#include "BasicDefOrg_DefOrgViewerAdapter.h"

BasicDefOrg_DefOrgViewerAdapter::BasicDefOrg_DefOrgViewerAdapter(){
	geomLayerPointer = new GeometricType();
	AddOrganismProperty("Sigma",0,10,1.0,0.1,"Sigma for Gradient Sensor");
	AddOrganismProperty("Chu",0,100,50);
}

int BasicDefOrg_DefOrgViewerAdapter::MaxNumberOfOutputItkSpatialObjects(){
	return 1;
}


int BasicDefOrg_DefOrgViewerAdapter::MaxNumberOfOutputImages(){
	return 1;
}

void BasicDefOrg_DefOrgViewerAdapter::PopulateItkScene(){
	itkScenePointer itkScene = m_OutputItkSpatialObjects[0].theItkScene;
	m_OutputItkSpatialObjects[0].isModified=true;
	/*itkScenePointer itkScene2 = m_OutputItkSpatialObjects[1].theItkScene;
	m_OutputItkSpatialObjects[1].isModified=true;*/
	geomLayerPointer->readTopologyFromFile( m_MeshFileName );
	itkScene->AddSpatialObject(geomLayerPointer->theMeshSpatialObject);  
	//itkScene2->AddSpatialObject(geomLayerPointer->theMeshSpatialObject);  
}

void BasicDefOrg_DefOrgViewerAdapter::PopulateVtkImage(){
	vtkImageImport* vtkImporter = m_OutputImages[0].first;
	m_OutputImages[0].second=true;
	m_InputImageReader = ImageFileReader::New();
	m_InputImageReader->SetFileName(m_ImageFileName.c_str());
	
	m_InputImageReader->Update();
	ImageType::Pointer image = m_InputImageReader->GetOutput();	
	PopulateVtkImageHelper(image, vtkImporter);
}


void BasicDefOrg_DefOrgViewerAdapter::UpdateOrganism(){
	itkScenePointer itkScene = m_OutputItkSpatialObjects[0].theItkScene;
	m_OutputItkSpatialObjects[0].isModified=true;
	testOrg->run();
	itkScene->AddSpatialObject(geomLayerPointer->theMeshSpatialObject);  
}


void BasicDefOrg_DefOrgViewerAdapter::SetupOrganism()
{
	m_Initialized=true;
	//TODO:: make this robust (i.e. flag errors if image not set, geom not set etc).
	
	// Instantiate the organism:
	testOrg = OrganismType::New();
	std::cout << "Organism created..." << std::endl;

	//Setup the sensor
	GradientSensorType::sensorIn input;
		
	input.sigma = GetOrganismProperty("Sigma");
	this->m_InputImageReader->Update();
	input.imageIn = this->m_InputImageReader->GetOutput();
	gradientSensor.run((void *)&input);
	std::cout << "Gradient sensor setup complete..." << std::endl;
	GradientSensorType::sensorOut * output = (GradientSensorType::sensorOut *) gradientSensor.getOuput();


	//Instantiate geomtery and physics layers
	eulerPhysLayerPointer = new EulerPhysicsType(0,0,10);	
			
	//physLayer.setInput(reader->GetOutput());
	eulerPhysLayerPointer->setExternalForces((void *) &(output->imageOut));
	eulerPhysLayerPointer->setGeometry(geomLayerPointer);

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

	//TEST BEHAVIOR
	//TODO figure out how to make sure it gets deleted.
	//TODO should we attach things by value instead by ref?
	cognitiveLayerPointer = new CognitiveType(5);
	beh1 = new Beh_TranslateAllType();
	def1 = new Def_TranslateAllType();
	cognitiveLayerPointer->setSchedule(m_ScheduleFileName);
	//Beh_TranslateAll<float, 3> beh1;
	//Def_Translation<float, 3> def1;								
	this->testOrg->setCognitiveLayer(cognitiveLayerPointer);
	this->testOrg->addBehaviour(beh1);
	this->testOrg->addDeformation(def1);

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


void BasicDefOrg_DefOrgViewerAdapter::PopulateVtkUnstructuredGrid(vtkUnstructuredGrid* vtkGrid /*in/out*/){
	geomLayerPointer->readTopologyFromFile( m_MeshFileName );
	MeshToUnstructuredGrid( geomLayerPointer->theMesh, vtkGrid/*in/out*/ );
}