/**
* Here we test that the scale factors for the TT model do what they are expected to
* We check that they modify APD in a way that is expected.
*/
void TestScaleFactorsForTT06(void)
{
double simulation_end=500;/*end time, in milliseconds for this model*/
// Set the stimulus, the following values are appropriate for single cell simulations of this model.
double magnitude = -38.0; // pA/pF
double duration = 1.0; // ms
double start = 100; // ms
boost::shared_ptr<SimpleStimulus> p_stimulus(new SimpleStimulus(magnitude,
duration,
start));
boost::shared_ptr<EulerIvpOdeSolver> p_solver(new EulerIvpOdeSolver); //define the solver
HeartConfig::Instance()->SetOdeTimeStep(0.001);// with Forward Euler, this must be as small as 0.001.
const std::string control_file = "TT_epi";
const std::string mid_file = "TT_mid";
const std::string endo_file = "TT_endo";
const std::string LQT_file = "TT_LQT";
CellTenTusscher2006EpiFromCellML TT_model_epi(p_solver, p_stimulus);
TT_model_epi.SetParameter("ScaleFactorIto", 1.0);
TT_model_epi.SetParameter("ScaleFactorGkr", 1.0);
TT_model_epi.SetParameter("ScaleFactorGks", 1.0);
//run the model
RunOdeSolverWithIonicModel(&TT_model_epi,
simulation_end,
control_file,
100,
false);
CellTenTusscher2006EpiFromCellML TT_model_mid(p_solver, p_stimulus);
TT_model_mid.SetParameter("ScaleFactorIto", 1.0);
TT_model_mid.SetParameter("ScaleFactorGkr", 1.0);
TT_model_mid.SetParameter("ScaleFactorGks", 0.25);
RunOdeSolverWithIonicModel(&TT_model_mid,
simulation_end,
mid_file,
100,
false);
CellTenTusscher2006EpiFromCellML TT_model_endo(p_solver, p_stimulus);
TT_model_endo.SetParameter("ScaleFactorIto", 0.165);
TT_model_endo.SetParameter("ScaleFactorGkr", 1.0);
TT_model_endo.SetParameter("ScaleFactorGks", 0.66);
RunOdeSolverWithIonicModel(&TT_model_endo,
simulation_end,
endo_file,
100,
false);
CellTenTusscher2006EpiFromCellML TT_model_LQT(p_solver, p_stimulus);
TT_model_LQT.SetParameter("ScaleFactorIto", 1.0);
TT_model_LQT.SetParameter("ScaleFactorGkr", 0.0);
TT_model_LQT.SetParameter("ScaleFactorGks", 1.0);
RunOdeSolverWithIonicModel(&TT_model_LQT,
simulation_end,
LQT_file,
100,
false);
ColumnDataReader data_reader1("TestIonicModels", control_file);
std::vector<double> voltages1 = GetVoltages(data_reader1);
ColumnDataReader data_reader2("TestIonicModels", mid_file);
std::vector<double> voltages2 = GetVoltages(data_reader2);
ColumnDataReader data_reader3("TestIonicModels", endo_file);
std::vector<double> voltages3 = GetVoltages(data_reader3);
ColumnDataReader data_reader4("TestIonicModels", LQT_file);
std::vector<double> voltages4 = GetVoltages(data_reader4);
TS_ASSERT_EQUALS(voltages1.size(), voltages2.size());
TS_ASSERT_EQUALS(voltages2.size(), voltages3.size());
TS_ASSERT_EQUALS(voltages3.size(), voltages4.size());
//create the times vector
std::vector<double> times;
double k =0;
for (unsigned i=0; i<voltages2.size(); i++)
{
times.push_back(k);
k=k+0.1;
}
CellProperties cell_properties_control(voltages1, times);
CellProperties cell_properties_mid(voltages2, times);
CellProperties cell_properties_endo(voltages3, times);
CellProperties cell_properties_LQT(voltages4, times);
double control_APD = cell_properties_control.GetLastActionPotentialDuration(90);
double mid_APD = cell_properties_mid.GetLastActionPotentialDuration(90);
double endo_APD = cell_properties_endo.GetLastActionPotentialDuration(90);
double LQT_APD = cell_properties_LQT.GetLastActionPotentialDuration(90);
TS_ASSERT_DELTA(control_APD, 300.4789, 0.1);
TS_ASSERT_DELTA(mid_APD, 392.1871, 0.1);
TS_ASSERT_DELTA(endo_APD, 329.2048, 0.1);
TS_ASSERT_DELTA(LQT_APD , 347.8374, 0.1);
}
void TestScaleFactorsMaleckar(void) throw (Exception)
{
double end_time =500;
boost::shared_ptr<RegularStimulus> p_stimulus(new RegularStimulus(-5.6,
6,
1000,
4.0));
boost::shared_ptr<EulerIvpOdeSolver> p_solver(new EulerIvpOdeSolver); //define the solver
HeartConfig::Instance()->SetOdeTimeStep(0.001);
CellMaleckar2008FromCellML atrial_ode_system(p_solver, p_stimulus);
const std::string control_file = "control";
const std::string first_set_file = "first_scale_factor_set";
const std::string second_set_file = "second_scale_factor_set";
const std::string AZD_file = "AZD_scale_factor_set";
OdeSolution control_solution;
OdeSolution first_scale_factor_set_solution;
OdeSolution second_scale_factor_set_solution;
OdeSolution AZD_scale_factor_set_solution;
double time_step=0.001;
double sampling_time=0.001;
std::vector<double> state_variables= atrial_ode_system.GetInitialConditions();
//default values
atrial_ode_system.SetParameter("ScaleFactorGks",1.0);
atrial_ode_system.SetParameter("ScaleFactorIto",1.0);
atrial_ode_system.SetParameter("ScaleFactorGkr",1.0);
atrial_ode_system.SetParameter("ScaleFactorGna",1.0);
atrial_ode_system.SetParameter("ScaleFactorAch",1e-24);
atrial_ode_system.SetParameter("ScaleFactorGNaK",1.0);
atrial_ode_system.SetParameter("ScaleFactorGNaCa",1.0);
atrial_ode_system.SetParameter("ScaleFactorGKur",1.0);
atrial_ode_system.SetParameter("ScaleFactorGK1",1.0);
atrial_ode_system.SetParameter("ScaleFactorGCaL",1.0);
atrial_ode_system.SetParameter("ScaleFactorAZD",0.0);
control_solution = p_solver->Solve(&atrial_ode_system, state_variables, 0, end_time, time_step, sampling_time);
control_solution.WriteToFile("TestIonicModels",
control_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
//now apply the first scale factor set, decreases outward currents
atrial_ode_system.SetParameter("ScaleFactorGks",0.8);
atrial_ode_system.SetParameter("ScaleFactorIto",1.0);
atrial_ode_system.SetParameter("ScaleFactorGkr",0.9);
atrial_ode_system.SetParameter("ScaleFactorGna",1.0);
atrial_ode_system.SetParameter("ScaleFactorAch",1e-24);
atrial_ode_system.SetParameter("ScaleFactorGNaK",1.0);
atrial_ode_system.SetParameter("ScaleFactorGNaCa",1.0);
atrial_ode_system.SetParameter("ScaleFactorGKur",0.7);
atrial_ode_system.SetParameter("ScaleFactorGK1",0.6);
atrial_ode_system.SetParameter("ScaleFactorGCaL",1.0);
atrial_ode_system.SetParameter("ScaleFactorAZD",0.0);
state_variables= atrial_ode_system.GetInitialConditions();
first_scale_factor_set_solution = p_solver->Solve(&atrial_ode_system, state_variables, 0, end_time, time_step, sampling_time);
first_scale_factor_set_solution.WriteToFile("TestIonicModels",
first_set_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
//now apply the secondscale factor set, this one increases inward currents
atrial_ode_system.SetParameter("ScaleFactorGks",1.0);
atrial_ode_system.SetParameter("ScaleFactorIto",1.0);
atrial_ode_system.SetParameter("ScaleFactorGkr",1.0);
atrial_ode_system.SetParameter("ScaleFactorGna",1.5);
atrial_ode_system.SetParameter("ScaleFactorAch",1e-24);
atrial_ode_system.SetParameter("ScaleFactorGNaK",1.0);
atrial_ode_system.SetParameter("ScaleFactorGNaCa",2.0);
atrial_ode_system.SetParameter("ScaleFactorGKur",1.0);
atrial_ode_system.SetParameter("ScaleFactorGK1",1.0);
atrial_ode_system.SetParameter("ScaleFactorGCaL",1.6);
atrial_ode_system.SetParameter("ScaleFactorAZD",0.0);
state_variables= atrial_ode_system.GetInitialConditions();
second_scale_factor_set_solution = p_solver->Solve(&atrial_ode_system, state_variables, 0, end_time, time_step, sampling_time);
second_scale_factor_set_solution.WriteToFile("TestIonicModels",
second_set_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
//check the AZD scale factor (vs control)
atrial_ode_system.SetParameter("ScaleFactorGks",1.0);
atrial_ode_system.SetParameter("ScaleFactorIto",1.0);
atrial_ode_system.SetParameter("ScaleFactorGkr",1.0);
atrial_ode_system.SetParameter("ScaleFactorGna",1.0);
atrial_ode_system.SetParameter("ScaleFactorAch",1e-24);
atrial_ode_system.SetParameter("ScaleFactorGNaK",1.0);
atrial_ode_system.SetParameter("ScaleFactorGNaCa",1.0);
atrial_ode_system.SetParameter("ScaleFactorGKur",1.0);
atrial_ode_system.SetParameter("ScaleFactorGK1",1.0);
atrial_ode_system.SetParameter("ScaleFactorGCaL",1.0);
atrial_ode_system.SetParameter("ScaleFactorAZD",5.0);
AZD_scale_factor_set_solution = p_solver->Solve(&atrial_ode_system, state_variables, 0, end_time, time_step, sampling_time);
AZD_scale_factor_set_solution.WriteToFile("TestIonicModels",
AZD_file,
"ms",//time units
100,//steps per row
false);/*true cleans the directory*/
ColumnDataReader data_reader1("TestIonicModels", control_file);
std::vector<double> voltages1 = GetVoltages(data_reader1);
ColumnDataReader data_reader2("TestIonicModels", first_set_file);
std::vector<double> voltages2 = GetVoltages(data_reader2);
ColumnDataReader data_reader3("TestIonicModels", second_set_file);
std::vector<double> voltages3 = GetVoltages(data_reader3);
ColumnDataReader data_reader4("TestIonicModels", AZD_file);
std::vector<double> voltages4 = GetVoltages(data_reader4);
TS_ASSERT_EQUALS(voltages1.size(), voltages2.size());
TS_ASSERT_EQUALS(voltages2.size(), voltages3.size());
TS_ASSERT_EQUALS(voltages3.size(), voltages4.size());
//create the times vector
std::vector<double> times;
double k =0;
for (unsigned i=0; i<voltages2.size(); i++)
{
times.push_back(k);
k=k+0.1;
}
CellProperties cell_properties_control(voltages1, times);
CellProperties cell_properties_first(voltages2, times);
CellProperties cell_properties_second(voltages3, times);
CellProperties cell_properties_AZD(voltages4, times);
double control_APD = cell_properties_control.GetLastActionPotentialDuration(90);
double first_APD = cell_properties_first.GetLastActionPotentialDuration(90);
double second_APD = cell_properties_second.GetLastActionPotentialDuration(90);
double AZD_APD = cell_properties_AZD.GetLastActionPotentialDuration(90);
//test that the aps are actually longer than control (all interventions were meant to have that effect except the last one)
TS_ASSERT_LESS_THAN(control_APD, first_APD);
TS_ASSERT_LESS_THAN(control_APD, second_APD);
TS_ASSERT_LESS_THAN(AZD_APD, control_APD);
//leave some hardcoded value for testing
TS_ASSERT_DELTA(control_APD, 206.1278, 0.1);
TS_ASSERT_DELTA(first_APD, 403.8293, 0.1);
TS_ASSERT_DELTA(second_APD, 320.0195, 0.1);
TS_ASSERT_DELTA(AZD_APD , 187.8073, 0.1);
}
void TestSMCmodelModified(void) throw (Exception)
{
// Set stimulus (no stimulus in this case)
double magnitude_stimulus = 0.0; // dimensionless
double duration_stimulus = 0.05; // ms
double start_stimulus = 0.01; // ms
double period=1;//
boost::shared_ptr<RegularStimulus> stimulus(new RegularStimulus(magnitude_stimulus,
duration_stimulus,
period,
start_stimulus));
boost::shared_ptr<EulerIvpOdeSolver> solver(new EulerIvpOdeSolver); //define the solver
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.1,0.1,1);
CorriasBuistSMCModified smc_ode_system(solver, stimulus);
TS_ASSERT_EQUALS(smc_ode_system.GetCarbonMonoxideScaleFactor(), 1.0); //coverage
smc_ode_system.SetCarbonMonoxideScaleFactor(1.0);//coverage
// Solve and write to file
RunOdeSolverWithIonicModel(&smc_ode_system,
60000,/*end time, in milliseconds*/
"SMCmodel_modified",
1000);
// Calculate APDs and compare with hardcoded values
ColumnDataReader data_reader1("TestIonicModels", "SMCmodel_modified");
std::vector<double> voltages = data_reader1.GetValues("Vm_SM");
//create the times vector
double k =0;
std::vector<double> times;
for (unsigned i=0; i<voltages.size(); i++)
{
times.push_back(k);
k=k+100;
}
CellProperties cell_properties(voltages, times, -45.0);//note the lower threshold for SMC calculation of 'AP');
TS_ASSERT_DELTA(cell_properties.GetLastActionPotentialDuration(50), 8331.3835, 0.1);
TS_ASSERT_DELTA(cell_properties.GetLastActionPotentialDuration(70), 8571.1671, 0.1);
TS_ASSERT_DELTA(cell_properties.GetLastActionPotentialDuration(80), 8722.6543, 0.1);
TS_ASSERT_DELTA(cell_properties.GetLastActionPotentialDuration(90), 8955.8126, 0.1);
CorriasBuistSMCModified smc_ode_system_no_stim(solver, stimulus);
//check the default value of the presence of ICC stimulus
TS_ASSERT_EQUALS(smc_ode_system_no_stim.GetFakeIccStimulusPresent(), true);
//Switch off ICC stimulus and check the voltage is almost flat
smc_ode_system_no_stim.SetFakeIccStimulusPresent(false);
//check member variable was switched correctly
TS_ASSERT_EQUALS(smc_ode_system_no_stim.GetFakeIccStimulusPresent(), false);
// Solve and write to file
RunOdeSolverWithIonicModel(&smc_ode_system_no_stim,
60000,/*end time, in milliseconds*/
"SMCmodel_modified_nostim",
1000);
// Calculate APDs and compare with hardcoded values
ColumnDataReader data_reader2("TestIonicModels", "SMCmodel_modified_nostim");
std::vector<double> voltages_flat = data_reader2.GetValues("Vm_SM");
CellProperties cell_properties_2(voltages_flat, times, -45.0);
//it should be flat now, no AP and cell properties should throw
TS_ASSERT_THROWS_THIS(cell_properties_2.GetLastActionPotentialDuration(90),
"AP did not occur, never exceeded threshold voltage.");
}