void
IoParams::parse(int ac,
char* av[])
{
namespace po = boost::program_options;
typedef std::vector<std::string> StringVectorType;
StringVectorType vItems;
po::options_description desc("Allowed Options");
desc.add_options()
("help", " produce help message")
("out", po::value(&strOut), " output transform file (.tm3d)")
("template", po::value(&strTemplate), " template volume (only for geometry) - if a gcam is present, it needs to be specified")
("subject", po::value(&strSubject), " subject volume (only for geometry)" )
("in", po::value(&vItems)->multitoken(), " input transforms - affine|volume|morph|mesh|gcam + fname")
("dbg", po::value(&vDbgCoords)->multitoken(), " enter debug coordinates ")
;
po::variables_map vm;
po::store( po::parse_command_line(ac,av,desc), vm);
po::notify(vm);
if ( vm.count("help") )
{
std::cout << desc << std::endl;
exit(0);
}
if ( strOut.empty() )
{
std::cerr << " Empty output file name\n";
exit(1);
}
// parse input terms
if ( vItems.empty() )
{
std::cout << " nothing to do - no transforms specified\n";
exit(0);
}
if ( vItems.size() % 2 )
{
std::cerr << " odd number of transform tokens\n";
exit(1);
}
for ( StringVectorType::iterator it = vItems.begin();
it != vItems.end(); )
{
MorphItem item;
item.type = *it++;
item.file = *it++;
this->items.push_back(item);
} // next it
}
void buildImageIntensityModelOnROI(const char* referenceFilename, const char* maskFilename, const char* dir, const char* outputImageFilename) {
typedef itk::PCAModelBuilder<RepresenterType> ModelBuilderType;
typedef itk::StatisticalModel<RepresenterType> StatisticalModelType;
typedef std::vector<std::string> StringVectorType;
typedef itk::DataManager<RepresenterType> DataManagerType;
RepresenterType::Pointer representer = RepresenterType::New();
typedef itk::ImageFileReader< ImageType > MaskReaderType;
MaskReaderType::Pointer maskReader = MaskReaderType::New();
maskReader->SetFileName( maskFilename );
maskReader->Update();
representer->SetReference( ReadImageFromFile(referenceFilename), maskReader->GetOutput() );
StringVectorType filenames;
getdir(dir, filenames, ".vtk");
DataManagerType::Pointer dataManager = DataManagerType::New();
dataManager->SetRepresenter(representer);
for (StringVectorType::const_iterator it = filenames.begin(); it != filenames.end(); it++) {
std::string fullpath = (std::string(dir) + "/") + *it;
dataManager->AddDataset( ReadImageFromFile(fullpath), fullpath.c_str());
}
ModelBuilderType::Pointer pcaModelBuilder = ModelBuilderType::New();
StatisticalModelType::Pointer model = pcaModelBuilder->BuildNewModel(dataManager->GetSampleDataStructure(), 0);
std::cout<<"dimensionality of the data: "<<model->GetDomain().GetNumberOfPoints()<<", dimension of the images: "<<(*dataManager->GetSampleDataStructure().begin())->GetSample()->GetLargestPossibleRegion().GetNumberOfPixels()<<std::endl;
std::cout<<"writing the mean sample to a png file..."<<std::endl;
typedef itk::ImageFileWriter< ImageType > ImageWriterType;
ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName( outputImageFilename );
writer->SetInput(model->DrawSample());
writer->Update();
}
//
// Build a new shape model from vtkPolyData, given in datadir.
//
int main(int argc, char** argv) {
if (argc < 3) {
std::cout << "Usage " << argv[0] << " datadir modelname" << std::endl;
exit(-1);
}
std::string datadir(argv[1]);
std::string modelname(argv[2]);
// All the statismo classes have to be parameterized with the RepresenterType.
// For building a shape model with vtk, we use the vtkPolyDataRepresenter.
typedef vtkStandardMeshRepresenter RepresenterType;
typedef DataManager<vtkPolyData> DataManagerType;
typedef PCAModelBuilder<vtkPolyData> ModelBuilderType;
typedef StatisticalModel<vtkPolyData> StatisticalModelType;
typedef std::vector<std::string> StringVectorType;
StringVectorType filenames;
getdir(datadir, filenames, ".vtk");
if (filenames.size() == 0) {
std::cerr << "did not find any vtk files in directory " << datadir << " exiting.";
exit(-1);
}
try {
// We create a new representer object. For the vtkPolyDataRepresenter, we have to set a reference
// and the alignmentType. The alignmenttype (which is here RIGID) determines how the dataset that we
// will use will later be aligned to the reference.
vtkPolyData* reference = loadVTKPolyData(datadir + "/" + filenames[0]);
boost::scoped_ptr<RepresenterType> representer(RepresenterType::Create(reference));
// We create a datamanager and provide it with a pointer to the representer
boost::scoped_ptr<DataManagerType> dataManager(DataManagerType::Create(representer.get()));
// Now we add our data to the data manager
// load the data and add it to the data manager. We take the first 17 hand shapes that we find in the data folder
for (unsigned i = 0; i < filenames.size() ; i++) {
vtkPolyData* dataset = loadVTKPolyData(datadir + "/" + filenames[i]);
// We provde the filename as a second argument.
// It will be written as metadata, and allows us to more easily figure out what we did later.
dataManager->AddDataset(dataset, filenames[i]);
// it is save to delete the dataset after it was added, as the datamanager direclty copies it.
dataset->Delete();
}
// To actually build a model, we need to create a model builder object.
// Calling the build model with a list of samples from the data manager, returns a new model.
// The second parameter to BuildNewModel is the variance of the noise on our data
boost::scoped_ptr<ModelBuilderType> modelBuilder(ModelBuilderType::Create());
boost::scoped_ptr<StatisticalModelType> model(modelBuilder->BuildNewModel(dataManager->GetData(), 0.01));
// Once we have built the model, we can save it to disk.
model->Save(modelname);
std::cout << "Successfully saved shape model as " << modelname << std::endl;
reference->Delete();
} catch (StatisticalModelException& e) {
std::cout << "Exception occured while building the shape model" << std::endl;
std::cout << e.what() << std::endl;
}
}
