int main(int argc, char *argv[])
{
// load the data
typedef utils::MatrixReader MatReader;
MatReader::Pointer reader = MatReader::New();
reader->SetFilename(argv[1]);
reader->Read();
utils::MatrixDataSet::Pointer data = reader->GetOutput();
typedef manifold::DiffusionMap DiffMap;
DiffMap::Pointer diffMap = DiffMap::New();
diffMap->Fit(data->doubleData["swiss"].transpose());
DiffMap::MatrixType E;
diffMap->GetEmbedding(E);
utils::MatrixDataSet::Pointer output = utils::MatrixDataSet::New();
output->AddData("E",E);
typedef utils::MatrixWriter Writer;
Writer::Pointer writer = Writer::New();
writer->SetInput(output);
writer->SetFilename("E.mat");
writer->Write();
return 0;
}
void output_mosaic_image(const IPF_Ptr& ipf, int layerIndex, int width, int height)
{
typedef itk::Image<unsigned char,2> Image;
Image::Pointer image = layerIndex > 0 ?
make_mosaic_image_with_boundaries(ipf, layerIndex, width, height) :
make_mosaic_image(ipf, layerIndex, width, height);
typedef itk::ImageFileWriter<Image> Writer;
Writer::Pointer writer = Writer::New();
writer->SetInput(image);
writer->SetFileName(OSSWrapper() << "../resources/partition" << layerIndex << ".bmp");
writer->Update();
}
void real_image_test()
{
typedef itk::Image<unsigned char,2> UCImage;
typedef itk::ImageFileReader<UCImage> UCReader;
// Read in the image (when debugging in VC++, it may be necessary to set the working directory to "$(TargetDir)").
UCReader::Pointer reader = UCReader::New();
reader->SetFileName("../resources/test.bmp");
reader->Update();
UCImage::Pointer windowedImage = reader->GetOutput();
// Cast the windowed image to make a dummy Hounsfield image.
typedef itk::Image<int,2> IntImage;
typedef itk::CastImageFilter<UCImage,IntImage> UC2IntCastFilter;
UC2IntCastFilter::Pointer uc2intCastFilter = UC2IntCastFilter::New();
uc2intCastFilter->SetInput(windowedImage);
uc2intCastFilter->Update();
IntImage::Pointer hounsfieldImage = uc2intCastFilter->GetOutput();
// Cast the windowed image to make its pixels real-valued.
typedef itk::Image<float,2> RealImage;
typedef itk::CastImageFilter<UCImage,RealImage> UC2RealCastFilter;
UC2RealCastFilter::Pointer uc2realCastFilter = UC2RealCastFilter::New();
uc2realCastFilter->SetInput(windowedImage);
// Smooth this real image using anisotropic diffusion.
typedef itk::GradientAnisotropicDiffusionImageFilter<RealImage,RealImage> AnisotropicDiffusionFilter;
AnisotropicDiffusionFilter::Pointer adFilter = AnisotropicDiffusionFilter::New();
adFilter->SetInput(uc2realCastFilter->GetOutput());
adFilter->SetConductanceParameter(1.0);
adFilter->SetNumberOfIterations(5); // a typical value (see the ITK software guide)
adFilter->SetTimeStep(0.125);
// Calculate the gradient magnitude of the smoothed image.
typedef itk::Image<short,2> GradientMagnitudeImage;
typedef itk::GradientMagnitudeImageFilter<RealImage,GradientMagnitudeImage> GradientMagnitudeFilter;
GradientMagnitudeFilter::Pointer gradientMagnitudeFilter = GradientMagnitudeFilter::New();
gradientMagnitudeFilter->SetInput(adFilter->GetOutput());
gradientMagnitudeFilter->SetUseImageSpacingOff();
gradientMagnitudeFilter->Update();
GradientMagnitudeImage::Pointer gradientMagnitudeImage = gradientMagnitudeFilter->GetOutput();
// Run the watershed algorithm on the gradient magnitude image.
typedef MeijsterRoerdinkWatershed<GradientMagnitudeImage::PixelType,2> WS;
WS ws(gradientMagnitudeImage, ITKImageUtil::make_4_connected_offsets());
std::cout << "Label Count: " << ws.label_count() << '\n';
// Convert the watershed label image to a colour RGB image.
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType,2> RGBImage;
typedef itk::Functor::ScalarToRGBPixelFunctor<long> ColourMapFunctorType;
typedef itk::UnaryFunctorImageFilter<WS::LabelImage, RGBImage, ColourMapFunctorType> ColourMapFilter;
ColourMapFilter::Pointer colourMapper = ColourMapFilter::New();
colourMapper->SetInput(ws.labels());
// Output the result to a file.
typedef itk::ImageFileWriter<RGBImage> Writer;
Writer::Pointer writer = Writer::New();
writer->SetInput(colourMapper->GetOutput());
writer->SetFileName("../resources/output.bmp");
writer->Update();
// Create the initial partition forest.
typedef PartitionForest<CTImageLeafLayer,CTImageBranchLayer> IPF;
typedef shared_ptr<IPF> IPF_Ptr;
shared_ptr<CTImageLeafLayer> leafLayer(new CTImageLeafLayer(hounsfieldImage, windowedImage, gradientMagnitudeImage));
shared_ptr<CTImageBranchLayer> lowestBranchLayer = IPF::make_lowest_branch_layer(leafLayer, ws.calculate_groups());
IPF_Ptr ipf(new IPF(leafLayer, lowestBranchLayer));
}