Title here
Summary here
This tutorial was generated from the file projects/MouseLesion/test/TestFibroblastsLiteratePaper.hpp at revision r27528. Note that the code is given in full at the bottom of the page.
Two dimensional mouse ventricle with lesion simulation
This is the code that was used to perform the simulation in Mahoney et al. (2016).
Code Walkthrough
#include <cxxtest/TestSuite.h>
These two includes are in this project, and not a standard part of Chaste v3.3
#include "ScarCellFactory.hpp"
#include "ScarConductivityModifier.hpp"
The rest of these includes are standard Chaste files…
#include "GmshMeshReader.hpp"
#include "MonodomainProblem.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "CellProperties.hpp" // For analysing APs
#include "PetscSetupAndFinalize.hpp"
class TestFibroblasts2d : public CxxTest::TestSuite
{
private:
/** Width of the 2D domain we're simulating. */
double mRegionWidth;
/** Radius of the scar in the centre. */
double mScarRadius;
/** Width of the boundary region (myocytes but different conductivity) */
double mBoundaryWidth;
public:
void Test2dPropagation() throw (Exception)
{
#ifdef CHASTE_CVODE
if (*(CommandLineArguments::Instance()->p_argc) == 1)
{
std::cout << "TestFibroblasts takes the following arguments:\n"
" Mandatory:\n"
" * --scar-conduction-scaling <x> The proportion of the intra-cellular conduction to\n"
" apply in the central scar region.\n"
"\n"
" Optional:\n"
" * --use-neutral-cells <true or false> Whether to use neutral cells OR,\n"
" * --use-fibroblasts <true or false> a fibroblast electrophysiology model,\n"
" in the scar region.\n"
" * --scar-membrane-area-scaling <x> the scaling factor for membrane area (per unit vol) in scar region\n"
" * --boundary-conduction-scaling <x> The proportion of intra-cellular conduction to\n"
" apply in the boundary of the scar (still myocytes).\n"
" * --scar-shape <x> Whether the scar should be a 'CIRCLE' or a 'SQUARE'\n"
"\n"
" * --pacing-period <x> The time between paces applied on x=0 (defaults to 100ms)\n"
" * --end-time <x> How long to perform the simulation for (defaults to pacing period).\n"
" * --lesion-pacing Whether to perform pacing in the centre of the lesion (default false).\n"
" * --cut Whether to introduce a cut with complete conduction block (defaults to false).\n";
return;
}
/**
* SET OPTIONS FOR THIS RUN
*
* These are the defaults.
*/
double pacing_cycle_length = 100;
bool use_neutral_cell_model = false;
bool use_fibroblasts = false;
bool lesion_pacing = false; // Alternative is remote/sinus pacing.
ScarShape shape = CIRCLE;
double scar_membrane_area_scaling = 1.0;
const std::string output_folder = "FibroblastSims/";
if (CommandLineArguments::Instance()->OptionExists("--pacing-period"))
{
pacing_cycle_length = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--pacing-period");
}
double end_time = pacing_cycle_length; // Default end time is pacing cycle length
if (CommandLineArguments::Instance()->OptionExists("--end-time"))
{
end_time = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--end-time");
}
if (CommandLineArguments::Instance()->OptionExists("--scar-shape"))
{
if (CommandLineArguments::Instance()->GetStringCorrespondingToOption("--scar-shape")=="CIRCLE")
{
shape = CIRCLE;
}
else if (CommandLineArguments::Instance()->GetStringCorrespondingToOption("--scar-shape")=="SQUARE")
{
shape = SQUARE;
}
else
{
EXCEPTION("The --scar-shape argument should be 'CIRCLE' or 'SQUARE'.");
}
}
// Here we say what proportion of the normal conductivity we want in the scar
double scaling_factor;
if (CommandLineArguments::Instance()->OptionExists("--scar-conduction-scaling"))
{
scaling_factor = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--scar-conduction-scaling");
assert(scaling_factor >= 0.0);
assert(scaling_factor <= 1.0);
}
else
{
EXCEPTION("Please provide the command line option '--scar-conduction-scaling' with a value between 0 and 1.");
}
double scaling_factor_boundary = 1.0;
if (CommandLineArguments::Instance()->OptionExists("--boundary-conduction-scaling"))
{
scaling_factor_boundary = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--boundary-conduction-scaling");
assert(scaling_factor_boundary >= 0.0);
assert(scaling_factor_boundary <= 1.0);
}
// And decide whether to use a neutral cell model, or normal mytocytes.
if (CommandLineArguments::Instance()->OptionExists("--use-neutral-cells"))
{
use_neutral_cell_model = CommandLineArguments::Instance()->GetBoolCorrespondingToOption("--use-neutral-cells");
}
// And decide whether to use a fibroblast model
if (CommandLineArguments::Instance()->OptionExists("--use-fibroblasts"))
{
use_fibroblasts = CommandLineArguments::Instance()->GetBoolCorrespondingToOption("--use-fibroblasts");
}
if (use_neutral_cell_model && use_fibroblasts)
{
EXCEPTION("You can only set '--use-neutral-cells true' OR '--use-fibroblasts true', not both.");
}
if (CommandLineArguments::Instance()->OptionExists("--scar-membrane-area-scaling"))
{
scar_membrane_area_scaling = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--scar-membrane-area-scaling");
assert(scar_membrane_area_scaling >= 0.0);
assert(scar_membrane_area_scaling <= 1.0);
}
bool create_cut = false;
if (CommandLineArguments::Instance()->OptionExists("--cut"))
{
create_cut = true;
}
if (CommandLineArguments::Instance()->OptionExists("--lesion-pacing"))
{
lesion_pacing = true;
}
// Set up a unique output folder for these options
std::stringstream sub_directory;
if (use_neutral_cell_model)
{
sub_directory << "Neutral";
}
else if (use_fibroblasts)
{
sub_directory << "Fibroblast";
}
else
{
sub_directory << "Myocyte";
}
sub_directory << "_scar_cond_" << scaling_factor << "_cap_" << scar_membrane_area_scaling << "_boundary_cond_" << scaling_factor_boundary << "_period_" << pacing_cycle_length << "_end_" << end_time;
if (shape==SQUARE)
{
sub_directory << "_Square";
}
if (create_cut)
{
sub_directory << "_WithCut";
}
if (lesion_pacing)
{
sub_directory << "_LesionPacing";
}
SET UP MESH
DistributedTetrahedralMesh<2,2> mesh;
if (create_cut)
{
GmshMeshReader<2,2> gmsh_reader("projects/MouseLesion/test/data/meshes/2D_with_cuts_7_by_9_mm.msh");
mesh.ConstructFromMeshReader(gmsh_reader);
// Mesh properties we will use in the cell factory and conductivity modifier.
mRegionWidth = 0.7; //cm
mScarRadius = 0.2325; //cm
mBoundaryWidth = 0.01; //cm
}
else
{
// Mesh properties we will use in the cell factory and conductivity modifier.
mRegionWidth = 0.5; //cm
mScarRadius = 0.1; //cm
mBoundaryWidth = 0.01; //cm
double h=0.005;
mesh.ConstructRegularSlabMesh(h, mRegionWidth, mRegionWidth);
}
SET STANDARD OPTIONS
HeartConfig::Instance()->SetSimulationDuration(end_time); //ms
HeartConfig::Instance()->SetOutputDirectory(output_folder + sub_directory.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetVisualizeWithVtk(true);
NUMERICAL METHOD PARAMETERS
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.1, 0.1, 0.1);
SET UP HETEROGENEOUS CONDUCTIVITY
double intra_conductivity = 1.75; // Chaste Defaults
double extra_conductivity = 7.0; // Chaste Defaults
// Set up the defaults.
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(intra_conductivity, intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(extra_conductivity, extra_conductivity));
COMPLETE THE SET UP OF PROBLEM
// Make a scar cell factory
ScarCellFactory<2> cell_factory(mRegionWidth,
mScarRadius,
pacing_cycle_length,
scar_membrane_area_scaling, // chi scaling factor.
use_neutral_cell_model,
use_fibroblasts,
shape,
lesion_pacing,
create_cut);
// Create a conductivity modifier
ScarConductivityModifier<2> modifier(&mesh,
shape,
mRegionWidth,
mScarRadius,
scaling_factor, // D scaling factor.
scar_membrane_area_scaling, // chi scaling factor.
mBoundaryWidth,
scaling_factor_boundary, // D scaling factor (chi not implemented for boundary yet).
true, // whether a lesion applied
create_cut);
MonodomainProblem<2> problem( &cell_factory );
problem.SetMesh( &mesh );
problem.SetWriteInfo(); // Writes max and min voltages out.
problem.Initialise();
problem.GetTissue()->SetConductivityModifier(&modifier);
// Check that the Scar cell factory is doing the index tracking I expect.
// These should have been calculated during the initialisation step.
// These were checked in Paraview for the h = 0.005 slab mesh.
// If these lines fail it isn't a problem if you have intentionally
// changed the mesh for some reason (as we have when there's a cut).
if (!create_cut)
{
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexCentreOfScar(), 5100u);
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexCentralTissue(), 8130u);
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexLeftTissue(), 5070u);
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexRightTissue(), 5130u);
}
problem.Solve();
// Print out a couple of node traces to file for easy plotting.
// Output file handler should be called collectively, the 'false' says "don't wipe the folder!"
OutputFileHandler handler(output_folder + sub_directory.str(), false);
// These methods must be called in parallel.
std::vector<unsigned> node_indices;
node_indices.push_back(cell_factory.GetNodeIndexCentreOfScar()); // 0
node_indices.push_back(cell_factory.GetNodeIndexCentralTissue()); // 1 - best "control" half way through
node_indices.push_back(cell_factory.GetNodeIndexLeftTissue()); // 2
node_indices.push_back(cell_factory.GetNodeIndexRightTissue()); // 3
node_indices.push_back(cell_factory.GetNodeIndexLeftOfScar()); // 4
node_indices.push_back(cell_factory.GetNodeIndexRightOfScar()); // 5
node_indices.push_back(cell_factory.GetNodeIndexSideOfScar()); // 6
node_indices.push_back(cell_factory.GetNodeIndexBaseOfTissue()); // 7
// But we only want the master to write out the actual file.
if (PetscTools::AmMaster())
{
FileFinder hdf5_dir(output_folder + sub_directory.str(), RelativeTo::ChasteTestOutput);
Hdf5DataReader reader(hdf5_dir, "results");
// Retrieve the voltage traces at nodes of interest
std::vector<std::vector<double> > voltage_traces;
for (unsigned i=0; i<node_indices.size(); i++)
{
voltage_traces.push_back(reader.GetVariableOverTime("V", node_indices[i]));
}
// Output the full voltage traces at these nodes
std::vector<double> times = reader.GetUnlimitedDimensionValues();
out_stream output_file = handler.OpenOutputFile("voltage_traces_at_selected_nodes.dat");
for (unsigned i=0; i<times.size(); i++)
{
*output_file << times[i];
for (unsigned j=0; j<node_indices.size(); j++)
{
*output_file << "\t" << voltage_traces[j][i] ;
}
*output_file << "\n";
}
output_file->close();
// Also output some of our action potential summary statistics
output_file = handler.OpenOutputFile("action_potential_properties_at_selected_nodes.dat");
*output_file << "Node\tAPD90(ms)\tAPD70(ms)\tAPD50(ms)\tMaxUpstroke(mV/ms)\tPeakVoltage(mV)\tAmplitude(mV)\tResting(mV)" << std::endl;
const double voltage_AP_threshold = -70.0;
for (unsigned i=0; i<node_indices.size(); i++)
{
CellProperties voltage_properties(voltage_traces[i], times, voltage_AP_threshold);
double apd90, apd70, apd50, upstroke, peak, amplitude, resting;
try
{
apd90 = voltage_properties.GetLastActionPotentialDuration(90);
apd70 = voltage_properties.GetLastActionPotentialDuration(70);
apd50 = voltage_properties.GetLastActionPotentialDuration(50);
upstroke = voltage_properties.GetLastCompleteMaxUpstrokeVelocity();
peak = voltage_properties.GetLastCompletePeakPotential();
amplitude = voltage_properties.GetLastActionPotentialAmplitude();
resting = voltage_properties.GetRestingPotentials().back();
}
catch (Exception& e)
{ // In case there is no action potential at all.
apd90 = 0.0;
apd70 = 0.0;
apd50 = 0.0;
upstroke = 0.0;
peak = 0.0;
amplitude = 0.0;
resting = voltage_traces[i].back();
}
*output_file << i << "\t"
<< apd90 << "\t" << apd70 << "\t" << apd50 << "\t"
<< upstroke << "\t" << peak << "\t" << amplitude << "\t" << resting << std::endl;
}
output_file->close();
}
#else
std::cout << "CVODE is not installed, or CHASTE is not configured to use it, check your hostconfig settings." << std::endl;
// TS_ASSERT(false); // uncomment if you want to ensure CVODE is set up on your system.
#endif // CHASTE_CVODE
}
};
Code
The full code is given below
File name TestFibroblastsLiteratePaper.hpp
#include <cxxtest/TestSuite.h>
#include "ScarCellFactory.hpp"
#include "ScarConductivityModifier.hpp"
#include "GmshMeshReader.hpp"
#include "MonodomainProblem.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "CellProperties.hpp" // For analysing APs
#include "PetscSetupAndFinalize.hpp"
class TestFibroblasts2d : public CxxTest::TestSuite
{
private:
/** Width of the 2D domain we're simulating. */
double mRegionWidth;
/** Radius of the scar in the centre. */
double mScarRadius;
/** Width of the boundary region (myocytes but different conductivity) */
double mBoundaryWidth;
public:
void Test2dPropagation() throw (Exception)
{
#ifdef CHASTE_CVODE
if (*(CommandLineArguments::Instance()->p_argc) == 1)
{
std::cout << "TestFibroblasts takes the following arguments:\n"
" Mandatory:\n"
" * --scar-conduction-scaling <x> The proportion of the intra-cellular conduction to\n"
" apply in the central scar region.\n"
"\n"
" Optional:\n"
" * --use-neutral-cells <true or false> Whether to use neutral cells OR,\n"
" * --use-fibroblasts <true or false> a fibroblast electrophysiology model,\n"
" in the scar region.\n"
" * --scar-membrane-area-scaling <x> the scaling factor for membrane area (per unit vol) in scar region\n"
" * --boundary-conduction-scaling <x> The proportion of intra-cellular conduction to\n"
" apply in the boundary of the scar (still myocytes).\n"
" * --scar-shape <x> Whether the scar should be a 'CIRCLE' or a 'SQUARE'\n"
"\n"
" * --pacing-period <x> The time between paces applied on x=0 (defaults to 100ms)\n"
" * --end-time <x> How long to perform the simulation for (defaults to pacing period).\n"
" * --lesion-pacing Whether to perform pacing in the centre of the lesion (default false).\n"
" * --cut Whether to introduce a cut with complete conduction block (defaults to false).\n";
return;
}
/**
* SET OPTIONS FOR THIS RUN
*
* These are the defaults.
*/
double pacing_cycle_length = 100;
bool use_neutral_cell_model = false;
bool use_fibroblasts = false;
bool lesion_pacing = false; // Alternative is remote/sinus pacing.
ScarShape shape = CIRCLE;
double scar_membrane_area_scaling = 1.0;
const std::string output_folder = "FibroblastSims/";
if (CommandLineArguments::Instance()->OptionExists("--pacing-period"))
{
pacing_cycle_length = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--pacing-period");
}
double end_time = pacing_cycle_length; // Default end time is pacing cycle length
if (CommandLineArguments::Instance()->OptionExists("--end-time"))
{
end_time = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--end-time");
}
if (CommandLineArguments::Instance()->OptionExists("--scar-shape"))
{
if (CommandLineArguments::Instance()->GetStringCorrespondingToOption("--scar-shape")=="CIRCLE")
{
shape = CIRCLE;
}
else if (CommandLineArguments::Instance()->GetStringCorrespondingToOption("--scar-shape")=="SQUARE")
{
shape = SQUARE;
}
else
{
EXCEPTION("The --scar-shape argument should be 'CIRCLE' or 'SQUARE'.");
}
}
// Here we say what proportion of the normal conductivity we want in the scar
double scaling_factor;
if (CommandLineArguments::Instance()->OptionExists("--scar-conduction-scaling"))
{
scaling_factor = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--scar-conduction-scaling");
assert(scaling_factor >= 0.0);
assert(scaling_factor <= 1.0);
}
else
{
EXCEPTION("Please provide the command line option '--scar-conduction-scaling' with a value between 0 and 1.");
}
double scaling_factor_boundary = 1.0;
if (CommandLineArguments::Instance()->OptionExists("--boundary-conduction-scaling"))
{
scaling_factor_boundary = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--boundary-conduction-scaling");
assert(scaling_factor_boundary >= 0.0);
assert(scaling_factor_boundary <= 1.0);
}
// And decide whether to use a neutral cell model, or normal mytocytes.
if (CommandLineArguments::Instance()->OptionExists("--use-neutral-cells"))
{
use_neutral_cell_model = CommandLineArguments::Instance()->GetBoolCorrespondingToOption("--use-neutral-cells");
}
// And decide whether to use a fibroblast model
if (CommandLineArguments::Instance()->OptionExists("--use-fibroblasts"))
{
use_fibroblasts = CommandLineArguments::Instance()->GetBoolCorrespondingToOption("--use-fibroblasts");
}
if (use_neutral_cell_model && use_fibroblasts)
{
EXCEPTION("You can only set '--use-neutral-cells true' OR '--use-fibroblasts true', not both.");
}
if (CommandLineArguments::Instance()->OptionExists("--scar-membrane-area-scaling"))
{
scar_membrane_area_scaling = CommandLineArguments::Instance()->GetDoubleCorrespondingToOption("--scar-membrane-area-scaling");
assert(scar_membrane_area_scaling >= 0.0);
assert(scar_membrane_area_scaling <= 1.0);
}
bool create_cut = false;
if (CommandLineArguments::Instance()->OptionExists("--cut"))
{
create_cut = true;
}
if (CommandLineArguments::Instance()->OptionExists("--lesion-pacing"))
{
lesion_pacing = true;
}
// Set up a unique output folder for these options
std::stringstream sub_directory;
if (use_neutral_cell_model)
{
sub_directory << "Neutral";
}
else if (use_fibroblasts)
{
sub_directory << "Fibroblast";
}
else
{
sub_directory << "Myocyte";
}
sub_directory << "_scar_cond_" << scaling_factor << "_cap_" << scar_membrane_area_scaling << "_boundary_cond_" << scaling_factor_boundary << "_period_" << pacing_cycle_length << "_end_" << end_time;
if (shape==SQUARE)
{
sub_directory << "_Square";
}
if (create_cut)
{
sub_directory << "_WithCut";
}
if (lesion_pacing)
{
sub_directory << "_LesionPacing";
}
DistributedTetrahedralMesh<2,2> mesh;
if (create_cut)
{
GmshMeshReader<2,2> gmsh_reader("projects/MouseLesion/test/data/meshes/2D_with_cuts_7_by_9_mm.msh");
mesh.ConstructFromMeshReader(gmsh_reader);
// Mesh properties we will use in the cell factory and conductivity modifier.
mRegionWidth = 0.7; //cm
mScarRadius = 0.2325; //cm
mBoundaryWidth = 0.01; //cm
}
else
{
// Mesh properties we will use in the cell factory and conductivity modifier.
mRegionWidth = 0.5; //cm
mScarRadius = 0.1; //cm
mBoundaryWidth = 0.01; //cm
double h=0.005;
mesh.ConstructRegularSlabMesh(h, mRegionWidth, mRegionWidth);
}
HeartConfig::Instance()->SetSimulationDuration(end_time); //ms
HeartConfig::Instance()->SetOutputDirectory(output_folder + sub_directory.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetVisualizeWithVtk(true);
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.1, 0.1, 0.1);
double intra_conductivity = 1.75; // Chaste Defaults
double extra_conductivity = 7.0; // Chaste Defaults
// Set up the defaults.
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(intra_conductivity, intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(extra_conductivity, extra_conductivity));
// Make a scar cell factory
ScarCellFactory<2> cell_factory(mRegionWidth,
mScarRadius,
pacing_cycle_length,
scar_membrane_area_scaling, // chi scaling factor.
use_neutral_cell_model,
use_fibroblasts,
shape,
lesion_pacing,
create_cut);
// Create a conductivity modifier
ScarConductivityModifier<2> modifier(&mesh,
shape,
mRegionWidth,
mScarRadius,
scaling_factor, // D scaling factor.
scar_membrane_area_scaling, // chi scaling factor.
mBoundaryWidth,
scaling_factor_boundary, // D scaling factor (chi not implemented for boundary yet).
true, // whether a lesion applied
create_cut);
MonodomainProblem<2> problem( &cell_factory );
problem.SetMesh( &mesh );
problem.SetWriteInfo(); // Writes max and min voltages out.
problem.Initialise();
problem.GetTissue()->SetConductivityModifier(&modifier);
// Check that the Scar cell factory is doing the index tracking I expect.
// These should have been calculated during the initialisation step.
// These were checked in Paraview for the h = 0.005 slab mesh.
// If these lines fail it isn't a problem if you have intentionally
// changed the mesh for some reason (as we have when there's a cut).
if (!create_cut)
{
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexCentreOfScar(), 5100u);
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexCentralTissue(), 8130u);
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexLeftTissue(), 5070u);
TS_ASSERT_EQUALS(cell_factory.GetNodeIndexRightTissue(), 5130u);
}
problem.Solve();
// Print out a couple of node traces to file for easy plotting.
// Output file handler should be called collectively, the 'false' says "don't wipe the folder!"
OutputFileHandler handler(output_folder + sub_directory.str(), false);
// These methods must be called in parallel.
std::vector<unsigned> node_indices;
node_indices.push_back(cell_factory.GetNodeIndexCentreOfScar()); // 0
node_indices.push_back(cell_factory.GetNodeIndexCentralTissue()); // 1 - best "control" half way through
node_indices.push_back(cell_factory.GetNodeIndexLeftTissue()); // 2
node_indices.push_back(cell_factory.GetNodeIndexRightTissue()); // 3
node_indices.push_back(cell_factory.GetNodeIndexLeftOfScar()); // 4
node_indices.push_back(cell_factory.GetNodeIndexRightOfScar()); // 5
node_indices.push_back(cell_factory.GetNodeIndexSideOfScar()); // 6
node_indices.push_back(cell_factory.GetNodeIndexBaseOfTissue()); // 7
// But we only want the master to write out the actual file.
if (PetscTools::AmMaster())
{
FileFinder hdf5_dir(output_folder + sub_directory.str(), RelativeTo::ChasteTestOutput);
Hdf5DataReader reader(hdf5_dir, "results");
// Retrieve the voltage traces at nodes of interest
std::vector<std::vector<double> > voltage_traces;
for (unsigned i=0; i<node_indices.size(); i++)
{
voltage_traces.push_back(reader.GetVariableOverTime("V", node_indices[i]));
}
// Output the full voltage traces at these nodes
std::vector<double> times = reader.GetUnlimitedDimensionValues();
out_stream output_file = handler.OpenOutputFile("voltage_traces_at_selected_nodes.dat");
for (unsigned i=0; i<times.size(); i++)
{
*output_file << times[i];
for (unsigned j=0; j<node_indices.size(); j++)
{
*output_file << "\t" << voltage_traces[j][i] ;
}
*output_file << "\n";
}
output_file->close();
// Also output some of our action potential summary statistics
output_file = handler.OpenOutputFile("action_potential_properties_at_selected_nodes.dat");
*output_file << "Node\tAPD90(ms)\tAPD70(ms)\tAPD50(ms)\tMaxUpstroke(mV/ms)\tPeakVoltage(mV)\tAmplitude(mV)\tResting(mV)" << std::endl;
const double voltage_AP_threshold = -70.0;
for (unsigned i=0; i<node_indices.size(); i++)
{
CellProperties voltage_properties(voltage_traces[i], times, voltage_AP_threshold);
double apd90, apd70, apd50, upstroke, peak, amplitude, resting;
try
{
apd90 = voltage_properties.GetLastActionPotentialDuration(90);
apd70 = voltage_properties.GetLastActionPotentialDuration(70);
apd50 = voltage_properties.GetLastActionPotentialDuration(50);
upstroke = voltage_properties.GetLastCompleteMaxUpstrokeVelocity();
peak = voltage_properties.GetLastCompletePeakPotential();
amplitude = voltage_properties.GetLastActionPotentialAmplitude();
resting = voltage_properties.GetRestingPotentials().back();
}
catch (Exception& e)
{ // In case there is no action potential at all.
apd90 = 0.0;
apd70 = 0.0;
apd50 = 0.0;
upstroke = 0.0;
peak = 0.0;
amplitude = 0.0;
resting = voltage_traces[i].back();
}
*output_file << i << "\t"
<< apd90 << "\t" << apd70 << "\t" << apd50 << "\t"
<< upstroke << "\t" << peak << "\t" << amplitude << "\t" << resting << std::endl;
}
output_file->close();
}
#else
std::cout << "CVODE is not installed, or CHASTE is not configured to use it, check your hostconfig settings." << std::endl;
// TS_ASSERT(false); // uncomment if you want to ensure CVODE is set up on your system.
#endif // CHASTE_CVODE
}
};