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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;
}
Also used : Color(java.awt.Color) Arrays(java.util.Arrays) HistogramPlotBuilder(uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder) ConfigurationException(uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException) TextWindow(ij.text.TextWindow) RealVector(org.apache.commons.math3.linear.RealVector) ImageJPluginLoggerHelper(uk.ac.sussex.gdsc.core.ij.ImageJPluginLoggerHelper) StoredDataStatistics(uk.ac.sussex.gdsc.core.utils.StoredDataStatistics) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) MathUtils(uk.ac.sussex.gdsc.core.utils.MathUtils) CalibrationWriter(uk.ac.sussex.gdsc.smlm.data.config.CalibrationWriter) Path(java.nio.file.Path) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) ArrayPeakResultStore(uk.ac.sussex.gdsc.smlm.results.ArrayPeakResultStore) ClusteringSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.ClusteringSettings) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) InputSource(uk.ac.sussex.gdsc.smlm.ij.plugins.ResultsManager.InputSource) ConvergenceException(org.apache.commons.math3.exception.ConvergenceException) MultivariateVectorFunction(org.apache.commons.math3.analysis.MultivariateVectorFunction) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) Gaussian2DPeakResultHelper(uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultHelper) Logger(java.util.logging.Logger) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) Plot(ij.gui.Plot) CalibrationHelper(uk.ac.sussex.gdsc.smlm.data.config.CalibrationHelper) List(java.util.List) LeastSquaresBuilder(org.apache.commons.math3.fitting.leastsquares.LeastSquaresBuilder) Converter(uk.ac.sussex.gdsc.core.data.utils.Converter) SimpleArrayUtils(uk.ac.sussex.gdsc.core.utils.SimpleArrayUtils) FileUtils(uk.ac.sussex.gdsc.core.utils.FileUtils) PlugIn(ij.plugin.PlugIn) JumpDistanceAnalysis(uk.ac.sussex.gdsc.smlm.fitting.JumpDistanceAnalysis) TraceManager(uk.ac.sussex.gdsc.smlm.results.TraceManager) LevenbergMarquardtOptimizer(org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer) WindowOrganiser(uk.ac.sussex.gdsc.core.ij.plugin.WindowOrganiser) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) DmttConfiguration(uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration) AtomicReference(java.util.concurrent.atomic.AtomicReference) Function(java.util.function.Function) TextField(java.awt.TextField) OptionListener(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionListener) ArrayList(java.util.ArrayList) Level(java.util.logging.Level) Trace(uk.ac.sussex.gdsc.smlm.results.Trace) MultiDialog(uk.ac.sussex.gdsc.core.ij.gui.MultiDialog) CurveLogger(uk.ac.sussex.gdsc.smlm.fitting.JumpDistanceAnalysis.CurveLogger) Statistics(uk.ac.sussex.gdsc.core.utils.Statistics) SimpleImageJTrackProgress(uk.ac.sussex.gdsc.core.ij.SimpleImageJTrackProgress) Files(java.nio.file.Files) Checkbox(java.awt.Checkbox) BufferedWriter(java.io.BufferedWriter) StdMath(uk.ac.sussex.gdsc.smlm.utils.StdMath) IOException(java.io.IOException) LeastSquaresProblem(org.apache.commons.math3.fitting.leastsquares.LeastSquaresProblem) DynamicMultipleTargetTracing(uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing) TooManyIterationsException(org.apache.commons.math3.exception.TooManyIterationsException) CalibrationReader(uk.ac.sussex.gdsc.smlm.data.config.CalibrationReader) Consumer(java.util.function.Consumer) Gaussian2DPeakResultCalculator(uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultCalculator) Paths(java.nio.file.Paths) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) IJ(ij.IJ) DiagonalMatrix(org.apache.commons.math3.linear.DiagonalMatrix) PeakResultStoreList(uk.ac.sussex.gdsc.smlm.results.PeakResultStoreList) Optimum(org.apache.commons.math3.fitting.leastsquares.LeastSquaresOptimizer.Optimum) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) DmttConfiguration(uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing.DmttConfiguration) Checkbox(java.awt.Checkbox) TextField(java.awt.TextField) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog)

Aggregations

IJ (ij.IJ)1 Plot (ij.gui.Plot)1 PlugIn (ij.plugin.PlugIn)1 TextWindow (ij.text.TextWindow)1 Checkbox (java.awt.Checkbox)1 Color (java.awt.Color)1 TextField (java.awt.TextField)1 BufferedWriter (java.io.BufferedWriter)1 IOException (java.io.IOException)1 Files (java.nio.file.Files)1 Path (java.nio.file.Path)1 Paths (java.nio.file.Paths)1 ArrayList (java.util.ArrayList)1 Arrays (java.util.Arrays)1 List (java.util.List)1 AtomicReference (java.util.concurrent.atomic.AtomicReference)1 Consumer (java.util.function.Consumer)1 Function (java.util.function.Function)1 Level (java.util.logging.Level)1 Logger (java.util.logging.Logger)1