void ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::GenerateData()
{
typename InputImageType::Pointer rgbaImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
typename OutputImageType::Pointer outputImage =
static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
typename InputImageType::RegionType region = rgbaImage->GetLargestPossibleRegion();
outputImage->SetSpacing( m_ReferenceImage->GetSpacing() ); // Set the image spacing
outputImage->SetOrigin( m_ReferenceImage->GetOrigin() ); // Set the image origin
outputImage->SetDirection( m_ReferenceImage->GetDirection() ); // Set the image direction
outputImage->SetRegions( m_ReferenceImage->GetLargestPossibleRegion());
outputImage->Allocate();
outputImage->FillBuffer(0);
float* outImageBufferPointer = outputImage->GetBufferPointer();
itk::Image< short, 3 >::Pointer counterImage = itk::Image< short, 3 >::New();
counterImage->SetSpacing( m_ReferenceImage->GetSpacing() ); // Set the image spacing
counterImage->SetOrigin( m_ReferenceImage->GetOrigin() ); // Set the image origin
counterImage->SetDirection( m_ReferenceImage->GetDirection() ); // Set the image direction
counterImage->SetRegions( m_ReferenceImage->GetLargestPossibleRegion());
counterImage->Allocate();
counterImage->FillBuffer(0);
short* counterImageBufferPointer = counterImage->GetBufferPointer();
int w = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(0);
int h = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(1);
int d = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(2);
typedef ImageRegionConstIterator< InputImageType > InImageIteratorType;
InImageIteratorType rgbaIt(rgbaImage, region);
rgbaIt.GoToBegin();
while(!rgbaIt.IsAtEnd()){
InPixelType x = rgbaIt.Get();
++rgbaIt;
itk::Point<float, 3> vertex;
itk::Index<3> index = rgbaIt.GetIndex();
rgbaImage->TransformIndexToPhysicalPoint(index, vertex);
outputImage->TransformPhysicalPointToIndex(vertex, index);
itk::ContinuousIndex<float, 3> contIndex;
outputImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
float frac_x = contIndex[0] - index[0];
float frac_y = contIndex[1] - index[1];
float frac_z = contIndex[2] - index[2];
int px = index[0];
if (frac_x<0)
{
px -= 1;
frac_x += 1;
}
int py = index[1];
if (frac_y<0)
{
py -= 1;
frac_y += 1;
}
int pz = index[2];
if (frac_z<0)
{
pz -= 1;
frac_z += 1;
}
frac_x = 1-frac_x;
frac_y = 1-frac_y;
frac_z = 1-frac_z;
// int coordinates inside image?
if (px < 0 || px >= w-1)
continue;
if (py < 0 || py >= h-1)
continue;
if (pz < 0 || pz >= d-1)
continue;
OutPixelType out;
switch (m_Channel)
{
case RED:
out = (float)x.GetRed()/255;
break;
case GREEN:
out = (float)x.GetGreen()/255;
break;
case BLUE:
out = (float)x.GetBlue()/255;
break;
case ALPHA:
out = (float)x.GetAlpha()/255;
}
outImageBufferPointer[( px + w*(py + h*pz ))] += out*( frac_x)*( frac_y)*( frac_z);
outImageBufferPointer[( px + w*(py+1+ h*pz ))] += out*( frac_x)*(1-frac_y)*( frac_z);
outImageBufferPointer[( px + w*(py + h*pz+h))] += out*( frac_x)*( frac_y)*(1-frac_z);
outImageBufferPointer[( px + w*(py+1+ h*pz+h))] += out*( frac_x)*(1-frac_y)*(1-frac_z);
outImageBufferPointer[( px+1 + w*(py + h*pz ))] += out*(1-frac_x)*( frac_y)*( frac_z);
outImageBufferPointer[( px+1 + w*(py + h*pz+h))] += out*(1-frac_x)*( frac_y)*(1-frac_z);
outImageBufferPointer[( px+1 + w*(py+1+ h*pz ))] += out*(1-frac_x)*(1-frac_y)*( frac_z);
outImageBufferPointer[( px+1 + w*(py+1+ h*pz+h))] += out*(1-frac_x)*(1-frac_y)*(1-frac_z);
counterImageBufferPointer[( px + w*(py + h*pz ))] += 1;
counterImageBufferPointer[( px + w*(py+1+ h*pz ))] += 1;
counterImageBufferPointer[( px + w*(py + h*pz+h))] += 1;
counterImageBufferPointer[( px + w*(py+1+ h*pz+h))] += 1;
counterImageBufferPointer[( px+1 + w*(py + h*pz ))] += 1;
counterImageBufferPointer[( px+1 + w*(py + h*pz+h))] += 1;
counterImageBufferPointer[( px+1 + w*(py+1+ h*pz ))] += 1;
counterImageBufferPointer[( px+1 + w*(py+1+ h*pz+h))] += 1;
}
typedef ImageRegionIterator< OutputImageType > OutImageIteratorType;
OutImageIteratorType outIt(outputImage, outputImage->GetLargestPossibleRegion());
outIt.GoToBegin();
typedef ImageRegionConstIterator< itk::Image< short, 3 > > CountImageIteratorType;
CountImageIteratorType counterIt(counterImage, counterImage->GetLargestPossibleRegion());
counterIt.GoToBegin();
while(!outIt.IsAtEnd() && !counterIt.IsAtEnd()){
if (counterIt.Value()>0)
outIt.Set(outIt.Value()/counterIt.Value());
++outIt;
++counterIt;
}
}
void TractDensityImageFilter< OutputImageType >::GenerateData()
{
// generate upsampled image
mitk::Geometry3D::Pointer geometry = m_FiberBundle->GetGeometry();
typename OutputImageType::Pointer outImage = this->GetOutput();
// calculate new image parameters
mitk::Vector3D newSpacing;
mitk::Point3D newOrigin;
itk::Matrix<double, 3, 3> newDirection;
ImageRegion<3> upsampledRegion;
if (m_UseImageGeometry && !m_InputImage.IsNull())
{
MITK_INFO << "TractDensityImageFilter: using image geometry";
newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor;
upsampledRegion = m_InputImage->GetLargestPossibleRegion();
newOrigin = m_InputImage->GetOrigin();
typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize();
size[0] *= m_UpsamplingFactor;
size[1] *= m_UpsamplingFactor;
size[2] *= m_UpsamplingFactor;
upsampledRegion.SetSize(size);
newDirection = m_InputImage->GetDirection();
}
else
{
MITK_INFO << "TractDensityImageFilter: using fiber bundle geometry";
newSpacing = geometry->GetSpacing()/m_UpsamplingFactor;
newOrigin = geometry->GetOrigin();
mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
newOrigin[0] += bounds.GetElement(0);
newOrigin[1] += bounds.GetElement(2);
newOrigin[2] += bounds.GetElement(4);
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
newDirection[j][i] = geometry->GetMatrixColumn(i)[j];
upsampledRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
upsampledRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
upsampledRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
}
typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize();
// apply new image parameters
outImage->SetSpacing( newSpacing );
outImage->SetOrigin( newOrigin );
outImage->SetDirection( newDirection );
outImage->SetRegions( upsampledRegion );
outImage->Allocate();
outImage->FillBuffer(0.0);
int w = upsampledSize[0];
int h = upsampledSize[1];
int d = upsampledSize[2];
// set/initialize output
OutPixelType* outImageBufferPointer = (OutPixelType*)outImage->GetBufferPointer();
// resample fiber bundle
float minSpacing = 1;
if(newSpacing[0]<newSpacing[1] && newSpacing[0]<newSpacing[2])
minSpacing = newSpacing[0];
else if (newSpacing[1] < newSpacing[2])
minSpacing = newSpacing[1];
else
minSpacing = newSpacing[2];
MITK_INFO << "TractDensityImageFilter: resampling fibers to ensure sufficient voxel coverage";
m_FiberBundle = m_FiberBundle->GetDeepCopy();
m_FiberBundle->ResampleFibers(minSpacing);
MITK_INFO << "TractDensityImageFilter: starting image generation";
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
vtkSmartPointer<vtkCellArray> vLines = fiberPolyData->GetLines();
vLines->InitTraversal();
int numFibers = m_FiberBundle->GetNumFibers();
boost::progress_display disp(numFibers);
for( int i=0; i<numFibers; i++ )
{
++disp;
vtkIdType numPoints(0);
vtkIdType* points(NULL);
vLines->GetNextCell ( numPoints, points );
// fill output image
for( int j=0; j<numPoints; j++)
{
itk::Point<float, 3> vertex = GetItkPoint(fiberPolyData->GetPoint(points[j]));
itk::Index<3> index;
itk::ContinuousIndex<float, 3> contIndex;
outImage->TransformPhysicalPointToIndex(vertex, index);
outImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
float frac_x = contIndex[0] - index[0];
float frac_y = contIndex[1] - index[1];
float frac_z = contIndex[2] - index[2];
if (frac_x<0)
{
index[0] -= 1;
frac_x += 1;
}
if (frac_y<0)
{
index[1] -= 1;
frac_y += 1;
}
if (frac_z<0)
{
index[2] -= 1;
frac_z += 1;
}
frac_x = 1-frac_x;
frac_y = 1-frac_y;
frac_z = 1-frac_z;
// int coordinates inside image?
if (index[0] < 0 || index[0] >= w-1)
continue;
if (index[1] < 0 || index[1] >= h-1)
continue;
if (index[2] < 0 || index[2] >= d-1)
continue;
if (m_BinaryOutput)
{
outImageBufferPointer[( index[0] + w*(index[1] + h*index[2] ))] = 1;
outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2] ))] = 1;
outImageBufferPointer[( index[0] + w*(index[1] + h*index[2]+h))] = 1;
outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2]+h))] = 1;
outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2] ))] = 1;
outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2]+h))] = 1;
outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2] ))] = 1;
outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2]+h))] = 1;
}
else
{
outImageBufferPointer[( index[0] + w*(index[1] + h*index[2] ))] += ( frac_x)*( frac_y)*( frac_z);
outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2] ))] += ( frac_x)*(1-frac_y)*( frac_z);
outImageBufferPointer[( index[0] + w*(index[1] + h*index[2]+h))] += ( frac_x)*( frac_y)*(1-frac_z);
outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2]+h))] += ( frac_x)*(1-frac_y)*(1-frac_z);
outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2] ))] += (1-frac_x)*( frac_y)*( frac_z);
outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2]+h))] += (1-frac_x)*( frac_y)*(1-frac_z);
outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2] ))] += (1-frac_x)*(1-frac_y)*( frac_z);
outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2]+h))] += (1-frac_x)*(1-frac_y)*(1-frac_z);
}
}
}
if (!m_OutputAbsoluteValues && !m_BinaryOutput)
{
MITK_INFO << "TractDensityImageFilter: max-normalizing output image";
OutPixelType max = 0;
for (int i=0; i<w*h*d; i++)
if (max < outImageBufferPointer[i])
max = outImageBufferPointer[i];
if (max>0)
for (int i=0; i<w*h*d; i++)
outImageBufferPointer[i] /= max;
}
if (m_InvertImage)
{
MITK_INFO << "TractDensityImageFilter: inverting image";
for (int i=0; i<w*h*d; i++)
outImageBufferPointer[i] = 1-outImageBufferPointer[i];
}
MITK_INFO << "TractDensityImageFilter: finished processing";
}
void TractsToFiberEndingsImageFilter< OutputImageType >::GenerateData()
{
// generate upsampled image
mitk::Geometry3D::Pointer geometry = m_FiberBundle->GetGeometry();
typename OutputImageType::Pointer outImage = this->GetOutput();
// calculate new image parameters
mitk::Vector3D newSpacing;
mitk::Point3D newOrigin;
itk::Matrix<double, 3, 3> newDirection;
ImageRegion<3> upsampledRegion;
if (m_UseImageGeometry && !m_InputImage.IsNull())
{
newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor;
upsampledRegion = m_InputImage->GetLargestPossibleRegion();
newOrigin = m_InputImage->GetOrigin();
typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize();
size[0] *= m_UpsamplingFactor;
size[1] *= m_UpsamplingFactor;
size[2] *= m_UpsamplingFactor;
upsampledRegion.SetSize(size);
newDirection = m_InputImage->GetDirection();
}
else
{
newSpacing = geometry->GetSpacing()/m_UpsamplingFactor;
newOrigin = geometry->GetOrigin();
mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
newOrigin[0] += bounds.GetElement(0);
newOrigin[1] += bounds.GetElement(2);
newOrigin[2] += bounds.GetElement(4);
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
newDirection[j][i] = geometry->GetMatrixColumn(i)[j];
upsampledRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
upsampledRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
upsampledRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
}
typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize();
// apply new image parameters
outImage->SetSpacing( newSpacing );
outImage->SetOrigin( newOrigin );
outImage->SetDirection( newDirection );
outImage->SetRegions( upsampledRegion );
outImage->Allocate();
int w = upsampledSize[0];
int h = upsampledSize[1];
int d = upsampledSize[2];
// set/initialize output
OutPixelType* outImageBufferPointer = (OutPixelType*)outImage->GetBufferPointer();
for (int i=0; i<w*h*d; i++)
outImageBufferPointer[i] = 0;
// resample fiber bundle
float minSpacing = 1;
if(newSpacing[0]<newSpacing[1] && newSpacing[0]<newSpacing[2])
minSpacing = newSpacing[0];
else if (newSpacing[1] < newSpacing[2])
minSpacing = newSpacing[1];
else
minSpacing = newSpacing[2];
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
vtkSmartPointer<vtkCellArray> vLines = fiberPolyData->GetLines();
vLines->InitTraversal();
int numFibers = m_FiberBundle->GetNumFibers();
boost::progress_display disp(numFibers);
for( int i=0; i<numFibers; i++ )
{
++disp;
vtkIdType numPoints(0);
vtkIdType* points(NULL);
vLines->GetNextCell ( numPoints, points );
// fill output image
if (numPoints>0)
{
itk::Point<float, 3> vertex = GetItkPoint(fiberPolyData->GetPoint(points[0]));
itk::Index<3> index;
outImage->TransformPhysicalPointToIndex(vertex, index);
if (m_BinaryOutput)
outImage->SetPixel(index, 1);
else
outImage->SetPixel(index, outImage->GetPixel(index)+1);
}
if (numPoints>2)
{
itk::Point<float, 3> vertex = GetItkPoint(fiberPolyData->GetPoint(points[numPoints-1]));
itk::Index<3> index;
outImage->TransformPhysicalPointToIndex(vertex, index);
if (m_BinaryOutput)
outImage->SetPixel(index, 1);
else
outImage->SetPixel(index, outImage->GetPixel(index)+1);
}
}
if (m_InvertImage)
for (int i=0; i<w*h*d; i++)
outImageBufferPointer[i] = 1-outImageBufferPointer[i];
}