Chaste  Release::3.4
PseudoEcgCalculator.cpp
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35 
36 #include "PseudoEcgCalculator.hpp"
37 #include "HeartRegionCodes.hpp"
38 #include "HeartConfig.hpp"
39 #include "PetscTools.hpp"
40 #include "Version.hpp"
41 #include <iostream>
42 
43 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
45  c_vector<double,PROBLEM_DIM>& rU,
46  c_matrix<double,PROBLEM_DIM,SPACE_DIM>& rGradU)
47 {
48  c_vector<double,SPACE_DIM> r_vector = rX.rGetLocation()- mProbeElectrode.rGetLocation();
49  double norm_r = norm_2(r_vector);
50  if (norm_r <= DBL_EPSILON)
51  {
52  EXCEPTION("Probe is on a mesh Gauss point.");
53  }
54  c_vector<double,SPACE_DIM> grad_one_over_r = - (r_vector)*SmallPow( (1/norm_r) , 3);
55  matrix_row<c_matrix<double, PROBLEM_DIM, SPACE_DIM> > grad_u_row(rGradU, 0);
56  double integrand = inner_prod(grad_u_row, grad_one_over_r);
57 
58  return -mDiffusionCoefficient*integrand;
59 }
60 
61 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
63  const ChastePoint<SPACE_DIM>& rProbeElectrode,
64  const FileFinder& rDirectory,
65  const std::string& rHdf5FileName,
66  const std::string& rVariableName,
67  unsigned timestepStride)
68  : mrMesh(rMesh),
69  mProbeElectrode(rProbeElectrode),
70  mVariableName(rVariableName),
71  mTimestepStride(timestepStride)
72 {
73  mpDataReader = new Hdf5DataReader(rDirectory, rHdf5FileName);
77  //check that the hdf file was generated by simulations from the same mesh
78  assert(mNumberOfNodes == mrMesh.GetNumNodes());
79 }
80 
81 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
83 {
84  bool result = false; // Don't skip usually
85  if (mVariableName=="V")
86  {
87  // If we are integrating voltage and this element is in the bath then skip it.
89  }
90  return result;
91 }
92 
93 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
95 {
96  delete mpDataReader;
97 }
98 
99 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
101 {
102  assert(diffusionCoefficient>=0);
103  mDiffusionCoefficient = diffusionCoefficient;
104 }
105 
106 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
108 {
109  Vec solution_at_one_time_step = PetscTools::CreateVec(mNumberOfNodes);
110  mpDataReader->GetVariableOverNodes(solution_at_one_time_step, mVariableName , timeStep);
111 
112  double pseudo_ecg_at_one_timestep;
113  try
114  {
115  pseudo_ecg_at_one_timestep = this->Calculate(mrMesh, solution_at_one_time_step);
116  }
117  catch (Exception &e)
118  {
119  PetscTools::Destroy(solution_at_one_time_step);
120  throw e;
121  }
122  PetscTools::Destroy(solution_at_one_time_step);
123  return pseudo_ecg_at_one_timestep;
124 }
125 
126 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
128 {
129  // Cache the time values so that we can plot a decent x-axis
130  std::vector<double> time_points = mpDataReader->GetUnlimitedDimensionValues();
131 
132  std::stringstream stream;
133  stream << "PseudoEcgFromElectrodeAt" << "_" << mProbeElectrode.GetWithDefault(0)
134  << "_" << mProbeElectrode.GetWithDefault(1)
135  << "_" << mProbeElectrode.GetWithDefault(2) << ".dat";
136  OutputFileHandler output_file_handler(HeartConfig::Instance()->GetOutputDirectory() + "/output", false);
137  out_stream p_file=out_stream(NULL);
138  if (PetscTools::AmMaster())
139  {
140  p_file = output_file_handler.OpenOutputFile(stream.str());
141  *p_file << "#Time(ms)\tPseudo-ECG\n";
142  }
143  for (unsigned time_step = 0; time_step < mNumTimeSteps; time_step+=mTimestepStride)
144  {
145  double pseudo_ecg_at_one_timestep = ComputePseudoEcgAtOneTimeStep(time_step);
146  if (PetscTools::AmMaster())
147  {
148  *p_file << time_points[time_step] << "\t" <<pseudo_ecg_at_one_timestep << "\n";
149  }
150  }
151  if (PetscTools::AmMaster())
152  {
153  //write provenance info
154  std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
155  *p_file << comment;
156  p_file->close();
157  }
158 }
160 // Explicit instantiation
162 
163 template class PseudoEcgCalculator<1,1,1>;
164 template class PseudoEcgCalculator<1,2,1>;
165 template class PseudoEcgCalculator<1,3,1>;
166 template class PseudoEcgCalculator<2,2,1>;
167 //template class PseudoEcgCalculator<2,3,1>;
168 template class PseudoEcgCalculator<3,3,1>;
169 
void SetDiffusionCoefficient(double diffusionCoefficient)
static bool IsRegionBath(HeartRegionType regionId)
unsigned GetNumberOfRows()
double GetIntegrand(ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU)
c_vector< double, DIM > & rGetLocation()
Definition: ChastePoint.cpp:76
double SmallPow(double x, unsigned exponent)
#define EXCEPTION(message)
Definition: Exception.hpp:143
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
static bool AmMaster()
Definition: PetscTools.cpp:120
static Vec CreateVec(int size, int localSize=PETSC_DECIDE, bool ignoreOffProcEntries=true)
Definition: PetscTools.cpp:214
bool ShouldSkipThisElement(Element< ELEMENT_DIM, SPACE_DIM > &rElement)
out_stream OpenOutputFile(const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
PseudoEcgCalculator(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, const ChastePoint< SPACE_DIM > &rProbeElectrode, const FileFinder &rDirectory, const std::string &rHdf5FileName, const std::string &rVariableName="V", unsigned timestepStride=1)
static void Destroy(Vec &rVec)
Definition: PetscTools.hpp:351
std::vector< double > GetVariableOverTime(const std::string &rVariableName, unsigned nodeIndex)
unsigned GetUnsignedAttribute()
static std::string GetProvenanceString()
Hdf5DataReader * mpDataReader
static HeartConfig * Instance()
double ComputePseudoEcgAtOneTimeStep(unsigned timeStep)