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());
}
void readwarpfile(int nlhs,
mxArray *plhs[],
int nrhs,
const mxArray *prhs[])
{
typedef int PixelType;
typedef itk::Image< PixelType, Dimension > ImageType;
// mexPrintf("the dimentsion is ", Dimension);
// typedef PixelType;
typedef itk::Vector<PixelType, Dimension> VectorPixelType;
typedef itk::Image<VectorPixelType, Dimension> DeformationFieldType;
typedef itk::WarpImageFilter
<ImageType, ImageType, DeformationFieldType> WarperType;
mexPrintf("input number is: %d", nrhs);
mexPrintf("output parameternumber is: %d", nlhs);
// mexPrintf("the dimentsion is :%d", Dimension);
//boost::timer timer;
typename DeformationFieldType::SizeType size;
typename DeformationFieldType::IndexType start;
unsigned int numPix(1u);
char * inputDfFilename;
mwSize matlabdims[Dimension];
// here, we should read image parameter
for (unsigned int d=0; d<Dimension; d++)
{
matlabdims[d]= mxGetDimensions(prhs[1])[d];
size[d] = matlabdims[d];
start[d] = 0;
numPix *= size[d];
// inptrs[d] = static_cast<const MatlabPixelType *>(mxGetData(prhs[d]));
}
inputDfFilename = mxArrayToString(prhs[0]);
mexPrintf("output file name is %s", inputDfFilename);
typename itk::ImageFileReader<DeformationFieldType>::Pointer df_reader = itk::ImageFileReader<DeformationFieldType>::New();
df_reader->SetFileName(inputDfFilename);
df_reader->Update();
// Allocate images and deformation field
typename ImageType::Pointer image
= ImageType::New();
typename DeformationFieldType::Pointer field = DeformationFieldType::New();
// typename DeformationFieldType::Pointer field = 0;
typename DeformationFieldType::SpacingType spacing;
spacing.Fill( 1.0 );
typename DeformationFieldType::PointType origin;
origin.Fill( 0.0 );
typename DeformationFieldType::RegionType region;
field = df_reader->GetOutput();
region = field->GetLargestPossibleRegion();
// initialize output point
const mxClassID classID = mxGetClassID(prhs[1]);
MatlabPixelType * fieldoutptrs[Dimension];
for (unsigned int d=0; d<Dimension; d++)
{
plhs[d] = mxCreateNumericArray(
Dimension, matlabdims, classID, mxREAL);
fieldoutptrs[d] = static_cast<MatlabPixelType *>(mxGetData(plhs[d]));
}
// read field
VectorPixelType * fieldptr = field->GetBufferPointer();
const VectorPixelType * const buff_end = fieldptr + numPix;
while ( fieldptr != buff_end )
{
for (unsigned int d=0; d<Dimension; d++)
{
*(fieldoutptrs[d])++ = (*fieldptr)[d];
}
++fieldptr;
}
}