public double[,] Simulate(double[] y0, IStimulus stimulus)
{
Initialize(y0);
double[,] retValue = new double[y.Length + 1, Nsave];
int ns = skip;
int p = 0;
try
{
for (int n = 0; n < N; ++n)
{
if (ns == skip)
{
if (p < Nsave)
{
retValue[0, p] = t1 + n * h;
for (int k = 0; k < y.Length; ++k)
retValue[k + 1, p] = y[k];
}
p = p + 1;
ns = 0;
}
++ns;
Integrate(t1 + n * h, stimulus);
}
}
catch { }
return retValue;
}
public double[,] Simulate(double[] y0, IStimulus stimulus)
{
Initialize(y0);
double[,] retValue = new double[y.Length + 1, Nsave];
int ns = skip;
int p = 0;
try
{
for (int n = 0; n < N; ++n)
{
if (ns == skip)
{
if (p < Nsave)
{
retValue[0, p] = t1 + n * h;
for (int k = 0; k < y.Length; ++k)
{
retValue[k + 1, p] = y[k];
}
}
p = p + 1;
ns = 0;
}
++ns;
Integrate(t1 + n * h, stimulus);
}
}
catch { }
return(retValue);
}
protected virtual void WriteStimulus(Epoch e, IExternalDevice ed, IStimulus s)
{
// write s.StimulusID
Console.WriteLine("Epoch stimulus id {0} for device {1}", s.StimulusID, ed.Name);
WriteStimulusParameters(e, ed, s, s.Parameters);
}
protected virtual void WriteStimulusParameters(Epoch e, IExternalDevice ed, IStimulus s, IDictionary <string, object> p)
{
foreach (var k in s.Parameters.Keys)
{
var v = s.Parameters[k];
WriteStimulusParameter(e, ed, s, k, v);
}
}
public static void AssertStimuliEqual(IStimulus expected, IPersistentStimulus actual)
{
Assert.AreEqual(expected.StimulusID, actual.StimulusID);
Assert.AreEqual(expected.Units, actual.Units);
Assert.AreEqual(expected.SampleRate, actual.SampleRate);
Assert.AreEqual(expected.Duration, actual.Duration);
Assert.AreEqual(expected.Data, actual.Data);
CollectionAssert.AreEquivalent(expected.Parameters, actual.Parameters);
AssertConfigurationSpansEqual(expected.OutputConfigurationSpans.Consolidate(), actual.ConfigurationSpans);
}
public static double Threshold(AnalysisParameters P, PatchModel M, IStimulus Is)
{
var solver = new ModelSolver()
{
Model = M,
H = 2e-6,
T1 = P.T1,
T2 = P.T2
};
return solver.EstimateThreshold(P.y0, Is);
}
public virtual void dydt(double[] dydt, double t, double[] y, IStimulus stimulus)
{
double En = y[0];
double Ei = y[1];
alpha(a, y);
beta(b, y);
dydt[0] = -(Iion_n(y) - stimulus.GetValue(t) - (Ei - En) / Ril) / (Cn + Cm);
dydt[1] = -(Iion_i(y) + (Ei - En) / Ril - Cm * dydt[0]) / Ci;
for (int n = 0; n < Ngating; ++n)
dydt[n + 2] = a[n] * (1 - y[n + 2]) - b[n] * y[n + 2];
}
public double[] GetFinalState(double[] y0, IStimulus stimulus)
{
Initialize(y0);
double[] retValue = new double[y.Length];
try
{
for (int n = 0; n < N; ++n)
Integrate(t1 + n * h, stimulus);
for (int n = 0; n < y.Length; ++n)
retValue[n] = y[n];
}
catch { }
return retValue;
}
public double EstimateThreshold(double[] y0, IStimulus stimulus)
{
const int max_iter = 200;
int count = 0;
double I1 = 0;
double I2 = 1e-9;
try
{
while (!IsActivated(y0, stimulus, I2))
{
I1 = I2;
I2 = 2 * I2;
++count;
if (count > max_iter)
{
break;
}
}
while (Math.Abs(I2 - I1) > 1e-12)
{
double Itest = (I2 - I1) / 2 + I1;
if (IsActivated(y0, stimulus, Itest))
{
I2 = Itest;
}
else
{
I1 = Itest;
}
++count;
if (count > max_iter)
{
break;
}
}
}
catch { }
return(I2);
}
public bool IsActivated(double[] y0, IStimulus stimulus)
{
bool retValue = false;
try
{
Initialize(y0);
for (int n = 0; n < N; ++n)
{
Integrate(t1 + n * h, stimulus);
if (y[0] > 0)
{
retValue = true;
break;
}
}
}
catch { }
return retValue;
}
/// <summary>
/// Constructs an output data stream around a given Stimulus with a hint at the block duration
/// to use for enumerating the stimulus data.
/// </summary>
/// <param name="stimulus">Stimulus to stream</param>
/// <param name="blockDuration">Block duration to use for enumerating the stimulus data</param>
public StimulusOutputDataStream(IStimulus stimulus, TimeSpan blockDuration)
{
if (stimulus == null)
throw new ArgumentNullException("stimulus");
if (blockDuration <= TimeSpan.Zero)
throw new ArgumentOutOfRangeException("blockDuration");
Stimulus = stimulus;
StimulusDataEnumerator = stimulus.DataBlocks(blockDuration).GetEnumerator();
Position = TimeSpan.Zero;
OutputPosition = TimeSpan.Zero;
}
private void WriteStimulusDataConfigurationSpans(H5GroupId sId, IStimulus s)
{
WriteConfigurationSpans(sId, s.OutputConfigurationSpans);
}
private void WriteStimulusConfigurationSpans(IStimulus s)
{
WriteConfigurationSpans(s.OutputConfigurationSpans);
}
protected override void WriteStimulus(Epoch e, IExternalDevice ed, IStimulus s)
{
writer.WriteStartElement("stimulus");
writer.WriteAttributeString("device", ed.Name);
writer.WriteAttributeString("stimulusID", s.StimulusID);
writer.WriteAttributeString("stimulusUnits", s.Units);
WriteDictionary("parameters", s.Parameters);
WriteStimulusConfigurationSpans(s);
writer.WriteEndElement();
}
protected virtual void WriteStimulusParameter(Epoch e, IExternalDevice ed, IStimulus s, string k, object v)
{
Console.WriteLine("Epoch stimulus parameter {0}={1}", k, v);
}
protected virtual void WriteStimulus(Epoch e, IExternalDevice ed, IStimulus s)
{
// write s.StimulusID
Console.WriteLine("Epoch stimulus id {0} for device {1}", s.StimulusID, ed.Name);
WriteStimulusParameters(e, ed, s, s.Parameters);
}
protected virtual void WriteStimulusParameter(Epoch e, IExternalDevice ed, IStimulus s, string k, object v)
{
Console.WriteLine("Epoch stimulus parameter {0}={1}", k, v);
}
public double EstimateThreshold(double[] y0, IStimulus stimulus)
{
const int max_iter = 200;
int count = 0;
double I1 = 0;
double I2 = 1e-9;
try
{
while (!IsActivated(y0, stimulus, I2))
{
I1 = I2;
I2 = 2 * I2;
++count;
if (count > max_iter)
break;
}
while (Math.Abs(I2 - I1) > 1e-12)
{
double Itest = (I2 - I1) / 2 + I1;
if (IsActivated(y0, stimulus, Itest))
I2 = Itest;
else
I1 = Itest;
++count;
if (count > max_iter)
break;
}
}
catch { }
return I2;
}
public bool IsActivated(double[] y0, IStimulus stimulus, double Is)
{
stimulus.Is = Is;
return IsActivated(y0, stimulus);
}
public override void dydt(double[] dydt, double t, double[] y, IStimulus stimulus)
{
double En = y[0];
double Ei = y[1];
double Rbb = getRbb(y);
alpha(a, y);
beta(b, y);
dydt[0] = -(Iion_n(y) - stimulus.GetValue(t) - (Ei - En) / Rbb) / (Cn + Cm);
dydt[1] = -(Iion_i(y) + (Ei - En) / Rbb - Cm * dydt[0]) / Ci;
if (ClampKo == 1)
dydt[2] = 0;
else
dydt[2] = (jK_i(y) + jPump(y))/Vpa;
for (int n = 0; n < Ngating; ++n)
dydt[n + 3] = a[n] * (1 - y[n + 3]) - b[n] * y[n + 3];
}
protected virtual void WriteStimulusParameters(Epoch e, IExternalDevice ed, IStimulus s, IDictionary<string, object> p)
{
foreach (var k in s.Parameters.Keys)
{
var v = s.Parameters[k];
WriteStimulusParameter(e, ed, s, k, v);
}
}
public void SetUp()
{
const int srate = 1000;
IList<IMeasurement> list = Enumerable.Range(0, srate * 2).Select(i => new Measurement(i, "V") as IMeasurement).ToList();
data = new OutputData(list, new Measurement(srate, "Hz"));
stim = new RenderedStimulus("stimID", new Dictionary<string, object>(), data);
stream = new StimulusOutputDataStream(stim, TimeSpan.FromSeconds(0.13));
indefiniteStim = new RenderedStimulus("indefID", new Dictionary<string, object>(), data, Option<TimeSpan>.None());
indefiniteStream = new StimulusOutputDataStream(indefiniteStim, TimeSpan.FromSeconds(0.52));
}
private void Integrate(double t, IStimulus stimulus)
{
model.dydt(dydt, t, y, stimulus);
for (int n = 0; n < y.Length; ++n)
{
y[n] += h * dydt[n];
if (y[n] > 1)
y[n] = 1;
if (y[n] < -1)
y[n] = -1;
}
}
