#include <HeartConfigRelatedCellFactory.hpp>
Inheritance diagram for HeartConfigRelatedCellFactory< SPACE_DIM >:
Collaboration diagram for HeartConfigRelatedCellFactory< SPACE_DIM >:
Detailed Description
template<unsigned SPACE_DIM>
class HeartConfigRelatedCellFactory< SPACE_DIM >
This is a cardiac cell factory which uses the settings from HeartConfig to set up the cells.
It thus supports such features as heterogeneities (in both the type of cell, and for some cells, cell model parameters), and the ability to dynamically convert CellML files into C++ code, compile this, and load the resulting model.
Definition at line 96 of file HeartConfigRelatedCellFactory.hpp.
Constructor & Destructor Documentation
| HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory | ( | ) |
Constructor reads settings from the configuration file.
- Note:
- Must be called collectively.
Definition at line 50 of file HeartConfigRelatedCellFactory.cpp.
References EXCEPTION, HeartConfig::GetCellHeterogeneities(), HeartConfig::GetIonicModelRegions(), HeartConfig::GetStimuli(), HeartConfig::Instance(), HeartConfig::IsElectrodesPresent(), HeartConfigRelatedCellFactory< SPACE_DIM >::mCellHeterogeneityAreas, HeartConfigRelatedCellFactory< SPACE_DIM >::mIonicModelRegions, HeartConfigRelatedCellFactory< SPACE_DIM >::mIonicModelsDefined, HeartConfigRelatedCellFactory< SPACE_DIM >::mParameterSettings, HeartConfigRelatedCellFactory< SPACE_DIM >::mScaleFactorGkr, HeartConfigRelatedCellFactory< SPACE_DIM >::mScaleFactorGks, HeartConfigRelatedCellFactory< SPACE_DIM >::mScaleFactorIto, HeartConfigRelatedCellFactory< SPACE_DIM >::mStimulatedAreas, HeartConfigRelatedCellFactory< SPACE_DIM >::mStimuliApplied, and HeartConfigRelatedCellFactory< SPACE_DIM >::PreconvertCellmlFiles().
| HeartConfigRelatedCellFactory< SPACE_DIM >::~HeartConfigRelatedCellFactory | ( | ) |
Destructor
Definition at line 106 of file HeartConfigRelatedCellFactory.cpp.
Member Function Documentation
| AbstractCardiacCellInterface * HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCardiacCellForTissueNode | ( | unsigned | nodeIndex | ) | [virtual] |
Create the correct stimulated tissue cell for a given region in the mesh The stimulus is determined in this method (using the list of stimulation regions). The cardiac cell type (and parameters) are determined in the CreateCellWithIntracellularStimulus method
- Parameters:
-
nodeIndex is the global index within the mesh
Implements AbstractCardiacCellFactory< SPACE_DIM >.
Definition at line 342 of file HeartConfigRelatedCellFactory.cpp.
| AbstractCardiacCellInterface * HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus | ( | boost::shared_ptr< AbstractStimulusFunction > | intracellularStimulus, |
| unsigned | nodeIndex | ||
| ) |
Create the correct tissue cell for a given region in the mesh
- Parameters:
-
intracellularStimulus is computed in CreateCardiacCellForTissueNode determined by the list of stimulation regions nodeIndex is the global index within the mesh
Definition at line 111 of file HeartConfigRelatedCellFactory.cpp.
References EXCEPTION, HeartConfig::GetCheckpointSimulation(), AbstractCardiacCellInterface::GetLookupTableCollection(), HeartConfig::Instance(), and NEVER_REACHED.
| void HeartConfigRelatedCellFactory< 3u >::FillInCellularTransmuralAreas | ( | ) | [virtual] |
Method that fills in the vector of heterogeneity areas with the NodesLists that correspond to a given layer (implemented in subclasses)
Reimplemented from AbstractCardiacCellFactory< SPACE_DIM >.
Definition at line 367 of file HeartConfigRelatedCellFactory.cpp.
References HeartGeometryInformation< SPACE_DIM >::DetermineLayerForEachNode(), HeartConfig::GetEndoLayerFraction(), HeartConfig::GetEndoLayerIndex(), HeartConfig::GetEpiLayerFraction(), HeartConfig::GetEpiLayerIndex(), HeartConfig::GetMeshName(), HeartConfig::GetMidLayerIndex(), HeartConfig::Instance(), NEVER_REACHED, and HeartGeometryInformation< SPACE_DIM >::rGetLayerForEachNode().
| void HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas | ( | ) | [virtual] |
Helper method to calculate and fill in the heterogeneities areas (mCellHeterogeneityAreas)
Reimplemented from AbstractCardiacCellFactory< SPACE_DIM >.
Definition at line 361 of file HeartConfigRelatedCellFactory.cpp.
References NEVER_REACHED.
| DynamicCellModelLoaderPtr HeartConfigRelatedCellFactory< SPACE_DIM >::LoadDynamicModel | ( | const cp::ionic_model_selection_type & | rModel, |
| bool | isCollective | ||
| ) | [private] |
Get a loader for the given (dynamically loadable) cell model.
- Parameters:
-
rModel model to load isCollective whether we are being called collectively
Definition at line 95 of file HeartConfigRelatedCellFactory.cpp.
References CellMLToSharedLibraryConverter::Convert().
| void HeartConfigRelatedCellFactory< SPACE_DIM >::PreconvertCellmlFiles | ( | ) | [private] |
Called by the constructor to convert any CellML files used as dynamically loaded cell models to shared libraries. This is necessary since the conversion process must be done collectively.
- Note:
- Must be called collectively.
Definition at line 79 of file HeartConfigRelatedCellFactory.cpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
| void HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellIntracellularStimulus | ( | AbstractCardiacCellInterface * | pCell, |
| unsigned | nodeIndex | ||
| ) |
Set the intracellular stimulus for a cell based on the definitions in HeartConfig.
- Parameters:
-
pCell the cell to set stimulus of nodeIndex the index of the node corresponding to this cell in the mesh
Definition at line 323 of file HeartConfigRelatedCellFactory.cpp.
References AbstractCardiacCellInterface::SetIntracellularStimulusFunction().
Referenced by CardiacSimulation::CreateAndRun().
| void HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters | ( | AbstractCardiacCellInterface * | pCell, |
| unsigned | nodeIndex | ||
| ) |
Set parameters of a cell based on heterogeneity definitions in HeartConfig.
- Parameters:
-
pCell the cell to set parameters of nodeIndex the index of the node corresponding to this cell in the mesh
#1166 applying Hill function for drug action
Definition at line 256 of file HeartConfigRelatedCellFactory.cpp.
References HeartConfig::GetDrugDose(), HeartConfig::GetIc50Values(), AbstractCardiacCellInterface::GetParameter(), HeartConfig::Instance(), and AbstractCardiacCellInterface::SetParameter().
Referenced by CardiacSimulation::CreateAndRun().
Member Data Documentation
std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > HeartConfigRelatedCellFactory< SPACE_DIM >::mCellHeterogeneityAreas [private] |
List of regions which represent areas in which to give parametric heterogeneity (scaling gating parameters) This vector will be filled in by the HeartConfig::GetCellHeterogeneity method if the user requested to specify the heterogeneity areas by cuboids, or, alternatively, by the FillInCellularTransmuralAreas method in the cell factory called by the problem class AFTER setting the mesh (which is needed for the calculations of the distance maps for the calculations of heterogeneities).
When creating a cardiac cell for each node (CreateCardiacCellForTissueNode) the code will check whether that node is contained in the heterogeneity area or not.
Definition at line 122 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
cp::ionic_model_selection_type HeartConfigRelatedCellFactory< SPACE_DIM >::mDefaultIonicModel [private] |
Default cardiac cell model to be used in all tissue (except heterogeneous regions)
Definition at line 100 of file HeartConfigRelatedCellFactory.hpp.
std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > HeartConfigRelatedCellFactory< SPACE_DIM >::mIonicModelRegions [private] |
List of axis-aligned box regions which contain heterogeneous cardiac ionic model types
Definition at line 102 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<cp::ionic_model_selection_type> HeartConfigRelatedCellFactory< SPACE_DIM >::mIonicModelsDefined [private] |
List of ionic model (size matches that of mIonicModelRegions)
Definition at line 104 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<std::map<std::string, double> > HeartConfigRelatedCellFactory< SPACE_DIM >::mParameterSettings [private] |
Named parameters to be set in each region (size of list matches that of mCellHeterogeneityAreas)
Definition at line 131 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<double> HeartConfigRelatedCellFactory< SPACE_DIM >::mScaleFactorGkr [private] |
List of scale factors for Gkr scaling in each region (size of list matches that of mCellHeterogeneityAreas)
Definition at line 128 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<double> HeartConfigRelatedCellFactory< SPACE_DIM >::mScaleFactorGks [private] |
List of scale factors for Gks scaling in each region (size of list matches that of mCellHeterogeneityAreas)
Definition at line 124 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<double> HeartConfigRelatedCellFactory< SPACE_DIM >::mScaleFactorIto [private] |
List of scale factors for Ito scaling in each region (size of list matches that of mCellHeterogeneityAreas)
Definition at line 126 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > HeartConfigRelatedCellFactory< SPACE_DIM >::mStimulatedAreas [private] |
List of axis-aligned box or ellipsoid regions which represent areas to stimulate
Definition at line 107 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
std::vector<boost::shared_ptr<AbstractStimulusFunction> > HeartConfigRelatedCellFactory< SPACE_DIM >::mStimuliApplied [private] |
List of intracellular current stimuli to apply (size matches that of mStimulatedAreas)
Definition at line 109 of file HeartConfigRelatedCellFactory.hpp.
Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().
The documentation for this class was generated from the following files:
- heart/src/problem/cell_factories/HeartConfigRelatedCellFactory.hpp
- heart/src/problem/cell_factories/HeartConfigRelatedCellFactory.cpp
