Examples with ClusteringSettings uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.ClusteringSettings used on opensource projects

Example 1 with ClusteringSettings

use of uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.ClusteringSettings 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;
}