use of ij.plugin.WindowOrganiser in project GDSC-SMLM by aherbert.
the class PSFEstimator method calculateStatistics.
private boolean calculateStatistics(PeakFit fitter, double[] params, double[] params_dev) {
debug(" Fitting PSF");
swapStatistics();
// Create the fit engine using the PeakFit plugin
FitConfiguration fitConfig = config.getFitConfiguration();
fitConfig.setInitialAngle((float) params[0]);
fitConfig.setInitialPeakStdDev0((float) params[1]);
fitConfig.setInitialPeakStdDev1((float) params[2]);
ImageStack stack = imp.getImageStack();
Rectangle roi = stack.getProcessor(1).getRoi();
ImageSource source = new IJImageSource(imp);
// Allow interlaced data by wrapping the image source
if (interlacedData) {
source = new InterlacedImageSource(source, dataStart, dataBlock, dataSkip);
}
// Allow frame aggregation by wrapping the image source
if (integrateFrames > 1) {
source = new AggregatedImageSource(source, integrateFrames);
}
fitter.initialiseImage(source, roi, true);
fitter.addPeakResults(this);
fitter.initialiseFitting();
FitEngine engine = fitter.createFitEngine();
// Use random slices
int[] slices = new int[stack.getSize()];
for (int i = 0; i < slices.length; i++) slices[i] = i + 1;
Random rand = new Random();
rand.shuffle(slices);
IJ.showStatus("Fitting ...");
// Use multi-threaded code for speed
int i;
for (i = 0; i < slices.length; i++) {
int slice = slices[i];
//debug(" Processing slice = %d\n", slice);
IJ.showProgress(size(), settings.numberOfPeaks);
ImageProcessor ip = stack.getProcessor(slice);
// stack processor does not set the bounds required by ImageConverter
ip.setRoi(roi);
FitJob job = new FitJob(slice, ImageConverter.getData(ip), roi);
engine.run(job);
if (sampleSizeReached() || Utils.isInterrupted()) {
break;
}
}
if (Utils.isInterrupted()) {
IJ.showProgress(1);
engine.end(true);
return false;
}
// Wait until we have enough results
while (!sampleSizeReached() && !engine.isQueueEmpty()) {
IJ.showProgress(size(), settings.numberOfPeaks);
try {
Thread.sleep(50);
} catch (InterruptedException e) {
break;
}
}
// End now if we have enough samples
engine.end(sampleSizeReached());
IJ.showStatus("");
IJ.showProgress(1);
// This count will be an over-estimate given that the provider is ahead of the consumer
// in this multi-threaded system
debug(" Processed %d/%d slices (%d peaks)", i, slices.length, size());
setParams(ANGLE, params, params_dev, sampleNew[ANGLE]);
setParams(X, params, params_dev, sampleNew[X]);
setParams(Y, params, params_dev, sampleNew[Y]);
if (settings.showHistograms) {
int[] idList = new int[NAMES.length];
int count = 0;
boolean requireRetile = false;
for (int ii = 0; ii < 3; ii++) {
if (sampleNew[ii].getN() == 0)
continue;
StoredDataStatistics stats = new StoredDataStatistics(sampleNew[ii].getValues());
idList[count++] = Utils.showHistogram(TITLE, stats, NAMES[ii], 0, 0, settings.histogramBins, "Mean = " + Utils.rounded(stats.getMean()) + ". Median = " + Utils.rounded(sampleNew[ii].getPercentile(50)));
requireRetile = requireRetile || Utils.isNewWindow();
}
if (requireRetile && count > 0) {
new WindowOrganiser().tileWindows(Arrays.copyOf(idList, count));
}
}
if (size() < 2) {
log("ERROR: Insufficient number of fitted peaks, terminating ...");
return false;
}
return true;
}
use of ij.plugin.WindowOrganiser in project GDSC-SMLM by aherbert.
the class FilterAnalysis method showPlots.
private void showPlots() {
if (plots.isEmpty())
return;
// Display the top N plots
int[] list = new int[plots.size()];
int i = 0;
for (NamedPlot p : plots) {
Plot2 plot = new Plot2(p.name, p.xAxisName, "Jaccard", p.xValues, p.yValues);
plot.setLimits(p.xValues[0], p.xValues[p.xValues.length - 1], 0, 1);
plot.setColor(Color.RED);
plot.draw();
plot.setColor(Color.BLUE);
plot.addPoints(p.xValues, p.yValues, Plot2.CROSS);
PlotWindow plotWindow = Utils.display(p.name, plot);
list[i++] = plotWindow.getImagePlus().getID();
}
new WindowOrganiser().tileWindows(list);
}
use of ij.plugin.WindowOrganiser in project GDSC-SMLM by aherbert.
the class DiffusionRateTest method run.
/*
* (non-Javadoc)
*
* @see ij.plugin.PlugIn#run(java.lang.String)
*/
public void run(String arg) {
SMLMUsageTracker.recordPlugin(this.getClass(), arg);
if (IJ.controlKeyDown()) {
simpleTest();
return;
}
extraOptions = Utils.isExtraOptions();
if (!showDialog())
return;
lastSimulatedDataset[0] = lastSimulatedDataset[1] = "";
lastSimulatedPrecision = 0;
final int totalSteps = (int) Math.ceil(settings.seconds * settings.stepsPerSecond);
conversionFactor = 1000000.0 / (settings.pixelPitch * settings.pixelPitch);
// Diffusion rate is um^2/sec. Convert to pixels per simulation frame.
final double diffusionRateInPixelsPerSecond = settings.diffusionRate * conversionFactor;
final double diffusionRateInPixelsPerStep = diffusionRateInPixelsPerSecond / settings.stepsPerSecond;
final double precisionInPixels = myPrecision / settings.pixelPitch;
final boolean addError = myPrecision != 0;
Utils.log(TITLE + " : D = %s um^2/sec, Precision = %s nm", Utils.rounded(settings.diffusionRate, 4), Utils.rounded(myPrecision, 4));
Utils.log("Mean-displacement per dimension = %s nm/sec", Utils.rounded(1e3 * ImageModel.getRandomMoveDistance(settings.diffusionRate), 4));
if (extraOptions)
Utils.log("Step size = %s, precision = %s", Utils.rounded(ImageModel.getRandomMoveDistance(diffusionRateInPixelsPerStep)), Utils.rounded(precisionInPixels));
// Convert diffusion co-efficient into the standard deviation for the random walk
final double diffusionSigma = (settings.getDiffusionType() == DiffusionType.LINEAR_WALK) ? // Q. What should this be? At the moment just do 1D diffusion on a random vector
ImageModel.getRandomMoveDistance(diffusionRateInPixelsPerStep) : ImageModel.getRandomMoveDistance(diffusionRateInPixelsPerStep);
Utils.log("Simulation step-size = %s nm", Utils.rounded(settings.pixelPitch * diffusionSigma, 4));
// Move the molecules and get the diffusion rate
IJ.showStatus("Simulating ...");
final long start = System.nanoTime();
final long seed = System.currentTimeMillis() + System.identityHashCode(this);
RandomGenerator[] random = new RandomGenerator[3];
RandomGenerator[] random2 = new RandomGenerator[3];
for (int i = 0; i < 3; i++) {
random[i] = new Well19937c(seed + i * 12436);
random2[i] = new Well19937c(seed + i * 678678 + 3);
}
Statistics[] stats2D = new Statistics[totalSteps];
Statistics[] stats3D = new Statistics[totalSteps];
StoredDataStatistics jumpDistances2D = new StoredDataStatistics(totalSteps);
StoredDataStatistics jumpDistances3D = new StoredDataStatistics(totalSteps);
for (int j = 0; j < totalSteps; j++) {
stats2D[j] = new Statistics();
stats3D[j] = new Statistics();
}
SphericalDistribution dist = new SphericalDistribution(settings.confinementRadius / settings.pixelPitch);
Statistics asymptote = new Statistics();
// Save results to memory
MemoryPeakResults results = new MemoryPeakResults(totalSteps);
Calibration cal = new Calibration(settings.pixelPitch, 1, 1000.0 / settings.stepsPerSecond);
results.setCalibration(cal);
results.setName(TITLE);
int peak = 0;
// Store raw coordinates
ArrayList<Point> points = new ArrayList<Point>(totalSteps);
StoredData totalJumpDistances1D = new StoredData(settings.particles);
StoredData totalJumpDistances2D = new StoredData(settings.particles);
StoredData totalJumpDistances3D = new StoredData(settings.particles);
for (int i = 0; i < settings.particles; i++) {
if (i % 16 == 0) {
IJ.showProgress(i, settings.particles);
if (Utils.isInterrupted())
return;
}
// Increment the frame so that tracing analysis can distinguish traces
peak++;
double[] origin = new double[3];
final int id = i + 1;
MoleculeModel m = new MoleculeModel(id, origin.clone());
if (addError)
origin = addError(origin, precisionInPixels, random);
if (useConfinement) {
// Note: When using confinement the average displacement should asymptote
// at the average distance of a point from the centre of a ball. This is 3r/4.
// See: http://answers.yahoo.com/question/index?qid=20090131162630AAMTUfM
// The equivalent in 2D is 2r/3. However although we are plotting 2D distance
// this is a projection of the 3D position onto the plane and so the particles
// will not be evenly spread (there will be clustering at centre caused by the
// poles)
final double[] axis = (settings.getDiffusionType() == DiffusionType.LINEAR_WALK) ? nextVector() : null;
for (int j = 0; j < totalSteps; j++) {
double[] xyz = m.getCoordinates();
double[] originalXyz = xyz.clone();
for (int n = confinementAttempts; n-- > 0; ) {
if (settings.getDiffusionType() == DiffusionType.GRID_WALK)
m.walk(diffusionSigma, random);
else if (settings.getDiffusionType() == DiffusionType.LINEAR_WALK)
m.slide(diffusionSigma, axis, random[0]);
else
m.move(diffusionSigma, random);
if (!dist.isWithin(m.getCoordinates())) {
// Reset position
for (int k = 0; k < 3; k++) xyz[k] = originalXyz[k];
} else {
// The move was allowed
break;
}
}
points.add(new Point(id, xyz));
if (addError)
xyz = addError(xyz, precisionInPixels, random2);
peak = record(xyz, id, peak, stats2D[j], stats3D[j], jumpDistances2D, jumpDistances3D, origin, results);
}
asymptote.add(distance(m.getCoordinates()));
} else {
if (settings.getDiffusionType() == DiffusionType.GRID_WALK) {
for (int j = 0; j < totalSteps; j++) {
m.walk(diffusionSigma, random);
double[] xyz = m.getCoordinates();
points.add(new Point(id, xyz));
if (addError)
xyz = addError(xyz, precisionInPixels, random2);
peak = record(xyz, id, peak, stats2D[j], stats3D[j], jumpDistances2D, jumpDistances3D, origin, results);
}
} else if (settings.getDiffusionType() == DiffusionType.LINEAR_WALK) {
final double[] axis = nextVector();
for (int j = 0; j < totalSteps; j++) {
m.slide(diffusionSigma, axis, random[0]);
double[] xyz = m.getCoordinates();
points.add(new Point(id, xyz));
if (addError)
xyz = addError(xyz, precisionInPixels, random2);
peak = record(xyz, id, peak, stats2D[j], stats3D[j], jumpDistances2D, jumpDistances3D, origin, results);
}
} else {
for (int j = 0; j < totalSteps; j++) {
m.move(diffusionSigma, random);
double[] xyz = m.getCoordinates();
points.add(new Point(id, xyz));
if (addError)
xyz = addError(xyz, precisionInPixels, random2);
peak = record(xyz, id, peak, stats2D[j], stats3D[j], jumpDistances2D, jumpDistances3D, origin, results);
}
}
}
// Debug: record all the particles so they can be analysed
// System.out.printf("%f %f %f\n", m.getX(), m.getY(), m.getZ());
final double[] xyz = m.getCoordinates();
double d2 = 0;
totalJumpDistances1D.add(d2 = xyz[0] * xyz[0]);
totalJumpDistances2D.add(d2 += xyz[1] * xyz[1]);
totalJumpDistances3D.add(d2 += xyz[2] * xyz[2]);
}
final double time = (System.nanoTime() - start) / 1000000.0;
IJ.showProgress(1);
MemoryPeakResults.addResults(results);
lastSimulatedDataset[0] = results.getName();
lastSimulatedPrecision = myPrecision;
// Convert pixels^2/step to um^2/sec
final double msd2D = (jumpDistances2D.getMean() / conversionFactor) / (results.getCalibration().getExposureTime() / 1000);
final double msd3D = (jumpDistances3D.getMean() / conversionFactor) / (results.getCalibration().getExposureTime() / 1000);
Utils.log("Raw data D=%s um^2/s, Precision = %s nm, N=%d, step=%s s, mean2D=%s um^2, MSD 2D = %s um^2/s, mean3D=%s um^2, MSD 3D = %s um^2/s", Utils.rounded(settings.diffusionRate), Utils.rounded(myPrecision), jumpDistances2D.getN(), Utils.rounded(results.getCalibration().getExposureTime() / 1000), Utils.rounded(jumpDistances2D.getMean() / conversionFactor), Utils.rounded(msd2D), Utils.rounded(jumpDistances3D.getMean() / conversionFactor), Utils.rounded(msd3D));
aggregateIntoFrames(points, addError, precisionInPixels, random2);
IJ.showStatus("Analysing results ...");
if (showDiffusionExample) {
showExample(totalSteps, diffusionSigma, random);
}
// Plot a graph of mean squared distance
double[] xValues = new double[stats2D.length];
double[] yValues2D = new double[stats2D.length];
double[] yValues3D = new double[stats3D.length];
double[] upper2D = new double[stats2D.length];
double[] lower2D = new double[stats2D.length];
double[] upper3D = new double[stats3D.length];
double[] lower3D = new double[stats3D.length];
SimpleRegression r2D = new SimpleRegression(false);
SimpleRegression r3D = new SimpleRegression(false);
final int firstN = (useConfinement) ? fitN : totalSteps;
for (int j = 0; j < totalSteps; j++) {
// Convert steps to seconds
xValues[j] = (double) (j + 1) / settings.stepsPerSecond;
// Convert values in pixels^2 to um^2
final double mean2D = stats2D[j].getMean() / conversionFactor;
final double mean3D = stats3D[j].getMean() / conversionFactor;
final double sd2D = stats2D[j].getStandardDeviation() / conversionFactor;
final double sd3D = stats3D[j].getStandardDeviation() / conversionFactor;
yValues2D[j] = mean2D;
yValues3D[j] = mean3D;
upper2D[j] = mean2D + sd2D;
lower2D[j] = mean2D - sd2D;
upper3D[j] = mean3D + sd3D;
lower3D[j] = mean3D - sd3D;
if (j < firstN) {
r2D.addData(xValues[j], yValues2D[j]);
r3D.addData(xValues[j], yValues3D[j]);
}
}
// TODO - Fit using the equation for 2D confined diffusion:
// MSD = 4s^2 + R^2 (1 - 0.99e^(-1.84^2 Dt / R^2)
// s = localisation precision
// R = confinement radius
// D = 2D diffusion coefficient
// t = time
final PolynomialFunction fitted2D, fitted3D;
if (r2D.getN() > 0) {
// Do linear regression to get diffusion rate
final double[] best2D = new double[] { r2D.getIntercept(), r2D.getSlope() };
fitted2D = new PolynomialFunction(best2D);
final double[] best3D = new double[] { r3D.getIntercept(), r3D.getSlope() };
fitted3D = new PolynomialFunction(best3D);
// For 2D diffusion: d^2 = 4D
// where: d^2 = mean-square displacement
double D = best2D[1] / 4.0;
String msg = "2D Diffusion rate = " + Utils.rounded(D, 4) + " um^2 / sec (" + Utils.timeToString(time) + ")";
IJ.showStatus(msg);
Utils.log(msg);
D = best3D[1] / 6.0;
Utils.log("3D Diffusion rate = " + Utils.rounded(D, 4) + " um^2 / sec (" + Utils.timeToString(time) + ")");
} else {
fitted2D = fitted3D = null;
}
// Create plots
plotMSD(totalSteps, xValues, yValues2D, lower2D, upper2D, fitted2D, 2);
plotMSD(totalSteps, xValues, yValues3D, lower3D, upper3D, fitted3D, 3);
plotJumpDistances(TITLE, jumpDistances2D, 2, 1);
plotJumpDistances(TITLE, jumpDistances3D, 3, 1);
if (idCount > 0)
new WindowOrganiser().tileWindows(idList);
if (useConfinement)
Utils.log("3D asymptote distance = %s nm (expected %.2f)", Utils.rounded(asymptote.getMean() * settings.pixelPitch, 4), 3 * settings.confinementRadius / 4);
}
use of ij.plugin.WindowOrganiser in project GDSC-SMLM by aherbert.
the class DiffusionRateTest method simpleTest.
/**
* Perform a simple diffusion test. This can be used to understand the distributions that are generated during
* 3D diffusion.
*/
private void simpleTest() {
if (!showSimpleDialog())
return;
StoredDataStatistics[] stats2 = new StoredDataStatistics[3];
StoredDataStatistics[] stats = new StoredDataStatistics[3];
RandomGenerator[] random = new RandomGenerator[3];
final long seed = System.currentTimeMillis() + System.identityHashCode(this);
for (int i = 0; i < 3; i++) {
stats2[i] = new StoredDataStatistics(simpleParticles);
stats[i] = new StoredDataStatistics(simpleParticles);
random[i] = new Well19937c(seed + i);
}
final double scale = Math.sqrt(2 * simpleD);
final int report = Math.max(1, simpleParticles / 200);
for (int particle = 0; particle < simpleParticles; particle++) {
if (particle % report == 0)
IJ.showProgress(particle, simpleParticles);
double[] xyz = new double[3];
if (linearDiffusion) {
double[] dir = nextVector();
for (int step = 0; step < simpleSteps; step++) {
final double d = ((random[1].nextDouble() > 0.5) ? -1 : 1) * random[0].nextGaussian();
for (int i = 0; i < 3; i++) {
xyz[i] += dir[i] * d;
}
}
} else {
for (int step = 0; step < simpleSteps; step++) {
for (int i = 0; i < 3; i++) {
xyz[i] += random[i].nextGaussian();
}
}
}
for (int i = 0; i < 3; i++) xyz[i] *= scale;
double msd = 0;
for (int i = 0; i < 3; i++) {
msd += xyz[i] * xyz[i];
stats2[i].add(msd);
// Store the actual distances
stats[i].add(xyz[i]);
}
}
IJ.showProgress(1);
for (int i = 0; i < 3; i++) {
plotJumpDistances(TITLE, stats2[i], i + 1);
// Save stats to file for fitting
save(stats2[i], i + 1, "msd");
save(stats[i], i + 1, "d");
}
if (idCount > 0)
new WindowOrganiser().tileWindows(idList);
}
use of ij.plugin.WindowOrganiser in project GDSC-SMLM by aherbert.
the class TraceDiffusion method tileNewWindows.
private void tileNewWindows() {
if (idCount > 0) {
idList = Arrays.copyOf(idList, idCount);
new WindowOrganiser().tileWindows(idList);
}
}
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