();
ImageRegion<3> upsampledRegion;
upsampledRegion.SetSize(0, bounds[0]);
upsampledRegion.SetSize(1, bounds[1]);
upsampledRegion.SetSize(2, bounds[2]);
typename InputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize();
for (unsigned int n = 0; n < 3; n++)
{
upsampledSize[n] = upsampledSize[n] * m_UpsamplingFactor;
}
upsampledRegion.SetSize( upsampledSize );
outImage->SetRegions( upsampledRegion );
outImage->Allocate();
int w = upsampledSize[0];
int h = upsampledSize[1];
int d = upsampledSize[2];
unsigned char* accuout;
accuout = reinterpret_cast<unsigned char*>(outImage->GetBufferPointer());
for (int i=0; i<w*h*d; i++) accuout[i] = 0;
typedef mitk::FiberBundle::ContainerTractType ContainerTractType;
typedef mitk::FiberBundle::ContainerType ContainerType;
typedef mitk::FiberBundle::ContainerPointType ContainerPointType;
ContainerType::Pointer tractContainer = m_FiberBundle->GetTractContainer();
for (int i=0; i<tractContainer->Size(); i++)
{
ContainerTractType::Pointer tract = tractContainer->GetElement(i);
int tractsize = tract->Size();
if (tractsize>1)
{
ContainerPointType start = tract->GetElement(0);
ContainerPointType end = tract->GetElement(tractsize-1);
start[0] = (start[0]+0.5) * m_UpsamplingFactor;
start[1] = (start[1]+0.5) * m_UpsamplingFactor;
start[2] = (start[2]+0.5) * m_UpsamplingFactor;
// int coordinates inside image?
int px = (int) (start[0]);
if (px < 0 || px >= w)
continue;
int py = (int) (start[1]);
if (py < 0 || py >= h)
continue;
int pz = (int) (start[2]);
if (pz < 0 || pz >= d)
continue;
accuout[( px + w*(py + h*pz ))] += 1;
end[0] = (end[0]+0.5) * m_UpsamplingFactor;
end[1] = (end[1]+0.5) * m_UpsamplingFactor;
end[2] = (end[2]+0.5) * m_UpsamplingFactor;
// int coordinates inside image?
px = (int) (end[0]);
if (px < 0 || px >= w)
continue;
py = (int) (end[1]);
if (py < 0 || py >= h)
continue;
pz = (int) (end[2]);
if (pz < 0 || pz >= d)
continue;
accuout[( px + w*(py + h*pz ))] += 1;
}
}
MITK_INFO << "2D fiber endings image generated";
}
