use of org.apache.commons.math3.stat.descriptive.rank.Max in project GDSC-SMLM by aherbert.
the class ErfTest method erfxxHasLowError.
private void erfxxHasLowError(BaseErf erf, double expected) {
RandomGenerator rg = new Well19937c(30051977);
int range = 3;
double max = 0;
for (int xi = -range; xi <= range; xi++) {
for (int xi2 = -range; xi2 <= range; xi2++) {
for (int i = 0; i < 5; i++) {
double x = xi + rg.nextDouble();
for (int j = 0; j < 5; j++) {
double x2 = xi2 + rg.nextDouble();
double o = erf.erf(x, x2);
double e = org.apache.commons.math3.special.Erf.erf(x, x2);
double error = Math.abs(o - e);
if (max < error)
max = error;
//System.out.printf("x=%f, x2=%f, e=%f, o=%f, error=%f\n", x, x2, e, o, error);
Assert.assertTrue(error < expected);
}
}
}
}
System.out.printf("erfxx %s max error = %g\n", erf.name, max);
}
use of org.apache.commons.math3.stat.descriptive.rank.Max in project lucene-solr by apache.
the class DescribeEvaluator method evaluate.
public Tuple evaluate(Tuple tuple) throws IOException {
if (subEvaluators.size() != 1) {
throw new IOException("describe expects 1 column as a parameters");
}
StreamEvaluator colEval = subEvaluators.get(0);
List<Number> numbers = (List<Number>) colEval.evaluate(tuple);
DescriptiveStatistics descriptiveStatistics = new DescriptiveStatistics();
for (Number n : numbers) {
descriptiveStatistics.addValue(n.doubleValue());
}
Map map = new HashMap();
map.put("max", descriptiveStatistics.getMax());
map.put("mean", descriptiveStatistics.getMean());
map.put("min", descriptiveStatistics.getMin());
map.put("stdev", descriptiveStatistics.getStandardDeviation());
map.put("sum", descriptiveStatistics.getSum());
map.put("N", descriptiveStatistics.getN());
map.put("var", descriptiveStatistics.getVariance());
map.put("kurtosis", descriptiveStatistics.getKurtosis());
map.put("skewness", descriptiveStatistics.getSkewness());
map.put("popVar", descriptiveStatistics.getPopulationVariance());
map.put("geometricMean", descriptiveStatistics.getGeometricMean());
map.put("sumsq", descriptiveStatistics.getSumsq());
return new Tuple(map);
}
use of org.apache.commons.math3.stat.descriptive.rank.Max in project GDSC-SMLM by aherbert.
the class PCPALMMolecules method performDistanceAnalysis.
private void performDistanceAnalysis(double[][] intraHist, int p99) {
// We want to know the fraction of distances between molecules at the 99th percentile
// that are intra- rather than inter-molecule.
// Do single linkage clustering of closest pair at this distance and count the number of
// links that are inter and intra.
// Convert molecules for clustering
ArrayList<ClusterPoint> points = new ArrayList<ClusterPoint>(molecules.size());
for (Molecule m : molecules) // Precision was used to store the molecule ID
points.add(ClusterPoint.newClusterPoint((int) m.precision, m.x, m.y, m.photons));
ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), ClusteringAlgorithm.PARTICLE_SINGLE_LINKAGE, new IJTrackProgress());
IJ.showStatus("Clustering to check inter-molecule distances");
engine.setTrackJoins(true);
ArrayList<Cluster> clusters = engine.findClusters(points, intraHist[0][p99]);
IJ.showStatus("");
if (clusters != null) {
double[] intraIdDistances = engine.getIntraIdDistances();
double[] interIdDistances = engine.getInterIdDistances();
int all = interIdDistances.length + intraIdDistances.length;
log(" * Fraction of inter-molecule particle linkage @ %s nm = %s %%", Utils.rounded(intraHist[0][p99], 4), (all > 0) ? Utils.rounded(100.0 * interIdDistances.length / all, 4) : "0");
// Show a double cumulative histogram plot
double[][] intraIdHist = Maths.cumulativeHistogram(intraIdDistances, false);
double[][] interIdHist = Maths.cumulativeHistogram(interIdDistances, false);
// Plot
String title = TITLE + " molecule linkage distance";
Plot2 plot = new Plot2(title, "Distance", "Frequency", intraIdHist[0], intraIdHist[1]);
double max = (intraIdHist[1].length > 0) ? intraIdHist[1][intraIdHist[1].length - 1] : 0;
if (interIdHist[1].length > 0)
max = FastMath.max(max, interIdHist[1][interIdHist[1].length - 1]);
plot.setLimits(0, intraIdHist[0][intraIdHist[0].length - 1], 0, max);
plot.setColor(Color.blue);
plot.addPoints(interIdHist[0], interIdHist[1], Plot2.LINE);
plot.setColor(Color.black);
Utils.display(title, plot);
} else {
log("Aborted clustering to check inter-molecule distances");
}
}
use of org.apache.commons.math3.stat.descriptive.rank.Max in project GDSC-SMLM by aherbert.
the class PCPALMMolecules method runSimulation.
private void runSimulation(boolean resultsAvailable) {
if (resultsAvailable && !showSimulationDialog())
return;
startLog();
log("Simulation parameters");
if (blinkingDistribution == 3) {
log(" - Clusters = %d", nMolecules);
log(" - Simulation size = %s um", Utils.rounded(simulationSize, 4));
log(" - Molecules/cluster = %s", Utils.rounded(blinkingRate, 4));
log(" - Blinking distribution = %s", BLINKING_DISTRIBUTION[blinkingDistribution]);
log(" - p-Value = %s", Utils.rounded(p, 4));
} else {
log(" - Molecules = %d", nMolecules);
log(" - Simulation size = %s um", Utils.rounded(simulationSize, 4));
log(" - Blinking rate = %s", Utils.rounded(blinkingRate, 4));
log(" - Blinking distribution = %s", BLINKING_DISTRIBUTION[blinkingDistribution]);
}
log(" - Average precision = %s nm", Utils.rounded(sigmaS, 4));
log(" - Clusters simulation = " + CLUSTER_SIMULATION[clusterSimulation]);
if (clusterSimulation > 0) {
log(" - Cluster number = %s +/- %s", Utils.rounded(clusterNumber, 4), Utils.rounded(clusterNumberSD, 4));
log(" - Cluster radius = %s nm", Utils.rounded(clusterRadius, 4));
}
final double nmPerPixel = 100;
double width = simulationSize * 1000.0;
// Allow a border of 3 x sigma for +/- precision
//if (blinkingRate > 1)
width -= 3 * sigmaS;
RandomGenerator randomGenerator = new Well19937c(System.currentTimeMillis() + System.identityHashCode(this));
RandomDataGenerator dataGenerator = new RandomDataGenerator(randomGenerator);
UniformDistribution dist = new UniformDistribution(null, new double[] { width, width, 0 }, randomGenerator.nextInt());
molecules = new ArrayList<Molecule>(nMolecules);
// Create some dummy results since the calibration is required for later analysis
results = new MemoryPeakResults();
results.setCalibration(new gdsc.smlm.results.Calibration(nmPerPixel, 1, 100));
results.setSource(new NullSource("Molecule Simulation"));
results.begin();
int count = 0;
// Generate a sequence of coordinates
ArrayList<double[]> xyz = new ArrayList<double[]>((int) (nMolecules * 1.1));
Statistics statsRadius = new Statistics();
Statistics statsSize = new Statistics();
String maskTitle = TITLE + " Cluster Mask";
ByteProcessor bp = null;
double maskScale = 0;
if (clusterSimulation > 0) {
// Simulate clusters.
// Note: In the Veatch et al. paper (Plos 1, e31457) correlation functions are built using circles
// with small radii of 4-8 Arbitrary Units (AU) or large radii of 10-30 AU. A fluctuations model is
// created at T = 1.075 Tc. It is not clear exactly how the particles are distributed.
// It may be that a mask is created first using the model. The particles are placed on the mask using
// a specified density. This simulation produces a figure to show either a damped cosine function
// (circles) or an exponential (fluctuations). The number of particles in each circle may be randomly
// determined just by density. The figure does not discuss the derivation of the cluster size
// statistic.
//
// If this plugin simulation is run with a uniform distribution and blinking rate of 1 then the damped
// cosine function is reproduced. The curve crosses g(r)=1 at a value equivalent to the average
// distance to the centre-of-mass of each drawn cluster, not the input cluster radius parameter (which
// is a hard upper limit on the distance to centre).
final int maskSize = lowResolutionImageSize;
int[] mask = null;
// scale is in nm/pixel
maskScale = width / maskSize;
ArrayList<double[]> clusterCentres = new ArrayList<double[]>();
int totalSteps = 1 + (int) Math.ceil(nMolecules / clusterNumber);
if (clusterSimulation == 2 || clusterSimulation == 3) {
// Clusters are non-overlapping circles
// Ensure the circles do not overlap by using an exclusion mask that accumulates
// out-of-bounds pixels by drawing the last cluster (plus some border) on an image. When no
// more pixels are available then stop generating molecules.
// This is done by cumulatively filling a mask and using the MaskDistribution to select
// a new point. This may be slow but it works.
// TODO - Allow clusters of different sizes...
mask = new int[maskSize * maskSize];
Arrays.fill(mask, 255);
MaskDistribution maskDistribution = new MaskDistribution(mask, maskSize, maskSize, 0, maskScale, maskScale, randomGenerator);
double[] centre;
IJ.showStatus("Computing clusters mask");
int roiRadius = (int) Math.round((clusterRadius * 2) / maskScale);
if (clusterSimulation == 3) {
// Generate a mask of circles then sample from that.
// If we want to fill the mask completely then adjust the total steps to be the number of
// circles that can fit inside the mask.
totalSteps = (int) (maskSize * maskSize / (Math.PI * Math.pow(clusterRadius / maskScale, 2)));
}
while ((centre = maskDistribution.next()) != null && clusterCentres.size() < totalSteps) {
IJ.showProgress(clusterCentres.size(), totalSteps);
// The mask returns the coordinates with the centre of the image at 0,0
centre[0] += width / 2;
centre[1] += width / 2;
clusterCentres.add(centre);
// Fill in the mask around the centre to exclude any more circles that could overlap
double cx = centre[0] / maskScale;
double cy = centre[1] / maskScale;
fillMask(mask, maskSize, (int) cx, (int) cy, roiRadius, 0);
//Utils.display("Mask", new ColorProcessor(maskSize, maskSize, mask));
try {
maskDistribution = new MaskDistribution(mask, maskSize, maskSize, 0, maskScale, maskScale, randomGenerator);
} catch (IllegalArgumentException e) {
// This can happen when there are no more non-zero pixels
log("WARNING: No more room for clusters on the mask area (created %d of estimated %d)", clusterCentres.size(), totalSteps);
break;
}
}
IJ.showProgress(1);
IJ.showStatus("");
} else {
// Pick centres randomly from the distribution
while (clusterCentres.size() < totalSteps) clusterCentres.add(dist.next());
}
if (showClusterMask || clusterSimulation == 3) {
// Show the mask for the clusters
if (mask == null)
mask = new int[maskSize * maskSize];
else
Arrays.fill(mask, 0);
int roiRadius = (int) Math.round((clusterRadius) / maskScale);
for (double[] c : clusterCentres) {
double cx = c[0] / maskScale;
double cy = c[1] / maskScale;
fillMask(mask, maskSize, (int) cx, (int) cy, roiRadius, 1);
}
if (clusterSimulation == 3) {
// We have the mask. Now pick points at random from the mask.
MaskDistribution maskDistribution = new MaskDistribution(mask, maskSize, maskSize, 0, maskScale, maskScale, randomGenerator);
// Allocate each molecule position to a parent circle so defining clusters.
int[][] clusters = new int[clusterCentres.size()][];
int[] clusterSize = new int[clusters.length];
for (int i = 0; i < nMolecules; i++) {
double[] centre = maskDistribution.next();
// The mask returns the coordinates with the centre of the image at 0,0
centre[0] += width / 2;
centre[1] += width / 2;
xyz.add(centre);
// Output statistics on cluster size and number.
// TODO - Finding the closest cluster could be done better than an all-vs-all comparison
double max = distance2(centre, clusterCentres.get(0));
int cluster = 0;
for (int j = 1; j < clusterCentres.size(); j++) {
double d2 = distance2(centre, clusterCentres.get(j));
if (d2 < max) {
max = d2;
cluster = j;
}
}
// Assign point i to cluster
centre[2] = cluster;
if (clusterSize[cluster] == 0) {
clusters[cluster] = new int[10];
}
if (clusters[cluster].length <= clusterSize[cluster]) {
clusters[cluster] = Arrays.copyOf(clusters[cluster], (int) (clusters[cluster].length * 1.5));
}
clusters[cluster][clusterSize[cluster]++] = i;
}
// Generate real cluster size statistics
for (int j = 0; j < clusterSize.length; j++) {
final int size = clusterSize[j];
if (size == 0)
continue;
statsSize.add(size);
if (size == 1) {
statsRadius.add(0);
continue;
}
// Find centre of cluster and add the distance to each point
double[] com = new double[2];
for (int n = 0; n < size; n++) {
double[] xy = xyz.get(clusters[j][n]);
for (int k = 0; k < 2; k++) com[k] += xy[k];
}
for (int k = 0; k < 2; k++) com[k] /= size;
for (int n = 0; n < size; n++) {
double dx = xyz.get(clusters[j][n])[0] - com[0];
double dy = xyz.get(clusters[j][n])[1] - com[1];
statsRadius.add(Math.sqrt(dx * dx + dy * dy));
}
}
}
if (showClusterMask) {
bp = new ByteProcessor(maskSize, maskSize);
for (int i = 0; i < mask.length; i++) if (mask[i] != 0)
bp.set(i, 128);
Utils.display(maskTitle, bp);
}
}
// Use the simulated cluster centres to create clusters of the desired size
if (clusterSimulation == 1 || clusterSimulation == 2) {
for (double[] clusterCentre : clusterCentres) {
int clusterN = (int) Math.round((clusterNumberSD > 0) ? dataGenerator.nextGaussian(clusterNumber, clusterNumberSD) : clusterNumber);
if (clusterN < 1)
continue;
//double[] clusterCentre = dist.next();
if (clusterN == 1) {
// No need for a cluster around a point
xyz.add(clusterCentre);
statsRadius.add(0);
statsSize.add(1);
} else {
// Generate N random points within a circle of the chosen cluster radius.
// Locate the centre-of-mass and the average distance to the centre.
double[] com = new double[3];
int j = 0;
while (j < clusterN) {
// Generate a random point within a circle uniformly
// http://stackoverflow.com/questions/5837572/generate-a-random-point-within-a-circle-uniformly
double t = 2.0 * Math.PI * randomGenerator.nextDouble();
double u = randomGenerator.nextDouble() + randomGenerator.nextDouble();
double r = clusterRadius * ((u > 1) ? 2 - u : u);
double x = r * Math.cos(t);
double y = r * Math.sin(t);
double[] xy = new double[] { clusterCentre[0] + x, clusterCentre[1] + y };
xyz.add(xy);
for (int k = 0; k < 2; k++) com[k] += xy[k];
j++;
}
// Add the distance of the points from the centre of the cluster.
// Note this does not account for the movement due to precision.
statsSize.add(j);
if (j == 1) {
statsRadius.add(0);
} else {
for (int k = 0; k < 2; k++) com[k] /= j;
while (j > 0) {
double dx = xyz.get(xyz.size() - j)[0] - com[0];
double dy = xyz.get(xyz.size() - j)[1] - com[1];
statsRadius.add(Math.sqrt(dx * dx + dy * dy));
j--;
}
}
}
}
}
} else {
// Random distribution
for (int i = 0; i < nMolecules; i++) xyz.add(dist.next());
}
// The Gaussian sigma should be applied so the overall distance from the centre
// ( sqrt(x^2+y^2) ) has a standard deviation of sigmaS?
final double sigma1D = sigmaS / Math.sqrt(2);
// Show optional histograms
StoredDataStatistics intraDistances = null;
StoredData blinks = null;
if (showHistograms) {
int capacity = (int) (xyz.size() * blinkingRate);
intraDistances = new StoredDataStatistics(capacity);
blinks = new StoredData(capacity);
}
Statistics statsSigma = new Statistics();
for (int i = 0; i < xyz.size(); i++) {
int nOccurrences = getBlinks(dataGenerator, blinkingRate);
if (showHistograms)
blinks.add(nOccurrences);
final int size = molecules.size();
// Get coordinates in nm
final double[] moleculeXyz = xyz.get(i);
if (bp != null && nOccurrences > 0) {
bp.putPixel((int) Math.round(moleculeXyz[0] / maskScale), (int) Math.round(moleculeXyz[1] / maskScale), 255);
}
while (nOccurrences-- > 0) {
final double[] localisationXy = Arrays.copyOf(moleculeXyz, 2);
// Add random precision
if (sigma1D > 0) {
final double dx = dataGenerator.nextGaussian(0, sigma1D);
final double dy = dataGenerator.nextGaussian(0, sigma1D);
localisationXy[0] += dx;
localisationXy[1] += dy;
if (!dist.isWithinXY(localisationXy))
continue;
// Calculate mean-squared displacement
statsSigma.add(dx * dx + dy * dy);
}
final double x = localisationXy[0];
final double y = localisationXy[1];
molecules.add(new Molecule(x, y, i, 1));
// Store in pixels
float[] params = new float[7];
params[Gaussian2DFunction.X_POSITION] = (float) (x / nmPerPixel);
params[Gaussian2DFunction.Y_POSITION] = (float) (y / nmPerPixel);
results.addf(i + 1, (int) x, (int) y, 0, 0, 0, params, null);
}
if (molecules.size() > size) {
count++;
if (showHistograms) {
int newCount = molecules.size() - size;
if (newCount == 1) {
//intraDistances.add(0);
continue;
}
// Get the distance matrix between these molecules
double[][] matrix = new double[newCount][newCount];
for (int ii = size, x = 0; ii < molecules.size(); ii++, x++) {
for (int jj = size + 1, y = 1; jj < molecules.size(); jj++, y++) {
final double d2 = molecules.get(ii).distance2(molecules.get(jj));
matrix[x][y] = matrix[y][x] = d2;
}
}
// Get the maximum distance for particle linkage clustering of this molecule
double max = 0;
for (int x = 0; x < newCount; x++) {
// Compare to all-other molecules and get the minimum distance
// needed to join at least one
double linkDistance = Double.POSITIVE_INFINITY;
for (int y = 0; y < newCount; y++) {
if (x == y)
continue;
if (matrix[x][y] < linkDistance)
linkDistance = matrix[x][y];
}
// Check if this is larger
if (max < linkDistance)
max = linkDistance;
}
intraDistances.add(Math.sqrt(max));
}
}
}
results.end();
if (bp != null)
Utils.display(maskTitle, bp);
// Used for debugging
//System.out.printf(" * Molecules = %d (%d activated)\n", xyz.size(), count);
//if (clusterSimulation > 0)
// System.out.printf(" * Cluster number = %s +/- %s. Radius = %s +/- %s\n",
// Utils.rounded(statsSize.getMean(), 4), Utils.rounded(statsSize.getStandardDeviation(), 4),
// Utils.rounded(statsRadius.getMean(), 4), Utils.rounded(statsRadius.getStandardDeviation(), 4));
log("Simulation results");
log(" * Molecules = %d (%d activated)", xyz.size(), count);
log(" * Blinking rate = %s", Utils.rounded((double) molecules.size() / xyz.size(), 4));
log(" * Precision (Mean-displacement) = %s nm", (statsSigma.getN() > 0) ? Utils.rounded(Math.sqrt(statsSigma.getMean()), 4) : "0");
if (showHistograms) {
if (intraDistances.getN() == 0) {
log(" * Mean Intra-Molecule particle linkage distance = 0 nm");
log(" * Fraction of inter-molecule particle linkage @ 0 nm = 0 %%");
} else {
plot(blinks, "Blinks/Molecule", true);
double[][] intraHist = plot(intraDistances, "Intra-molecule particle linkage distance", false);
// Determine 95th and 99th percentile
int p99 = intraHist[0].length - 1;
double limit1 = 0.99 * intraHist[1][p99];
double limit2 = 0.95 * intraHist[1][p99];
while (intraHist[1][p99] > limit1 && p99 > 0) p99--;
int p95 = p99;
while (intraHist[1][p95] > limit2 && p95 > 0) p95--;
log(" * Mean Intra-Molecule particle linkage distance = %s nm (95%% = %s, 99%% = %s, 100%% = %s)", Utils.rounded(intraDistances.getMean(), 4), Utils.rounded(intraHist[0][p95], 4), Utils.rounded(intraHist[0][p99], 4), Utils.rounded(intraHist[0][intraHist[0].length - 1], 4));
if (distanceAnalysis) {
performDistanceAnalysis(intraHist, p99);
}
}
}
if (clusterSimulation > 0) {
log(" * Cluster number = %s +/- %s", Utils.rounded(statsSize.getMean(), 4), Utils.rounded(statsSize.getStandardDeviation(), 4));
log(" * Cluster radius = %s +/- %s nm (mean distance to centre-of-mass)", Utils.rounded(statsRadius.getMean(), 4), Utils.rounded(statsRadius.getStandardDeviation(), 4));
}
}
use of org.apache.commons.math3.stat.descriptive.rank.Max in project uPortal by Jasig.
the class JpaStatisticalSummaryTest method testSummaryStatisticsJson.
// @Test
// public void testJpaStatisticalSummary() {
// final long id = this.executeInTransaction(new Callable<Long>() {
// @Override
// public Long call() throws Exception {
// final JpaStatisticalSummary jpaStatisticalSummary = new
// JpaStatisticalSummary();
//
// final Random r = new Random(0);
// for (int i = 0; i < 10; i++) {
// final int nextInt = r.nextInt(100000000);
// jpaStatisticalSummary.addValue(nextInt);
// }
//
// getEntityManager().persist(jpaStatisticalSummary);
//
// System.out.println(jpaStatisticalSummary);
//
// return jpaStatisticalSummary.getStatSummaryId();
// }
// });
//
// System.out.println(id);
//
// this.executeInTransaction(new CallableWithoutResult() {
// @Override
// protected void callWithoutResult() {
// final JpaStatisticalSummary jpaStatisticalSummary =
// getEntityManager().find(JpaStatisticalSummary.class, id);
//
// System.out.println(jpaStatisticalSummary);
// }
// });
// }
@Ignore
@Test
public void testSummaryStatisticsJson() throws Exception {
final SecondMoment secondMoment = new SecondMoment();
final Sum sum = new Sum();
final SumOfSquares sumsq = new SumOfSquares();
final Min min = new Min();
final Max max = new Max();
final SumOfLogs sumLog = new SumOfLogs();
final Random r = new Random(0);
for (int i = 0; i < 10; i++) {
final int nextInt = r.nextInt(100000000);
secondMoment.increment(nextInt);
sum.increment(nextInt);
sumsq.increment(nextInt);
min.increment(nextInt);
max.increment(nextInt);
sumLog.increment(nextInt);
}
testStorelessUnivariateStatistic(secondMoment, 7.513432791665536E15);
testStorelessUnivariateStatistic(sum, 6.01312177E8);
testStorelessUnivariateStatistic(sumsq, 4.3671066212513456E16);
testStorelessUnivariateStatistic(min, 2116447.0);
testStorelessUnivariateStatistic(max, 8.5505948E7);
testStorelessUnivariateStatistic(sumLog, 175.91713800250577);
}
Aggregations