TestPseudoEcgCalculator.hpp

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#ifndef TESTPSEUDOECGCALCULATOR_HPP_
#define TESTPSEUDOECGCALCULATOR_HPP_

#include <cxxtest/TestSuite.h>
#include <iostream>

#include "TetrahedralMesh.hpp" //must be first, it gets UblasIncludes from the mesh classes (ChastePoint.hpp)
#include "DistributedTetrahedralMesh.hpp"
#include "PseudoEcgCalculator.hpp"
#include "ReplicatableVector.hpp"
#include "Hdf5DataReader.hpp"
#include "Hdf5DataWriter.hpp"
#include "OutputFileHandler.hpp"
#include "TrianglesMeshReader.hpp"
#include "TrianglesMeshReader.hpp"
#include "TetrahedralMesh.hpp"
#include "HeartConfig.hpp"
#include "PetscSetupAndFinalize.hpp"
#include "FileComparison.hpp"
#include "SimpleBathProblemSetup.hpp"
#include "BidomainWithBathProblem.hpp"

/* HOW_TO_TAG Cardiac/Post-processing
 * Compute pseudo-ECGs
 */
class TestPseudoEcgCalculator : public CxxTest::TestSuite
{

public:

    void TestCalculator1DLinearGradient()
    {

        //read in the 1D mesh, from 0 to 1
        TrianglesMeshReader<1,1> reader("mesh/test/data/1D_0_to_1_100_elements");
        TetrahedralMesh<1,1> mesh;
        mesh.ConstructFromMeshReader(reader);

        for (AbstractTetrahedralMesh<1,1>::ElementIterator it = mesh.GetElementIteratorBegin();
             it != mesh.GetElementIteratorEnd();
             ++it)
        {
            // A correct calculation depends on this not breaking!
            TS_ASSERT(!HeartRegionCode::IsRegionBath((*it).GetUnsignedAttribute()));
        }

        ////////////////////////////////////////////////////
        //First we write an hdf5 file with a gradient of V
        // i.e. V(x) = x; We write 4 time steps.
        ///////////////////////////////////////////////////
        unsigned number_nodes = mesh.GetNumNodes();

        DistributedVectorFactory factory(number_nodes);
        Hdf5DataWriter writer(factory, "hdf5", "gradient_V", false);
        writer.DefineFixedDimension(number_nodes);

        int node_id = writer.DefineVariable("Node", "dimensionless");
        //we call the variable like the default for the pseudoecg calculator
        int V_id = writer.DefineVariable("V", "mV");
        writer.DefineUnlimitedDimension("Time", "msec");
        writer.EndDefineMode();

        Vec petsc_data_1 = factory.CreateVec();
        DistributedVector distributed_vector_1 = factory.CreateDistributedVector(petsc_data_1);

        Vec petsc_data_2 = factory.CreateVec();
        DistributedVector distributed_vector_2 = factory.CreateDistributedVector(petsc_data_2);

        //4 time steps
        unsigned number_of_time_steps = 4;
        for (unsigned time_step=0; time_step<number_of_time_steps; time_step++)
        {
            // Write some values, the value of V is the same as the x coordinate, i.e. a gradient
            for (DistributedVector::Iterator index = distributed_vector_1.Begin();
                 index!= distributed_vector_1.End();
                 ++index)
            {
                distributed_vector_1[index] = index.Global;
                distributed_vector_2[index] = index.Global/100.0;
            }
            distributed_vector_1.Restore();
            distributed_vector_2.Restore();

            // Write the vector
            writer.PutVector(node_id, petsc_data_1);
            writer.PutVector(V_id, petsc_data_2);
            writer.PutUnlimitedVariable(time_step);
            writer.AdvanceAlongUnlimitedDimension();
        }

        writer.Close();

        PetscTools::Destroy(petsc_data_1);
        PetscTools::Destroy(petsc_data_2);

        ///////////////////////////////////////////////////
        // Now we compute the pseudo ECG. We set an electrode at x=15.
        ///////////////////////////////////////////////////
        ChastePoint<1> probe_electrode(15.0);

        PseudoEcgCalculator<1,1,1> calculator (mesh, probe_electrode,
                                               FileFinder("hdf5",RelativeTo::ChasteTestOutput),
                                               "gradient_V");
        double pseudo_ecg;

        // The expected result is the integral of: - d(gradV)*dgrad(1/r) in dx
        // Because in this simple case d(gradV)=1, the result is simply -1/(15-x) evaluated
        // between 0 and 1
        double expected_result = -(1/14.0-1/15.0);
        for (unsigned k = 0; k< number_of_time_steps; k++)
        {
            pseudo_ecg = calculator.ComputePseudoEcgAtOneTimeStep(k);
            TS_ASSERT_DELTA(pseudo_ecg, expected_result,1e-6);
        }

        //now we test the writer method
        calculator.WritePseudoEcg();

        std::string output_dir = "ChasteResults/output";//default value
        {
            FileComparison comparer(OutputFileHandler::GetChasteTestOutputDirectory() + output_dir + "/PseudoEcgFromElectrodeAt_15_0_0.dat",
                                    "heart/test/data/ValidPseudoEcg1D.dat");
            TS_ASSERT(comparer.CompareFiles());
        }

        {
            // Time-step striding
            PseudoEcgCalculator<1,1,1> course_calculator (mesh, probe_electrode,
                                                   FileFinder("hdf5",RelativeTo::ChasteTestOutput),
                                                   "gradient_V", "V" /*Voltage name*/, 2 /*Time stride*/);
            course_calculator.WritePseudoEcg();
            FileComparison comparer(OutputFileHandler::GetChasteTestOutputDirectory() + output_dir + "/PseudoEcgFromElectrodeAt_15_0_0.dat",
                    "heart/test/data/CoarsePseudoEcg1D.dat");
            TS_ASSERT(comparer.CompareFiles());
        }

        ChastePoint<1> bad_probe_electrode(0.0021132486540519);
        PseudoEcgCalculator<1,1,1> bad_calculator (mesh,
                                                   bad_probe_electrode,
                                                   FileFinder("hdf5",RelativeTo::ChasteTestOutput),
                                                   "gradient_V");
        TS_ASSERT_THROWS_THIS(bad_calculator.ComputePseudoEcgAtOneTimeStep(0), "Probe is on a mesh Gauss point.");

    }

    void TestCalculator1DParabolic()
    {
        TrianglesMeshReader<1,1> reader("mesh/test/data/1D_0_to_1_100_elements");
        DistributedTetrahedralMesh<1,1> mesh;
        mesh.ConstructFromMeshReader(reader);

        for (AbstractTetrahedralMesh<1,1>::ElementIterator it = mesh.GetElementIteratorBegin();
             it != mesh.GetElementIteratorEnd();
             ++it)
        {
            // A correct calculation depends on this not breaking!
            TS_ASSERT(!HeartRegionCode::IsRegionBath((*it).GetUnsignedAttribute()));
        }

        ////////////////////////////////////////////////////
        //First we write an hdf5 file with V as a parabolic function of x
        // i.e. V(x) = x^2; We write 4 time steps.
        ///////////////////////////////////////////////////
        unsigned number_nodes = mesh.GetNumNodes();

        DistributedVectorFactory factory(number_nodes);

        Hdf5DataWriter writer(factory, "hdf5", "parabolic_V", false);
        writer.DefineFixedDimension(number_nodes);

        int node_id = writer.DefineVariable("Node", "dimensionless");
        //we call the variable like the default for the pseudoecg calculator
        int V_id = writer.DefineVariable("V", "mV");
        writer.DefineUnlimitedDimension("Time", "msec");
        writer.EndDefineMode();

        Vec petsc_data_1 = factory.CreateVec();
        DistributedVector distributed_vector_1 = factory.CreateDistributedVector(petsc_data_1);

        Vec petsc_data_2 = factory.CreateVec();
        DistributedVector distributed_vector_2 = factory.CreateDistributedVector(petsc_data_2);

        //4 time steps
        unsigned number_of_time_steps = 4;
        for (unsigned time_step=0; time_step<number_of_time_steps; time_step++)
        {
            // Write some values, the value of V is x^2, i.e. a parabola
            for (DistributedVector::Iterator index = distributed_vector_1.Begin();
                 index!= distributed_vector_1.End();
                 ++index)
            {
                distributed_vector_1[index] = index.Global;
                distributed_vector_2[index] = (index.Global/100.0)*(index.Global/100.0);
            }
            distributed_vector_1.Restore();
            distributed_vector_2.Restore();

            // Write the vector
            writer.PutVector(node_id, petsc_data_1);
            writer.PutVector(V_id, petsc_data_2);
            writer.PutUnlimitedVariable(time_step);
            writer.AdvanceAlongUnlimitedDimension();
        }

        writer.Close();

        PetscTools::Destroy(petsc_data_1);
        PetscTools::Destroy(petsc_data_2);

        ///////////////////////////////////////////////////
        // Now we compute the pseudo ECG. We set an electrode at x=15.
        ///////////////////////////////////////////////////

        ChastePoint<1> probe_electrode(15.0);

        PseudoEcgCalculator<1,1,1> calculator (mesh, probe_electrode,
                FileFinder("hdf5",RelativeTo::ChasteTestOutput), "parabolic_V", "V");

        double pseudo_ecg; //stores the results

        calculator.SetDiffusionCoefficient(1.0);

        // The expected result is the integral of: - d(gradV)*dgrad(1/r) in dx
        // In this case d(gradV)/dx=2x, hence the result is the integral of: - (2x * d(1/(15-x))/dx)
        // Integrating by parts with f = 2x and g = 1/(15-x) and evaluating between 0 and 1

        double expected_result = -( (2/14.0) - 2.0*log(1/14.0) + 2.0*log(1/15.0));
        for (unsigned k = 0; k< number_of_time_steps; k++)
        {
            pseudo_ecg = calculator.ComputePseudoEcgAtOneTimeStep(k);
            TS_ASSERT_DELTA(pseudo_ecg, expected_result,1e-6);
        }

        // Now try a different diffusion coefficient
        double diff_coeff = 2.0;
        calculator.SetDiffusionCoefficient(diff_coeff);

        //since we are assuming D to be constant, the expected result is just mulitplied by diff_coeff
        for (unsigned k = 0; k< number_of_time_steps; k++)
        {
            pseudo_ecg = calculator.ComputePseudoEcgAtOneTimeStep(k);
            TS_ASSERT_DELTA(pseudo_ecg, diff_coeff*expected_result,1e-6);
        }
    }

    /**
     * Test for BidomainWithBath problems.
     */
    void TestBathEcgCalculations()
    {
        HeartConfig::Instance()->SetSimulationDuration(2.0);  //ms - set to 500 to see whole AP trace.
        HeartConfig::Instance()->SetOutputDirectory("BidomainBath1d_PseudoEcg");
        HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_1d");

        c_vector<double,1> centre;
        centre(0) = 0.5;
        BathCellFactory<1> cell_factory(-1e6, centre); // stimulates x=0.5 node

        BidomainWithBathProblem<1> bidomain_problem( &cell_factory );

        TrianglesMeshReader<1,1> reader("mesh/test/data/1D_0_to_1_100_elements");
        TetrahedralMesh<1,1> mesh;
        mesh.ConstructFromMeshReader(reader);

        // Set the x<0.25 and x>0.75 regions as the bath region
        for (unsigned i=0; i<mesh.GetNumElements(); i++)
        {
            double x = mesh.GetElement(i)->CalculateCentroid()[0];
            if ((x<0.25) || (x>0.75))
            {
                mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidBathId());
            }
        }

        bidomain_problem.SetMesh(&mesh);
        bidomain_problem.Initialise();

        bidomain_problem.Solve();

        Vec sol = bidomain_problem.GetSolution();
        ReplicatableVector sol_repl(sol);

        // Test some Pseudo ECG calculation methods #2107
        ChastePoint<1> point1(0.0); // Point at which to calculate a pseudo-ECG - this is allowed.
        PseudoEcgCalculator<1,1,1>  ecg_calculator1(mesh, point1, FileFinder("BidomainBath1d_PseudoEcg",RelativeTo::ChasteTestOutput), "bidomain_bath_1d");

        // At the beginning we should have zero as voltage is uniform (in the tissue, this failed before #2107)
        double pseudo_ecg1_at_t_0 = ecg_calculator1.ComputePseudoEcgAtOneTimeStep(0);
        TS_ASSERT_DELTA(pseudo_ecg1_at_t_0, 0.0, 1e-9);

        ChastePoint<1> point2(0.3); // Point at which to calculate a pseudo-ECG - this should look decent
        PseudoEcgCalculator<1,1,1> ecg_calculator2(mesh, point2, FileFinder("BidomainBath1d_PseudoEcg",RelativeTo::ChasteTestOutput), "bidomain_bath_1d");

        // At the beginning we should have zero as voltage is uniform (in the tissue, this failed before #2107)
        double pseudo_ecg2_at_t_0 = ecg_calculator2.ComputePseudoEcgAtOneTimeStep(0);
        TS_ASSERT_DELTA(pseudo_ecg2_at_t_0, 0.0, 1e-9);

        // For completeness
        ecg_calculator1.WritePseudoEcg();
        ecg_calculator2.WritePseudoEcg();
    }

 };


#endif /*TESTPSEUDOECGCALCULATOR_HPP_*/