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

Example 51 with PathObject

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

the class AbstractPathROITool method commitObjectToHierarchy.

/**
 * When drawing an object is complete, add it to the hierarchy - or whatever else is required.
 *
 * @param e
 * @param pathObject
 */
void commitObjectToHierarchy(MouseEvent e, PathObject pathObject) {
    if (pathObject == null)
        return;
    var viewer = getViewer();
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    var currentROI = pathObject.getROI();
    // If we are in selection mode, try to get objects to select
    if (PathPrefs.selectionModeProperty().get()) {
        var pathClass = PathPrefs.autoSetAnnotationClassProperty().get();
        var toSelect = hierarchy.getObjectsForROI(null, currentROI);
        if (!toSelect.isEmpty() && pathClass != null) {
            boolean retainIntensityClass = !(PathClassTools.isPositiveOrGradedIntensityClass(pathClass) || PathClassTools.isNegativeClass(pathClass));
            var reclassified = toSelect.stream().filter(p -> p.getPathClass() != pathClass).map(p -> new Reclassifier(p, pathClass, retainIntensityClass)).filter(r -> r.apply()).map(r -> r.getPathObject()).collect(Collectors.toList());
            if (!reclassified.isEmpty()) {
                hierarchy.fireObjectClassificationsChangedEvent(this, reclassified);
            }
        }
        if (pathObject.getParent() != null)
            hierarchy.removeObject(pathObject, true);
        // viewer.getHierarchy().fireHierarchyChangedEvent(this);
        if (toSelect.isEmpty())
            viewer.setSelectedObject(null);
        else if (e.isShiftDown()) {
            hierarchy.getSelectionModel().deselectObject(pathObject);
            hierarchy.getSelectionModel().selectObjects(toSelect);
        } else
            hierarchy.getSelectionModel().setSelectedObjects(toSelect, null);
    } else {
        if (!requestParentClipping(e)) {
            if (currentROI.isEmpty()) {
                pathObject = null;
            } else
                // Ensure object is within the hierarchy
                hierarchy.addPathObject(pathObject);
        } else {
            ROI roiNew = refineROIByParent(pathObject.getROI());
            if (roiNew.isEmpty()) {
                hierarchy.removeObject(pathObject, true);
                pathObject = null;
            } else {
                ((PathAnnotationObject) pathObject).setROI(roiNew);
                hierarchy.addPathObjectBelowParent(getCurrentParent(), pathObject, true);
            }
        }
        if (pathObject != null)
            viewer.setSelectedObject(pathObject);
        else
            viewer.getHierarchy().getSelectionModel().clearSelection();
    }
    var editor = viewer.getROIEditor();
    editor.ensureHandlesUpdated();
    editor.resetActiveHandle();
    if (preferReturnToMove()) {
        var qupath = QuPathGUI.getInstance();
        if (qupath != null)
            qupath.setSelectedTool(PathTools.MOVE);
    }
}

Example 52 with PathObject

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

the class AbstractPolyROITool method mouseMoved.

@Override
public void mouseMoved(MouseEvent e) {
    super.mouseMoved(e);
    var viewer = getViewer();
    ROI currentROI = viewer.getCurrentROI();
    RoiEditor editor = viewer.getROIEditor();
    if (isPolyROI(currentROI) && editor.getROI() == currentROI) {
        Point2D p = mouseLocationToImage(e, true, requestPixelSnapping());
        ROI roiUpdated = editor.setActiveHandlePosition(p.getX(), p.getY(), viewer.getDownsampleFactor(), e.isShiftDown());
        PathObject pathObject = viewer.getSelectedObject();
        if (roiUpdated != currentROI && pathObject instanceof PathROIObject) {
            ((PathROIObject) pathObject).setROI(roiUpdated);
            viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(pathObject), true);
        }
    }
}

Example 53 with PathObject

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

the class AbstractPolyROITool method mouseReleased.

@Override
public void mouseReleased(MouseEvent e) {
    super.mouseReleased(e);
    if (isFreehandPolyROI) {
        var viewer = getViewer();
        PathObject currentObject = viewer.getSelectedObject();
        ROI currentROI = currentObject == null ? null : currentObject.getROI();
        if (isPolyROI(currentROI) && currentROI.isEmpty()) {
            isFreehandPolyROI = false;
        } else if (PathPrefs.enableFreehandToolsProperty().get()) {
            RoiEditor editor = viewer.getROIEditor();
            Point2D p2 = mouseLocationToImage(e, true, requestPixelSnapping());
            ROI roiUpdated = editor.setActiveHandlePosition(p2.getX(), p2.getY(), viewer.getDownsampleFactor(), e.isShiftDown());
            if (currentObject != null && currentObject.getROI() != roiUpdated && currentObject instanceof PathROIObject) {
                ((PathROIObject) currentObject).setROI(roiUpdated);
            }
            commitObjectToHierarchy(e, currentObject);
        // completePolygon(e);
        }
    }
}

Example 54 with PathObject

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

the class AbstractPolyROITool method mousePressed.

@Override
public void mousePressed(MouseEvent e) {
    super.mousePressed(e);
    // If we double-clicked a polygon, we're done with it
    var viewer = getViewer();
    PathObject currentObject = viewer == null ? null : viewer.getSelectedObject();
    if (currentObject != null && e.getClickCount() == 1) {
        RoiEditor editor = viewer.getROIEditor();
        logger.trace("Adjusting polygon {}", e);
        Point2D p2 = mouseLocationToImage(e, true, requestPixelSnapping());
        ROI roiUpdated = editor.requestNewHandle(p2.getX(), p2.getY());
        if (currentObject != null && currentObject.getROI() != roiUpdated && currentObject instanceof PathROIObject) {
            ((PathROIObject) currentObject).setROI(roiUpdated);
        }
        isFreehandPolyROI = false;
        viewer.repaint();
    } else {
        commitObjectToHierarchy(e, currentObject);
    }
    ROI currentROI = currentObject == null ? null : currentObject.getROI();
    if (isPolyROI(currentROI) && currentROI.isEmpty() && (currentROI.getNumPoints() == 1 || new HashSet<>(currentROI.getAllPoints()).size() == 1))
        isFreehandPolyROI = true;
}

Example 55 with PathObject

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

the class AbstractPolyROITool 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);
    if (!e.isPrimaryButtonDown()) {
        return;
    }
    var viewer = getViewer();
    ROI currentROI = viewer.getCurrentROI();
    RoiEditor editor = viewer.getROIEditor();
    if (isPolyROI(currentROI) && editor.getROI() == currentROI) {
        Point2D p = mouseLocationToImage(e, true, requestPixelSnapping());
        ROI roiUpdated = editor.requestNewHandle(p.getX(), p.getY());
        PathObject pathObject = viewer.getSelectedObject();
        if (roiUpdated != currentROI && pathObject instanceof PathROIObject) {
            ((PathROIObject) pathObject).setROI(roiUpdated);
            viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(pathObject), true);
        }
    }
}