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

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

//#include "itkImage.h"
#include <iostream>
#include "itkOrganism.h"
#include "Phys_Euler.h"
#include "Ctrl_ScheduleDriven.h"
#include "Beh_TranslateAll.h"
#include "Def_Translation.h"
#include "Beh_UniformScale.h"
#include "Def_UniformScale.h"
#include "Sense_Gradient.h"
#include "Geom_MeshSpatialObject.h"

using namespace mial;
int main(int argc, char ** argv)
{
        if( argc < 4 )
        {
                std::cerr << "Usage: " << std::endl;
                std::cerr << argv[0] << "  inputImageFile   outputImageFile  inputEulerScheduleFile inputMesh" << std::endl;
                return EXIT_FAILURE;
        }
        std::string inputImageFileName = argv[1];
        std::string outputImageFileName = argv[2];
        std::string topologyInputFileName = argv[4];
        std::string scheduleFileName = argv[3];
        
        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());
        writer->SetFileName(outputImageFileName.c_str());



        // Instantiate the organism:
        typedef itk::ItkOrganism <ImageType, ImageType, GradientImageType, float, 3> organismType;
        organismType::Pointer testOrg = organismType::New();
        std::cout << "Organism created..." << std::endl;

        //Instatiate a sensor
        typedef Sense_Gradient<float,ImageType,GradientImageType,3> gradientSensorType;
        gradientSensorType::sensorIn::Pointer input = gradientSensorType::sensorIn::New();
        gradientSensorType::Pointer gradientSensor = gradientSensorType::New();
        input->sigma = 1.0;
        reader->Update();
        input->imageIn = reader->GetOutput();
        gradientSensor->run(input);
        gradientSensorType::sensorOut::Pointer output = (gradientSensorType::sensorOut *) (gradientSensor->getOutput()).GetPointer();


        //Instantiate geomtery and physics layers
        typedef Phys_Euler<float,GradientImageType,3> PhysLayerType;
        typedef Geom_MeshSpatialObject<float,3> GeometricType;

        PhysLayerType::Pointer physLayer = PhysLayerType::New();
        GeometricType::Pointer geomLayer = GeometricType::New();
        
        physLayer->setExternalForces((void *) &(output->imageOut));
        physLayer->setGeometry(geomLayer);

        testOrg->setPhysicsLayer(physLayer);
        testOrg->setGeometricLayer(geomLayer);
        std::cout << "Physics layer added..." << std::endl;

        //Load the topology
        geomLayer->readTopologyFromFile(topologyInputFileName);
        std::cout << "Topology read from '" << topologyInputFileName << "'..." << std::endl;
        
        //Add cogntive, behavioral, and deformations
        Ctrl_ScheduleDriven<float, 3>::Pointer cgL = Ctrl_ScheduleDriven<float, 3>::New();
        cgL->setSchedule(scheduleFileName);
        Beh_TranslateAll<float, 3>::Pointer beh1 = Beh_TranslateAll<float,3>::New();
        Beh_UniformScale<float, 3>::Pointer beh2 = Beh_UniformScale<float,3>::New();
        Def_Translation<float, 3>::Pointer def1 = Def_Translation<float,3>::New();                                                              
        Def_UniformScale<float, 3>::Pointer def2 = Def_UniformScale<float,3>::New();                                                            
        testOrg->setCognitiveLayer(cgL);
        testOrg->addBehaviour(beh1);
        testOrg->addBehaviour(beh2);
        testOrg->addDeformation(def1);
        testOrg->addDeformation(def2);

        //Pass the output of the reader to the filter, then to the writer.
        testOrg->SetInput(reader->GetOutput());

        writer->SetInput(testOrg->GetOutput());
        try
        {
                std::cout << "Running organism..." << std::endl;
                for(int i=0; i<25;i++)
                {
                        testOrg->run();
                        std::cout << "one run" << std::endl;
                }
                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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