Examples with PathROIObject qupath.lib.objects.PathROIObject used on opensource projects

Example 6 with PathROIObject

use of qupath.lib.objects.PathROIObject in project qupath by qupath.

the class RefineAnnotationsPlugin method getTasks.

@Override
protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
    Collection<? extends PathObject> parentObjects = getParentObjects(runner);
    if (parentObjects == null || parentObjects.isEmpty())
        return Collections.emptyList();
    // Add a single task, to avoid multithreading - which may complicate setting parents
    List<Runnable> tasks = new ArrayList<>(1);
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    double minFragmentSize;
    double maxHoleSize, maxHoleSizeTemp;
    ImageServer<T> server = getServer(runner);
    PixelCalibration cal = server.getPixelCalibration();
    if (cal.hasPixelSizeMicrons()) {
        double pixelAreaMicrons = cal.getPixelWidthMicrons() * cal.getPixelHeightMicrons();
        minFragmentSize = params.getDoubleParameterValue("minFragmentSizeMicrons") / pixelAreaMicrons;
        maxHoleSizeTemp = params.getDoubleParameterValue("maxHoleSizeMicrons") / pixelAreaMicrons;
    } else {
        minFragmentSize = params.getDoubleParameterValue("minFragmentSizePixels");
        maxHoleSizeTemp = params.getDoubleParameterValue("maxHoleSizePixels");
    }
    // Handle negative values
    if (maxHoleSizeTemp < 0)
        maxHoleSize = Double.POSITIVE_INFINITY;
    else
        maxHoleSize = maxHoleSizeTemp;
    // Want to reset selection
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    Collection<PathObject> previousSelection = new ArrayList<>(hierarchy.getSelectionModel().getSelectedObjects());
    tasks.add(() -> {
        List<PathObject> toRemove = new ArrayList<>();
        Map<PathROIObject, ROI> toUpdate = new HashMap<>();
        for (PathObject pathObject : parentObjects) {
            ROI roiOrig = pathObject.getROI();
            if (roiOrig == null || !roiOrig.isArea())
                continue;
            ROI roiUpdated = RoiTools.removeSmallPieces(roiOrig, minFragmentSize, maxHoleSize);
            if (roiUpdated == null || roiUpdated.isEmpty())
                toRemove.add(pathObject);
            else if (roiOrig != roiUpdated && pathObject instanceof PathROIObject) {
                toUpdate.put((PathROIObject) pathObject, roiUpdated);
            }
        }
        if (toRemove.isEmpty() && toUpdate.isEmpty())
            return;
        hierarchy.getSelectionModel().clearSelection();
        if (!toRemove.isEmpty())
            hierarchy.removeObjects(toRemove, true);
        if (!toUpdate.isEmpty()) {
            hierarchy.removeObjects(toUpdate.keySet(), true);
            toUpdate.forEach((p, r) -> p.setROI(r));
            hierarchy.addPathObjects(toUpdate.keySet());
        }
        hierarchy.getSelectionModel().selectObjects(previousSelection);
        hierarchy.getSelectionModel().setSelectedObject(selected, true);
    });
    return tasks;
}

Example 7 with PathROIObject

use of qupath.lib.objects.PathROIObject in project qupath by qupath.

the class MoveTool method mouseDragged.

@Override
public void mouseDragged(MouseEvent e) {
    if (mover != null)
        mover.stopMoving();
    super.mouseDragged(e);
    if (!e.isPrimaryButtonDown() || e.isConsumed())
        return;
    // Handle ROIs if the spacebar isn't down
    var viewer = getViewer();
    if (!viewer.isSpaceDown()) {
        RoiEditor editor = viewer.getROIEditor();
        Point2D p = mouseLocationToImage(e, true, false);
        // Try moving handle
        if (editor != null && editor.hasActiveHandle()) {
            double x = p.getX();
            double y = p.getY();
            if (PathPrefs.usePixelSnappingProperty().get() && editor.getROI() != null && editor.getROI().isArea()) {
                x = (int) x;
                y = (int) y;
            }
            ROI updatedROI = editor.setActiveHandlePosition(x, y, viewer.getDownsampleFactor() / 2.0, e.isShiftDown());
            if (updatedROI == null)
                // This shouldn't occur...?
                logger.warn("Updated ROI is null! Will be skipped...");
            else {
                PathObject selectedObject = viewer.getSelectedObject();
                if (selectedObject.getROI() != updatedROI && selectedObject instanceof PathROIObject)
                    ((PathROIObject) selectedObject).setROI(updatedROI);
                // TODO: Check event firing frequency!
                viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(selectedObject), true);
                // viewer.repaint();
                e.consume();
                return;
            }
        }
        // Try to translate, if that's what is happening
        ROI currentROI = viewer.getCurrentROI();
        if (editor != null && editor.isTranslating()) {
            Rectangle2D boundsBefore = AwtTools.getBounds2D(currentROI);
            ROI translatedROI = editor.updateTranslation(p.getX(), p.getY(), viewer.getServerBounds());
            if (translatedROI != null) {
                Rectangle2D boundsAfter = AwtTools.getBounds2D(currentROI);
                Rectangle2D boundsIntersection = new Rectangle2D.Double();
                Rectangle2D.union(boundsBefore, boundsAfter, boundsIntersection);
                ((PathROIObject) viewer.getSelectedObject()).setROI(translatedROI);
                viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(viewer.getSelectedObject()), true);
            // System.err.println("Changing... " + viewer.getHierarchy().nObjects());
            // viewer.repaintImageRegion(boundsIntersection, false);
            }
            pDragging = null;
            return;
        }
        // Try to select objects, if alt is down
        if (e.isAltDown()) {
            tryToSelect(p.getX(), p.getY(), e.getClickCount() - 1, true, false);
            e.consume();
            return;
        }
    }
    // Don't allow dragging if 'zoom to fit' selected
    if (viewer.getZoomToFit())
        return;
    // If we don't have a previous point, we aren't dragging (e.g. there was an alt-click)
    if (pDragging == null)
        return;
    // Extract previous coordinates so we can reuse the Point2D object
    double xPrevious = pDragging.getX();
    double yPrevious = pDragging.getY();
    // Calculate how much the image was dragged
    pDragging = mouseLocationToImage(e, false, false);
    dx = pDragging.getX() - xPrevious;
    dy = pDragging.getY() - yPrevious;
    // Update the viewer
    viewer.setDoFasterRepaint(true);
    viewer.setCenterPixelLocation(viewer.getCenterPixelX() - dx, viewer.getCenterPixelY() - dy);
    // viewer.setDoFasterRepaint(false);
    pDragging = mouseLocationToImage(e, false, false);
    lastDragTimestamp = System.currentTimeMillis();
}

Example 8 with PathROIObject

use of qupath.lib.objects.PathROIObject in project qupath by qupath.

the class AbstractPathDraggingROITool method mouseDragged.

@Override
public void mouseDragged(MouseEvent e) {
    super.mouseDragged(e);
    if (!e.isPrimaryButtonDown()) {
        return;
    }
    var viewer = getViewer();
    ROI currentROI = viewer.getCurrentROI() instanceof ROI ? (ROI) viewer.getCurrentROI() : null;
    RoiEditor editor = viewer.getROIEditor();
    if (currentROI != null && editor.getROI() == currentROI && editor.hasActiveHandle()) {
        PathObject pathObject = viewer.getSelectedObject();
        Point2D p = mouseLocationToImage(e, true, requestPixelSnapping());
        ROI roiUpdated = editor.setActiveHandlePosition(p.getX(), p.getY(), 0.25, e.isShiftDown());
        if (roiUpdated != currentROI) {
            ((PathROIObject) pathObject).setROI(roiUpdated);
            viewer.repaint();
        }
        viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(pathObject), true);
        // editor.setActiveHandlePosition(x, y, minDisplacement, shiftDown)
        // currentROI.updateAdjustment(p.getX(), p.getY(), e.isShiftDown());
        viewer.repaint();
    }
}

Example 9 with PathROIObject

use of qupath.lib.objects.PathROIObject in project qupath by qupath.

the class PointsTool method handleAltClick.

/**
 * Alt-clicks remove the selected point, or selects a new 'family' of points (i.e. a different object) if
 * a point from the current object isn't clicked.
 *
 * @param x
 * @param y
 * @param currentObject
 * @return
 */
private boolean handleAltClick(double x, double y, PathObject currentObject) {
    var viewer = getViewer();
    var viewerPlane = viewer.getImagePlane();
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    double distance = PathPrefs.pointRadiusProperty().get();
    // Remove a point if the current selection has one
    if (currentObject != null && PathObjectTools.hasPointROI(currentObject)) {
        PointsROI points = (PointsROI) currentObject.getROI();
        if (points.getImagePlane().equals(viewerPlane)) {
            ROI points2 = removeNearbyPoint(points, x, y, distance);
            if (points != points2) {
                ((PathROIObject) currentObject).setROI(points2);
                hierarchy.updateObject(currentObject, false);
                // hierarchy.fireHierarchyChangedEvent(this, currentObject);
                return true;
            }
        }
    }
    // Activate a points object if there is one
    for (PathObject pathObject : hierarchy.getPointObjects(PathObject.class)) {
        // Don't check the current object again
        if (pathObject == currentObject || !pathObject.getROI().getImagePlane().equals(viewerPlane))
            continue;
        // See if we've almost clicked on a point
        if (((PointsROI) pathObject.getROI()).getNearest(x, y, distance) != null) {
            viewer.setSelectedObject(pathObject);
            // hierarchy.getSelectionModel().setSelectedPathObject(pathObject);
            return true;
        }
    }
    // Select nothing
    viewer.setSelectedObject(null);
    return true;
}

Example 10 with PathROIObject

use of qupath.lib.objects.PathROIObject in project qupath by qupath.

the class PointsTool method mouseDragged.

@Override
public void mouseDragged(MouseEvent e) {
    super.mouseDragged(e);
    if (!e.isPrimaryButtonDown() || e.isConsumed()) {
        return;
    }
    var viewer = getViewer();
    RoiEditor editor = viewer.getROIEditor();
    if (!(editor.getROI() instanceof PointsROI) || !editor.hasActiveHandle())
        return;
    PointsROI points = getCurrentPoints();
    // Find out the coordinates in the image domain & update the adjustment
    Point2D pAdjusting = mouseLocationToImage(e, true, requestPixelSnapping());
    // double radius = PointsROI.defaultPointRadiusProperty().get();
    PointsROI points2 = (PointsROI) editor.setActiveHandlePosition(pAdjusting.getX(), pAdjusting.getY(), 0.25, e.isShiftDown());
    if (points2 == points)
        return;
    PathROIObject currentObject = (PathROIObject) viewer.getSelectedObject();
    currentObject.setROI(points2);
    viewer.repaint();
// viewer.getHierarchy().fireHierarchyChangedEvent(this, currentObject);
// //		points.updateAdjustment(pAdjusting.getX(), pAdjusting.getY(), e.isShiftDown());
// 
// //		Point2 p = points.getNearest(pAdjusting.getX(), pAdjusting.getY(), radius);
// if (p == null) {
// } else {
// p.setLocation(pAdjusting.getX(), pAdjusting.getY());
// //			points.resetMeasurements();
// viewer.repaint();
// }
}