Examples with PluginRunner qupath.lib.plugins.PluginRunner used on opensource projects

Example 1 with PluginRunner

use of qupath.lib.plugins.PluginRunner in project qupath by qupath.

the class QPEx method runPlugin.

@SuppressWarnings({ "unchecked", "rawtypes" })
public static boolean runPlugin(final String className, final ImageData<?> imageData, final String args) throws InterruptedException {
    if (imageData == null)
        return false;
    boolean completed = false;
    String pluginName = className;
    boolean cancelled = false;
    try {
        Class<?> cPlugin = QP.class.getClassLoader().loadClass(className);
        Constructor<?> cons = cPlugin.getConstructor();
        final PathPlugin plugin = (PathPlugin) cons.newInstance();
        pluginName = plugin.getName();
        PluginRunner runner;
        // TODO: Give potential of passing a plugin runner
        var qupath = getQuPath();
        if (isBatchMode() || imageData != qupath.getImageData()) {
            runner = new CommandLinePluginRunner(imageData);
            completed = plugin.runPlugin(runner, args);
            cancelled = runner.isCancelled();
        } else {
            completed = qupath.runPlugin(plugin, args, false);
            cancelled = !completed;
        // runner = new PluginRunnerFX(qupath);
        }
    } catch (Exception e) {
        logger.error("Error running plugin {}: {}", className, e.getLocalizedMessage());
        logger.error("", e);
    }
    // Notify caller that this failed
    if (cancelled)
        throw new InterruptedException(pluginName + " cancelled!");
    // }
    return completed;
}

Example 2 with PluginRunner

use of qupath.lib.plugins.PluginRunner in project qupath by qupath.

the class ImageJMacroRunner method getParentObjects.

@Override
protected Collection<? extends PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
    // Try to get currently-selected objects
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    List<PathObject> pathObjects = hierarchy.getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation() || p.isTMACore()).collect(Collectors.toList());
    if (pathObjects.isEmpty()) {
        if (GuiTools.promptForParentObjects(this.getName(), runner.getImageData(), false, getSupportedParentObjectClasses()))
            pathObjects = new ArrayList<>(hierarchy.getSelectionModel().getSelectedObjects());
    }
    return pathObjects;
// // TODO: Give option to analyse annotations, even when TMA grid is present
// ImageData<BufferedImage> imageData = runner.getImageData();
// TMAGrid tmaGrid = imageData.getHierarchy().getTMAGrid();
// if (tmaGrid != null && tmaGrid.nCores() > 0)
// return PathObjectTools.getTMACoreObjects(imageData.getHierarchy(), false);
// else
// return imageData.getHierarchy().getObjects(null, PathAnnotationObject.class);
}