private static void displayForBrian(Izhikevich9pModelMC model, int idx) {
String forBrian = "";
forBrian =
"\n\nk"
+ idx
+ "="
+ model.getK()[idx]
+ "/ms/mV\na"
+ idx
+ "="
+ model.getA()[idx]
+ "\nb"
+ idx
+ "="
+ model.getB()[idx]
+ "\nd"
+ idx
+ "="
+ model.getD()[idx]
+ "\nC"
+ idx
+ "="
+ model.getcM()[idx]
+ "\nvR"
+ idx
+ "="
+ model.getvR()[idx]
+ "*mV\nvT"
+ idx
+ "="
+ model.getvT()[idx]
+ "*mV\nvPeak"
+ idx
+ "="
+ model.getvPeak()[idx]
+ "*mV\nc"
+ idx
+ "="
+ model.getvMin()[idx]
+ "*mV";
System.out.println(forBrian);
}
private static void runWithUserParmValues() {
Izhikevich9pModelMC model = getRightInstanceForModel();
double k0, k1, k2;
double a0, a1, a2;
double b0, b1, b2;
double d0, d1, d2;
double C0, C1, C2;
double vR0;
double vT0, vT1, vT2;
double vPeak0, vPeak1, vPeak2;
double c0, c1, c2;
double Gt_1, P_1, Gt_2, P_2;
double[] newCurrents = new double[] {408}; // , currents[1]};
k0 = 1.029252f;
a0 = 0.0015812784f;
b0 = 2.3435593f;
d0 = 3.0f;
C0 = 85.0f;
vR0 = -60.772045f;
vT0 = -30.712957f;
vPeak0 = 19.3511f;
c0 = -53.59736f;
model.setK(getDouble1dArray(k0));
model.setA(getDouble1dArray(a0));
model.setB(getDouble1dArray(b0));
model.setD(getDouble1dArray(d0));
model.setcM(getDouble1dArray(C0));
model.setvR(vR0);
model.setvT(getDouble1dArray(vT0));
model.setvMin(getDouble1dArray(c0));
model.setvPeak(getDouble1dArray(vPeak0));
model.setG(getDouble1dArray(0));
model.setP(getDouble1dArray(0));
double[] weights = new double[] {};
ModelEvaluatorMC evaluator =
new ModelEvaluatorMC(
model,
ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS,
ModelEvaluatorWrapper.INPUT_PHENOTYPE_CONSTRAINT,
ModelEvaluatorWrapper.INPUT_PAT_REP_WEIGHTS,
ModelEvaluatorWrapper.INPUT_MC_CONS,
newCurrents,
weights);
evaluator.setDisplayAll(true);
evaluator.getFitness();
System.out.println("\nSpike Times: ");
GeneralUtils.displayArray(evaluator.getModelSomaSpikePatternHolder().getSpikeTimes());
}
public static Izhikevich9pModelMC readModel(String exp, int trial) {
File newFile = new File("output/" + exp + "/job." + trial + ".Full");
if (!(newFile).exists()) {
System.out.println("file not found! skipping.." + "file: " + newFile.getAbsolutePath());
return null;
}
double[] parms =
ECStatOutputReader.readBestSolution("output/" + exp + "/job." + trial + ".Full", 50);
Izhikevich9pModelMC model = getRightInstanceForModel();
EAGenes genes = new EAGenes(parms, iso_comp);
model.setK(genes.getK());
model.setA(genes.getA());
model.setB(genes.getB());
model.setD(genes.getD());
model.setcM(genes.getCM());
model.setvR(genes.getVR());
model.setvT(genes.getVT());
model.setvMin(genes.getVMIN());
model.setvPeak(genes.getVPEAK());
model.setG(genes.getG());
model.setP(genes.getP());
double[] I = genes.getI();
// System.out.println(I[0]);
model.setInputParameters(new double[] {I[0]}, 0d, 0d);
return model;
}
private static void runPrimary(
double[] parms,
String opFolder,
boolean displayParms,
boolean displayErrors,
boolean drawPlots) {
Izhikevich9pModelMC model = getRightInstanceForModel();
EAGenes genes = new EAGenes(parms, iso_comp);
model.setK(genes.getK());
model.setA(genes.getA());
model.setB(genes.getB());
model.setD(genes.getD());
model.setcM(genes.getCM());
model.setvR(genes.getVR());
model.setvT(genes.getVT());
model.setvMin(genes.getVMIN());
model.setvPeak(genes.getVPEAK());
model.setG(genes.getG());
model.setP(genes.getP());
double[] currents = genes.getI();
// float[] newCurrents = new float[currents.length];
// for(int i=0;i<newCurrents.length;i++)
// newCurrents[i] = currents[i];
double[] weights = new double[model.getNCompartments() - 1]; // genes.getW();
for (int wi = 0; wi < weights.length; wi++) {
weights[wi] = 1;
}
ModelEvaluatorMC evaluator =
new ModelEvaluatorMC(
model,
ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS,
ModelEvaluatorWrapper.INPUT_PHENOTYPE_CONSTRAINT,
ModelEvaluatorWrapper.INPUT_PAT_REP_WEIGHTS,
ModelEvaluatorWrapper.INPUT_MC_CONS,
currents,
weights);
evaluator.setRampRheo(false);
if (displayErrors || displayOnlyFitness) {
if (displayOnlyFitness) {
evaluator.setDisplayAll(false);
evaluator.setDisplayOnlyClass(true);
} else {
evaluator.setDisplayAll(true);
}
// evaluator.setDisplayForPlotIdx(0);
float f = evaluator.getFitness();
if (displayOnlyFitness) {
System.out.print("\t" + f + "\t");
}
// System.out.println();
// evaluator.get
double[] spikeTimes = evaluator.getModelSomaSpikePatternHolder().getSpikeTimes();
spikeTimes = GeneralUtils.roundOff(spikeTimes);
// GeneralUtils.displayArray(spikeTimes);
}
if (displayParms) {
for (int idx = 0; idx < model.getNCompartments(); idx++) {
displayForBrian(model, idx);
}
for (int idx = 0; idx < model.getNCompartments() - 1; idx++) {
System.out.println("Gt_" + (idx + 1) + "=" + model.getG()[idx] + "/ms");
System.out.println("P_" + (idx + 1) + "=" + model.getP()[idx]);
System.out.println("W" + idx + "=" + weights[idx]);
}
// System.out.println();
GeneralUtils.displayArrayUnformatWithSpace(parms, 1, 3);
}
if (drawPlots) {
// float I = currents[0];
double[][] Is = null;
double[] Idurs = null;
if (model.getNCompartments() > 1) {
Idurs =
new double
[ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length + 4]; // exc., ir., sp., EPSP
int i;
for (i = 0; i < ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length; i++) {
Idurs[i] = (float) ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS[i].getCurrentDuration();
}
if (!ModelEvaluatorWrapper.ISO_COMPS) {
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[0].getAttribute(
MCConstraintAttributeID.current_duration); // exc.
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[1].getAttribute(
MCConstraintAttributeID.current_duration); // ir.
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_duration); // sp.
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[3].getAttribute(
MCConstraintAttributeID.sim_duration); // epsp.
}
// *** similarly additional mc currents
double[] somaCurrents = new double[currents.length + 4];
double[] dend1Currents = new double[currents.length + 4];
for (i = 0; i < currents.length; i++) {
somaCurrents[i] = currents[i]; // somatic scenarios
dend1Currents[i] = 0; // no dend current for somatic scenarios
}
double[] rheoComp = model.getRheoBases();
somaCurrents[i] = rheoComp[0]; // exc.
dend1Currents[i++] = rheoComp[1]; // exc.
if (!ModelEvaluatorWrapper.ISO_COMPS) {
somaCurrents[i] =
(double)
ModelEvaluatorWrapper.INPUT_MC_CONS[1].getAttribute(
MCConstraintAttributeID.current); // ir
dend1Currents[i++] =
(double)
ModelEvaluatorWrapper.INPUT_MC_CONS[1].getAttribute(
MCConstraintAttributeID.current); // ir
somaCurrents[i] =
0; // indirectly get the I required for single spike prop as below: (have to go
// through unnecessary steps?!)
float dend_curr_min =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_min);
float dend_curr_max =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_max);
float dend_current_time_min =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_time_min);
float dend_current_duration =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_duration);
float dend_current_step =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_step);
float dend_target_spike_freq =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_target_spike_freq);
for (int c = 1; c < model.getNCompartments(); c++) {
float[] spikeCounts =
evaluator
.getMcEvalholder()
.propagatedSpikeCounts(
c,
MultiCompConstraintEvaluator.forwardConnectionIdcs[c],
dend_curr_min,
dend_curr_max,
dend_current_time_min,
dend_current_duration,
dend_current_step,
dend_target_spike_freq);
dend1Currents[i++] =
spikeCounts[2]; // MUST HAVE 2D ARRAY for dend currents for more than 2 comps!!!!
}
}
somaCurrents[i] = 0; // epsp; syn simulation
dend1Currents[i++] = 0; // epsp; syn simulation
Is = new double[model.getNCompartments()][];
Is[0] = somaCurrents;
Is[1] = dend1Currents;
} else {
Is = new double[1][];
Idurs = new double[ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length];
for (int i = 0; i < ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length; i++) {
Idurs[i] = (float) ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS[i].getCurrentDuration();
}
Is[0] = currents;
}
BrianInvoker invoker = new BrianInvoker(opFolder, Is, Idurs);
invoker.setDisplayErrorStream(true);
invoker.invoke(model);
}
}