private List<Vector2D> makeBlobs(int centers, double clusterStd, double min, double max) {
NormalDistribution dist = new NormalDistribution(random, 0.0, clusterStd, 1e-9);
double range = max - min;
Vector2D[] centerPoints = new Vector2D[centers];
for (int i = 0; i < centers; i++) {
centerPoints[i] =
new Vector2D(random.nextDouble() * range + min, random.nextDouble() * range + min);
}
int[] nSamplesPerCenter = new int[centers];
int count = samples / centers;
Arrays.fill(nSamplesPerCenter, count);
for (int i = 0; i < samples % centers; i++) {
nSamplesPerCenter[i]++;
}
List<Vector2D> points = new ArrayList<>();
for (int i = 0; i < centers; i++) {
for (int j = 0; j < nSamplesPerCenter[i]; j++) {
points.add(new Vector2D(dist.sample(), dist.sample()).add(centerPoints[i]));
}
}
return points;
}
@Override
protected OperationData process(IDataset input, IMonitor monitor) {
double theta = 0;
try {
theta = ScanMetadata.getTheta(input);
} catch (Exception e) {
}
NormalDistribution beamfootprint =
new NormalDistribution(
0, (1e-3 * model.getBeamHeight() / 2 * Math.sqrt(2 * Math.log(2) - 0.5)));
double areaCorrection =
2
* (beamfootprint.cumulativeProbability(
(model.getFootprint()
* Math.sin((theta + model.getAngularFudgeFactor()) * Math.PI / 180))));
Dataset output = DatasetUtils.cast(input, Dataset.FLOAT64);
output = Maths.multiply(input, areaCorrection);
Dataset outputSum =
DatasetFactory.createFromObject((DatasetUtils.cast(output, Dataset.FLOAT64)).sum());
return new OperationData(output, outputSum);
}
@Test
/** Test of integrator for the sine function. */
public void testSinFunction() {
UnivariateFunction f = new Gaussian(10, 2);
UnivariateIntegrator integrator = new SimpsonIntegrator();
double a, b, expected, tolerance, result;
a = 8;
b = 12;
expected = 0.68269;
tolerance = 0.00001;
tolerance = Math.abs(expected * integrator.getRelativeAccuracy());
result = integrator.integrate(MAX_EVAL, f, a, b);
assertEquals(expected, result, tolerance);
log.info(
"Result: "
+ result
+ ", tolerance: "
+ tolerance
+ " - Relative accuracy: "
+ integrator.getRelativeAccuracy()
+ " - Absolute accuracy: "
+ integrator.getAbsoluteAccuracy()
+ " - Iterations: "
+ integrator.getIterations());
NormalDistribution distribution = new NormalDistribution(10, 2);
result = distribution.cumulativeProbability(a, b);
log.info("Distribution result: " + result);
}
/**
* As described by Bernt Arne Ødegaard in Financial Numerical Recipes in C++.
*
* <p>Returns P(X < a, Y < b) where X, Y are gaussian random variables N(0, 1) of the bivariate
* normal distribution with correlation c in [-1, 1] between X and Y.
*/
public static double cdf(double a, double b, double c) {
if (a == Double.NaN || b == Double.NaN || c == Double.NaN) {
throw new IllegalArgumentException("Arguments must be a number.");
}
if (a == Double.NaN) {
System.out.println("");
}
a = handleInfinity(a);
b = handleInfinity(b);
c = handleInfinity(c);
if (a == Double.NaN) {
System.out.println("");
}
if (a <= 0 && b <= 0 && c <= 0) {
final double aprime = a / FastMath.sqrt(2d * (1d - c * c));
final double bprime = b / FastMath.sqrt(2d * (1d - c * c));
double sum = 0;
for (int i = 0; i < A.length; i++) {
for (int j = 0; j < A.length; j++) {
sum += A[i] * A[j] * f(B[i], B[j], aprime, bprime, c);
}
}
sum *= FastMath.sqrt(1d - c * c) / FastMath.PI;
return sum;
}
// a or b may be too big and their multiplication may result in NaN.
if (c * a * b
<= 0) { // c is smaller (between [-1, 1]) and will help to avoid NaNs. So we multiply c
// first.
if ((a <= 0) && (b >= 0) && (c >= 0)) {
return normal.cumulativeProbability(a) - cdf(a, -b, -c);
} else if ((a >= 0) && (b <= 0) && (c >= 0)) {
return normal.cumulativeProbability(b) - cdf(-a, b, -c);
} else if ((a >= 0) && (b >= 0) && (c <= 0)) {
return normal.cumulativeProbability(a)
+ normal.cumulativeProbability(b)
- 1
+ cdf(-a, -b, c);
}
} else if (c * a * b >= 0) {
final double denum = FastMath.sqrt(a * a - 2d * c * a * b + b * b);
final double rho1 = ((c * a - b) * FastMath.signum(a)) / denum;
final double rho2 = ((c * b - a) * FastMath.signum(b)) / denum;
final double delta = (1d - FastMath.signum(a) * FastMath.signum(b)) / 4d;
return cdf(a, 0, rho1) + cdf(b, 0, rho2) - delta;
}
throw new RuntimeException(
"Should never get here. Values of [a; b ; c] = [" + a + "; " + b + "; " + c + "].");
}
private static SparseRealMatrix initializeMatrix(SparseRealMatrix matrix, double sigma) {
NormalDistribution normRandom = new NormalDistribution(0.0, sigma);
int r = matrix.getRowDimension();
int c = matrix.getColumnDimension();
for (int i = 0; i < r; i++) {
for (int j = 0; j < c; j++) {
double x = normRandom.sample();
matrix.setEntry(i, j, x);
}
}
return matrix;
}
// ======== per-timeslot activities ========
@Override
public void step() {
// check for end-of-shift
Shift newShift = shiftSchedule[indexOfShift(getNowInstant())];
if (newShift != currentShift) {
log.info(getName() + " start of shift");
// Take all batteries out of service
double totalEnergy = getEnergyCharging() + getEnergyInUse();
setEnergyCharging(getEnergyCharging() + getEnergyInUse());
setCapacityInUse(0.0);
setEnergyInUse(0.0);
// Put the strongest batteries in trucks for the next shift
if (null != newShift) {
setCapacityInUse(newShift.getTrucks() * batteryCapacity);
setEnergyInUse(Math.min(getCapacityInUse(), totalEnergy));
setEnergyCharging(totalEnergy - getEnergyInUse());
}
log.info(
getName()
+ ": new shift cInUse "
+ capacityInUse
+ ", eInUse "
+ energyInUse
+ ", eCharging "
+ energyCharging);
currentShift = newShift;
}
// discharge batteries on active trucks
if (null != currentShift) {
double usage = Math.max(0.0, normal.sample() * truckStd + truckKW * currentShift.getTrucks());
double deficit = usage - getEnergyInUse();
log.debug(getName() + ": trucks use " + usage + " kWh");
if (deficit > 0.0) {
log.warn(getName() + ": trucks use more energy than available by " + deficit + " kWh");
addEnergyInUse(deficit);
addEnergyCharging(-deficit);
}
addEnergyInUse(-usage);
}
// use energy on chargers, accounting for regulation
double regulation = getSubscription().getRegulation();
log.info(getName() + ": regulation " + regulation);
double energyUsed = useEnergy(regulation);
// Record energy used
getSubscription().usePower(energyUsed);
log.info(
getName()
+ " cInUse "
+ capacityInUse
+ ", eInUse "
+ energyInUse
+ ", eCharging "
+ energyCharging);
}
private void initial() {
NormalDistribution nd = new NormalDistribution();
String[] seqList = this.sequence.split(";");
for (String seq : seqList) {
BaseIsotopomer bIso = new BaseIsotopomer(seq, this.isotopomerWidth);
TIntDoubleMap chargeScaleMap = new TIntDoubleHashMap();
int centralCharge = bIso.getCentralChargeState();
int totalChargeState = (bIso.getMaxChargeState() - centralCharge) * 2;
double step = 6.0 / totalChargeState;
// calculate right side of the central charge state (inclusive) to 10+ charge
double x = 0.0;
for (int i = centralCharge; i > 8; i--) {
double factor = nd.density(x);
x += step;
chargeScaleMap.put(i, factor);
}
// calculate left side of the central charge state (exclusive) to max charge
x = step;
for (int i = centralCharge + 1; i <= bIso.getMaxChargeState(); i++) {
double factor = nd.density(x);
x += step;
chargeScaleMap.put(i, factor);
}
// build list of Isotopomer
for (int charge : chargeScaleMap.keys()) {
ChargedIsotopomer cIso = new ChargedIsotopomer(bIso, charge);
isotopomerList.add(cIso);
TDoubleDoubleMap tempPeakMap = cIso.getScaledPeakMap(chargeScaleMap.get(charge));
for (double mz : tempPeakMap.keys()) {
double intensity = peakMap.get(mz);
if (intensity == peakMap.getNoEntryValue()) {
peakMap.put(mz, tempPeakMap.get(mz));
} else {
peakMap.put(mz, intensity + tempPeakMap.get(mz));
}
}
}
}
}
// Model "a" with a normal distribution, and test whether cdf(mean(b)) > pvalue
public boolean significantIncrease(List<Double> a, List<Double> b, double pvalue) {
double meanA = mean(a);
double sd = 0;
for (Double val : a) {
sd += (val - meanA) * (val - meanA);
}
sd = Math.sqrt(sd / (a.size() - 1));
if (sd <= 0) {
return true;
}
double meanB = mean(b);
NormalDistribution dist = new NormalDistribution(meanA, sd);
double p = dist.cumulativeProbability(meanB);
boolean significant = (p > pvalue);
System.out.println("p-value=" + p + ", " + (significant ? "increase" : "no increase"));
return significant;
}
/** {@inheritDoc} */
public ConfidenceInterval createInterval(
int numberOfTrials, int numberOfSuccesses, double confidenceLevel) {
IntervalUtils.checkParameters(numberOfTrials, numberOfSuccesses, confidenceLevel);
final double alpha = (1.0 - confidenceLevel) / 2;
final NormalDistribution normalDistribution = new NormalDistribution();
final double z = normalDistribution.inverseCumulativeProbability(1 - alpha);
final double zSquared = FastMath.pow(z, 2);
final double mean = (double) numberOfSuccesses / (double) numberOfTrials;
final double factor = 1.0 / (1 + (1.0 / numberOfTrials) * zSquared);
final double modifiedSuccessRatio = mean + (1.0 / (2 * numberOfTrials)) * zSquared;
final double difference =
z
* FastMath.sqrt(
1.0 / numberOfTrials * mean * (1 - mean)
+ (1.0 / (4 * FastMath.pow(numberOfTrials, 2)) * zSquared));
final double lowerBound = factor * (modifiedSuccessRatio - difference);
final double upperBound = factor * (modifiedSuccessRatio + difference);
return new ConfidenceInterval(lowerBound, upperBound, confidenceLevel);
}
// Gets a new random-number opSeed just in case we don't already have one.
// Useful for mock-based testing.
private void ensureSeeds() {
if (null == opSeed) {
opSeed =
service
.getRandomSeedRepo()
.getRandomSeed(LiftTruck.class.getName() + "-" + name, 0, "model");
evalSeed =
service
.getRandomSeedRepo()
.getRandomSeed(LiftTruck.class.getName() + "-" + name, 0, "eval");
normal = new NormalDistribution(0.0, 1.0);
normal.reseedRandomGenerator(opSeed.nextLong());
}
}
public static double normalInverseCDF(double pValue, double mean, double sigma) {
NormalDistribution normDist = new NormalDistribution(mean, sigma);
double ret = normDist.inverseCumulativeProbability(pValue);
return ret;
}
public static double normalCDF(double x, double mean, double sigma) {
NormalDistribution normDist = new NormalDistribution(mean, sigma);
double ret = normDist.cumulativeProbability(x);
return ret;
}
private Vector2D generateNoiseVector(NormalDistribution distribution) {
return new Vector2D(distribution.sample(), distribution.sample());
}
