Examples with PathObjectHierarchy qupath.lib.objects.hierarchy.PathObjectHierarchy used on opensource projects

Example 1 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class SplitAnnotationsPlugin method getTasks.

@Override
protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
    Collection<? extends PathObject> parentObjects = getParentObjects(runner);
    if (parentObjects == null || parentObjects.isEmpty())
        return Collections.emptyList();
    // Add a single task, to avoid multithreading - which may complicate setting parents
    List<Runnable> tasks = new ArrayList<>(1);
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    // Want to reset selection
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    tasks.add(() -> {
        /*
			 * Resolving the hierarchy with many objects can be very slow.
			 * Here, we take an object, split it and then add it below the original object in the hierarchy.
			 * We then just need to remove the originals, allowing the newly-added objects to have their 
			 * parents reassigned.
			 */
        List<PathObject> toAdd = new ArrayList<>();
        List<PathObject> toRemove = new ArrayList<>();
        List<PathObject> localSplit = new ArrayList<>();
        Set<PathObject> toSelect = new HashSet<>();
        for (PathObject pathObject : parentObjects) {
            localSplit.clear();
            ROI roiOrig = pathObject.getROI();
            if (roiOrig == null) {
                toSelect.add(pathObject);
                continue;
            }
            var splitROIs = RoiTools.splitROI(roiOrig);
            if (splitROIs.size() == 1)
                continue;
            toRemove.add(pathObject);
            for (var r : splitROIs) {
                var annotation = PathObjects.createAnnotationObject(r, pathObject.getPathClass());
                annotation.setLocked(pathObject.isLocked());
                localSplit.add(annotation);
            }
            if (pathObject.hasChildren()) {
                for (var temp : localSplit) hierarchy.addPathObjectBelowParent(pathObject, temp, false);
            } else
                pathObject.addPathObjects(localSplit);
            toAdd.addAll(localSplit);
        }
        if (toAdd.isEmpty() && toRemove.isEmpty())
            return;
        hierarchy.getSelectionModel().clearSelection();
        toSelect.addAll(toAdd);
        hierarchy.removeObjects(toRemove, true);
        // hierarchy.addPathObjects(toAdd, false);
        hierarchy.getSelectionModel().selectObjects(toSelect);
        if (toSelect.contains(selected))
            hierarchy.getSelectionModel().setSelectedObject(selected, true);
    });
    return tasks;
}

Example 2 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class QP method clearTMAGrid.

/**
 * Remove the TMA grid from the current {@code PathObjectHierarchy}.
 *
 * @see #getCurrentHierarchy
 */
public static void clearTMAGrid() {
    PathObjectHierarchy hierarchy = getCurrentHierarchy();
    if (hierarchy == null)
        return;
    hierarchy.setTMAGrid(null);
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    if (selected instanceof TMACoreObject)
        hierarchy.getSelectionModel().setSelectedObject(null);
}

Example 3 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class Commands method promptToDeleteObjects.

/**
 * Prompt to delete objects of a specified type, or all objects.
 * @param imageData
 * @param cls
 */
public static void promptToDeleteObjects(ImageData<?> imageData, Class<? extends PathObject> cls) {
    if (imageData == null)
        return;
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    // Handle no specified class - indicates all objects of all types should be cleared
    if (cls == null) {
        int n = hierarchy.nObjects();
        if (n == 0)
            return;
        String message;
        if (n == 1)
            message = "Delete object?";
        else
            message = "Delete all " + n + " objects?";
        if (Dialogs.showYesNoDialog("Delete objects", message)) {
            hierarchy.clearAll();
            hierarchy.getSelectionModel().setSelectedObject(null);
            imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Clear all objects", "clearAllObjects();"));
        }
        return;
    }
    // Handle clearing TMA grid
    if (TMACoreObject.class.equals(cls)) {
        if (hierarchy.getTMAGrid() != null) {
            if (Dialogs.showYesNoDialog("Delete objects", "Clear TMA grid?")) {
                hierarchy.setTMAGrid(null);
                PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
                if (selected instanceof TMACoreObject)
                    hierarchy.getSelectionModel().setSelectedObject(null);
                imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Clear TMA Grid", "clearTMAGrid();"));
            }
            return;
        }
    }
    // Handle clearing objects of another specified type
    Collection<PathObject> pathObjects = hierarchy.getObjects(null, cls);
    if (pathObjects.isEmpty())
        return;
    int n = pathObjects.size();
    String message = n == 1 ? "Delete 1 object?" : "Delete " + n + " objects?";
    if (Dialogs.showYesNoDialog("Delete objects", message)) {
        hierarchy.removeObjects(pathObjects, true);
        PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
        if (selected != null && selected.getClass().isAssignableFrom(cls))
            hierarchy.getSelectionModel().setSelectedObject(null);
        if (selected != null && selected.getClass().isAssignableFrom(cls))
            hierarchy.getSelectionModel().setSelectedObject(null);
        if (cls == PathDetectionObject.class)
            imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Clear detections", "clearDetections();"));
        else if (cls == PathAnnotationObject.class)
            imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Clear annotations", "clearAnnotations();"));
        else if (cls == TMACoreObject.class)
            imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Clear TMA grid", "clearTMAGrid();"));
        else
            logger.warn("Cannot clear all objects for class {}", cls);
    }
}

Example 4 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class Commands method mergeSelectedAnnotations.

// /**
// * Merge the points ROIs of different objects to create a single object containing all points with a specific {@link PathClass}.
// * @param imageData the image data containing points to merge
// * @param selectedOnly if true, use only classes found within the currently selected objects
// */
// public static void mergePointsForClasses(ImageData<?> imageData, boolean selectedOnly) {
// var hierarchy = imageData == null ? null : imageData.getHierarchy();
// if (hierarchy == null) {
// Dialogs.showNoImageError("Merge points");
// return;
// }
// if (selectedOnly) {
// PathObjectTools.mergePointsForSelectedObjectClasses(hierarchy);
// imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep(
// "Merge points for selected classifications",
// "mergePointsForSelectedObjectClasses();"
// ));
// } else {
// PathObjectTools.mergePointsForAllClasses(hierarchy);
// imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep(
// "Merge points for all classifications",
// "mergePointsForAllClasses();"
// ));
// }
// }
/**
 * Merge the currently-selected annotations for an image, replacing them with a single new annotation.
 * @param imageData
 */
public static void mergeSelectedAnnotations(ImageData<?> imageData) {
    if (imageData == null)
        return;
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    logger.debug("Merging selected annotations");
    QP.mergeSelectedAnnotations(hierarchy);
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Merge selected annotations", "mergeSelectedAnnotations()"));
}

Example 5 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class ExportObjectsCommand method runGeoJsonExport.

/**
 * Run the path object GeoJSON export command.
 * @param qupath
 * @return success
 * @throws IOException
 */
public static boolean runGeoJsonExport(QuPathGUI qupath) throws IOException {
    // Get ImageData
    var imageData = qupath.getImageData();
    if (imageData == null)
        return false;
    // Get hierarchy
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    String allObjects = "All objects";
    String selectedObjects = "Selected objects";
    String defaultObjects = hierarchy.getSelectionModel().noSelection() ? allObjects : selectedObjects;
    // Params
    var parameterList = new ParameterList().addChoiceParameter("exportOptions", "Export ", defaultObjects, Arrays.asList(allObjects, selectedObjects), "Choose which objects to export - run a 'Select annotations/detections' command first if needed").addBooleanParameter("excludeMeasurements", "Exclude measurements", false, "Exclude object measurements during export - for large numbers of detections this can help reduce the file size").addBooleanParameter("doPretty", "Pretty JSON", false, "Pretty GeoJSON is more human-readable but results in larger file sizes").addBooleanParameter("doFeatureCollection", "Export as FeatureCollection", true, "Export as a 'FeatureCollection', which is a standard GeoJSON way to represent multiple objects; if not, a regular JSON object/array will be export").addBooleanParameter("doZip", "Compress data (zip)", false, "Compressed files take less memory");
    if (!Dialogs.showParameterDialog("Export objects", parameterList))
        return false;
    Collection<PathObject> toProcess;
    var comboChoice = parameterList.getChoiceParameterValue("exportOptions");
    if (comboChoice.equals("Selected objects")) {
        if (hierarchy.getSelectionModel().noSelection()) {
            Dialogs.showErrorMessage("No selection", "No selection detected!");
            return false;
        }
        toProcess = hierarchy.getSelectionModel().getSelectedObjects();
    } else
        toProcess = hierarchy.getObjects(null, null);
    // Remove PathRootObject
    toProcess = toProcess.stream().filter(e -> !e.isRootObject()).collect(Collectors.toList());
    // Check if includes ellipse(s), as they will need to be polygonized
    var nEllipses = toProcess.stream().filter(ann -> isEllipse(ann)).count();
    if (nEllipses > 0) {
        String message = nEllipses == 1 ? "1 ellipse will be polygonized, continue?" : String.format("%d ellipses will be polygonized, continue?", nEllipses);
        var response = Dialogs.showYesNoDialog("Ellipse polygonization", message);
        if (!response)
            return false;
    }
    File outFile;
    // Get default name & output directory
    var project = qupath.getProject();
    String defaultName = imageData.getServer().getMetadata().getName();
    if (project != null) {
        var entry = project.getEntry(imageData);
        if (entry != null)
            defaultName = entry.getImageName();
    }
    defaultName = GeneralTools.getNameWithoutExtension(defaultName);
    File defaultDirectory = project == null || project.getPath() == null ? null : project.getPath().toFile();
    while (defaultDirectory != null && !defaultDirectory.isDirectory()) defaultDirectory = defaultDirectory.getParentFile();
    if (parameterList.getBooleanParameterValue("doZip"))
        outFile = Dialogs.promptToSaveFile("Export to file", defaultDirectory, defaultName + ".zip", "ZIP archive", ".zip");
    else
        outFile = Dialogs.promptToSaveFile("Export to file", defaultDirectory, defaultName + ".geojson", "GeoJSON", ".geojson");
    // If user cancels
    if (outFile == null)
        return false;
    List<GeoJsonExportOptions> options = new ArrayList<>();
    if (parameterList.getBooleanParameterValue("excludeMeasurements"))
        options.add(GeoJsonExportOptions.EXCLUDE_MEASUREMENTS);
    if (parameterList.getBooleanParameterValue("doPretty"))
        options.add(GeoJsonExportOptions.PRETTY_JSON);
    if (parameterList.getBooleanParameterValue("doFeatureCollection"))
        options.add(GeoJsonExportOptions.FEATURE_COLLECTION);
    // Export
    QP.exportObjectsToGeoJson(toProcess, outFile.getAbsolutePath(), options.toArray(GeoJsonExportOptions[]::new));
    // Notify user of success
    int nObjects = toProcess.size();
    String message = nObjects == 1 ? "1 object was exported to " + outFile.getAbsolutePath() : String.format("%d objects were exported to %s", nObjects, outFile.getAbsolutePath());
    Dialogs.showInfoNotification("Succesful export", message);
    // Get history workflow
    var historyWorkflow = imageData.getHistoryWorkflow();
    // args for workflow step
    Map<String, String> map = new LinkedHashMap<>();
    map.put("path", outFile.getPath());
    String method = comboChoice.equals(allObjects) ? "exportAllObjectsToGeoJson" : "exportSelectedObjectsToGeoJson";
    String methodTitle = comboChoice.equals(allObjects) ? "Export all objects" : "Export selected objects";
    String optionsString = options.stream().map(o -> "\"" + o.name() + "\"").collect(Collectors.joining(", "));
    map.put("options", optionsString);
    if (!optionsString.isEmpty())
        optionsString = ", " + optionsString;
    String methodString = String.format("%s(%s%s)", method, "\"" + GeneralTools.escapeFilePath(outFile.getPath()) + "\"", optionsString);
    historyWorkflow.addStep(new DefaultScriptableWorkflowStep(methodTitle, map, methodString));
    return true;
}