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

Example 46 with PathObject

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

the class IJTools method convertToPathObject.

/**
 * Create a {@link PathObject} for a specific ImageJ Roi, using an {@link ImagePlus} to help set properties.
 *
 * @param roi the ImageJ ROI
 * @param downsampleFactor the downsample factor used for rescaling (or 1.0 for no rescaling)
 * @param creator a function
 * @param imp the {@link ImagePlus} associated with this Roi; it is used to determine the xOrigin, yOrigin and image plane
 * @return a {@link PathObject} or null if no object could be created (e.g. the ImageJ roi is null or incompatible)
 *
 * @see #convertToPathObject(Roi, double, double, double, Function, ImagePlane)
 * @since v0.4.0
 */
public static PathObject convertToPathObject(Roi roi, double downsampleFactor, Function<ROI, PathObject> creator, ImagePlus imp) {
    Calibration cal = imp == null ? null : imp.getCalibration();
    var plane = getImagePlane(roi, imp);
    ROI pathROI = IJTools.convertToROI(roi, cal, downsampleFactor, plane);
    if (pathROI == null)
        return null;
    PathObject pathObject = creator.apply(pathROI);
    calibrateObject(pathObject, roi);
    return pathObject;
}

Example 47 with PathObject

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

the class SubcellularDetection method getParentObjects.

@Override
protected Collection<PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
    Collection<Class<? extends PathObject>> parentClasses = getSupportedParentObjectClasses();
    List<PathObject> parents = new ArrayList<>();
    for (PathObject parent : getHierarchy(runner).getSelectionModel().getSelectedObjects()) {
        for (Class<? extends PathObject> cls : parentClasses) {
            if (cls.isAssignableFrom(parent.getClass())) {
                parents.add(parent);
                break;
            }
        }
    }
    return parents;
}

Example 48 with PathObject

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

the class IJExtension method extractOverlay.

/**
 * Extract an ImageJ overlay for the specified region.
 * @param hierarchy
 * @param request
 * @param options options to control which objects are being displayed
 * @param filter optional additional filter used to determine which objects will be included (may be used in combination with options)
 * @return
 */
public static Overlay extractOverlay(PathObjectHierarchy hierarchy, RegionRequest request, OverlayOptions options, Predicate<PathObject> filter) {
    Overlay overlay = new Overlay();
    double downsample = request.getDownsample();
    double xOrigin = -request.getX() / downsample;
    double yOrigin = -request.getY() / downsample;
    // TODO: Permit filling/unfilling ROIs
    for (PathObject child : hierarchy.getObjectsForRegion(PathObject.class, request, null)) {
        if (filter != null && !filter.test(child))
            continue;
        if (child.hasROI()) {
            // Check if this is displayed - skip it not
            if (options != null && ((child instanceof PathDetectionObject && !options.getShowDetections()) || (child instanceof PathAnnotationObject && !options.getShowAnnotations()) || (child instanceof TMACoreObject && !options.getShowTMAGrid())))
                continue;
            boolean isCell = child instanceof PathCellObject;
            Color color = ColorToolsAwt.getCachedColor(ColorToolsFX.getDisplayedColorARGB(child));
            if (!(isCell && (options == null || !options.getShowCellBoundaries()))) {
                Roi roi = IJTools.convertToIJRoi(child.getROI(), xOrigin, yOrigin, downsample);
                roi.setStrokeColor(color);
                roi.setName(child.getDisplayedName());
                // roi.setStrokeWidth(2);
                overlay.add(roi);
            }
            if (isCell && (options == null || options.getShowCellNuclei())) {
                ROI nucleus = ((PathCellObject) child).getNucleusROI();
                if (nucleus == null)
                    continue;
                Roi roi = IJTools.convertToIJRoi(((PathCellObject) child).getNucleusROI(), xOrigin, yOrigin, downsample);
                roi.setStrokeColor(color);
                roi.setName(child.getDisplayedName() + " - nucleus");
                overlay.add(roi);
            }
        }
    }
    return overlay;
}

Example 49 with PathObject

use of qupath.lib.objects.PathObject 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 50 with PathObject

use of qupath.lib.objects.PathObject 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;
}