Examples with ROI qupath.lib.roi.interfaces.ROI used on opensource projects

Example 31 with ROI

use of qupath.lib.roi.interfaces.ROI 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 32 with ROI

use of qupath.lib.roi.interfaces.ROI 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 33 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class ObservableMeasurementTableDataTest method test.

@SuppressWarnings("javadoc")
@Test
public void test() {
    // See https://github.com/locationtech/jts/issues/571
    for (int counter = 0; counter < 50; counter++) {
        ImageData<BufferedImage> imageData = new ImageData<>(null);
        PathClass tumorClass = PathClassFactory.getPathClass(StandardPathClasses.TUMOR);
        PathClass stromaClass = PathClassFactory.getPathClass(StandardPathClasses.STROMA);
        // PathClass otherClass = PathClassFactory.getDefaultPathClass(PathClasses.OTHER);
        PathClass artefactClass = PathClassFactory.getPathClass("Artefact");
        PathObjectHierarchy hierarchy = imageData.getHierarchy();
        // Add a parent annotation
        PathObject parent = PathObjects.createAnnotationObject(ROIs.createRectangleROI(500, 500, 1000, 1000, ImagePlane.getDefaultPlane()));
        // Create 100 tumor detections
        // ROI emptyROI = ROIs.createEmptyROI();
        ROI smallROI = ROIs.createRectangleROI(500, 500, 1, 1, ImagePlane.getDefaultPlane());
        for (int i = 0; i < 100; i++) {
            if (i < 25)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getNegative(tumorClass)));
            else if (i < 50)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getOnePlus(tumorClass)));
            else if (i < 75)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getTwoPlus(tumorClass)));
            else if (i < 100)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getThreePlus(tumorClass)));
        }
        // Create 100 stroma detections
        for (int i = 0; i < 100; i++) {
            if (i < 50)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getNegative(stromaClass)));
            else if (i < 60)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getOnePlus(stromaClass)));
            else if (i < 70)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getTwoPlus(stromaClass)));
            else if (i < 100)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getThreePlus(stromaClass)));
        }
        // Create 50 artefact detections
        for (int i = 0; i < 50; i++) {
            parent.addPathObject(PathObjects.createDetectionObject(smallROI, artefactClass));
        }
        hierarchy.addPathObject(parent);
        ObservableMeasurementTableData model = new ObservableMeasurementTableData();
        model.setImageData(imageData, Collections.singletonList(parent));
        // Check tumor counts
        assertEquals(100, model.getNumericValue(parent, "Num Tumor (base)"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: Negative"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 1+"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 2+"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 3+"), EPSILON);
        assertTrue(Double.isNaN(model.getNumericValue(parent, "Num Tumor: 4+")));
        // Check tumor H-score, Allred score & positive %
        assertEquals(150, model.getNumericValue(parent, "Tumor: H-score"), EPSILON);
        assertEquals(75, model.getNumericValue(parent, "Tumor: Positive %"), EPSILON);
        assertEquals(2, model.getNumericValue(parent, "Tumor: Allred intensity"), EPSILON);
        assertEquals(5, model.getNumericValue(parent, "Tumor: Allred proportion"), EPSILON);
        assertEquals(7, model.getNumericValue(parent, "Tumor: Allred score"), EPSILON);
        // Check tumor H-score unaffected when tumor detections added without intensity classification
        for (int i = 0; i < 10; i++) parent.addPathObject(PathObjects.createDetectionObject(smallROI, tumorClass));
        hierarchy.fireHierarchyChangedEvent(this);
        model.refreshEntries();
        // model.setImageData(imageData, Collections.singletonList(parent));
        assertEquals(100, model.getNumericValue(parent, "Num Stroma (base)"), EPSILON);
        assertEquals(50, model.getNumericValue(parent, "Num Stroma: Negative"), EPSILON);
        assertEquals(150, model.getNumericValue(parent, "Tumor: H-score"), EPSILON);
        assertEquals(75, model.getNumericValue(parent, "Tumor: Positive %"), EPSILON);
        // Check stroma scores
        assertEquals(100, model.getNumericValue(parent, "Num Stroma (base)"), EPSILON);
        assertEquals(120, model.getNumericValue(parent, "Stroma: H-score"), EPSILON);
        // Check complete scores
        assertEquals(135, model.getNumericValue(parent, "Stroma + Tumor: H-score"), EPSILON);
        // Add a new parent that completely contains the current object, and confirm complete scores agree
        PathObject parentNew = PathObjects.createAnnotationObject(ROIs.createRectangleROI(0, 0, 2000, 2000, ImagePlane.getDefaultPlane()));
        hierarchy.addPathObject(parentNew);
        model.refreshEntries();
        assertEquals(135, model.getNumericValue(parent, "Stroma + Tumor: H-score"), EPSILON);
        assertEquals(135, model.getNumericValue(parentNew, "Stroma + Tumor: H-score"), EPSILON);
        // Create a new object and demonstrate Allred dependence on a single cell
        PathObject parentAllred = PathObjects.createAnnotationObject(ROIs.createRectangleROI(4000, 4000, 1000, 1000, ImagePlane.getDefaultPlane()));
        ROI newROI = ROIs.createEllipseROI(4500, 4500, 10, 10, ImagePlane.getDefaultPlane());
        for (int i = 0; i < 100; i++) parentAllred.addPathObject(PathObjects.createDetectionObject(newROI, PathClassFactory.getNegative(tumorClass)));
        hierarchy.addPathObject(parentAllred);
        model.refreshEntries();
        assertEquals(0, model.getNumericValue(parentAllred, "Tumor: Allred score"), EPSILON);
        parentAllred.addPathObject(PathObjects.createDetectionObject(newROI, PathClassFactory.getThreePlus(tumorClass)));
        hierarchy.fireHierarchyChangedEvent(parentAllred);
        model.refreshEntries();
        assertEquals(4, model.getNumericValue(parentAllred, "Tumor: Allred score"), EPSILON);
    }
}

Example 34 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class MoveTool method mouseMoved.

@Override
public void mouseMoved(MouseEvent e) {
    super.mouseMoved(e);
    // We don't want to change a waiting cursor unnecessarily
    var viewer = getViewer();
    Cursor cursorType = viewer.getCursor();
    if (cursorType == Cursor.WAIT)
        return;
    // If we are already translating, we must need a move cursor
    if (viewer.getROIEditor().isTranslating()) {
        if (cursorType != Cursor.MOVE)
            viewer.setCursor(Cursor.MOVE);
        return;
    }
    // Check if we should have a panning or moving cursor, changing if required
    ROI currentROI = viewer.getCurrentROI();
    if (currentROI != null && canAdjust(viewer.getSelectedObject())) {
        Point2D p2 = mouseLocationToImage(e, true, false);
        double xx = p2.getX();
        double yy = p2.getY();
        if (RoiTools.areaContains(currentROI, xx, yy)) {
            ensureCursorType(Cursor.MOVE);
            return;
        }
    }
    ensureCursorType(Cursor.HAND);
}

Example 35 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class MoveTool method mouseReleased.

@Override
public void mouseReleased(MouseEvent e) {
    super.mouseReleased(e);
    if (e.isConsumed())
        return;
    var viewer = getViewer();
    RoiEditor editor = viewer.getROIEditor();
    if (editor != null && (editor.hasActiveHandle() || editor.isTranslating())) {
        boolean roiChanged = (editor.isTranslating() && editor.finishTranslation()) || editor.hasActiveHandle();
        editor.resetActiveHandle();
        // if (editor.isTranslating())
        // editor.finishTranslation();
        e.consume();
        PathObject pathObject = viewer.getSelectedObject();
        if (requestParentClipping(e) && pathObject instanceof PathAnnotationObject) {
            ROI roiNew = refineROIByParent(pathObject.getROI());
            ((PathAnnotationObject) pathObject).setROI(roiNew);
        }
        if (pathObject != null && pathObject.hasROI() && pathObject.getROI().isEmpty()) {
            if (pathObject.getParent() != null)
                viewer.getHierarchy().removeObject(pathObject, true);
            viewer.setSelectedObject(null);
        } else {
            PathObjectHierarchy hierarchy = viewer.getHierarchy();
            if (pathObject instanceof TMACoreObject) {
                hierarchy.fireHierarchyChangedEvent(pathObject);
            } else if (pathObject != null) {
                // Handle ROI changes only if required
                if (roiChanged) {
                    var updatedROI = editor.getROI();
                    if (pathObject.getROI() != updatedROI && pathObject instanceof PathROIObject)
                        ((PathROIObject) pathObject).setROI(updatedROI);
                    // PathObject parentPrevious = pathObject.getParent();
                    hierarchy.removeObjectWithoutUpdate(pathObject, true);
                    if (getCurrentParent() == null || !PathPrefs.clipROIsForHierarchyProperty().get() || e.isShiftDown())
                        hierarchy.addPathObject(pathObject);
                    else
                        hierarchy.addPathObjectBelowParent(getCurrentParent(), pathObject, true);
                // PathObject parentNew = pathObject.getParent();
                // if (parentPrevious == parentNew)
                // hierarchy.fireHierarchyChangedEvent(this, parentPrevious);
                // else
                // hierarchy.fireHierarchyChangedEvent(this);
                }
            }
            viewer.setSelectedObject(pathObject);
        }
    }
    // Optionally continue a dragging movement until the canvas comes to a standstill
    if (pDragging != null && requestDynamicDragging && System.currentTimeMillis() - lastDragTimestamp < 100 && (dx * dx + dy * dy > viewer.getDownsampleFactor())) {
        mover = new ViewerMover(viewer);
        mover.startMoving(dx, dy, false);
    } else
        viewer.setDoFasterRepaint(false);
    // Make sure we don't have a previous point (to prevent weird dragging artefacts)
    pDragging = null;
// // If we were translating, stop
// if (editor.isTranslating()) {
// editor.finishTranslation();
// // TODO: Make this more efficient!
// viewer.getPathObjectHierarchy().fireHierarchyChangedEvent();
// return;
// }
}