Examples with RoiManager ij.plugin.frame.RoiManager used on opensource projects

Example 1 with RoiManager

use of ij.plugin.frame.RoiManager in project imagej1 by imagej.

the class OverlayCommands method hide.

void hide() {
    ImagePlus imp = IJ.getImage();
    imp.setHideOverlay(true);
    RoiManager rm = RoiManager.getInstance();
    if (rm != null)
        rm.runCommand("show none");
}

Example 2 with RoiManager

use of ij.plugin.frame.RoiManager in project imagej1 by imagej.

the class OverlayCommands method toRoiManager.

void toRoiManager() {
    ImagePlus imp = IJ.getImage();
    Overlay overlay = imp.getOverlay();
    if (overlay == null) {
        IJ.error("Overlay required");
        return;
    }
    RoiManager rm = RoiManager.getInstance2();
    if (rm == null)
        rm = new RoiManager();
    if (overlay.size() >= 4 && overlay.get(3).getPosition() != 0)
        Prefs.showAllSliceOnly = true;
    rm.runCommand("reset");
    rm.setEditMode(imp, false);
    for (int i = 0; i < overlay.size(); i++) rm.add(imp, overlay.get(i), i + 1);
    rm.setEditMode(imp, true);
    rm.runCommand("show all");
    imp.setOverlay(null);
}

Example 3 with RoiManager

use of ij.plugin.frame.RoiManager in project imagej1 by imagej.

the class RoiInterpolator method run.

public void run(String arg) {
    RoiManager roiman = RoiManager.getInstance();
    if (roiman == null || roiman.getCount() < 2) {
        IJ.error("RoiInterpolator", "Please populate the ROI Manager with at least two ROIs");
        return;
    }
    Roi[] rois = roiman.getRoisAsArray();
    int xmax = 0;
    int xmin = Integer.MAX_VALUE;
    int ymax = 0;
    int ymin = Integer.MAX_VALUE;
    int zmax = 1;
    int zmin = Integer.MAX_VALUE;
    ArrayList<Integer> templateSlices = new ArrayList<Integer>();
    for (Roi roi : rois) {
        int slice = roiman.getSliceNumber(roi.getName());
        if (!templateSlices.contains(new Integer(slice)))
            templateSlices.add(new Integer(slice));
        if (// ignore non-slice associated ROIs
        slice == 0)
            continue;
        zmin = Math.min(slice, zmin);
        zmax = Math.max(slice, zmax);
        Rectangle bounds = roi.getBounds();
        xmin = Math.min(xmin, bounds.x);
        ymin = Math.min(ymin, bounds.y);
        xmax = Math.max(xmax, bounds.x + bounds.width);
        ymax = Math.max(ymax, bounds.y + bounds.height);
    }
    if (templateSlices.size() < 2) {
        IJ.error("RoiInterpolator", "ROIs are all on the same slice, nothing to interpolate");
        return;
    }
    // create the binary stack
    final int stackW = xmax - xmin + 1;
    final int stackH = ymax - ymin + 1;
    final int nSlices = zmax - zmin + 1;
    ImageStack stack = new ImageStack(stackW, stackH);
    for (int s = 0; s < nSlices; s++) {
        ByteProcessor bp = new ByteProcessor(stackW, stackH);
        bp.setColor(255);
        for (Roi roi : rois) {
            int slice = roiman.getSliceNumber(roi.getName());
            if (slice == zmin + s) {
                Rectangle bounds = roi.getBounds();
                roi.setLocation(bounds.x - xmin, bounds.y - ymin);
                bp.setRoi(roi);
                if (roi.getType() == Roi.RECTANGLE)
                    bp.fill();
                else
                    bp.fill(roi);
            }
        }
        stack.addSlice("" + s, bp);
    }
    // do the binary interpolation
    BinaryInterpolator bi = new BinaryInterpolator();
    bi.run(stack);
    ImagePlus binary = new ImagePlus("interpolated", stack);
    // get the ROIs
    ThresholdToSelection ts = new ThresholdToSelection();
    ts.setup("", binary);
    for (int s = 0; s < nSlices; s++) {
        if (templateSlices.contains(new Integer(s + zmin)))
            continue;
        ImageProcessor bp = stack.getProcessor(s + 1);
        int threshold = 255;
        bp.setThreshold(threshold, threshold, ImageProcessor.NO_LUT_UPDATE);
        Roi roi = ts.convert(bp);
        roi.setPosition(s + zmin);
        Rectangle bounds = roi.getBounds();
        roi.setLocation(bounds.x + xmin, bounds.y + ymin);
        roiman.addRoi(roi);
    }
    for (Roi roi : rois) {
        Rectangle bounds = roi.getBounds();
        roi.setLocation(bounds.x + xmin, bounds.y + ymin);
    }
    roiman.runCommand("sort");
    IJ.showStatus("ROIs interpolated");
}

Example 4 with RoiManager

use of ij.plugin.frame.RoiManager in project GDSC-SMLM by aherbert.

the class TcPalmAnalysis method analyseRois.

/**
 * Analyses all the ROIs in the ROI manager.
 *
 * @param event the event
 */
private void analyseRois(ActionEvent event) {
    final RoiManager manager = RoiManager.getInstance();
    if (manager == null) {
        IJ.error(TITLE, "ROI manager is not open");
        return;
    }
    final LocalList<Roi> rois = Arrays.stream(manager.getRoisAsArray()).filter(Roi::isArea).collect(LocalCollectors.toLocalList());
    if (rois.isEmpty()) {
        IJ.error(TITLE, "No area ROIs");
        return;
    }
    // Check for overlaps.
    if (!settings.getDisableOverlapCheck() && anyOverlap(rois)) {
        final GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage(TextUtils.wrap("WARNING - Bounding rectangles of ROIs overlap. You can verify " + "the ROIs on the image using the ROI manager 'Show all' function.", 80));
        gd.setOKLabel("Continue");
        gd.showDialog();
        if (gd.wasCanceled()) {
            return;
        }
    }
    // For each ROI:
    // - Extract the current groups
    // - Build the cumulative count plot
    // - Identify the bursts
    // - Extract ClusterData for each burst
    final TcPalmAnalysisSettings settings = this.settings.build();
    final LocalList<ClusterData> allClusters = rois.parallelStream().map(roi -> {
        final Rectangle2D scaledBounds = createScaledBounds(roi);
        final BiPredicate<ClusterData, Rectangle2D> filter = createSelectionFilter(roi, settings);
        // Filter all cluster groups
        final LocalList<ClusterData> clusters = new LocalList<>();
        clusterData.forEach(c -> {
            if (filter.test(c, scaledBounds)) {
                clusters.add(c);
            }
        });
        // Extract activation bursts
        final CumulativeCountData countData = createCumulativeCountData(clusters, false);
        final LocalList<int[]> bursts = runBurstAnalysis(settings, countData);
        final LocalList<LocalList<PeakResult>> burstLocalisations = createBurstLocalisations(clusters, bursts);
        clusters.clear();
        burstLocalisations.forEach(list -> {
            final ClusterData d = new ClusterData(clusters.size() + 1, list);
            // Save this for analysis
            d.sourceRoi = roi;
            d.getArea();
            clusters.add(d);
        });
        return clusters;
    }).collect(LocalList::new, LocalList::addAll, LocalList::addAll);
    // Reorder
    final Counter count = new Counter();
    allClusters.forEach(c -> c.id = count.incrementAndGet());
    // Display in a table
    final ClusterDataTableModelFrame frame = createAllClustersTable();
    frame.getModel().setData(allClusters, dataCalibration);
    // Allow the results to be repeated
    frame.selectedAction = clusters -> {
        // Expecting a single cluster. No clusters occurs when the table (and selection) is cleared.
        if (clusters.size() == 1) {
            final ClusterData c = clusters.get(0);
            // Push the correct ROI and settings to the analysis action.
            // We do not directly update the ROI or dialog settings as
            // these trigger events that are processed to add work with a delay.
            // Updating them at the end should generate events that are
            // ignored when finally executed as the ROI/settings should be the same.
            addWork(0, c.sourceRoi, settings, () -> {
                // When analysis has finished update the settings and image ROI.
                image.getImagePlus().setRoi(c.sourceRoi);
                darkTimeToleranceTextField.setText(Integer.toString(settings.getDarkTimeTolerance()));
                minClusterSizeTextField.setText(Integer.toString(settings.getMinClusterSize()));
                // When analysis has finished the cluster should be selected in the
                // current clusters table.
                final ClusterDataTableModelFrame currentClusters = currentClustersTable.get();
                if (currentClusters != null) {
                    currentClusters.select(c);
                }
            });
        }
    };
    // Show histogram of cluster size/duration
    reportAnalysis(settings, allClusters, dataCalibration);
    // Save clusters to memory
    final Trace[] traces = allClusters.stream().map(c -> {
        final Trace t = new Trace();
        t.setId(c.id);
        c.results.forEach(t::add);
        return t;
    }).toArray(Trace[]::new);
    TraceMolecules.saveResults(results, traces, "TC PALM");
    IJ.showStatus(TITLE + ": " + TextUtils.pleural(allClusters.size(), "cluster"));
}

Example 5 with RoiManager

use of ij.plugin.frame.RoiManager in project imagej1 by imagej.

the class ImageCanvas method roiManagerSelect.

public boolean roiManagerSelect(Roi roi, boolean delete) {
    RoiManager rm = RoiManager.getInstance();
    if (rm == null)
        return false;
    int index = rm.getRoiIndex(roi);
    if (index < 0)
        return false;
    if (delete) {
        rm.select(imp, index);
        rm.runCommand("delete");
    } else
        rm.selectAndMakeVisible(imp, index);
    return true;
}