Examples with DmttConfiguration uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration used on opensource projects

Example 6 with DmttConfiguration

use of uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration in project GDSC-SMLM by aherbert.

the class TraceDiffusion method showTraceDialog.

private boolean showTraceDialog(ArrayList<MemoryPeakResults> allResults) {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("trace-diffusion"));
    if (!multiMode) {
        ResultsManager.addInput(gd, settings.inputOption, InputSource.MEMORY);
    }
    clusteringSettings = SettingsManager.readClusteringSettings(0).toBuilder();
    gd.addChoice("Mode", TRACE_MODE, clusteringSettings.getTraceDiffusionMode(), new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer value) {
            clusteringSettings.setTraceDiffusionMode(value);
            return collectOptions(false);
        }

        @Override
        public boolean collectOptions() {
            return collectOptions(true);
        }

        private boolean collectOptions(boolean silent) {
            final ExtendedGenericDialog egd = new ExtendedGenericDialog("Trace diffusion options", null);
            // Only 2 modes
            if (clusteringSettings.getTraceDiffusionMode() == 1) {
                // Dynamic Multiple Target Tracing
                final TextField tfD = egd.addAndGetNumericField("Diffusion_coefficient", clusteringSettings.getDiffusionCoefficentMaximum(), 3, 6, "um^2/s");
                final TextField tfW = egd.addAndGetNumericField("Temporal_window", clusteringSettings.getTemporalWindow(), 0, 6, "frames");
                final TextField tfLdw = egd.addAndGetNumericField("Local_diffusion_weight", clusteringSettings.getLocalDiffusionWeight(), 2);
                final TextField tfOiw = egd.addAndGetNumericField("On_intensity_weight", clusteringSettings.getOnIntensityWeight(), 2);
                final TextField tfDdf = egd.addAndGetNumericField("Disappearance_decay_factor", clusteringSettings.getDisappearanceDecayFactor(), 0, 6, "frames");
                final TextField tfDt = egd.addAndGetNumericField("Disappearance_threshold", clusteringSettings.getDisappearanceThreshold(), 0, 6, "frames");
                final Checkbox cbDld = egd.addAndGetCheckbox("Disable_local_diffusion_model", clusteringSettings.getDisableLocalDiffusionModel());
                final Checkbox cbDim = egd.addAndGetCheckbox("Disable_intensity_model", clusteringSettings.getDisableIntensityModel());
                // Allow reset to defaults
                egd.addAndGetButton("Defaults", e -> {
                    final DmttConfiguration config = DmttConfiguration.newBuilder(1).build();
                    tfD.setText(String.valueOf(clusteringSettings.getDiffusionCoefficentMaximum()));
                    tfW.setText(String.valueOf(config.getTemporalWindow()));
                    tfLdw.setText(String.valueOf(config.getLocalDiffusionWeight()));
                    tfOiw.setText(String.valueOf(config.getOnIntensityWeight()));
                    tfDdf.setText(String.valueOf(config.getDisappearanceDecayFactor()));
                    tfDt.setText(String.valueOf(config.getDisappearanceThreshold()));
                    cbDld.setState(config.isDisableLocalDiffusionModel());
                    cbDim.setState(config.isDisableIntensityModel());
                });
            } else {
                // Nearest Neighbour
                egd.addNumericField("Distance_Threshold (nm)", clusteringSettings.getDistanceThreshold(), 0);
                egd.addNumericField("Distance_Exclusion (nm)", clusteringSettings.getDistanceExclusion(), 0);
            }
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            if (clusteringSettings.getTraceDiffusionMode() == 1) {
                // Dynamic Multiple Target Tracing
                clusteringSettings.setDiffusionCoefficentMaximum(egd.getNextNumber());
                clusteringSettings.setTemporalWindow((int) egd.getNextNumber());
                clusteringSettings.setLocalDiffusionWeight(egd.getNextNumber());
                clusteringSettings.setOnIntensityWeight(egd.getNextNumber());
                clusteringSettings.setDisappearanceDecayFactor(egd.getNextNumber());
                clusteringSettings.setDisappearanceThreshold((int) egd.getNextNumber());
                clusteringSettings.setDisableLocalDiffusionModel(egd.getNextBoolean());
                clusteringSettings.setDisableIntensityModel(egd.getNextBoolean());
            } else {
                // Nearest Neighbour
                clusteringSettings.setDistanceThreshold(egd.getNextNumber());
                clusteringSettings.setDistanceExclusion(Math.abs(egd.getNextNumber()));
            }
            return true;
        }
    });
    gd.addSlider("Min_trace_length", 2, 20, clusteringSettings.getMinimumTraceLength());
    gd.addCheckbox("Ignore_ends", clusteringSettings.getIgnoreEnds());
    gd.addCheckbox("Save_traces", clusteringSettings.getSaveTraces());
    gd.showDialog();
    if (gd.wasCanceled() || !readTraceDialog(gd)) {
        return false;
    }
    // Update the settings
    SettingsManager.writeSettings(clusteringSettings.build());
    // Load the results
    if (!multiMode) {
        final MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, true, null, null);
        if (MemoryPeakResults.isEmpty(results)) {
            IJ.error(TITLE, "No results could be loaded");
            IJ.showStatus("");
            return false;
        }
        if (!checkCalibration(results)) {
            return false;
        }
        allResults.add(results);
    }
    return true;
}

Example 7 with DmttConfiguration

use of uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration in project GDSC-SMLM by aherbert.

the class DynamicMultipleTargetTracingTest method checkBuilderDefaults.

@SeededTest
void checkBuilderDefaults(RandomSeed seed) {
    final UniformRandomProvider rng = RngUtils.create(seed.getSeed());
    final double diffusionCoefficientMaximum = 1 + rng.nextDouble();
    final DmttConfiguration.Builder b = DmttConfiguration.newBuilder(diffusionCoefficientMaximum);
    final DmttConfiguration c1 = b.build();
    // Check round-trip
    for (final DmttConfiguration config : new DmttConfiguration[] { c1, c1.toBuilder().build() }) {
        Assertions.assertEquals(diffusionCoefficientMaximum, config.getDiffusionCoefficientMaximum());
        Assertions.assertTrue(config.getTemporalWindow() > 1);
        Assertions.assertTrue(config.getLocalDiffusionWeight() >= 0);
        Assertions.assertTrue(config.getLocalDiffusionWeight() <= 1);
        Assertions.assertTrue(config.getOnIntensityWeight() >= 0);
        Assertions.assertTrue(config.getOnIntensityWeight() <= 1);
        Assertions.assertTrue(config.getDisappearanceDecayFactor() > 0);
        Assertions.assertTrue(config.getDisappearanceThreshold() > 0);
        Assertions.assertFalse(config.isDisableIntensityModel());
        Assertions.assertFalse(config.isDisableLocalDiffusionModel());
    }
}

Example 8 with DmttConfiguration

use of uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration in project GDSC-SMLM by aherbert.

the class DynamicMultipleTargetTracingTest method testTraceMoleculesDisableLocalDiffusionModel.

/**
 * Test trace molecules using 2 molecules. One is fixed and the other moves past it. The tracing
 * should assign the fixed molecule correctly as it has a low local diffusion rate.
 */
@Test
void testTraceMoleculesDisableLocalDiffusionModel() {
    // The test is not very robust and fails 20% of the time. A fixed seed corrects this.
    final UniformRandomProvider rng = RngUtils.create(0x12345L);
    final NormalizedGaussianSampler gauss = SamplerUtils.createNormalizedGaussianSampler(rng);
    // localisation precision (in pixels)
    final double s = 0.1;
    final SharedStateContinuousSampler intensity1 = SamplerUtils.createGaussianSampler(rng, 1000, 100);
    final SharedStateContinuousSampler intensity2 = SamplerUtils.createGaussianSampler(rng, 500, 50);
    final MemoryPeakResults results = new MemoryPeakResults(100);
    final CalibrationWriter writer = results.getCalibrationWriterSafe();
    // 0.1 um pixels, 1 second exposure time
    writer.setDistanceUnit(DistanceUnit.PIXEL);
    writer.setNmPerPixel(100);
    writer.setExposureTime(1000);
    results.setCalibration(writer.getCalibration());
    // First molecule diffuses roughly across the field from top-left to bottom-right.
    // 5 frames is the default for local stats, 15 frames for trajectory removal.
    // Use 20 so we build local stats and can expire a trajectory.
    final int size = 20;
    for (int i = 0; i < size; i++) {
        results.add(new PeakResult(i, (float) (i + gauss.sample() * s), (float) (i + gauss.sample() * s), (float) (intensity1.sample())));
    }
    // Second molecule is fixed in the centre with a lower intensity (allow
    // correct matching when tracks overlap)
    final int x = size / 2;
    for (int i = 0; i < size; i++) {
        results.add(new PeakResult(i, (float) (x + gauss.sample() * s), (float) (x + gauss.sample() * s), (float) (intensity2.sample())));
    }
    // Add a single molecule that will not connect to anything in the second frame.
    // This should create a trajectory that will expire.
    results.add(new PeakResult(1, size, size, (float) (intensity1.sample())));
    // Move centre to centre each jump => sqrt(2 * 0.1^2) = 0.141 um or 0.02 um^2
    // MSD = 4D => D = 0.02 / 4 = 0.005
    final DmttConfiguration config = DmttConfiguration.newBuilder(0.005).setDisableLocalDiffusionModel(true).setTemporalWindow(10).build();
    final List<Trace> traces = new DynamicMultipleTargetTracing(results).traceMolecules(config);
    // Should have 3 traces
    Assertions.assertEquals(3, traces.size());
    // Assert ids start from 1
    for (int i = 0; i < traces.size(); i++) {
        Assertions.assertEquals(i + 1, traces.get(i).getId());
    }
    // Traces should be 2 full length and 1 single peak
    Assertions.assertEquals(size, traces.get(0).size());
    Assertions.assertEquals(size, traces.get(1).size());
    Assertions.assertEquals(1, traces.get(2).size());
    // Do an analysis on the actual tracks.
    // One should be based in the centre and the other should have parts close to position (i,i)
    // for each frame i.
    final PeakResult[] peaks = results.toArray();
    // Assume traces are initially created using the input order of the results.
    final Trace t1 = traces.get(0);
    final Trace t2 = traces.get(1);
    for (int i = 0; i < size; i++) {
        Assertions.assertSame(peaks[i], t1.get(i));
        Assertions.assertSame(peaks[i + size], t2.get(i));
    }
}

Example 9 with DmttConfiguration

use of uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration in project GDSC-SMLM by aherbert.

the class DynamicMultipleTargetTracingTest method testTraceMolecules.

/**
 * Test trace molecules using 2 molecules. One is fixed and the other moves across it. The tracing
 * should assign the fixed molecule correctly as it has a low local diffusion rate and different
 * intensity.
 */
@Test
void testTraceMolecules() {
    // The test is not very robust and fails 10% of the time. A fixed seed corrects this.
    final UniformRandomProvider rng = RngUtils.create(0x12345L);
    final NormalizedGaussianSampler gauss = SamplerUtils.createNormalizedGaussianSampler(rng);
    // localisation precision (in pixels)
    final double s = 0.1;
    final SharedStateContinuousSampler intensity1 = SamplerUtils.createGaussianSampler(rng, 1000, 100);
    final SharedStateContinuousSampler intensity2 = SamplerUtils.createGaussianSampler(rng, 500, 50);
    final MemoryPeakResults results = new MemoryPeakResults(100);
    final CalibrationWriter writer = results.getCalibrationWriterSafe();
    // 0.1 um pixels, 1 second exposure time
    writer.setDistanceUnit(DistanceUnit.PIXEL);
    writer.setNmPerPixel(100);
    writer.setExposureTime(1000);
    results.setCalibration(writer.getCalibration());
    // First molecule diffuses roughly across the field from top-left to bottom-right.
    // 5 frames is the default for local stats, 15 frames for trajectory removal.
    // Use 20 so we build local stats and can expire a trajectory.
    final int size = 20;
    for (int i = 0; i < size; i++) {
        results.add(new PeakResult(i, (float) (i + gauss.sample() * s), (float) (i + gauss.sample() * s), (float) (intensity1.sample())));
    }
    // Second molecule is fixed in the centre with a lower intensity (allow
    // correct matching when tracks overlap)
    final int x = size / 2;
    for (int i = 0; i < size; i++) {
        results.add(new PeakResult(i, (float) (x + gauss.sample() * s), (float) (x + gauss.sample() * s), (float) (intensity2.sample())));
    }
    // Add a single molecule that will not connect to anything in the second frame.
    // This should create a trajectory that will expire.
    results.add(new PeakResult(1, size, size, (float) (intensity1.sample())));
    // 1 diffuses top-left to bottom-right.
    // 2 is fixed in the centre.
    // 3 is in the bottom-right for 1 frame.
    // 
    // 1
    // 1
    // 1
    // 12
    // 1
    // 1
    // 13
    // 
    // Molecule 3 can sometimes connect to the long lifetime molecules once they have been alive
    // long enough to create a local probability model. The default lifetime is 5 frames.
    // Setting this to 10 frames allows a better local model to be created.
    // Move centre to centre each jump => sqrt(2 * 0.1^2) = 0.141 um or 0.02 um^2
    // MSD = 4D => D = 0.02 / 4 = 0.005
    final DmttConfiguration config = DmttConfiguration.newBuilder(0.005).setTemporalWindow(10).build();
    final List<Trace> traces = new DynamicMultipleTargetTracing(results).traceMolecules(config);
    // Should have 3 traces
    Assertions.assertEquals(3, traces.size());
    // Assert ids start from 1
    for (int i = 0; i < traces.size(); i++) {
        Assertions.assertEquals(i + 1, traces.get(i).getId());
    }
    // Traces should be 2 full length and 1 single peak
    Assertions.assertEquals(size, traces.get(0).size());
    Assertions.assertEquals(size, traces.get(1).size());
    Assertions.assertEquals(1, traces.get(2).size());
    // Do an analysis on the actual tracks.
    // One should be based in the centre and the other should have parts close to position (i,i)
    // for each frame i.
    final PeakResult[] peaks = results.toArray();
    // Assume traces are initially created using the input order of the results.
    final Trace t1 = traces.get(0);
    final Trace t2 = traces.get(1);
    for (int i = 0; i < size; i++) {
        Assertions.assertSame(peaks[i], t1.get(i));
        Assertions.assertSame(peaks[i + size], t2.get(i));
    }
}