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

Example 21 with DefaultScriptableWorkflowStep

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

the class Commands method duplicateSelectedAnnotations.

/**
 * Duplicate the selected annotations.
 * @param imageData
 */
public static void duplicateSelectedAnnotations(ImageData<?> imageData) {
    if (imageData == null) {
        Dialogs.showNoImageError("Duplicate annotations");
        return;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    PathObjectTools.duplicateSelectedAnnotations(hierarchy);
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Duplicate selected annotations", "duplicateSelectedAnnotations()"));
}

Example 22 with DefaultScriptableWorkflowStep

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

the class Commands method promptToResolveHierarchy.

/**
 * Resolve parent-child relationships within the object hierarchy.
 * This means that objects will be arranged hierarchically, rather than as a flat list.
 * @param imageData the image data to process
 */
public static void promptToResolveHierarchy(ImageData<?> imageData) {
    if (imageData == null) {
        Dialogs.showNoImageError("Resolve hierarchy");
        return;
    }
    var hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null)
        return;
    if (!Dialogs.showConfirmDialog("Resolve hierarchy", "Are you sure you want to resolve object relationships?\n" + "For large object hierarchies this can take a long time.")) {
        return;
    }
    hierarchy.resolveHierarchy();
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Resolve hierarchy", "resolveHierarchy()"));
}

Example 23 with DefaultScriptableWorkflowStep

use of qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep 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 24 with DefaultScriptableWorkflowStep

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

the class ImageData method addColorDeconvolutionStainsToWorkflow.

// TODO: REINTRODUCE LOGGING!
private static void addColorDeconvolutionStainsToWorkflow(ImageData<?> imageData) {
    // logger.warn("Color deconvolution stain logging not currently enabled!");
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    if (stains == null) {
        return;
    }
    String arg = ColorDeconvolutionStains.getColorDeconvolutionStainsAsString(imageData.getColorDeconvolutionStains(), 5);
    Map<String, String> map = GeneralTools.parseArgStringValues(arg);
    WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
    String commandName = "Set color deconvolution stains";
    WorkflowStep newStep = new DefaultScriptableWorkflowStep(commandName, map, "setColorDeconvolutionStains(\'" + arg + "');");
    // else
    if (!Objects.equals(newStep, lastStep))
        imageData.getHistoryWorkflow().addStep(newStep);
// ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
// if (stains == null)
// return;
// 
// String arg = ColorDeconvolutionStains.getColorDeconvolutionStainsAsString(imageData.getColorDeconvolutionStains(), 5);
// Map<String, String> map = GeneralTools.parseArgStringValues(arg);
// WorkflowStep lastStep = imageData.getWorkflow().getLastStep();
// String commandName = "Set color deconvolution stains";
// WorkflowStep newStep = new DefaultScriptableWorkflowStep(commandName,
// map,
// QP.class.getSimpleName() + ".setColorDeconvolutionStains(\'" + arg + "');");
// 
// if (lastStep != null && commandName.equals(lastStep.getName()))
// imageData.getWorkflow().replaceLastStep(newStep);
// else
// imageData.getWorkflow().addStep(newStep);
}

Example 25 with DefaultScriptableWorkflowStep

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

the class PathClassPane method selectObjectsByClassification.

/**
 * Select objects by classification, logging the step (if performed) in the history workflow.
 * @param imageData the {@link ImageData} containing objects to be selected
 * @param pathClasses classifications that will result in an object being selected
 * @return true if a selection command was run, false otherwise (e.g. if no pathClasses were specified)
 */
public static boolean selectObjectsByClassification(ImageData<?> imageData, PathClass... pathClasses) {
    var hierarchy = imageData.getHierarchy();
    if (pathClasses.length == 0) {
        logger.warn("Cannot select objects by classification - no classifications selected!");
        return false;
    }
    QP.selectObjectsByPathClass(hierarchy, pathClasses);
    var s = Arrays.stream(pathClasses).map(p -> p == null || p == PathClassFactory.getPathClassUnclassified() ? "null" : "\"" + p.toString() + "\"").collect(Collectors.joining(", "));
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Select objects by classification", "selectObjectsByClassification(" + s + ");"));
    return true;
}