Examples with ImageData qupath.lib.images.ImageData used on opensource projects

Example 26 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class ProjectBrowser method getPopup.

ContextMenu getPopup() {
    Action actionOpenImage = new Action("Open image", e -> qupath.openImageEntry(getSelectedEntry()));
    Action actionRemoveImage = new Action("Remove image(s)", e -> {
        Collection<ImageRow> imageRows = getSelectedImageRowsRecursive();
        Collection<ProjectImageEntry<BufferedImage>> entries = ProjectTreeRow.getEntries(imageRows);
        if (entries.isEmpty())
            return;
        // Don't allow us to remove any entries that are currently open (in any viewer)
        for (var viewer : qupath.getViewers()) {
            var imageData = viewer.getImageData();
            var entry = imageData == null ? null : getProject().getEntry(imageData);
            if (entry != null && entries.contains(entry)) {
                Dialogs.showErrorMessage("Remove project entries", "Please close all images you want to remove!");
                return;
            }
        }
        if (entries.size() == 1) {
            if (!Dialogs.showConfirmDialog("Remove project entry", "Remove " + entries.iterator().next().getImageName() + " from project?"))
                return;
        } else if (!Dialogs.showYesNoDialog("Remove project entries", String.format("Remove %d entries?", entries.size())))
            return;
        var result = Dialogs.showYesNoCancelDialog("Remove project entries", "Delete all associated data?");
        if (result == DialogButton.CANCEL)
            return;
        project.removeAllImages(entries, result == DialogButton.YES);
        refreshTree(null);
        syncProject(project);
        if (tree != null) {
            boolean isExpanded = tree.getRoot() != null && tree.getRoot().isExpanded();
            tree.setRoot(model.getRoot());
            tree.getRoot().setExpanded(isExpanded);
        }
    });
    Action actionDuplicateImages = new Action("Duplicate image(s)", e -> {
        Collection<ImageRow> imageRows = getSelectedImageRowsRecursive();
        if (imageRows.isEmpty()) {
            logger.debug("Nothing to duplicate - no entries selected");
            return;
        }
        boolean singleImage = false;
        String name = "";
        String title = "Duplicate images";
        String namePrompt = "Append to image name";
        String nameHelp = "Specify text to append to the image name to distinguish duplicated images";
        if (imageRows.size() == 1) {
            title = "Duplicate image";
            namePrompt = "Duplicate image name";
            nameHelp = "Specify name for the duplicated image";
            singleImage = true;
            name = imageRows.iterator().next().getDisplayableString();
            name = GeneralTools.generateDistinctName(name, project.getImageList().stream().map(p -> p.getImageName()).collect(Collectors.toSet()));
        }
        var params = new ParameterList().addStringParameter("name", namePrompt, name, nameHelp).addBooleanParameter("copyData", "Also duplicate data files", true, "Duplicate any associated data files along with the image");
        if (!Dialogs.showParameterDialog(title, params))
            return;
        boolean copyData = params.getBooleanParameterValue("copyData");
        name = params.getStringParameterValue("name");
        // Ensure we have a single space and then the text to append, with extra whitespace removed
        if (!singleImage && !name.isBlank())
            name = " " + name.strip();
        for (var imageRow : imageRows) {
            try {
                var newEntry = project.addDuplicate(ProjectTreeRow.getEntry(imageRow), copyData);
                if (newEntry != null && !name.isBlank()) {
                    if (singleImage)
                        newEntry.setImageName(name);
                    else
                        newEntry.setImageName(newEntry.getImageName() + name);
                }
            } catch (Exception ex) {
                Dialogs.showErrorNotification("Duplicating image", "Error duplicating " + ProjectTreeRow.getEntry(imageRow).getImageName());
                logger.error(ex.getLocalizedMessage(), ex);
            }
        }
        try {
            project.syncChanges();
        } catch (Exception ex) {
            logger.error("Error synchronizing project changes: " + ex.getLocalizedMessage(), ex);
        }
        refreshProject();
        if (imageRows.size() == 1)
            logger.debug("Duplicated 1 image entry");
        else
            logger.debug("Duplicated {} image entries");
    });
    Action actionSetImageName = new Action("Rename image", e -> {
        TreeItem<ProjectTreeRow> path = tree.getSelectionModel().getSelectedItem();
        if (path == null)
            return;
        if (path.getValue().getType() == ProjectTreeRow.Type.IMAGE) {
            if (setProjectEntryImageName(ProjectTreeRow.getEntry(path.getValue())) && project != null)
                syncProject(project);
        }
    });
    // Add a metadata value
    Action actionAddMetadataValue = new Action("Add metadata", e -> {
        Project<BufferedImage> project = getProject();
        Collection<ImageRow> imageRows = getSelectedImageRowsRecursive();
        if (project != null && !imageRows.isEmpty()) {
            TextField tfMetadataKey = new TextField();
            var suggestions = project.getImageList().stream().map(p -> p.getMetadataKeys()).flatMap(Collection::stream).distinct().sorted().collect(Collectors.toList());
            TextFields.bindAutoCompletion(tfMetadataKey, suggestions);
            TextField tfMetadataValue = new TextField();
            Label labKey = new Label("New key");
            Label labValue = new Label("New value");
            labKey.setLabelFor(tfMetadataKey);
            labValue.setLabelFor(tfMetadataValue);
            tfMetadataKey.setTooltip(new Tooltip("Enter the name for the metadata entry"));
            tfMetadataValue.setTooltip(new Tooltip("Enter the value for the metadata entry"));
            ProjectImageEntry<BufferedImage> entry = imageRows.size() == 1 ? ProjectTreeRow.getEntry(imageRows.iterator().next()) : null;
            int nMetadataValues = entry == null ? 0 : entry.getMetadataKeys().size();
            GridPane pane = new GridPane();
            pane.setVgap(5);
            pane.setHgap(5);
            pane.add(labKey, 0, 0);
            pane.add(tfMetadataKey, 1, 0);
            pane.add(labValue, 0, 1);
            pane.add(tfMetadataValue, 1, 1);
            String name = imageRows.size() + " images";
            if (entry != null) {
                name = entry.getImageName();
                if (nMetadataValues > 0) {
                    Label labelCurrent = new Label("Current metadata");
                    TextArea textAreaCurrent = new TextArea();
                    textAreaCurrent.setEditable(false);
                    String keyString = entry.getMetadataSummaryString();
                    if (keyString.isEmpty())
                        textAreaCurrent.setText("No metadata entries yet");
                    else
                        textAreaCurrent.setText(keyString);
                    textAreaCurrent.setPrefRowCount(3);
                    labelCurrent.setLabelFor(textAreaCurrent);
                    pane.add(labelCurrent, 0, 2);
                    pane.add(textAreaCurrent, 1, 2);
                }
            }
            Dialog<ButtonType> dialog = new Dialog<>();
            dialog.setTitle("Metadata");
            dialog.getDialogPane().getButtonTypes().setAll(ButtonType.OK, ButtonType.CANCEL);
            dialog.getDialogPane().setHeaderText("Set metadata for " + name);
            dialog.getDialogPane().setContent(pane);
            Optional<ButtonType> result = dialog.showAndWait();
            if (result.isPresent() && result.get() == ButtonType.OK) {
                String key = tfMetadataKey.getText().trim();
                String value = tfMetadataValue.getText();
                if (key.isEmpty()) {
                    logger.warn("Attempted to set metadata value for {}, but key was empty!", name);
                } else {
                    // Set metadata for all entries
                    for (var temp : imageRows) ProjectTreeRow.getEntry(temp).putMetadataValue(key, value);
                    syncProject(project);
                    tree.refresh();
                }
            }
        } else {
            Dialogs.showErrorMessage("Edit image description", "No entry is selected!");
        }
    });
    // Edit the description for the image
    Action actionEditDescription = new Action("Edit description", e -> {
        Project<?> project = getProject();
        ProjectImageEntry<?> entry = getSelectedEntry();
        if (project != null && entry != null) {
            if (showDescriptionEditor(entry)) {
                descriptionText.set(entry.getDescription());
                syncProject(project);
            }
        } else {
            Dialogs.showErrorMessage("Edit image description", "No entry is selected!");
        }
    });
    // Mask the name of the images and shuffle the entry
    Action actionMaskImageNames = ActionTools.createSelectableAction(PathPrefs.maskImageNamesProperty(), "Mask image names");
    // Refresh thumbnail according to current display settings
    Action actionRefreshThumbnail = new Action("Refresh thumbnail", e -> {
        TreeItem<ProjectTreeRow> path = tree.getSelectionModel().getSelectedItem();
        if (path == null)
            return;
        if (path.getValue().getType() == ProjectTreeRow.Type.IMAGE) {
            ProjectImageEntry<BufferedImage> entry = ProjectTreeRow.getEntry(path.getValue());
            if (!isCurrentImage(entry)) {
                logger.warn("Cannot refresh entry for image that is not open!");
                return;
            }
            BufferedImage imgThumbnail = qupath.getViewer().getRGBThumbnail();
            imgThumbnail = resizeForThumbnail(imgThumbnail);
            try {
                entry.setThumbnail(imgThumbnail);
            } catch (IOException e1) {
                logger.error("Error writing thumbnail", e1);
            }
            tree.refresh();
        }
    });
    // Open the project directory using Explorer/Finder etc.
    Action actionOpenProjectDirectory = createBrowsePathAction("Project...", () -> getProjectPath());
    Action actionOpenProjectEntryDirectory = createBrowsePathAction("Project entry...", () -> getProjectEntryPath());
    Action actionOpenImageServerDirectory = createBrowsePathAction("Image server...", () -> getImageServerPath());
    Menu menuSort = new Menu("Sort by...");
    ContextMenu menu = new ContextMenu();
    var hasProjectBinding = qupath.projectProperty().isNotNull();
    var menuOpenDirectories = MenuTools.createMenu("Open directory...", actionOpenProjectDirectory, actionOpenProjectEntryDirectory, actionOpenImageServerDirectory);
    menuOpenDirectories.visibleProperty().bind(hasProjectBinding);
    // MenuItem miOpenProjectDirectory = ActionUtils.createMenuItem(actionOpenProjectDirectory);
    MenuItem miOpenImage = ActionUtils.createMenuItem(actionOpenImage);
    MenuItem miRemoveImage = ActionUtils.createMenuItem(actionRemoveImage);
    MenuItem miDuplicateImage = ActionUtils.createMenuItem(actionDuplicateImages);
    MenuItem miSetImageName = ActionUtils.createMenuItem(actionSetImageName);
    MenuItem miRefreshThumbnail = ActionUtils.createMenuItem(actionRefreshThumbnail);
    MenuItem miEditDescription = ActionUtils.createMenuItem(actionEditDescription);
    MenuItem miAddMetadata = ActionUtils.createMenuItem(actionAddMetadataValue);
    MenuItem miMaskImages = ActionUtils.createCheckMenuItem(actionMaskImageNames);
    // Set visibility as menu being displayed
    menu.setOnShowing(e -> {
        TreeItem<ProjectTreeRow> selected = tree.getSelectionModel().getSelectedItem();
        ProjectImageEntry<BufferedImage> selectedEntry = selected == null ? null : ProjectTreeRow.getEntry(selected.getValue());
        var entries = getSelectedImageRowsRecursive();
        boolean isImageEntry = selectedEntry != null;
        // miOpenProjectDirectory.setVisible(project != null && project.getBaseDirectory().exists());
        miOpenImage.setVisible(isImageEntry);
        miDuplicateImage.setVisible(isImageEntry);
        miSetImageName.setVisible(isImageEntry);
        miAddMetadata.setVisible(!entries.isEmpty());
        miEditDescription.setVisible(isImageEntry);
        miRefreshThumbnail.setVisible(isImageEntry && isCurrentImage(selectedEntry));
        miRemoveImage.setVisible(selected != null && project != null && !project.getImageList().isEmpty());
        if (project == null) {
            menuSort.setVisible(false);
            return;
        }
        Map<String, MenuItem> newItems = new TreeMap<>();
        for (ProjectImageEntry<?> entry : project.getImageList()) {
            // Add all entry metadata keys
            for (String key : entry.getMetadataKeys()) {
                if (!newItems.containsKey(key))
                    newItems.put(key, ActionUtils.createMenuItem(createSortByKeyAction(key, key)));
            }
            // Add all additional keys
            for (String key : baseMetadataKeys) {
                if (!newItems.containsKey(key))
                    newItems.put(key, ActionUtils.createMenuItem(createSortByKeyAction(key, key)));
            }
        }
        menuSort.getItems().setAll(newItems.values());
        menuSort.getItems().add(0, ActionUtils.createMenuItem(createSortByKeyAction("None", null)));
        menuSort.getItems().add(1, new SeparatorMenuItem());
        menuSort.setVisible(true);
        if (menu.getItems().isEmpty())
            e.consume();
    });
    SeparatorMenuItem separator = new SeparatorMenuItem();
    separator.visibleProperty().bind(menuSort.visibleProperty());
    menu.getItems().addAll(miOpenImage, miRemoveImage, miDuplicateImage, new SeparatorMenuItem(), miSetImageName, miAddMetadata, miEditDescription, miMaskImages, miRefreshThumbnail, separator, menuSort);
    separator = new SeparatorMenuItem();
    separator.visibleProperty().bind(menuOpenDirectories.visibleProperty());
    if (Desktop.isDesktopSupported()) {
        menu.getItems().addAll(separator, menuOpenDirectories);
    }
    return menu;
}

Example 27 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class DefaultScriptEditor method createInsertAction.

Action createInsertAction(final String name) {
    Action action = new Action(name, e -> {
        var control = getCurrentTextComponent();
        String join = "," + System.lineSeparator() + "  ";
        String listFormat = "[" + System.lineSeparator() + "  %s" + System.lineSeparator() + "]";
        if (name.toLowerCase().equals("pixel classifiers")) {
            try {
                String classifiers = qupath.getProject().getPixelClassifiers().getNames().stream().map(classifierName -> "\"" + classifierName + "\"").collect(Collectors.joining(join));
                String s = classifiers.isEmpty() ? "[]" : String.format(listFormat, classifiers);
                control.paste(s);
            } catch (IOException ex) {
                logger.error("Could not fetch classifiers", ex.getLocalizedMessage());
            }
        } else if (name.toLowerCase().equals("object classifiers")) {
            try {
                String classifiers = qupath.getProject().getObjectClassifiers().getNames().stream().map(classifierName -> "\"" + classifierName + "\"").collect(Collectors.joining(join));
                String s = classifiers.isEmpty() ? "[]" : String.format(listFormat, classifiers);
                control.paste(s);
            } catch (IOException ex) {
                logger.error("Could not fetch classifiers", ex.getLocalizedMessage());
            }
        } else if (name.toLowerCase().equals("detection")) {
            var imageData = qupath.getImageData();
            String measurements = "";
            if (imageData != null) {
                measurements = imageData.getHierarchy().getDetectionObjects().stream().flatMap(d -> d.getMeasurementList().getMeasurementNames().stream()).distinct().map(m -> "\"" + m + "\"").collect(Collectors.joining(join));
            }
            String s = measurements.isEmpty() ? "[]" : String.format(listFormat, measurements);
            control.paste(s);
        } else if (name.toLowerCase().equals(GeneralTools.SYMBOL_MU + ""))
            control.paste(GeneralTools.SYMBOL_MU + "");
        else {
        // TODO: fix
        // // Imports (end with a new line)
        // if (name.toLowerCase().equals("qpex"))
        // control.insertText(0, "import static qupath.lib.gui.scripting.QPEx.*");
        // else if (name.toLowerCase().equals("qp"))
        // control.insertText(0, "import static qupath.lib.gui.scripting.QP.*");
        // else if (name.toLowerCase().equals("all default"))
        // control.insertText(0, QPEx.getDefaultImports(false));
        // currentLanguage.get().getSyntax().handleNewLine(control, smartEditing.get());
        }
        e.consume();
    });
    if (name.equals(GeneralTools.SYMBOL_MU + ""))
        action.setAccelerator(new KeyCodeCombination(KeyCode.M, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    else if (name.toLowerCase().equals("pixel classifiers") || name.toLowerCase().equals("object classifiers"))
        action.disabledProperty().bind(qupath.projectProperty().isNull());
    else if (name.toLowerCase().equals("detection"))
        action.disabledProperty().bind(qupath.imageDataProperty().isNull());
    return action;
}

Example 28 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class DensityMapDataOp method apply.

@Override
public Mat apply(ImageData<BufferedImage> imageData, RegionRequest request) throws IOException {
    ensureInitialized();
    logger.trace("Applying density map op for {}", request);
    // Calculate how much padding we need
    var padding = op.getPadding();
    if (!padding.isEmpty()) {
        // Add padding to the request
        double downsample = request.getDownsample();
        var padding2 = Padding.getPadding((int) Math.round(padding.getX1() * downsample), (int) Math.round(padding.getX2() * downsample), (int) Math.round(padding.getY1() * downsample), (int) Math.round(padding.getY2() * downsample));
        request = request.pad2D(padding2);
    }
    // Get all objects within the padded region
    var allPathObjects = imageData.getHierarchy().getObjectsForRegion(null, request, null).stream().filter(allObjects).collect(Collectors.toList());
    if (allPathObjects.size() == 1)
        logger.trace("Generating counts tile for 1 object");
    else
        logger.trace("Generating counts tile for {} objects", allPathObjects.size());
    // Create an output mat
    int nChannels = getChannelCount();
    int width = (int) Math.round(request.getWidth() / request.getDownsample());
    int height = (int) Math.round(request.getHeight() / request.getDownsample());
    var mat = new Mat(height, width, opencv_core.CV_64FC(nChannels), Scalar.ZERO);
    DoubleIndexer idx = mat.createIndexer();
    // Get points representing all the centroids of each subpopulation of object
    // Use these to increment pixel values in a counts image
    int c = 0;
    for (var entry : primaryObjects.entrySet()) {
        var predicate = entry.getValue();
        var primaryROIs = allPathObjects.stream().filter(predicate).map(p -> PathObjectTools.getROI(p, true)).collect(Collectors.toList());
        var points = objectsToPoints(primaryROIs);
        incrementCounts(idx, points, request, width, height, c);
        c++;
    }
    // Get points for all objects, if we need them
    if (c < getChannelCount()) {
        var allObjectROIs = allPathObjects.stream().map(p -> PathObjectTools.getROI(p, true)).collect(Collectors.toList());
        var points = objectsToPoints(allObjectROIs);
        incrementCounts(idx, points, request, width, height, c);
        c++;
    }
    idx.close();
    // Now apply the op
    var output = this.op.apply(mat);
    return output;
}

Example 29 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class OMEPyramidWriterCommand method run.

@Override
public void run() {
    if (currentTask != null && !currentTask.isDone()) {
        if (!Dialogs.showConfirmDialog("OME Pyramid writer", "Do you want to stop the current export?"))
            // TODO: Delete exporting file?
            return;
        else {
            currentTask.cancel(true);
        }
    }
    QuPathViewer viewer = qupath.getViewer();
    int zPos = viewer.getZPosition();
    int tPos = viewer.getTPosition();
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (imageData == null) {
        Dialogs.showNoImageError("OME Pyramid writer");
        return;
    }
    ImageServer<BufferedImage> server = imageData.getServer();
    // Region
    PathObject selected = imageData.getHierarchy().getSelectionModel().getSelectedObject();
    ImageRegion region = null;
    int width, height;
    if (selected == null || !selected.hasROI() || !selected.getROI().isArea()) {
        width = server.getWidth();
        height = server.getHeight();
    } else {
        region = ImageRegion.createInstance(selected.getROI());
        width = region.getWidth();
        height = region.getHeight();
    }
    // Set compression - with a sanity check for validity, defaulting to another comparable method if necessary
    CompressionType compression = getDefaultPyramidCompression();
    List<String> compatibleCompression = Arrays.stream(CompressionType.values()).filter(c -> c.supportsImage(server)).map(c -> c.toFriendlyString()).collect(Collectors.toList());
    if (!compatibleCompression.contains(compression.toFriendlyString()))
        compression = CompressionType.DEFAULT;
    var params = new ParameterList().addChoiceParameter("compression", "Compression type", compression.toFriendlyString(), compatibleCompression).addIntParameter("scaledDownsample", "Pyramidal downsample", scaledDownsample.get(), "", 1, 8, "Amount to downsample each consecutive pyramidal level; use 1 to indicate the image should not be pyramidal").addIntParameter("tileSize", "Tile size", getDefaultTileSize(), "px", "Tile size for export (should be between 128 and 8192)").addBooleanParameter("parallelize", "Parallelize export", parallelizeTiling.get(), "Export image tiles in parallel - " + "this should be faster, best keep it on unless you encounter export problems").addBooleanParameter("allZ", "All z-slices", allZ.get(), "Include all z-slices in the stack").addBooleanParameter("allT", "All timepoints", allT.get(), "Include all timepoints in the time-series");
    boolean singleTile = server.getTileRequestManager().getTileRequests(RegionRequest.createInstance(server)).size() == 1;
    params.setHiddenParameters(server.nZSlices() == 1, "allZ");
    params.setHiddenParameters(server.nTimepoints() == 1, "allT");
    params.setHiddenParameters(singleTile, "tileSize", "parallelize");
    if (!Dialogs.showParameterDialog("Export OME-TIFF", params))
        return;
    compression = CompressionType.fromFriendlyString((String) params.getChoiceParameterValue("compression"));
    defaultPyramidCompression.set(compression);
    int downsampleScale = params.getIntParameterValue("scaledDownsample");
    scaledDownsample.set(downsampleScale);
    int tileSize = params.getIntParameterValue("tileSize");
    boolean parallelize = params.getBooleanParameterValue("parallelize");
    if (!singleTile) {
        tileSize = GeneralTools.clipValue(tileSize, 128, 8192);
        defaultTileSize.set(tileSize);
        parallelizeTiling.set(parallelize);
    }
    boolean doAllZ = false;
    boolean doAllT = false;
    if (server.nZSlices() > 1) {
        doAllZ = params.getBooleanParameterValue("allZ");
        allZ.set(doAllZ);
    }
    if (server.nTimepoints() > 1) {
        doAllT = params.getBooleanParameterValue("allT");
        allT.set(doAllT);
    }
    OMEPyramidWriter.Builder builder = new OMEPyramidWriter.Builder(server);
    if (region != null) {
        builder = builder.region(region);
    } else {
        if (server.nZSlices() > 1 && !doAllZ)
            builder.zSlice(zPos);
        if (server.nTimepoints() > 1 && !doAllT)
            builder.timePoint(tPos);
    }
    builder.compression(compression);
    if (downsampleScale <= 1 || Math.max(width, height) / server.getDownsampleForResolution(0) < minSizeForTiling.get())
        builder.downsamples(server.getDownsampleForResolution(0));
    else
        builder.scaledDownsampling(server.getDownsampleForResolution(0), downsampleScale);
    // Set tile size; if we just have one tile, use the image width & height
    if (singleTile)
        builder = builder.tileSize(width, height);
    else
        builder = builder.tileSize(tileSize).parallelize(parallelize);
    if (server.nZSlices() > 1 && doAllZ)
        builder.allZSlices();
    if (server.nTimepoints() > 1 && doAllT)
        builder.allTimePoints();
    // Prompt for file
    File fileOutput = Dialogs.promptToSaveFile("Write pyramid", null, null, "OME TIFF pyramid", ".ome.tif");
    if (fileOutput == null)
        return;
    String name = fileOutput.getName();
    // We can have trouble with only the '.tif' part of the name being included
    if (name.endsWith(".tif") && !name.endsWith(".ome.tif"))
        fileOutput = new File(fileOutput.getParentFile(), name.substring(0, name.length() - 4) + ".ome.tif");
    OMEPyramidSeries writer = builder.build();
    if (pool == null) {
        pool = Executors.newSingleThreadExecutor(ThreadTools.createThreadFactory("ome-pyramid-export", false));
    }
    currentTask = pool.submit(new WriterTask(OMEPyramidWriter.createWriter(writer), fileOutput.getAbsolutePath()));
}

Example 30 with ImageData

use of qupath.lib.images.ImageData 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;
}