use of gdsc.core.utils.StoredDataStatistics in project GDSC-SMLM by aherbert.
the class TraceDiffusion method summarise.
private void summarise(Trace[] traces, double[] fitMSDResult, int n, double[][] jdParams) {
IJ.showStatus("Calculating summary ...");
// Create summary table
createSummaryTable();
Statistics[] stats = new Statistics[NAMES.length];
for (int i = 0; i < stats.length; i++) {
stats[i] = (settings.showHistograms) ? new StoredDataStatistics() : new Statistics();
}
for (Trace trace : traces) {
stats[T_ON].add(trace.getOnTime() * exposureTime);
final double signal = trace.getSignal() / results.getGain();
stats[TOTAL_SIGNAL].add(signal);
stats[SIGNAL_PER_FRAME].add(signal / trace.size());
}
// Add to the summary table
StringBuilder sb = new StringBuilder(title);
sb.append('\t').append(createCombinedName());
sb.append("\t");
sb.append(Utils.rounded(exposureTime * 1000, 3)).append("\t");
sb.append(Utils.rounded(settings.distanceThreshold, 3)).append("\t");
sb.append(Utils.rounded(settings.distanceExclusion, 3)).append("\t");
sb.append(settings.minimumTraceLength).append("\t");
sb.append(settings.ignoreEnds).append("\t");
sb.append(settings.truncate).append("\t");
sb.append(settings.internalDistances).append("\t");
sb.append(settings.fitLength).append("\t");
sb.append(settings.msdCorrection).append("\t");
sb.append(settings.precisionCorrection).append("\t");
sb.append(settings.mle).append("\t");
sb.append(traces.length).append("\t");
sb.append(Utils.rounded(precision, 4)).append("\t");
double D = 0, s = 0;
if (fitMSDResult != null) {
D = fitMSDResult[0];
s = fitMSDResult[1];
}
sb.append(Utils.rounded(D, 4)).append("\t");
sb.append(Utils.rounded(s * 1000, 4)).append("\t");
sb.append(Utils.rounded(settings.jumpDistance * exposureTime)).append("\t");
sb.append(n).append("\t");
sb.append(Utils.rounded(beta, 4)).append("\t");
if (jdParams == null) {
sb.append("\t\t\t");
} else {
sb.append(format(jdParams[0])).append("\t");
sb.append(format(jdParams[1])).append("\t");
sb.append(Utils.rounded(ic)).append("\t");
}
for (int i = 0; i < stats.length; i++) {
sb.append(Utils.rounded(stats[i].getMean(), 3)).append("\t");
}
if (java.awt.GraphicsEnvironment.isHeadless()) {
IJ.log(sb.toString());
return;
} else {
summaryTable.append(sb.toString());
}
if (settings.showHistograms) {
IJ.showStatus("Calculating histograms ...");
for (int i = 0; i < NAMES.length; i++) {
if (displayHistograms[i]) {
showHistogram((StoredDataStatistics) stats[i], NAMES[i], alwaysRemoveOutliers[i], ROUNDED[i], false);
}
}
}
tileNewWindows();
IJ.showStatus("Finished " + TITLE);
}
use of gdsc.core.utils.StoredDataStatistics in project GDSC-SMLM by aherbert.
the class BlinkEstimatorTest method estimateBlinking.
private TIntHashSet estimateBlinking(double nBlinks, double tOn, double tOff, int particles, double fixedFraction, boolean timeAtLowerBound, boolean doAssert) {
SpatialIllumination activationIllumination = new UniformIllumination(100);
int totalSteps = 100;
double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
ImageModel imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, tOn, 0, tOff, 0, nBlinks);
imageModel.setRandomGenerator(rand);
double[] max = new double[] { 256, 256, 32 };
double[] min = new double[3];
SpatialDistribution distribution = new UniformDistribution(min, max, rand.nextInt());
List<CompoundMoleculeModel> compounds = new ArrayList<CompoundMoleculeModel>(1);
CompoundMoleculeModel c = new CompoundMoleculeModel(1, 0, 0, 0, Arrays.asList(new MoleculeModel(0, 0, 0, 0)));
c.setDiffusionRate(diffusionRate);
c.setDiffusionType(DiffusionType.RANDOM_WALK);
compounds.add(c);
List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, particles, distribution, false);
// Activate fluorophores
List<? extends FluorophoreSequenceModel> fluorophores = imageModel.createFluorophores(molecules, totalSteps);
totalSteps = checkTotalSteps(totalSteps, fluorophores);
List<LocalisationModel> localisations = imageModel.createImage(molecules, fixedFraction, totalSteps, photons, 0.5, false);
// // Remove localisations to simulate missed counts.
// List<LocalisationModel> newLocalisations = new ArrayList<LocalisationModel>(localisations.size());
// boolean[] id = new boolean[fluorophores.size() + 1];
// Statistics photonStats = new Statistics();
// for (LocalisationModel l : localisations)
// {
// photonStats.add(l.getIntensity());
// // Remove by intensity threshold and optionally at random.
// if (l.getIntensity() < minPhotons || rand.nextDouble() < pDelete)
// continue;
// newLocalisations.add(l);
// id[l.getId()] = true;
// }
// localisations = newLocalisations;
// System.out.printf("Photons = %f\n", photonStats.getMean());
//
// List<FluorophoreSequenceModel> newFluorophores = new ArrayList<FluorophoreSequenceModel>(fluorophores.size());
// for (FluorophoreSequenceModel f : fluorophores)
// {
// if (id[f.getId()])
// newFluorophores.add(f);
// }
// fluorophores = newFluorophores;
MemoryPeakResults results = new MemoryPeakResults();
results.setCalibration(new Calibration(pixelPitch, 1, msPerFrame));
for (LocalisationModel l : localisations) {
// Remove by intensity threshold and optionally at random.
if (l.getIntensity() < minPhotons || rand.nextDouble() < pDelete)
continue;
float[] params = new float[7];
params[Gaussian2DFunction.X_POSITION] = (float) l.getX();
params[Gaussian2DFunction.Y_POSITION] = (float) l.getY();
params[Gaussian2DFunction.X_SD] = params[Gaussian2DFunction.Y_SD] = psfWidth;
params[Gaussian2DFunction.SIGNAL] = (float) (l.getIntensity());
results.addf(l.getTime(), 0, 0, 0, 0, 0, params, null);
}
// Add random localisations
for (int i = (int) (localisations.size() * pAdd); i-- > 0; ) {
float[] params = new float[7];
params[Gaussian2DFunction.X_POSITION] = (float) (rand.nextDouble() * max[0]);
params[Gaussian2DFunction.Y_POSITION] = (float) (rand.nextDouble() * max[1]);
params[Gaussian2DFunction.X_SD] = params[Gaussian2DFunction.Y_SD] = psfWidth;
// Intensity doesn't matter at the moment for tracing
params[Gaussian2DFunction.SIGNAL] = (float) (photons);
results.addf(1 + rand.nextInt(totalSteps), 0, 0, 0, 0, 0, params, null);
}
// Get actual simulated stats ...
Statistics statsNBlinks = new Statistics();
Statistics statsTOn = new Statistics();
Statistics statsTOff = new Statistics();
Statistics statsSampledNBlinks = new Statistics();
Statistics statsSampledTOn = new Statistics();
StoredDataStatistics statsSampledTOff = new StoredDataStatistics();
for (FluorophoreSequenceModel f : fluorophores) {
statsNBlinks.add(f.getNumberOfBlinks());
statsTOn.add(f.getOnTimes());
statsTOff.add(f.getOffTimes());
int[] on = f.getSampledOnTimes();
statsSampledNBlinks.add(on.length);
statsSampledTOn.add(on);
statsSampledTOff.add(f.getSampledOffTimes());
}
System.out.printf("N = %d (%d), N-blinks = %f, tOn = %f, tOff = %f, Fixed = %f\n", fluorophores.size(), localisations.size(), nBlinks, tOn, tOff, fixedFraction);
System.out.printf("Actual N-blinks = %f (%f), tOn = %f (%f), tOff = %f (%f), 95%% = %f, max = %f\n", statsNBlinks.getMean(), statsSampledNBlinks.getMean(), statsTOn.getMean(), statsSampledTOn.getMean(), statsTOff.getMean(), statsSampledTOff.getMean(), statsSampledTOff.getStatistics().getPercentile(95), statsSampledTOff.getStatistics().getMax());
System.out.printf("-=-=--=-\n");
BlinkEstimator be = new BlinkEstimator();
be.maxDarkTime = (int) (tOff * 10);
be.msPerFrame = msPerFrame;
be.relativeDistance = false;
double d = ImageModel.getRandomMoveDistance(diffusionRate);
be.searchDistance = (fixedFraction < 1) ? Math.sqrt(2 * d * d) * 3 : 0;
be.timeAtLowerBound = timeAtLowerBound;
be.showPlots = false;
//Assert.assertTrue("Max dark time must exceed the dark time of the data (otherwise no plateau)",
// be.maxDarkTime > statsSampledTOff.getStatistics().getMax());
int nMolecules = fluorophores.size();
if (usePopulationStatistics) {
nBlinks = statsNBlinks.getMean();
tOff = statsTOff.getMean();
} else {
nBlinks = statsSampledNBlinks.getMean();
tOff = statsSampledTOff.getMean();
}
// See if any fitting regime gets a correct answer
TIntHashSet ok = new TIntHashSet();
for (int nFittedPoints = MIN_FITTED_POINTS; nFittedPoints <= MAX_FITTED_POINTS; nFittedPoints++) {
be.nFittedPoints = nFittedPoints;
be.computeBlinkingRate(results, true);
double moleculesError = DoubleEquality.relativeError(nMolecules, be.getNMolecules());
double blinksError = DoubleEquality.relativeError(nBlinks, be.getNBlinks());
double offError = DoubleEquality.relativeError(tOff * msPerFrame, be.getTOff());
System.out.printf("Error %d: N = %f, blinks = %f, tOff = %f : %f\n", nFittedPoints, moleculesError, blinksError, offError, (moleculesError + blinksError + offError) / 3);
if (moleculesError < relativeError && blinksError < relativeError && offError < relativeError) {
ok.add(nFittedPoints);
System.out.printf("-=-=--=-\n");
System.out.printf("*** Correct at %d fitted points ***\n", nFittedPoints);
if (doAssert)
break;
}
//if (!be.isIncreaseNFittedPoints())
// break;
}
System.out.printf("-=-=--=-\n");
if (doAssert)
Assert.assertFalse(ok.isEmpty());
//Assert.assertEquals("Invalid t-off", tOff * msPerFrame, be.getTOff(), tOff * msPerFrame * relativeError);
return ok;
}
use of gdsc.core.utils.StoredDataStatistics in project GDSC-SMLM by aherbert.
the class EMGainAnalysis method pdfEMGain.
/**
* Calculate the probability density function for EM-gain. The maximum count to evaluate is calculated dynamically
* so that the cumulative probability does not change.
* <p>
* See Ulbrich & Isacoff (2007). Nature Methods 4, 319-321, SI equation 3.
*
* @param p
* The average number of photons per pixel input to the EM-camera
* @param m
* The multiplication factor (gain)
* @return The PDF
*/
private double[] pdfEMGain(final double p, final double m) {
StoredDataStatistics stats = new StoredDataStatistics(100);
stats.add(FastMath.exp(-p));
for (int c = 1; ; c++) {
final double g = pEMGain(c, p, m);
stats.add(g);
final double delta = g / stats.getSum();
if (delta < 1e-5)
break;
}
return stats.getValues();
}
use of gdsc.core.utils.StoredDataStatistics in project GDSC-SMLM by aherbert.
the class FIRE method runQEstimation.
private void runQEstimation() {
IJ.showStatus(TITLE + " ...");
if (!showQEstimationInputDialog())
return;
MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
if (results == null || results.size() == 0) {
IJ.error(TITLE, "No results could be loaded");
return;
}
if (results.getCalibration() == null) {
IJ.error(TITLE, "The results are not calibrated");
return;
}
results = cropToRoi(results);
if (results.size() < 2) {
IJ.error(TITLE, "No results within the crop region");
return;
}
initialise(results, null);
// We need localisation precision.
// Build a histogram of the localisation precision.
// Get the initial mean and SD and plot as a Gaussian.
PrecisionHistogram histogram = calculatePrecisionHistogram();
if (histogram == null) {
IJ.error(TITLE, "No localisation precision available.\n \nPlease choose " + PrecisionMethod.FIXED + " and enter a precision mean and SD.");
return;
}
StoredDataStatistics precision = histogram.precision;
//String name = results.getName();
double fourierImageScale = SCALE_VALUES[imageScaleIndex];
int imageSize = IMAGE_SIZE_VALUES[imageSizeIndex];
// Create the image and compute the numerator of FRC.
// Do not use the signal so results.size() is the number of localisations.
IJ.showStatus("Computing FRC curve ...");
FireImages images = createImages(fourierImageScale, imageSize, false);
// DEBUGGING - Save the two images to disk. Load the images into the Matlab
// code that calculates the Q-estimation and make this plugin match the functionality.
//IJ.save(new ImagePlus("i1", images.ip1), "/scratch/i1.tif");
//IJ.save(new ImagePlus("i2", images.ip2), "/scratch/i2.tif");
FRC frc = new FRC();
frc.progress = progress;
frc.setFourierMethod(fourierMethod);
frc.setSamplingMethod(samplingMethod);
frc.setPerimeterSamplingFactor(perimeterSamplingFactor);
FRCCurve frcCurve = frc.calculateFrcCurve(images.ip1, images.ip2, images.nmPerPixel);
if (frcCurve == null) {
IJ.error(TITLE, "Failed to compute FRC curve");
return;
}
IJ.showStatus("Running Q-estimation ...");
// Note:
// The method implemented here is based on Matlab code provided by Bernd Rieger.
// The idea is to compute the spurious correlation component of the FRC Numerator
// using an initial estimate of distribution of the localisation precision (assumed
// to be Gaussian). This component is the contribution of repeat localisations of
// the same molecule to the numerator and is modelled as an exponential decay
// (exp_decay). The component is scaled by the Q-value which
// is the average number of times a molecule is seen in addition to the first time.
// At large spatial frequencies the scaled component should match the numerator,
// i.e. at high resolution (low FIRE number) the numerator is made up of repeat
// localisations of the same molecule and not actual structure in the image.
// The best fit is where the numerator equals the scaled component, i.e. num / (q*exp_decay) == 1.
// The FRC Numerator is plotted and Q can be determined by
// adjusting Q and the precision mean and SD to maximise the cost function.
// This can be done interactively by the user with the effect on the FRC curve
// dynamically updated and displayed.
// Compute the scaled FRC numerator
double qNorm = (1 / frcCurve.mean1 + 1 / frcCurve.mean2);
double[] frcnum = new double[frcCurve.getSize()];
for (int i = 0; i < frcnum.length; i++) {
FRCCurveResult r = frcCurve.get(i);
frcnum[i] = qNorm * r.getNumerator() / r.getNumberOfSamples();
}
// Compute the spatial frequency and the region for curve fitting
double[] q = FRC.computeQ(frcCurve, false);
int low = 0, high = q.length;
while (high > 0 && q[high - 1] > maxQ) high--;
while (low < q.length && q[low] < minQ) low++;
// Require we fit at least 10% of the curve
if (high - low < q.length * 0.1) {
IJ.error(TITLE, "Not enough points for Q estimation");
return;
}
// Obtain initial estimate of Q plateau height and decay.
// This can be done by fitting the precision histogram and then fixing the mean and sigma.
// Or it can be done by allowing the precision to be sampled and the mean and sigma
// become parameters for fitting.
// Check if we can sample precision values
boolean sampleDecay = precision != null && FIRE.sampleDecay;
double[] exp_decay;
if (sampleDecay) {
// Random sample of precision values from the distribution is used to
// construct the decay curve
int[] sample = Random.sample(10000, precision.getN(), new Well19937c());
final double four_pi2 = 4 * Math.PI * Math.PI;
double[] pre = new double[q.length];
for (int i = 1; i < q.length; i++) pre[i] = -four_pi2 * q[i] * q[i];
// Sample
final int n = sample.length;
double[] hq = new double[n];
for (int j = 0; j < n; j++) {
// Scale to SR pixels
double s2 = precision.getValue(sample[j]) / images.nmPerPixel;
s2 *= s2;
for (int i = 1; i < q.length; i++) hq[i] += FastMath.exp(pre[i] * s2);
}
for (int i = 1; i < q.length; i++) hq[i] /= n;
exp_decay = new double[q.length];
exp_decay[0] = 1;
for (int i = 1; i < q.length; i++) {
double sinc_q = sinc(Math.PI * q[i]);
exp_decay[i] = sinc_q * sinc_q * hq[i];
}
} else {
// Note: The sigma mean and std should be in the units of super-resolution
// pixels so scale to SR pixels
exp_decay = computeExpDecay(histogram.mean / images.nmPerPixel, histogram.sigma / images.nmPerPixel, q);
}
// Smoothing
double[] smooth;
if (loessSmoothing) {
// Note: This computes the log then smooths it
double bandwidth = 0.1;
int robustness = 0;
double[] l = new double[exp_decay.length];
for (int i = 0; i < l.length; i++) {
// Original Matlab code computes the log for each array.
// This is equivalent to a single log on the fraction of the two.
// Perhaps the two log method is more numerically stable.
//l[i] = Math.log(Math.abs(frcnum[i])) - Math.log(exp_decay[i]);
l[i] = Math.log(Math.abs(frcnum[i] / exp_decay[i]));
}
try {
LoessInterpolator loess = new LoessInterpolator(bandwidth, robustness);
smooth = loess.smooth(q, l);
} catch (Exception e) {
IJ.error(TITLE, "LOESS smoothing failed");
return;
}
} else {
// Note: This smooths the curve before computing the log
double[] norm = new double[exp_decay.length];
for (int i = 0; i < norm.length; i++) {
norm[i] = frcnum[i] / exp_decay[i];
}
// Median window of 5 == radius of 2
MedianWindow mw = new MedianWindow(norm, 2);
smooth = new double[exp_decay.length];
for (int i = 0; i < norm.length; i++) {
smooth[i] = Math.log(Math.abs(mw.getMedian()));
mw.increment();
}
}
// Fit with quadratic to find the initial guess.
// Note: example Matlab code frc_Qcorrection7.m identifies regions of the
// smoothed log curve with low derivative and only fits those. The fit is
// used for the final estimate. Fitting a subset with low derivative is not
// implemented here since the initial estimate is subsequently optimised
// to maximise a cost function.
Quadratic curve = new Quadratic();
SimpleCurveFitter fit = SimpleCurveFitter.create(curve, new double[2]);
WeightedObservedPoints points = new WeightedObservedPoints();
for (int i = low; i < high; i++) points.add(q[i], smooth[i]);
double[] estimate = fit.fit(points.toList());
double qValue = FastMath.exp(estimate[0]);
//System.out.printf("Initial q-estimate = %s => %.3f\n", Arrays.toString(estimate), qValue);
// This could be made an option. Just use for debugging
boolean debug = false;
if (debug) {
// Plot the initial fit and the fit curve
double[] qScaled = FRC.computeQ(frcCurve, true);
double[] line = new double[q.length];
for (int i = 0; i < q.length; i++) line[i] = curve.value(q[i], estimate);
String title = TITLE + " Initial fit";
Plot2 plot = new Plot2(title, "Spatial Frequency (nm^-1)", "FRC Numerator");
String label = String.format("Q = %.3f", qValue);
plot.addPoints(qScaled, smooth, Plot.LINE);
plot.setColor(Color.red);
plot.addPoints(qScaled, line, Plot.LINE);
plot.setColor(Color.black);
plot.addLabel(0, 0, label);
Utils.display(title, plot, Utils.NO_TO_FRONT);
}
if (fitPrecision) {
// Q - Should this be optional?
if (sampleDecay) {
// If a sample of the precision was used to construct the data for the initial fit
// then update the estimate using the fit result since it will be a better start point.
histogram.sigma = precision.getStandardDeviation();
// Normalise sum-of-squares to the SR pixel size
double meanSumOfSquares = (precision.getSumOfSquares() / (images.nmPerPixel * images.nmPerPixel)) / precision.getN();
histogram.mean = images.nmPerPixel * Math.sqrt(meanSumOfSquares - estimate[1] / (4 * Math.PI * Math.PI));
}
// Do a multivariate fit ...
SimplexOptimizer opt = new SimplexOptimizer(1e-6, 1e-10);
PointValuePair p = null;
MultiPlateauness f = new MultiPlateauness(frcnum, q, low, high);
double[] initial = new double[] { histogram.mean / images.nmPerPixel, histogram.sigma / images.nmPerPixel, qValue };
p = findMin(p, opt, f, scale(initial, 0.1));
p = findMin(p, opt, f, scale(initial, 0.5));
p = findMin(p, opt, f, initial);
p = findMin(p, opt, f, scale(initial, 2));
p = findMin(p, opt, f, scale(initial, 10));
if (p != null) {
double[] point = p.getPointRef();
histogram.mean = point[0] * images.nmPerPixel;
histogram.sigma = point[1] * images.nmPerPixel;
qValue = point[2];
}
} else {
// If so then this should be optional.
if (sampleDecay) {
if (precisionMethod != PrecisionMethod.FIXED) {
histogram.sigma = precision.getStandardDeviation();
// Normalise sum-of-squares to the SR pixel size
double meanSumOfSquares = (precision.getSumOfSquares() / (images.nmPerPixel * images.nmPerPixel)) / precision.getN();
histogram.mean = images.nmPerPixel * Math.sqrt(meanSumOfSquares - estimate[1] / (4 * Math.PI * Math.PI));
}
exp_decay = computeExpDecay(histogram.mean / images.nmPerPixel, histogram.sigma / images.nmPerPixel, q);
}
// Estimate spurious component by promoting plateauness.
// The Matlab code used random initial points for a Simplex optimiser.
// A Brent line search should be pretty deterministic so do simple repeats.
// However it will proceed downhill so if the initial point is wrong then
// it will find a sub-optimal result.
UnivariateOptimizer o = new BrentOptimizer(1e-3, 1e-6);
Plateauness f = new Plateauness(frcnum, exp_decay, low, high);
UnivariatePointValuePair p = null;
p = findMin(p, o, f, qValue, 0.1);
p = findMin(p, o, f, qValue, 0.2);
p = findMin(p, o, f, qValue, 0.333);
p = findMin(p, o, f, qValue, 0.5);
// Do some Simplex repeats as well
SimplexOptimizer opt = new SimplexOptimizer(1e-6, 1e-10);
p = findMin(p, opt, f, qValue * 0.1);
p = findMin(p, opt, f, qValue * 0.5);
p = findMin(p, opt, f, qValue);
p = findMin(p, opt, f, qValue * 2);
p = findMin(p, opt, f, qValue * 10);
if (p != null)
qValue = p.getPoint();
}
QPlot qplot = new QPlot(frcCurve, qValue, low, high);
// Interactive dialog to estimate Q (blinking events per flourophore) using
// sliders for the mean and standard deviation of the localisation precision.
showQEstimationDialog(histogram, qplot, frcCurve, images.nmPerPixel);
IJ.showStatus(TITLE + " complete");
}
use of gdsc.core.utils.StoredDataStatistics in project GDSC-SMLM by aherbert.
the class FIRE method calculatePrecisionHistogram.
/**
* Calculate a histogram of the precision. The precision can be either stored in the results or calculated using the
* Mortensen formula. If the precision method for Q estimation is not fixed then the histogram is fitted with a
* Gaussian to create an initial estimate.
*
* @param precisionMethod
* the precision method
* @return The precision histogram
*/
private PrecisionHistogram calculatePrecisionHistogram() {
boolean logFitParameters = false;
String title = results.getName() + " Precision Histogram";
// Check if the results has the precision already or if it can be computed.
boolean canUseStored = canUseStoredPrecision(results);
boolean canCalculatePrecision = canCalculatePrecision(results);
// Set the method to compute a histogram. Default to the user selected option.
PrecisionMethod m = null;
if (canUseStored && precisionMethod == PrecisionMethod.STORED)
m = precisionMethod;
else if (canCalculatePrecision && precisionMethod == PrecisionMethod.CALCULATE)
m = precisionMethod;
if (m == null) {
// We only have two choices so if one is available then select it.
if (canUseStored)
m = PrecisionMethod.STORED;
else if (canCalculatePrecision)
m = PrecisionMethod.CALCULATE;
// If the user selected a method not available then log a warning
if (m != null && precisionMethod != PrecisionMethod.FIXED) {
IJ.log(String.format("%s : Selected precision method '%s' not available, switching to '%s'", TITLE, precisionMethod, m.getName()));
}
if (m == null) {
// This does not matter if the user has provide a fixed input.
if (precisionMethod == PrecisionMethod.FIXED) {
PrecisionHistogram histogram = new PrecisionHistogram(title);
histogram.mean = mean;
histogram.sigma = sigma;
return histogram;
}
// No precision
return null;
}
}
// We get here if we can compute precision.
// Build the histogram
StoredDataStatistics precision = new StoredDataStatistics(results.size());
if (m == PrecisionMethod.STORED) {
for (PeakResult r : results.getResults()) {
precision.add(r.getPrecision());
}
} else {
final double nmPerPixel = results.getNmPerPixel();
final double gain = results.getGain();
final boolean emCCD = results.isEMCCD();
for (PeakResult r : results.getResults()) {
precision.add(r.getPrecision(nmPerPixel, gain, emCCD));
}
}
//System.out.printf("Raw p = %f\n", precision.getMean());
double yMin = Double.NEGATIVE_INFINITY, yMax = 0;
// Set the min and max y-values using 1.5 x IQR
DescriptiveStatistics stats = precision.getStatistics();
double lower = stats.getPercentile(25);
double upper = stats.getPercentile(75);
if (Double.isNaN(lower) || Double.isNaN(upper)) {
if (logFitParameters)
Utils.log("Error computing IQR: %f - %f", lower, upper);
} else {
double iqr = upper - lower;
yMin = FastMath.max(lower - iqr, stats.getMin());
yMax = FastMath.min(upper + iqr, stats.getMax());
if (logFitParameters)
Utils.log(" Data range: %f - %f. Plotting 1.5x IQR: %f - %f", stats.getMin(), stats.getMax(), yMin, yMax);
}
if (yMin == Double.NEGATIVE_INFINITY) {
int n = 5;
yMin = Math.max(stats.getMin(), stats.getMean() - n * stats.getStandardDeviation());
yMax = Math.min(stats.getMax(), stats.getMean() + n * stats.getStandardDeviation());
if (logFitParameters)
Utils.log(" Data range: %f - %f. Plotting mean +/- %dxSD: %f - %f", stats.getMin(), stats.getMax(), n, yMin, yMax);
}
// Get the data within the range
double[] data = precision.getValues();
precision = new StoredDataStatistics(data.length);
for (double d : data) {
if (d < yMin || d > yMax)
continue;
precision.add(d);
}
int histogramBins = Utils.getBins(precision, Utils.BinMethod.SCOTT);
float[][] hist = Utils.calcHistogram(precision.getFloatValues(), yMin, yMax, histogramBins);
PrecisionHistogram histogram = new PrecisionHistogram(hist, precision, title);
if (precisionMethod == PrecisionMethod.FIXED) {
histogram.mean = mean;
histogram.sigma = sigma;
return histogram;
}
// Fitting of the histogram to produce the initial estimate
// Extract non-zero data
float[] x = Arrays.copyOf(hist[0], hist[0].length);
float[] y = hist[1];
int count = 0;
float dx = (x[1] - x[0]) * 0.5f;
for (int i = 0; i < y.length; i++) if (y[i] > 0) {
x[count] = x[i] + dx;
y[count] = y[i];
count++;
}
x = Arrays.copyOf(x, count);
y = Arrays.copyOf(y, count);
// Sense check to fitted data. Get mean and SD of histogram
double[] stats2 = Utils.getHistogramStatistics(x, y);
if (logFitParameters)
Utils.log(" Initial Statistics: %f +/- %f", stats2[0], stats2[1]);
histogram.mean = stats2[0];
histogram.sigma = stats2[1];
// Standard Gaussian fit
double[] parameters = fitGaussian(x, y);
if (parameters == null) {
Utils.log(" Failed to fit initial Gaussian");
return histogram;
}
double newMean = parameters[1];
double error = Math.abs(stats2[0] - newMean) / stats2[1];
if (error > 3) {
Utils.log(" Failed to fit Gaussian: %f standard deviations from histogram mean", error);
return histogram;
}
if (newMean < yMin || newMean > yMax) {
Utils.log(" Failed to fit Gaussian: %f outside data range %f - %f", newMean, yMin, yMax);
return histogram;
}
if (logFitParameters)
Utils.log(" Initial Gaussian: %f @ %f +/- %f", parameters[0], parameters[1], parameters[2]);
histogram.mean = parameters[1];
histogram.sigma = parameters[2];
return histogram;
}
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