Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
AbstractPurkinjeCellFactory.cpp
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35
36
37#include "AbstractPurkinjeCellFactory.hpp"
38#include "PurkinjeVentricularJunctionStimulus.hpp"
39#include "MultiStimulus.hpp"
40#include "HeartConfig.hpp"
41#include "Warnings.hpp"
42
43template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
45 : AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>(),
46 mpMixedDimensionMesh(NULL)
47{
48}
49
50template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
52{
53 std::string pvj_file_name;
54 bool file_specified = true;
55
56 try
57 {
58 // HeartConfig::Instance()->GetMeshName() will throw an exception if no mesh name is defined
59 pvj_file_name = HeartConfig::Instance()->GetMeshName() + ".pvj";
60 }
61 catch(Exception&)
62 {
63 file_specified = false;
64 }
65
66 FileFinder junction_file(pvj_file_name, RelativeTo::AbsoluteOrCwd);
67 if (!file_specified || !junction_file.Exists() )
68 {
69 // In this case we expect the user to specify PVJ programmatically, so return immediately.
70 WARNING("No Purkinje-Ventricular junction (.pvj) file found. Junctions must be specified manually.");
71 return;
72 }
73
74 std::ifstream junction_stream(junction_file.GetAbsolutePath().c_str());
75
76 if (!junction_stream.good())
77 { // file couldn't be opened
78 EXCEPTION("Couldn't open data file: " << junction_file.GetAbsolutePath());
79 }
80
81 // Reads in file defining nodes and resistance (separated by space)
82 while (junction_stream.good())
83 {
84 std::string this_line;
85 getline(junction_stream, this_line);
86
87 if (this_line=="" || this_line=="\r")
88 {
89 if (junction_stream.eof())
90 { // If the blank line is the last line carry on OK.
91 break;
92 }
93 else
94 {
95 EXCEPTION("No data found on line in file: " << junction_file.GetAbsolutePath());
96 }
97 }
98 std::stringstream line(this_line);
99
100 unsigned node_id;
101 line >> node_id;
102 double resistance;
103 line >> resistance;
104
105 if (mpMixedDimensionMesh->rGetNodePermutation().size() != 0) //Do we have a permuted mesh?
106 {
107 unsigned mapped_node_id = mpMixedDimensionMesh->rGetNodePermutation()[node_id];
108
109 mJunctionMap[mapped_node_id] = resistance;
110 }
111 else
112 {
113 mJunctionMap[node_id] = resistance;
114 }
115 }
116}
117
118template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
120 AbstractCardiacCellInterface* pPurkinjeCell,
121 AbstractCardiacCellInterface* pCardiacCell,
122 double resistance)
123{
124 // Figure out the effective resistance for this mesh, in kOhm.cm^3
125 if (pNode) // Should always be provided apart from low-level tests!
126 {
127 assert(mpMixedDimensionMesh);
128 typedef typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::CableRangeAtNode CableRangeAtNode;
129 CableRangeAtNode cable_range = mpMixedDimensionMesh->GetCablesAtNode(pNode);
130 double total_cross_sectional_area = 0.0;
131 for (typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::NodeCableIterator iter=cable_range.first;
132 iter != cable_range.second;
133 ++iter)
134 {
135 Element<1u,SPACE_DIM>* p_cable = iter->second;
136 double cable_radius = p_cable->GetAttribute();
137 total_cross_sectional_area += M_PI*cable_radius*cable_radius;
138 }
139 resistance *= total_cross_sectional_area / HeartConfig::Instance()->GetPurkinjeSurfaceAreaToVolumeRatio();
140 }
141 // Create the junction stimuli, and associate them with the cells
142 boost::shared_ptr<PurkinjeVentricularJunctionStimulus> p_pvj_ventricular_stim(new PurkinjeVentricularJunctionStimulus(resistance));
143 boost::shared_ptr<PurkinjeVentricularJunctionStimulus> p_pvj_purkinje_stim(new PurkinjeVentricularJunctionStimulus(resistance));
144 p_pvj_purkinje_stim->SetAppliedToPurkinjeCellModel();
145 p_pvj_ventricular_stim->SetVentricularCellModel(pCardiacCell);
146 p_pvj_ventricular_stim->SetPurkinjeCellModel(pPurkinjeCell);
147 p_pvj_purkinje_stim->SetVentricularCellModel(pCardiacCell);
148 p_pvj_purkinje_stim->SetPurkinjeCellModel(pPurkinjeCell);
149
150 // Create new combined stimuli which add the junction stimuli to those already in the cells
151 boost::shared_ptr<MultiStimulus> p_multi_stim_ventricular(new MultiStimulus);
152 p_multi_stim_ventricular->AddStimulus(p_pvj_ventricular_stim);
153 p_multi_stim_ventricular->AddStimulus(pCardiacCell->GetStimulusFunction());
154 pCardiacCell->SetStimulusFunction(p_multi_stim_ventricular);
155
156 boost::shared_ptr<MultiStimulus> p_multi_stim_purkinje(new MultiStimulus);
157 p_multi_stim_purkinje->AddStimulus(p_pvj_purkinje_stim);
158 p_multi_stim_purkinje->AddStimulus(pPurkinjeCell->GetStimulusFunction());
159 pPurkinjeCell->SetStimulusFunction(p_multi_stim_purkinje);
160}
161
162template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
164{
165 mpMixedDimensionMesh = dynamic_cast<MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>*>(pMesh);
166 if (mpMixedDimensionMesh == NULL)
167 {
168 EXCEPTION("AbstractPurkinjeCellFactory must take a MixedDimensionMesh");
169 }
170 mLocalPurkinjeNodes.clear();
171 for (typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::CableElementIterator iter = mpMixedDimensionMesh->GetCableElementIteratorBegin();
172 iter != mpMixedDimensionMesh->GetCableElementIteratorEnd();
173 ++iter)
174 {
175 mLocalPurkinjeNodes.insert((*iter)->GetNodeGlobalIndex(0u));
176 mLocalPurkinjeNodes.insert((*iter)->GetNodeGlobalIndex(1u));
177 }
179
180 ReadJunctionsFile();
181}
182
183template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
185 Node<SPACE_DIM>* pNode,
186 AbstractCardiacCellInterface* pCardiacCell)
187{
188 unsigned node_index = pNode->GetIndex();
189 if (mLocalPurkinjeNodes.count(node_index)>0)
190 {
191 return CreatePurkinjeCellForTissueNode(pNode, pCardiacCell);
192 }
193 else
194 {
195 return new FakeBathCell(this->mpSolver, this->mpZeroStimulus);
196 }
197}
198
199template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
201{
202 if (mpMixedDimensionMesh == NULL)
203 {
204 EXCEPTION("The mixed dimension mesh object has not been set in the cell factory");
205 }
206 return mpMixedDimensionMesh;
207}
208
209template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
211 AbstractCardiacCellInterface* pPurkinjeCell,
212 AbstractCardiacCellInterface* pCardiacCell)
213{
214 std::map<unsigned, double>::iterator iter = mJunctionMap.find(pNode->GetIndex());
215 if (iter != mJunctionMap.end())
216 {
217 CreateJunction(pNode, pPurkinjeCell, pCardiacCell, iter->second);
218 }
219}
220
221// Explicit instantiation
#define EXCEPTION(message)
virtual void SetMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
boost::shared_ptr< AbstractStimulusFunction > GetStimulusFunction()
void SetStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus)
void CreateJunctionFromFile(const Node< SPACE_DIM > *pNode, AbstractCardiacCellInterface *pPurkinjeCell, AbstractCardiacCellInterface *pCardiacCell)
AbstractCardiacCellInterface * CreatePurkinjeCellForNode(Node< SPACE_DIM > *pNode, AbstractCardiacCellInterface *pCardiacCell)
void SetMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > * GetMixedDimensionMesh()
void CreateJunction(const Node< SPACE_DIM > *pNode, AbstractCardiacCellInterface *pPurkinjeCell, AbstractCardiacCellInterface *pCardiacCell, double resistance)
std::string GetAbsolutePath() const
bool Exists() const
std::string GetMeshName() const
double GetPurkinjeSurfaceAreaToVolumeRatio()
static HeartConfig * Instance()
std::vector< Element< 1, SPACE_DIM > * >::const_iterator CableElementIterator
std::pair< NodeCableIterator, NodeCableIterator > CableRangeAtNode
std::multimap< constNode< SPACE_DIM > *, Element< 1u, SPACE_DIM > * >::iterator NodeCableIterator
Definition Node.hpp:59
unsigned GetIndex() const
Definition Node.cpp:158