static mitk::Image::Pointer GenerateMaskImage(unsigned int dimX,
unsigned int dimY,
unsigned int dimZ,
float spacingX = 1,
float spacingY = 1,
float spacingZ = 1)
{
typedef itk::Image< TPixelType, 3 > ImageType;
typename ImageType::RegionType imageRegion;
imageRegion.SetSize(0, dimX);
imageRegion.SetSize(1, dimY);
imageRegion.SetSize(2, dimZ);
typename ImageType::SpacingType spacing;
spacing[0] = spacingX;
spacing[1] = spacingY;
spacing[2] = spacingZ;
mitk::Point3D origin; origin.Fill(0.0);
itk::Matrix<double, 3, 3> directionMatrix; directionMatrix.SetIdentity();
typename ImageType::Pointer image = ImageType::New();
image->SetSpacing( spacing );
image->SetOrigin( origin );
image->SetDirection( directionMatrix );
image->SetLargestPossibleRegion( imageRegion );
image->SetBufferedRegion( imageRegion );
image->SetRequestedRegion( imageRegion );
image->Allocate();
image->FillBuffer(1);
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( image.GetPointer() );
mitkImage->SetVolume( image->GetBufferPointer() );
return mitkImage;
}
typename PatchExtractor<PValue>::ImageType::Pointer
PatchExtractor<PValue>::ExtractPatch()
{
ContIndexType startIndex;
for(unsigned int i = 0; i < 2; i++)
{
startIndex[i] = m_Center[i] - (m_Size[i] / 2.0);
}
startIndex[2] = 0;
PointType newOrigin;
m_Image->TransformContinuousIndexToPhysicalPoint(startIndex, newOrigin);
typename ImageType::Pointer patch = ImageType::New();
patch->SetDirection(m_Image->GetDirection());
patch->SetOrigin(newOrigin);
patch->SetSpacing(m_Image->GetSpacing());
typename ImageType::RegionType region;
m_Size[2] = 1;
region.SetSize(m_Size);
patch->SetRegions(region);
patch->Allocate();
typedef itk::NearestNeighborInterpolateImageFunction<ImageType, double> InterpolatorType;
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetInputImage(m_Image);
itk::ImageRegionIterator<ImageType> imageIt(patch, region);
while(!imageIt.IsAtEnd())
{
typename ImageType::IndexType index = imageIt.GetIndex();
PointType point;
patch->TransformIndexToPhysicalPoint(index, point);
if(interpolator->IsInsideBuffer(point))
imageIt.Set(interpolator->Evaluate(point));
else
imageIt.Set(0);
++imageIt;
}
return patch;
}
static mitk::Image::Pointer GenerateGradientWithDimXImage(unsigned int dimX,
unsigned int dimY,
unsigned int dimZ,
float spacingX = 1,
float spacingY = 1,
float spacingZ = 1)
{
typedef itk::Image< TPixelType, 3 > ImageType;
typename ImageType::RegionType imageRegion;
imageRegion.SetSize(0, dimX);
imageRegion.SetSize(1, dimY);
imageRegion.SetSize(2, dimZ);
typename ImageType::SpacingType spacing;
spacing[0] = spacingX;
spacing[1] = spacingY;
spacing[2] = spacingZ;
mitk::Point3D origin; origin.Fill(0.0);
itk::Matrix<double, 3, 3> directionMatrix; directionMatrix.SetIdentity();
typename ImageType::Pointer image = ImageType::New();
image->SetSpacing( spacing );
image->SetOrigin( origin );
image->SetDirection( directionMatrix );
image->SetLargestPossibleRegion( imageRegion );
image->SetBufferedRegion( imageRegion );
image->SetRequestedRegion( imageRegion );
image->Allocate();
image->FillBuffer(0.0);
typedef itk::ImageRegionIterator<ImageType> IteratorOutputType;
IteratorOutputType it(image, imageRegion);
it.GoToBegin();
TPixelType val = 0;
while(!it.IsAtEnd())
{
it.Set(val % dimX);
val++;
++it;
}
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( image.GetPointer() );
mitkImage->SetVolume( image->GetBufferPointer() );
return mitkImage;
}
void WorkbenchUtils::addPaddingItk(itk::Image <PixelType, ImageDimension> *itkImage, Axis axis, bool append,
int numberOfSlices, float pixelValue, Image::Pointer outImage) {
// pixel type is templated. The input field for the value is set to float, so the user might enter some invalid values for the image type at hand.
// since all primitive built-in types have well defined casting behaviour between each other, we'll just do a typecast. we will clip the entered
// value at PixelTypes min/max to prevent an overflow. The possible loss of precision is ignored.
float lower = itk::NumericTraits<PixelType>::min();
float upper = itk::NumericTraits<PixelType>::max();
float clippedPixelValue = std::max(lower, std::min(pixelValue, upper));
PixelType paddingPixelValue = (PixelType) clippedPixelValue;
typedef itk::Image <PixelType, ImageDimension> ImageType;
// gather all data
typename ImageType::SizeType lowerBound;
typename ImageType::SizeType upperBound;
lowerBound.Fill(0);
upperBound.Fill(0);
unsigned int itkAxis = convertToItkAxis(axis);
if (append) {
upperBound[itkAxis] = numberOfSlices;
} else {
lowerBound[itkAxis] = numberOfSlices;
}
// setup the filter
typedef itk::ConstantPadImageFilter <ImageType, ImageType> PadFilterType;
typename PadFilterType::Pointer padFilter = PadFilterType::New();
padFilter->SetInput(itkImage);
padFilter->SetConstant(paddingPixelValue);
padFilter->SetPadLowerBound(lowerBound);
padFilter->SetPadUpperBound(upperBound);
padFilter->UpdateLargestPossibleRegion();
// Update the origin, since padding creates negative index that is lost when returned to MITK
typename ImageType::Pointer paddedImage = padFilter->GetOutput();
typename ImageType::RegionType paddedImageRegion = paddedImage->GetLargestPossibleRegion();
typename ImageType::PointType origin;
paddedImage->TransformIndexToPhysicalPoint(paddedImageRegion.GetIndex(), origin);
paddedImage->SetOrigin(origin);
// get the results and cast them back to mitk. return via out parameter.
outImage->InitializeByItk(paddedImage.GetPointer());
CastToMitkImage(paddedImage, outImage);
}
void invcondemonsforces(int nlhs,
mxArray *plhs[],
int nrhs,
const mxArray *prhs[])
{
typedef float PixelType;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef float VectorComponentType;
typedef itk::Vector<VectorComponentType, Dimension> VectorPixelType;
typedef itk::Image<VectorPixelType, Dimension> DeformationFieldType;
typedef itk::ESMInvConDemonsRegistrationFunction
<ImageType,ImageType,DeformationFieldType> DemonsRegistrationFunctionType;
//boost::timer timer;
// Allocate images and deformation field
typename ImageType::Pointer fixedimage
= ImageType::New();
typename ImageType::Pointer movingimage
= ImageType::New();
typename ImageType::Pointer fw_weightimage
= ImageType::New();
typename DeformationFieldType::Pointer field
= DeformationFieldType::New();
typename ImageType::Pointer jacobianimage
= ImageType::New();
typename DeformationFieldType::Pointer inv_field
= DeformationFieldType::New();
typename DeformationFieldType::Pointer update
= DeformationFieldType::New();
typename DeformationFieldType::SpacingType spacing;
spacing.Fill( 1.0 );
typename DeformationFieldType::PointType origin;
origin.Fill( 0.0 );
typename DeformationFieldType::RegionType region;
typename DeformationFieldType::SizeType size;
typename DeformationFieldType::IndexType start;
unsigned int numPix(1u);
const MatlabPixelType * fixinptr = static_cast<const MatlabPixelType *>(mxGetData(prhs[0]));
const MatlabPixelType * movinptr = static_cast<const MatlabPixelType *>(mxGetData(prhs[1]));
const MatlabPixelType * fieldinptrs[Dimension];
const MatlabPixelType * inv_fieldinptrs[Dimension];
mwSize matlabdims[Dimension];
for (unsigned int d=0; d<Dimension; d++)
{
matlabdims[d]= mxGetDimensions(prhs[0])[d];
size[d] = matlabdims[d];
start[d] = 0;
numPix *= size[d];
fieldinptrs[d] = static_cast<const MatlabPixelType *>(mxGetData(prhs[2+d]));
inv_fieldinptrs[d] = static_cast<const MatlabPixelType *>(mxGetData(prhs[2+Dimension+d]));
}
const MatlabPixelType * jacobianptr = static_cast<const MatlabPixelType *> (mxGetData(prhs[2*Dimension + 2]));
const MatlabPixelType * fw_weightptr = static_cast<const MatlabPixelType *> (mxGetData(prhs[2*Dimension + 3]));
const double RegWeight = static_cast<double>( mxGetPr(prhs[2*Dimension+4])[0] );
const unsigned int UseJacFlag = 1;
//std::cout << "RegWeight : " << RegWeight << std::endl;
region.SetSize( size );
region.SetIndex( start );
fixedimage->SetOrigin( origin );
fixedimage->SetSpacing( spacing );
fixedimage->SetRegions( region );
fixedimage->Allocate();
movingimage->SetOrigin( origin );
movingimage->SetSpacing( spacing );
movingimage->SetRegions( region );
movingimage->Allocate();
fw_weightimage->SetOrigin( origin );
fw_weightimage->SetSpacing( spacing );
fw_weightimage->SetRegions( region );
fw_weightimage->Allocate();
field->SetOrigin( origin );
field->SetSpacing( spacing );
field->SetRegions( region );
field->Allocate();
inv_field->SetOrigin( origin );
inv_field->SetSpacing( spacing );
inv_field->SetRegions( region );
inv_field->Allocate();
update->SetOrigin( origin );
update->SetSpacing( spacing );
update->SetRegions( region );
update->Allocate();
if (UseJacFlag > 0)
{
jacobianimage->SetOrigin( origin );
jacobianimage->SetSpacing( spacing );
jacobianimage->SetRegions( region );
jacobianimage->Allocate();
}
//mexPrintf("done Allocate(); %f sec\n", timer.elapsed());
//timer.restart();
PixelType * fixptr = fixedimage->GetBufferPointer();
const PixelType * const fixbuff_end = fixptr + numPix;
PixelType * movptr = movingimage->GetBufferPointer();
PixelType * fwweightptr = NULL;
PixelType * jacptr = NULL;
if (UseJacFlag > 0)
{
jacptr = jacobianimage->GetBufferPointer();
}
fwweightptr = fw_weightimage->GetBufferPointer();
VectorPixelType * fieldptr = field->GetBufferPointer();
VectorPixelType * inv_fieldptr = inv_field->GetBufferPointer();
while ( fixptr != fixbuff_end )
{
*fixptr++ = *fixinptr++;
*movptr++ = *movinptr++;
*fwweightptr++ = *fw_weightptr++;
for (unsigned int d=0; d<Dimension; d++)
{
(*fieldptr)[d] = *(fieldinptrs[d])++;
}
if (UseJacFlag > 0)
{
*jacptr++ = *jacobianptr++;
}
++fieldptr;
for (unsigned int d=0; d<Dimension; d++)
{
(*inv_fieldptr)[d] = *(inv_fieldinptrs[d])++;
}
++inv_fieldptr;
}
// Create demons function
typename DemonsRegistrationFunctionType::Pointer drfp
= DemonsRegistrationFunctionType::New();
//mexPrintf("step size: %f\n",mxGetPr(prhs[2*Dimension+2])[0]);
//drfp->SetMaximumUpdateStepLength( mxGetPr(prhs[2*Dimension+2])[0] );
typename DemonsRegistrationFunctionType::GradientType gtype = DemonsRegistrationFunctionType::Symmetric;
drfp->SetUseGradientType( gtype );
drfp->SetDeformationField( field );
drfp->SetInvDeformationField( inv_field);
drfp->SetFixedImage( fixedimage );
drfp->SetMovingImage( movingimage );
drfp->SetRegWeight(RegWeight);
drfp->SetUseFwWeight(true);
drfp->SetFwWeightImage(fw_weightimage);
if (UseJacFlag > 0)
{
drfp->SetUseJacobian(true);
drfp->SetJacobianDetImage(jacobianimage);
}
else
{
drfp->SetUseJacobian(false);
}
drfp->InitializeIteration();
//mexPrintf("done demons function init %f sec\n", timer.elapsed());
//timer.restart();
const itk::Size<Dimension> radius = drfp->GetRadius();
// Break the input into a series of regions. The first region is free
// of boundary conditions, the rest with boundary conditions. We operate
// on the output region because input has been copied to output.
typedef itk::NeighborhoodAlgorithm::ImageBoundaryFacesCalculator
<DeformationFieldType> FaceCalculatorType;
typedef typename FaceCalculatorType::FaceListType FaceListType;
typedef typename DemonsRegistrationFunctionType::NeighborhoodType
NeighborhoodIteratorType;
typedef itk::ImageRegionIterator<DeformationFieldType> UpdateIteratorType;
FaceCalculatorType faceCalculator;
FaceListType faceList = faceCalculator(field, region, radius);
typename FaceListType::iterator fIt = faceList.begin();
// Ask the function object for a pointer to a data structure it
// will use to manage any global values it needs. We'll pass this
// back to the function object at each calculation and then
// again so that the function object can use it to determine a
// time step for this iteration.
void * globalData = drfp->GetGlobalDataPointer();
// Process the non-boundary region.
NeighborhoodIteratorType nD(radius, field, *fIt);
UpdateIteratorType nU(update, *fIt);
nD.GoToBegin();
while( !nD.IsAtEnd() )
{
nU.Value() = drfp->ComputeUpdate(nD, globalData);
++nD;
++nU;
}
// Process each of the boundary faces.
NeighborhoodIteratorType bD;
UpdateIteratorType bU;
for (++fIt; fIt != faceList.end(); ++fIt)
{
bD = NeighborhoodIteratorType(radius, field, *fIt);
bU = UpdateIteratorType(update, *fIt);
bD.GoToBegin();
bU.GoToBegin();
while ( !bD.IsAtEnd() )
{
bU.Value() = drfp->ComputeUpdate(bD, globalData);
++bD;
++bU;
}
}
// Ask the finite difference function to compute the time step for
// this iteration. We give it the global data pointer to use, then
// ask it to free the global data memory.
//timeStep = df->ComputeGlobalTimeStep(globalData);
drfp->ReleaseGlobalDataPointer(globalData);
//mexPrintf("done actual computations %f sec\n", timer.elapsed());
//timer.restart();
// Allocate outputs
const mxClassID classID = mxGetClassID(prhs[0]);
MatlabPixelType * outptrs[Dimension];
for (unsigned int d=0; d<Dimension; d++)
{
plhs[d] = mxCreateNumericArray(
Dimension, matlabdims, classID, mxREAL);
outptrs[d] = static_cast<MatlabPixelType *>(mxGetData(plhs[d]));
}
//mexPrintf("done allocate outputs %f sec\n", timer.elapsed());
//timer.restart();
// put result into outputs
const VectorPixelType * upptr = update->GetBufferPointer();
const VectorPixelType * const upbuff_end = upptr + numPix;
while ( upptr != upbuff_end )
{
for (unsigned int d=0; d<Dimension; d++)
{
*(outptrs[d])++ = (*upptr)[d];
}
++upptr;
}
//mexPrintf("done outputs copy %f sec\n", timer.elapsed());
}