Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
RunAndCheckIonicModels.hpp
1/*
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34*/
35
36
37#ifndef _RUNANDCHECKIONICMODELS_HPP_
38#define _RUNANDCHECKIONICMODELS_HPP_
39
40#include <vector>
41#include <string>
42
43#include "OdeSolution.hpp"
44
45#include "ColumnDataWriter.hpp"
46#include "ColumnDataReader.hpp"
47
48#include "AbstractCardiacCell.hpp"
49#include "HeartConfig.hpp"
50
51#include <cxxtest/TestSuite.h>
52
53void RunOdeSolverWithIonicModel(AbstractCardiacCellInterface* pOdeSystem,
54 double endTime,
55 std::string filename,
56 int stepPerRow=100,
57 bool doComputeExceptVoltage=true,
58 bool useSamplingInterval=false);
59
60void CheckCellModelResults(const std::string& rBaseResultsFilename,
61 std::string validResultsBasename = "",
62 double tolerance = 1e-3,
63 std::string referenceFolder = "heart/test/data/ionicmodels");
64
65std::vector<double> GetVoltages(ColumnDataReader& rReader);
66
67void CompareCellModelResults(std::string baseResultsFilename1, std::string baseResultsFilename2,
68 double tolerance, bool vOnly=false, std::string folderName="TestIonicModels");
69
70
71/*
72 * Note: we have to have the function definitions here, rather than in a .cpp file, if we're
73 * to include them in heart/src, as otherwise linking of the heart library fails because
74 * CxxTest routines are not defined.
75 */
76
77#include <cmath>
78
79void RunOdeSolverWithIonicModel(AbstractCardiacCellInterface* pOdeSystem,
80 double endTime,
81 std::string filename,
82 int stepPerRow,
83 bool doComputeExceptVoltage,
84 bool useSamplingInterval)
85{
86 double start_time = 0.0;
87
88 if (doComputeExceptVoltage)
89 {
90 // Store the current system state
91 std::vector<double> state_variables_copy = pOdeSystem->GetStdVecStateVariables();
92
93 // Test ComputeExceptVoltage
94 double v_init = pOdeSystem->GetVoltage();
95 pOdeSystem->ComputeExceptVoltage(start_time, start_time + 100.0 /*ms*/);
96 double v_end = pOdeSystem->GetVoltage();
97 TS_ASSERT_DELTA(v_init, v_end, 1e-6);
98
99 // Test SetVoltage
100 pOdeSystem->SetVoltage(1e6);
101 TS_ASSERT_DELTA(pOdeSystem->GetVoltage(), 1e6, 1e-6);
102
103 // Reset the system
104 pOdeSystem->SetStateVariables(state_variables_copy);
105 }
106
107 // Solve and write to file
108 if (useSamplingInterval)
109 {
110 OdeSolution solution = pOdeSystem->Compute(start_time, endTime, HeartConfig::Instance()->GetOdeTimeStep() * stepPerRow);
111 solution.WriteToFile("TestIonicModels", filename, "ms", 1, false, 4);
112 }
113 else
114 {
115 OdeSolution solution = pOdeSystem->Compute(start_time, endTime);
116 solution.WriteToFile("TestIonicModels", filename, "ms", stepPerRow, false, 4);
117 }
118}
119
120std::vector<double> GetVoltages(ColumnDataReader& rReader)
121{
122 //Rather Ugly, we can't currently guarantee what the name of the voltage column is,
123 //hence we try to cover the most common possibilities
124 std::vector<double> voltages;
125 if (rReader.HasValues("V"))
126 {
127 voltages = rReader.GetValues("V");
128 }
129 else if (rReader.HasValues("membrane_voltage"))
130 {
131 voltages = rReader.GetValues("membrane_voltage");
132 }
133 else if (rReader.HasValues("membrane__V"))
134 {
135 voltages = rReader.GetValues("membrane__V");
136 }
137 else
138 {
139 EXCEPTION("Model membrane voltage not recognised.");
140 }
141 return voltages;
142}
143
144std::vector<double> GetIntracellularCalcium(ColumnDataReader& rReader)
145{
146 //Rather Ugly, we can't currently guarantee what the name of the calcium column is,
147 //hence we try to cover the most common possibilities
148 std::vector<double> cai;
149 if (rReader.HasValues("CaI"))
150 {
151 cai = rReader.GetValues("CaI");
152 }
153 else if (rReader.HasValues("cytosolic_calcium_concentration"))
154 {
155 cai = rReader.GetValues("cytosolic_calcium_concentration");
156 }
157 else if (rReader.HasValues("Cai"))
158 {
159 cai = rReader.GetValues("Cai");
160 }
161 else
162 {
163 EXCEPTION("Model intracellular calcium is not recognised.");
164 }
165 return cai;
166}
167
168std::vector<double> GetHGate(ColumnDataReader& rReader)
169{
170 //Rather Ugly, we can't currently guarantee what the name of the h gate column is,
171 //hence we try to cover the most common possibilities
172 std::vector<double> h_values;
173 if (rReader.HasValues("h"))
174 {
175 h_values = rReader.GetValues("h");
176 }
177 else if (rReader.HasValues("fast_sodium_current_h_gate__h"))
178 {
179 h_values = rReader.GetValues("fast_sodium_current_h_gate__h");
180 }
181 else if (rReader.HasValues("membrane_fast_sodium_current_h_gate"))
182 {
183 h_values = rReader.GetValues("membrane_fast_sodium_current_h_gate");
184 }
185 else
186 {
187 EXCEPTION("Model h gate is not recognised.");
188 }
189 return h_values;
190}
191
192/*
193 * Check the cell model against a previous version
194 * or another source e.g. Alan's COR
195 */
196void CheckCellModelResults(const std::string& rBaseResultsFilename,
197 std::string validResultsBasename,
198 double tolerance,
199 std::string referenceFolder)
200{
201 // read data entries for the new file
202 ColumnDataReader data_reader("TestIonicModels", rBaseResultsFilename);
203 std::vector<double> times = data_reader.GetValues("Time");
204 std::vector<double> voltages = GetVoltages(data_reader);
205
206 if (validResultsBasename == "")
207 {
208 validResultsBasename = rBaseResultsFilename;
209 }
210
211 ColumnDataReader valid_reader(referenceFolder, validResultsBasename + "ValidData",
212 false);
213 std::vector<double> valid_times = valid_reader.GetValues("Time");
214 std::vector<double> valid_voltages = GetVoltages(valid_reader);
215
216 TS_ASSERT_EQUALS(times.size(), valid_times.size());
217 for (unsigned i=0; i<valid_times.size(); i++)
218 {
219 TS_ASSERT_DELTA(times[i], valid_times[i], 1e-12);
220 TS_ASSERT_DELTA(voltages[i], valid_voltages[i], tolerance);
221 }
222}
223
224void CompareCellModelResults(std::string baseResultsFilename1, std::string baseResultsFilename2,
225 double tolerance, bool vOnly, std::string folderName)
226{
227 // Compare 2 sets of results, e.g. from 2 different solvers for the same model.
228 // If the time series differ, the finer resolution must be given first.
229 ColumnDataReader data_reader1(folderName, baseResultsFilename1);
230 std::vector<double> times1 = data_reader1.GetValues("Time");
231 std::vector<double> voltages1 = GetVoltages(data_reader1);
232 std::vector<double> calcium1;
233 std::vector<double> h1;
234
235 ColumnDataReader data_reader2(folderName, baseResultsFilename2);
236 std::vector<double> times2 = data_reader2.GetValues("Time");
237 std::vector<double> voltages2 = GetVoltages(data_reader2);
238 std::vector<double> calcium2;
239 std::vector<double> h2;
240
241 if (!vOnly)
242 {
243 calcium1 = GetIntracellularCalcium(data_reader1);
244 h1 = GetHGate(data_reader1);
245 calcium2 = GetIntracellularCalcium(data_reader2);
246 h2 = GetHGate(data_reader2);
247 }
248
249 TS_ASSERT(times1.size() >= times2.size());
250 double last_v = voltages2[0];
251 double tol = tolerance;
252 for (unsigned i=0, j=0; i<times2.size(); i++)
253 {
254 // Find corresponding time index
255 while (j<times1.size() && times1[j] < times2[i] - 1e-12)
256 {
257 j++;
258 }
259
260 // Set tolerance higher in upstroke
261 if (fabs(voltages2[i] - last_v) > 0.05)
262 {
263 tol = tolerance * 25;
264 }
265 else
266 {
267 tol = tolerance;
268 }
269 last_v = voltages2[i];
270
271 TS_ASSERT_DELTA(times1[j], times2[i], 1e-12);
272 // adjust tol to data
273 TS_ASSERT_DELTA(voltages1[j], voltages2[i], tol);
274 if (!vOnly)
275 {
276 TS_ASSERT_DELTA(calcium1[j], calcium2[i], tol/100);
277 TS_ASSERT_DELTA(h1[j], h2[i], tol/10);
278 }
279 }
280}
281
282
283#endif //_RUNANDCHECKIONICMODELS_HPP_
#define EXCEPTION(message)
virtual void SetStateVariables(const std::vector< double > &rVariables)=0
virtual void ComputeExceptVoltage(double tStart, double tEnd)=0
virtual double GetVoltage()=0
virtual std::vector< double > GetStdVecStateVariables()=0
virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)=0
virtual void SetVoltage(double voltage)=0
bool HasValues(const std::string &rVariableName)
std::vector< double > GetValues(const std::string &rVariableName)
static HeartConfig * Instance()
void WriteToFile(std::string directoryName, std::string baseResultsFilename, std::string timeUnits, unsigned stepsPerRow=1, bool cleanDirectory=true, unsigned precision=8, bool includeDerivedQuantities=false)