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

Example 56 with PathObject

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

the class BrushTool method createShape.

/**
 * Create a new Geometry using the specified tool, assuming a user click/drag at the provided x & y coordinates.
 * @param e
 *
 * @param x
 * @param y
 * @param useTiles If true, request generating a shape from existing tile objects.
 * @param addToShape If provided, it can be assumed that any new shape ought to be added to this one.
 *                   The purpose is that this method may (optionally) use the shape to refine the one it will generate,
 *                   e.g. to avoid having isolated or jagged boundaries.
 * @return
 */
protected Geometry createShape(MouseEvent e, double x, double y, boolean useTiles, Geometry addToShape) {
    // See if we're on top of a tile
    if (useTiles) {
        List<PathObject> listSelectable = getSelectableObjectList(x, y);
        for (PathObject temp : listSelectable) {
            // if ((temp instanceof PathDetectionObject) && temp.getROI() instanceof PathArea)
            if (temp instanceof PathTileObject && temp.hasROI() && temp.getROI().isArea() && !(temp.getROI() instanceof RectangleROI)) {
                creatingTiledROI = true;
                return temp.getROI().getGeometry();
            }
        }
        // If we're currently creating a tiled, ROI, but now not clicked on a tile, just return
        if (creatingTiledROI)
            return null;
    }
    // Compute a diameter scaled according to the pressure being applied
    double diameter = Math.max(1, getBrushDiameter());
    Geometry geometry;
    if (lastPoint == null) {
        var shapeFactory = new GeometricShapeFactory(getGeometryFactory());
        shapeFactory.setCentre(new Coordinate(x, y));
        shapeFactory.setSize(diameter);
        // shapeFactory.setCentre(new Coordinate(x-diameter/2, y-diameter/2));
        geometry = shapeFactory.createEllipse();
    } else {
        if (lastPoint.distanceSq(x, y) == 0)
            return null;
        var factory = getGeometryFactory();
        geometry = factory.createLineString(new Coordinate[] { new Coordinate(lastPoint.getX(), lastPoint.getY()), new Coordinate(x, y) }).buffer(diameter / 2.0);
    }
    return geometry;
}

Example 57 with PathObject

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

the class BrushTool method mouseDragged.

@Override
public void mouseDragged(MouseEvent e) {
    // Note: if the 'freehand' part of the polygon creation isn't desired, just comment out this whole method
    super.mouseDragged(e);
    ensureCursorType(getRequestedCursor());
    if (!e.isPrimaryButtonDown()) {
        return;
    }
    // Can only modify annotations
    var viewer = getViewer();
    PathObject pathObject = viewer.getSelectedObject();
    if (pathObject == null || !pathObject.isAnnotation() || !pathObject.isEditable())
        return;
    if (pathObject != currentObject) {
        logger.warn("Selected object has changed from {} to {}", currentObject, pathObject);
        return;
    }
    ROI currentROI = pathObject.getROI();
    if (!(currentROI instanceof ROI))
        return;
    ROI shapeROI = currentROI;
    PathObject pathObjectUpdated = getUpdatedObject(e, shapeROI, pathObject, -1);
    if (pathObject != pathObjectUpdated) {
        viewer.setSelectedObject(pathObjectUpdated, PathPrefs.selectionModeProperty().get());
    } else {
        viewer.repaint();
    }
}

Example 58 with PathObject

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

the class BrushTool method getUpdatedObject.

private PathObject getUpdatedObject(MouseEvent e, ROI shapeROI, PathObject currentObject, double flatness) {
    Point2D p = mouseLocationToImage(e, true, requestPixelSnapping());
    var viewer = getViewer();
    ImagePlane plane = shapeROI == null ? ImagePlane.getPlane(viewer.getZPosition(), viewer.getTPosition()) : shapeROI.getImagePlane();
    Geometry shapeNew;
    boolean subtractMode = isSubtractMode(e);
    Geometry shapeCurrent = shapeROI == null ? null : shapeROI.getGeometry();
    Geometry shapeDrawn = createShape(e, p.getX(), p.getY(), PathPrefs.useTileBrushProperty().get() && !e.isShiftDown(), subtractMode ? null : shapeCurrent);
    if (shapeDrawn == null)
        return currentObject;
    // Do our pixel snapping now, with the simpler geometry (rather than latter when things are already complex)
    if (requestPixelSnapping())
        shapeDrawn = GeometryTools.roundCoordinates(shapeDrawn);
    lastPoint = p;
    try {
        if (shapeROI != null) {
            // Check to see if any changes are required at all
            if (shapeDrawn == null || (subtractMode && !shapeCurrent.intersects(shapeDrawn)) || (!subtractMode && shapeCurrent.covers(shapeDrawn)))
                return currentObject;
            // TODO: Consider whether a preference should be used rather than the shift key?
            // Anyhow, this will switch to 'dodge' mode, and avoid overlapping existing annotations
            boolean avoidOtherAnnotations = requestParentClipping(e);
            if (subtractMode) {
                // If subtracting... then just subtract
                shapeNew = shapeROI.getGeometry().difference(shapeDrawn);
            } else if (avoidOtherAnnotations) {
                shapeNew = shapeCurrent.union(shapeDrawn);
                shapeNew = refineGeometryByParent(shapeNew);
            } else {
                // Just add, regardless of whether there are other annotations below or not
                var temp = shapeROI.getGeometry();
                try {
                    shapeNew = temp.union(shapeDrawn);
                } catch (Exception e2) {
                    shapeNew = shapeROI.getGeometry();
                }
            }
        } else {
            shapeNew = shapeDrawn;
        }
        // If we aren't snapping, at least remove some vertices
        if (!requestPixelSnapping()) {
            try {
                shapeNew = VWSimplifier.simplify(shapeNew, 0.1);
            } catch (Exception e2) {
                logger.error("Error simplifying ROI: " + e2.getLocalizedMessage(), e2);
            }
        }
        // Make sure we fit inside the image
        shapeNew = GeometryTools.constrainToBounds(shapeNew, 0, 0, viewer.getServerWidth(), viewer.getServerHeight());
        // Sometimes we can end up with a GeometryCollection containing lines/non-areas... if so, remove these
        if (shapeNew instanceof GeometryCollection) {
            shapeNew = GeometryTools.ensurePolygonal(shapeNew);
        }
        ROI roiNew = GeometryTools.geometryToROI(shapeNew, plane);
        if (currentObject instanceof PathAnnotationObject) {
            ((PathAnnotationObject) currentObject).setROI(roiNew);
            return currentObject;
        }
        // shapeNew = new PathAreaROI(new Area(shapeNew.getShape()));
        PathObject pathObjectNew = PathObjects.createAnnotationObject(roiNew, PathPrefs.autoSetAnnotationClassProperty().get());
        if (currentObject != null) {
            pathObjectNew.setName(currentObject.getName());
            pathObjectNew.setColorRGB(currentObject.getColorRGB());
            pathObjectNew.setPathClass(currentObject.getPathClass());
        }
        return pathObjectNew;
    } catch (Exception ex) {
        logger.error("Error updating ROI", ex);
        return currentObject;
    }
}

Example 59 with PathObject

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

the class AbstractPathDraggingROITool method mouseReleased.

@Override
public void mouseReleased(MouseEvent e) {
    if (e.getButton() != MouseButton.PRIMARY) {
        return;
    }
    var viewer = getViewer();
    PathObject selectedObject = viewer.getSelectedObject();
    if (selectedObject == null)
        return;
    RoiEditor editor = viewer.getROIEditor();
    ROI currentROI = selectedObject.getROI();
    if (currentROI != null && editor.getROI() == currentROI && editor.hasActiveHandle()) {
        editor.setROI(null);
        // Remove empty ROIs
        if (currentROI.isEmpty()) {
            if (selectedObject.getParent() != null)
                viewer.getHierarchy().removeObject(selectedObject, true);
            viewer.setSelectedObject(null);
        } else {
            commitObjectToHierarchy(e, selectedObject);
        }
    // editor.ensureHandlesUpdated();
    // editor.resetActiveHandle();
    // if (PathPrefs.getReturnToMoveMode())
    // modes.setMode(Modes.MOVE);
    }
}

Example 60 with PathObject

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

the class AbstractPathTool method getSelectableObjectList.

/**
 * Get a list of all selectable objects overlapping the specified x, y coordinates, ordered by depth in the hierarchy
 * @param x
 * @param y
 * @return
 */
List<PathObject> getSelectableObjectList(double x, double y) {
    var viewer = getViewer();
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    if (hierarchy == null)
        return Collections.emptyList();
    Collection<PathObject> pathObjects = PathObjectTools.getObjectsForLocation(hierarchy, x, y, viewer.getZPosition(), viewer.getTPosition(), viewer.getMaxROIHandleSize());
    if (pathObjects.isEmpty())
        return Collections.emptyList();
    List<PathObject> pathObjectList = new ArrayList<>(pathObjects);
    if (pathObjectList.size() == 1)
        return pathObjectList;
    Collections.sort(pathObjectList, PathObjectHierarchy.HIERARCHY_COMPARATOR);
    return pathObjectList;
}