Chaste  Release::2018.1
AbstractCvodeCellWithDataClamp.cpp
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35 
36 #ifdef CHASTE_CVODE
37 
38 #include <sstream>
39 #include <iostream>
40 #include <cmath>
41 
42 #include "AbstractCvodeCellWithDataClamp.hpp"
43 #include "Exception.hpp"
44 #include "HeartConfig.hpp"
46 #include <algorithm>
47 
48 
49 AbstractCvodeCellWithDataClamp::AbstractCvodeCellWithDataClamp(boost::shared_ptr<AbstractIvpOdeSolver> pSolver/* unused */,
50  unsigned numberOfStateVariables,
51  unsigned voltageIndex,
52  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
53  : AbstractCvodeCell(pSolver, numberOfStateVariables, voltageIndex, pIntracellularStimulus),
54  mDataAvailable(false),
55  mDataClampIsOn(false)
56 {
57 }
58 
60 {
61 }
62 
63 void AbstractCvodeCellWithDataClamp::SetExperimentalData(std::vector<double> experimentalTimes,
64  std::vector<double> experimentalVoltages)
65 {
66  assert(experimentalVoltages.size()==experimentalTimes.size());
67  assert(experimentalVoltages.size()>1u);
68  mExperimentalTimes = experimentalTimes;
69  mExperimentalVoltages = experimentalVoltages;
70  mDataAvailable = true;
71 }
72 
73 double AbstractCvodeCellWithDataClamp::GetExperimentalVoltageAtTimeT(const double& rTime) // Linearly interpolate between data points
74 {
75  if (!mDataClampIsOn)
76  {
77  // For speed we want to be able to skip this method.
78  return DOUBLE_UNSET;
79  }
80 
81  if (rTime > mExperimentalTimes.back() || rTime < mExperimentalTimes[0])
82  {
83  EXCEPTION("The requested time " << rTime << " is outside the times stored in the data clamp.");
84  }
85 
86  std::vector<double>::iterator upper_vec =
87  std::upper_bound(mExperimentalTimes.begin(), mExperimentalTimes.end(), rTime);
88  // upper_vec points to first element that is (strictly) > rTime (so it can't be first one if rTime is in range)
89 
90  // Special case - here the lower bound is equal to upper bound and both are pointing to end!
91  if (upper_vec == mExperimentalTimes.end())
92  {
93  return mExperimentalVoltages.back();
94  }
95 
96  unsigned upper_index = upper_vec - mExperimentalTimes.begin();
97 
98  assert(upper_index>0u); // Sanity check to avoid seg faults below.
99  // if this assert ever fails we may need the code below, but I can't see how it could!
100 // if (upper_index == 0u)
101 // {
102 // // Special case - here the lower bound is equal to upper bound and no interpolation needed
103 // return mExperimentalVoltages[0];
104 // }
105 
106  double lower_time = mExperimentalTimes[upper_index-1];
107  double increment = rTime - lower_time;
108  double time_step = mExperimentalTimes[upper_index] - mExperimentalTimes[upper_index-1];
109  double voltage_step = mExperimentalVoltages[upper_index] - mExperimentalVoltages[upper_index-1];
110  return mExperimentalVoltages[upper_index-1] + increment * voltage_step / time_step;
111 }
112 
114 {
115  this->SetParameter("membrane_data_clamp_current_conductance",0);
116  mDataClampIsOn = false;
117 }
118 
120 {
121  if (!mDataAvailable)
122  {
123  EXCEPTION("Before calling TurnOnDataClamp(), please provide experimental data via the SetExperimentalData() method.");
124  }
125  assert(mExperimentalTimes.size() > 1u);
126  this->SetParameter("membrane_data_clamp_current_conductance", conductance);
127  mDataClampIsOn = true;
128 }
129 
130 #endif // CHASTE_CVODEWITHDATACLAMP
AbstractCvodeCellWithDataClamp(boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
#define EXCEPTION(message)
Definition: Exception.hpp:143
void SetParameter(const std::string &rParameterName, double value)
const double DOUBLE_UNSET
Definition: Exception.hpp:56
double GetExperimentalVoltageAtTimeT(const double &rTime)
void SetExperimentalData(std::vector< double > experimentalTimes, std::vector< double > experimentalVoltages)