void CreateKernel(ImageType::Pointer kernel, unsigned int width)
{
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
size.Fill(width);
ImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
kernel->SetRegions(region);
kernel->Allocate();
itk::ImageRegionIterator<ImageType> imageIterator(kernel, region);
while(!imageIterator.IsAtEnd())
{
//imageIterator.Set(255);
imageIterator.Set(1);
++imageIterator;
}
}
void setUp()
{
typedef itk::Image<double, 3> ImageType;
typedef itk::VectorImage<double, 3> VectorImageType;
typedef itk::ImageRegionIterator<ImageType> ImageIteratorType;
typedef itk::ImageDuplicator<ImageType> DuplicatorType;
typedef itk::ComposeImageFilter<ImageType> CompositeFilterType;
// generate two images with one component
ImageType::Pointer imageComponent1 = itk::Image<double, 3>::New();
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
size.Fill(5);
ImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
imageComponent1->SetRegions(region);
imageComponent1->Allocate();
DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(imageComponent1);
duplicator->Update();
ImageType::Pointer imageComponent2 = duplicator->GetOutput();
// give them differing data
ImageIteratorType iterator1(imageComponent1, imageComponent1->GetLargestPossibleRegion());
iterator1.GoToBegin();
int i = 0;
while (!iterator1.IsAtEnd())
{
iterator1.Set((double)i);
++iterator1;
++i;
}
ImageIteratorType iterator2(imageComponent2, imageComponent2->GetLargestPossibleRegion());
iterator2.GoToBegin();
i = 2000;
while (!iterator2.IsAtEnd())
{
iterator2.Set((double)i);
++iterator2;
++i;
}
// copy into single VectorImage
CompositeFilterType::Pointer compositeFilter = CompositeFilterType::New();
compositeFilter->SetInput(0, imageComponent1);
compositeFilter->SetInput(1, imageComponent2);
compositeFilter->Update();
itk::VectorImage<double, 3>::Pointer multiComponentImage = compositeFilter->GetOutput();
// cast images to mitk
mitk::CastToMitkImage(multiComponentImage, m_mitkMultiComponentImage);
mitk::CastToMitkImage(imageComponent1, m_mitkImageComponent1);
mitk::CastToMitkImage(imageComponent2, m_mitkImageComponent2);
}
ImageType::Pointer SBImageUtils::ResizeImage(ImageType::Pointer input, uint width, uint height)
{
ResampleImageFilterType::Pointer resample = ResampleImageFilterType::New();
ImageType::SizeType outputSize;
outputSize.Fill(width);
ImageType::SizeType inputSize = input->GetLargestPossibleRegion().GetSize();
ImageType::SpacingType outputSpacing;
outputSpacing[0] = input->GetSpacing()[0] * (static_cast<double>(inputSize[0]) / static_cast<double>(outputSize[0]));
outputSpacing[1] = input->GetSpacing()[1] * (static_cast<double>(inputSize[1]) / static_cast<double>(outputSize[1]));
//default will be white
resample->SetDefaultPixelValue(0xFFFF);
resample->SetInput(input);
resample->SetSize(outputSize);
resample->SetOutputSpacing(outputSpacing);
resample->SetTransform(TransformType::New());
resample->UpdateLargestPossibleRegion();
return resample->GetOutput();
}
/*
* mexFunction(): entry point for the mex function
*/
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
// interface to deal with input arguments from Matlab
enum InputIndexType {IN_TRI, IN_X, IN_RES, IN_SIZE, IN_ORIGIN, InputIndexType_MAX};
MatlabImportFilter::Pointer matlabImport = MatlabImportFilter::New();
matlabImport->ConnectToMatlabFunctionInput(nrhs, prhs);
// check the number of input arguments
matlabImport->CheckNumberOfArguments(2, InputIndexType_MAX);
// register the inputs for this function at the import filter
typedef MatlabImportFilter::MatlabInputPointer MatlabInputPointer;
MatlabInputPointer inTRI = matlabImport->RegisterInput(IN_TRI, "TRI");
MatlabInputPointer inX = matlabImport->RegisterInput(IN_X, "X"); // (x, y, z)
MatlabInputPointer inRES = matlabImport->RegisterInput(IN_RES, "RES"); // (r, c, s)
MatlabInputPointer inSIZE = matlabImport->RegisterInput(IN_SIZE, "SIZE"); // (r, c, s)
MatlabInputPointer inORIGIN = matlabImport->RegisterInput(IN_ORIGIN, "ORIGIN"); // (x, y, z)
// interface to deal with outputs to Matlab
enum OutputIndexType {OUT_IM, OutputIndexType_MAX};
MatlabExportFilter::Pointer matlabExport = MatlabExportFilter::New();
matlabExport->ConnectToMatlabFunctionOutput(nlhs, plhs);
// check that the number of outputs the user is asking for is valid
matlabExport->CheckNumberOfArguments(0, OutputIndexType_MAX);
// register the outputs for this function at the export filter
typedef MatlabExportFilter::MatlabOutputPointer MatlabOutputPointer;
MatlabOutputPointer outIM = matlabExport->RegisterOutput(OUT_IM, "IM");
// if any input point set is empty, the outputs are empty too
if (mxIsEmpty(inTRI->pm) || mxIsEmpty(inX->pm)) {
matlabExport->CopyEmptyArrayToMatlab(outIM);
return;
}
// get number of rows in inputs X and TRI
mwSize nrowsX = mxGetM(inX->pm);
mwSize nrowsTRI = mxGetM(inTRI->pm);
// instantiate mesh
MeshType::Pointer mesh = MeshType::New();
// read vertices
PointSetType::Pointer xDef = PointSetType::New(); // default: empty point set
PointSetType::Pointer x = PointSetType::New();
x->GetPoints()->CastToSTLContainer()
= matlabImport->ReadVectorOfVectorsFromMatlab<PointType::CoordRepType, PointType>
(inX, xDef->GetPoints()->CastToSTLContainer());
#ifdef DEBUG
std::cout << "Number of X points read = " << x->GetNumberOfPoints() << std::endl;
#endif
// assertion check
if (nrowsX != x->GetNumberOfPoints()) {
mexErrMsgTxt(("Input " + inX->name
+ ": Number of points read different from number of points provided by user").c_str());
}
// swap XY coordinates to make them compliant with ITK convention
// (see important programming note at the help header above)
matlabImport->SwapXYInVectorOfVectors<PointType::CoordRepType, std::vector<PointType> >
(x->GetPoints()->CastToSTLContainer(), x->GetNumberOfPoints());
// populate mesh with vertices
mesh->SetPoints(x->GetPoints());
// read triangles
PointType triDef;
triDef.Fill(mxGetNaN());
for (mwIndex i = 0; i < nrowsTRI; ++i) {
PointType triangle = matlabImport->ReadRowVectorFromMatlab<CoordType, PointType>(inTRI, i, triDef);
// create a triangle cell to read the vertex indices of the current input triangle
CellAutoPointer cell;
cell.TakeOwnership(new TriangleType);
// assign to the 0, 1, 2 elements in the triangle cell the vertex
// indices that we have just read. Note that we have to substract
// 1 to convert Matlab's index convention 1, 2, 3, ... to C++
// convention 0, 1, 2, ...
cell->SetPointId(0, triangle[0] - 1);
cell->SetPointId(1, triangle[1] - 1);
cell->SetPointId(2, triangle[2] - 1);
// insert cell into the mesh
mesh->SetCell(i, cell);
}
#ifdef DEBUG
std::cout << "Number of triangles read = " << mesh->GetNumberOfCells() << std::endl;
#endif
// assertion check
if (nrowsTRI != mesh->GetNumberOfCells()) {
mexErrMsgTxt(("Input " + inTRI->name
+ ": Number of triangles read different from number of triangles provided by user").c_str());
}
// get user input parameters for the output rasterization
ImageType::SpacingType spacingDef;
spacingDef.Fill(1.0);
ImageType::SpacingType spacing = matlabImport->
ReadRowVectorFromMatlab<ImageType::SpacingValueType, ImageType::SpacingType>(inRES, spacingDef);
ImageType::SizeType sizeDef;
sizeDef.Fill(10);
ImageType::SizeType size = matlabImport->
ReadRowVectorFromMatlab<ImageType::SizeValueType, ImageType::SizeType>(inSIZE, sizeDef);
ImageType::PointType originDef;
originDef.Fill(0.0);
ImageType::PointType origin = matlabImport->
ReadRowVectorFromMatlab<ImageType::PointType::ValueType, ImageType::PointType>(inORIGIN, originDef);
// (see important programming note at the help header above)
matlabImport->SwapXYInVector<ImageType::PointType::ValueType, ImageType::PointType>(origin);
// instantiate rasterization filter
MeshFilterType::Pointer meshFilter = MeshFilterType::New();
// smallest voxel side length
ImageType::SpacingValueType minSpacing = spacing[0];
for (mwIndex i = 1; i < Dimension; ++i) {
minSpacing = std::min(minSpacing, spacing[i]);
}
// pass input parameters to the filter
meshFilter->SetInput(mesh);
meshFilter->SetSpacing(spacing);
meshFilter->SetSize(size);
meshFilter->SetOrigin(origin);
meshFilter->SetTolerance(minSpacing / 10.0);
meshFilter->SetInsideValue(1);
meshFilter->SetOutsideValue(0);
ImageType::IndexType start;
start.Fill(0);
meshFilter->SetIndex(start);
// convert image size from itk::Size format to std::vector<mwSize>
// so that we can use it in GraftItkImageOntoMatlab
std::vector<mwSize> sizeStdVector(Dimension);
for (unsigned int i = 0; i < Dimension; ++i) {
sizeStdVector[i] = size[i];
}
// graft ITK filter output onto Matlab output
matlabExport->GraftItkImageOntoMatlab<PixelType, Dimension>
(outIM, meshFilter->GetOutput(), sizeStdVector);
#ifdef DEBUG
std::cout << "Resolution (spacing) = " << meshFilter->GetSpacing() << std::endl;
std::cout << "Size = " << meshFilter->GetSize() << std::endl;
std::cout << "Origin = " << meshFilter->GetOrigin() << std::endl;
#endif
// run rasterization
meshFilter->Update();
}
