TestStreeterFibreGenerator.hpp

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*/
#ifndef TESTSTREETERFIBREGENERATOR_HPP_
#define TESTSTREETERFIBREGENERATOR_HPP_

#include "TetrahedralMesh.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "StreeterFibreGenerator.hpp"
#include "OutputFileHandler.hpp"
#include "TrianglesMeshReader.hpp"
#include "FibreReader.hpp"

#include "PetscSetupAndFinalize.hpp"

/*
 * HOW_TO_TAG Cardiac/Problem definition
 * Generate fibre field definitions for cardiac geometries using a mathematical rule approach
 *
 */
class TestStreeterFibreGenerator : public CxxTest::TestSuite
{
private:
    void CompareGeneratedWithReferenceFile(FileFinder& rGeneratedFile, FibreFileType generatedFileType, FileFinder& rReferenceFile, FibreFileType referenceFileType)
    {
        // Make sure that any parallel file writers have finished before attempting to open
        PetscTools::Barrier("Wait for WriteData()");
        FibreReader<3> fibre_reader1(rGeneratedFile, generatedFileType);
        FibreReader<3> fibre_reader2(rReferenceFile, referenceFileType);

        double tol = 1e-10;

        std::vector< c_vector<double, 3> > fibres1;
        std::vector< c_vector<double, 3> > second1;
        std::vector< c_vector<double, 3> > third1;

        std::vector< c_vector<double, 3> > fibres2;
        std::vector< c_vector<double, 3> > second2;
        std::vector< c_vector<double, 3> > third2;

        if (generatedFileType == ORTHO)
        {
            fibre_reader1.GetAllOrtho(fibres1, second1, third1);
        }
        else
        {
            fibre_reader1.GetAllAxi(fibres1);
        }

        if (referenceFileType == ORTHO)
        {
            fibre_reader2.GetAllOrtho(fibres2, second2, third2);
        }
        else
        {
            fibre_reader2.GetAllAxi(fibres2);
        }

        TS_ASSERT_EQUALS(fibres1.size(), fibres2.size());
        if (generatedFileType == ORTHO && referenceFileType == ORTHO)
        {
            TS_ASSERT_EQUALS(second1.size(), second2.size());
            TS_ASSERT_EQUALS(third1.size(), third2.size());
        }

        for (unsigned i = 0u; i < fibres1.size(); i++)
        {
            for (unsigned j=0u; j<3u; j++)
            {
                TS_ASSERT_DELTA( fibres1[i][j] , fibres2[i][j] , tol);
                if (generatedFileType == ORTHO && referenceFileType == ORTHO)
                {
                    TS_ASSERT_DELTA( second1[i][j] , second2[i][j] , tol);
                    TS_ASSERT_DELTA( third1[i][j] , third2[i][j] , tol);
                }
            }
        }
    }

public:

    void TestSimpleOrthotropic()
    {
        TrianglesMeshReader<3,3> mesh_reader("heart/test/data/box_shaped_heart/box_heart");
        std::string epi_face_file = "heart/test/data/box_shaped_heart/epi.tri";
        std::string rv_face_file = "heart/test/data/box_shaped_heart/rv.tri";
        std::string lv_face_file = "heart/test/data/box_shaped_heart/lv.tri";

        DistributedTetrahedralMesh<3,3> mesh;
        mesh.ConstructFromMeshReader(mesh_reader);

        StreeterFibreGenerator<3> fibre_generator(mesh);
        fibre_generator.SetSurfaceFiles(epi_face_file, rv_face_file, lv_face_file, false);
        fibre_generator.SetApexToBase(0);

        OutputFileHandler handler("shorter_streeter", false);
        fibre_generator.WriteData(handler, "box_heart.ortho");

        FileFinder fibre_file_ascii = handler.FindFile("box_heart.ortho");
        FileFinder fibre_file_reference("heart/test/data/box_shaped_heart/box_heart.ortho", RelativeTo::ChasteSourceRoot);

        CompareGeneratedWithReferenceFile(fibre_file_ascii, ORTHO, fibre_file_reference, ORTHO);

        fibre_generator.SetWriteFileAsBinary();
        fibre_generator.WriteData(handler, "box_heart_binary.ortho");

        FileFinder fibre_file_binary = handler.FindFile("box_heart_binary.ortho");

        CompareGeneratedWithReferenceFile(fibre_file_binary, ORTHO, fibre_file_reference, ORTHO);
    }

    void TestSimpleOrthotropicNotDistributed()
    {
        TrianglesMeshReader<3,3> mesh_reader("heart/test/data/box_shaped_heart/box_heart");
        std::string epi_face_file = "heart/test/data/box_shaped_heart/epi.tri";
        std::string rv_face_file = "heart/test/data/box_shaped_heart/rv.tri";
        std::string lv_face_file = "heart/test/data/box_shaped_heart/lv.tri";

        TetrahedralMesh<3,3> mesh;
        mesh.ConstructFromMeshReader(mesh_reader);

        StreeterFibreGenerator<3> fibre_generator(mesh);
        fibre_generator.SetSurfaceFiles(epi_face_file, rv_face_file, lv_face_file, false);
        fibre_generator.SetApexToBase(0);

        OutputFileHandler handler("shorter_streeter", false);
        fibre_generator.WriteData(handler, "box_heart_not_dist.ortho");

        FileFinder fibre_file1 = handler.FindFile("box_heart_not_dist.ortho");
        FileFinder fibre_file2("heart/test/data/box_shaped_heart/box_heart.ortho", RelativeTo::ChasteSourceRoot);

        CompareGeneratedWithReferenceFile(fibre_file1, ORTHO, fibre_file2, ORTHO);
    }

    void TestExceptions()
    {
        TrianglesMeshReader<3,3> mesh_reader("heart/test/data/box_shaped_heart/box_heart");

        DistributedTetrahedralMesh<3,3> mesh;
        mesh.ConstructFromMeshReader(mesh_reader);

        StreeterFibreGenerator<3> fibre_generator(mesh);

        // No surfaces defined
        OutputFileHandler handler("streeter", false);
        TS_ASSERT_THROWS_THIS(fibre_generator.WriteData(handler, "file.fibres"),
                "Files defining the heart surfaces not set");

        // Wrong surface filename
        TS_ASSERT_THROWS_THIS(fibre_generator.SetSurfaceFiles("wrong_name", "wrong_name", "wrong_name", false),
                "Wrong surface definition file name wrong_name");

        std::string epi_face_file = "heart/test/data/box_shaped_heart/epi.tri";
        std::string rv_face_file = "heart/test/data/box_shaped_heart/rv.tri";
        std::string lv_face_file = "heart/test/data/box_shaped_heart/lv.tri";


        fibre_generator.SetSurfaceFiles(epi_face_file, rv_face_file, lv_face_file, false);
        OutputFileHandler shorter_handler("shorter_streeter", false);
        TS_ASSERT_THROWS_THIS(fibre_generator.WriteData(shorter_handler, "vector_not_set.ortho"),
            "Apex to base vector has not been set");
        TS_ASSERT_THROWS_THIS(fibre_generator.SetApexToBase(999),
            "Apex to base coordinate axis was out of range");

        c_vector<double, 3> axis;
        axis[0] = 0.0;
        axis[1] = 0.0;
        axis[2] = 0.0;
        TS_ASSERT_THROWS_THIS(fibre_generator.SetApexToBase(axis),
            "Apex to base vector should be non-zero");
        axis[1] = 42.0; //Will be normalised
        fibre_generator.SetApexToBase(axis);
    }

    void TestConstructStreeterOnLeftWedge()
    {
        TrianglesMeshReader<3,3> mesh_reader("heart/test/data/human_wedge_mesh/HumanWedgeMesh");
        std::string epi_face_file = "heart/test/data/human_wedge_mesh/epi.tri";
        std::string endo_face_file = "heart/test/data/human_wedge_mesh/endo.tri";

        DistributedTetrahedralMesh<3,3> mesh;
        mesh.ConstructFromMeshReader(mesh_reader);

        StreeterFibreGenerator<3> fibre_generator(mesh);

        //Assume we are in the left ventricle
        fibre_generator.SetSurfaceFiles(epi_face_file, "", endo_face_file, true);

        fibre_generator.SetApexToBase(0);
        fibre_generator.SetWriteFileAsBinary();

        OutputFileHandler handler("human_wedge_mesh", false);

        fibre_generator.WriteData(handler, "HumanWedgeMeshLeft.ortho");

        FileFinder fibre_file1 = handler.FindFile("HumanWedgeMeshLeft.ortho");
        FileFinder fibre_file2("heart/test/data/human_wedge_mesh/HumanWedgeMeshLeft.ortho", RelativeTo::ChasteSourceRoot);

        CompareGeneratedWithReferenceFile(fibre_file1, ORTHO, fibre_file2, ORTHO);
    }

    void TestConstructStreeterOnRightWedge()
    {
        TrianglesMeshReader<3,3> mesh_reader("heart/test/data/human_wedge_mesh/HumanWedgeMesh");
        std::string epi_face_file = "heart/test/data/human_wedge_mesh/epi.tri";
        std::string endo_face_file = "heart/test/data/human_wedge_mesh/endo.tri";

        DistributedTetrahedralMesh<3,3> mesh;
        mesh.ConstructFromMeshReader(mesh_reader);

        StreeterFibreGenerator<3> fibre_generator(mesh);

        //Assume we are in the left ventricle
        fibre_generator.SetSurfaceFiles(epi_face_file, endo_face_file, "", true);

        fibre_generator.SetApexToBase(0);
        fibre_generator.SetWriteFileAsBinary();

        OutputFileHandler handler("human_wedge_mesh", false);

        fibre_generator.WriteData(handler, "HumanWedgeMeshRight.ortho");

        FileFinder fibre_file1 = handler.FindFile("HumanWedgeMeshRight.ortho");
        FileFinder fibre_file2("heart/test/data/human_wedge_mesh/HumanWedgeMeshRight.ortho", RelativeTo::ChasteSourceRoot);

        CompareGeneratedWithReferenceFile(fibre_file1, ORTHO, fibre_file2, ORTHO);
    }

    void TestSetLogInfo()
    {
        TrianglesMeshReader<3,3> mesh_reader("heart/test/data/box_shaped_heart/box_heart");
        std::string epi_face_file = "heart/test/data/box_shaped_heart/epi.tri";
        std::string rv_face_file = "heart/test/data/box_shaped_heart/rv.tri";
        std::string lv_face_file = "heart/test/data/box_shaped_heart/lv.tri";

        DistributedTetrahedralMesh<3,3> mesh;
        mesh.ConstructFromMeshReader(mesh_reader);

        StreeterFibreGenerator<3> fibre_generator(mesh);
        fibre_generator.SetSurfaceFiles(epi_face_file, rv_face_file, lv_face_file, false);
        fibre_generator.SetApexToBase(0);

        OutputFileHandler handler("shorter_streeter_loginfo");

        fibre_generator.WriteData(handler, "box_heart.ortho");

        FileFinder node_regions_file = handler.FindFile("node_regions.data");
        FileFinder wall_thickness_file = handler.FindFile("wall_thickness.data");
        FileFinder averaged_thickness_file = handler.FindFile("averaged_thickness.data");

        TS_ASSERT_EQUALS(node_regions_file.IsFile(), false);
        TS_ASSERT_EQUALS(wall_thickness_file.IsFile(), false);
        TS_ASSERT_EQUALS(averaged_thickness_file.IsFile(), false);

        // Make the above parallel tests finish before the next part.
        // (When master process enters PreWriteCalculations it will create empty files for the node_regions etc.)
        PetscTools::Barrier("Wait for tests that files don't exist yet");
        fibre_generator.SetLogInfo(true);
        fibre_generator.WriteData(handler, "box_heart.ortho");

        TS_ASSERT_EQUALS(node_regions_file.IsFile(), true);
        TS_ASSERT_EQUALS(wall_thickness_file.IsFile(), true);
        TS_ASSERT_EQUALS(averaged_thickness_file.IsFile(), true);
    }
};

#endif /*TESTSTREETERFIBREGENERATOR_HPP_*/