Examples with ClusterPoint uk.ac.sussex.gdsc.core.clustering.ClusterPoint used on opensource projects

Example 1 with ClusterPoint

use of uk.ac.sussex.gdsc.core.clustering.ClusterPoint in project GDSC-SMLM by aherbert.

the class PcPalmClusters method convertToPoint.

/**
 * Convert molecules for clustering.
 *
 * @param molecules the molecules
 * @return the list of cluster points
 */
private List<ClusterPoint> convertToPoint(List<Molecule> molecules) {
    final ArrayList<ClusterPoint> points = new ArrayList<>(molecules.size());
    int id = 0;
    for (final Molecule m : molecules) {
        points.add(ClusterPoint.newClusterPoint(id++, m.x, m.y, (weightedClustering) ? m.photons : 1));
    }
    return points;
}

Example 2 with ClusterPoint

use of uk.ac.sussex.gdsc.core.clustering.ClusterPoint in project GDSC-SMLM by aherbert.

the class TraceMolecules method convertToTraces.

/**
 * Convert the clusters from the clustering engine into traces composed of the original list of
 * peak results.
 *
 * @param results the results
 * @param clusters the clusters
 * @return the traces
 */
public static Trace[] convertToTraces(MemoryPeakResults results, List<Cluster> clusters) {
    final Trace[] traces = new Trace[clusters.size()];
    int index = 0;
    for (final Cluster cluster : clusters) {
        final Trace trace = new Trace();
        trace.setId(index + 1);
        for (ClusterPoint point = cluster.getHeadClusterPoint(); point != null; point = point.getNext()) {
            // The point Id was the position in the original results array
            trace.add(results.get(point.getId()));
        }
        trace.sort();
        traces[index++] = trace;
    }
    return traces;
}

Example 3 with ClusterPoint

use of uk.ac.sussex.gdsc.core.clustering.ClusterPoint in project GDSC-SMLM by aherbert.

the class TraceMolecules method convertToClusterPoints.

/**
 * Convert a list of peak results into points for the clustering engine.
 *
 * @param results the results
 * @return the list of clusters
 */
public static List<ClusterPoint> convertToClusterPoints(MemoryPeakResults results) {
    final ArrayList<ClusterPoint> points = new ArrayList<>(results.size());
    final Counter counter = new Counter();
    results.forEach((PeakResultProcedure) result -> points.add(ClusterPoint.newTimeClusterPoint(counter.getAndIncrement(), result.getXPosition(), result.getYPosition(), result.getIntensity(), result.getFrame(), result.getEndFrame())));
    return points;
}

Example 4 with ClusterPoint

use of uk.ac.sussex.gdsc.core.clustering.ClusterPoint in project GDSC-SMLM by aherbert.

the class PcPalmMolecules method performDistanceAnalysis.

private void performDistanceAnalysis(double[][] intraHist, int p99) {
    // We want to know the fraction of distances between molecules at the 99th percentile
    // that are intra- rather than inter-molecule.
    // Do single linkage clustering of closest pair at this distance and count the number of
    // links that are inter and intra.
    // Convert molecules for clustering
    final ArrayList<ClusterPoint> points = new ArrayList<>(settings.molecules.size());
    for (final Molecule m : settings.molecules) {
        // Precision was used to store the molecule ID
        points.add(ClusterPoint.newClusterPoint((int) m.precision, m.x, m.y, m.photons));
    }
    final ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), ClusteringAlgorithm.PARTICLE_SINGLE_LINKAGE, SimpleImageJTrackProgress.getInstance());
    IJ.showStatus("Clustering to check inter-molecule distances");
    engine.setTrackJoins(true);
    final List<Cluster> clusters = engine.findClusters(points, intraHist[0][p99]);
    IJ.showStatus("");
    if (clusters != null) {
        final double[] intraIdDistances = engine.getIntraIdDistances();
        final double[] interIdDistances = engine.getInterIdDistances();
        final int all = interIdDistances.length + intraIdDistances.length;
        log("  * Fraction of inter-molecule particle linkage @ %s nm = %s %%", MathUtils.rounded(intraHist[0][p99], 4), (all > 0) ? MathUtils.rounded(100.0 * interIdDistances.length / all, 4) : "0");
        // Show a double cumulative histogram plot
        final double[][] intraIdHist = MathUtils.cumulativeHistogram(intraIdDistances, false);
        final double[][] interIdHist = MathUtils.cumulativeHistogram(interIdDistances, false);
        // Plot
        final String title = TITLE + " molecule linkage distance";
        final Plot plot = new Plot(title, "Distance", "Frequency");
        plot.addPoints(intraIdHist[0], intraIdHist[1], Plot.LINE);
        double max = (intraIdHist[1].length > 0) ? intraIdHist[1][intraIdHist[1].length - 1] : 0;
        if (interIdHist[1].length > 0) {
            max = Math.max(max, interIdHist[1][interIdHist[1].length - 1]);
        }
        plot.setLimits(0, intraIdHist[0][intraIdHist[0].length - 1], 0, max);
        plot.setColor(Color.blue);
        plot.addPoints(interIdHist[0], interIdHist[1], Plot.LINE);
        plot.setColor(Color.black);
        plot.addLegend("Intra-molecule\nInter-molecule");
        ImageJUtils.display(title, plot);
    } else {
        log("Aborted clustering to check inter-molecule distances");
    }
}