Examples with RunSavedClassifierWorkflowStep qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep used on opensource projects

Example 1 with RunSavedClassifierWorkflowStep

use of qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep in project qupath by qupath.

the class PathClassifierPane method runClassifier.

void runClassifier() {
    QuPathViewer viewer = viewerValue.getValue();
    if (viewer == null)
        return;
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (classifier == null || imageData == null || !classifier.isValid())
        return;
    Collection<PathObject> pathObjects = imageData.getHierarchy().getDetectionObjects();
    var availableFeatures = PathClassifierTools.getAvailableFeatures(pathObjects);
    var requiredFeatures = classifier.getRequiredMeasurements();
    String missingFeatures = requiredFeatures.stream().filter(p -> !availableFeatures.contains(p)).collect(Collectors.joining("\n\t"));
    if (!missingFeatures.isEmpty())
        logger.warn("Detection objects are missing the following feature(s):\n\t" + missingFeatures + "\nWill proceed with classification anyway..");
    // SwingUtilities.getRoot(viewer).setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    try {
        PathClassifierTools.runClassifier(imageData.getHierarchy(), classifier);
        // Log the classifier
        if (pathClassifier != null) {
            imageData.getHistoryWorkflow().addStep(new RunSavedClassifierWorkflowStep(pathClassifier));
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        // SwingUtilities.getRoot(viewer).setCursor(cursor);
        // Update displayed list - names may have changed - and classifier summary
        updateClassifierSummary();
    }
}

Example 2 with RunSavedClassifierWorkflowStep

use of qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep in project qupath by qupath.

the class QP method runClassifier.

/**
 * Run a detection object classifier for the current image data, reading the classifier from a specified path
 * @param path
 */
@Deprecated
public static void runClassifier(final String path) {
    ImageData<?> imageData = getCurrentImageData();
    if (imageData == null)
        return;
    PathObjectClassifier classifier = PathClassifierTools.loadClassifier(new File(path));
    if (classifier == null) {
        logger.error("Could not load classifier from {}", path);
        return;
    }
    runClassifier(imageData, classifier);
    // Log the step
    imageData.getHistoryWorkflow().addStep(new RunSavedClassifierWorkflowStep(path));
}