use of uk.ac.sussex.gdsc.smlm.model.ImageModel in project GDSC-SMLM by aherbert.
the class CreateData method run.
@Override
public void run(String arg) {
SmlmUsageTracker.recordPlugin(this.getClass(), arg);
extraOptions = ImageJUtils.isExtraOptions();
simpleMode = (arg != null && arg.contains("simple"));
benchmarkMode = (arg != null && arg.contains("benchmark"));
spotMode = (arg != null && arg.contains("spot"));
trackMode = (arg != null && arg.contains("track"));
if ("load".equals(arg)) {
loadBenchmarkData();
return;
}
// Each localisation set is a collection of localisations that represent all localisations
// with the same ID that are on in the same image time frame (Note: the simulation
// can create many localisations per fluorophore per time frame which is useful when
// modelling moving particles)
List<LocalisationModelSet> localisationSets = null;
// Each fluorophore contains the on and off times when light was emitted
List<? extends FluorophoreSequenceModel> fluorophores = null;
if (simpleMode || benchmarkMode || spotMode) {
if (!showSimpleDialog()) {
return;
}
resetMemory();
// 1 second frames
settings.setExposureTime(1000);
areaInUm = settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 1e6;
// Number of spots per frame
int count = 0;
int[] nextN = null;
SpatialDistribution dist;
if (benchmarkMode) {
// --------------------
// BENCHMARK SIMULATION
// --------------------
// Draw the same point on the image repeatedly
count = 1;
dist = createFixedDistribution();
try {
reportAndSaveFittingLimits(dist);
} catch (final Exception ex) {
// This will be from the computation of the CRLB
IJ.error(TITLE, ex.getMessage());
return;
}
} else if (spotMode) {
// ---------------
// SPOT SIMULATION
// ---------------
// The spot simulation draws 0 or 1 random point per frame.
// Ensure we have 50% of the frames with a spot.
nextN = new int[settings.getParticles() * 2];
Arrays.fill(nextN, 0, settings.getParticles(), 1);
RandomUtils.shuffle(nextN, UniformRandomProviders.create());
// Only put spots in the central part of the image
final double border = settings.getSize() / 4.0;
dist = createUniformDistribution(border);
} else {
// -----------------
// SIMPLE SIMULATION
// -----------------
// The simple simulation draws n random points per frame to achieve a specified density.
// No points will appear in multiple frames.
// Each point has a random number of photons sampled from a range.
// We can optionally use a mask. Create his first as it updates the areaInUm
dist = createDistribution();
// Randomly sample (i.e. not uniform density in all frames)
if (settings.getSamplePerFrame()) {
final double mean = areaInUm * settings.getDensity();
ImageJUtils.log("Mean samples = %f", mean);
if (mean < 0.5) {
final GenericDialog gd = new GenericDialog(TITLE);
gd.addMessage("The mean samples per frame is low: " + MathUtils.rounded(mean) + "\n \nContinue?");
gd.enableYesNoCancel();
gd.hideCancelButton();
gd.showDialog();
if (!gd.wasOKed()) {
return;
}
}
final PoissonSampler poisson = new PoissonSampler(createRandomGenerator(), mean);
final StoredDataStatistics samples = new StoredDataStatistics(settings.getParticles());
while (samples.getSum() < settings.getParticles()) {
samples.add(poisson.sample());
}
nextN = new int[samples.getN()];
for (int i = 0; i < nextN.length; i++) {
nextN[i] = (int) samples.getValue(i);
}
} else {
// Use the density to get the number per frame
count = (int) Math.max(1, Math.round(areaInUm * settings.getDensity()));
}
}
UniformRandomProvider rng = null;
localisationSets = new ArrayList<>(settings.getParticles());
final int minPhotons = (int) settings.getPhotonsPerSecond();
final int range = (int) settings.getPhotonsPerSecondMaximum() - minPhotons + 1;
if (range > 1) {
rng = createRandomGenerator();
}
// Add frames at the specified density until the number of particles has been reached
int id = 0;
int time = 0;
while (id < settings.getParticles()) {
// Allow the number per frame to be specified
if (nextN != null) {
if (time >= nextN.length) {
break;
}
count = nextN[time];
}
// Simulate random positions in the frame for the specified density
time++;
for (int j = 0; j < count; j++) {
final double[] xyz = dist.next();
// Ignore within border. We do not want to draw things we cannot fit.
// if (!distBorder.isWithinXy(xyz))
// continue;
// Simulate random photons
final int intensity = minPhotons + ((rng != null) ? rng.nextInt(range) : 0);
final LocalisationModel m = new LocalisationModel(id, time, xyz, intensity, LocalisationModel.CONTINUOUS);
// Each localisation can be a separate localisation set
final LocalisationModelSet set = new LocalisationModelSet(id, time);
set.add(m);
localisationSets.add(set);
id++;
}
}
} else {
if (!showDialog()) {
return;
}
resetMemory();
areaInUm = settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 1e6;
int totalSteps;
double correlation = 0;
ImageModel imageModel;
if (trackMode) {
// ----------------
// TRACK SIMULATION
// ----------------
// In track mode we create fixed lifetime fluorophores that do not overlap in time.
// This is the simplest simulation to test moving molecules.
settings.setSeconds((int) Math.ceil(settings.getParticles() * (settings.getExposureTime() + settings.getTOn()) / 1000));
totalSteps = 0;
final double simulationStepsPerFrame = (settings.getStepsPerSecond() * settings.getExposureTime()) / 1000.0;
imageModel = new FixedLifetimeImageModel(settings.getStepsPerSecond() * settings.getTOn() / 1000.0, simulationStepsPerFrame, createRandomGenerator());
} else {
// ---------------
// FULL SIMULATION
// ---------------
// The full simulation draws n random points in space.
// The same molecule may appear in multiple frames, move and blink.
//
// Points are modelled as fluorophores that must be activated and then will
// blink and photo-bleach. The molecules may diffuse and this can be simulated
// with many steps per image frame. All steps from a frame are collected
// into a localisation set which can be drawn on the output image.
final SpatialIllumination activationIllumination = createIllumination(settings.getPulseRatio(), settings.getPulseInterval());
// Generate additional frames so that each frame has the set number of simulation steps
totalSteps = (int) Math.ceil(settings.getSeconds() * settings.getStepsPerSecond());
// Since we have an exponential decay of activations
// ensure half of the particles have activated by 30% of the frames.
final double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
// Q. Does tOn/tOff change depending on the illumination strength?
imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, settings.getStepsPerSecond() * settings.getTOn() / 1000.0, settings.getStepsPerSecond() * settings.getTOffShort() / 1000.0, settings.getStepsPerSecond() * settings.getTOffLong() / 1000.0, settings.getNBlinksShort(), settings.getNBlinksLong(), createRandomGenerator());
imageModel.setUseGeometricDistribution(settings.getNBlinksGeometricDistribution());
// Only use the correlation if selected for the distribution
if (PHOTON_DISTRIBUTION[PHOTON_CORRELATED].equals(settings.getPhotonDistribution())) {
correlation = settings.getCorrelation();
}
}
imageModel.setPhotonBudgetPerFrame(true);
imageModel.setDiffusion2D(settings.getDiffuse2D());
imageModel.setRotation2D(settings.getRotate2D());
IJ.showStatus("Creating molecules ...");
final SpatialDistribution distribution = createDistribution();
final List<CompoundMoleculeModel> compounds = createCompoundMolecules();
if (compounds == null) {
return;
}
final List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, settings.getParticles(), distribution, settings.getRotateInitialOrientation());
// Activate fluorophores
IJ.showStatus("Creating fluorophores ...");
// Note: molecules list will be converted to compounds containing fluorophores
fluorophores = imageModel.createFluorophores(molecules, totalSteps);
if (fluorophores.isEmpty()) {
IJ.error(TITLE, "No fluorophores created");
return;
}
// Map the fluorophore ID to the compound for mixtures
if (compounds.size() > 1) {
idToCompound = new TIntIntHashMap(fluorophores.size());
for (final FluorophoreSequenceModel l : fluorophores) {
idToCompound.put(l.getId(), l.getLabel());
}
}
IJ.showStatus("Creating localisations ...");
// TODO - Output a molecule Id for each fluorophore if using compound molecules. This allows
// analysis
// of the ratio of trimers, dimers, monomers, etc that could be detected.
totalSteps = checkTotalSteps(totalSteps, fluorophores);
if (totalSteps == 0) {
return;
}
imageModel.setPhotonDistribution(createPhotonDistribution());
try {
imageModel.setConfinementDistribution(createConfinementDistribution());
} catch (final ConfigurationException ex) {
// We asked the user if it was OK to continue and they said no
return;
}
// This should be optimised
imageModel.setConfinementAttempts(10);
final List<LocalisationModel> localisations = imageModel.createImage(molecules, settings.getFixedFraction(), totalSteps, settings.getPhotonsPerSecond() / settings.getStepsPerSecond(), correlation, settings.getRotateDuringSimulation());
// Re-adjust the fluorophores to the correct time
if (settings.getStepsPerSecond() != 1) {
final double scale = 1.0 / settings.getStepsPerSecond();
for (final FluorophoreSequenceModel f : fluorophores) {
f.adjustTime(scale);
}
}
// Integrate the frames
localisationSets = combineSimulationSteps(localisations);
localisationSets = filterToImageBounds(localisationSets);
}
datasetNumber.getAndIncrement();
final List<LocalisationModel> localisations = drawImage(localisationSets);
if (localisations == null || localisations.isEmpty()) {
IJ.error(TITLE, "No localisations created");
return;
}
fluorophores = removeFilteredFluorophores(fluorophores, localisations);
final double signalPerFrame = showSummary(fluorophores, localisations);
if (!benchmarkMode) {
final boolean fullSimulation = (!(simpleMode || spotMode));
saveSimulationParameters(localisations.size(), fullSimulation, signalPerFrame);
}
IJ.showStatus("Saving data ...");
saveFluorophores(fluorophores);
saveImageResults(results);
saveLocalisations(localisations);
// The settings for the filenames may have changed
SettingsManager.writeSettings(settings.build());
IJ.showStatus("Done");
}
use of uk.ac.sussex.gdsc.smlm.model.ImageModel in project GDSC-SMLM by aherbert.
the class BlinkEstimatorTest method estimateBlinking.
private TIntHashSet estimateBlinking(UniformRandomProvider rg, double blinkingRate, double ton, double toff, int particles, double fixedFraction, boolean timeAtLowerBound, boolean doAssert) {
Assumptions.assumeTrue(TestSettings.allow(TestComplexity.MAXIMUM));
final SpatialIllumination activationIllumination = new UniformIllumination(100);
int totalSteps = 100;
final double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
final ImageModel imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, ton, 0, toff, 0, blinkingRate, rg);
final double[] max = new double[] { 256, 256, 32 };
final double[] min = new double[3];
final SpatialDistribution distribution = new UniformDistribution(min, max, rg.nextInt());
final List<CompoundMoleculeModel> compounds = new ArrayList<>(1);
final 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);
final List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, particles, distribution, false);
// Activate fluorophores
final List<? extends FluorophoreSequenceModel> fluorophores = imageModel.createFluorophores(molecules, totalSteps);
totalSteps = checkTotalSteps(totalSteps, fluorophores);
final 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;
// logger.info("Photons = %f", photonStats.getMean());
//
// List<FluorophoreSequenceModel> newFluorophores = new
// ArrayList<FluorophoreSequenceModel>(fluorophores.size());
// for (FluorophoreSequenceModel f : fluorophores)
// {
// if (id[f.getId()])
// newFluorophores.add(f);
// }
// fluorophores = newFluorophores;
final MemoryPeakResults results = new MemoryPeakResults();
final CalibrationWriter calibration = new CalibrationWriter();
calibration.setNmPerPixel(pixelPitch);
calibration.setExposureTime(msPerFrame);
calibration.setCountPerPhoton(1);
results.setCalibration(calibration.getCalibration());
results.setPsf(PsfHelper.create(PSFType.ONE_AXIS_GAUSSIAN_2D));
final float b = 0;
float intensity;
final float z = 0;
for (final LocalisationModel l : localisations) {
// Remove by intensity threshold and optionally at random.
if (l.getIntensity() < minPhotons || rg.nextDouble() < probabilityDelete) {
continue;
}
final int frame = l.getTime();
intensity = (float) l.getIntensity();
final float x = (float) l.getX();
final float y = (float) l.getY();
final float[] params = Gaussian2DPeakResultHelper.createParams(b, intensity, x, y, z, psfWidth);
results.add(frame, 0, 0, 0, 0, 0, 0, params, null);
}
// Add random localisations
// Intensity doesn't matter at the moment for tracing
intensity = (float) photons;
for (int i = (int) (localisations.size() * probabilityAdd); i-- > 0; ) {
final int frame = 1 + rg.nextInt(totalSteps);
final float x = (float) (rg.nextDouble() * max[0]);
final float y = (float) (rg.nextDouble() * max[1]);
final float[] params = Gaussian2DPeakResultHelper.createParams(b, intensity, x, y, z, psfWidth);
results.add(frame, 0, 0, 0, 0, 0, 0, params, null);
}
// Get actual simulated stats ...
final Statistics statsNBlinks = new Statistics();
final Statistics statsTOn = new Statistics();
final Statistics statsTOff = new Statistics();
final Statistics statsSampledNBlinks = new Statistics();
final Statistics statsSampledTOn = new Statistics();
final StoredDataStatistics statsSampledTOff = new StoredDataStatistics();
for (final FluorophoreSequenceModel f : fluorophores) {
statsNBlinks.add(f.getNumberOfBlinks());
statsTOn.add(f.getOnTimes());
statsTOff.add(f.getOffTimes());
final int[] on = f.getSampledOnTimes();
statsSampledNBlinks.add(on.length);
statsSampledTOn.add(on);
statsSampledTOff.add(f.getSampledOffTimes());
}
logger.info(FunctionUtils.getSupplier("N = %d (%d), N-blinks = %f, tOn = %f, tOff = %f, Fixed = %f", fluorophores.size(), localisations.size(), blinkingRate, ton, toff, fixedFraction));
logger.info(FunctionUtils.getSupplier("Actual N-blinks = %f (%f), tOn = %f (%f), tOff = %f (%f), 95%% = %f, max = %f", statsNBlinks.getMean(), statsSampledNBlinks.getMean(), statsTOn.getMean(), statsSampledTOn.getMean(), statsTOff.getMean(), statsSampledTOff.getMean(), statsSampledTOff.getStatistics().getPercentile(95), statsSampledTOff.getStatistics().getMax()));
logger.info("-=-=--=-");
final BlinkEstimator be = new BlinkEstimator();
be.setMaxDarkTime((int) (toff * 10));
be.setMsPerFrame(msPerFrame);
be.setRelativeDistance(false);
final double d = ImageModel.getRandomMoveDistance(diffusionRate);
be.setSearchDistance((fixedFraction < 1) ? Math.sqrt(2 * d * d) * 3 : 0);
be.setTimeAtLowerBound(timeAtLowerBound);
// Assertions.assertTrue("Max dark time must exceed the dark time of the data (otherwise no
// plateau)",
// be.maxDarkTime > statsSampledTOff.getStatistics().getMax());
final int nMolecules = fluorophores.size();
if (usePopulationStatistics) {
blinkingRate = statsNBlinks.getMean();
toff = statsTOff.getMean();
} else {
blinkingRate = statsSampledNBlinks.getMean();
toff = statsSampledTOff.getMean();
}
// See if any fitting regime gets a correct answer
final TIntHashSet ok = new TIntHashSet();
for (int numberOfFittedPoints = MIN_FITTED_POINTS; numberOfFittedPoints <= MAX_FITTED_POINTS; numberOfFittedPoints++) {
be.setNumberOfFittedPoints(numberOfFittedPoints);
be.computeBlinkingRate(results, true);
final double moleculesError = DoubleEquality.relativeError(nMolecules, be.getNMolecules());
final double blinksError = DoubleEquality.relativeError(blinkingRate, be.getNBlinks());
final double offError = DoubleEquality.relativeError(toff * msPerFrame, be.getTOff());
logger.info(FunctionUtils.getSupplier("Error %d: N = %f, blinks = %f, tOff = %f : %f", numberOfFittedPoints, moleculesError, blinksError, offError, (moleculesError + blinksError + offError) / 3));
if (moleculesError < relativeError && blinksError < relativeError && offError < relativeError) {
ok.add(numberOfFittedPoints);
logger.info("-=-=--=-");
logger.info(FunctionUtils.getSupplier("*** Correct at %d fitted points ***", numberOfFittedPoints));
if (doAssert) {
break;
}
}
// if (!be.isIncreaseNFittedPoints())
// break;
}
logger.info("-=-=--=-");
if (doAssert) {
Assertions.assertFalse(ok.isEmpty());
}
// relativeError);
return ok;
}
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