void mitk::CreateDistanceImageFromSurfaceFilter::CreateEmptyDistanceImage()
{
// Determine the bounds of the input points in index- and world-coordinates
DistanceImageType::PointType minPointInWorldCoordinates, maxPointInWorldCoordinates;
DistanceImageType::IndexType minPointInIndexCoordinates, maxPointInIndexCoordinates;
DetermineBounds( minPointInWorldCoordinates, maxPointInWorldCoordinates,
minPointInIndexCoordinates, maxPointInIndexCoordinates );
// Calculate the extent of the region that contains all given points in MM.
// To do this, we take the difference between the maximal and minimal
// index-coordinates (must not be less than 1) and multiply it with the
// spacing of the reference-image.
Vector3D extentMM;
for (unsigned int dim = 0; dim < 3; ++dim)
{
extentMM[dim] = (std::abs(maxPointInIndexCoordinates[dim] - minPointInIndexCoordinates[dim])) * m_ReferenceImage->GetSpacing()[dim];
}
/*
* Now create an empty distance image. The created image will always have the same number of pixels, independent from
* the original image (e.g. always consists of 500000 pixels) and will have an isotropic spacing.
* The spacing is calculated like the following:
* The image's volume = 500000 Pixels = extentX*spacing*extentY*spacing*extentZ*spacing
* So the spacing is: spacing = ( extentX*extentY*extentZ / 500000 )^(1/3)
*/
double basis = (extentMM[0]*extentMM[1]*extentMM[2]) / m_DistanceImageVolume;
double exponent = 1.0/3.0;
m_DistanceImageSpacing = pow(basis, exponent);
// calculate the number of pixels of the distance image for each direction
unsigned int numberOfXPixel = extentMM[0] / m_DistanceImageSpacing;
unsigned int numberOfYPixel = extentMM[1] / m_DistanceImageSpacing;
unsigned int numberOfZPixel = extentMM[2] / m_DistanceImageSpacing;
// We increase the sizeOfRegion by 4 as we decrease the origin by 2 later.
// This expansion of the region is necessary to achieve a complete
// interpolation.
DistanceImageType::SizeType sizeOfRegion;
sizeOfRegion[0] = numberOfXPixel + 8;
sizeOfRegion[1] = numberOfYPixel + 8;
sizeOfRegion[2] = numberOfZPixel + 8;
// The region starts at index 0,0,0
DistanceImageType::IndexType initialOriginAsIndex;
initialOriginAsIndex.Fill(0);
DistanceImageType::PointType originAsWorld = minPointInWorldCoordinates;
DistanceImageType::RegionType lpRegion;
lpRegion.SetSize(sizeOfRegion);
lpRegion.SetIndex(initialOriginAsIndex);
// We initialize the itk::Image with
// * origin and direction to have it correctly placed and rotated in the world
// * the largest possible region to set the extent to be calculated
// * the isotropic spacing that we have calculated above
m_DistanceImageITK = DistanceImageType::New();
m_DistanceImageITK->SetOrigin( originAsWorld );
m_DistanceImageITK->SetDirection( m_ReferenceImage->GetDirection() );
m_DistanceImageITK->SetRegions( lpRegion );
m_DistanceImageITK->SetSpacing( m_DistanceImageSpacing );
m_DistanceImageITK->Allocate();
//First of all the image is initialized with the value 10*m_DistanceImageSpacing for each pixel
m_DistanceImageDefaultBufferValue = 10*m_DistanceImageSpacing;
m_DistanceImageITK->FillBuffer(m_DistanceImageDefaultBufferValue);
// Now we move the origin of the distanceImage 2 index-Coordinates
// in all directions
DistanceImageType::IndexType originAsIndex;
m_DistanceImageITK->TransformPhysicalPointToIndex( originAsWorld, originAsIndex );
originAsIndex[0] -= 2;
originAsIndex[1] -= 2;
originAsIndex[2] -= 2;
m_DistanceImageITK->TransformIndexToPhysicalPoint( originAsIndex, originAsWorld );
m_DistanceImageITK->SetOrigin( originAsWorld );
}
void mitk::CreateDistanceImageFromSurfaceFilter::CreateDistanceImage()
{
DistanceImageType::Pointer distanceImg = DistanceImageType::New();
// Determine the bounds of the input points in index- and world-coordinates
DistanceImageType::PointType minPointInWorldCoordinates, maxPointInWorldCoordinates;
DistanceImageType::IndexType minPointInIndexCoordinates, maxPointInIndexCoordinates;
DetermineBounds( minPointInWorldCoordinates, maxPointInWorldCoordinates,
minPointInIndexCoordinates, maxPointInIndexCoordinates );
// Calculate the extent of the region that contains all given points in MM.
// To do this, we take the difference between the maximal and minimal
// index-coordinates (must not be less than 1) and multiply it with the
// spacing of the reference-image.
Vector3D extentMM;
for (unsigned int dim = 0; dim < 3; ++dim)
{
extentMM[dim] = (int)
(
(std::max( std::abs(maxPointInIndexCoordinates[dim] - minPointInIndexCoordinates[dim]),
(DistanceImageType::IndexType::IndexValueType) 1
) + 1.0) // (max-index - min-index)+1 because the pixels between index 3 and 5 cover 2+1=3 pixels (pixel 3,4, and 5)
* m_ReferenceImage->GetSpacing()[dim]
) + 1; // (int) ((...) + 1) -> we round up to the next BIGGER int value
}
/*
* Now create an empty distance image. The create image will always have the same sizeOfRegion, independent from
* the original image (e.g. always consists of 500000 pixels) and will have an isotropic spacing.
* The spacing is calculated like the following:
* The image's volume = 500000 Pixels = extentX*spacing*extentY*spacing*extentZ*spacing
* So the spacing is: spacing = ( 500000 / extentX*extentY*extentZ )^(1/3)
*/
double basis = (extentMM[0]*extentMM[1]*extentMM[2]) / m_DistanceImageVolume;
double exponent = 1.0/3.0;
double distImgSpacing = pow(basis, exponent);
int tempSpacing = (distImgSpacing+0.05)*10;
m_DistanceImageSpacing = (double)tempSpacing/10.0;
// calculate the number of pixels of the distance image for each direction
unsigned int numberOfXPixel = extentMM[0] / m_DistanceImageSpacing;
unsigned int numberOfYPixel = extentMM[1] / m_DistanceImageSpacing;
unsigned int numberOfZPixel = extentMM[2] / m_DistanceImageSpacing;
// We increase the sizeOfRegion by 4 as we decrease the origin by 2 later.
// This expansion of the region is necessary to achieve a complete
// interpolation.
DistanceImageType::SizeType sizeOfRegion;
sizeOfRegion[0] = numberOfXPixel + 4;
sizeOfRegion[1] = numberOfYPixel + 4;
sizeOfRegion[2] = numberOfZPixel + 4;
// The region starts at index 0,0,0
DistanceImageType::IndexType initialOriginAsIndex;
initialOriginAsIndex.Fill(0);
DistanceImageType::PointType originAsWorld = minPointInWorldCoordinates;
DistanceImageType::RegionType lpRegion;
lpRegion.SetSize(sizeOfRegion);
lpRegion.SetIndex(initialOriginAsIndex);
// We initialize the itk::Image with
// * origin and direction to have it correctly placed and rotated in the world
// * the largest possible region to set the extent to be calculated
// * the isotropic spacing that we have calculated above
distanceImg->SetOrigin( originAsWorld );
distanceImg->SetDirection( m_ReferenceImage->GetDirection() );
distanceImg->SetRegions( lpRegion );
distanceImg->SetSpacing( m_DistanceImageSpacing );
distanceImg->Allocate();
//First of all the image is initialized with the value 10 for each pixel
distanceImg->FillBuffer(10);
// Now we move the origin of the distanceImage 2 index-Coordinates
// in all directions
DistanceImageType::IndexType originAsIndex;
distanceImg->TransformPhysicalPointToIndex( originAsWorld, originAsIndex );
originAsIndex[0] -= 2;
originAsIndex[1] -= 2;
originAsIndex[2] -= 2;
distanceImg->TransformIndexToPhysicalPoint( originAsIndex, originAsWorld );
distanceImg->SetOrigin( originAsWorld );
/*
* Now we must calculate the distance for each pixel. But instead of calculating the distance value
* for all of the image's pixels we proceed similar to the region growing algorithm:
*
* 1. Take the first pixel from the narrowband_point_list and calculate the distance for each neighbor (6er)
* 2. If the current index's distance value is below a certain threshold push it into the list
* 3. Next iteration take the next index from the list and originAsIndex with 1. again
*
* This is done until the narrowband_point_list is empty.
*/
std::queue<DistanceImageType::IndexType> narrowbandPoints;
PointType currentPoint = m_Centers.at(0);
double distance = this->CalculateDistanceValue(currentPoint);
// create itk::Point from vnl_vector
DistanceImageType::PointType currentPointAsPoint;
currentPointAsPoint[0] = currentPoint[0];
currentPointAsPoint[1] = currentPoint[1];
currentPointAsPoint[2] = currentPoint[2];
// Transform the input point in world-coordinates to index-coordinates
DistanceImageType::IndexType currentIndex;
distanceImg->TransformPhysicalPointToIndex( currentPointAsPoint, currentIndex );
assert( lpRegion.IsInside(currentIndex) ); // we are quite certain this should hold
narrowbandPoints.push(currentIndex);
distanceImg->SetPixel(currentIndex, distance);
NeighborhoodImageIterator::RadiusType radius;
radius.Fill(1);
NeighborhoodImageIterator nIt(radius, distanceImg, distanceImg->GetLargestPossibleRegion());
unsigned int relativeNbIdx[] = {4, 10, 12, 14, 16, 22};
bool isInBounds = false;
while ( !narrowbandPoints.empty() )
{
nIt.SetLocation(narrowbandPoints.front());
narrowbandPoints.pop();
unsigned int* relativeNb = &relativeNbIdx[0];
for (int i = 0; i < 6; i++)
{
nIt.GetPixel(*relativeNb, isInBounds);
if( isInBounds && nIt.GetPixel(*relativeNb) == 10)
{
currentIndex = nIt.GetIndex(*relativeNb);
// Transform the currently checked point from index-coordinates to
// world-coordinates
distanceImg->TransformIndexToPhysicalPoint( currentIndex, currentPointAsPoint );
// create a vnl_vector
currentPoint[0] = currentPointAsPoint[0];
currentPoint[1] = currentPointAsPoint[1];
currentPoint[2] = currentPointAsPoint[2];
// and check the distance
distance = this->CalculateDistanceValue(currentPoint);
if ( abs(distance) <= m_DistanceImageSpacing )
{
nIt.SetPixel(*relativeNb, distance);
narrowbandPoints.push(currentIndex);
}
}
relativeNb++;
}
}
// Fist we set the border slices of the image to value 1000 so that we can perform a
// region growing afterwards starting from the middle of the image
DistanceImageType::SizeType reqSize;
reqSize[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0];
reqSize[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1];
reqSize[2] = 1;
DistanceImageType::IndexType reqStart;
reqStart[0] = 0;
reqStart[1] = 0;
reqStart[2] = 0;
DistanceImageType::RegionType reqRegion;
reqRegion.SetSize(reqSize);
reqRegion.SetIndex(reqStart);
this->FillImageRegion(reqRegion, 1000, distanceImg);
reqStart[0] = 0;
reqStart[1] = 0;
reqStart[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2]-1;
reqRegion.SetIndex(reqStart);
this->FillImageRegion(reqRegion, 1000, distanceImg);
reqSize[0] = 1;
reqSize[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1];
reqSize[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2];;
reqStart[0] = 0;
reqStart[1] = 0;
reqStart[2] = 0;
reqRegion.SetSize(reqSize);
reqRegion.SetIndex(reqStart);
this->FillImageRegion(reqRegion, 1000, distanceImg);
reqStart[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0]-1;
reqStart[1] = 0;
reqStart[2] = 0;
reqRegion.SetIndex(reqStart);
this->FillImageRegion(reqRegion, 1000, distanceImg);
reqSize[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0];
reqSize[1] = 1;
reqSize[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2];;
reqStart[0] = 0;
reqStart[1] = 0;
reqStart[2] = 0;
reqRegion.SetSize(reqSize);
reqRegion.SetIndex(reqStart);
this->FillImageRegion(reqRegion, 1000, distanceImg);
reqStart[0] = 0;
reqStart[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1]-1;
reqStart[2] = 0;
reqRegion.SetIndex(reqStart);
this->FillImageRegion(reqRegion, 1000, distanceImg);
// Now we make some kind of region growing from the middle of the image to set all
// inner pixels to -10. In this way we assure to extract a valid surface
NeighborhoodImageIterator nIt2(radius, distanceImg, distanceImg->GetLargestPossibleRegion());
currentIndex[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0]*0.5;
currentIndex[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1]*0.5;
currentIndex[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2]*0.5;
narrowbandPoints.push(currentIndex);
distanceImg->SetPixel(currentIndex, -10);
while ( !narrowbandPoints.empty() )
{
nIt2.SetLocation(narrowbandPoints.front());
narrowbandPoints.pop();
for (int i = 0; i < 6; i++)
{
if( nIt2.GetPixel(relativeNbIdx[i]) == 10)
{
currentIndex = nIt2.GetIndex(relativeNbIdx[i]);
nIt2.SetPixel(relativeNbIdx[i], -10);
narrowbandPoints.push(currentIndex);
}
}
}
Image::Pointer resultImage = this->GetOutput();
// Cast the created distance-Image from itk::Image to the mitk::Image
// that is our output.
CastToMitkImage(distanceImg, resultImage);
}
