/**
* Create a simulation of a NodeBasedCellPopulation with all Buske forces.
* Test that no exceptions are thrown.
*/
void TestAllBuskeForces() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesn't work in parallel
// Create a simple mesh
HoneycombMeshGenerator generator(5, 5, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
// Create a node-based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestAllBuskeForces");
simulator.SetEndTime(5.0);
// Create a force law and pass it to the simulation
MAKE_PTR(BuskeCompressionForce<2>, p_buske_compression_force);
MAKE_PTR(BuskeElasticForce<2>, p_buske_elastic_force);
MAKE_PTR(BuskeAdhesiveForce<2>, p_buske_adhesive_force);
p_buske_compression_force->SetCompressionEnergyParameter(0.01);
simulator.AddForce(p_buske_compression_force);
simulator.AddForce(p_buske_elastic_force);
simulator.AddForce(p_buske_adhesive_force);
simulator.Solve();
}
/*
* === Using the modifier in a cell-based simulation ===
*
* We conclude with a brief test demonstrating how {{{CellHeightTrackingModifier}}} can be used
* in a cell-based simulation.
*/
void TestOffLatticeSimulationWithCellHeightTrackingModifier()
{
/*
* In this case, we choose to create a small {{{NodeBasedCellPopulation}}} comprising 25 cells.
* We choose a cut-off for mechanical interactions between cells of 1.5 units and add a
* simple {{{ReplusionForce}}} to the simulation. We use a {{{UniformCellCycleModel}}}
* to implement some random proliferation in the simulation.
*/
HoneycombMeshGenerator generator(2, 2, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<UniformCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
NodeBasedCellPopulation<2> cell_population(mesh, cells);
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithCellHeightTrackingModifier");
simulator.SetSamplingTimestepMultiple(12);
simulator.SetEndTime(20.0);
MAKE_PTR(RepulsionForce<2>, p_force);
simulator.AddForce(p_force);
/*
* Finally, we add a {{{CellHeightTrackingModifier}}} to the simulation.
*/
MAKE_PTR(CellHeightTrackingModifier, p_modifier);
simulator.AddSimulationModifier(p_modifier);
/* To run the simulation, we call {{{Solve()}}}. */
simulator.Solve();
}
void TestSave() throw (Exception)
{
EXIT_IF_PARALLEL;
PottsMeshGenerator<2> generator(10, 0, 0, 10, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, 10, p_diff_type);
std::vector<unsigned> location_indices;
for (unsigned index=0; index<10; index++)
{
location_indices.push_back(index);
}
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices, 4);
// Set up cell-based simulation
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOnLatticeSimulationWithCaBasedCellPopulationSaveAndLoad");
simulator.SetDt(1);
simulator.SetEndTime(10);
// Add update rule
MAKE_PTR(DiffusionCaUpdateRule<2>, p_diffusion_update_rule);
p_diffusion_update_rule->SetDiffusionParameter(0.1);
simulator.AddCaUpdateRule(p_diffusion_update_rule);
// Run simulation
simulator.Solve();
// Save the results
CellBasedSimulationArchiver<2, OnLatticeSimulation<2> >::Save(&simulator);
}
/**
* Create a simulation of a NodeBasedCellPopulation with a BuskeInteractionForce system.
* Test that no exceptions are thrown, and write the results to file.
*/
void TestSimpleMonolayerWithBuskeAdhesiveForce() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesn't work in parallel
// Create a simple mesh
HoneycombMeshGenerator generator(5, 5, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes());
// Create a node-based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithBuskeAdhesiveForce");
simulator.SetEndTime(5.0);
// Create a force law and pass it to the simulation
MAKE_PTR(BuskeAdhesiveForce<2>, p_buske_adhesive_force);
p_buske_adhesive_force->SetAdhesionEnergyParameter(0.002);
simulator.AddForce(p_buske_adhesive_force);
simulator.Solve();
// Check that nothing's gone badly wrong by testing that nodes aren't too close together
double min_distance_between_cells = 1.0;
for (unsigned i=0; i<simulator.rGetCellPopulation().GetNumNodes(); i++)
{
for (unsigned j=i+1; j<simulator.rGetCellPopulation().GetNumNodes(); j++)
{
double distance = norm_2(simulator.rGetCellPopulation().GetNode(i)->rGetLocation()-simulator.rGetCellPopulation().GetNode(j)->rGetLocation());
if (distance < min_distance_between_cells)
{
min_distance_between_cells = distance;
}
}
}
TS_ASSERT_LESS_THAN_EQUALS(1e-3, min_distance_between_cells);
}
void TestSave() throw (Exception)
{
EXIT_IF_PARALLEL; // Potts simulations don't work in parallel because they depend on NodesOnlyMesh for writing.
// Create a simple 2D PottsMesh
PottsMeshGenerator<2> generator(10, 1, 4, 10, 1, 4);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(StemCellProliferativeType, p_stem_type);
CellsGenerator<UniformlyDistributedGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, p_mesh->GetNumElements(), p_stem_type);
// Create cell population
PottsBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set up cell-based simulation
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOnLatticeSimulationWithPottsBasedCellPopulationSaveAndLoad");
simulator.SetDt(0.1);
simulator.SetEndTime(10);
simulator.SetSamplingTimestepMultiple(10);
// Create update rules and pass to the simulation
MAKE_PTR(VolumeConstraintPottsUpdateRule<2>, p_volume_constraint_update_rule);
simulator.AddPottsUpdateRule(p_volume_constraint_update_rule);
MAKE_PTR(AdhesionPottsUpdateRule<2>, p_adhesion_update_rule);
simulator.AddPottsUpdateRule(p_adhesion_update_rule);
// Run simulation
simulator.Solve();
// Save the results
CellBasedSimulationArchiver<2, OnLatticeSimulation<2> >::Save(&simulator);
}
/*
* Now test the switching rules.
*/
void TestRandomCaSwitchingUpdateRuleIn2d()
{
// Set the timestep and size of domain to let us calculate the probabilities of movement
double delta_t = 0.1;
double delta_x = 1;
double switching_parameter = 0.1;
// Create an update law system
RandomCaSwitchingUpdateRule<2> random_switching_update_rule;
// Test get/set methods
TS_ASSERT_DELTA(random_switching_update_rule.GetSwitchingParameter(), 0.5, 1e-12);
random_switching_update_rule.SetSwitchingParameter(1.0);
TS_ASSERT_DELTA(random_switching_update_rule.GetSwitchingParameter(), 1.0, 1e-12);
random_switching_update_rule.SetSwitchingParameter(switching_parameter);
// Test EvaluateProbability()
// Create a simple 2D PottsMesh
PottsMeshGenerator<2> generator(3, 0, 0, 3, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedG1GenerationalCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, 6u, p_diff_type);
// Specify where cells lie here we have cells on the bottom two rows
std::vector<unsigned> location_indices;
for (unsigned i=0; i<6; i++)
{
location_indices.push_back(i);
}
// Create cell population
CaBasedCellPopulation<2u> cell_population(*p_mesh, cells, location_indices);
TS_ASSERT_DELTA(random_switching_update_rule.EvaluateSwitchingProbability(0,1,cell_population, delta_t, delta_x),switching_parameter*delta_t,1e-6);
TS_ASSERT_DELTA(random_switching_update_rule.EvaluateSwitchingProbability(0,6,cell_population, delta_t, delta_x),switching_parameter*delta_t,1e-6);
TS_ASSERT_DELTA(random_switching_update_rule.EvaluateSwitchingProbability(0,5,cell_population, delta_t, delta_x),switching_parameter*delta_t,1e-6);
// Note this is independent of node index and population so even returns for nodes not in the mesh
TS_ASSERT_DELTA(random_switching_update_rule.EvaluateSwitchingProbability(UNSIGNED_UNSET,UNSIGNED_UNSET,cell_population, delta_t, delta_x),switching_parameter*delta_t,1e-6);
}
/*
* RemoveFirst -- remove the first entry in the free list of ProcGlobal.
*
* Use compare_and_swap to avoid using lock and guarantee atomic operation.
*/
static PGPROC *
RemoveFirst()
{
volatile PROC_HDR *procglobal = ProcGlobal;
SHMEM_OFFSET myOffset;
PGPROC *freeProc = NULL;
/*
* Decrement numFreeProcs before removing the first entry from the
* free list.
*/
gp_atomic_add_32(&procglobal->numFreeProcs, -1);
int32 casResult = false;
while(!casResult)
{
myOffset = procglobal->freeProcs;
if (myOffset == INVALID_OFFSET)
{
break;
}
freeProc = (PGPROC *) MAKE_PTR(myOffset);
casResult = compare_and_swap_ulong(&((PROC_HDR *)procglobal)->freeProcs,
myOffset,
freeProc->links.next);
if (gp_debug_pgproc && !casResult)
{
elog(LOG, "need to retry allocating a PGPROC entry: pid=%d (oldHeadOffset=%ld, newHeadOffset=%ld)",
MyProcPid, myOffset, procglobal->freeProcs);
}
}
if (freeProc == NULL)
{
/*
* Increment numFreeProcs since we didn't remove any entry from
* the free list.
*/
gp_atomic_add_32(&procglobal->numFreeProcs, 1);
}
return freeProc;
}
StatechartCellCycleModelSerializable::StatechartCellCycleModelSerializable(bool LoadingFromArchive): AbstractCellCycleModel(){
mLoadingFromArchive=LoadingFromArchive;
TempVariableStorage=std::vector<double>();
TempStateStorage=0;
//Set some sensible C.Elegans germ cell defaults
mSDuration=8.33;
mG2Duration=6.66;
mMDuration=1.66;
mG1Duration=3.33;
mDimension=3;
mCurrentCellCyclePhase=G_ONE_PHASE;
MAKE_PTR(CellStatechart,newStatechart);
pStatechart=newStatechart;
};
void TestCalculateWriteResultsToFile()
{
std::string output_directory = "TestDiscreteSystemForceCalculator";
// Set up a cell population
HoneycombMeshGenerator mesh_generator(7, 5, 0, 2.0);
MutableMesh<2,2>* p_mesh = mesh_generator.GetMesh();
CellsGenerator<FixedG1GenerationalCellCycleModel, 2> cells_generator;
std::vector<CellPtr> cells;
cells_generator.GenerateBasic(cells, p_mesh->GetNumNodes());
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Create the force law and pass in to a std::list
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
std::vector<boost::shared_ptr<AbstractTwoBodyInteractionForce<2> > > force_collection;
force_collection.push_back(p_force);
// Create a force calculator
DiscreteSystemForceCalculator calculator(cell_population, force_collection);
// Test WriteResultsToFile
calculator.WriteResultsToFile(output_directory);
// Compare output with saved files of what they should look like
OutputFileHandler handler(output_directory, false);
std::string results_file = handler.GetOutputDirectoryFullPath() + "results_from_time_0/results.vizstress";
NumericFileComparison node_velocities(results_file, "cell_based/test/data/TestDiscreteSystemForceCalculator/results.vizstress");
TS_ASSERT(node_velocities.CompareFiles(1e-4));
// Run a simulation to generate some results.viz<other things> files
// so the visualizer can display the results.vizstress file.
// (These lines are not actually necessary for generating results.vizstress)
OffLatticeSimulation<2> simulator(cell_population);
simulator.AddForce(p_force);
simulator.SetEndTime(0.05);
simulator.SetOutputDirectory(output_directory+"_rerun");
simulator.Solve();
}
void
InitBufferPool () {
int i;
PrivateRefCount = (long *) malloc(NBuffers * sizeof(long));
// Altered to use regular memory
BufferDescriptors = (BufferDesc *) malloc (NBuffers * sizeof(BufferDesc));
BufferBlocks = (char *) malloc (NBuffers * BLCKSZ);
ShmemBase = BufferBlocks;
// ShmemBase = (unsigned long) BufferBlocks;
if (false)
{
}
else
{
BufferDesc *buf;
buf = BufferDescriptors;
for (i = 0; i < NBuffers; buf++, i++)
{
CLEAR_BUFFERTAG(buf->tag);
buf->flags = 0;
buf->usage_count = 0;
buf->refcount = 0;
buf->wait_backend_pid = 0;
buf->freeNext = i + 1;
buf->buf_id = i;
*((char *) MAKE_PTR(i * BLCKSZ)) = '#';
buf->io_in_progress_lock = LWLockAssign();
buf->content_lock = LWLockAssign();
}
/* close the circular queue */
BufferDescriptors[NBuffers - 1].freeNext = -1;
StrategyInitialize(true);
}
}
// Testing Save
void TestSave() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenereator does not work in parallel
// Create a simple mesh
int num_cells_depth = 5;
int num_cells_width = 5;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes());
// Create a node based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithNodeBasedCellPopulationSaveAndLoad");
simulator.SetEndTime(0.1);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Create some boundary conditions and pass them to the simulation
c_vector<double,2> normal = zero_vector<double>(2);
normal(1) =-1.0;
MAKE_PTR_ARGS(PlaneBoundaryCondition<2>, p_bc, (&node_based_cell_population, zero_vector<double>(2), normal)); // y>0
simulator.AddCellPopulationBoundaryCondition(p_bc);
// Solve
simulator.Solve();
// Save the results
CellBasedSimulationArchiver<2, OffLatticeSimulation<2> >::Save(&simulator);
}
/*
* Initialize access to shared buffer pool
*
* This is called during backend startup (whether standalone or under the
* postmaster). It sets up for this backend's access to the already-existing
* buffer pool.
*
* NB: this is called before InitProcess(), so we do not have a PGPROC and
* cannot do LWLockAcquire; hence we can't actually access the bufmgr's
* shared memory yet. We are only initializing local data here.
*/
void
InitBufferPoolAccess(void)
{
int i;
/*
* Allocate and zero local arrays of per-buffer info.
*/
BufferBlockPointers = (Block *) calloc(NBuffers, sizeof(Block));
PrivateRefCount = (long *) calloc(NBuffers, sizeof(long));
BufferLocks = (bits8 *) calloc(NBuffers, sizeof(bits8));
/*
* Convert shmem offsets into addresses as seen by this process. This
* is just to speed up the BufferGetBlock() macro.
*/
for (i = 0; i < NBuffers; i++)
BufferBlockPointers[i] = (Block) MAKE_PTR(BufferDescriptors[i].data);
}
void TestMoreOnLatticeSimulationExceptions()
{
// Create a simple 2D PottsMesh
PottsMeshGenerator<2> generator(6, 2, 2, 6, 2, 2);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, p_mesh->GetNumElements(), p_diff_type);
// Create cell population
PottsBasedCellPopulation<2> potts_based_cell_population(*p_mesh, cells);
// Try to set up off lattice simulation
TS_ASSERT_THROWS_THIS(OffLatticeSimulation<2> simulator(potts_based_cell_population),
"OffLatticeSimulations require a subclass of AbstractOffLatticeCellPopulation.");
}
/*
* GetOldestXmin -- returns oldest transaction that was running
* when any current transaction was started.
*
* If allDbs is TRUE then all backends are considered; if allDbs is FALSE
* then only backends running in my own database are considered.
*
* This is used by VACUUM to decide which deleted tuples must be preserved
* in a table. allDbs = TRUE is needed for shared relations, but allDbs =
* FALSE is sufficient for non-shared relations, since only backends in my
* own database could ever see the tuples in them.
*
* Note: we include the currently running xids in the set of considered xids.
* This ensures that if a just-started xact has not yet set its snapshot,
* when it does set the snapshot it cannot set xmin less than what we compute.
*/
TransactionId
GetOldestXmin(bool allDbs)
{
SISeg *segP = shmInvalBuffer;
ProcState *stateP = segP->procState;
TransactionId result;
int index;
result = GetCurrentTransactionId();
LWLockAcquire(SInvalLock, LW_SHARED);
for (index = 0; index < segP->lastBackend; index++)
{
SHMEM_OFFSET pOffset = stateP[index].procStruct;
if (pOffset != INVALID_OFFSET)
{
PGPROC *proc = (PGPROC *) MAKE_PTR(pOffset);
if (allDbs || proc->databaseId == MyDatabaseId)
{
/* Fetch xid just once - see GetNewTransactionId */
TransactionId xid = proc->xid;
if (TransactionIdIsNormal(xid))
{
if (TransactionIdPrecedes(xid, result))
result = xid;
xid = proc->xmin;
if (TransactionIdIsNormal(xid))
if (TransactionIdPrecedes(xid, result))
result = xid;
}
}
}
}
LWLockRelease(SInvalLock);
return result;
}
/*
* ProcLockWakeup -- routine for waking up processes when a lock is
* released.
*/
int
ProcLockWakeup(PROC_QUEUE *queue, char *ltable, char *lock)
{
PROC *proc;
int count;
if (! queue->size)
return(STATUS_NOT_FOUND);
proc = (PROC *) MAKE_PTR(queue->links.prev);
count = 0;
while ((LockResolveConflicts ((LOCKTAB *) ltable,
(LOCK *) lock,
proc->token,
proc->xid) == STATUS_OK))
{
/* there was a waiting process, grant it the lock before waking it
* up. This will prevent another process from seizing the lock
* between the time we release the lock master (spinlock) and
* the time that the awoken process begins executing again.
*/
GrantLock((LOCK *) lock, proc->token);
queue->size--;
/*
* ProcWakeup removes proc from the lock waiting process queue and
* returns the next proc in chain. If a writer just dropped
* its lock and there are several waiting readers, wake them all up.
*/
proc = ProcWakeup(proc, NO_ERROR);
count++;
if (!proc || queue->size == 0)
break;
}
if (count)
return(STATUS_OK);
else
/* Something is still blocking us. May have deadlocked. */
return(STATUS_NOT_FOUND);
}
/*
* BackendIdGetProc - given a BackendId, find its PGPROC structure
*
* This is a trivial lookup in the ProcState array. We assume that the caller
* knows that the backend isn't going to go away, so we do not bother with
* locking.
*/
struct PGPROC *
BackendIdGetProc(BackendId procId)
{
SISeg *segP = shmInvalBuffer;
if (procId > 0 && procId <= segP->lastBackend)
{
ProcState *stateP = &segP->procState[procId - 1];
SHMEM_OFFSET pOffset = stateP->procStruct;
if (pOffset != INVALID_OFFSET)
{
PGPROC *proc = (PGPROC *) MAKE_PTR(pOffset);
return proc;
}
}
return NULL;
}
/*
* Initialize access to shared buffer pool
*
* This is called during backend startup (whether standalone or under the
* postmaster). It sets up for this backend's access to the already-existing
* buffer pool.
*
* NB: this is called before InitProcess(), so we do not have a PGPROC and
* cannot do LWLockAcquire; hence we can't actually access the bufmgr's
* shared memory yet. We are only initializing local data here.
*/
void
InitBufferPoolAccess(void)
{
int i;
/*
* Allocate and zero local arrays of per-buffer info.
*/
BufferBlockPointers = (Block *) calloc(NBuffers,
sizeof(*BufferBlockPointers));
PrivateRefCount = (int32 *) calloc(NBuffers,
sizeof(*PrivateRefCount));
/*
* Convert shmem offsets into addresses as seen by this process. This
* is just to speed up the BufferGetBlock() macro. It is OK to do this
* without any lock since the data pointers never change.
*/
for (i = 0; i < NBuffers; i++)
BufferBlockPointers[i] = (Block) MAKE_PTR(BufferDescriptors[i].data);
}
/*
* SHMQueueInsertBefore -- put elem in queue before the given queue
* element. Inserting "before" the queue head puts the elem
* at the tail of the queue.
*/
void
SHMQueueInsertBefore(SHM_QUEUE *queue, SHM_QUEUE *elem)
{
SHM_QUEUE *prevPtr = (SHM_QUEUE *) MAKE_PTR((queue)->prev);
SHMEM_OFFSET elemOffset = MAKE_OFFSET(elem);
Assert(SHM_PTR_VALID(queue));
Assert(SHM_PTR_VALID(elem));
#ifdef SHMQUEUE_DEBUG
dumpQ(queue, "in SHMQueueInsertBefore: begin");
#endif
(elem)->next = prevPtr->next;
(elem)->prev = queue->prev;
(queue)->prev = elemOffset;
prevPtr->next = elemOffset;
#ifdef SHMQUEUE_DEBUG
dumpQ(queue, "in SHMQueueInsertBefore: end");
#endif
}
void TestSimpleTargetAreaModifierOutputParameters()
{
EXIT_IF_PARALLEL;
std::string output_directory = "TestSimpleTargetAreaModifierOutputParameters";
OutputFileHandler output_file_handler(output_directory, false);
MAKE_PTR(SimpleTargetAreaModifier<2>, p_modifier);
TS_ASSERT_EQUALS(p_modifier->GetIdentifier(), "SimpleTargetAreaModifier-2");
out_stream modifier_parameter_file = output_file_handler.OpenOutputFile("SimpleTargetAreaModifier.parameters");
p_modifier->OutputSimulationModifierParameters(modifier_parameter_file);
modifier_parameter_file->close();
{
// Compare the generated file in test output with a reference copy in the source code
FileFinder generated = output_file_handler.FindFile("SimpleTargetAreaModifier.parameters");
FileFinder reference("cell_based/test/data/TestSimulationModifierOutputParameters/SimpleTargetAreaModifier.parameters",
RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated, reference);
TS_ASSERT(comparer.CompareFiles());
}
}
/*
* ProcWakeup -- wake up a process by releasing its private semaphore.
*
* remove the process from the wait queue and set its links invalid.
* RETURN: the next process in the wait queue.
*/
PROC *
ProcWakeup(PROC *proc, int errType)
{
PROC *retProc;
/* assume that spinlock has been acquired */
if (proc->links.prev == INVALID_OFFSET ||
proc->links.next == INVALID_OFFSET)
return((PROC *) NULL);
retProc = (PROC *) MAKE_PTR(proc->links.prev);
/* you have to update waitLock->waitProcs.size yourself */
SHMQueueDelete(&(proc->links));
SHMQueueElemInit(&(proc->links));
proc->errType = errType;
IpcSemaphoreUnlock(proc->sem.semId, proc->sem.semNum, IpcExclusiveLock);
return retProc;
}
/**
* Create a simulation of a NodeBasedCellPopulation to test movement threshold.
*/
void TestMovementThreshold() throw (Exception)
{
EXIT_IF_PARALLEL; // This test doesn't work in parallel because only one process will throw.
// Creates nodes and mesh
std::vector<Node<2>*> nodes;
nodes.push_back(new Node<2>(0, false, 0.0, 0.0));
nodes.push_back(new Node<2>(0, false, 0.0, 0.3));
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(nodes, 1.5);
// Create cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes());
// Create a node based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
node_based_cell_population.SetAbsoluteMovementThreshold(1e-6);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetEndTime(0.1);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithNodeBasedCellPopulationThreshold");
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Solve
TS_ASSERT_THROWS_CONTAINS(simulator.Solve(),
"which is more than the AbsoluteMovementThreshold:");
// Avoid memory leak
delete nodes[0];
delete nodes[1];
}
AbstractCellCycleModel* StatechartCellCycleModelSerializable::CreateCellCycleModel(){
//Create a new cell cycle model
StatechartCellCycleModelSerializable* newStatechartCellCycleModelSerializable = new StatechartCellCycleModelSerializable();
//Ensure values are inhereted from parent as appropriate
newStatechartCellCycleModelSerializable->SetBirthTime(mBirthTime);
newStatechartCellCycleModelSerializable->SetMinimumGapDuration(mMinimumGapDuration);
newStatechartCellCycleModelSerializable->SetStemCellG1Duration(mStemCellG1Duration);
newStatechartCellCycleModelSerializable->SetTransitCellG1Duration(mTransitCellG1Duration);
newStatechartCellCycleModelSerializable->SetSDuration(mSDuration);
newStatechartCellCycleModelSerializable->SetG2Duration(mG2Duration);
newStatechartCellCycleModelSerializable->SetMDuration(mMDuration);
newStatechartCellCycleModelSerializable->SetDimension(mDimension);
newStatechartCellCycleModelSerializable->mG1Duration=mG1Duration;
newStatechartCellCycleModelSerializable->mLoadingFromArchive=mLoadingFromArchive;
//Create a new statechart.
MAKE_PTR(CellStatechart, newStatechart);
//Set its cell pointer to the parent cell to avoid it being null when constructors are called.
newStatechart->SetCell(mpCell);
//Copy the state of the parent. Give result to the daughter cell cycle model.
newStatechartCellCycleModelSerializable->pStatechart=pStatechart->Copy(newStatechart);
//Return the new cell cycle model. The cell pointer will be made to point to the daughter when SetCell is called.
return newStatechartCellCycleModelSerializable;
};
void TestSetupSolveException() throw (Exception)
{
// First set up SimulationTime (this is usually handled by a simulation object)
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0, 1);
// Create a SimpleTargetAreaModifier
MAKE_PTR(SimpleTargetAreaModifier<2>, p_modifier);
// Create a cell population whose type should not be used with a SimpleTargetAreaModifier
HoneycombMeshGenerator generator(4, 4, 0);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, p_mesh->GetNumNodes());
MeshBasedCellPopulation<2> population(*p_mesh, cells);
// Test that the correct exception is thrown if we try to call UpdateTargetAreas() on the population
TS_ASSERT_THROWS_THIS(p_modifier->SetupSolve(population, "unused_argument"),
"AbstractTargetAreaModifiers are to be used with a VertexBasedCellPopulation only");
CellBasedEventHandler::Reset(); // Otherwise logging has been started but not stopped due to exception above.
}
static uim_lisp
uim_xml_parser_create(uim_lisp encoding_)
{
uim_xml_ctx *ctx;
const XML_Char *encoding = REFER_C_STR(encoding_);
XML_Parser parser;
parser = XML_ParserCreate(encoding);
if (parser) {
XML_SetElementHandler(parser, xml_start_element_handler, xml_end_element_handler);
XML_SetCharacterDataHandler(parser, xml_characterdata_handler);
}
ctx = uim_calloc(1, sizeof(uim_xml_ctx *));
ctx->parser = parser;
ctx->data = uim_malloc(sizeof(uim_xml_userdata *));
ctx->data->start_ = NULL;
ctx->data->end_ = NULL;
ctx->data->characterdata_ = NULL;
return MAKE_PTR(ctx);
}
/*
* ProcRemove -
* used by the postmaster to clean up the global tables. This also frees
* up the semaphore used for the lmgr of the process. (We have to do
* this is the postmaster instead of doing a IpcSemaphoreKill on exiting
* the process because the semaphore set is shared among backends and
* we don't want to remove other's semaphores on exit.)
*/
bool
ProcRemove(int pid)
{
SHMEM_OFFSET location;
PROC *proc;
location = INVALID_OFFSET;
location = ShmemPIDDestroy(pid);
if (location == INVALID_OFFSET)
return(FALSE);
proc = (PROC *) MAKE_PTR(location);
SpinAcquire(ProcStructLock);
ProcFreeSem(proc->sem.semKey, proc->sem.semNum);
proc->links.next = ProcGlobal->freeProcs;
ProcGlobal->freeProcs = MAKE_OFFSET(proc);
SpinRelease(ProcStructLock);
return(TRUE);
}
/**
* 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);
}
/*
* === 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();
}
void TestAddCellwithExclusionBasedDivisionRule()
{
/**
* In this test we basically test that the AbstractCaBasedDivisionRule is implemented and joined with the population
* correctly. We make a new ExclusionCaBasedDivisionRule, divide a cell with it and check that the new cells
* are in the correct locations.
*/
// Make a simple Potts mesh
PottsMeshGenerator<2> generator(3, 0, 0, 3, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create 6 cells in the bottom 2 rows
std::vector<unsigned> location_indices;
for (unsigned index=0; index<6; index++)
{
location_indices.push_back(index);
}
std::vector<CellPtr> cells;
CellsGenerator<FixedG1GenerationalCellCycleModel, 1> cells_generator;
cells_generator.GenerateBasic(cells, location_indices.size());
// Create cell population
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
CellPtr p_cell_0 = cell_population.GetCellUsingLocationIndex(0);
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(StemCellProliferativeType, p_stem_type);
FixedG1GenerationalCellCycleModel* p_model = new FixedG1GenerationalCellCycleModel();
CellPtr p_temp_cell(new Cell(p_state, p_model));
p_temp_cell->SetCellProliferativeType(p_stem_type);
p_temp_cell->SetBirthTime(-1);
// Set the division rule for our population to be the exclusion division rule (note that this is the default
boost::shared_ptr<AbstractCaBasedDivisionRule<2> > p_division_rule_to_set(new ExclusionCaBasedDivisionRule<2>());
cell_population.SetCaBasedDivisionRule(p_division_rule_to_set);
// Get the division rule back from the population and try to add new cell by dividing cell at site 0;
boost::shared_ptr<AbstractCaBasedDivisionRule<2> > p_division_rule = cell_population.GetCaBasedDivisionRule();
CellPtr p_parent_cell = cell_population.GetCellUsingLocationIndex(0);
TS_ASSERT(!(p_division_rule->IsRoomToDivide(p_parent_cell,cell_population)));
// Test adding the new cell in the population (note this calls CalculateDaughterNodeIndex)
TS_ASSERT_THROWS_THIS(cell_population.AddCell(p_cell_0, p_parent_cell),
"Trying to divide when there is no room to divide, check your division rule");
// Test adding it in a free space
p_parent_cell = cell_population.GetCellUsingLocationIndex(4);
TS_ASSERT(p_division_rule->IsRoomToDivide(p_parent_cell,cell_population));
TS_ASSERT_EQUALS(p_division_rule->CalculateDaughterNodeIndex(p_cell_0,p_parent_cell,cell_population), 7u);
// Test adding the new cell in the population (note this calls CalculateDaughterNodeIndex)
cell_population.AddCell(p_cell_0, p_parent_cell);
// Now check the cells are in the correct place
TS_ASSERT_EQUALS(cell_population.GetNumRealCells(), 7u);
}
static uim_lisp
c_ffi_call(uim_lisp result_, uim_lisp fun_, uim_lisp argv_)
{
ffi_cif cif;
ffi_type **arg_types;
void **arg_values;
ffi_status status;
ffi_type *result_type = NULL;
void *result;
int args;
int i;
void *p;
uim_lisp ret_;
object_type return_object_type;
int input_void = 0;
args = uim_scm_length(argv_);
arg_types = uim_malloc(args * sizeof(void *));
arg_values = uim_malloc(args * sizeof(ffi_type *));
return_object_type = select_object_type(result_);
switch (return_object_type) {
case RET_UNKNOWN:
break;
case RET_VOID:
result_type = &ffi_type_void;
break;
case RET_UCHAR:
result_type = &ffi_type_uchar;
break;
case RET_SCHAR:
result_type = &ffi_type_schar;
break;
case RET_USHORT:
result_type = &ffi_type_ushort;
break;
case RET_SSHORT:
result_type = &ffi_type_sshort;
break;
case RET_ULONG:
result_type = &ffi_type_ulong;
break;
case RET_SLONG:
result_type = &ffi_type_slong;
break;
case RET_UINT:
result_type = &ffi_type_uint;
break;
case RET_SINT:
result_type = &ffi_type_sint;
break;
case RET_FLOAT:
result_type = &ffi_type_float;
break;
case RET_DOUBLE:
result_type = &ffi_type_double;
break;
case RET_STR:
result_type = &ffi_type_pointer;
break;
case RET_PTR:
result_type = &ffi_type_pointer;
break;
case RET_SCM:
result_type = &ffi_type_pointer;
break;
}
result = uim_malloc(1024); /* huge? */
for (i = 0; i < args; i++) {
uim_lisp arg_ = CAR(argv_);
switch (select_object_type(CAR(arg_))) {
case RET_UNKNOWN:
break;
case RET_VOID:
input_void = 1;
break;
case RET_UCHAR:
p = uim_malloc(sizeof(unsigned char));
*((unsigned char *)p) = C_CHAR(CDR(arg_));
arg_types[i] = &ffi_type_uchar;
arg_values[i] = p;
break;
case RET_SCHAR:
p = uim_malloc(sizeof(signed char));
*((signed char *)p) = C_CHAR(CDR(arg_));
arg_types[i] = &ffi_type_schar;
arg_values[i] = p;
break;
case RET_USHORT:
p = uim_malloc(sizeof(unsigned short));
*((unsigned short *)p) = C_INT(CDR(arg_));
arg_types[i] = &ffi_type_ushort;
arg_values[i] = p;
break;
case RET_SSHORT:
p = uim_malloc(sizeof(unsigned short));
*((signed short *)p) = C_INT(CDR(arg_));
arg_types[i] = &ffi_type_sshort;
arg_values[i] = p;
break;
case RET_UINT:
p = uim_malloc(sizeof(unsigned int));
*((unsigned int *)p) = C_INT(CDR(arg_));
arg_types[i] = &ffi_type_uint;
arg_values[i] = p;
break;
case RET_SINT:
p = uim_malloc(sizeof(signed int));
*((signed int *)p) = C_INT(CDR(arg_));
arg_types[i] = &ffi_type_sint;
arg_values[i] = p;
break;
case RET_ULONG:
p = uim_malloc(sizeof(unsigned long));
*((unsigned long *)p) = C_INT(CDR(arg_));
arg_types[i] = &ffi_type_ulong;
arg_values[i] = p;
break;
case RET_SLONG:
p = uim_malloc(sizeof(signed long));
*((signed long *)p) = C_INT(CDR(arg_));
arg_types[i] = &ffi_type_slong;
arg_values[i] = p;
break;
case RET_FLOAT:
{
char *endptr;
p = uim_malloc(sizeof(float));
*((double *)p) = strtof(REFER_C_STR(CDR(arg_)), &endptr);
arg_types[i] = &ffi_type_float;
arg_values[i] = p;
}
break;
case RET_DOUBLE:
{
char *endptr;
p = uim_malloc(sizeof(double));
*((double *)p) = strtod(REFER_C_STR(CDR(arg_)), &endptr);
arg_types[i] = &ffi_type_double;
arg_values[i] = p;
}
break;
case RET_STR:
p = uim_malloc(sizeof(void *));
*((void **)p) = (void *)REFER_C_STR(CDR(arg_));
arg_types[i] = &ffi_type_pointer;
arg_values[i] = p;
break;
case RET_PTR:
p = uim_malloc(sizeof(void *));
if (NULLP(CDR(arg_)))
*((void **)p) = NULL;
else
*((void **)p) = C_PTR(CDR(arg_));
arg_types[i] = &ffi_type_pointer;
arg_values[i] = p;
break;
case RET_SCM:
p = uim_malloc(sizeof(void *));
*((void **)p) = CDR(arg_);
arg_types[i] = &ffi_type_pointer;
arg_values[i] = p;
}
argv_ = CDR(argv_);
}
if (input_void)
args = 0;
status = ffi_prep_cif(&cif, FFI_DEFAULT_ABI, args, result_type, arg_types);
switch (status) {
case FFI_OK:
break;
case FFI_BAD_TYPEDEF:
ffi_strerr_ = ffi_strerr_messages[FFI_STRERR_BAD_TYPEDEF];
break;
case FFI_BAD_ABI:
ffi_strerr_ = ffi_strerr_messages[FFI_STRERR_BAD_ABI];
break;
default:
ffi_strerr_ = ffi_strerr_messages[FFI_STRERR_UNKOWN];
}
if (status == FFI_OK)
ffi_call(&cif, (void (*)(void))C_PTR(fun_), result, arg_values);
for (i = 0; i < args; i++)
free(arg_values[i]);
free(arg_types);
free(arg_values);
if (status != FFI_OK) {
free(result);
return uim_scm_f();
}
ret_ = uim_scm_f();
switch (return_object_type) {
case RET_UNKNOWN:
case RET_VOID:
break;
case RET_UCHAR:
ret_ = MAKE_CHAR(*(unsigned char *)result);
break;
case RET_SCHAR:
ret_ = MAKE_CHAR(*(signed char *)result);
break;
case RET_USHORT:
ret_ = MAKE_INT(*(unsigned short *)result);
break;
case RET_SSHORT:
ret_ = MAKE_INT(*(signed short *)result);
break;
case RET_UINT:
ret_ = MAKE_INT(*(unsigned int *)result);
break;
case RET_SINT:
ret_ = MAKE_INT(*(signed int *)result);
break;
case RET_ULONG:
ret_ = MAKE_INT(*(unsigned long *)result);
break;
case RET_SLONG:
ret_ = MAKE_INT(*(signed long *)result);
break;
case RET_FLOAT:
{
char str[1024];
snprintf(str, sizeof(str), "%f", *((float *)result));
ret_ = MAKE_STR(str);
}
break;
case RET_DOUBLE:
{
char str[1024];
snprintf(str, sizeof(str), "%f", *((double *)result));
ret_ = MAKE_STR(str);
}
break;
case RET_STR:
ret_ = MAKE_STR(*((char **)result));
break;
case RET_PTR:
ret_ = MAKE_PTR(*((void **)result));
break;
case RET_SCM:
ret_ = *(uim_lisp *)result;
break;
}
free(result);
ffi_strerr_ = NULL;
return ret_;
}
void TestAddCellWithShovingBasedDivisionRule()
{
/**
* In this test we create a new ShovingCaBasedDivisionRule, divide a cell with it
* and check that the new cells are in the correct locations. First, we test where
* there is space around the cells. This is the default setup.
*/
// Create a simple Potts mesh
PottsMeshGenerator<2> generator(5, 0, 0, 5, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create 9 cells in the central nodes
std::vector<unsigned> location_indices;
for (unsigned row=1; row<4; row++)
{
location_indices.push_back(1+row*5);
location_indices.push_back(2+row*5);
location_indices.push_back(3+row*5);
}
std::vector<CellPtr> cells;
CellsGenerator<FixedG1GenerationalCellCycleModel, 1> cells_generator;
cells_generator.GenerateBasic(cells, location_indices.size());
// Create cell population
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
// Check the cell locations
unsigned cell_locations[9] = {6, 7, 8, 11, 12, 13, 16, 17, 18};
unsigned index = 0;
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_EQUALS(cell_population.GetLocationIndexUsingCell(*cell_iter),cell_locations[index])
++index;
}
// Make a new cell to add
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(StemCellProliferativeType, p_stem_type);
FixedG1GenerationalCellCycleModel* p_model = new FixedG1GenerationalCellCycleModel();
CellPtr p_new_cell(new Cell(p_state, p_model));
p_new_cell->SetCellProliferativeType(p_stem_type);
p_new_cell->SetBirthTime(-1);
// Set the division rule for our population to be the shoving division rule
boost::shared_ptr<AbstractCaBasedDivisionRule<2> > p_division_rule_to_set(new ShovingCaBasedDivisionRule<2>());
cell_population.SetCaBasedDivisionRule(p_division_rule_to_set);
// Get the division rule back from the population and try to add new cell by dividing cell at site 0
boost::shared_ptr<AbstractCaBasedDivisionRule<2> > p_division_rule = cell_population.GetCaBasedDivisionRule();
// Select central cell
CellPtr p_cell_12 = cell_population.GetCellUsingLocationIndex(12);
// The ShovingCaBasedDivisionRule method IsRoomToDivide() always returns true
TS_ASSERT_EQUALS((p_division_rule->IsRoomToDivide(p_cell_12, cell_population)), true);
/*
* Test adding the new cell to the population; this calls CalculateDaughterNodeIndex().
* The new cell moves into node 13.
*/
cell_population.AddCell(p_new_cell, p_cell_12);
// Now check the cells are in the correct place
TS_ASSERT_EQUALS(cell_population.GetNumRealCells(), 10u);
// Note the cell originally on node 13 has been shoved to node 14 and the new cell is on node 13
unsigned new_cell_locations[10] = {6, 7, 8, 11, 12, 14, 16, 17, 18, 13};
index = 0;
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
TS_ASSERT_EQUALS(cell_population.GetLocationIndexUsingCell(*cell_iter), new_cell_locations[index])
++index;
}
}