Examples with ImageData qupath.lib.images.ImageData used on opensource projects

Example 31 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class Commands method promptToSimplifySelectedAnnotations.

/**
 * Show a prompt to selected annotations in a hierarchy.
 * @param imageData the current image data
 * @param altitudeThreshold default altitude value for simplification
 */
public static void promptToSimplifySelectedAnnotations(ImageData<?> imageData, double altitudeThreshold) {
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    List<PathObject> pathObjects = hierarchy.getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation() && p.hasROI() && p.isEditable() && !p.getROI().isPoint()).collect(Collectors.toList());
    if (pathObjects.isEmpty()) {
        Dialogs.showErrorMessage("Simplify annotations", "No unlocked shape annotations selected!");
        return;
    }
    String input = Dialogs.showInputDialog("Simplify shape", "Set altitude threshold in pixels.\nHigher values give simpler shapes.", Double.toString(altitudeThreshold));
    if (input == null || !(input instanceof String) || ((String) input).trim().length() == 0)
        return;
    try {
        altitudeThreshold = Double.parseDouble(((String) input).trim());
    } catch (NumberFormatException e) {
        logger.error("Could not parse altitude threshold from {}", input);
        return;
    }
    if (altitudeThreshold <= 0) {
        Dialogs.showErrorMessage("Simplify shape", "Amplitude threshold should be greater than zero!");
        return;
    }
    long startTime = System.currentTimeMillis();
    for (var pathObject : pathObjects) {
        ROI pathROI = pathObject.getROI();
        if (pathROI instanceof PolygonROI) {
            PolygonROI polygonROI = (PolygonROI) pathROI;
            pathROI = ShapeSimplifier.simplifyPolygon(polygonROI, altitudeThreshold);
        } else {
            pathROI = ShapeSimplifier.simplifyShape(pathROI, altitudeThreshold);
        }
        ((PathAnnotationObject) pathObject).setROI(pathROI);
    }
    long endTime = System.currentTimeMillis();
    logger.debug("Shapes simplified in " + (endTime - startTime) + " ms");
    hierarchy.fireObjectsChangedEvent(hierarchy, pathObjects);
}

Example 32 with ImageData

use of qupath.lib.images.ImageData 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);
}