Examples with PointPair uk.ac.sussex.gdsc.core.match.PointPair used on opensource projects

Example 1 with PointPair

use of uk.ac.sussex.gdsc.core.match.PointPair in project GDSC-SMLM by aherbert.

the class TraceMatchCalculator method addPointPairResult.

private void addPointPairResult(StringBuilder sb, Pulse p1, Pulse p2) {
    addPoint(sb, p2);
    final PointPair pair = new PointPair(p1, p2);
    final double d = pair.getXyDistance();
    if (d >= 0) {
        sb.append(MathUtils.rounded(d, 4)).append('\t');
    } else {
        sb.append("-\t");
    }
    if (p1 != null && p2 != null) {
        sb.append(MathUtils.rounded(p1.score(p2, d * d, settings.distanceThreshold), 4)).append('\t');
    } else {
        sb.append("-\t");
    }
}

Example 2 with PointPair

use of uk.ac.sussex.gdsc.core.match.PointPair in project GDSC-SMLM by aherbert.

the class TraceMatchCalculator method compareCoordinates.

@SuppressWarnings("null")
private void compareCoordinates(MemoryPeakResults results1, MemoryPeakResults results2, MemoryPeakResults results3, double distanceThreshold) {
    final Pulse[] p1 = extractPulses(results1);
    final Pulse[] p2 = extractPulses(results2);
    final Pulse[] p3 = extractPulses(results3);
    final List<Pulse> tp = null;
    List<Pulse> fp = null;
    List<Pulse> fn = null;
    List<PointPair> pairs = null;
    final List<Pulse> tp2 = null;
    List<Pulse> fp2 = null;
    List<Pulse> fn2 = null;
    List<PointPair> pairs2 = null;
    if (settings.showPairs) {
        pairs = new LinkedList<>();
        fp = new LinkedList<>();
        fn = new LinkedList<>();
        pairs2 = new LinkedList<>();
        fp2 = new LinkedList<>();
        fn2 = new LinkedList<>();
    }
    final MatchResult result = MatchCalculator.analyseResults2D(p1, p2, distanceThreshold, tp, fp, fn, pairs);
    final MatchResult result2 = MatchCalculator.analyseResults2D(p1, p3, distanceThreshold, tp2, fp2, fn2, pairs2);
    // Create output
    Consumer<String> resultsOutput;
    if (!java.awt.GraphicsEnvironment.isHeadless()) {
        final TextWindow resultsWindow = ImageJUtils.refresh(resultsWindowRef, () -> new TextWindow(TITLE + " Results", createResultsHeader(), "", 900, 300));
        resultsOutput = resultsWindow::append;
        if (settings.showPairs) {
            if (p3 == null) {
                // Produce a pairs output
                final WindowAndPainter wap = refresh(pairsWindowRef, true, resultsWindow, results1);
                // Add the unmatched points
                WindowManager.getIDList();
                for (final Coordinate c : fn) {
                    pairs.add(new PointPair(c, null));
                }
                for (final Coordinate c : fp) {
                    pairs.add(new PointPair(null, c));
                }
                final List<? extends PointPair> sortedPairs = sort(pairs);
                for (final PointPair pair : sortedPairs) {
                    addPairResult(wap.textWindow, pair);
                }
            } else {
                // Produce a triple output
                final WindowAndPainter wap = refresh(triplesWindowRef, false, resultsWindow, results1);
                final HashMap<Pulse, Triple> map = new HashMap<>();
                final ArrayList<Triple> triples = new ArrayList<>(pairs.size());
                for (final PointPair pair : pairs) {
                    final Pulse p = (Pulse) pair.getPoint1();
                    final Triple t = new Triple(p, (Pulse) pair.getPoint2(), null);
                    triples.add(t);
                    map.put(p, t);
                }
                // Complete the reference set of points
                for (final Coordinate c : fn) {
                    final Pulse p = (Pulse) c;
                    final Triple t = new Triple(p, null, null);
                    triples.add(t);
                    map.put(p, t);
                }
                // Add the unmatched points
                for (final Coordinate c : fp) {
                    triples.add(new Triple(null, (Pulse) c, null));
                }
                for (final Coordinate c : fp2) {
                    triples.add(new Triple(null, null, (Pulse) c));
                }
                // Add the results from the second match
                for (final PointPair pair : pairs2) {
                    final Pulse p = (Pulse) pair.getPoint1();
                    final Pulse pp = (Pulse) pair.getPoint2();
                    final Triple triple = map.get(p);
                    if (triple != null) {
                        triple.p3 = pp;
                    } else {
                        triples.add(new Triple(null, null, pp));
                    }
                }
                final List<? extends Triple> sortedTriples = sort(triples);
                for (final Triple t : sortedTriples) {
                    addTripleResult(wap.textWindow, t);
                }
            }
        }
    } else {
        if (writeHeader.compareAndSet(true, false)) {
            IJ.log(createResultsHeader());
        }
        resultsOutput = IJ::log;
    }
    final StringBuilder sb = new StringBuilder();
    addResult(resultsOutput, sb, settings.inputOption1, settings.inputOption2, distanceThreshold, result);
    if (p3 != null) {
        addResult(resultsOutput, sb, settings.inputOption1, settings.inputOption3, distanceThreshold, result2);
    }
}

Example 3 with PointPair

use of uk.ac.sussex.gdsc.core.match.PointPair in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method savePairs.

private void savePairs(MemoryPeakResults results1, MemoryPeakResults results2, List<PointPair> allMatches) {
    if (!settings.savePairs) {
        return;
    }
    // Get the directory
    final String directory = ImageJUtils.getDirectory("Pairs_directory", settings.pairsDirectory);
    if (directory == null) {
        return;
    }
    settings.pairsDirectory = directory;
    final double[] distanceThresholds = getDistances(settings.distanceThreshold, settings.increments, settings.delta);
    // Create output files for each distance band
    final PeakResults[] output1 = new PeakResults[distanceThresholds.length];
    final PeakResults[] output2 = new PeakResults[distanceThresholds.length];
    double high = 0;
    for (int i = 0; i < distanceThresholds.length; i++) {
        final double low = high;
        high = distanceThresholds[i];
        output1[i] = createFilePeakResults(directory, 1, results1, low, high);
        output2[i] = createFilePeakResults(directory, 2, results2, low, high);
    }
    // Square the thresholds
    SimpleArrayUtils.apply(distanceThresholds, v -> v * v);
    final double[] pairDistances = getPairDistances(allMatches);
    int index = 0;
    for (final PointPair pair : allMatches) {
        final int insert = search(distanceThresholds, pairDistances[index++]);
        if (insert != -1) {
            final PeakResult r1 = ((PeakResultPoint) pair.getPoint1()).getPeakResult();
            final PeakResult r2 = ((PeakResultPoint) pair.getPoint2()).getPeakResult();
            output1[insert].add(r1);
            output2[insert].add(r2);
        }
    }
    for (int i = 0; i < output1.length; i++) {
        output1[i].end();
        output2[i].end();
    }
}

Example 4 with PointPair

use of uk.ac.sussex.gdsc.core.match.PointPair in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method showPairs.

/**
 * Show the match pairs in a results table.
 *
 * <p>Adds an ROI painter for the original image source of results set 1 (if it is visible) to the
 * table.
 *
 * @param results1 the first set of results
 * @param pairs the pairs
 * @param resultsWindow the results window
 */
private void showPairs(MemoryPeakResults results1, final List<PointPair> pairs, final TextWindow resultsWindow) {
    if (!settings.showPairs) {
        return;
    }
    final TextWindow pairsWindow = createPairsWindow(resultsWindow, results1.getSource());
    pairsWindow.getTextPanel().clear();
    final Ticker ticker = ImageJUtils.createTicker(pairs.size(), 0, "Writing pairs table");
    try (final BufferedTextWindow bw = new BufferedTextWindow(pairsWindow)) {
        final StringBuilder sb = new StringBuilder();
        for (final PointPair pair : pairs) {
            bw.append(addPairResult(sb, pair));
            ticker.tick();
        }
    }
    ImageJUtils.finished();
}

Example 5 with PointPair

use of uk.ac.sussex.gdsc.core.match.PointPair in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method getPairDistances.

private static double[] getPairDistances(List<PointPair> pairs) {
    final double[] d = new double[pairs.size()];
    int index = 0;
    for (final PointPair pair : pairs) {
        d[index++] = pair.getXyDistanceSquared();
    }
    return d;
}