Java tutorial
package gdsc.smlm.ij.plugins; /*----------------------------------------------------------------------------- * GDSC SMLM Software * * Copyright (C) 2013 Alex Herbert * Genome Damage and Stability Centre * University of Sussex, UK * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 3 of the License, or * (at your option) any later version. *---------------------------------------------------------------------------*/ import gdsc.smlm.ij.IJTrackProgress; import gdsc.smlm.ij.plugins.ResultsManager.InputSource; import gdsc.smlm.ij.utils.Utils; import gdsc.smlm.results.MemoryPeakResults; import gdsc.smlm.results.PeakResult; import gdsc.smlm.results.Trace; import gdsc.smlm.results.TraceManager; import gdsc.smlm.results.clustering.Cluster; import gdsc.smlm.results.clustering.ClusteringAlgorithm; import gdsc.smlm.results.clustering.ClusteringEngine; import gdsc.smlm.utils.StoredDataStatistics; import ij.IJ; import ij.Prefs; import ij.gui.GenericDialog; import ij.gui.Plot2; import ij.plugin.PlugIn; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import org.apache.commons.math3.util.FastMath; /** * Computes a graph of the dark time and estimates the time threshold for the specified point in the * cumulative histogram. */ public class DarkTimeAnalysis implements PlugIn { private static String TITLE = "Dark-time Analysis"; private static String[] METHOD; private static ClusteringAlgorithm[] algorithms = new ClusteringAlgorithm[] { ClusteringAlgorithm.CENTROID_LINKAGE_TIME_PRIORITY, ClusteringAlgorithm.CENTROID_LINKAGE_DISTANCE_PRIORITY, ClusteringAlgorithm.PARTICLE_CENTROID_LINKAGE_TIME_PRIORITY, ClusteringAlgorithm.PARTICLE_CENTROID_LINKAGE_DISTANCE_PRIORITY }; static { ArrayList<String> methods = new ArrayList<String>(); methods.add("Tracing"); for (ClusteringAlgorithm c : algorithms) methods.add("Clustering (" + c.toString() + ")"); METHOD = methods.toArray(new String[methods.size()]); } private static String inputOption = ""; private static int method = 0; private static double msPerFrame = 50; private static double searchDistance = 100; private static double maxDarkTime = 0; private static double percentile = 99; private static int nBins = 100; /* * (non-Javadoc) * * @see ij.plugin.PlugIn#run(java.lang.String) */ public void run(String arg) { // Require some fit results and selected regions if (MemoryPeakResults.countMemorySize() == 0) { IJ.error(TITLE, "There are no fitting results in memory"); return; } if (!showDialog()) return; MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, true); if (results == null || results.size() == 0) { IJ.error(TITLE, "No results could be loaded"); IJ.showStatus(""); return; } msPerFrame = results.getCalibration().exposureTime; Utils.log("%s: %d localisations", TITLE, results.size()); if (results.size() == 0) { IJ.error(TITLE, "No results were loaded"); return; } analyse(results); } private boolean showDialog() { GenericDialog gd = new GenericDialog(TITLE); gd.addHelp(About.HELP_URL); gd.addMessage("Compute the cumulative dark-time histogram"); ResultsManager.addInput(gd, inputOption, InputSource.MEMORY); gd.addChoice("Method", METHOD, METHOD[method]); gd.addSlider("Search_distance (nm)", 5, 150, searchDistance); gd.addNumericField("Max_dark_time (seconds)", maxDarkTime, 2); gd.addSlider("Percentile", 0, 100, percentile); gd.addSlider("Histogram_bins", 0, 100, nBins); gd.showDialog(); if (gd.wasCanceled()) return false; inputOption = gd.getNextChoice(); method = gd.getNextChoiceIndex(); searchDistance = gd.getNextNumber(); maxDarkTime = gd.getNextNumber(); percentile = gd.getNextNumber(); nBins = (int) Math.abs(gd.getNextNumber()); // Check arguments try { Parameters.isAboveZero("Search distance", searchDistance); Parameters.isPositive("Percentile", percentile); } catch (IllegalArgumentException e) { IJ.error(TITLE, e.getMessage()); return false; } return true; } private void analyse(MemoryPeakResults results) { // Find min and max time frames results.sort(); int min = results.getResults().get(0).peak; int max = results.getResults().get(results.size() - 1).getEndFrame(); // Trace results double d = searchDistance / results.getCalibration().nmPerPixel; int range = max - min + 1; if (maxDarkTime > 0) range = FastMath.max(1, (int) Math.round(maxDarkTime * 1000 / msPerFrame)); IJTrackProgress tracker = new IJTrackProgress(); tracker.status("Analysing ..."); tracker.log("Analysing (d=%s nm (%s px) t=%s s (%d frames)) ...", Utils.rounded(searchDistance), Utils.rounded(d), Utils.rounded(range * msPerFrame / 1000.0), range); Trace[] traces; if (method == 0) { TraceManager tm = new TraceManager(results); tm.setTracker(tracker); tm.traceMolecules(d, range); traces = tm.getTraces(); } else { ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), algorithms[method - 1], tracker); List<PeakResult> peakResults = results.getResults(); ArrayList<Cluster> clusters = engine.findClusters(TraceMolecules.convertToClusterPoints(peakResults), d, range); traces = TraceMolecules.convertToTraces(peakResults, clusters); } tracker.status("Computing histogram ..."); // Build dark-time histogram int[] times = new int[range]; StoredDataStatistics stats = new StoredDataStatistics(); for (Trace trace : traces) { if (trace.getNBlinks() > 1) { for (int t : trace.getOffTimes()) { times[t]++; } stats.add(trace.getOffTimes()); } } plotDarkTimeHistogram(stats); // Cumulative histogram for (int i = 1; i < times.length; i++) times[i] += times[i - 1]; int total = times[times.length - 1]; // Plot dark-time up to 100% double[] x = new double[range]; double[] y = new double[range]; int truncate = 0; for (int i = 0; i < x.length; i++) { x[i] = i * msPerFrame; y[i] = (100.0 * times[i]) / total; if (times[i] == total) // 100% { truncate = i + 1; break; } } if (truncate > 0) { x = Arrays.copyOf(x, truncate); y = Arrays.copyOf(y, truncate); } String title = "Cumulative Dark-time"; Plot2 plot = new Plot2(title, "Time (ms)", "Percentile", x, y); Utils.display(title, plot); // Report percentile for (int i = 0; i < y.length; i++) { if (y[i] >= percentile) { Utils.log("Dark-time Percentile %.1f @ %s ms = %s s", percentile, Utils.rounded(x[i]), Utils.rounded(x[i] / 1000)); break; } } tracker.status(""); } private void plotDarkTimeHistogram(StoredDataStatistics stats) { if (nBins > 0) { // Convert the X-axis to milliseconds double[] xValues = stats.getValues(); for (int i = 0; i < xValues.length; i++) xValues[i] *= msPerFrame; // Ensure the bin width is never less than 1 Utils.showHistogram("Dark-time", new StoredDataStatistics(xValues), "Time (ms)", 1, 0, nBins); } } }