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

Example 16 with DefaultScriptableWorkflowStep

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

the class Commands method createFullImageAnnotation.

/**
 * Create a full image annotation for the image in the specified viewer.
 * The z and t positions of the viewer will be used.
 * @param viewer the viewer containing the image to be processed
 */
public static void createFullImageAnnotation(QuPathViewer viewer) {
    if (viewer == null)
        return;
    ImageData<?> imageData = viewer.getImageData();
    if (imageData == null)
        return;
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    // Check if we already have a comparable annotation
    int z = viewer.getZPosition();
    int t = viewer.getTPosition();
    ImageRegion bounds = viewer.getServerBounds();
    ROI roi = ROIs.createRectangleROI(bounds.getX(), bounds.getY(), bounds.getWidth(), bounds.getHeight(), ImagePlane.getPlane(z, t));
    for (PathObject pathObject : hierarchy.getAnnotationObjects()) {
        ROI r2 = pathObject.getROI();
        if (r2 instanceof RectangleROI && roi.getBoundsX() == r2.getBoundsX() && roi.getBoundsY() == r2.getBoundsY() && roi.getBoundsWidth() == r2.getBoundsWidth() && roi.getBoundsHeight() == r2.getBoundsHeight() && roi.getImagePlane().equals(r2.getImagePlane())) {
            logger.info("Full image annotation already exists! {}", pathObject);
            viewer.setSelectedObject(pathObject);
            return;
        }
    }
    PathObject pathObject = PathObjects.createAnnotationObject(roi);
    hierarchy.addPathObject(pathObject);
    viewer.setSelectedObject(pathObject);
    // Log in the history
    if (z == 0 && t == 0)
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Create full image annotation", "createSelectAllObject(true);"));
    else
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Create full image annotation", String.format("createSelectAllObject(true, %d, %d);", z, t)));
}

Example 17 with DefaultScriptableWorkflowStep

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

the class Commands method distanceToAnnotations2D.

/**
 * Compute the distance between all detections and the closest annotation, for all annotation classifications.
 * @param imageData the image data to process
 */
public static void distanceToAnnotations2D(ImageData<?> imageData) {
    String title = "Distance to annotations 2D";
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return;
    }
    if (imageData.getServer().nZSlices() > 1) {
        logger.debug("Warning user that measurements will be 2D...");
        if (!Dialogs.showConfirmDialog(title, "Distance to annotations command works only in 2D - distances will not be calculated for objects on different z-slices or time-points")) {
            logger.debug("Command cancelled");
            return;
        }
    }
    var result = Dialogs.showYesNoCancelDialog(title, "Split multi-part classifications?\nIf yes, each component of classifications such as \"Class1: Class2\" will be treated separately.");
    boolean doSplit = false;
    if (result == DialogButton.YES)
        doSplit = true;
    else if (result != DialogButton.NO)
        return;
    DistanceTools.detectionToAnnotationDistances(imageData, doSplit);
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Distance to annotations 2D", doSplit ? "detectionToAnnotationDistances(true)" : "detectionToAnnotationDistances(false)"));
}

Example 18 with DefaultScriptableWorkflowStep

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

the class Commands method resetTMAMetadata.

/**
 * Reset TMA metadata, if available.
 * @param imageData
 * @return true if changes were made, false otherwise
 */
public static boolean resetTMAMetadata(ImageData<?> imageData) {
    if (imageData == null || imageData.getHierarchy().getTMAGrid() == null) {
        logger.warn("No TMA grid available!");
        return false;
    }
    QP.resetTMAMetadata(imageData.getHierarchy(), true);
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Reset TMA metadata", "resetTMAMetadata(true);"));
    return true;
}

Example 19 with DefaultScriptableWorkflowStep

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

the class MeasurementManager method promptToRemoveMeasurements.

private boolean promptToRemoveMeasurements() {
    var selectedItems = new ArrayList<>(listView.getSelectionModel().getSelectedItems());
    if (selectedItems.isEmpty()) {
        Dialogs.showErrorMessage("Remove measurements", "No measurements selected!");
        return false;
    }
    String number = selectedItems.size() == 1 ? String.format("'%s'", selectedItems.iterator().next()) : selectedItems.size() + " measurements";
    if (!Dialogs.showConfirmDialog("Remove measurements", "Are you sure you want to permanently remove " + number + "?"))
        return false;
    String removeString = selectedItems.stream().map(m -> "\"" + m + "\"").collect(Collectors.joining(", "));
    logger.info("Removing measurements: {}", removeString);
    Class<? extends PathObject> cls = comboBox.getSelectionModel().getSelectedItem();
    QP.removeMeasurements(imageData.getHierarchy(), cls, selectedItems.toArray(String[]::new));
    // Keep for scripting
    WorkflowStep step = new DefaultScriptableWorkflowStep("Remove measurements", String.format("removeMeasurements(%s, %s);", cls.getName(), removeString));
    imageData.getHistoryWorkflow().addStep(step);
    // Update
    refreshMeasurements();
    updateCurrentList();
    filterText.set("");
    return true;
}

Example 20 with DefaultScriptableWorkflowStep

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

the class Commands method detectionCentroidDistances2D.

/**
 * Compute the distance between the centroids of all detections, for all available classifications.
 * @param imageData the image data to process
 */
public static void detectionCentroidDistances2D(ImageData<?> imageData) {
    String title = "Detection centroid distances 2D";
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return;
    }
    if (imageData.getServer().nZSlices() > 1) {
        logger.debug("Warning user that measurements will be 2D...");
        if (!Dialogs.showConfirmDialog(title, "Detection centroid distances command works only in 2D - distances will not be calculated for objects on different z-slices or time-points")) {
            logger.debug("Command cancelled");
            return;
        }
    }
    var result = Dialogs.showYesNoCancelDialog(title, "Split multi-part classifications?\nIf yes, each component of classifications such as \"Class1: Class2\" will be treated separately.");
    boolean doSplit = false;
    if (result == DialogButton.YES)
        doSplit = true;
    else if (result != DialogButton.NO)
        return;
    DistanceTools.detectionCentroidDistances(imageData, doSplit);
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Detection centroid distances 2D", doSplit ? "detectionCentroidDistances(true)" : "detectionCentroidDistances(false)"));
}