Examples with OffsetPointRoi uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi used on opensource projects

Example 1 with OffsetPointRoi

use of uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi in project GDSC-SMLM by aherbert.

the class PeakResultTableModelFrame method doSourceOverlay.

private void doSourceOverlay() {
    final PeakResultTableModel model = getModel();
    if (model == null) {
        return;
    }
    final PeakResult[] list = table.getSelectedData();
    if (list.length == 0) {
        return;
    }
    final ImageSource source = model.getSource();
    if (source == null) {
        return;
    }
    final String title = source.getOriginal().getName();
    final ImagePlus imp = WindowManager.getImage(title);
    if (imp == null) {
        return;
    }
    // Assumes 3D stack (no channel/time)
    if (imp.getNDimensions() > 3) {
        return;
    }
    try {
        final TypeConverter<DistanceUnit> converter = CalibrationHelper.getDistanceConverter(model.getCalibration(), DistanceUnit.PIXEL);
        final Overlay o = new Overlay();
        if (list.length == 1) {
            final PeakResult p = list[0];
            final PointRoi roi = new OffsetPointRoi(converter.convert(p.getXPosition()), converter.convert(p.getYPosition()));
            roi.setPointType(3);
            roi.setPosition(p.getFrame());
            o.add(roi);
        } else {
            Arrays.sort(list, FramePeakResultComparator.INSTANCE);
            final TFloatArrayList ox = new TFloatArrayList(list.length);
            final TFloatArrayList oy = new TFloatArrayList(list.length);
            int frame = list[0].getFrame() - 1;
            for (int i = 0; i < list.length; i++) {
                if (frame != list[i].getFrame()) {
                    if (ox.size() > 0) {
                        final PointRoi roi = new OffsetPointRoi(ox.toArray(), oy.toArray());
                        roi.setPointType(3);
                        roi.setPosition(frame);
                        ox.resetQuick();
                        oy.resetQuick();
                        o.add(roi);
                    }
                    frame = list[i].getFrame();
                }
                ox.add(converter.convert(list[i].getXPosition()));
                oy.add(converter.convert(list[i].getYPosition()));
            }
            if (ox.size() > 0) {
                final PointRoi roi = new OffsetPointRoi(ox.toArray(), oy.toArray());
                roi.setPointType(3);
                roi.setPosition(frame);
                o.add(roi);
            }
        }
        imp.setOverlay(o);
        final PeakResult p = list[0];
        imp.setSlice(p.getFrame());
        ImageJUtils.adjustSourceRect(imp, 0, (int) converter.convert(p.getXPosition()), (int) converter.convert(p.getYPosition()));
        imp.getWindow().toFront();
    } catch (final ConversionException ex) {
    // Ignore
    }
}

Example 2 with OffsetPointRoi

use of uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi in project GDSC-SMLM by aherbert.

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus localImp = this.imp;
    if (fitMaxima && singleFrame > 0 && source instanceof IJImageSource) {
        final String title = source.getName();
        localImp = WindowManager.getImage(title);
    }
    if (singleFrame > 0 && localImp != null) {
        MemoryPeakResults memoryResults = null;
        for (final PeakResults r : this.results.toArray()) {
            if (r instanceof MemoryPeakResults) {
                memoryResults = (MemoryPeakResults) r;
                break;
            }
        }
        if (memoryResults == null || memoryResults.size() == 0) {
            return;
        }
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed()) {
            return;
        }
        final LUT lut = LutHelper.createLut(LutColour.ICE);
        final Overlay o = new Overlay();
        final int size = memoryResults.size();
        final Counter j = new Counter(size);
        final ImagePlus finalImp = localImp;
        memoryResults.forEach(DistanceUnit.PIXEL, (XyResultProcedure) (x, y) -> {
            final PointRoi roi = new OffsetPointRoi(x, y);
            final Color c = LutHelper.getColour(lut, j.decrementAndGet(), size);
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (finalImp.getStackSize() > 1) {
                roi.setPosition(singleFrame);
            }
            o.add(roi);
        });
        localImp.setOverlay(o);
        localImp.getWindow().toFront();
    }
}

Example 3 with OffsetPointRoi

use of uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi in project GDSC-SMLM by aherbert.

the class TcPalmAnalysis method runBurstOverlay.

/**
 * Overlay the clusters on the image.
 *
 * @param bursts the bursts
 * @param image the image
 * @param colourMap the colour map
 */
private static void runBurstOverlay(LocalList<LocalList<PeakResult>> bursts, ImageJImagePeakResults image, ColourMap colourMap) {
    if (bursts.isEmpty()) {
        image.getImagePlus().setOverlay(null);
        return;
    }
    final Overlay overlay = new Overlay();
    for (int i = 0; i < bursts.size(); i++) {
        final LocalList<PeakResult> results = bursts.unsafeGet(i);
        final int np = results.size();
        final float[] xp = new float[np];
        final float[] yp = new float[np];
        for (int j = 0; j < np; j++) {
            final PeakResult r = results.unsafeGet(j);
            xp[j] = image.mapX(r.getXPosition());
            yp[j] = image.mapY(r.getYPosition());
        }
        final PointRoi roi = new OffsetPointRoi(xp, yp, np);
        roi.setShowLabels(false);
        roi.setPointType(3);
        final Color c = colourMap.getColour(i);
        roi.setFillColor(c);
        roi.setStrokeColor(c);
        overlay.add(roi);
    }
    image.getImagePlus().setOverlay(overlay);
}

Example 4 with OffsetPointRoi

use of uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi in project GDSC-SMLM by aherbert.

the class SpotInspector method mouseClicked.

private void mouseClicked(MouseEvent event) {
    if (id != currentId.get()) {
        return;
    }
    // Show the result that was double clicked in the result table
    if (event.getClickCount() > 1) {
        final int rank = textPanel.getSelectionStart() + 1;
        // Show the spot that was double clicked
        final ImagePlus imp = WindowManager.getImage(TITLE);
        if (imp != null && rank > 0 && rank <= imp.getStackSize()) {
            imp.setSlice(rank);
            if (imp.getWindow() != null) {
                imp.getWindow().toFront();
            }
            final PeakResult r = rankedResults.get(rank - 1).peakResult;
            final TypeConverter<DistanceUnit> dc = results.getDistanceConverter(DistanceUnit.PIXEL);
            final float rx = dc.convert(r.getXPosition());
            final float ry = dc.convert(r.getYPosition());
            final int x = (int) rx;
            final int y = (int) ry;
            // Find bounds
            final int minX = x - settings.radius;
            final int minY = y - settings.radius;
            // Require the Shift key to add all spots
            if (!event.isShiftDown()) {
                // Add the single clicked spot
                imp.setRoi(new OffsetPointRoi(rx - minX, ry - minY));
                return;
            }
            // Add all the spots
            final int maxX = x + settings.radius + 1;
            final int maxY = y + settings.radius + 1;
            // Create ROIs
            final HashSet<Point2D.Float> spots = new HashSet<>();
            results.forEach(DistanceUnit.PIXEL, (XyResultProcedure) (xp, yp) -> {
                if (xp > minX && xp < maxX && yp > minY && yp < maxY) {
                    // Use only unique points
                    spots.add(new Point2D.Float(xp - minX, yp - minY));
                }
            });
            final int points = spots.size();
            final float[] ox = new float[points];
            final float[] oy = new float[points];
            final Counter c = new Counter();
            spots.forEach(p -> {
                ox[c.getCount()] = p.x;
                oy[c.getAndIncrement()] = p.y;
            });
            imp.setRoi(new OffsetPointRoi(ox, oy, points));
        }
    }
}

Example 5 with OffsetPointRoi

use of uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi in project GDSC-SMLM by aherbert.

the class PsfCreator method createRoi.

private static Roi createRoi(float x, float y, Color color) {
    final Roi roi = new OffsetPointRoi(x, y);
    roi.setStrokeColor(color);
    roi.setFillColor(color);
    return roi;
}