Eigen::VectorXd operator()(Eigen::VectorXd v){
_joint_vel=v/20;
_joint+=_joint_vel;
_pos=forward_model(_joint);
return _joint;
}
/**
* Here we test the scale factors methiods for the mahajan model.
* The idea is to set the scale factors for the 3 different cell types (epi, mid and endo)
* and check that the rsulting APD makes sense if compared to experiemntal results
*/
void TestScaleFactorsForMahajanModel(void) throw(Exception)
{
double end_time=300;
double time_step=0.01;
double sampling_time=time_step;
// Set stimulus
double magnitude_stimulus = -70.0; // pA/pF
double duration_stimulus = 1.0; // ms
double start_stimulus = 10.0; // ms
double period=1000;//here, this is ms
boost::shared_ptr<RegularStimulus> p_stimulus(new RegularStimulus(magnitude_stimulus,
duration_stimulus,
period,
start_stimulus));
boost::shared_ptr<EulerIvpOdeSolver> p_forward_solver(new EulerIvpOdeSolver); //define the solver
CellMahajan2008FromCellML forward_model(p_forward_solver, p_stimulus);
boost::shared_ptr<BackwardEulerIvpOdeSolver> p_backward_solver(new BackwardEulerIvpOdeSolver(
forward_model.GetNumberOfStateVariables()));
CellMahajan2008FromCellML epicardial_model(p_backward_solver, p_stimulus);
CellMahajan2008FromCellML endocardial_model(p_backward_solver, p_stimulus);
CellMahajan2008FromCellML midmyocardial_model(p_backward_solver, p_stimulus);
epicardial_model.SetParameter("ScaleFactorGks",1.0);
epicardial_model.SetParameter("ScaleFactorIto",1.0);
epicardial_model.SetParameter("ScaleFactorGkr",1.0);
midmyocardial_model.SetParameter("ScaleFactorGks",0.09);
midmyocardial_model.SetParameter("ScaleFactorIto",1.0);
midmyocardial_model.SetParameter("ScaleFactorGkr",1.0);
endocardial_model.SetParameter("ScaleFactorGks",0.86);
endocardial_model.SetParameter("ScaleFactorIto",0.2);
endocardial_model.SetParameter("ScaleFactorGkr",1.0);
std::vector<double> state_variables_epi = epicardial_model.GetInitialConditions();
std::vector<double> state_variables_endo = endocardial_model.GetInitialConditions();
std::vector<double> state_variables_mid = midmyocardial_model.GetInitialConditions();
const std::string mahajan_epi_file = "Mahajan_epi";
const std::string mahajan_mid_file = "Mahajan_mid";
const std::string mahajan_endo_file = "Mahajan_endo";
// Solve and write to file
OdeSolution epi_solution;
epi_solution = p_backward_solver->Solve(&epicardial_model, state_variables_epi, 0, end_time, time_step, sampling_time);
epi_solution.WriteToFile("TestIonicModels",
mahajan_epi_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
OdeSolution mid_solution;
mid_solution = p_backward_solver->Solve(&midmyocardial_model, state_variables_mid, 0, end_time, time_step, sampling_time);
mid_solution.WriteToFile("TestIonicModels",
mahajan_mid_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
OdeSolution endo_solution;
endo_solution = p_backward_solver->Solve(&endocardial_model, state_variables_endo, 0, end_time, time_step, sampling_time);
endo_solution.WriteToFile("TestIonicModels",
mahajan_endo_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
ColumnDataReader data_reader_epi("TestIonicModels", mahajan_epi_file);
ColumnDataReader data_reader_mid("TestIonicModels", mahajan_mid_file);
ColumnDataReader data_reader_endo("TestIonicModels", mahajan_endo_file);
std::vector<double> times = data_reader_epi.GetValues("Time");
std::vector<double> v_endo = data_reader_endo.GetValues("membrane_voltage");
std::vector<double> v_epi = data_reader_epi.GetValues("membrane_voltage");
std::vector<double> v_mid = data_reader_mid.GetValues("membrane_voltage");
CellProperties cell_properties_endo(v_endo, times);
CellProperties cell_properties_epi(v_epi, times);
CellProperties cell_properties_mid(v_mid, times);
double epi_APD = cell_properties_epi.GetLastActionPotentialDuration(90);
double endo_APD = cell_properties_endo.GetLastActionPotentialDuration(90);
double mid_APD = cell_properties_mid.GetLastActionPotentialDuration(90);
// Check that percentage increase from epi to mid and endo (roughly*) matches results
// from McIntosh et al. Card Res, 45:397-409. 200 (Figure 1 and 2)
// *this is cardiac modelling after all...
TS_ASSERT_DELTA((mid_APD-epi_APD)*100/epi_APD, 48.6, 2); // new values because gtos and gtof were the wrong way round (in Mahajan paper - they copied and pasted from Shannon wrong!)
TS_ASSERT_DELTA((endo_APD-epi_APD)*100/epi_APD, 15.7, 2); // ""
}
Arm():_state(Eigen::VectorXd::Zero((NB_JOINT+1)*3)),
_joint(Eigen::VectorXd::Zero(NB_JOINT)),
_joint_vel(Eigen::VectorXd::Zero(NB_JOINT))
{
_pos=forward_model(_joint);
}
