Examples with TIntProcedure gnu.trove.procedure.TIntProcedure used on opensource projects

Example 6 with TIntProcedure

use of gnu.trove.procedure.TIntProcedure in project GDSC-SMLM by aherbert.

the class DoubletAnalysis method run.

/**
	 * Run.
	 */
private void run() {
    doubletResults = null;
    final ImageStack stack = imp.getImageStack();
    // Get the coordinates per frame
    TIntObjectHashMap<ArrayList<Coordinate>> actualCoordinates = ResultsMatchCalculator.getCoordinates(results.getResults(), false);
    final long[] sumCount = new long[1];
    actualCoordinates.forEachValue(new TObjectProcedure<ArrayList<Coordinate>>() {

        public boolean execute(ArrayList<Coordinate> list) {
            sumCount[0] += list.size();
            return true;
        }
    });
    final double density = 1e6 * sumCount[0] / (simulationParameters.a * simulationParameters.a * results.getBounds().getWidth() * results.getBounds().getHeight() * actualCoordinates.size());
    // Create a pool of workers
    final int nThreads = Prefs.getThreads();
    final BlockingQueue<Integer> jobs = new ArrayBlockingQueue<Integer>(nThreads * 2);
    List<Worker> workers = new LinkedList<Worker>();
    List<Thread> threads = new LinkedList<Thread>();
    Overlay overlay = (showOverlay) ? new Overlay() : null;
    for (int i = 0; i < nThreads; i++) {
        Worker worker = new Worker(jobs, stack, actualCoordinates, fitConfig, overlay);
        Thread t = new Thread(worker);
        workers.add(worker);
        threads.add(t);
        t.start();
    }
    // Fit the frames
    long runTime = System.nanoTime();
    totalProgress = actualCoordinates.size();
    stepProgress = Utils.getProgressInterval(totalProgress);
    progress = 0;
    actualCoordinates.forEachKey(new TIntProcedure() {

        public boolean execute(int frame) {
            put(jobs, frame);
            return true;
        }
    });
    // Finish all the worker threads by passing in a null job
    for (int i = 0; i < threads.size(); i++) {
        put(jobs, -1);
    }
    // Wait for all to finish
    for (int i = 0; i < threads.size(); i++) {
        try {
            threads.get(i).join();
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
    threads.clear();
    threads = null;
    IJ.showProgress(1);
    IJ.showStatus("Collecting results ...");
    runTime = System.nanoTime() - runTime;
    // Collect the results
    int cic = 0, daic = 0, dbic = 0;
    ArrayList<DoubletResult> results = null;
    int maxH = 0, maxH2 = 0, maxH3 = 0;
    for (Worker worker : workers) {
        if (results == null)
            results = worker.results;
        else
            results.addAll(worker.results);
        cic += worker.cic;
        daic += worker.daic;
        dbic += worker.dbic;
        maxH = Maths.max(maxH, worker.spotHistogram.length);
        for (int k = 0; k < 3; k++) {
            maxH2 = Maths.max(maxH2, worker.neighbourHistogram[k].length);
            maxH3 = Maths.max(maxH3, worker.almostNeighbourHistogram[k].length);
        }
    }
    if (cic > 0)
        System.out.printf("Difference AIC %d, BIC %d, Total %d\n", daic, dbic, cic);
    if (showHistograms) {
        double[] spotHistogram = new double[maxH];
        double[] resultHistogram = new double[maxH];
        double[][] neighbourHistogram = new double[3][maxH2];
        double[][] almostNeighbourHistogram = new double[3][maxH3];
        for (Worker worker : workers) {
            final int[] h1a = worker.spotHistogram;
            final int[] h1b = worker.resultHistogram;
            for (int j = 0; j < h1a.length; j++) {
                spotHistogram[j] += h1a[j];
                resultHistogram[j] += h1b[j];
            }
            final int[][] h2 = worker.neighbourHistogram;
            final int[][] h3 = worker.almostNeighbourHistogram;
            for (int k = 0; k < 3; k++) {
                for (int j = 0; j < h2[k].length; j++) neighbourHistogram[k][j] += h2[k][j];
                for (int j = 0; j < h3[k].length; j++) almostNeighbourHistogram[k][j] += h3[k][j];
            }
        }
        showHistogram(0, spotHistogram);
        showHistogram(1, resultHistogram);
        showHistogram(2, neighbourHistogram[0]);
        showHistogram(3, neighbourHistogram[1]);
        showHistogram(4, neighbourHistogram[2]);
        showHistogram(5, almostNeighbourHistogram[0]);
        showHistogram(6, almostNeighbourHistogram[1]);
        showHistogram(7, almostNeighbourHistogram[2]);
    }
    workers.clear();
    workers = null;
    if (overlay != null)
        imp.setOverlay(overlay);
    MemoryPeakResults.freeMemory();
    Collections.sort(results);
    summariseResults(results, density, runTime);
    windowOrganiser.tile();
    IJ.showStatus("");
}

Example 7 with TIntProcedure

use of gnu.trove.procedure.TIntProcedure in project ProPPR by TeamCohen.

the class PosNegRWExample method toString.

public String toString() {
    final StringBuilder sb = new StringBuilder("PosNegRWExample[");
    sb.append(this.name).append(" ");
    sb.append(graph.nodeSize()).append("/").append(graph.edgeSize()).append("; [");
    queryVec.forEachKey(new TIntProcedure() {

        @Override
        public boolean execute(int q) {
            sb.append(q).append(",");
            return true;
        }
    });
    if (sb.length() > 0)
        sb.deleteCharAt(sb.length() - 1);
    sb.append("] -> +[");
    if (posList.length > 0) {
        Dictionary.buildString(posList, sb, ",", true);
    }
    ;
    sb.append("]; -[");
    if (negList.length > 0) {
        Dictionary.buildString(negList, sb, ",", true);
    }
    ;
    sb.append("]]");
    return sb.toString();
}

Example 8 with TIntProcedure

use of gnu.trove.procedure.TIntProcedure in project ProPPR by TeamCohen.

the class LightweightStateGraph method near.

public List<State> near(State u) {
    int ui = this.nodeTab.getId(u);
    if (!near.containsKey(ui))
        return DEFAULT_NEAR;
    TIntArrayList vs = near.get(ui);
    final ArrayList<State> ret = new ArrayList<State>(vs.size());
    vs.forEach(new TIntProcedure() {

        @Override
        public boolean execute(int vi) {
            ret.add(nodeTab.getSymbol(vi));
            return true;
        }
    });
    return ret;
}