C:/cmcintos/defOrgs/examples/advanced/defOrg.cxx

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkMeanImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkCovariantVector.h"

//#include "itkImage.h"
#include <iostream>
#include "Org_EulerSchedule.h"
#include "Org_LevelSetSchedule.h"
#include "Geometric.h"

using namespace mial;
int main(int argc, char * argv[] )
{
        if( argc < 5 )
        {
                std::cerr << "Usage: " << std::endl;
                std::cerr << argv[0] << "  inputImageFile   outputImageFile  inputEulerScheduleFile inputLeveSetScheduleFile inputMesh" << std::endl;
                return EXIT_FAILURE;
        }
        std::string inputImageFileName = argv[1];
        std::string outputImageFileName = argv[2];
        std::string eulerScheduleFileName = argv[3];
        std::string levelSetScheduleFileName = argv[4];
        std::string topologyInputFileName = argv[5];

        typedef unsigned char PixelType;
        const unsigned int Dimension = 3;
        typedef itk::Image< PixelType, Dimension > ImageType; 


        typedef itk::CovariantVector< float, 3 >  GradientPixelType;
        typedef itk::Image< GradientPixelType, 3 > GradientImageType;

        //Instantiate the reader/writer:
        typedef itk::ImageFileReader< ImageType >  ReaderType;
        typedef itk::ImageFileWriter< ImageType >  WriterType;
        ReaderType::Pointer reader = ReaderType::New();
        WriterType::Pointer writer = WriterType::New();

        reader->SetFileName(inputImageFileName.c_str());
        //TODO Make sensors pipelinable to avoid forcing update of reader
        reader->Update();
        writer->SetFileName(outputImageFileName.c_str());


        // Instantiate the organism:
        typedef itk::Org_EulerSchedule<ImageType, Geometric<float,3>::BinaryImageType, GradientImageType, float, 3> eulerOrganismType;
        eulerOrganismType::Pointer eulerOrg = eulerOrganismType::New();
        std::cout << "Euler organism created..." << std::endl;

        //Add Springs:
        eulerOrg->setTopology(topologyInputFileName);
        std::cout << "Topology read from '" << topologyInputFileName << "'..." << std::endl;
        //eulerOrg->writeNodesToFile(nodeOutputFileName);

        //TEST BEHAVIOR
        eulerOrg->setSchedule(eulerScheduleFileName);
        
        //Pass the output of the reader to the filter, then to the writer.
        eulerOrg->SetInput(reader->GetOutput());
        

        
        eulerOrg->setUp();

        //Deform the euler organism
        std::cout << "Running Euler organism..." << std::endl;
        for(int i=0; i<25;i++)
        {
                eulerOrg->run();
                std::cout << "one run" << std::endl;
        }
        //Prepare the euler organisms output
        eulerOrg->Update();


        //Use a level set organism to smooth the euler's final shape
        typedef itk::Org_LevelSetSchedule<ImageType, ImageType, GradientImageType, float, 3> levelSetOrganismType;
        levelSetOrganismType::Pointer levelSetOrg = levelSetOrganismType::New();
        levelSetOrg->SetInput(reader->GetOutput());
        levelSetOrg->setSchedule(levelSetScheduleFileName);
        levelSetOrg->setUp();
        //Use the eulerOrg's output to create the shape for the levelSetOrg (creates the mesh and the distance image).
        levelSetOrg->setTopologyFromBinaryImage(eulerOrg->GetOutput());
        
        std::cout << "Running levelSet organism..." << std::endl;
        for(int i=0; i<25;i++)
        {
                levelSetOrg->run();
                std::cout << "one run" << std::endl;
        }

        writer->SetInput(levelSetOrg->GetOutput());
        try
        {
                writer->Update(); //Will cause an update on the reader, because it depends on it
                std::cout << "Output written to '" << outputImageFileName << "'." << std::endl;
        }
        catch(itk::ExceptionObject & err)
        {
                std::cout << "ExceptionObject caught!" << std::endl;
                std::cout << err << std::endl;
                return -1;
        }
        return 0;
}

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