/*
* 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();
}
int main(int, char ** argv)
{
OptionsData options;
readXMLValues(argv[2], options);
exit(1);
// parse the dicom directory
gdcm::Directory dir;
dir.Load(argv[1], true);
gdcm::Directory::FilenamesType filenames = dir.GetFilenames();
gdcm::Tag seriesDescription = gdcm::Tag(0x0008,0x103e);
gdcm::Tag seriesNumber = gdcm::Tag(0x0020,0x0011);
gdcm::Tag instanceNumber = gdcm::Tag(0x0020,0x0013);
gdcm::Tag sliceThickness = gdcm::Tag(0x0018,0x0050);
gdcm::Tag triggerTime = gdcm::Tag(0x0018,0x1060);
gdcm::Tag numberOfImages = gdcm::Tag(0x0018,0x1090);
gdcm::Tag slicePosition = gdcm::Tag(0x0019,0x1015);
gdcm::Tag imagePosition = gdcm::Tag(0x0020,0x0032);
gdcm::Tag imageOrientation = gdcm::Tag(0x0020,0x0037);
gdcm::Tag sliceLocation = gdcm::Tag(0x0020,0x1041);
gdcm::Tag rows = gdcm::Tag(0x0028,0x0010);
gdcm::Tag cols = gdcm::Tag(0x0028,0x0011);
gdcm::Tag pixelSpacing = gdcm::Tag(0x0028,0x0030);
gdcm::Scanner scanner;
scanner.AddTag(seriesDescription);
scanner.AddTag(seriesNumber);
scanner.AddTag(instanceNumber);
scanner.AddTag(sliceThickness);
scanner.AddTag(triggerTime);
scanner.AddTag(numberOfImages);
scanner.AddTag(slicePosition);
scanner.AddTag(imagePosition);
scanner.AddTag(imageOrientation);
scanner.AddTag(sliceLocation);
scanner.AddTag(rows);
scanner.AddTag(cols);
scanner.AddTag(pixelSpacing);
scanner.Scan(filenames);
gdcm::Scanner::MappingType mapping = scanner.GetMappings();
// extract all the images that are Short axis and are the first instance
gdcm::Directory::FilenamesType targetFilenames;
for(unsigned int i = 0; i < filenames.size(); i++)
{
const char * fname = filenames[i].c_str();
if(mapping.count(fname) == 0) continue;
// extract the image information
std::string descriptionStr = mapping[fname][seriesDescription];
std::string instanceNumberStr = mapping[fname][instanceNumber];
QString description = QString::fromStdString(descriptionStr);
unsigned int instanceNumber = QString::fromStdString(instanceNumberStr).toInt();
// check that the description is a short axis one and is instance 1
if(instanceNumber == 1 && description.contains("sa", Qt::CaseInsensitive))
{
targetFilenames.push_back(filenames[i]);
}
}
// sort the images based on their slice position
/*
gdcm::Sorter sorter;
sorter.SetSortFunction(position_sort);
sorter.StableSort(targetFilenames);
gdcm::Directory::FilenamesType sorted = sorter.GetFilenames();
for(unsigned int i = 0; i < sorted.size(); i++)
{
const char * fname = sorted[i].c_str();
std::string position = mapping[fname][imagePosition];
std::cout << position << std::endl;
std::cout << mapping[fname][sliceLocation] << std::endl;
}
*/
std::cout << targetFilenames.size() << std::endl;
// find the slice with the smallest slice position
double smallest = 1000000.0;
int smallestIndex;
for(unsigned int i = 0; i < targetFilenames.size(); i++)
{
const char * fname = targetFilenames[i].c_str();
std::string slicePosition = mapping[fname][sliceLocation];
double pos = QString::fromStdString(slicePosition).toDouble();
std::cout << pos << std::endl;
if(pos < smallest)
{
smallest = pos;
smallestIndex = i;
}
}
// load the image
typedef itk::Image<unsigned short, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(targetFilenames[smallestIndex]);
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(reader->GetOutput());
flipper->Update();
ImageType::Pointer referenceImage = flipper->GetOutput();
ImageType::DirectionType direction = referenceImage->GetDirection();
direction.SetIdentity();
referenceImage->SetDirection(direction);
ImageType::PointType origin = referenceImage->GetOrigin();
origin.Fill(20.0);
referenceImage->SetOrigin(origin);
ImageType::SpacingType spacing;
spacing.Fill(1.0);
referenceImage->SetSpacing(spacing);
flipper->GetOutput()->Print(std::cout);
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(referenceImage);
writer->SetImageIO(itk::NrrdImageIO::New());
writer->SetFileName("test.nrrd");
writer->Update();
std::cout << targetFilenames[smallestIndex] << std::endl;
return 0;
}
// ------------------------------------------------------------------------
void NormaliseImage(const ImageType::Pointer &input,
const ImageType::Pointer &reference,
ImageType::Pointer &output,
SeriesTransform &trans)
{
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(input);
flipper->Update();
output = flipper->GetOutput();
// get the reference offset
vnl_vector<double> refOrigin(3);
refOrigin[0] = reference->GetOrigin()[0];// + trans.translation[0];
refOrigin[1] = reference->GetOrigin()[1];// + trans.translation[1];
refOrigin[2] = reference->GetOrigin()[2];// + trans.translation[2];
vnl_matrix<double> refRot = reference->GetDirection().GetVnlMatrix();
vnl_matrix<double> refRotInv = vnl_inverse(refRot);
vnl_vector<double> refOffset = refRotInv * refOrigin;
// get the image origin
vnl_vector<double> origin(3);
origin[0] = output->GetOrigin()[0];
origin[1] = output->GetOrigin()[1];
origin[2] = output->GetOrigin()[2];
// apply the rotation to the origin
origin = refRotInv * origin;
// apply the offset to the origin
origin = origin - refOffset;
// apply the scaling
origin /= reference->GetSpacing()[0];
// put the values into the output image
ImageType::PointType itkOrigin;
itkOrigin[0] = origin[0];
itkOrigin[1] = origin[1];
itkOrigin[2] = origin[2];
ImageType::SpacingType spacing;
spacing.Fill(output->GetSpacing()[0] / reference->GetSpacing()[0]);
// get the new direction
ImageType::DirectionType dirOut = output->GetDirection();
dirOut = reference->GetDirection().GetInverse() * dirOut.GetVnlMatrix();
output->SetSpacing(spacing);
output->SetDirection(dirOut);
output->SetOrigin(itkOrigin);
}