Examples with QuPathGUI qupath.lib.gui.QuPathGUI used on opensource projects

Example 6 with QuPathGUI

use of qupath.lib.gui.QuPathGUI in project qupath by qupath.

the class ImportObjectsCommand method runObjectImport.

/**
 * Import objects or ROIs and adds them to the current hierarchy.
 *
 * @param qupath
 * @return success
 * @throws IOException
 */
public static boolean runObjectImport(QuPathGUI qupath) throws IOException {
    var imageData = qupath.getImageData();
    if (imageData == null)
        return false;
    var file = Dialogs.promptForFile("Choose file to import", null, "QuPath objects", PathIO.getObjectFileExtensions(true).toArray(String[]::new));
    // User cancel
    if (file == null)
        return false;
    List<PathObject> objs;
    try {
        objs = PathIO.readObjects(file);
    } catch (IOException | IllegalArgumentException ex) {
        Dialogs.showErrorNotification("Error importing objects", ex.getLocalizedMessage());
        return false;
    }
    if (objs.isEmpty()) {
        Dialogs.showWarningNotification("Import objects", "No objects found in " + file.getAbsolutePath());
        return false;
    }
    int nObjects = objs.stream().mapToInt(p -> 1 + PathObjectTools.countDescendants(p)).sum();
    String message = nObjects == 1 ? "Add 1 object to the hierarchy?" : String.format("Add %d objects to the hierarchy?", nObjects);
    var confirm = Dialogs.showConfirmDialog("Add to hierarchy", message);
    if (!confirm)
        return false;
    var hierarchy = imageData.getHierarchy();
    hierarchy.addPathObjects(objs);
    Map<String, String> map = new HashMap<>();
    map.put("path", file.getPath());
    String method = "Import objects";
    String methodString = String.format("%s(%s%s%s)", "importObjectsFromFile", "\"", GeneralTools.escapeFilePath(file.getPath()), "\"");
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep(method, map, methodString));
    return true;
}

Example 7 with QuPathGUI

use of qupath.lib.gui.QuPathGUI in project qupath by qupath.

the class TMASummaryViewer method setTMAEntriesFromOpenImage.

private void setTMAEntriesFromOpenImage() {
    QuPathGUI qupath = QuPathGUI.getInstance();
    if (qupath == null || qupath.getImageData() == null || qupath.getImageData().getHierarchy().getTMAGrid() == null) {
        Dialogs.showErrorMessage("Show TMA summary", "No TMA data available!");
        return;
    }
    ImageData<BufferedImage> imageData = qupath.getImageData();
    setTMAEntriesFromImageData(imageData);
}

Example 8 with QuPathGUI

use of qupath.lib.gui.QuPathGUI in project qupath by qupath.

the class GuiTools method createAnnotationsMenuImpl.

private static void createAnnotationsMenuImpl(QuPathGUI qupath, Object menu) {
    // Add annotation options
    CheckMenuItem miLockAnnotations = new CheckMenuItem("Lock");
    CheckMenuItem miUnlockAnnotations = new CheckMenuItem("Unlock");
    miLockAnnotations.setOnAction(e -> setSelectedAnnotationLock(qupath.getImageData(), true));
    miUnlockAnnotations.setOnAction(e -> setSelectedAnnotationLock(qupath.getImageData(), false));
    MenuItem miSetProperties = new MenuItem("Set properties");
    miSetProperties.setOnAction(e -> {
        var hierarchy = qupath.getViewer().getHierarchy();
        if (hierarchy != null)
            GuiTools.promptToSetActiveAnnotationProperties(hierarchy);
    });
    var actionInsertInHierarchy = qupath.createImageDataAction(imageData -> Commands.insertSelectedObjectsInHierarchy(imageData));
    actionInsertInHierarchy.setText("Insert in hierarchy");
    var miInsertHierarchy = ActionTools.createMenuItem(actionInsertInHierarchy);
    var actionMerge = qupath.createImageDataAction(imageData -> Commands.mergeSelectedAnnotations(imageData));
    actionMerge.setText("Merge selected");
    var actionSubtract = qupath.createImageDataAction(imageData -> Commands.combineSelectedAnnotations(imageData, CombineOp.SUBTRACT));
    actionSubtract.setText("Subtract selected");
    var actionIntersect = qupath.createImageDataAction(imageData -> Commands.combineSelectedAnnotations(imageData, CombineOp.INTERSECT));
    actionIntersect.setText("Intersect selected");
    var actionInverse = qupath.createImageDataAction(imageData -> Commands.makeInverseAnnotation(imageData));
    actionInverse.setText("Make inverse");
    Menu menuCombine = MenuTools.createMenu("Edit multiple", actionMerge, // TODO: Make this less ambiguous!
    actionSubtract, actionIntersect);
    Menu menuEdit = MenuTools.createMenu("Edit single", actionInverse, qupath.createPluginAction("Split", SplitAnnotationsPlugin.class, null));
    // Menu menuPoints = MenuTools.createMenu(
    // "Points",
    // QuPathGUI.createCommandAction(new MergePointsCommand(qupath, true), "Merge all points for class"),
    // QuPathGUI.createCommandAction(new MergePointsCommand(qupath, true), "Merge selected points for class")
    // );
    MenuItem separator = new SeparatorMenuItem();
    Runnable validator = () -> {
        var imageData = qupath.getImageData();
        PathObject selected = null;
        Collection<PathObject> allSelected = Collections.emptyList();
        boolean allSelectedAnnotations = false;
        boolean hasSelectedAnnotation = false;
        if (imageData != null) {
            selected = imageData.getHierarchy().getSelectionModel().getSelectedObject();
            allSelected = new ArrayList<>(imageData.getHierarchy().getSelectionModel().getSelectedObjects());
            hasSelectedAnnotation = selected != null && selected.isAnnotation();
            allSelectedAnnotations = allSelected.stream().allMatch(p -> p.isAnnotation());
        }
        miLockAnnotations.setDisable(!hasSelectedAnnotation);
        miUnlockAnnotations.setDisable(!hasSelectedAnnotation);
        if (hasSelectedAnnotation) {
            boolean isLocked = selected.isLocked();
            miLockAnnotations.setSelected(isLocked);
            miUnlockAnnotations.setSelected(!isLocked);
        }
        miSetProperties.setDisable(!hasSelectedAnnotation);
        miInsertHierarchy.setVisible(selected != null);
        menuEdit.setVisible(hasSelectedAnnotation);
        menuCombine.setVisible(allSelectedAnnotations && allSelected.size() > 1);
        separator.setVisible(menuEdit.isVisible() || menuCombine.isVisible());
    };
    List<MenuItem> items;
    if (menu instanceof Menu) {
        Menu m = (Menu) menu;
        items = m.getItems();
        m.setOnMenuValidation(e -> validator.run());
    } else if (menu instanceof ContextMenu) {
        ContextMenu m = (ContextMenu) menu;
        items = m.getItems();
        m.setOnShowing(e -> validator.run());
    } else
        throw new IllegalArgumentException("Menu must be either a standard Menu or a ContextMenu!");
    MenuTools.addMenuItems(items, miLockAnnotations, miUnlockAnnotations, miSetProperties, miInsertHierarchy, separator, menuEdit, menuCombine);
}