/*
* == Using the SRN model in a cell-based simulation ==
*
* We conclude with a brief test demonstrating how {{{MySrnModel}}} can be used
* in a cell-based simulation.
*/
void TestOffLatticeSimulationWithMySrnModel() throw(Exception)
{
/* We use the honeycomb vertex mesh generator to create a vertex mesh.
*/
HoneycombVertexMeshGenerator generator(2, 2);
MutableVertexMesh<2,2>* p_mesh = generator.GetMesh();
/* Next, we create some cells. First, define the cells vector. */
std::vector<CellPtr> cells;
/* We must create a shared_ptr to a {{{CellMutationState}}} with which to bestow the cells.
* We make use of the macro MAKE_PTR to do this: the first argument is the class and
* the second argument is the name of the shared_ptr. */
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(StemCellProliferativeType, p_stem_type);
/* Then we loop over the nodes. */
for (unsigned i=0; i<p_mesh->GetNumElements(); i++)
{
/* For each node we create a cell with our SRN model and simple Stochastic cell cycle model. */
StochasticDurationCellCycleModel* p_cell_cycle_model = new StochasticDurationCellCycleModel();
MySrnModel* p_srn_model = new MySrnModel;
/* We choose to initialise the concentrations to random levels in each cell. */
std::vector<double> initial_conditions;
initial_conditions.push_back(1.0-2.0*RandomNumberGenerator::Instance()->ranf());
initial_conditions.push_back(1.0-2.0*RandomNumberGenerator::Instance()->ranf());
p_srn_model->SetInitialConditions(initial_conditions);
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model, p_srn_model));
p_cell->SetCellProliferativeType(p_stem_type);
/* Now, we define a random birth time, chosen from [-T,0], where
* T = t,,1,, + t,,2,,, where t,,1,, is a parameter representing the G,,1,, duration
* of a stem cell, and t,,2,, is the basic S+G,,2,,+M phases duration.
*/
double birth_time = - RandomNumberGenerator::Instance()->ranf() * (p_cell_cycle_model->GetStemCellG1Duration() + p_cell_cycle_model->GetSG2MDuration());
/* We then set the birth time and push the cell back into the vector of cells. */
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
/* Now that we have defined the mesh and cells, we can define the cell population, forces, areas modifier, and simulation
* in the same way as the other tutorials. */
VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithMySrnModel");
simulator.SetEndTime(10.0);
simulator.SetSamplingTimestepMultiple(50);
MAKE_PTR(NagaiHondaForce<2>, p_force);
simulator.AddForce(p_force);
MAKE_PTR(SimpleTargetAreaModifier<2>, p_growth_modifier);
simulator.AddSimulationModifier(p_growth_modifier);
/* Finally to run the simulation, we call {{{Solve()}}}. */
simulator.Solve();
}
void CellsGenerator<CELL_CYCLE_MODEL,DIM>::GenerateGivenLocationIndices(std::vector<CellPtr>& rCells,
const std::vector<unsigned> locationIndices,
boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
assert(!locationIndices.empty());
unsigned num_cells = locationIndices.size();
rCells.clear();
rCells.reserve(num_cells);
CellPropertyRegistry::Instance()->Clear();
for (unsigned i=0; i<num_cells; i++)
{
CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
p_cell_cycle_model->SetDimension(DIM);
boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
if (!pCellProliferativeType)
{
p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
}
else
{
p_cell->SetCellProliferativeType(pCellProliferativeType);
}
double birth_time = 0.0 - locationIndices[i];
p_cell->SetBirthTime(birth_time);
rCells.push_back(p_cell);
}
}
void TestArchiveTysonNovakCellCycleModels()
{
// Set up
OutputFileHandler handler("archive", false);
std::string archive_filename = handler.GetOutputDirectoryFullPath() + "TysonNovakCellCycleModel.arch";
{
// We must set up SimulationTime to avoid memory leaks
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0, 1);
// As usual, we archive via a pointer to the most abstract class possible
AbstractCellCycleModel* const p_model = new TysonNovakCellCycleModel;
p_model->SetDimension(3);
p_model->SetBirthTime(-1.5);
static_cast<TysonNovakCellCycleModel*>(p_model)->SetDt(0.085);
// We must create a cell to be able to initialise the cell cycle model's ODE system
MAKE_PTR(WildTypeCellMutationState, p_healthy_state);
MAKE_PTR(StemCellProliferativeType, p_stem_type);
CellPtr p_cell(new Cell(p_healthy_state, p_model));
p_cell->SetCellProliferativeType(p_stem_type);
p_cell->InitialiseCellCycleModel();
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
output_arch << p_model;
// Note that here, deletion of the cell-cycle model is handled by the cell destructor
SimulationTime::Destroy();
}
{
// We must set SimulationTime::mStartTime here to avoid tripping an assertion
SimulationTime::Instance()->SetStartTime(0.0);
AbstractCellCycleModel* p_model2;
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
input_arch >> p_model2;
TS_ASSERT_EQUALS(p_model2->GetDimension(), 3u);
TS_ASSERT_DELTA(p_model2->GetBirthTime(), -1.5, 1e-12);
TS_ASSERT_DELTA(static_cast<TysonNovakCellCycleModel*>(p_model2)->GetDt(), 0.085, 1e-3);
TysonNovakCellCycleModel* p_static_cast_model =
static_cast<TysonNovakCellCycleModel*>(p_model2);
TysonNovak2001OdeSystem* p_ode_system =
static_cast<TysonNovak2001OdeSystem*>(p_static_cast_model->GetOdeSystem());
TS_ASSERT(p_ode_system != NULL);
// Avoid memory leaks
delete p_model2;
}
}
void TestVertexCryptBoundaryForceMethods() throw (Exception)
{
// Create a simple 2D VertexMesh
HoneycombVertexMeshGenerator generator(5, 5, false, 0.1, 0.5);
MutableVertexMesh<2,2>* p_mesh = generator.GetMesh();
// Translate mesh so that some points are below y=0
p_mesh->Translate(0.0, -3.0);
// Set up cells, one for each VertexElement. Give each cell
// a birth time of -elem_index, so its age is elem_index
std::vector<CellPtr> cells;
boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
boost::shared_ptr<AbstractCellProliferativeType> p_diff_type(new DifferentiatedCellProliferativeType);
for (unsigned elem_index=0; elem_index<p_mesh->GetNumElements(); elem_index++)
{
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_diff_type);
double birth_time = 0.0 - elem_index;
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
// Create cell population
VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Create a force system
VertexCryptBoundaryForce<2> force(100);
for (unsigned i=0; i<cell_population.GetNumNodes(); i++)
{
cell_population.GetNode(i)->ClearAppliedForce();
}
force.AddForceContribution(cell_population);
// Check forces are correct
for (unsigned i=0; i<cell_population.GetNumNodes(); i++)
{
TS_ASSERT_DELTA(cell_population.GetNode(i)->rGetAppliedForce()[0], 0.0, 1e-4);
double y = cell_population.GetNode(i)->rGetLocation()[1];
if (y >= 0.0)
{
// If y > 0, the force contribution should be zero...
TS_ASSERT_DELTA(cell_population.GetNode(i)->rGetAppliedForce()[1], 0.0, 1e-4);
}
else
{
// ...otherwise, the force contribution should be quadratic in y
double expected_force = force.GetForceStrength()*y*y;
TS_ASSERT_DELTA(cell_population.GetNode(i)->rGetAppliedForce()[1], expected_force, 1e-4);
}
}
}
void Test2DMonolayerRepresentativeSimulationForProfiling() throw (Exception)
{
// Set start time
SimulationTime::Instance()->SetStartTime(0.0);
// Create a simple mesh
HoneycombMeshGenerator generator(5, 5, 0);
MutableMesh<2,2>* p_mesh = generator.GetCircularMesh(3.5);
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
StochasticDurationGenerationBasedCellCycleModel* p_model = new StochasticDurationGenerationBasedCellCycleModel();
p_model->SetMaxTransitGenerations(UINT_MAX);
p_model->SetTransitCellG1Duration(1.0);
p_model->SetStemCellG1Duration(1.0);
double birth_time = -RandomNumberGenerator::Instance()->ranf()*
( p_model->GetStemCellG1Duration()
+ p_model->GetSG2MDuration() );
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_transit_type);
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
// Create a cell population
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("Test2DMonolayerRepresentativeSimulationForProfiling");
simulator.SetEndTime(50.0);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
p_force->SetCutOffLength(1.5);
simulator.AddForce(p_force);
// Run simulation
simulator.Solve();
// Tidy up
SimulationTime::Destroy();
RandomNumberGenerator::Destroy();
}
void CellsGenerator<CELL_CYCLE_MODEL,DIM>::GenerateBasic(std::vector<CellPtr>& rCells,
unsigned numCells,
const std::vector<unsigned> locationIndices,
boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
rCells.clear();
if (!locationIndices.empty())
{
// If location indices is given, then it needs to match the number of output cells
if (numCells != locationIndices.size())
{
EXCEPTION("The size of the locationIndices vector must match the required number of output cells");
}
}
rCells.reserve(numCells);
// Create cells
for (unsigned i=0; i<numCells; i++)
{
CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
p_cell_cycle_model->SetDimension(DIM);
boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
if (!pCellProliferativeType)
{
p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
}
else
{
p_cell->SetCellProliferativeType(pCellProliferativeType);
}
double birth_time;
if (!locationIndices.empty())
{
birth_time = 0.0 - locationIndices[i];
}
else
{
birth_time = 0.0 - i;
}
p_cell->SetBirthTime(birth_time);
rCells.push_back(p_cell);
}
}
void TestGetCellUsingLocationIndexWithHaloCell() throw (Exception)
{
boost::shared_ptr<Node<3> > p_node(new Node<3>(10, false, 0.0, 0.0, 0.0));
// Create a cell.
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_type);
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPtr p_cell(new Cell(p_state, p_model));
mpNodeBasedCellPopulation->AddHaloCell(p_cell, p_node);
TS_ASSERT_THROWS_NOTHING(mpNodeBasedCellPopulation->GetCellUsingLocationIndex(10));
TS_ASSERT_EQUALS(mpNodeBasedCellPopulation->GetCellUsingLocationIndex(10), p_cell);
}
void TestNonPhaseBasedCcmException() throw (Exception)
{
// First set up SimulationTime (this is usually handled by a simulation object)
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0, 1);
// Create a cell mutation state
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_type);
// Create a cell-cycle model
UniformlyDistributedCellCycleModel* p_model = new UniformlyDistributedCellCycleModel();
// Create a cell
CellPtr p_cell(new Cell(p_state, p_model));
// Create a SimpleTargetAreaModifier
MAKE_PTR(SimpleTargetAreaModifier<2>, p_modifier);
// Test that the correct exception is thrown if we try to call UpdateTargetAreas() on the population
TS_ASSERT_THROWS_THIS(p_modifier->UpdateTargetAreaOfCell(p_cell),
"SimpleTargetAreaModifier is to be used with a AbstractPhaseBasedCellCycleModel only");
CellBasedEventHandler::Reset(); // Otherwise logging has been started but not stopped due to exception above.
}
void CellsGenerator<CELL_CYCLE_MODEL,DIM>::GenerateBasicRandom(std::vector<CellPtr>& rCells,
unsigned numCells,
boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
rCells.clear();
rCells.reserve(numCells);
// Create cells
for (unsigned i=0; i<numCells; i++)
{
CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
p_cell_cycle_model->SetDimension(DIM);
boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
if (!pCellProliferativeType)
{
p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
}
else
{
p_cell->SetCellProliferativeType(pCellProliferativeType);
}
double birth_time = -p_cell_cycle_model->GetAverageStemCellCycleTime()*RandomNumberGenerator::Instance()->ranf();
if (p_cell->GetCellProliferativeType()->IsType<TransitCellProliferativeType>())
{
birth_time = -p_cell_cycle_model->GetAverageTransitCellCycleTime()*RandomNumberGenerator::Instance()->ranf();
}
p_cell->SetBirthTime(birth_time);
rCells.push_back(p_cell);
}
}
void TestNodeBasedSimulationWithContactInhibition()
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator does not work in parallel
// Create a simple 2D NodeBasedCellPopulation
HoneycombMeshGenerator generator(5, 5, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
ContactInhibitionCellCycleModel* p_cycle_model = new ContactInhibitionCellCycleModel();
p_cycle_model->SetDimension(2);
p_cycle_model->SetBirthTime(-10.0);
p_cycle_model->SetQuiescentVolumeFraction(0.9);
p_cycle_model->SetEquilibriumVolume(0.7854); //pi *(0.5)^2
p_cycle_model->SetStemCellG1Duration(0.1);
p_cycle_model->SetTransitCellG1Duration(0.1);
CellPtr p_cell(new Cell(p_state, p_cycle_model));
p_cell->SetCellProliferativeType(p_transit_type);
cells.push_back(p_cell);
}
NodeBasedCellPopulation<2> cell_population(mesh, cells);
cell_population.AddPopulationWriter<CellMutationStatesCountWriter>();
cell_population.AddCellWriter<CellVolumesWriter>();
cell_population.AddPopulationWriter<NodeVelocityWriter>();
// Create a simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestNodeBasedSimulationWithVolumeTracked");
TS_ASSERT_EQUALS(simulator.GetDt(), 1.0/120.0); // Default value for off-lattice simulations
simulator.SetEndTime(simulator.GetDt()/2.0);
// Create a volume-tracking modifier and pass it to the simulation
MAKE_PTR(VolumeTrackingModifier<2>, p_modifier);
simulator.AddSimulationModifier(p_modifier);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
p_force->SetCutOffLength(1.5);
simulator.AddForce(p_force);
// Run simulation
simulator.Solve();
// Test that the node velocities file exists
OutputFileHandler output_file_handler("TestNodeBasedSimulationWithVolumeTracked", false);
FileFinder generated = output_file_handler.FindFile("results_from_time_0/nodevelocities.dat");
TS_ASSERT(generated.Exists());
// Test that the volumes of the cells are correct in CellData at the first timestep
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_population.GetVolumeOfCell(*cell_iter), cell_iter->GetCellData()->GetItem("volume"), 1e-4);
}
simulator.SetEndTime(2.0);
// Run simulation
simulator.Solve();
// Test that the volumes of the cells are correct in CellData at the end time
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_population.GetVolumeOfCell(*cell_iter), cell_iter->GetCellData()->GetItem("volume"), 1e-4);
}
// Check that the correct number of cells are labelled (i.e. experiencing contact inhibition)
TS_ASSERT_EQUALS(cell_population.GetCellPropertyRegistry()->Get<CellLabel>()->GetCellCount(), 2u);
}
void TestArchivingOfCell() throw(Exception)
{
OutputFileHandler handler("archive", false);
handler.SetArchiveDirectory();
std::string archive_filename = handler.GetOutputDirectoryFullPath() + "cell.arch";
// Archive a cell
{
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(2.0, 4);
// Create mutation state
boost::shared_ptr<AbstractCellProperty> p_healthy_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
boost::shared_ptr<AbstractCellProperty> p_type(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
// Create cell-cycle model
FixedDurationGenerationBasedCellCycleModel* p_cell_model = new FixedDurationGenerationBasedCellCycleModel();
// Create SRN
Goldbeter1991SrnModel* p_srn_model = new Goldbeter1991SrnModel();
// Create cell property collection
CellPropertyCollection collection;
MAKE_PTR(CellLabel, p_label);
collection.AddProperty(p_label);
// Create cell
CellPtr p_cell(new Cell(p_healthy_state, p_cell_model, p_srn_model, false, collection));
p_cell->SetCellProliferativeType(p_type);
p_cell->InitialiseCellCycleModel();
p_cell->InitialiseSrnModel();
p_simulation_time->IncrementTimeOneStep();
TS_ASSERT_EQUALS(p_cell->GetAge(), 0.5);
TS_ASSERT_EQUALS(p_cell->GetAncestor(), UNSIGNED_UNSET);
// Set ancestor
MAKE_PTR_ARGS(CellAncestor, p_cell_ancestor, (2u));
p_cell->SetAncestor(p_cell_ancestor);
TS_ASSERT_EQUALS(p_cell->GetAncestor(), 2u);
// Set CellVecData with some actual content
boost::shared_ptr<AbstractCellProperty> p_vec_data(CellPropertyRegistry::Instance()->Get<CellVecData>());
p_cell->AddCellProperty(p_vec_data);
Vec item_1 = PetscTools::CreateAndSetVec(2, -17.3); // <-17.3, -17.3>
p_cell->GetCellVecData()->SetItem("item 1", item_1);
// Check properties set correctly
CellPropertyCollection& final_collection = p_cell->rGetCellPropertyCollection();
TS_ASSERT_EQUALS(final_collection.GetSize(), 7u);
TS_ASSERT_EQUALS(final_collection.HasProperty<WildTypeCellMutationState>(), true);
TS_ASSERT_EQUALS(final_collection.HasProperty<ApcOneHitCellMutationState>(), false);
TS_ASSERT_EQUALS(final_collection.HasProperty<ApcTwoHitCellMutationState>(), false);
TS_ASSERT_EQUALS(final_collection.HasProperty<CellLabel>(), true);
TS_ASSERT_EQUALS(final_collection.HasPropertyType<AbstractCellProperty>(), true);
TS_ASSERT_EQUALS(final_collection.HasPropertyType<AbstractCellMutationState>(), true);
TS_ASSERT_EQUALS(final_collection.HasPropertyType<CellAncestor>(), true);
TS_ASSERT_EQUALS(final_collection.HasPropertyType<CellId>(), true);
TS_ASSERT_EQUALS(p_cell->GetAncestor(), 2u);
for (CellPropertyCollection::Iterator it = final_collection.Begin(); it != final_collection.End(); ++it)
{
TS_ASSERT_EQUALS(final_collection.HasProperty(*it), true);
bool is_wildtype = (*it)->IsType<WildTypeCellMutationState>();
bool is_label = (*it)->IsType<CellLabel>();
bool is_ancestor = (*it)->IsType<CellAncestor>();
bool is_cellid = (*it)->IsType<CellId>();
bool is_data = (*it)->IsType<CellData>();
bool is_vec_data = (*it)->IsType<CellVecData>();
bool is_stem = (*it)->IsType<StemCellProliferativeType>();
bool is_any_of_above = is_wildtype || is_label || is_ancestor || is_cellid || is_data || is_vec_data || is_stem;
TS_ASSERT_EQUALS(is_any_of_above, true);
}
// Create another cell
boost::shared_ptr<AbstractCellProperty> p_another_healthy_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
FixedDurationGenerationBasedCellCycleModel* p_another_cell_model = new FixedDurationGenerationBasedCellCycleModel();
Goldbeter1991SrnModel* p_another_srn_model = new Goldbeter1991SrnModel();
CellPtr p_another_cell(new Cell(p_another_healthy_state, p_another_cell_model, p_another_srn_model, false, collection));
boost::shared_ptr<AbstractCellProperty> p_another_vec_data(new CellVecData);
p_another_cell->AddCellProperty(p_another_vec_data);
TS_ASSERT_EQUALS(p_cell->GetCellVecData()->GetNumItems(), 1u);
TS_ASSERT_EQUALS(p_another_cell->GetCellVecData()->GetNumItems(), 0u);
Vec another_item_1 = PetscTools::CreateAndSetVec(2, 42.0); // <42, 42>
p_another_cell->GetCellVecData()->SetItem("item 1", another_item_1);
// Create an output archive
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
CellPtr const p_const_cell = p_cell;
// Write the cell to the archive
output_arch << static_cast<const SimulationTime&> (*p_simulation_time);
output_arch << p_const_cell;
// Write the second cell also
CellPtr const p_another_const_cell = p_another_cell;
output_arch << p_another_const_cell;
// Tidy up
SimulationTime::Destroy();
PetscTools::Destroy(item_1);
PetscTools::Destroy(another_item_1);
}
// Restore CellPtr
{
// Need to set up time to initialize a cell
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetStartTime(1.0);
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(2.0, 1); // will be restored
// Initialize a cell
CellPtr p_cell;
// Restore the cell
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
input_arch >> *p_simulation_time;
input_arch >> p_cell;
// Check the simulation time has been restored (through the cell)
TS_ASSERT_EQUALS(p_simulation_time->GetTime(), 0.5);
TS_ASSERT_EQUALS(p_simulation_time->GetTimeStep(), 0.5);
TS_ASSERT_EQUALS(p_cell->GetAge(), 0.5);
TS_ASSERT_EQUALS(static_cast<FixedDurationGenerationBasedCellCycleModel*>(p_cell->GetCellCycleModel())->GetGeneration(), 0u);
TS_ASSERT(dynamic_cast<Goldbeter1991SrnModel*>(p_cell->GetSrnModel()));
TS_ASSERT_EQUALS(p_cell->GetCellProliferativeType()->IsType<StemCellProliferativeType>(), true);
AbstractCellCycleModel* p_cc_model = p_cell->GetCellCycleModel();
TS_ASSERT_EQUALS(p_cc_model->GetCell(), p_cell);
AbstractSrnModel* p_srn_model = p_cell->GetSrnModel();
TS_ASSERT_EQUALS(p_srn_model->GetCell(), p_cell);
CellPropertyCollection& collection = p_cell->rGetCellPropertyCollection();
TS_ASSERT_EQUALS(collection.GetSize(), 7u);
TS_ASSERT_EQUALS(collection.HasProperty<WildTypeCellMutationState>(), true);
TS_ASSERT_EQUALS(collection.HasProperty<ApcOneHitCellMutationState>(), false);
TS_ASSERT_EQUALS(collection.HasProperty<ApcTwoHitCellMutationState>(), false);
TS_ASSERT_EQUALS(collection.HasProperty<CellLabel>(), true);
TS_ASSERT_EQUALS(collection.HasPropertyType<AbstractCellProperty>(), true);
TS_ASSERT_EQUALS(collection.HasPropertyType<AbstractCellMutationState>(), true);
TS_ASSERT_EQUALS(collection.HasPropertyType<CellAncestor>(), true);
TS_ASSERT_EQUALS(collection.HasPropertyType<CellId>(), true);
TS_ASSERT_EQUALS(p_cell->GetAncestor(), 2u);
// Check explicitly for CellVecData as it is not available by default as CellData
TS_ASSERT_EQUALS(collection.HasPropertyType<CellVecData>(), true);
// Check that the Vec stored in CellVecData was unarchived correctly
boost::shared_ptr<CellVecData> p_cell_vec_data = boost::static_pointer_cast<CellVecData>(collection.GetPropertiesType<CellVecData>().GetProperty());
PetscInt vec_size;
VecGetSize(p_cell_vec_data->GetItem("item 1"), &vec_size);
TS_ASSERT_EQUALS(vec_size, 2);
ReplicatableVector rep_item_1(p_cell_vec_data->GetItem("item 1"));
TS_ASSERT_DELTA(rep_item_1[0], -17.3, 2e-14);
for (CellPropertyCollection::Iterator it = collection.Begin(); it != collection.End(); ++it)
{
TS_ASSERT_EQUALS(collection.HasProperty(*it), true);
bool is_wildtype = (*it)->IsType<WildTypeCellMutationState>();
bool is_label = (*it)->IsType<CellLabel>();
bool is_ancestor = (*it)->IsType<CellAncestor>();
bool is_cellid = (*it)->IsType<CellId>();
bool is_data = (*it)->IsType<CellData>();
bool is_vec_data = (*it)->IsType<CellVecData>();
bool is_stem = (*it)->IsType<StemCellProliferativeType>();
bool is_any_of_above = is_wildtype || is_label || is_ancestor || is_cellid || is_data || is_vec_data || is_stem;
TS_ASSERT_EQUALS(is_any_of_above, true);
}
// Try another cell
CellPtr p_another_cell;
input_arch >> p_another_cell;
ReplicatableVector rep_another_item_1(p_another_cell->GetCellVecData()->GetItem("item 1"));
TS_ASSERT_DELTA(rep_another_item_1[0], 42.0, 2e-14);
}
}
void TestTargetAreaOfDaughterCells()
{
// Plan: initialise a cell and have it divide at a fixed time. If cell divides at t, check that:
// target area of mother cell at t - dt = mature target area
// target area of daughter cells at t = half of that
// target area of daughter cells at t + dt = half of mature target area + little increment
// Create a simple 2D MutableVertexMesh with only one cell
HoneycombVertexMeshGenerator generator(1, 1);
MutableVertexMesh<2,2>* p_mesh = generator.GetMesh();
// Set up cell
std::vector<CellPtr> cells;
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_transit_type);
double birth_time = -11.0; // The cell cycle duration is 12
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
// Create cell population
VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestTargetAreaOfDaughterCells");
simulator.SetEndTime(0.997);
// Create a force law and pass it to the simulation
MAKE_PTR(NagaiHondaForce<2>, p_nagai_honda_force);
simulator.AddForce(p_nagai_honda_force);
// Create a SimpleTargetAreaModifier
MAKE_PTR(SimpleTargetAreaModifier<2>, p_growth_modifier);
simulator.AddSimulationModifier(p_growth_modifier);
// Run simulation
simulator.Solve();
// We should only have one cell now
unsigned num_cells_before_division = simulator.rGetCellPopulation().GetNumRealCells();
TS_ASSERT_EQUALS(num_cells_before_division, 1u);
// This is the cell from before; let's see what its target area is
double target_area_before_division = p_cell->GetCellData()->GetItem("target area");
TS_ASSERT_DELTA(target_area_before_division,1.0,1e-9);
// We now adjust the end time and run the simulation a bit further
simulator.SetEndTime(1.001);
simulator.Solve();
// We should now have two cells
unsigned num_cells_at_division = simulator.rGetCellPopulation().GetNumRealCells();
TS_ASSERT_EQUALS(num_cells_at_division, 2u);
// Iterate over the cells, checking their target areas
for (VertexBasedCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
double target_area_at_division = cell_iter->GetCellData()->GetItem("target area");
TS_ASSERT_DELTA(target_area_at_division,0.5,1e-9);
}
// We now do the same thing again
simulator.SetEndTime(1.003);
simulator.Solve();
// We should still have two cells
unsigned num_cells_after_division = simulator.rGetCellPopulation().GetNumRealCells();
TS_ASSERT_EQUALS(num_cells_after_division, 2u);
for (VertexBasedCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
double target_area_after_division = cell_iter->GetCellData()->GetItem("target area");
// line to verify: cell_target_area *= 0.5*(1 + cell_age/g1_duration)
double supposed_target_area_after_division = 0.5*(1+0.002/2.);
TS_ASSERT_DELTA(target_area_after_division,supposed_target_area_after_division,1e-9);
}
}
void TestCryptProjectionForceMethods() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesnt work in parallel.
// Create a mesh
unsigned num_cells_width = 10;
unsigned num_cells_depth = 10;
unsigned thickness_of_ghost_layer = 0;
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0,1);
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, thickness_of_ghost_layer);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
// Centre the mesh at (0,0)
ChasteCuboid<2> bounding_box=p_mesh->CalculateBoundingBox();
double width_of_mesh = (num_cells_width/(num_cells_width+2.0*thickness_of_ghost_layer))*(bounding_box.GetWidth(0));
double height_of_mesh = (num_cells_depth/(num_cells_depth+2.0*thickness_of_ghost_layer))*(bounding_box.GetWidth(1));
p_mesh->Translate(-width_of_mesh/2, -height_of_mesh/2);
// Create some cells
std::vector<CellPtr> cells;
boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
boost::shared_ptr<AbstractCellProperty> p_stem_type(new StemCellProliferativeType);
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPtr p_cell(new Cell(p_state, p_model));
if (i==4 || i==5)
{
p_cell->SetBirthTime(-0.5);
}
else
{
p_cell->SetBirthTime(-10.0);
}
p_cell->SetCellProliferativeType(p_stem_type);
cells.push_back(p_cell);
}
// Create a cell population
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
std::pair<CellPtr,CellPtr> cell_pair_4_5 = cell_population.CreateCellPair(cell_population.GetCellUsingLocationIndex(4), cell_population.GetCellUsingLocationIndex(5));
cell_population.MarkSpring(cell_pair_4_5);
// Create a spring system with crypt surface z = 2*r
WntConcentration<2>::Instance()->SetCryptProjectionParameterA(2.0);
WntConcentration<2>::Instance()->SetCryptProjectionParameterB(1.0);
CryptProjectionForce crypt_projection_force;
// Test get methods
TS_ASSERT_DELTA(crypt_projection_force.GetA(), 2.0, 1e-12);
TS_ASSERT_DELTA(crypt_projection_force.GetB(), 1.0, 1e-12);
// Test crypt height and gradient calculations
c_vector<double, 2> node_location_2d = p_mesh->GetNode(0)->rGetLocation();
TS_ASSERT_DELTA(crypt_projection_force.CalculateCryptSurfaceHeightAtPoint(node_location_2d), 2.0*pow(norm_2(node_location_2d),1.0), 1e-12);
TS_ASSERT_DELTA(crypt_projection_force.CalculateCryptSurfaceDerivativeAtPoint(node_location_2d), 2.0, 1e-12);
// Test updating of mNode3dLocationMap
crypt_projection_force.UpdateNode3dLocationMap(cell_population);
// Move a node slightly
ChastePoint<2> new_point;
new_point.rGetLocation()[0] = node_location_2d[0]+0.05;
new_point.rGetLocation()[1] = node_location_2d[1];
p_mesh->SetNode(0, new_point, false);
// Test UpdateNode3dLocationMap()
c_vector<double, 2> new_node_location_2d;
new_node_location_2d[0] = new_point.rGetLocation()[0];
new_node_location_2d[1] = new_point.rGetLocation()[1];
crypt_projection_force.UpdateNode3dLocationMap(cell_population);
// Check the map updates correctly (note that we have used no ghost nodes, so the map does contain 0)
c_vector<double, 3> calculated_new_node_location_3d = crypt_projection_force.mNode3dLocationMap[0];
c_vector<double, 3> correct_new_node_location_3d;
correct_new_node_location_3d[0] = new_node_location_2d[0];
correct_new_node_location_3d[1] = new_node_location_2d[1];
correct_new_node_location_3d[2] = crypt_projection_force.CalculateCryptSurfaceHeightAtPoint(new_node_location_2d);
TS_ASSERT_DELTA(calculated_new_node_location_3d[0], correct_new_node_location_3d[0], 1e-12);
TS_ASSERT_DELTA(calculated_new_node_location_3d[1], correct_new_node_location_3d[1], 1e-12);
TS_ASSERT_DELTA(calculated_new_node_location_3d[2], correct_new_node_location_3d[2], 1e-12);
// Test force calculation on a normal spring
c_vector<double,2> force_on_spring; // between nodes 0 and 1
// Find one of the elements that nodes 0 and 1 live on
ChastePoint<2> new_point2;
new_point2.rGetLocation()[0] = new_point[0] + 0.01;
new_point2.rGetLocation()[1] = new_point[1] + 0.01;
unsigned elem_index = p_mesh->GetContainingElementIndex(new_point2, false);
Element<2,2>* p_element = p_mesh->GetElement(elem_index);
force_on_spring = crypt_projection_force.CalculateForceBetweenNodes(p_element->GetNodeGlobalIndex(1),
p_element->GetNodeGlobalIndex(0),
cell_population);
TS_ASSERT_DELTA(force_on_spring[0], -5.7594, 1e-4);
TS_ASSERT_DELTA(force_on_spring[1], 0.0230, 1e-4);
// Test force calculation with a cutoff
double dist = norm_2(p_mesh->GetVectorFromAtoB(p_element->GetNode(0)->rGetLocation(),
p_element->GetNode(1)->rGetLocation()));
crypt_projection_force.SetCutOffLength(dist - 0.1);
force_on_spring = crypt_projection_force.CalculateForceBetweenNodes(p_element->GetNodeGlobalIndex(1),
p_element->GetNodeGlobalIndex(0),
cell_population);
TS_ASSERT_DELTA(force_on_spring[0], 0.0, 1e-4);
TS_ASSERT_DELTA(force_on_spring[1], 0.0, 1e-4);
// Test force calculation for a pair of newly born neighbouring cells
force_on_spring = crypt_projection_force.CalculateForceBetweenNodes(4, 5, cell_population);
TS_ASSERT_DELTA(force_on_spring[0], 0.0, 1e-4);
TS_ASSERT_DELTA(force_on_spring[1], 0.0, 1e-4);
cell_population.UnmarkSpring(cell_pair_4_5);
// For coverage, test force calculation for a pair of neighbouring apoptotic cells
cell_population.GetCellUsingLocationIndex(6)->StartApoptosis();
cell_population.GetCellUsingLocationIndex(7)->StartApoptosis();
force_on_spring = crypt_projection_force.CalculateForceBetweenNodes(6, 7, cell_population);
TS_ASSERT_DELTA(force_on_spring[0], 0.0, 1e-4);
TS_ASSERT_DELTA(force_on_spring[1], 0.0, 1e-4);
// Test force calculation for a particular node
for (unsigned i=0; i<cell_population.GetNumNodes(); i++)
{
cell_population.GetNode(i)->ClearAppliedForce();
}
crypt_projection_force.AddForceContribution(cell_population);
TS_ASSERT_DELTA(cell_population.GetNode(0)->rGetAppliedForce()[0], 0.0, 1e-4);
TS_ASSERT_DELTA(cell_population.GetNode(0)->rGetAppliedForce()[1], 0.0, 1e-4);
// Test that in the case of a flat crypt surface (mA=mB=0), the results are the same as for Meineke2001SpringSystem
WntConcentration<2>::Instance()->SetCryptProjectionParameterA(0.001);
WntConcentration<2>::Instance()->SetCryptProjectionParameterB(0.001);
CryptProjectionForce flat_crypt_projection_force;
GeneralisedLinearSpringForce<2> linear_force;
// Normally this would be set up at the start of rCalculateforcesOfEachNode
flat_crypt_projection_force.UpdateNode3dLocationMap(cell_population);
for (MeshBasedCellPopulation<2>::SpringIterator spring_iterator = cell_population.SpringsBegin();
spring_iterator != cell_population.SpringsEnd();
++spring_iterator)
{
unsigned nodeA_global_index = spring_iterator.GetNodeA()->GetIndex();
unsigned nodeB_global_index = spring_iterator.GetNodeB()->GetIndex();
c_vector<double, 2> force_flat = flat_crypt_projection_force.CalculateForceBetweenNodes(nodeA_global_index, nodeB_global_index, cell_population);
c_vector<double, 2> force_meineke = linear_force.CalculateForceBetweenNodes(nodeA_global_index, nodeB_global_index, cell_population);
TS_ASSERT_DELTA(force_flat[0], force_meineke[0], 1e-3);
TS_ASSERT_DELTA(force_flat[1], force_meineke[1], 1e-3);
}
WntConcentration<2>::Destroy();
}
void TestTysonNovakCellCycleModel() throw(Exception)
{
// Set up
SimulationTime* p_simulation_time = SimulationTime::Instance();
unsigned num_timesteps = 50;
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(3.0, num_timesteps);
double standard_divide_time = 75.19/60.0;
// Test TysonNovakCellCycleModel methods for a healthy cell
TysonNovakCellCycleModel* p_cell_model = new TysonNovakCellCycleModel;
p_cell_model->SetBirthTime(p_simulation_time->GetTime());
TS_ASSERT_EQUALS(p_cell_model->CanCellTerminallyDifferentiate(), false);
MAKE_PTR(WildTypeCellMutationState, p_healthy_state);
MAKE_PTR(StemCellProliferativeType, p_stem_type);
CellPtr p_cell(new Cell(p_healthy_state, p_cell_model));
p_cell->SetCellProliferativeType(p_stem_type);
p_cell->InitialiseCellCycleModel();
p_cell_model->SetDt(0.1/60.0);
/*
* For coverage, we create another cell-cycle model that is identical except that we
* manually pass in an ODE solver. In this case, our ODE solver (BackwardEulerIvpOdeSolver)
* is the same type as the solver used by the cell-cycle model if no solver is provided
* (unless CVODE is used), so our results should be identical.
*/
boost::shared_ptr<CellCycleModelOdeSolver<TysonNovakCellCycleModel, BackwardEulerIvpOdeSolver> >
p_solver(CellCycleModelOdeSolver<TysonNovakCellCycleModel, BackwardEulerIvpOdeSolver>::Instance());
p_solver->SetSizeOfOdeSystem(6);
p_solver->Initialise();
TysonNovakCellCycleModel* p_other_cell_model = new TysonNovakCellCycleModel(p_solver);
p_other_cell_model->SetBirthTime(p_simulation_time->GetTime());
// Timestep for non-adaptive solvers defaults to 0.0001
TS_ASSERT_EQUALS(p_other_cell_model->GetDt(), 0.0001);
p_other_cell_model->SetDt(0.1/60.0);
CellPtr p_other_cell(new Cell(p_healthy_state, p_other_cell_model));
p_other_cell->SetCellProliferativeType(p_stem_type);
p_other_cell->InitialiseCellCycleModel();
// Test the cell is ready to divide at the right time
for (unsigned i=0; i<num_timesteps/2; i++)
{
p_simulation_time->IncrementTimeOneStep();
double time = p_simulation_time->GetTime();
bool result = p_cell_model->ReadyToDivide();
bool other_result = p_other_cell_model->ReadyToDivide();
if (time > standard_divide_time)
{
TS_ASSERT_EQUALS(result, true);
TS_ASSERT_EQUALS(other_result, true);
}
else
{
TS_ASSERT_EQUALS(result, false);
TS_ASSERT_EQUALS(other_result, false);
}
}
// Test ODE solution
std::vector<double> proteins = p_cell_model->GetProteinConcentrations();
TS_ASSERT_EQUALS(proteins.size(), 6u);
TS_ASSERT_DELTA(proteins[0], 0.10000000000000, 1e-2);
TS_ASSERT_DELTA(proteins[1], 0.98913684535843, 1e-2);
TS_ASSERT_DELTA(proteins[2], 1.54216806705641, 1e-1);
TS_ASSERT_DELTA(proteins[3], 1.40562614481544, 2e-2);
TS_ASSERT_DELTA(proteins[4], 0.67083371879876, 1e-2);
TS_ASSERT_DELTA(proteins[5], 0.95328206604519, 2e-2);
std::vector<double> other_proteins = p_other_cell_model->GetProteinConcentrations();
TS_ASSERT_EQUALS(other_proteins.size(), 6u);
TS_ASSERT_DELTA(other_proteins[0], 0.10000000000000, 1e-2);
TS_ASSERT_DELTA(other_proteins[1], 0.98913684535843, 1e-2);
TS_ASSERT_DELTA(other_proteins[2], 1.54216806705641, 1e-1);
TS_ASSERT_DELTA(other_proteins[3], 1.40562614481544, 2e-2);
TS_ASSERT_DELTA(other_proteins[4], 0.67083371879876, 1e-2);
TS_ASSERT_DELTA(other_proteins[5], 0.95328206604519, 2e-2);
TS_ASSERT_EQUALS(p_cell_model->ReadyToDivide(),true);
// For coverage, we also test TysonNovakCellCycleModel methods for a mutant cell
p_cell_model->ResetForDivision();
TS_ASSERT_EQUALS(p_cell_model->ReadyToDivide(),false);
TysonNovakCellCycleModel* p_cell_model2 = static_cast<TysonNovakCellCycleModel*> (p_cell_model->CreateCellCycleModel());
MAKE_PTR(ApcOneHitCellMutationState, p_mutation);
CellPtr p_stem_cell_2(new Cell(p_mutation, p_cell_model2));
TS_ASSERT_EQUALS(p_cell_model2->ReadyToDivide(),false);
p_stem_cell_2->SetCellProliferativeType(p_stem_type);
TS_ASSERT_EQUALS(p_cell_model->ReadyToDivide(),false);
TS_ASSERT_EQUALS(p_cell_model2->ReadyToDivide(),false);
// Test the cell is ready to divide at the right time
for (unsigned i=0; i<num_timesteps/2; i++)
{
p_simulation_time->IncrementTimeOneStep();
double time = p_simulation_time->GetTime();
bool result = p_cell_model->ReadyToDivide();
bool result2 = p_cell_model2->ReadyToDivide();
if (time > 2.0* standard_divide_time)
{
TS_ASSERT_EQUALS(result, true);
TS_ASSERT_EQUALS(result2, true);
}
else
{
TS_ASSERT_EQUALS(result, false);
TS_ASSERT_EQUALS(result2, false);
}
}
// Test ODE solution
proteins = p_cell_model->GetProteinConcentrations();
TS_ASSERT_EQUALS(proteins.size(), 6u);
TS_ASSERT_DELTA(proteins[0], 0.10000000000000, 1e-2);
TS_ASSERT_DELTA(proteins[1], 0.98913684535843, 1e-2);
TS_ASSERT_DELTA(proteins[2], 1.54216806705641, 1e-1);
TS_ASSERT_DELTA(proteins[3], 1.40562614481544, 1e-1);
TS_ASSERT_DELTA(proteins[4], 0.67083371879876, 1e-2);
TS_ASSERT_DELTA(proteins[5], 0.9662, 1e-2);
// Coverage of AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly()
std::vector<double> test_results(6);
for (unsigned i=0; i<6; i++)
{
test_results[i] = (double)i;
}
p_cell_model->SetProteinConcentrationsForTestsOnly(1.0, test_results);
proteins = p_cell_model->GetProteinConcentrations();
for (unsigned i=0; i<6; i++)
{
TS_ASSERT_DELTA(proteins[i], test_results[i], 1e-6);
}
}
void RunTest(const std::string& rOutputDirName,
const std::string& rModelName,
const std::vector<std::string>& rArgs,
bool testLookupTables=false,
double tableTestV=-1000)
{
// Copy CellML file (and .out if present) into output dir
OutputFileHandler handler(rOutputDirName, true);
FileFinder cellml_file("heart/test/data/cellml/" + rModelName + ".cellml", RelativeTo::ChasteSourceRoot);
handler.CopyFileTo(cellml_file);
FileFinder out_file("heart/test/data/cellml/" + rModelName + ".out", RelativeTo::ChasteSourceRoot);
if (out_file.Exists())
{
handler.CopyFileTo(out_file);
}
// Create options file
std::vector<std::string> args(rArgs);
// args.push_back("--profile");
CellMLToSharedLibraryConverter converter(true);
if (!args.empty())
{
converter.CreateOptionsFile(handler, rModelName, args);
}
// Do the conversion
FileFinder copied_file(rOutputDirName + "/" + rModelName + ".cellml", RelativeTo::ChasteTestOutput);
DynamicCellModelLoaderPtr p_loader = converter.Convert(copied_file);
// Apply a stimulus of -40 uA/cm^2 - should work for all models
boost::shared_ptr<AbstractCardiacCellInterface> p_cell(CreateCellWithStandardStimulus(*p_loader, -40.0));
// Check that the default stimulus units are correct
if (p_cell->HasCellMLDefaultStimulus())
{
// Record the existing stimulus and re-apply it at the end
boost::shared_ptr<AbstractStimulusFunction> original_stim = p_cell->GetStimulusFunction();
// Tell the cell to use the default stimulus and retrieve it
boost::shared_ptr<RegularStimulus> p_reg_stim = p_cell->UseCellMLDefaultStimulus();
if (rModelName!="aslanidi_model_2009") // Even before recent changes aslanidi model has stimulus of -400 !
{
// Stimulus magnitude should be approximately between -5 and -81 uA/cm^2
TS_ASSERT_LESS_THAN(p_reg_stim->GetMagnitude(),-5);
TS_ASSERT_LESS_THAN(-81,p_reg_stim->GetMagnitude());
}
// Stimulus duration should be approximately between 0.1 and 5 ms.
TS_ASSERT_LESS_THAN(p_reg_stim->GetDuration(),6.01);
TS_ASSERT_LESS_THAN(0.1,p_reg_stim->GetDuration());
// Stimulus period should be approximately between 70 (for bondarenko - seems fast! - would expect 8-10 beats per second for mouse) and 2000ms.
TS_ASSERT_LESS_THAN(p_reg_stim->GetPeriod(),2000);
TS_ASSERT_LESS_THAN(70,p_reg_stim->GetPeriod());
p_cell->SetIntracellularStimulusFunction(original_stim);
}
// Check lookup tables exist if they should
if (testLookupTables && rModelName != "hodgkin_huxley_squid_axon_model_1952_modified")
{
double v = p_cell->GetVoltage();
p_cell->SetVoltage(tableTestV);
TS_ASSERT_THROWS_CONTAINS(p_cell->GetIIonic(), "outside lookup table range");
p_cell->SetVoltage(v);
}
Simulate(rOutputDirName, rModelName, p_cell);
}
void Test2DVertexCryptRepresentativeSimulationForProfiling()
{
// Set start time
SimulationTime::Instance()->SetStartTime(0.0);
// Create mesh
unsigned crypt_width = 18;
unsigned crypt_height = 25;
CylindricalHoneycombVertexMeshGenerator generator(crypt_width, crypt_height, true);
Cylindrical2dVertexMesh* p_mesh = generator.GetCylindricalMesh();
// Make crypt shorter for sloughing
double crypt_length = 20.0;
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
for (unsigned elem_index=0; elem_index<p_mesh->GetNumElements(); elem_index++)
{
SimpleWntCellCycleModel* p_model = new SimpleWntCellCycleModel;
p_model->SetDimension(2);
double birth_time = - RandomNumberGenerator::Instance()->ranf()*
( p_model->GetTransitCellG1Duration()
+ p_model->GetSG2MDuration() );
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_transit_type);
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
// Create cell population
VertexBasedCellPopulation<2> crypt(*p_mesh, cells);
// Set up Wnt gradient
WntConcentration<2>::Instance()->SetType(LINEAR);
WntConcentration<2>::Instance()->SetCellPopulation(crypt);
WntConcentration<2>::Instance()->SetCryptLength(crypt_length);
// Create crypt simulation from cell population and force law
CryptSimulation2d simulator(crypt);
simulator.SetSamplingTimestepMultiple(50);
simulator.SetEndTime(30.0);
simulator.SetOutputDirectory("Test2DVertexCryptRepresentativeSimulationForProfiling");
// Create a force law and pass it to the simulation
MAKE_PTR(NagaiHondaForce<2>, p_nagai_honda_force);
simulator.AddForce(p_nagai_honda_force);
// ...and with that the target area modifier
MAKE_PTR(SimpleTargetAreaModifier<2>, p_growth_modifier);
simulator.AddSimulationModifier(p_growth_modifier);
// Add a cell killer
MAKE_PTR_ARGS(SloughingCellKiller<2>, p_killer, (&crypt, crypt_length));
simulator.AddCellKiller(p_killer);
// Run simulation
simulator.Solve();
// Tidy up
WntConcentration<2>::Destroy();
}
void TestVolumeTrackedOffLatticeSimulationArchiving() throw (Exception)
{
EXIT_IF_PARALLEL;
// Create a simple 2D MeshBasedCellPopulation
HoneycombMeshGenerator generator(2, 2, 0);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(StemCellProliferativeType, p_stem_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
ContactInhibitionCellCycleModel* p_cycle_model = new ContactInhibitionCellCycleModel();
p_cycle_model->SetDimension(2);
p_cycle_model->SetBirthTime(-1.0);
p_cycle_model->SetQuiescentVolumeFraction(0.7);
p_cycle_model->SetEquilibriumVolume(1.0);
p_cycle_model->SetStemCellG1Duration(0.1);
p_cycle_model->SetTransitCellG1Duration(0.1);
CellPtr p_cell(new Cell(p_state, p_cycle_model));
p_cell->SetCellProliferativeType(p_stem_type);
p_cell->InitialiseCellCycleModel();
cells.push_back(p_cell);
}
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Create a contact inhibition simulator
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestVolumeTrackedOffLatticeSimulationSaveAndLoad");
double end_time = 0.01;
simulator.SetEndTime(end_time);
// Create a volume-tracking modifier and pass it to the simulation
MAKE_PTR(VolumeTrackingModifier<2>, p_modifier);
simulator.AddSimulationModifier(p_modifier);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
p_force->SetCutOffLength(1.5);
simulator.AddForce(p_force);
// Run simulation
simulator.Solve();
CellBasedSimulationArchiver<2, OffLatticeSimulation<2> >::Save(&simulator);
TS_ASSERT_EQUALS(simulator.rGetCellPopulation().GetNumRealCells(), 4u);
TS_ASSERT_EQUALS((static_cast<MeshBasedCellPopulation<2>*>(&(simulator.rGetCellPopulation())))->GetNumRealCells(), 4u);
TS_ASSERT_DELTA(SimulationTime::Instance()->GetTime(), 0.01, 1e-9);
CellPtr p_cell = simulator.rGetCellPopulation().GetCellUsingLocationIndex(3);
TS_ASSERT_DELTA(p_cell->GetAge(), 1.01, 1e-4);
SimulationTime::Destroy();
SimulationTime::Instance()->SetStartTime(0.0);
// Load simulation
OffLatticeSimulation<2>* p_simulator
= CellBasedSimulationArchiver<2, OffLatticeSimulation<2> >::Load("TestVolumeTrackedOffLatticeSimulationSaveAndLoad", end_time);
p_simulator->SetEndTime(0.2);
TS_ASSERT_EQUALS(p_simulator->rGetCellPopulation().GetNumRealCells(), 4u);
TS_ASSERT_EQUALS((static_cast<MeshBasedCellPopulation<2>*>(&(p_simulator->rGetCellPopulation())))->GetNumRealCells(), 4u);
TS_ASSERT_DELTA(SimulationTime::Instance()->GetTime(), 0.01, 1e-9);
CellPtr p_cell2 = p_simulator->rGetCellPopulation().GetCellUsingLocationIndex(3);
TS_ASSERT_DELTA(p_cell2->GetAge(), 1.01, 1e-4);
// Run simulation
p_simulator->Solve();
// Tidy up
delete p_simulator;
// Test Warnings
TS_ASSERT_EQUALS(Warnings::Instance()->GetNumWarnings(), 2u);
Warnings::QuietDestroy();
}
void TestVertexBasedSimulationWithContactInhibition()
{
EXIT_IF_PARALLEL; // Output in cell-based simulations doesn't work in parallel ///\todo #2356
// Create a simple 2D VertexBasedCellPopulation
HoneycombVertexMeshGenerator generator(2, 2);
MutableVertexMesh<2,2>* p_mesh = generator.GetMesh();
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<p_mesh->GetNumElements(); i++)
{
ContactInhibitionCellCycleModel* p_cycle_model = new ContactInhibitionCellCycleModel();
p_cycle_model->SetDimension(2);
p_cycle_model->SetBirthTime(-10.0);
p_cycle_model->SetQuiescentVolumeFraction(0.99); // Very high as cells are not that compressed, as low in number and want to check that contact inhibition works.
p_cycle_model->SetEquilibriumVolume(1.0); // Target volume in NagaiHonda force
p_cycle_model->SetStemCellG1Duration(0.1);
p_cycle_model->SetTransitCellG1Duration(0.1);
CellPtr p_cell(new Cell(p_state, p_cycle_model));
p_cell->SetCellProliferativeType(p_transit_type);
cells.push_back(p_cell);
}
VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.AddPopulationWriter<CellMutationStatesCountWriter>();
cell_population.AddCellWriter<CellVolumesWriter>();
// Create a simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestVertexBasedSimulationWithVolumeTracked");
simulator.SetEndTime(simulator.GetDt()/2.0);
// Create a volume-tracking modifier and pass it to the simulation
MAKE_PTR(VolumeTrackingModifier<2>, p_modifier);
simulator.AddSimulationModifier(p_modifier);
// Create a force law and pass it to the simulation
MAKE_PTR(NagaiHondaForce<2>, p_nagai_honda_force);
simulator.AddForce(p_nagai_honda_force);
// A NagaiHondaForce has to be used together with an AbstractTargetAreaModifier #2488
MAKE_PTR(SimpleTargetAreaModifier<2>, p_growth_modifier);
simulator.AddSimulationModifier(p_growth_modifier);
// Run simulation
simulator.Solve();
// Test that the volumes of the cells are correct in CellData at the first timestep
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_population.GetVolumeOfCell(*cell_iter), (*cell_iter)->GetCellData()->GetItem("volume"), 1e-4);
}
simulator.SetEndTime(2.0);
// Run simulation
simulator.Solve();
// Test that the volumes of the cells are correct in CellData at the end time
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_population.GetVolumeOfCell(*cell_iter), (*cell_iter)->GetCellData()->GetItem("volume"), 1e-4);
}
// Check that the correct number of cells are labelled (i.e. experiencing contact inhibition)
TS_ASSERT_EQUALS(cell_population.GetCellPropertyRegistry()->Get<CellLabel>()->GetCellCount(),8u);
}
void TestMeshBasedSimulationWithGhostNodesAndContactInhibition()
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator does not work in parallel.
// Create a simple 2D MeshBasedCellPopulationWithGhostNodes
HoneycombMeshGenerator generator(3, 3, 3);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
std::vector<unsigned> location_indices = generator.GetCellLocationIndices();
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<location_indices.size(); i++)
{
ContactInhibitionCellCycleModel* p_cycle_model = new ContactInhibitionCellCycleModel();
p_cycle_model->SetDimension(2);
p_cycle_model->SetBirthTime(-10.0);
p_cycle_model->SetQuiescentVolumeFraction(0.9);
p_cycle_model->SetEquilibriumVolume(0.866); //sqrt(3.0)/2
p_cycle_model->SetStemCellG1Duration(0.1);
p_cycle_model->SetTransitCellG1Duration(0.1);
CellPtr p_cell(new Cell(p_state, p_cycle_model));
p_cell->SetCellProliferativeType(p_transit_type);
cells.push_back(p_cell);
}
MeshBasedCellPopulationWithGhostNodes<2> cell_population(*p_mesh, cells,location_indices);
cell_population.AddPopulationWriter<CellMutationStatesCountWriter>();
cell_population.AddCellWriter<CellVolumesWriter>();
// Create a simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestMeshBasedSimulationWithGhostNodesAndVolumeTracked");
simulator.SetEndTime(simulator.GetDt()/2.0);
// Create a volume-tracking modifier and pass it to the simulation
MAKE_PTR(VolumeTrackingModifier<2>, p_modifier);
simulator.AddSimulationModifier(p_modifier);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
p_force->SetCutOffLength(1.5);
simulator.AddForce(p_force);
// Run simulation
simulator.Solve();
// Test that the volumes of the cells are correct in CellData at the first timestep
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_population.GetVolumeOfCell(*cell_iter), (*cell_iter)->GetCellData()->GetItem("volume"), 1e-4);
}
simulator.SetEndTime(2.0);
// Run simulation
simulator.Solve();
// Test that the volumes of the cells are correct in CellData at the end time
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_population.GetVolumeOfCell(*cell_iter), (*cell_iter)->GetCellData()->GetItem("volume"), 1e-4);
}
// Check that the correct number of cells are labelled (i.e. experiencing contact inhibition)
TS_ASSERT_EQUALS(cell_population.GetCellPropertyRegistry()->Get<CellLabel>()->GetCellCount(), 12u);
}
void TestOffLatticeSimulationWithMotileCellPropertyAndWriters() throw(Exception)
{
/*
* We begin by creating a {{{NodeBasedCellPopulation}}}, just as in [wiki:UserTutorials/CreatingAndUsingANewCellProperty].
* We add the {{{MotileCellProperty}}} to a random selection of cells.
* We also add the {{{CellLabel}}} to these cells so that we can easily visualize the different cell types.
*/
EXIT_IF_PARALLEL;
HoneycombMeshGenerator generator(10, 10);
MutableMesh<2,2>* p_generating_mesh = generator.GetCircularMesh(5);
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
MAKE_PTR(MotileCellProperty, p_motile);
MAKE_PTR(CellLabel, p_label);
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPropertyCollection collection;
if (RandomNumberGenerator::Instance()->ranf() < 0.2)
{
collection.AddProperty(p_motile);
collection.AddProperty(p_label);
}
CellPtr p_cell(new Cell(p_state, p_model, false, collection));
p_cell->SetCellProliferativeType(p_diff_type);
double birth_time = - RandomNumberGenerator::Instance()->ranf() *
(p_model->GetStemCellG1Duration() + p_model->GetSG2MDuration());
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
NodeBasedCellPopulation<2> cell_population(mesh, cells);
/* In order to write cell motility data using our writer, we must add it to the list of writers
* used by the population. This is achieved using the {{{AddCellWriter()}}} method,
* which is templated. */
cell_population.AddCellWriter<CellMotilityWriter>();
/* We then pass in the cell population into an {{{OffLatticeSimulation}}},
* and set the output directory, output multiple, and end time. */
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithMotileCellPropertyAndWriters");
simulator.SetSamplingTimestepMultiple(12);
simulator.SetEndTime(10.0);
/* Next we create a force law and pass it to the {{{OffLatticeSimulation}}}, and call {{{Solve()}}} to run the simulation. */
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
simulator.Solve();
}
/*
* == Testing the SRN model ==
*
* We begin by testing that our new cell-cycle model is implemented correctly.
*/
void TestMySrnModel() throw(Exception)
{
/* Test that we can construct a {{{MySrnModel}}} object: */
TS_ASSERT_THROWS_NOTHING(MySrnModel srn_model);
/* Now we construct and initialise a cell with a {{{MySrnModel}}}.*/
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
StochasticDurationCellCycleModel* p_cell_cycle_model = new StochasticDurationCellCycleModel();
MySrnModel* p_srn_model = new MySrnModel;
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model, p_srn_model));
p_cell->SetCellProliferativeType(p_diff_type);
p_cell->InitialiseCellCycleModel();
p_cell->InitialiseSrnModel();
/* Now increment time and check the ODE in {{{MySrnModel}}} is solved correctly. */
double end_time = 10;
unsigned num_steps = 1000;
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(end_time, num_steps);
for (unsigned i=0; i<num_steps; i++)
{
SimulationTime::Instance()->IncrementTimeOneStep();
double current_time = SimulationTime::Instance()->GetTime();
/* Check that the ODE system is solved correctly */
p_srn_model->SimulateToCurrentTime();
// Test converged to steady state
TS_ASSERT_DELTA(p_cell->GetCellData()->GetItem("x"), cos(0.5*current_time), 1e-4);
}
/* Lastly, we briefly test that archiving of {{{MySrnModel}}} has
* been implemented correctly. Create an {{{OutputFileHandler}}} and use
* this to define a filename for the archive.
*/
OutputFileHandler handler("archive", false);
std::string archive_filename = handler.GetOutputDirectoryFullPath() + "my_srn_model.arch";
/* Create an output archive. */
{
/* Destroy the current instance of {{{SimulationTime}}} and create another instance.
* Set the start time, end time and number of time steps. */
SimulationTime::Destroy();
SimulationTime::Instance()->SetStartTime(0.0);
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(3.0, 4);
/* Create a cell with associated srn and cell-cycle model. */
StochasticDurationCellCycleModel* p_cell_cycle_model = new StochasticDurationCellCycleModel();
AbstractSrnModel* p_srn_model = new MySrnModel;
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model, p_srn_model));
p_cell->SetCellProliferativeType(p_diff_type);
p_cell->InitialiseCellCycleModel();
p_cell->InitialiseSrnModel();
/* Move forward two time steps. */
p_simulation_time->IncrementTimeOneStep();
p_simulation_time->IncrementTimeOneStep();
/* Solve the SRN. */
p_srn_model->SimulateToCurrentTime();
double current_time = 1.5;
TS_ASSERT_DELTA(p_cell->GetCellData()->GetItem("x"), cos(0.5*current_time), 1e-4);
/* Now archive the cell-cycle model through its cell. */
CellPtr const p_const_cell = p_cell;
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
output_arch << p_const_cell;
}
/* Now create an input archive. Begin by again destroying the current
* instance of {{{SimulationTime}}} and creating another instance. Set
* the start time, end time and number of time steps. note that this is
* overwritten when you load the archive.
*/
{
SimulationTime::Destroy();
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetStartTime(0.0);
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(1.0, 1);
TS_ASSERT_DELTA(p_simulation_time->GetTime(), 0.0, 1e-4);
/* Create a pointer to a cell. */
CellPtr p_cell;
/* Create an input archive and restore the cell from the archive. */
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
input_arch >> p_cell;
/* Test that the state of the ODES has been restored correctly. */
double current_time = 1.5;
TS_ASSERT_DELTA(p_simulation_time->GetTime(), current_time, 1e-4);
TS_ASSERT_DELTA(p_cell->GetCellData()->GetItem("x"), cos(0.5*current_time), 1e-4);
/* Move forward two more time steps. */
p_simulation_time->IncrementTimeOneStep();
p_simulation_time->IncrementTimeOneStep();
/* Solve the SRN. */
p_cell->GetSrnModel()->SimulateToCurrentTime();
/* Check it's moved on OK */
current_time = 3.0;
TS_ASSERT_DELTA(p_simulation_time->GetTime(), current_time, 1e-4);
TS_ASSERT_DELTA(p_cell->GetCellData()->GetItem("x"), cos(0.5*current_time), 1e-4);
}
}
/**
* Test a cell-based simulation with a non-Meineke spring system.
*
* This test consists of a standard crypt projection model simulation with a
* radial sloughing cell killer, a crypt projection cell-cycle model that
* depends on a radial Wnt gradient, and the crypt projection model spring
* system, and store the results for use in later archiving tests.
*/
void TestOffLatticeSimulationWithCryptProjectionSpringSystem() throw (Exception)
{
double a = 0.2;
double b = 2.0;
WntConcentration<2>::Instance()->SetCryptProjectionParameterA(a);
WntConcentration<2>::Instance()->SetCryptProjectionParameterB(b);
// Set up mesh
int num_cells_depth = 20;
int num_cells_width = 20;
unsigned thickness_of_ghost_layer = 3;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, thickness_of_ghost_layer);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
double crypt_length = (double)num_cells_depth *sqrt(3.0)/2.0;
std::vector<unsigned> location_indices = generator.GetCellLocationIndices();
ChasteCuboid<2> bounding_box=p_mesh->CalculateBoundingBox();
double width_of_mesh = (num_cells_width/(num_cells_width+2.0*thickness_of_ghost_layer))*(bounding_box.GetWidth(0));
double height_of_mesh = (num_cells_depth/(num_cells_depth+2.0*thickness_of_ghost_layer))*(bounding_box.GetWidth(1));
p_mesh->Translate(-width_of_mesh/2, -height_of_mesh/2);
// To start off with, set up all cells to have TransitCellProliferativeType
std::vector<CellPtr> cells;
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
for (unsigned i=0; i<location_indices.size(); i++)
{
SimpleWntCellCycleModel* p_model = new SimpleWntCellCycleModel();
p_model->SetDimension(2);
p_model->SetWntStemThreshold(0.95);
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_transit_type);
p_cell->InitialiseCellCycleModel();
double birth_time = - RandomNumberGenerator::Instance()->ranf()*
( p_model->GetTransitCellG1Duration()
+p_model->GetSG2MDuration());
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
// Make a cell population
MeshBasedCellPopulationWithGhostNodes<2> crypt(*p_mesh, cells, location_indices);
// Set up the Wnt gradient
WntConcentration<2>::Instance()->SetType(RADIAL);
WntConcentration<2>::Instance()->SetCellPopulation(crypt);
WntConcentration<2>::Instance()->SetCryptLength(crypt_length);
// Make a cell-based simulation
OffLatticeSimulation<2> crypt_projection_simulator(crypt, false, false);
// Create a force law and pass it to the simulation
MAKE_PTR(CryptProjectionForce, p_force);
crypt_projection_simulator.AddForce(p_force);
// Create a radial cell killer and pass it in to the cell-based simulation
c_vector<double,2> centre = zero_vector<double>(2);
double crypt_radius = pow(crypt_length/a, 1.0/b);
MAKE_PTR_ARGS(RadialSloughingCellKiller, p_killer, (&crypt, centre, crypt_radius));
crypt_projection_simulator.AddCellKiller(p_killer);
// Set up the simulation
crypt_projection_simulator.SetOutputDirectory("CryptProjectionSimulation");
crypt_projection_simulator.SetEndTime(0.25);
// Run the simulation
TS_ASSERT_THROWS_NOTHING(crypt_projection_simulator.Solve());
// These cells just divided and have been gradually moving apart.
// This is happening around (4, -1). The exact spring length is slightly
// compiler/architecture dependent.
// These results are from time 0.25.
std::vector<double> node_a_location = crypt_projection_simulator.GetNodeLocation(301);
std::vector<double> node_b_location = crypt_projection_simulator.GetNodeLocation(504);
c_vector<double, 2> distance_between;
distance_between(0) = node_a_location[0] - node_b_location[0];
distance_between(1) = node_a_location[1] - node_b_location[1];
// Note that this distance varies based on the quality of the original honeycomb mesh,
// the precision of the machine and the optimisation level
TS_ASSERT_DELTA(norm_2(distance_between), 0.6516, 4.0e-3);
// Test the Wnt concentration result
WntConcentration<2>* p_wnt = WntConcentration<2>::Instance();
TS_ASSERT_DELTA(p_wnt->GetWntLevel(crypt.GetCellUsingLocationIndex(257)), 0.7781, 1e-3);
TS_ASSERT_DELTA(p_wnt->GetWntLevel(crypt.GetCellUsingLocationIndex(503)), 0.9038, 1e-3);
// Tidy up
WntConcentration<2>::Destroy();
}
/*
* === Using the cell property in a cell-based simulation ===
*
* We conclude with a brief test demonstrating how {{{MotileCellProperty}}} can be used
* in a cell-based simulation.
*/
void TestOffLatticeSimulationWithMotileCellProperty() throw(Exception)
{
/* Note that HoneycombMeshGenerator, used in this test, is not
* yet implemented in parallel. */
/* We use the {{{HoneycombMeshGenerator}}} to create a honeycomb mesh covering a
* circular domain of given radius, and use this to generate a {{{NodesOnlyMesh}}}
* as follows. */
HoneycombMeshGenerator generator(10, 10);
MutableMesh<2,2>* p_generating_mesh = generator.GetCircularMesh(5);
NodesOnlyMesh<2> mesh;
/* We construct the mesh using the generating mesh and a cut-off 1.5 which defines the
* connectivity in the mesh.
*/
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
/* We now create a shared pointer to our new property, as follows. */
MAKE_PTR(MotileCellProperty, p_motile);
/*
* Also create a shared pointer to a cell label so we can visualize the
* different cell types. Note that this is also a {{{CellProperty}}}.
*/
MAKE_PTR(CellLabel, p_label);
/* Next, we create some cells. We don't use a Generator as we want to give some cells the new cell property, therefore
* we create the cells in a loop, as follows.*/
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
/* For each node we create a cell with our cell-cycle model and the wild-type cell mutation state.
* We then add the property {{{MotileCellProperty}}} to a random selection of the cells, as follows. */
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPropertyCollection collection;
if (RandomNumberGenerator::Instance()->ranf() < 0.2)
{
collection.AddProperty(p_motile);
collection.AddProperty(p_label);
}
CellPtr p_cell(new Cell(p_state, p_model, false, collection));
p_cell->SetCellProliferativeType(p_diff_type);
/* Now, we define a random birth time, chosen from [-T,0], where
* T = t,,1,, + t,,2,,, where t,,1,, is a parameter representing the G,,1,, duration
* of a stem cell, and t,,2,, is the basic S+G,,2,,+M phases duration.
*/
double birth_time = - RandomNumberGenerator::Instance()->ranf() *
(p_model->GetStemCellG1Duration()
+ p_model->GetSG2MDuration());
/* Finally, we set the birth time and push the cell back into the vector of cells. */
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
/* Now that we have defined the mesh and cells, we can define the cell population. The constructor
* takes in the mesh and the cells vector. */
NodeBasedCellPopulation<2> cell_population(mesh, cells);
/* In order to visualize labelled cells we need to use the following command.*/
cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>();
/* We then pass in the cell population into an {{{OffLatticeSimulation}}},
* and set the output directory, output multiple, and end time. */
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithMotileCellProperty");
simulator.SetSamplingTimestepMultiple(12);
simulator.SetEndTime(10.0);
/* We create a force law and pass it to the {{{OffLatticeSimulation}}}. */
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
/* Now create a {{{MotlieForce}}} and pass it to the {{{OffLatticeSimulation}}}. */
MAKE_PTR(MyMotiveForce, p_motive_force);
simulator.AddForce(p_motive_force);
/* To run the simulation, we call {{{Solve()}}}. */
simulator.Solve();
}
/**
* \todo WntBasedChemotaxis should be possible in other force laws. If/when
* this is implemented, this test should be moved to somewhere more appropriate.
*/
void TestCryptProjectionForceWithWntBasedChemotaxis() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesnt work in parallel.
double crypt_length = 22.0;
// Create a mesh
unsigned num_cells_width = 10;
unsigned num_cells_depth = 10;
unsigned thickness_of_ghost_layer = 0;
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0,1);
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, thickness_of_ghost_layer);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
// Centre the mesh at (0,0)
ChasteCuboid<2> bounding_box=p_mesh->CalculateBoundingBox();
double width_of_mesh = (num_cells_width/(num_cells_width+2.0*thickness_of_ghost_layer))*(bounding_box.GetWidth(0));
double height_of_mesh = (num_cells_depth/(num_cells_depth+2.0*thickness_of_ghost_layer))*(bounding_box.GetWidth(1));
p_mesh->Translate(-width_of_mesh/2, -height_of_mesh/2);
// Create some cells
std::vector<CellPtr> cells;
boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
boost::shared_ptr<AbstractCellProperty> p_stem_type(new StemCellProliferativeType);
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_stem_type);
p_cell->SetBirthTime(-10.0);
cells.push_back(p_cell);
}
// Create a cell population
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
std::pair<CellPtr,CellPtr> cell_pair_4_5 = cell_population.CreateCellPair(cell_population.GetCellUsingLocationIndex(4), cell_population.GetCellUsingLocationIndex(5));
cell_population.MarkSpring(cell_pair_4_5);
WntConcentration<2>::Instance()->SetType(RADIAL);
WntConcentration<2>::Instance()->SetCellPopulation(cell_population);
WntConcentration<2>::Instance()->SetCryptLength(crypt_length);
// Create a spring system with crypt surface z = 2*r
WntConcentration<2>::Instance()->SetCryptProjectionParameterA(2.0);
WntConcentration<2>::Instance()->SetCryptProjectionParameterB(1.0);
CryptProjectionForce crypt_projection_force;
crypt_projection_force.SetWntChemotaxis(false);
for (unsigned i=0; i<cell_population.GetNumNodes(); i++)
{
cell_population.GetNode(i)->ClearAppliedForce();
}
// Calculate node forces
crypt_projection_force.AddForceContribution(cell_population);
// Store the force of a particular node without Wnt-chemotaxis
c_vector<double,2> old_force;
old_force[0] = cell_population.GetNode(11)->rGetAppliedForce()[0];
old_force[1] = cell_population.GetNode(11)->rGetAppliedForce()[1];
// Now turn on Wnt-chemotaxis
crypt_projection_force.SetWntChemotaxis(true);
for (unsigned i=0; i<cell_population.GetNumNodes(); i++)
{
cell_population.GetNode(i)->ClearAppliedForce();
}
// Calculate node forces
crypt_projection_force.AddForceContribution(cell_population);
// Store the force of the same node, but now with Wnt-chemotaxis
c_vector<double,2> new_force = cell_population.GetNode(11)->rGetAppliedForce();
double wnt_chemotaxis_strength = crypt_projection_force.GetWntChemotaxisStrength();
CellPtr p_cell = cell_population.GetCellUsingLocationIndex(11u);
c_vector<double,2> wnt_component = wnt_chemotaxis_strength*WntConcentration<2>::Instance()->GetWntGradient(p_cell);
TS_ASSERT_DELTA(new_force[0], old_force[0]+wnt_component[0], 1e-4);
TS_ASSERT_DELTA(new_force[1], old_force[1]+wnt_component[1], 1e-4);
WntConcentration<2>::Destroy();
}
/**
* Test that post-#878, WntConcentration copes with a VertexBasedCellPopulation.
* \todo When vertex-based cell population code is added to cell_based folder, move this
* test to TestWntConcentration.hpp
*/
void TestWntConcentrationWithVertexBasedCellPopulation() throw(Exception)
{
// Make some nodes
std::vector<Node<2>*> nodes;
nodes.push_back(new Node<2>(0, true, 2.0, -1.0));
nodes.push_back(new Node<2>(1, true, 2.0, 1.0));
nodes.push_back(new Node<2>(2, true, -2.0, 1.0));
nodes.push_back(new Node<2>(3, true, -2.0, -1.0));
nodes.push_back(new Node<2>(4, true, 0.0, 2.0));
// Make a rectangular element out of nodes 0,1,2,3
std::vector<Node<2>*> nodes_elem_1;
nodes_elem_1.push_back(nodes[0]);
nodes_elem_1.push_back(nodes[1]);
nodes_elem_1.push_back(nodes[2]);
nodes_elem_1.push_back(nodes[3]);
// Make a triangular element out of nodes 1,4,2
std::vector<Node<2>*> nodes_elem_2;
nodes_elem_2.push_back(nodes[1]);
nodes_elem_2.push_back(nodes[4]);
nodes_elem_2.push_back(nodes[2]);
std::vector<VertexElement<2,2>*> vertex_elements;
vertex_elements.push_back(new VertexElement<2,2>(0, nodes_elem_1));
vertex_elements.push_back(new VertexElement<2,2>(1, nodes_elem_2));
// Make a vertex mesh
MutableVertexMesh<2,2> vertex_mesh(nodes, vertex_elements);
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
for (unsigned i=0; i<vertex_mesh.GetNumElements(); i++)
{
WntCellCycleModel* p_cell_cycle_model = new WntCellCycleModel;
p_cell_cycle_model->SetDimension(2);
CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
p_cell->SetCellProliferativeType(p_diff_type);
double birth_time = 0.0 - i;
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
// Create cell population
VertexBasedCellPopulation<2> cell_population(vertex_mesh, cells);
// Set the top of this cell_population, for the purposes of computing the WntConcentration
double crypt_length = 4.0;
// Set up an instance of the WntConcentration singleton object
WntConcentration<2>* p_wnt = WntConcentration<2>::Instance();
TS_ASSERT_EQUALS(p_wnt->IsWntSetUp(), false);
// Check that the singleton can be set up
p_wnt->SetType(LINEAR);
p_wnt->SetCellPopulation(cell_population);
p_wnt->SetCryptLength(crypt_length);
TS_ASSERT_EQUALS(p_wnt->IsWntSetUp(), true);
// Check that the singleton can be destroyed then recreated
WntConcentration<2>::Destroy();
WntConcentration<2>::Instance()->SetType(NONE);
WntConcentration<2>::Instance()->SetCellPopulation(cell_population);
WntConcentration<2>::Instance()->SetCryptLength(crypt_length);
TS_ASSERT_EQUALS(WntConcentration<2>::Instance()->IsWntSetUp(), false); // not fully set up now it is a NONE type
WntConcentration<2>::Destroy();
WntConcentration<2>::Instance()->SetType(LINEAR);
WntConcentration<2>::Instance()->SetCellPopulation(cell_population);
WntConcentration<2>::Instance()->SetCryptLength(crypt_length);
p_wnt = WntConcentration<2>::Instance();
TS_ASSERT_EQUALS(p_wnt->IsWntSetUp(), true); // set up again
double wnt_at_cell0 = p_wnt->GetWntLevel(cell_population.GetCellUsingLocationIndex(0));
double wnt_at_cell1 = p_wnt->GetWntLevel(cell_population.GetCellUsingLocationIndex(1));
// We have set the top of the cell population to be 4, so the WntConcentration should decrease linearly
// up the cell_population, from one at height 0 to zero at height 4.
// Cell 0 has centre of mass (0,0)
TS_ASSERT_DELTA(wnt_at_cell0, 1.0, 1e-4);
// Cell 1 has centre of mass (0, 4/3)
TS_ASSERT_DELTA(wnt_at_cell1, 2.0/3.0, 1e-4);
}
void TestCryptProjectionForceWithArchiving() throw (Exception)
{
EXIT_IF_PARALLEL; // Cell-based archiving doesn't work in parallel.
OutputFileHandler handler("archive", false); // don't erase contents of folder
std::string archive_filename = handler.GetOutputDirectoryFullPath() + "crypt_projection_spring_system.arch";
{
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_2_elements");
MutableMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0,1);
std::vector<CellPtr> cells;
boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
boost::shared_ptr<AbstractCellProperty> p_stem_type(new StemCellProliferativeType);
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPtr p_cell(new Cell(p_state, p_model));
p_cell->SetCellProliferativeType(p_stem_type);
p_cell->SetBirthTime(-50.0);
cells.push_back(p_cell);
}
MeshBasedCellPopulation<2> crypt(mesh, cells);
WntConcentration<2>::Instance()->SetCryptProjectionParameterA(1.0);
WntConcentration<2>::Instance()->SetCryptProjectionParameterB(2.0);
// Create force object
CryptProjectionForce crypt_projection_force;
TS_ASSERT_DELTA(crypt_projection_force.GetWntChemotaxisStrength(), 100.0, 1e-6);
crypt_projection_force.SetWntChemotaxisStrength(15.0);
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
// Serialize via pointer
CryptProjectionForce* const p_crypt_projection_force = &crypt_projection_force;
p_crypt_projection_force->SetCutOffLength(1.1);
output_arch << p_crypt_projection_force;
WntConcentration<2>::Destroy();
}
{
ArchiveLocationInfo::SetMeshPathname("mesh/test/data/", "square_2_elements");
// Create an input archive
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
CryptProjectionForce* p_crypt_projection_force;
// Restore from the archive
input_arch >> p_crypt_projection_force;
// Test the member data
TS_ASSERT_EQUALS(p_crypt_projection_force->mUseCutOffLength, true);
TS_ASSERT_DELTA(p_crypt_projection_force->GetA(), 1.0, 1e-12);
TS_ASSERT_DELTA(p_crypt_projection_force->GetB(), 2.0, 1e-12);
TS_ASSERT_DELTA(p_crypt_projection_force->GetWntChemotaxisStrength(), 15.0, 1e-6);
delete p_crypt_projection_force;
}
}
