Examples with TextWindow ij.text.TextWindow used on opensource projects

Example 16 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class TraceMolecules method createSummaryTable.

private void createSummaryTable() {
    if (java.awt.GraphicsEnvironment.isHeadless()) {
        if (header == null) {
            header = createHeader();
            IJ.log(header);
        }
    } else {
        if (summaryTable == null || !summaryTable.isVisible()) {
            summaryTable = new TextWindow(TITLE + " Data Summary", createHeader(), "", 800, 300);
            summaryTable.setVisible(true);
        }
    }
}

Example 17 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class ImageJTablePeakResults method createResultsWindow.

/**
 * Create the result window (if it is not available).
 */
private void createResultsWindow() {
    final String header = createResultsHeader();
    roiPainter = null;
    for (final Frame f : WindowManager.getNonImageWindows()) {
        if (f != null && tableTitle.equals(f.getTitle()) && f instanceof TextWindow) {
            resultsWindow = (TextWindow) f;
            // Check if the existing table matches the desired header
            final String currentHeader = resultsWindow.getTextPanel().getColumnHeadings();
            if (!currentHeader.startsWith(header)) {
                resultsWindow = null;
                continue;
            }
            roiPainter = map.get(resultsWindow.getTextPanel());
            break;
        }
    }
    newWindow = false;
    if (!ImageJUtils.isShowing(resultsWindow)) {
        newWindow = true;
        resultsWindow = new TextWindow(tableTitle, header, "", 800, 300);
        roiPainter = new ImageRoiPainter(resultsWindow.getTextPanel(), "", this);
        // The ROI painter adds itself to the TextPanel as a mouse listener. However
        // the TextPanel addMouseListener() adds to the private TextCanvas object so it
        // cannot be retrieved. Store the painter in a global lookup table.
        map.put(resultsWindow.getTextPanel(), roiPainter);
    }
    tp = resultsWindow.getTextPanel();
    if (roiPainter != null && getSource() != null) {
        roiPainter.setTitle(getSource().getOriginal().getName());
        // Update the coordinate provider (avoids memory leaks with old objects lying around)
        roiPainter.setCoordProvider(this);
        // Get the headings for extracting the coordinates
        final String[] headings = tp.getColumnHeadings().split("\t");
        indexT = indexX = indexY = -1;
        for (int i = 0; i < headings.length; i++) {
            if (headings[i].equals(frameColumnName)) {
                indexT = i;
                continue;
            }
            // Allow for units
            if (headings[i].equals("X") || headings[i].startsWith("X (")) {
                indexX = i;
                continue;
            }
            if (headings[i].equals("Y") || headings[i].startsWith("Y (")) {
                indexY = i;
                continue;
            }
        }
    }
}

Example 18 with TextWindow

use of ij.text.TextWindow 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 19 with TextWindow

use of ij.text.TextWindow 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 20 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class TrackPopulationAnalysis method createModelTable.

/**
 * Creates a table to show the final model. This uses the assignments to create a mixture model
 * from the original data.
 *
 * @param data the data
 * @param weights the weights for each component
 * @param component the component
 */
private static void createModelTable(double[][] data, double[] weights, int[] component) {
    final MixtureMultivariateGaussianDistribution model = MultivariateGaussianMixtureExpectationMaximization.createMixed(data, component);
    final MultivariateGaussianDistribution[] distributions = model.getDistributions();
    // Get the fraction of each component
    final int[] count = new int[MathUtils.max(component) + 1];
    Arrays.stream(component).forEach(c -> count[c]++);
    try (BufferedTextWindow tw = new BufferedTextWindow(ImageJUtils.refresh(modelTableRef, () -> new TextWindow("Track Population Model", createHeader(), "", 800, 300)))) {
        final StringBuilder sb = new StringBuilder();
        for (int i = 0; i < weights.length; i++) {
            sb.setLength(0);
            sb.append(i).append('\t');
            sb.append(MathUtils.rounded((double) count[i] / component.length)).append('\t');
            sb.append(MathUtils.rounded(weights[i]));
            final double[] means = distributions[i].getMeans();
            final double[] sd = distributions[i].getStandardDeviations();
            for (int j = 0; j < means.length; j++) {
                sb.append('\t').append(MathUtils.rounded(means[j])).append('\t').append(MathUtils.rounded(sd[j]));
            }
            tw.append(sb.toString());
        }
    }
}