Chaste  Release::2018.1
AbstractPurkinjeCellFactory.cpp
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36 
37 #include "AbstractPurkinjeCellFactory.hpp"
38 #include "PurkinjeVentricularJunctionStimulus.hpp"
39 #include "MultiStimulus.hpp"
40 #include "HeartConfig.hpp"
41 #include "Warnings.hpp"
42 
43 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
45  : AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>(),
46  mpMixedDimensionMesh(NULL)
47 {
48 }
49 
50 template<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 
118 template<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 
162 template<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 
183 template<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 
199 template<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 
209 template<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
222 template class AbstractPurkinjeCellFactory<1,1>;
223 template class AbstractPurkinjeCellFactory<2,2>;
224 template class AbstractPurkinjeCellFactory<3,3>;
225 template class AbstractPurkinjeCellFactory<1,2>;
226 template class AbstractPurkinjeCellFactory<1,3>;
double GetPurkinjeSurfaceAreaToVolumeRatio()
AbstractCardiacCellInterface * CreatePurkinjeCellForNode(Node< SPACE_DIM > *pNode, AbstractCardiacCellInterface *pCardiacCell)
Definition: Node.hpp:58
std::pair< NodeCableIterator, NodeCableIterator > CableRangeAtNode
std::string GetAbsolutePath() const
Definition: FileFinder.cpp:224
#define EXCEPTION(message)
Definition: Exception.hpp:143
MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > * GetMixedDimensionMesh()
void SetStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus)
std::string GetMeshName() const
std::multimap< const Node< SPACE_DIM > *, Element< 1u, SPACE_DIM > * >::iterator NodeCableIterator
void CreateJunctionFromFile(const Node< SPACE_DIM > *pNode, AbstractCardiacCellInterface *pPurkinjeCell, AbstractCardiacCellInterface *pCardiacCell)
bool Exists() const
Definition: FileFinder.cpp:183
void SetMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
virtual void SetMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
boost::shared_ptr< AbstractStimulusFunction > GetStimulusFunction()
unsigned GetIndex() const
Definition: Node.cpp:158
void CreateJunction(const Node< SPACE_DIM > *pNode, AbstractCardiacCellInterface *pPurkinjeCell, AbstractCardiacCellInterface *pCardiacCell, double resistance)
static HeartConfig * Instance()
std::vector< Element< 1, SPACE_DIM > * >::const_iterator CableElementIterator