void TestDeleteOrderSimpleMesh() throw(Exception)
{
TrianglesMeshReader<1,3> mesh_reader("lung/test/airway_generation/data/test_major_airways_mesh");
MutableMesh<1,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//Assign valid radii
for(unsigned node_index = 0; node_index < mesh.GetNumNodes(); ++node_index)
{
mesh.GetNode(node_index)->rGetNodeAttributes()[0] = 1.0;
}
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 6u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 5u);
MajorAirwaysCentreLinesCleaner cleaner(mesh, 0u);
cleaner.CleanUsingHorsfieldOrder(1u);
NodeMap node_map(mesh.GetNumAllNodes());
mesh.ReIndex(node_map);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 2u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 1u);
TS_ASSERT_DELTA(mesh.GetNode(0u)->rGetLocation()[0], 0.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(0u)->rGetLocation()[1], 0.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(0u)->rGetLocation()[2], -2.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(1u)->rGetLocation()[0], 0.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(1u)->rGetLocation()[1], 0.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(1u)->rGetLocation()[2], 0.0, 1e-6);
}
void TestCellwiseDataGradientVerySmallMesh() throw(Exception)
{
// Create a simple mesh
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_2_elements");
MutableMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Create a cell population
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
MeshBasedCellPopulation<2> cell_population(mesh, cells);
// Set up data: C(x,y) = x^2
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
double x = mesh.GetNode(i)->rGetLocation()[0];
CellPtr p_cell = cell_population.GetCellUsingLocationIndex(mesh.GetNode(i)->GetIndex());
p_cell->GetCellData()->SetItem("x^2", x*x);
}
CellwiseDataGradient<2> gradient;
gradient.SetupGradients(cell_population, "x^2");
// With the algorithm being used, the numerical gradient is (1,0)
// for each of the nodes
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
TS_ASSERT_DELTA(gradient.rGetGradient(i)(0), 1.0, 1e-9);
TS_ASSERT_DELTA(gradient.rGetGradient(i)(1), 0.0, 1e-9);
}
}
void TestDeleteFirstOrder() throw(Exception)
{
#ifdef CHASTE_VTK
VtkMeshReader<1,3> mesh_reader("lung/test/data/TestSubject002MajorAirways.vtu");
MutableMesh<1,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//Assign valid radii
for(unsigned node_index = 0; node_index < mesh.GetNumNodes(); ++node_index)
{
mesh.GetNode(node_index)->AddNodeAttribute(1.0);
}
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 12065u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 12064u);
MajorAirwaysCentreLinesCleaner cleaner(mesh, 0u);
cleaner.CleanUsingHorsfieldOrder(1u);
NodeMap node_map(mesh.GetNumAllNodes());
mesh.ReIndex(node_map);
//Confirmed visually to be correct
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 3683u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 3682u);
// Uncomment to visualise
// VtkMeshWriter<1,3> mesh_writer("TestMajorAirwaysCentreLinesCleaner", "Novartis002Trimmed");
// mesh_writer.WriteFilesUsingMesh(mesh);
#endif //CHASTE_VTK
}
void TestRemoveIsolatedNodesSimpleMesh() throw(Exception)
{
TrianglesMeshReader<1,3> mesh_reader("lung/test/airway_generation/data/test_isolated_nodes_major_airways_mesh");
MutableMesh<1,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//Assign valid radii
for(unsigned node_index = 0; node_index < mesh.GetNumNodes(); ++node_index)
{
mesh.GetNode(node_index)->rGetNodeAttributes()[0] = 1.0;
}
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 6u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 3u);
MajorAirwaysCentreLinesCleaner cleaner(mesh, 0u);
cleaner.CleanIsolatedNodes();
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 4u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 3u);
}
void TestRadialSloughingCellKillerMethods() throw(Exception)
{
// Create mesh
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_128_elements");
MutableMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
mesh.Translate(-0.5,-0.5);
// Get centre of mesh (we know it's at the origin, really)
c_vector<double,2> centre(2);
centre[0] = 0.0;
centre[1] = 0.0;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
centre += mesh.GetNode(i)->rGetLocation();
}
centre = centre/mesh.GetNumNodes();
// Choose radius of cell killer
double radius = 0.4;
// Create cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
// Create cell population
MeshBasedCellPopulation<2> cell_population(mesh, cells);
// Create cell killer and kill cells
RadialSloughingCellKiller radial_cell_killer(&cell_population, centre, radius);
radial_cell_killer.CheckAndLabelCellsForApoptosisOrDeath();
// Check that cells were labelled for death correctly
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
double r = norm_2(cell_population.GetLocationOfCellCentre(*cell_iter) - centre);
if (r > radius)
{
TS_ASSERT_EQUALS(cell_iter->IsDead(), true);
}
else
{
TS_ASSERT_EQUALS(cell_iter->IsDead(), false);
}
}
// Now get rid of dead cells
cell_population.RemoveDeadCells();
// Check that we are correctly left with cells inside the circle of death
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
double r = norm_2(cell_population.GetLocationOfCellCentre(*cell_iter) - centre);
TS_ASSERT_LESS_THAN_EQUALS(r, radius);
}
}
void TestHeuristicCleanSimpleMesh() throw(Exception)
{
{
TrianglesMeshReader<1,3> mesh_reader("lung/test/airway_generation/data/test_major_airways_mesh");
MutableMesh<1,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//Assign valid radii
for(unsigned node_index = 0; node_index < mesh.GetNumNodes(); ++node_index)
{
mesh.GetNode(node_index)->rGetNodeAttributes()[0] = 1.0;
}
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 6u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 5u);
MajorAirwaysCentreLinesCleaner cleaner(mesh, 0u);
cleaner.CleanTerminalsHueristic();
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 6u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 5u);
//Trips an added nodes exception. Not sure if this is needed!
//NodeMap node_map(mesh.GetNumAllNodes());
//mesh.ReIndex(node_map);
TS_ASSERT_DELTA(mesh.GetNode(2)->rGetLocation()[0], 1.6, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(3)->rGetLocation()[0], -1.6, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(4)->rGetLocation()[1], 1.6, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(5)->rGetLocation()[1], -1.6, 1e-6);
//Uncomment to visualise
// VtkMeshWriter<1,3> mesh_writer("TestMajorAirwaysCentreLinesCleaner", "heuristic_shorten", false);
// mesh_writer.WriteFilesUsingMesh(mesh);
}
{
TrianglesMeshReader<1,3> mesh_reader("lung/test/airway_generation/data/test_major_airways_mesh_short_terminals");
MutableMesh<1,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//Assign valid radii
for(unsigned node_index = 0; node_index < mesh.GetNumNodes(); ++node_index)
{
mesh.GetNode(node_index)->rGetNodeAttributes()[0] = 1.0;
}
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 6u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 5u);
MajorAirwaysCentreLinesCleaner cleaner(mesh, 0u);
cleaner.CleanTerminalsHueristic();
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 6u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 5u);
//Trips an added nodes exception. Not sure if this is needed!
//NodeMap node_map(mesh.GetNumAllNodes());
//mesh.ReIndex(node_map);
TS_ASSERT_DELTA(mesh.GetNode(2)->rGetLocation()[0], 1.4, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(3)->rGetLocation()[0], -1.4, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(4)->rGetLocation()[1], 1.4, 1e-6);
TS_ASSERT_DELTA(mesh.GetNode(5)->rGetLocation()[1], -1.4, 1e-6);
//Uncomment to visualise
// VtkMeshWriter<1,3> mesh_writer("TestMajorAirwaysCentreLinesCleaner", "heuristic_lengthen", false);
// mesh_writer.WriteFilesUsingMesh(mesh);
}
}
void TestCellwiseDataGradientFineMesh() throw(Exception)
{
// Create a mesh: [0,2]x[0,2]
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4096_elements");
MutableMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Create a cell population
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
MeshBasedCellPopulation<2> cell_population(mesh, cells);
//////////////////////////////////
// C(x,y) = const
//////////////////////////////////
cell_population.SetDataOnAllCells("const", 1.0);
CellwiseDataGradient<2> gradient;
gradient.SetupGradients(cell_population, "const");
// Check gradient
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
TS_ASSERT_DELTA(gradient.rGetGradient(i)(0), 0.0, 1e-9);
TS_ASSERT_DELTA(gradient.rGetGradient(i)(1), 0.0, 1e-9);
}
//////////////////////////////////
// Combined setup for
// C(x,y) = x-y
// and
// C(x,y) = x^2 - y^2
//////////////////////////////////
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
double x = mesh.GetNode(i)->rGetLocation()[0];
double y = mesh.GetNode(i)->rGetLocation()[1];
CellPtr p_cell = cell_population.GetCellUsingLocationIndex(mesh.GetNode(i)->GetIndex());
p_cell->GetCellData()->SetItem("x-y", x-y);
p_cell->GetCellData()->SetItem("x^2 - y^2", x*x - y*y);
}
// Check gradient
gradient.SetupGradients(cell_population, "x-y");
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
TS_ASSERT_DELTA(gradient.rGetGradient(i)(0), 1.0, 1e-9);
TS_ASSERT_DELTA(gradient.rGetGradient(i)(1), -1.0, 1e-9);
}
// Check gradient - here there is some numerical error
gradient.SetupGradients(cell_population, "x^2 - y^2");
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
double x = mesh.GetNode(i)->rGetLocation()[0];
double y = mesh.GetNode(i)->rGetLocation()[1];
double tol = 0.3;
if (x==0 || x==2 || y==0 || y==2) //ie on boundary
{
tol = 0.6;
}
TS_ASSERT_DELTA(gradient.rGetGradient(i)(0), 2*x, tol);
TS_ASSERT_DELTA(gradient.rGetGradient(i)(1), -2*y, tol);
}
}