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

Example 16 with PathObject

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

the class TMACommands method promptToDeleteTMAGridRowOrColumn.

private static boolean promptToDeleteTMAGridRowOrColumn(ImageData<?> imageData, TMARemoveType type) {
    String typeString = type.toString();
    String title = "Delete TMA " + typeString;
    boolean removeRow = type == TMARemoveType.ROW;
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return false;
    }
    if (imageData.getHierarchy().getTMAGrid() == null) {
        Dialogs.showErrorMessage(title, "No image with dearrayed TMA cores selected!");
        return false;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    TMACoreObject selectedCore = null;
    if (selected != null)
        selectedCore = PathObjectTools.getAncestorTMACore(selected);
    // Try to identify the row/column that we want
    TMAGrid grid = hierarchy.getTMAGrid();
    int row = -1;
    int col = -1;
    if (selectedCore != null) {
        for (int y = 0; y < grid.getGridHeight(); y++) {
            for (int x = 0; x < grid.getGridWidth(); x++) {
                if (grid.getTMACore(y, x) == selectedCore) {
                    row = y;
                    col = x;
                    break;
                }
            }
        }
    }
    // We need a selected core to know what to remove
    if (row < 0 || col < 0) {
        Dialogs.showErrorMessage(title, "Please select a TMA core to indicate which " + typeString + " to remove");
        return false;
    }
    // Check we have enough rows/columns - if not, this is just a clear operation
    if ((removeRow && grid.getGridHeight() <= 1) || (!removeRow && grid.getGridWidth() <= 1)) {
        if (Dialogs.showConfirmDialog(title, "Are you sure you want to delete the entire TMA grid?"))
            hierarchy.setTMAGrid(null);
        return false;
    }
    // Confirm the removal - add 1 due to 'base 0' probably not being expected by most users...
    int num = removeRow ? row : col;
    if (!Dialogs.showConfirmDialog(title, "Are you sure you want to delete " + typeString + " " + (num + 1) + " from TMA grid?"))
        return false;
    // Create a new grid
    List<TMACoreObject> coresNew = new ArrayList<>();
    for (int r = 0; r < grid.getGridHeight(); r++) {
        if (removeRow && row == r)
            continue;
        for (int c = 0; c < grid.getGridWidth(); c++) {
            if (!removeRow && col == c)
                continue;
            coresNew.add(grid.getTMACore(r, c));
        }
    }
    int newWidth = removeRow ? grid.getGridWidth() : grid.getGridWidth() - 1;
    TMAGrid gridNew = DefaultTMAGrid.create(coresNew, newWidth);
    hierarchy.setTMAGrid(gridNew);
    hierarchy.getSelectionModel().clearSelection();
    // Request new labels
    promptToRelabelTMAGrid(imageData);
    return true;
}

Example 17 with PathObject

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

the class Commands method promptToExportImageRegion.

/**
 * Prompt to export the current image region selected in the viewer.
 * @param viewer the viewer containing the image to export
 * @param renderedImage if true, export the rendered (RGB) image rather than original pixel values
 */
public static void promptToExportImageRegion(QuPathViewer viewer, boolean renderedImage) {
    if (viewer == null || viewer.getServer() == null) {
        Dialogs.showErrorMessage("Export image region", "No viewer & image selected!");
        return;
    }
    ImageServer<BufferedImage> server = viewer.getServer();
    if (renderedImage)
        server = RenderedImageServer.createRenderedServer(viewer);
    PathObject pathObject = viewer.getSelectedObject();
    ROI roi = pathObject == null ? null : pathObject.getROI();
    double regionWidth = roi == null ? server.getWidth() : roi.getBoundsWidth();
    double regionHeight = roi == null ? server.getHeight() : roi.getBoundsHeight();
    // Create a dialog
    GridPane pane = new GridPane();
    int row = 0;
    pane.add(new Label("Export format"), 0, row);
    ComboBox<ImageWriter<BufferedImage>> comboImageType = new ComboBox<>();
    Function<ImageWriter<BufferedImage>, String> fun = (ImageWriter<BufferedImage> writer) -> writer.getName();
    comboImageType.setCellFactory(p -> GuiTools.createCustomListCell(fun));
    comboImageType.setButtonCell(GuiTools.createCustomListCell(fun));
    var writers = ImageWriterTools.getCompatibleWriters(server, null);
    comboImageType.getItems().setAll(writers);
    comboImageType.setTooltip(new Tooltip("Choose export image format"));
    if (writers.contains(lastWriter))
        comboImageType.getSelectionModel().select(lastWriter);
    else
        comboImageType.getSelectionModel().selectFirst();
    comboImageType.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(comboImageType, Priority.ALWAYS);
    pane.add(comboImageType, 1, row++);
    TextArea textArea = new TextArea();
    textArea.setPrefRowCount(2);
    textArea.setEditable(false);
    textArea.setWrapText(true);
    // textArea.setPadding(new Insets(15, 0, 0, 0));
    comboImageType.setOnAction(e -> textArea.setText(((ImageWriter<BufferedImage>) comboImageType.getValue()).getDetails()));
    textArea.setText(((ImageWriter<BufferedImage>) comboImageType.getValue()).getDetails());
    pane.add(textArea, 0, row++, 2, 1);
    var label = new Label("Downsample factor");
    pane.add(label, 0, row);
    TextField tfDownsample = new TextField();
    label.setLabelFor(tfDownsample);
    pane.add(tfDownsample, 1, row++);
    tfDownsample.setTooltip(new Tooltip("Amount to scale down image - choose 1 to export at full resolution (note: for large images this may not succeed for memory reasons)"));
    ObservableDoubleValue downsample = Bindings.createDoubleBinding(() -> {
        try {
            return Double.parseDouble(tfDownsample.getText());
        } catch (NumberFormatException e) {
            return Double.NaN;
        }
    }, tfDownsample.textProperty());
    // Define a sensible limit for non-pyramidal images
    long maxPixels = 10000 * 10000;
    Label labelSize = new Label();
    labelSize.setMinWidth(400);
    labelSize.setTextAlignment(TextAlignment.CENTER);
    labelSize.setContentDisplay(ContentDisplay.CENTER);
    labelSize.setAlignment(Pos.CENTER);
    labelSize.setMaxWidth(Double.MAX_VALUE);
    labelSize.setTooltip(new Tooltip("Estimated size of exported image"));
    pane.add(labelSize, 0, row++, 2, 1);
    labelSize.textProperty().bind(Bindings.createStringBinding(() -> {
        if (!Double.isFinite(downsample.get())) {
            labelSize.setStyle("-fx-text-fill: red;");
            return "Invalid downsample value!  Must be >= 1";
        } else {
            long w = (long) (regionWidth / downsample.get() + 0.5);
            long h = (long) (regionHeight / downsample.get() + 0.5);
            String warning = "";
            var writer = comboImageType.getSelectionModel().getSelectedItem();
            boolean supportsPyramid = writer == null ? false : writer.supportsPyramidal();
            if (!supportsPyramid && w * h > maxPixels) {
                labelSize.setStyle("-fx-text-fill: red;");
                warning = " (too big!)";
            } else if (w < 5 || h < 5) {
                labelSize.setStyle("-fx-text-fill: red;");
                warning = " (too small!)";
            } else
                labelSize.setStyle(null);
            return String.format("Output image size: %d x %d pixels%s", w, h, warning);
        }
    }, downsample, comboImageType.getSelectionModel().selectedIndexProperty()));
    tfDownsample.setText(Double.toString(exportDownsample.get()));
    PaneTools.setMaxWidth(Double.MAX_VALUE, labelSize, textArea, tfDownsample, comboImageType);
    PaneTools.setHGrowPriority(Priority.ALWAYS, labelSize, textArea, tfDownsample, comboImageType);
    pane.setVgap(5);
    pane.setHgap(5);
    if (!Dialogs.showConfirmDialog("Export image region", pane))
        return;
    var writer = comboImageType.getSelectionModel().getSelectedItem();
    boolean supportsPyramid = writer == null ? false : writer.supportsPyramidal();
    int w = (int) (regionWidth / downsample.get() + 0.5);
    int h = (int) (regionHeight / downsample.get() + 0.5);
    if (!supportsPyramid && w * h > maxPixels) {
        Dialogs.showErrorNotification("Export image region", "Requested export region too large - try selecting a smaller region, or applying a higher downsample factor");
        return;
    }
    if (downsample.get() < 1 || !Double.isFinite(downsample.get())) {
        Dialogs.showErrorMessage("Export image region", "Downsample factor must be >= 1!");
        return;
    }
    exportDownsample.set(downsample.get());
    // Now that we know the output, we can create a new server to ensure it is downsampled as the necessary resolution
    if (renderedImage && downsample.get() != server.getDownsampleForResolution(0))
        server = new RenderedImageServer.Builder(viewer).downsamples(downsample.get()).build();
    // selectedImageType.set(comboImageType.getSelectionModel().getSelectedItem());
    // Create RegionRequest
    RegionRequest request = null;
    if (pathObject != null && pathObject.hasROI())
        request = RegionRequest.createInstance(server.getPath(), exportDownsample.get(), roi);
    // Create a sensible default file name, and prompt for the actual name
    String ext = writer.getDefaultExtension();
    String writerName = writer.getName();
    String defaultName = GeneralTools.getNameWithoutExtension(new File(ServerTools.getDisplayableImageName(server)));
    if (roi != null) {
        defaultName = String.format("%s (%s, x=%d, y=%d, w=%d, h=%d)", defaultName, GeneralTools.formatNumber(request.getDownsample(), 2), request.getX(), request.getY(), request.getWidth(), request.getHeight());
    }
    File fileOutput = Dialogs.promptToSaveFile("Export image region", null, defaultName, writerName, ext);
    if (fileOutput == null)
        return;
    try {
        if (request == null) {
            if (exportDownsample.get() == 1.0)
                writer.writeImage(server, fileOutput.getAbsolutePath());
            else
                writer.writeImage(ImageServers.pyramidalize(server, exportDownsample.get()), fileOutput.getAbsolutePath());
        } else
            writer.writeImage(server, request, fileOutput.getAbsolutePath());
        lastWriter = writer;
    } catch (IOException e) {
        Dialogs.showErrorMessage("Export region", e);
    }
}

Example 18 with PathObject

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

the class Commands method convertDetectionsToPoints.

/**
 * Convert detection objects to point annotations based upon their ROI centroids.
 * @param imageData the image data to process
 * @param preferNucleus if true, use a nucleus ROI for cell objects (if available
 */
public static void convertDetectionsToPoints(ImageData<?> imageData, boolean preferNucleus) {
    if (imageData == null) {
        Dialogs.showNoImageError("Convert detections to points");
        return;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    Collection<PathObject> pathObjects = hierarchy.getDetectionObjects();
    if (pathObjects.isEmpty()) {
        Dialogs.showErrorMessage("Detections to points", "No detections found!");
        return;
    }
    // Remove any detections that don't have a ROI - can't do much with them
    Iterator<PathObject> iter = pathObjects.iterator();
    while (iter.hasNext()) {
        if (!iter.next().hasROI())
            iter.remove();
    }
    if (pathObjects.isEmpty()) {
        logger.warn("No detections found with ROIs!");
        return;
    }
    // Check if existing objects should be deleted
    String message = pathObjects.size() == 1 ? "Delete detection after converting to a point?" : String.format("Delete %d detections after converting to points?", pathObjects.size());
    var button = Dialogs.showYesNoCancelDialog("Detections to points", message);
    if (button == Dialogs.DialogButton.CANCEL)
        return;
    boolean deleteDetections = button == Dialogs.DialogButton.YES;
    PathObjectTools.convertToPoints(hierarchy, pathObjects, preferNucleus, deleteDetections);
}

Example 19 with PathObject

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

the class QuPathGUI method setViewerPopupMenu.

private void setViewerPopupMenu(final QuPathViewerPlus viewer) {
    final ContextMenu popup = new ContextMenu();
    MenuItem miAddRow = new MenuItem("Add row");
    miAddRow.setOnAction(e -> viewerManager.addRow(viewer));
    MenuItem miAddColumn = new MenuItem("Add column");
    miAddColumn.setOnAction(e -> viewerManager.addColumn(viewer));
    MenuItem miRemoveRow = new MenuItem("Remove row");
    miRemoveRow.setOnAction(e -> viewerManager.removeViewerRow(viewer));
    MenuItem miRemoveColumn = new MenuItem("Remove column");
    miRemoveColumn.setOnAction(e -> viewerManager.removeViewerColumn(viewer));
    MenuItem miCloseViewer = new MenuItem("Close viewer");
    miCloseViewer.setOnAction(e -> {
        viewerManager.closeViewer(viewer);
    // viewerManager.removeViewer(viewer);
    });
    MenuItem miResizeGrid = new MenuItem("Reset grid size");
    miResizeGrid.setOnAction(e -> {
        viewerManager.resetGridSize();
    });
    MenuItem miToggleSync = ActionTools.createCheckMenuItem(defaultActions.TOGGLE_SYNCHRONIZE_VIEWERS, null);
    MenuItem miMatchResolutions = ActionTools.createMenuItem(defaultActions.MATCH_VIEWER_RESOLUTIONS);
    Menu menuMultiview = MenuTools.createMenu("Multi-view", miToggleSync, miMatchResolutions, miCloseViewer, null, miResizeGrid, null, // null,
    miAddRow, miAddColumn, null, miRemoveRow, miRemoveColumn);
    Menu menuView = MenuTools.createMenu("Display", ActionTools.createCheckMenuItem(defaultActions.SHOW_ANALYSIS_PANE, null), defaultActions.BRIGHTNESS_CONTRAST, null, ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 0.25), "400%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 1), "100%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 2), "50%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 10), "10%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 100), "1%"));
    ToggleGroup groupTools = new ToggleGroup();
    Menu menuTools = MenuTools.createMenu("Set tool", ActionTools.createCheckMenuItem(defaultActions.MOVE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.RECTANGLE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.ELLIPSE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.LINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYGON_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYLINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.BRUSH_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POINTS_TOOL, groupTools), null, ActionTools.createCheckMenuItem(defaultActions.SELECTION_MODE));
    // Handle awkward 'TMA core missing' option
    CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuTMA = new Menu("TMA");
    MenuTools.addMenuItems(menuTMA, miTMAValid, miTMAMissing, null, defaultActions.TMA_ADD_NOTE, null, MenuTools.createMenu("Add", createImageDataAction(imageData -> TMACommands.promptToAddRowBeforeSelected(imageData), "Add TMA row before"), createImageDataAction(imageData -> TMACommands.promptToAddRowAfterSelected(imageData), "Add TMA row after"), createImageDataAction(imageData -> TMACommands.promptToAddColumnBeforeSelected(imageData), "Add TMA column before"), createImageDataAction(imageData -> TMACommands.promptToAddColumnAfterSelected(imageData), "Add TMA column after")), MenuTools.createMenu("Remove", createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridRow(imageData), "Remove TMA row"), createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridColumn(imageData), "column")));
    // Create an empty placeholder menu
    Menu menuSetClass = MenuTools.createMenu("Set class");
    // CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    // miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    // CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    // miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuCells = MenuTools.createMenu("Cells", ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES_AND_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_CENTROIDS, null));
    MenuItem miClearSelectedObjects = new MenuItem("Delete object");
    miClearSelectedObjects.setOnAction(e -> {
        PathObjectHierarchy hierarchy = viewer.getHierarchy();
        if (hierarchy == null)
            return;
        if (hierarchy.getSelectionModel().singleSelection()) {
            GuiTools.promptToRemoveSelectedObject(hierarchy.getSelectionModel().getSelectedObject(), hierarchy);
        } else {
            GuiTools.promptToClearAllSelectedObjects(viewer.getImageData());
        }
    });
    // Create a standard annotations menu
    Menu menuAnnotations = GuiTools.populateAnnotationsMenu(this, new Menu("Annotations"));
    SeparatorMenuItem topSeparator = new SeparatorMenuItem();
    popup.setOnShowing(e -> {
        // Check if we have any cells
        ImageData<?> imageData = viewer.getImageData();
        if (imageData == null)
            menuCells.setVisible(false);
        else
            menuCells.setVisible(!imageData.getHierarchy().getDetectionObjects().isEmpty());
        // Check what to show for TMA cores or annotations
        Collection<PathObject> selectedObjects = viewer.getAllSelectedObjects();
        PathObject pathObject = viewer.getSelectedObject();
        menuTMA.setVisible(false);
        if (pathObject instanceof TMACoreObject) {
            boolean isMissing = ((TMACoreObject) pathObject).isMissing();
            miTMAValid.setSelected(!isMissing);
            miTMAMissing.setSelected(isMissing);
            menuTMA.setVisible(true);
        }
        // Add clear objects option if we have more than one non-TMA object
        if (imageData == null || imageData.getHierarchy().getSelectionModel().noSelection() || imageData.getHierarchy().getSelectionModel().getSelectedObject() instanceof TMACoreObject)
            miClearSelectedObjects.setVisible(false);
        else {
            if (imageData.getHierarchy().getSelectionModel().singleSelection()) {
                miClearSelectedObjects.setText("Delete object");
                miClearSelectedObjects.setVisible(true);
            } else {
                miClearSelectedObjects.setText("Delete objects");
                miClearSelectedObjects.setVisible(true);
            }
        }
        boolean hasAnnotations = pathObject instanceof PathAnnotationObject || (!selectedObjects.isEmpty() && selectedObjects.stream().allMatch(p -> p.isAnnotation()));
        updateSetAnnotationPathClassMenu(menuSetClass, viewer);
        menuAnnotations.setVisible(hasAnnotations);
        topSeparator.setVisible(hasAnnotations || pathObject instanceof TMACoreObject);
        // Occasionally, the newly-visible top part of a popup menu can have the wrong size?
        popup.setWidth(popup.getPrefWidth());
    });
    // popup.add(menuClassify);
    popup.getItems().addAll(miClearSelectedObjects, menuTMA, menuSetClass, menuAnnotations, topSeparator, menuMultiview, menuCells, menuView, menuTools);
    popup.setAutoHide(true);
    // Enable circle pop-up for quick classification on right-click
    CirclePopupMenu circlePopup = new CirclePopupMenu(viewer.getView(), null);
    viewer.getView().addEventHandler(MouseEvent.MOUSE_PRESSED, e -> {
        if ((e.isPopupTrigger() || e.isSecondaryButtonDown()) && e.isShiftDown() && !getAvailablePathClasses().isEmpty()) {
            circlePopup.setAnimationDuration(Duration.millis(200));
            updateSetAnnotationPathClassMenu(circlePopup, viewer);
            circlePopup.show(e.getScreenX(), e.getScreenY());
            e.consume();
            return;
        } else if (circlePopup.isShown())
            circlePopup.hide();
        if (e.isPopupTrigger() || e.isSecondaryButtonDown()) {
            popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
            e.consume();
        }
    });
// // It's necessary to make the Window the owner, since otherwise the context menu does not disappear when clicking elsewhere on the viewer
// viewer.getView().setOnContextMenuRequested(e -> {
// popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
// //			popup.show(viewer.getView(), e.getScreenX(), e.getScreenY());
// });
}

Example 20 with PathObject

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

the class QuPathGUI method setupViewer.

void setupViewer(final QuPathViewerPlus viewer) {
    viewer.getView().setFocusTraversable(true);
    // Update active viewer as required
    viewer.getView().focusedProperty().addListener((e, f, nowFocussed) -> {
        if (nowFocussed) {
            viewerManager.setActiveViewer(viewer);
        }
    });
    viewer.getView().addEventFilter(MouseEvent.MOUSE_PRESSED, e -> viewer.getView().requestFocus());
    viewer.zoomToFitProperty().bind(zoomToFit);
    // Create popup menu
    setViewerPopupMenu(viewer);
    viewer.getView().widthProperty().addListener((e, f, g) -> {
        if (viewer.getZoomToFit())
            updateMagnificationString();
    });
    viewer.getView().heightProperty().addListener((e, f, g) -> {
        if (viewer.getZoomToFit())
            updateMagnificationString();
    });
    // Enable drag and drop
    dragAndDrop.setupTarget(viewer.getView());
    // Listen to the scroll wheel
    viewer.getView().setOnScroll(e -> {
        if (viewer == viewerManager.getActiveViewer() || !viewerManager.getSynchronizeViewers()) {
            double scrollUnits = e.getDeltaY() * PathPrefs.getScaledScrollSpeed();
            // Use shift down to adjust opacity
            if (e.isShortcutDown()) {
                OverlayOptions options = viewer.getOverlayOptions();
                options.setOpacity((float) (options.getOpacity() + scrollUnits * 0.001));
                return;
            }
            // Avoid zooming at the end of a gesture when using touchscreens
            if (e.isInertia())
                return;
            if (PathPrefs.invertScrollingProperty().get())
                scrollUnits = -scrollUnits;
            double newDownsampleFactor = viewer.getDownsampleFactor() * Math.pow(viewer.getDefaultZoomFactor(), scrollUnits);
            newDownsampleFactor = Math.min(viewer.getMaxDownsample(), Math.max(newDownsampleFactor, viewer.getMinDownsample()));
            viewer.setDownsampleFactor(newDownsampleFactor, e.getX(), e.getY());
        }
    });
    viewer.getView().addEventFilter(RotateEvent.ANY, e -> {
        if (!PathPrefs.useRotateGesturesProperty().get())
            return;
        // logger.debug("Rotating: " + e.getAngle());
        viewer.setRotation(viewer.getRotation() + Math.toRadians(e.getAngle()));
        e.consume();
    });
    viewer.getView().addEventFilter(ZoomEvent.ANY, e -> {
        if (!PathPrefs.useZoomGesturesProperty().get())
            return;
        double zoomFactor = e.getZoomFactor();
        if (Double.isNaN(zoomFactor))
            return;
        logger.debug("Zooming: " + e.getZoomFactor() + " (" + e.getTotalZoomFactor() + ")");
        viewer.setDownsampleFactor(viewer.getDownsampleFactor() / zoomFactor, e.getX(), e.getY());
        e.consume();
    });
    viewer.getView().addEventFilter(ScrollEvent.ANY, new ScrollEventPanningFilter(viewer));
    viewer.getView().addEventHandler(KeyEvent.KEY_PRESSED, e -> {
        PathObject pathObject = viewer.getSelectedObject();
        if (!e.isConsumed() && pathObject != null) {
            if (pathObject.isTMACore()) {
                TMACoreObject core = (TMACoreObject) pathObject;
                if (e.getCode() == KeyCode.ENTER) {
                    defaultActions.TMA_ADD_NOTE.handle(new ActionEvent(e.getSource(), e.getTarget()));
                    e.consume();
                } else if (e.getCode() == KeyCode.BACK_SPACE) {
                    core.setMissing(!core.isMissing());
                    viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(core));
                    e.consume();
                }
            } else if (pathObject.isAnnotation()) {
                if (e.getCode() == KeyCode.ENTER) {
                    GuiTools.promptToSetActiveAnnotationProperties(viewer.getHierarchy());
                    e.consume();
                }
            }
        }
    });
}