/** Initialise the simplex and evaluate it. Returns null on failure. */
private List <double[]> makeSimplex(double[] initialParams, double[] initialParamVariations, Random random)
{
var simp = Java.NewDoubleArray2(numVertices, numParams + 1 + numExtraArrayElements);
/* simpTable.put(Thread.currentThread(), simp); */
if (initialParams != null)
{
for (int i = 0; i < numParams; i++)
{
if (double.IsNaN(initialParams[i]))
{
Array.Copy(initialParams, 0, simp[0], 0, Math.Min(initialParams.Length, numParams));
}
}
}
evaluate(simp[0]);
if (double.IsNaN(value(simp[0])))
{
findValidInitalParams(simp[0], initialParamVariations, random);
}
if (double.IsNaN(value(simp[0])))
{
return(null);
}
if (initializeSimplex(simp, initialParamVariations, random))
{
return(simp);
}
else
{
return(null);
}
}
/** Get the full simplex of the current thread. This may be useful if the target function
* wants to modify the simplex */
/* public List<double[]> getSimplex() {
* return simpTable.get(Thread.currentThread());
* } */
/** One minimization run (including reinitializations of the simplex until the result is stable) */
private void minimizeOnce(double[] initialParams, double[] initialParamVariations, int seed)
{
Random random = new Random(seed);
var simp = makeSimplex(initialParams, initialParamVariations, random);
if (simp == null)
{
status = wasInitialized ? REINITIALIZATION_FAILURE : INITIALIZATION_FAILURE;
return;
}
wasInitialized = true;
if (startTime == 0)
{
startTime = Java.SystemCurrentTimeMillis();
}
//if (io.binroot.regression.IJ.debugMode) showSimplex(simp, seed+" Initialized:");
int bestVertexNumber = minimize(simp); // first minimization
double bestValueSoFar = value(simp[bestVertexNumber]);
//reinitialize until converged or error/aborted (don't care about reinitialization failure in other thread)
bool reinitialisationFailure = false;
while (status == SUCCESS || status == REINITIALIZATION_FAILURE)
{
double[] paramVariations =
makeNewParamVariations(simp, bestVertexNumber, initialParams, initialParamVariations);
if (!reInitializeSimplex(simp, bestVertexNumber, paramVariations, random))
{
reinitialisationFailure = true;
break;
}
//if (io.binroot.regression.IJ.debugMode) showSimplex(simp, seed+" Reinitialized:");
bestVertexNumber = minimize(simp); // minimize with reinitialized simplex
if (belowErrorLimit(value(simp[bestVertexNumber]), bestValueSoFar, 2.0))
{
break;
}
bestValueSoFar = value(simp[bestVertexNumber]);
}
if (reinitialisationFailure)
{
status = REINITIALIZATION_FAILURE;
}
else if (status == SUCCESS || status == REINITIALIZATION_FAILURE) //i.e. not aborted, not max iterations exceeded
{
numCompletedMinimizations++; // it was a complete minimization
}
//if (io.binroot.regression.IJ.debugMode) showSimplex(simp, seed+" Final:");
if (resultsVector != null)
{
lock (resultsVector) {
resultsVector.Add(simp[bestVertexNumber]);
}
}
else
{
result = simp[bestVertexNumber];
}
}
/** Get the value of the minimum, i.e. the value associated with the resulting parameters
* as obtained by getParams(). May return NaN in case the minimize call has returned
* an INITIALIZATION_FAILURE status or that abort() has been called at the very
* beginning of the minimization.
* Do not call this method before minimization. */
public double getFunctionValue()
{
if (result == null)
{
result = new double[numParams + 1];
Java.DoubleArrayFill(result, double.NaN);
}
return(value(result));
}
/** Get the result, i.e., the set of parameter values (i.e., variable values)
* from the best corner of the simplex. Note that the array returned may have more
* elements than numParams; ignore the rest.
* May return an array with only NaN values in case the minimize call has returned
* an INITIALIZATION_FAILURE status or that abort() has been called at the very
* beginning of the minimization.
* Do not call this method before minimization. */
public double[] getParams()
{
if (result == null)
{
result = new double[numParams + 1 + numExtraArrayElements];
Java.DoubleArrayFill(result, double.NaN);
}
return(result);
}
/** Get center of all vertices except one to exclude
* (may be -1 to exclude none)
* Does not care about function values (i.e., last array elements) */
private void getCenter(List <double[]> simp, int excludeVertex, double[] center)
{
Java.DoubleArrayFill(center, 0.0);
int nV = 0;
for (int v = 0; v < numVertices; v++)
{
if (v != excludeVertex)
{
for (int i = 0; i < numParams; i++)
{
center[i] += simp[v][i];
}
nV++;
}
}
double norm = 1.0 / nV;
for (int i = 0; i < numParams; i++)
{
center[i] *= norm;
}
}
/** Minimizes the target function by variation of the simplex.
* Note that one call to this function never does more than 0.4*maxIter iterations.
* @return index of the best value in simp
*/
private int minimize(List <double[]> simp)
{
int[] worstNextBestArray = new int[3]; // used to pass these indices from 'order' function
double[] center = new double[numParams + 1 + numExtraArrayElements]; // center of all vertices except worst
double[] reflected = new double[numParams + 1 + numExtraArrayElements]; // the 1st new vertex to try
double[] secondTry = new double[numParams + 1 + numExtraArrayElements]; // expanded or contracted vertex
order(simp, worstNextBestArray);
int worst = worstNextBestArray[WORST];
int nextWorst = worstNextBestArray[NEXT_WORST];
int best = worstNextBestArray[BEST];
//showSimplex(simp, "before minimization, value="+value(simp[best]));
//String operation="ini";
int thisNumIter = 0;
while (true)
{
totalNumIter++; // global count over all threads
thisNumIter++; // local count for this minimize call
// THE MINIMIZAION ALGORITHM IS HERE
{
getCenter(simp, worst, center); // centroid of vertices except worst
// Reflect worst vertex through centriod of not-worst
getVertexAndEvaluate(center, simp[worst], -C_REFLECTION, reflected);
if (value(reflected) <= value(simp[best])) // if it's better than the best...
// try expanding it
{
getVertexAndEvaluate(center, simp[worst], -C_EXPANSION, secondTry);
if (value(secondTry) <= value(reflected))
{
copyVertex(secondTry, simp[worst]); // if expanded is better than reflected, keep it
//operation="expa";
goto iteration;
}
}
if (value(reflected) < value(simp[nextWorst]))
{
copyVertex(reflected, simp[worst]); // keep reflected if better than 2nd worst
//operation="refl";
goto iteration;
}
else if (value(reflected) < value(simp[worst]))
{
// try outer contraction
getVertexAndEvaluate(center, simp[worst], -C_CONTRACTION, secondTry);
if (value(secondTry) <= value(reflected))
{
copyVertex(secondTry, simp[worst]); // keep outer contraction
//operation="outC";
goto iteration;
}
}
else if (value(reflected) > value(simp[worst]) || double.IsNaN(value(reflected)))
{
// else inner contraction
getVertexAndEvaluate(center, simp[worst], C_CONTRACTION, secondTry);
if (value(secondTry) < value(simp[worst]))
{
copyVertex(secondTry, simp[worst]); // keep contracted if better than 2nd worst
//operation="innC";
goto iteration;
}
}
// if everything else has failed, contract simplex in on best
shrinkSimplexAndEvaluate(simp, best);
//operation="shri";
goto iteration;
} // iteration:
iteration:
bool checkParamResolution = // if new 'worst' is not close to 'best', don't check any further
paramResolutions != null && belowResolutionLimit(simp[worst], simp[best]);
order(simp, worstNextBestArray);
worst = worstNextBestArray[WORST];
nextWorst = worstNextBestArray[NEXT_WORST];
best = worstNextBestArray[BEST];
if (checkParamResolution)
{
if (belowResolutionLimit(simp, best)) // check whether all parameters are within the resolution limit
{
break;
}
}
if (belowErrorLimit(value(simp[best]), value(simp[worst]), 4.0)) // make sure we are at the minimum:
{
getCenter(simp, -1, secondTry); // check center of the simplex
evaluate(secondTry);
if (value(secondTry) < value(simp[best]))
{
copyVertex(secondTry, simp[best]); // better than best: keep
}
}
if (belowErrorLimit(value(simp[best]), value(simp[worst]), 4.0)) // no large spread of values
{
break; // looks like we are at the minimum
}
if (totalNumIter > maxIter || thisNumIter > 4 * (maxIter / 10))
{
status = MAX_ITERATIONS_EXCEEDED;
}
if (status != SUCCESS)
{
break;
}
if ((ijStatusString != null || checkEscape) && totalNumIter > nextIterationForStatus)
{
long time = Java.SystemCurrentTimeMillis();
nextIterationForStatus = totalNumIter + (int)(totalNumIter * 500L / (time - startTime + 1)); //next display 0.5 sec later
}
}
//showSimplex(simp, "after "+totalNumIter+" iterations: value="+value(simp[best]));
return(best);
}
