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

Example 51 with TextWindow

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

the class ResultsMatchCalculator method createResultsWindow.

private static TextWindow createResultsWindow(boolean doIdAnalysis) {
    final String header = createResultsHeader(doIdAnalysis);
    final TextWindow resultsWindow = ImageJUtils.refresh(resultsWindowRef, () -> new TextWindow(TITLE + " Results", header, "", 900, 300));
    ImageJUtils.refreshHeadings(resultsWindow, header, true);
    return resultsWindow;
}

Example 52 with TextWindow

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

the class ClassificationMatchCalculator method runCompareClassifications.

private void runCompareClassifications(MemoryPeakResults results1, MemoryPeakResults results2) {
    final List<PointPair> allMatches = new LinkedList<>();
    // Optionally exclude results which do not have an id and/or category
    Predicate<PeakResult> test = settings.useId == ClassAnalysis.IGNORE_ZERO ? r -> r.getId() != 0 : null;
    if (settings.useCategory == ClassAnalysis.IGNORE_ZERO) {
        final Predicate<PeakResult> test2 = r -> r.getCategory() != 0;
        test = test == null ? test2 : test.and(test2);
    } else if (test == null) {
        test = r -> true;
    }
    // Divide the results into time points
    final TIntObjectHashMap<List<PeakResultPoint>> coordinates1 = getCoordinates(results1, test);
    final TIntObjectHashMap<List<PeakResultPoint>> coordinates2 = getCoordinates(results2, test);
    // Process each time point
    int n1 = 0;
    int n2 = 0;
    for (final int t : getTimepoints(coordinates1, coordinates2)) {
        final Coordinate[] c1 = getCoordinates(coordinates1, t);
        final Coordinate[] c2 = getCoordinates(coordinates2, t);
        n1 += c1.length;
        n2 += c2.length;
        final List<PointPair> matches = new LinkedList<>();
        MatchCalculator.analyseResults3D(c1, c2, settings.matchDistance, null, null, null, matches);
        allMatches.addAll(matches);
    }
    if (allMatches.isEmpty()) {
        IJ.error(TITLE, "No localisation matches between the two results sets");
        return;
    }
    // Get the unique Ids and Categories in the matches.
    final Mapper ids = getMapper(allMatches, PeakResult::getId, settings.useId);
    final Mapper cats = getMapper(allMatches, PeakResult::getCategory, settings.useCategory);
    // Map id/category to an index = stride * cat + id
    final int stride = ids.size();
    // Any integer is allowed as an index
    if ((long) stride * cats.size() > 1L << 32) {
        IJ.error(TITLE, "Too many combinations of id and category to assigne unique labels");
        return;
    }
    // Extract indices
    final int[] set1 = new int[allMatches.size()];
    final int[] set2 = new int[allMatches.size()];
    int i = 0;
    for (final PointPair r : allMatches) {
        set1[i] = toIndex(stride, ids, cats, ((PeakResultPoint) r.getPoint1()).getPeakResult());
        set2[i] = toIndex(stride, ids, cats, ((PeakResultPoint) r.getPoint2()).getPeakResult());
        i++;
    }
    final Resequencer re = new Resequencer();
    re.setCacheMap(true);
    re.renumber(set1);
    re.renumber(set2);
    // Compare
    final RandIndex r = new RandIndex().compute(set1, set2);
    final TextWindow resultsWindow = ImageJUtils.refresh(resultsWindowRef, () -> new TextWindow(TITLE + " Results", "Results1\tResults2\tID\tCategory\tn1\tc1\tn2\tc2\tMatched\tRand Index\tAdjusted RI", "", 900, 300));
    try (BufferedTextWindow bw = new BufferedTextWindow(resultsWindow)) {
        final StringBuilder sb = new StringBuilder(2048);
        sb.append(results1.getName()).append('\t');
        sb.append(results2.getName()).append('\t');
        sb.append(ANALYSIS_OPTION[settings.useId.ordinal()]).append('\t');
        sb.append(ANALYSIS_OPTION[settings.useCategory.ordinal()]).append('\t');
        sb.append(n1).append('\t');
        sb.append(MathUtils.max(set1) + 1).append('\t');
        sb.append(n2).append('\t');
        sb.append(MathUtils.max(set2) + 1).append('\t');
        sb.append(set1.length).append('\t');
        sb.append(MathUtils.rounded(r.getRandIndex())).append('\t');
        sb.append(MathUtils.rounded(r.getAdjustedRandIndex())).append('\t');
        bw.append(sb.toString());
    }
}

Example 53 with TextWindow

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

the class ConfigurationTemplate method showTemplateInfo.

/**
 * Show the info from the template.
 *
 * @param name the name
 */
private void showTemplateInfo(String name) {
    final TemplateSettings settings = getTemplate(name);
    if (settings == null || settings.getNotesCount() == 0) {
        return;
    }
    if (infoWindow == null || !infoWindow.isVisible()) {
        infoWindow = new TextWindow(title + " Info", "", "", 450, 250);
        // Put underneath the results window
        if (resultsWindow != null) {
            final Point p = resultsWindow.getLocation();
            p.y += resultsWindow.getHeight();
            infoWindow.setLocation(p);
        }
    }
    infoWindow.getTextPanel().clear();
    for (final String note : settings.getNotesList()) {
        // Text window cannot show tabs
        infoWindow.append(note.replace('\t', ','));
    }
}

Example 54 with TextWindow

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

the class ConfigurationTemplate method updateResults.

/**
 * Update the results window using the current selected slice from the template image.
 *
 * @param slice the slice
 * @return the text window
 */
public TextWindow updateResults(int slice) {
    if (slice == currentSlice || text == null) {
        return resultsWindow;
    }
    currentSlice = slice;
    if (resultsWindow == null || !resultsWindow.isVisible()) {
        resultsWindow = new TextWindow(title + " Results", headings, "", 450, 250);
        // Put next to the image
        final ImagePlus tmpImp = WindowManager.getImage(templateId);
        if (tmpImp != null && tmpImp.getWindow() != null) {
            final ImageWindow iw = tmpImp.getWindow();
            final Point p = iw.getLocation();
            p.x += iw.getWidth();
            resultsWindow.setLocation(p);
        }
    }
    resultsWindow.getTextPanel().clear();
    final String data = text.get(slice);
    if (!TextUtils.isNullOrEmpty(data)) {
        resultsWindow.append(data);
    }
    return resultsWindow;
}

Example 55 with TextWindow

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

the class DiffusionRateTest method msdAnalysis.

/**
 * Tabulate the observed MSD for different jump distances.
 *
 * @param points the points
 */
private void msdAnalysis(ArrayList<Point> points) {
    if (myMsdAnalysisSteps == 0) {
        return;
    }
    IJ.showStatus("MSD analysis ...");
    IJ.showProgress(1, myMsdAnalysisSteps);
    // This will only be fast if the list is an array
    final Point[] list = points.toArray(new Point[0]);
    // Compute the base MSD
    final Point origin = new Point(0, 0, 0);
    double sum = origin.distance2(list[0]);
    int count = 1;
    for (int i = 1; i < list.length; i++) {
        final Point last = list[i - 1];
        final Point current = list[i];
        if (last.id == current.id) {
            sum += last.distance2(current);
        } else {
            sum += origin.distance2(current);
        }
        count++;
    }
    // Create a new set of points that have coordinates that
    // are the rolling average over the number of aggregate steps
    final DoubleRollingArray x = new DoubleRollingArray(pluginSettings.aggregateSteps);
    final DoubleRollingArray y = new DoubleRollingArray(pluginSettings.aggregateSteps);
    int id = 0;
    int length = 0;
    for (final Point p : points) {
        if (p.id != id) {
            x.clear();
            y.clear();
        }
        id = p.id;
        x.add(p.x);
        y.add(p.y);
        // Only create a point if the full aggregation size is reached
        if (x.isFull()) {
            list[length++] = new Point(id, x.getAverage(), y.getAverage());
        }
    }
    // Q - is this useful?
    final double p = myPrecision / settings.getPixelPitch();
    final UniformRandomProvider rng = UniformRandomProviders.create();
    final NormalizedGaussianSampler gauss = SamplerUtils.createNormalizedGaussianSampler(rng);
    final int totalSteps = (int) Math.ceil(settings.getSeconds() * settings.getStepsPerSecond() - pluginSettings.aggregateSteps);
    final int limit = Math.min(totalSteps, myMsdAnalysisSteps);
    final Ticker ticker = ImageJUtils.createTicker(limit, 1);
    final TextWindow msdTable = createMsdTable((sum / count) * settings.getStepsPerSecond() / conversionFactor);
    try (BufferedTextWindow bw = new BufferedTextWindow(msdTable)) {
        bw.setIncrement(0);
        for (int step = 1; step <= myMsdAnalysisSteps; step++) {
            sum = 0;
            count = 0;
            for (int i = step; i < length; i++) {
                final Point last = list[i - step];
                final Point current = list[i];
                if (last.id == current.id) {
                    if (p == 0) {
                        sum += last.distance2(current);
                        count++;
                    } else {
                        // is the same if enough samples are present
                        for (int ii = 1; ii-- > 0; ) {
                            sum += last.distance2(current, p, gauss);
                            count++;
                        }
                    }
                }
            }
            if (count == 0) {
                break;
            }
            bw.append(addResult(step, sum, count));
            ticker.tick();
        }
    }
    IJ.showProgress(1);
}