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

Example 21 with ROI

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

the class PathObjectIOTest method test_IOObjectsGeoJSONImpl.

private void test_IOObjectsGeoJSONImpl(boolean keepMeasurements, GeoJsonExportOptions... options) throws IOException {
    ROI roiDetection = ROIs.createRectangleROI(0, 0, 10, 10, ImagePlane.getDefaultPlane());
    ROI roiAnnotation = ROIs.createRectangleROI(100, 100, 10, 10, ImagePlane.getDefaultPlane());
    ROI roiCell1 = ROIs.createRectangleROI(25, 25, 25, 25, ImagePlane.getDefaultPlane());
    ROI roiCell2 = ROIs.createRectangleROI(12, 12, 5, 5, ImagePlane.getDefaultPlane());
    ROI roiTile = ROIs.createRectangleROI(100, 100, 10, 10, ImagePlane.getDefaultPlane());
    MeasurementList mlDetection = MeasurementListFactory.createMeasurementList(16, MeasurementList.MeasurementListType.GENERAL);
    MeasurementList mlCell = MeasurementListFactory.createMeasurementList(16, MeasurementList.MeasurementListType.GENERAL);
    PathObject myPDO = PathObjects.createDetectionObject(roiDetection, PathClassFactory.getPathClass("PathClassTest1", ColorTools.BLACK), mlDetection);
    PathObject myPAO = PathObjects.createAnnotationObject(roiAnnotation, PathClassFactory.getPathClass("PathClassTest1", ColorTools.BLACK));
    PathObject myPCO = PathObjects.createCellObject(roiCell1, roiCell2, PathClassFactory.getPathClass("PathClassTest2", ColorTools.GREEN), mlCell);
    PathObject myPTO = PathObjects.createTileObject(roiTile, PathClassFactory.getPathClass("PathClassTest2", ColorTools.GREEN), null);
    PathObject myTMA = PathObjects.createTMACoreObject(25, 25, 25, false);
    Collection<PathObject> objs = Arrays.asList(myPDO, myPCO, myPAO, myPTO, myTMA);
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    // Add measurements
    mlDetection.addMeasurement("TestMeasurement1", 5.0);
    mlDetection.addMeasurement("TestMeasurement2", 10.0);
    mlCell.addMeasurement("TestMeasurement3", 15.0);
    mlCell.addMeasurement("TestMeasurement4", 20.0);
    // Export to GeoJSON
    PathIO.exportObjectsAsGeoJSON(bos, objs, options);
    // Import from GeoJSON
    List<PathObject> objsBack = new ArrayList<>(PathIO.readObjectsFromGeoJSON(new ByteArrayInputStream(bos.toByteArray())));
    assertEquals(objs.size(), objsBack.size());
    // Array to count number of each PathObject type
    int[] countCheck = new int[] { 0, 0, 0, 0, 0 };
    for (PathObject po : objsBack) {
        if (po == null)
            continue;
        // Test whether po has a ROI
        assertTrue(po.hasROI());
        if (po.isTile()) {
            assertEquals(po.getPathClass(), PathClassFactory.getPathClass("PathClassTest2", ColorTools.GREEN));
            assertSameROIs(po.getROI(), roiTile);
            assertFalse(po.hasMeasurements());
            countCheck[0]++;
        } else if (po.isCell()) {
            assertEquals(po.getPathClass(), PathClassFactory.getPathClass("PathClassTest2", ColorTools.GREEN));
            assertSameROIs(po.getROI(), roiCell1);
            assertSameROIs(((PathCellObject) po).getNucleusROI(), roiCell2);
            if (keepMeasurements) {
                assertTrue(po.hasMeasurements());
                assertSameMeasurements(po.getMeasurementList(), myPCO.getMeasurementList());
            } else
                assertFalse(po.hasMeasurements());
            countCheck[1]++;
        } else if (po.isDetection()) {
            assertEquals(po.getPathClass(), PathClassFactory.getPathClass("PathClassTest1", ColorTools.BLACK));
            assertSameROIs(po.getROI(), roiDetection);
            if (keepMeasurements) {
                assertTrue(po.hasMeasurements());
                assertSameMeasurements(po.getMeasurementList(), myPDO.getMeasurementList());
            } else
                assertFalse(po.hasMeasurements());
            countCheck[2]++;
        } else if (po.isAnnotation()) {
            assertEquals(po.getPathClass(), PathClassFactory.getPathClass("PathClassTest1", ColorTools.BLACK));
            assertSameROIs(po.getROI(), roiAnnotation);
            assertFalse(po.hasMeasurements());
            countCheck[3]++;
        } else if (po.isTMACore()) {
            assertFalse(po.hasMeasurements());
            assertSameROIs(po.getROI(), myTMA.getROI());
            countCheck[4]++;
        }
    }
    assertArrayEquals(countCheck, new int[] { 1, 1, 1, 1, 1 });
}

Example 22 with ROI

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

the class TestROIs method checkROIMeasurements.

static void checkROIMeasurements(ROI roi, double pixelWidth, double pixelHeight, double delta) {
    if (roi.isPoint()) {
        checkROIPoints(roi);
        return;
    }
    ROI scaledROI = roi.scale(pixelWidth, pixelHeight);
    Geometry geometry = getGeometry(roi, pixelWidth, pixelHeight);
    if (roi instanceof EllipseROI)
        delta = roi.getArea() * delta;
    if (roi.isArea()) {
        ClosedShapeStatistics stats = new ClosedShapeStatistics(roi.getShape(), pixelWidth, pixelHeight);
        double area = roi.getScaledArea(pixelWidth, pixelHeight);
        assertEquals(area, stats.getArea(), delta);
        assertEquals(area, scaledROI.getArea(), delta);
        assertEquals(area, geometry.getArea(), delta);
    }
    if (roi.isLine()) {
        double length = roi.getScaledLength(pixelWidth, pixelHeight);
        assertEquals(length, scaledROI.getLength(), delta);
        assertEquals(length, geometry.getLength(), delta);
    }
}

Example 23 with ROI

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

the class TestROIs method roiSerialization.

@Test
public void roiSerialization() {
    double tol = 0.0;
    // Test serialization
    LineROI roi = new LineROI(100, 200, 300, 400);
    LineROI roi2 = (LineROI) objectFromBytes(objectToBytes(roi));
    testEqualBounds(roi, roi2, tol);
    testEqualLines(roi, roi2, tol);
    assertEquals(0, DefaultROIComparator.getInstance().compare(roi, roi2));
    RectangleROI rect = new RectangleROI(100, 200, 300, 400, ImagePlane.getPlaneWithChannel(0, 1, 2));
    ROI rect2 = (ROI) objectFromBytes(objectToBytes(rect));
    testEqualBounds(rect, rect2, tol);
    testEqualPolygonPoints(rect, rect2, tol);
    assertEquals(0, DefaultROIComparator.getInstance().compare(rect, rect2));
    EllipseROI ellipse = new EllipseROI(100, 200, 300, 400, ImagePlane.getPlaneWithChannel(0, 1, 2));
    ROI ellipse2 = (ROI) objectFromBytes(objectToBytes(ellipse));
    testEqualBounds(ellipse, ellipse2, tol);
    testEqualPolygonPoints(ellipse, ellipse2, tol);
    assertEquals(0, DefaultROIComparator.getInstance().compare(ellipse, ellipse2));
    PolygonROI poly = new PolygonROI(new float[] { 1.0f, 2.5f, 5.0f }, new float[] { 10.0f, 11.0f, 12.0f }, ImagePlane.getPlaneWithChannel(0, 1, 2));
    ROI poly2 = (ROI) objectFromBytes(objectToBytes(poly));
    testEqualBounds(poly, poly2, tol);
    testEqualPolygonPoints(poly, poly2, tol);
    assertEquals(0, DefaultROIComparator.getInstance().compare(poly, poly2));
    PolylineROI polyline = new PolylineROI(new float[] { 1.0f, 2.5f, 5.0f }, new float[] { 10.0f, 11.0f, 12.0f }, ImagePlane.getPlaneWithChannel(0, 1, 2));
    ROI polyline2 = (ROI) objectFromBytes(objectToBytes(poly));
    testEqualBounds(polyline, polyline2, tol);
    testEqualPolygonPoints(polyline, polyline2, tol);
    assertEquals(0, DefaultROIComparator.getInstance().compare(poly, poly2));
    // Test polygon construction from points
    PolygonROI poly3 = new PolygonROI(poly.getAllPoints(), ImagePlane.getPlaneWithChannel(0, 1, 2));
    testEqualBounds(poly, poly3, tol);
    testEqualPolygonPoints(poly, poly3, tol);
    assertEquals(0, DefaultROIComparator.getInstance().compare(poly, poly3));
}

Example 24 with ROI

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

the class AbstractPathROITool method createNewAnnotation.

/**
 * Create a new annotation & set it in the current viewer.
 * @param e
 * @param x
 * @param y
 * @return
 */
PathObject createNewAnnotation(MouseEvent e, double x, double y) {
    var viewer = getViewer();
    var currentObject = viewer.getSelectedObject();
    var editor = viewer.getROIEditor();
    if (currentObject != null && currentObject.getParent() == null && currentObject.getROI() == editor.getROI() && (editor.isTranslating() || editor.hasActiveHandle())) {
        logger.warn("Creating a new annotation before a previous one was complete - {} will be discarded!", currentObject);
    }
    logger.trace("Creating new annotation at ({}, {}", x, y);
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    if (hierarchy == null) {
        logger.warn("Cannot create new annotation - no hierarchy available!");
        return null;
    }
    ROI roi = createNewROI(e, x, y, viewer.getImagePlane());
    if (roi == null)
        return null;
    PathObject pathObject = PathObjects.createAnnotationObject(roi, PathPrefs.autoSetAnnotationClassProperty().get());
    var selectionModel = hierarchy.getSelectionModel();
    if (PathPrefs.selectionModeProperty().get() && !selectionModel.noSelection())
        viewer.setSelectedObject(pathObject, true);
    else
        viewer.setSelectedObject(pathObject);
    return pathObject;
}

Example 25 with ROI

use of qupath.lib.roi.interfaces.ROI 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);
    }
}