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);
}
// ------------------------------------------------------------------------
void buildShortAxisVolume(const SeriesTransform::Map &transforms,
const unsigned int seriesNumber, ImageType::Pointer &saVolume)
{
// get the short axis transforms
SeriesTransform::Map::const_iterator mapIt = transforms.begin();
std::vector<SeriesTransform> saSlices;
while(mapIt != transforms.end())
{
if(mapIt->second.series == seriesNumber)
{
unsigned int sliceNum = mapIt->second.slice;
if(saSlices.size() < (sliceNum+1))
saSlices.resize(sliceNum+1);
saSlices[sliceNum] = mapIt->second;
}
++mapIt;
}
// get the dimensions of the output image
ImageType::Pointer reference = saSlices[0].images[0];
unsigned int x,y,z;
x = reference->GetLargestPossibleRegion().GetSize()[0];
y = reference->GetLargestPossibleRegion().GetSize()[1];
z = saSlices.size();
ImageType::RegionType region;
ImageType::SizeType size;
ImageType::IndexType index;
size[0] = x;
size[1] = y;
size[2] = z;
index.Fill(0);
region.SetSize(size);
region.SetIndex(index);
// get the other parts
ImageType::SpacingType spacing = reference->GetSpacing();
spacing[2] = saSlices[0].sliceThickness;
ImageType::DirectionType direction = reference->GetDirection();
ImageType::PointType origin = reference->GetOrigin();
saVolume->SetOrigin(origin);
saVolume->SetDirection(direction);
saVolume->SetSpacing(spacing);
saVolume->SetRegions(region);
saVolume->Allocate();
saVolume->FillBuffer(0);
}
void RGBFilter::SetInput(ImageType::Pointer InputImage){
this->inputImage = InputImage;
// output image allocation
this->outputImage = ImageType::New();
ImageType::IndexType outputIndex;
outputIndex.Fill(0);
RegionType anotherRegion;
anotherRegion.SetIndex(outputIndex);
anotherRegion.SetSize(this->inputImage->GetLargestPossibleRegion().GetSize());
outputImage->SetLargestPossibleRegion(anotherRegion);
outputImage->SetBufferedRegion(anotherRegion);
outputImage->SetRequestedRegion(anotherRegion);
outputImage->Allocate();
this->ImRed = ChannelType::New();
ChannelType::IndexType outputIndex2;
outputIndex2.Fill(0);
RegionType anotherRegion2;
anotherRegion2.SetIndex(outputIndex2);
anotherRegion2.SetSize(this->inputImage->GetLargestPossibleRegion().GetSize());
ImRed->SetLargestPossibleRegion(anotherRegion2);
ImRed->SetBufferedRegion(anotherRegion2);
ImRed->SetRequestedRegion(anotherRegion2);
ImRed->Allocate();
this->ImGreen = ChannelType::New();
ChannelType::IndexType outputIndex3;
outputIndex3.Fill(0);
RegionType anotherRegion3;
anotherRegion3.SetIndex(outputIndex3);
anotherRegion3.SetSize(this->inputImage->GetLargestPossibleRegion().GetSize());
ImGreen->SetLargestPossibleRegion(anotherRegion3);
ImGreen->SetBufferedRegion(anotherRegion3);
ImGreen->SetRequestedRegion(anotherRegion3);
ImGreen->Allocate();
this->ImBlue = ChannelType::New();
ChannelType::IndexType outputIndex4;
outputIndex4.Fill(0);
RegionType anotherRegion4;
anotherRegion4.SetIndex(outputIndex4);
anotherRegion4.SetSize(this->inputImage->GetLargestPossibleRegion().GetSize());
ImBlue->SetLargestPossibleRegion(anotherRegion4);
ImBlue->SetBufferedRegion(anotherRegion4);
ImBlue->SetRequestedRegion(anotherRegion4);
ImBlue->Allocate();
}
int main(int argc, char ** argv)
{
std::string folderName = argv[1];
std::string filter = argv[2];
typedef utils::Directory Directory;
Directory::FilenamesType filenames = Directory::GetFiles(folderName, ".nrrd");
Directory::FilenamesType goodFilenames;
filterFilenames(filenames, filter, goodFilenames);
// load the images
std::vector<ImageType::Pointer> imageList;
for(unsigned int i = 0; i < goodFilenames.size(); i++)
{
std::cout << goodFilenames[i] << std::endl;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(goodFilenames[i]);
reader->SetImageIO(itk::NrrdImageIO::New());
reader->Update();
imageList.push_back(reader->GetOutput());
}
std::sort(imageList.begin(), imageList.end(), imageSort);
ImageType::Pointer outputImage = ImageType::New();
ImageType::RegionType outputRegion;
ImageType::SizeType outputSize = imageList.front()->GetLargestPossibleRegion().GetSize();
outputSize[2] = imageList.size();
ImageType::IndexType outputIndex;
outputIndex.Fill(0);
outputRegion.SetSize(outputSize);
outputRegion.SetIndex(outputIndex);
// compute the spacing
double meanSpacing = 0.0;
for(unsigned int i = 1; i < imageList.size(); i++)
{
ImageType::Pointer im1 = imageList[i-1];
ImageType::Pointer im2 = imageList[i];
meanSpacing += (im1->GetOrigin()-im2->GetOrigin()).GetNorm();
}
meanSpacing /= (double) (imageList.size()-1);
ImageType::SpacingType spacing = imageList.front()->GetSpacing();
spacing[2] = meanSpacing;
outputImage->SetRegions(outputRegion);
outputImage->SetSpacing(spacing);
outputImage->SetOrigin(imageList.front()->GetOrigin());
outputImage->SetDirection(imageList.front()->GetDirection());
outputImage->Allocate();
itk::ImageRegionIterator<ImageType> outIt(outputImage, outputImage->GetLargestPossibleRegion());
outIt.GoToBegin();
while(!outIt.IsAtEnd())
{
ImageType::IndexType index = outIt.GetIndex();
ImageType::IndexType testIndex = index;
testIndex[2] = 0;
outIt.Set(imageList[index[2]]->GetPixel(testIndex));
++outIt;
}
std::string stackFilename = folderName + "/stack.nrrd";
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(outputImage);
writer->SetFileName(stackFilename);
writer->SetImageIO(itk::NrrdImageIO::New());
writer->Update();
return 0;
}
void LabelsVolumeGenerator::postProcessTargetITK()
{
typedef unsigned char PixelType;
typedef Image<PixelType, 3> ImageType;
// create a new image from the target data
ImageType::Pointer input = ImageType::New();
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
for (int i = 0; i < 3; ++i) size[i] = m_targetVolume->dimensions[i];
ImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
input->SetRegions(region);
input->SetSpacing(m_targetVolume->spacing.data());
input->Allocate();
memcpy(input->GetBufferPointer(), m_targetVolume->data, m_bufferSize);
// create a grayscale dilation filter and a structuring element
typedef BinaryBallStructuringElement<PixelType, 3> StructureType;
typedef GrayscaleDilateImageFilter<ImageType, ImageType, StructureType> DilateFilterType;
DilateFilterType::Pointer filter = DilateFilterType::New();
StructureType structure;
structure.SetRadius(1);
filter->SetKernel(structure);
// set up progress reporting
if (m_progressReporter)
{
CStyleCommand::Pointer command = CStyleCommand::New();
command->SetClientData(m_progressReporter);
command->SetCallback(ProgressCallback);
filter->AddObserver(ProgressEvent(), command);
m_progressReporter->start("Post-Processing Label volume",
"Dilating label field...");
}
// hook up the filters and run
filter->SetInput(input);
filter->Update();
if (m_progressReporter)
m_progressReporter->finish();
// copy back into the target volume data
memcpy(m_targetVolume->data, filter->GetOutput()->GetBufferPointer(), m_bufferSize);
// threshold and gaussian blur to put a smooth version into the alpha channel
typedef BinaryThresholdImageFilter<ImageType, ImageType> ThresholderType;
// typedef DiscreteGaussianImageFilter<ImageType, ImageType> SmoothFilterType;
typedef SmoothingRecursiveGaussianImageFilter<ImageType, ImageType> SmoothFilterType;
ThresholderType::Pointer thresholder = ThresholderType::New();
thresholder->SetLowerThreshold(1);
thresholder->SetUpperThreshold(255);
thresholder->SetInsideValue(255);
thresholder->SetOutsideValue(0);
SmoothFilterType::Pointer smoother = SmoothFilterType::New();
// smoother->SetVariance(0.05); // in physical units
// smoother->SetMaximumKernelWidth(5);
smoother->SetSigma(0.2);
// set up progress reporting (again)
if (m_progressReporter)
{
CStyleCommand::Pointer command = CStyleCommand::New();
command->SetClientData(m_progressReporter);
command->SetCallback(ProgressCallback);
smoother->AddObserver(ProgressEvent(), command);
m_progressReporter->start("Post-Processing Label volume",
"Smoothing alpha mask...");
}
// hook up the filters and run
thresholder->SetInput(input);
smoother->SetInput(thresholder->GetOutput());
smoother->Update();
// copy back into the target volume data
memcpy(m_targetMask->data, smoother->GetOutput()->GetBufferPointer(), m_bufferSize);
if (m_progressReporter)
m_progressReporter->finish();
}
void
DistanceMapFilter::applyDistanceMapFilter(QString flnm,
QList<Vec> clipPos,
QList<Vec> clipNormal,
QList<CropObject> crops,
QList<PathObject> paths,
uchar *lut,
int chan)
{
int bpv = 1;
if (m_voxelType > 0) bpv = 2;
int nbytes = bpv*m_nY*m_nZ;
bool trim = (qRound(m_dataSize.x) < m_height ||
qRound(m_dataSize.y) < m_width ||
qRound(m_dataSize.z) < m_depth);
bool clipPresent = (clipPos.count() > 0);
m_cropPresent = false;
m_tearPresent = false;
m_blendPresent = false;
for(int ci=0; ci<m_crops.count(); ci++)
{
if (crops[ci].cropType() < CropObject::Tear_Tear)
m_cropPresent = true;
else if (crops[ci].cropType() < CropObject::View_Tear)
m_tearPresent = true;
else if (m_crops[ci].cropType() > CropObject::Displace_Displace &&
m_crops[ci].cropType() < CropObject::Glow_Ball)
m_blendPresent = true;
}
m_pathCropPresent = false;
m_pathBlendPresent = false;
for (int i=0; i<m_paths.count(); i++)
{
if (m_paths[i].blend()) m_pathBlendPresent = true;
if (m_paths[i].crop()) m_pathCropPresent = true;
}
m_meshLog->moveCursor(QTextCursor::End);
int d0 = 0;
int d1 = m_nX-1;
int d0z = d0 + qRound(m_dataMin.z);
int d1z = d1 + qRound(m_dataMin.z);
uchar *opacityVol = new uchar[m_nX*m_nY*m_nZ];
uchar *cropped = new uchar[nbytes];
uchar *tmp = new uchar[nbytes];
int i0 = 0;
for(int i=d0z; i<=d1z; i++)
{
m_meshProgress->setValue((int)(100.0*(float)i0/(float)m_nX));
qApp->processEvents();
int iv = qBound(0, i, m_depth-1);
uchar *vslice = m_vfm->getSlice(iv);
memset(cropped, 0, nbytes);
if (!trim)
memcpy(tmp, vslice, nbytes);
else
{
int wmin = qRound(m_dataMin.y);
int hmin = qRound(m_dataMin.x);
if (m_voxelType == 0)
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
tmp[w*m_nZ + h] = vslice[(wmin+w)*m_height + (hmin+h)];
}
else
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
((ushort*)tmp)[w*m_nZ + h] = ((ushort*)vslice)[(wmin+w)*m_height + (hmin+h)];
}
}
int jk = 0;
for(int j=0; j<m_nY; j++)
for(int k=0; k<m_nZ; k++)
{
Vec po = Vec(m_dataMin.x+k, m_dataMin.y+j, iv);
bool ok = true;
// we don't want to scale before pruning
int mop = 0;
{
Vec pp = po - m_dataMin;
int ppi = pp.x/m_pruneLod;
int ppj = pp.y/m_pruneLod;
int ppk = pp.z/m_pruneLod;
ppi = qBound(0, ppi, m_pruneX-1);
ppj = qBound(0, ppj, m_pruneY-1);
ppk = qBound(0, ppk, m_pruneZ-1);
int mopidx = ppk*m_pruneY*m_pruneX + ppj*m_pruneX + ppi;
mop = m_pruneData[3*mopidx + chan];
ok = (mop > 0);
}
po *= m_samplingLevel;
if (ok && clipPresent)
ok = StaticFunctions::getClip(po, clipPos, clipNormal);
if (ok && m_cropPresent)
ok = checkCrop(po);
if (ok && m_pathCropPresent)
ok = checkPathCrop(po);
if (ok && m_blendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkBlend(po, v, lut);
}
if (ok && m_pathBlendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkPathBlend(po, v, lut);
}
if (ok)
cropped[jk] = mop;
else
cropped[jk] = 0;
jk ++;
}
if (m_voxelType == 0)
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
tmp[j] = 0;
}
}
else
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
((ushort*)tmp)[j] = 0;
}
}
applyOpacity(iv, cropped, lut, tmp);
memcpy(opacityVol + i0*m_nY*m_nZ, tmp, m_nY*m_nZ);
i0++;
}
delete [] tmp;
delete [] cropped;
m_meshProgress->setValue(100);
qApp->processEvents();
//------------
if (m_tearPresent)
{
uchar *data0 = new uchar[m_nX*m_nY*m_nZ];
memcpy(data0, opacityVol, m_nX*m_nY*m_nZ);
applyTear(d0, d1, 0,
data0, opacityVol, false);
delete [] data0;
}
typedef uchar PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
size[0] = m_nZ;
size[1] = m_nY;
size[2] = m_nX;
ImageType::RegionType region(start, size);
ImageType::Pointer image = ImageType::New();
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
uchar *iptr = (uchar*)image->GetBufferPointer();
memcpy(iptr, opacityVol, m_nX*m_nY*m_nZ);
typedef itk::Image< float, 3 > OutputImageType;
typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, OutputImageType> DistanceMapFilter;
DistanceMapFilter::Pointer filter = DistanceMapFilter::New();
filter->SetInput( image );
filter->SetSquaredDistance(0);
filter->SetUseImageSpacing(0);
filter->SetInsideIsPositive(1);
filter->Update();
QFile fp;
fp.setFileName(flnm);
fp.open(QFile::WriteOnly);
uchar vt = 8;
fp.write((char*)&vt, 1);
fp.write((char*)&m_nX, 4);
fp.write((char*)&m_nY, 4);
fp.write((char*)&m_nZ, 4);
OutputImageType *dimg = filter->GetOutput();
char *tdata = (char*)(dimg->GetBufferPointer());
fp.write(tdata, 4*m_nX*m_nY*m_nZ);
fp.close();
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText("Signed Distance Map data saved in "+flnm);
QMessageBox::information(0, "", QString("Signed Distance Map saved in "+flnm));
}
/*
* 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();
}