use of uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure in project GDSC-SMLM by aherbert.
the class CreateData method showSummary.
private double showSummary(List<? extends FluorophoreSequenceModel> fluorophores, List<LocalisationModel> localisations) {
IJ.showStatus("Calculating statistics ...");
final Statistics[] stats = new Statistics[NAMES.length];
for (int i = 0; i < stats.length; i++) {
stats[i] = (settings.getShowHistograms() || alwaysRemoveOutliers[i]) ? new StoredDataStatistics() : new Statistics();
}
// Find the largest timepoint
final ImagePlus outputImp = WindowManager.getImage(benchmarkImageId);
int frameCount;
if (outputImp == null) {
sortLocalisationsByTime(localisations);
frameCount = localisations.get(localisations.size() - 1).getTime();
} else {
frameCount = outputImp.getStackSize();
}
final int[] countHistogram = new int[frameCount + 1];
// Use the localisations that were drawn to create the sampled on/off times
rebuildNeighbours(localisations);
// Assume that there is at least one localisation
final LocalisationModel first = localisations.get(0);
// The current localisation
int currentId = first.getId();
// The last time this localisation was on
int lastT = first.getTime();
// Number of blinks
int blinks = 0;
// On-time of current pulse
int currentT = 0;
double signal = 0;
final double centreOffset = settings.getSize() * 0.5;
// Used to convert the sampled times in frames into seconds
final double framesPerSecond = 1000.0 / settings.getExposureTime();
// final double gain = new CreateDataSettingsHelper(settings).getTotalGainSafe();
for (final LocalisationModel l : localisations) {
final double[] data = l.getData();
if (data == null) {
throw new IllegalStateException("No localisation data. This should not happen!");
}
final double noise = data[1];
final double sx = data[2];
final double sy = data[3];
final double intensityInPhotons = data[4];
// Q. What if the noise is zero, i.e. no background photon / read noise?
// Just ignore it at current. This is only an approximation to the SNR estimate
// if this is not a Gaussian spot.
final double snr = Gaussian2DPeakResultHelper.getMeanSignalUsingP05(intensityInPhotons, sx, sy) / noise;
stats[SIGNAL].add(intensityInPhotons);
stats[NOISE].add(noise);
if (noise != 0) {
stats[SNR].add(snr);
}
// if (l.isContinuous())
if (l.getNext() != null && l.getPrevious() != null) {
stats[SIGNAL_CONTINUOUS].add(intensityInPhotons);
if (noise != 0) {
stats[SNR_CONTINUOUS].add(snr);
}
}
final int id = l.getId();
// Check if this a new fluorophore
if (currentId != id) {
// Add previous fluorophore
stats[SAMPLED_BLINKS].add(blinks);
stats[SAMPLED_T_ON].add(currentT / framesPerSecond);
stats[TOTAL_SIGNAL].add(signal);
// Reset
blinks = 0;
currentT = 1;
currentId = id;
signal = intensityInPhotons;
} else {
signal += intensityInPhotons;
// Check if the current fluorophore pulse is broken (i.e. a blink)
if (l.getTime() - 1 > lastT) {
blinks++;
stats[SAMPLED_T_ON].add(currentT / framesPerSecond);
currentT = 1;
stats[SAMPLED_T_OFF].add(((l.getTime() - 1) - lastT) / framesPerSecond);
} else {
// Continuous on-time
currentT++;
}
}
lastT = l.getTime();
countHistogram[lastT]++;
stats[X].add((l.getX() - centreOffset) * settings.getPixelPitch());
stats[Y].add((l.getY() - centreOffset) * settings.getPixelPitch());
stats[Z].add(l.getZ() * settings.getPixelPitch());
}
// Final fluorophore
stats[SAMPLED_BLINKS].add(blinks);
stats[SAMPLED_T_ON].add(currentT / framesPerSecond);
stats[TOTAL_SIGNAL].add(signal);
// Samples per frame
for (int t = 1; t < countHistogram.length; t++) {
stats[SAMPLES].add(countHistogram[t]);
}
if (fluorophores != null) {
for (final FluorophoreSequenceModel f : fluorophores) {
stats[BLINKS].add(f.getNumberOfBlinks());
// On-time
for (final double t : f.getOnTimes()) {
stats[T_ON].add(t);
}
// Off-time
for (final double t : f.getOffTimes()) {
stats[T_OFF].add(t);
}
}
} else {
// show no blinks
stats[BLINKS].add(0);
stats[T_ON].add(1);
}
if (results != null) {
// Convert depth-of-field to pixels
final double depth = settings.getDepthOfField() / settings.getPixelPitch();
try {
// Get widths
final WidthResultProcedure wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
wp.getW();
stats[WIDTH].add(wp.wx);
} catch (final DataException ex) {
ImageJUtils.log("Unable to compute width: " + ex.getMessage());
}
try {
// Get z depth
final StandardResultProcedure sp = new StandardResultProcedure(results, DistanceUnit.PIXEL);
sp.getXyz();
// Get precision
final PrecisionResultProcedure pp = new PrecisionResultProcedure(results);
pp.getPrecision();
stats[PRECISION].add(pp.precisions);
for (int i = 0; i < pp.size(); i++) {
if (Math.abs(sp.z[i]) < depth) {
stats[PRECISION_IN_FOCUS].add(pp.precisions[i]);
}
}
} catch (final DataException ex) {
ImageJUtils.log("Unable to compute LSE precision: " + ex.getMessage());
}
// Compute density per frame. Multi-thread for speed
if (settings.getDensityRadius() > 0) {
final int threadCount = Prefs.getThreads();
final Ticker ticker = ImageJUtils.createTicker(results.getLastFrame(), threadCount, "Calculating density ...");
final ExecutorService threadPool = Executors.newFixedThreadPool(threadCount);
final List<Future<?>> futures = new LinkedList<>();
final TFloatArrayList coordsX = new TFloatArrayList();
final TFloatArrayList coordsY = new TFloatArrayList();
final Statistics densityStats = stats[DENSITY];
final float radius = (float) (settings.getDensityRadius() * getHwhm());
final Rectangle bounds = results.getBounds();
final double area = (double) bounds.width * bounds.height;
// Store the density for each result.
final int[] allDensity = new int[results.size()];
final FrameCounter counter = results.newFrameCounter();
results.forEach((PeakResultProcedure) result -> {
if (counter.advance(result.getFrame())) {
counter.increment(runDensityCalculation(threadPool, futures, coordsX, coordsY, densityStats, radius, area, allDensity, counter.getCount(), ticker));
}
coordsX.add(result.getXPosition());
coordsY.add(result.getYPosition());
});
runDensityCalculation(threadPool, futures, coordsX, coordsY, densityStats, radius, area, allDensity, counter.getCount(), ticker);
ConcurrencyUtils.waitForCompletionUnchecked(futures);
threadPool.shutdown();
ImageJUtils.finished();
// Split results into singles (density = 0) and clustered (density > 0)
final MemoryPeakResults singles = copyMemoryPeakResults("No Density");
final MemoryPeakResults clustered = copyMemoryPeakResults("Density");
counter.reset();
results.forEach((PeakResultProcedure) result -> {
final int density = allDensity[counter.getAndIncrement()];
result.setOrigValue(density);
if (density == 0) {
singles.add(result);
} else {
clustered.add(result);
}
});
}
}
final StringBuilder sb = new StringBuilder();
sb.append(datasetNumber).append('\t');
if (settings.getCameraType() == CameraType.SCMOS) {
sb.append("sCMOS (").append(settings.getCameraModelName()).append(") ");
final Rectangle bounds = cameraModel.getBounds();
sb.append(" ").append(bounds.x).append(",").append(bounds.y);
final int size = settings.getSize();
sb.append(" ").append(size).append("x").append(size);
} else if (CalibrationProtosHelper.isCcdCameraType(settings.getCameraType())) {
sb.append(CalibrationProtosHelper.getName(settings.getCameraType()));
final int size = settings.getSize();
sb.append(" ").append(size).append("x").append(size);
if (settings.getCameraType() == CameraType.EMCCD) {
sb.append(" EM=").append(settings.getEmGain());
}
sb.append(" CG=").append(settings.getCameraGain());
sb.append(" RN=").append(settings.getReadNoise());
sb.append(" B=").append(settings.getBias());
} else {
throw new IllegalStateException();
}
sb.append(" QE=").append(settings.getQuantumEfficiency()).append('\t');
sb.append(settings.getPsfModel());
if (psfModelType == PSF_MODEL_IMAGE) {
sb.append(" Image").append(settings.getPsfImageName());
} else if (psfModelType == PSF_MODEL_ASTIGMATISM) {
sb.append(" model=").append(settings.getAstigmatismModel());
} else {
sb.append(" DoF=").append(MathUtils.rounded(settings.getDepthOfFocus()));
if (settings.getEnterWidth()) {
sb.append(" SD=").append(MathUtils.rounded(settings.getPsfSd()));
} else {
sb.append(" λ=").append(MathUtils.rounded(settings.getWavelength()));
sb.append(" NA=").append(MathUtils.rounded(settings.getNumericalAperture()));
}
}
sb.append('\t');
sb.append((fluorophores == null) ? localisations.size() : fluorophores.size()).append('\t');
sb.append(stats[SAMPLED_BLINKS].getN() + (int) stats[SAMPLED_BLINKS].getSum()).append('\t');
sb.append(localisations.size()).append('\t');
sb.append(frameCount).append('\t');
sb.append(MathUtils.rounded(areaInUm)).append('\t');
sb.append(MathUtils.rounded(localisations.size() / (areaInUm * frameCount), 4)).append('\t');
sb.append(MathUtils.rounded(getHwhm(), 4)).append('\t');
double sd = getPsfSd();
sb.append(MathUtils.rounded(sd, 4)).append('\t');
sd *= settings.getPixelPitch();
final double sa = PsfCalculator.squarePixelAdjustment(sd, settings.getPixelPitch()) / settings.getPixelPitch();
sb.append(MathUtils.rounded(sa, 4)).append('\t');
// Width not valid for the Image PSF.
// Q. Is this true? We can approximate the FHWM for a spot-like image PSF.
final int nStats = (psfModelType == PSF_MODEL_IMAGE) ? stats.length - 1 : stats.length;
for (int i = 0; i < nStats; i++) {
final double centre = (alwaysRemoveOutliers[i]) ? ((StoredDataStatistics) stats[i]).getStatistics().getPercentile(50) : stats[i].getMean();
sb.append(MathUtils.rounded(centre, 4)).append('\t');
}
createSummaryTable().accept(sb.toString());
// Show histograms
if (settings.getShowHistograms() && !java.awt.GraphicsEnvironment.isHeadless()) {
IJ.showStatus("Calculating histograms ...");
final boolean[] chosenHistograms = getChoosenHistograms();
final WindowOrganiser wo = new WindowOrganiser();
final HistogramPlotBuilder builder = new HistogramPlotBuilder(TITLE);
for (int i = 0; i < NAMES.length; i++) {
if (chosenHistograms[i]) {
builder.setData((StoredDataStatistics) stats[i]).setName(NAMES[i]).setIntegerBins(integerDisplay[i]).setRemoveOutliersOption((settings.getRemoveOutliers() || alwaysRemoveOutliers[i]) ? 2 : 0).setNumberOfBins(settings.getHistogramBins()).show(wo);
}
}
wo.tile();
}
IJ.showStatus("");
return stats[SIGNAL].getMean();
}
use of uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure in project GDSC-SMLM by aherbert.
the class PcPalmMolecules method extractLocalisations.
/**
* Extract molecules for the PC-PALM analysis.
*
* <p>Estimate the localisation uncertainty (precision) of each molecule using the formula of
* Mortensen, et al (2010), Nature Methods 7, 377-381. Store distance in nm and signal in photons
* using the calibration
*
* @param results the results
* @return the array list
* @throws DataException If conversion to nm and photons with computed precision is not possible
*/
public List<Molecule> extractLocalisations(MemoryPeakResults results) {
final ArrayList<Molecule> list = new ArrayList<>(results.size());
// Access calibrated data
final StandardResultProcedure sp = new StandardResultProcedure(results, DistanceUnit.NM, IntensityUnit.PHOTON);
sp.getIxy();
final PrecisionResultProcedure pp = new PrecisionResultProcedure(results);
pp.getPrecision();
for (int i = 0, size = pp.size(); i < size; i++) {
list.add(new Molecule(sp.x[i], sp.y[i], pp.precisions[i], sp.intensity[i]));
}
return list;
}
use of uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure in project GDSC-SMLM by aherbert.
the class ImageJ3DResultsViewer method getPoints.
/**
* Gets the points.
*
* @param results the results
* @param settings the settings
* @return the points
*/
static LocalList<Point3f> getPoints(MemoryPeakResults results, ImageJ3DResultsViewerSettingsOrBuilder settings) {
final LocalList<Point3f> points = new LocalList<>(results.size());
if (results.is3D()) {
results.forEach(DistanceUnit.NM, (XyzResultProcedure) (x, y, z) -> {
points.push(new Point3f(x, y, z));
});
} else {
results.forEach(DistanceUnit.NM, (XyResultProcedure) (x, y) -> {
points.push(new Point3f(x, y, 0));
});
final double range = settings.getDepthRange();
if (range > 0 && results.size() > 1) {
final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
final double min = -settings.getDepthRange() / 2;
switch(mode) {
case DITHER:
final SplitMix r = SplitMix.new64(settings.getDitherSeed());
for (int i = points.size(); i-- > 0; ) {
points.unsafeGet(i).z += (min + r.nextDouble() * range);
}
break;
case INTENSITY:
// Rank by intensity, highest first
final StandardResultProcedure p = new StandardResultProcedure(results);
p.getI();
final int[] indices = SimpleArrayUtils.natural(results.size());
SortUtils.sortIndices(indices, p.intensity, true);
final double inc = range / indices.length;
for (int i = 0; i < indices.length; i++) {
// The standard rendering has +z going away so put the highest rank at min
points.unsafeGet(indices[i]).z += (min + i * inc);
}
break;
case NONE:
break;
default:
throw new IllegalStateException("Unknown depth mode: " + mode);
}
}
}
return points;
}
use of uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure in project GDSC-SMLM by aherbert.
the class ImageJ3DResultsViewer method createRankByDepth.
private static float[] createRankByDepth(MemoryPeakResults results) {
if (results.is3D()) {
final StandardResultProcedure procedure = new StandardResultProcedure(results);
procedure.getZ();
return procedure.z;
}
return null;
}
use of uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure in project GDSC-SMLM by aherbert.
the class DensityImage method createDensityManager.
private static DensityManager createDensityManager(MemoryPeakResults results) {
if (MemoryPeakResults.isEmpty(results)) {
throw new IllegalArgumentException("Results are null or empty");
}
final StandardResultProcedure sp = new StandardResultProcedure(results, DistanceUnit.PIXEL);
sp.getXy();
final Rectangle bounds = results.getBounds();
final double area = (double) bounds.width * bounds.height;
return new DensityManager(sp.x, sp.y, area);
}
Aggregations