Examples with XyResultProcedure uk.ac.sussex.gdsc.smlm.results.procedures.XyResultProcedure used on opensource projects

Example 1 with XyResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.XyResultProcedure 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 2 with XyResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.XyResultProcedure 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 3 with XyResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.XyResultProcedure in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method getPoints.

/**
 * Gets the points.
 *
 * @param results the results
 * @param settings the settings
 * @return the points
 */
static LocalList<Point3f> getPoints(MemoryPeakResults results, ImageJ3DResultsViewerSettingsOrBuilder settings) {
    final LocalList<Point3f> points = new LocalList<>(results.size());
    if (results.is3D()) {
        results.forEach(DistanceUnit.NM, (XyzResultProcedure) (x, y, z) -> {
            points.push(new Point3f(x, y, z));
        });
    } else {
        results.forEach(DistanceUnit.NM, (XyResultProcedure) (x, y) -> {
            points.push(new Point3f(x, y, 0));
        });
        final double range = settings.getDepthRange();
        if (range > 0 && results.size() > 1) {
            final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
            final double min = -settings.getDepthRange() / 2;
            switch(mode) {
                case DITHER:
                    final SplitMix r = SplitMix.new64(settings.getDitherSeed());
                    for (int i = points.size(); i-- > 0; ) {
                        points.unsafeGet(i).z += (min + r.nextDouble() * range);
                    }
                    break;
                case INTENSITY:
                    // Rank by intensity, highest first
                    final StandardResultProcedure p = new StandardResultProcedure(results);
                    p.getI();
                    final int[] indices = SimpleArrayUtils.natural(results.size());
                    SortUtils.sortIndices(indices, p.intensity, true);
                    final double inc = range / indices.length;
                    for (int i = 0; i < indices.length; i++) {
                        // The standard rendering has +z going away so put the highest rank at min
                        points.unsafeGet(indices[i]).z += (min + i * inc);
                    }
                    break;
                case NONE:
                    break;
                default:
                    throw new IllegalStateException("Unknown depth mode: " + mode);
            }
        }
    }
    return points;
}