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

Example 1 with Pulse

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

the class TraceMatchCalculator method extractPulses.

@Nullable
private static Pulse[] extractPulses(MemoryPeakResults results) {
    if (results == null) {
        return null;
    }
    final Pulse[] pulses = new Pulse[results.size()];
    final Counter i = new Counter();
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> pulses[i.getAndIncrement()] = new Pulse(x, y, result.getFrame(), result.getEndFrame()));
    return pulses;
}

Example 2 with Pulse

use of uk.ac.sussex.gdsc.core.match.Pulse 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 Pulse

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

the class TraceMatchCalculator method refresh.

private static WindowAndPainter refresh(AtomicReference<WindowAndPainter> ref, boolean pairs, TextWindow resultsWindow, MemoryPeakResults results1) {
    // Produce a pairs output
    final WindowAndPainter wap = ConcurrencyUtils.refresh(ref, // Test the window is showing
    w -> ImageJUtils.isShowing(w.textWindow), // Create
    () -> {
        final String title = TITLE + ((pairs) ? " Pairs" : " Triples");
        final String header = pairs ? createPairsHeader() : createTriplesHeader();
        final TextWindow window = new TextWindow(title, header, "", 900, 300);
        // Position relative to results window
        final Point p = resultsWindow.getLocation();
        p.y += resultsWindow.getHeight();
        window.setLocation(p);
        final CoordinateProvider coordinateProvider = line -> {
            // Extract the startT and x,y coordinates from the first pulse in the line
            final int[] index = { 0, 5, 12 };
            final String[] fields = line.split("\t");
            for (final int i : index) {
                if (i < fields.length) {
                    if (fields[i].equals("-")) {
                        continue;
                    }
                    final int startT = Integer.parseInt(fields[i]);
                    final double x = Double.parseDouble(fields[i + 2]);
                    final double y = Double.parseDouble(fields[i + 3]);
                    return new double[] { startT, x, y };
                }
            }
            return null;
        };
        final ImageRoiPainter painter = new ImageRoiPainter(window.getTextPanel(), results1.getSource().getOriginal().getName(), coordinateProvider);
        final WindowAndPainter result = new WindowAndPainter(window, painter);
        // Free memory on close
        window.addWindowListener(new WindowAdapter() {

            @Override
            public void windowClosed(WindowEvent event) {
                ref.compareAndSet(result, null);
                super.windowClosed(event);
            }
        });
        return result;
    });
    wap.textWindow.getTextPanel().clear();
    wap.painter.setTitle(results1.getSource().getOriginal().getName());
    return wap;
}

Example 4 with Pulse

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

the class TraceMatchCalculator method addTripleResult.

private void addTripleResult(TextWindow triplesWindow, Triple triple) {
    final StringBuilder sb = new StringBuilder();
    final Pulse p1 = triple.p1;
    final Pulse p2 = triple.p2;
    final Pulse p3 = triple.p3;
    addPoint(sb, p1);
    addPointPairResult(sb, p1, p2);
    addPointPairResult(sb, p1, p3);
    triplesWindow.append(sb.toString());
}

Example 5 with Pulse

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

the class TraceMatchCalculator method addPairResult.

private void addPairResult(TextWindow pairsWindow, PointPair pair) {
    final StringBuilder sb = new StringBuilder();
    final Pulse p1 = (Pulse) pair.getPoint1();
    final Pulse p2 = (Pulse) pair.getPoint2();
    addPoint(sb, p1);
    addPointPairResult(sb, p1, p2);
    pairsWindow.append(sb.toString());
}