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

Example 61 with PathObject

use of qupath.lib.objects.PathObject 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 62 with PathObject

use of qupath.lib.objects.PathObject 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;
// }
}

Example 63 with PathObject

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

the class PathClassifierTools method getAvailableFeatures.

/**
 * Get a set containing the names of all measurements found in the measurement lists of a specified object collection.
 *
 * @param pathObjects
 * @return
 */
public static Set<String> getAvailableFeatures(final Collection<? extends PathObject> pathObjects) {
    Set<String> featureSet = new LinkedHashSet<>();
    // This has a small optimization that takes into consideration the fact that many objects share references to exactly the same MeasurementLists -
    // so by checking the last list that was added, there is no need to bother the set to add the same thing again.
    List<String> lastNames = null;
    for (PathObject pathObject : pathObjects) {
        if (!pathObject.hasMeasurements())
            continue;
        List<String> list = pathObject.getMeasurementList().getMeasurementNames();
        if (lastNames != list)
            featureSet.addAll(list);
        lastNames = list;
    }
    return featureSet;
}

Example 64 with PathObject

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

the class PathClassifierTools method runClassifier.

/**
 * Apply a classifier to the detection objects in a hierarchy.
 * @param hierarchy
 * @param classifier
 */
public static void runClassifier(final PathObjectHierarchy hierarchy, final PathObjectClassifier classifier) {
    // Apply classifier to everything
    // If we have a TMA grid, do one core at a time
    long startTime = System.currentTimeMillis();
    TMAGrid tmaGrid = hierarchy.getTMAGrid();
    Collection<PathObject> pathObjects = new ArrayList<>();
    int nClassified = 0;
    // tmaGrid = null;
    if (tmaGrid != null) {
        for (TMACoreObject core : tmaGrid.getTMACoreList()) {
            pathObjects = PathObjectTools.getDescendantObjects(core, pathObjects, PathDetectionObject.class);
            nClassified += classifier.classifyPathObjects(pathObjects);
            pathObjects.clear();
        }
    } else {
        hierarchy.getObjects(pathObjects, PathDetectionObject.class);
        nClassified = classifier.classifyPathObjects(pathObjects);
    }
    long endTime = System.currentTimeMillis();
    logger.info(String.format("Classification time: %.2f seconds", (endTime - startTime) / 1000.));
    // Fire a change event for all detection objects
    if (nClassified > 0)
        hierarchy.fireObjectClassificationsChangedEvent(classifier, hierarchy.getObjects(null, PathDetectionObject.class));
    else
        logger.warn("No objects classified!");
}

Example 65 with PathObject

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

the class ImageJMacroRunner method runPlugin.

@Override
public boolean runPlugin(final PluginRunner<BufferedImage> runner, final String arg) {
    if (!parseArgument(runner.getImageData(), arg))
        return false;
    if (dialog == null) {
        dialog = new Stage();
        dialog.initOwner(qupath.getStage());
        dialog.setTitle("ImageJ macro runner");
        BorderPane pane = new BorderPane();
        if (arg != null)
            macroText = arg;
        // Create text area
        final TextArea textArea = new TextArea();
        textArea.setPrefRowCount(12);
        textArea.setPrefSize(400, 400);
        textArea.setWrapText(true);
        textArea.setFont(Font.font("Courier"));
        if (macroText != null)
            textArea.setText(macroText);
        BorderPane panelMacro = new BorderPane();
        // panelMacro.setBorder(BorderFactory.createTitledBorder("Macro"));
        panelMacro.setCenter(textArea);
        ParameterPanelFX parameterPanel = new ParameterPanelFX(getParameterList(runner.getImageData()));
        panelMacro.setBottom(parameterPanel.getPane());
        // Create button panel
        Button btnRun = new Button("Run");
        btnRun.setOnAction(e -> {
            macroText = textArea.getText().trim();
            if (macroText.length() == 0)
                return;
            PathObjectHierarchy hierarchy = getHierarchy(runner);
            PathObject pathObject = hierarchy.getSelectionModel().singleSelection() ? hierarchy.getSelectionModel().getSelectedObject() : null;
            if (pathObject instanceof PathAnnotationObject || pathObject instanceof TMACoreObject) {
                SwingUtilities.invokeLater(() -> {
                    runMacro(params, qupath.getViewer().getImageData(), qupath.getViewer().getImageDisplay(), pathObject, macroText);
                });
            } else {
                // DisplayHelpers.showErrorMessage(getClass().getSimpleName(), "Sorry, ImageJ macros can only be run for single selected images");
                // logger.warn("ImageJ macro being run in current thread");
                // runPlugin(runner, arg); // TODO: Consider running in a background thread?
                // Run in a background thread
                Collection<? extends PathObject> parents = getParentObjects(runner);
                if (parents.isEmpty()) {
                    Dialogs.showErrorMessage("ImageJ macro runner", "No annotation or TMA core objects selected!");
                    return;
                }
                List<Runnable> tasks = new ArrayList<>();
                for (PathObject parent : parents) addRunnableTasks(qupath.getViewer().getImageData(), parent, tasks);
                qupath.submitShortTask(() -> runner.runTasks(tasks, true));
            // runner.runTasks(tasks);
            // Runnable r = new Runnable() {
            // public void run() {
            // runPlugin(runner, arg);
            // }
            // };
            // new Thread(r).start();
            }
        });
        Button btnClose = new Button("Close");
        btnClose.setOnAction(e -> dialog.hide());
        GridPane panelButtons = PaneTools.createRowGridControls(btnRun, btnClose);
        pane.setCenter(panelMacro);
        pane.setBottom(panelButtons);
        panelButtons.setPadding(new Insets(5, 0, 0, 0));
        pane.setPadding(new Insets(10, 10, 10, 10));
        dialog.setScene(new Scene(pane));
    }
    dialog.show();
    return true;
}