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Example 1 with DefaultScriptableWorkflowStep

use of qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep 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);
    }
}
Also used : DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) PathObjectHierarchy(qupath.lib.objects.hierarchy.PathObjectHierarchy) PathAnnotationObject(qupath.lib.objects.PathAnnotationObject) PathObject(qupath.lib.objects.PathObject) TMACoreObject(qupath.lib.objects.TMACoreObject)

Example 2 with DefaultScriptableWorkflowStep

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

the class Commands method requestShapeFeatures.

private static void requestShapeFeatures(ImageData<?> imageData, Collection<ShapeFeatures> features) {
    if (imageData == null)
        return;
    var featureArray = features.toArray(ShapeFeatures[]::new);
    if (featureArray.length == 0)
        return;
    Collection<PathObject> selected = imageData.getHierarchy().getSelectionModel().getSelectedObjects();
    if (selected.isEmpty()) {
        Dialogs.showWarningNotification("Shape features", "No objects selected!");
    } else {
        selected = new ArrayList<>(selected);
        String featureString = Arrays.stream(featureArray).map(f -> "\"" + f.name() + "\"").collect(Collectors.joining(", "));
        QP.addShapeMeasurements(imageData, selected, featureArray);
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Add shape measurements", String.format("addShapeMeasurements(%s)", featureString)));
        if (selected.size() == 1)
            Dialogs.showInfoNotification("Shape features", "Shape features calculated for one object");
        else
            Dialogs.showInfoNotification("Shape features", "Shape features calculated for " + selected.size() + " objects");
    }
}
Also used : Arrays(java.util.Arrays) ServerTools(qupath.lib.images.servers.ServerTools) PathTileObject(qupath.lib.objects.PathTileObject) StackPane(javafx.scene.layout.StackPane) ImageWriter(qupath.lib.images.writers.ImageWriter) ParameterList(qupath.lib.plugins.parameters.ParameterList) ImageRegion(qupath.lib.regions.ImageRegion) Map(java.util.Map) PathObjects(qupath.lib.objects.PathObjects) Screen(javafx.stage.Screen) WorkflowStep(qupath.lib.plugins.workflow.WorkflowStep) PathAnnotationObject(qupath.lib.objects.PathAnnotationObject) Project(qupath.lib.projects.Project) ShapeFeatures(qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures) MeasurementMapPane(qupath.lib.gui.panes.MeasurementMapPane) BorderPane(javafx.scene.layout.BorderPane) StringProperty(javafx.beans.property.StringProperty) RectangleROI(qupath.lib.roi.RectangleROI) CheckBoxListCell(javafx.scene.control.cell.CheckBoxListCell) PathObjectHierarchy(qupath.lib.objects.hierarchy.PathObjectHierarchy) Supplier(java.util.function.Supplier) Bindings(javafx.beans.binding.Bindings) ViewTrackerControlPane(qupath.lib.gui.viewer.recording.ViewTrackerControlPane) Projects(qupath.lib.projects.Projects) ArrayList(java.util.ArrayList) CheckListView(org.controlsfx.control.CheckListView) ROIs(qupath.lib.roi.ROIs) ShapeSimplifier(qupath.lib.roi.ShapeSimplifier) TextAlignment(javafx.scene.text.TextAlignment) PathClassPane(qupath.lib.gui.panes.PathClassPane) GridPane(javafx.scene.layout.GridPane) Files(java.nio.file.Files) GeneralTools(qupath.lib.common.GeneralTools) RegionRequest(qupath.lib.regions.RegionRequest) Window(java.awt.Window) DistanceTools(qupath.lib.analysis.DistanceTools) IOException(java.io.IOException) File(java.io.File) OverlayOptions(qupath.lib.gui.viewer.OverlayOptions) PathObjectTools(qupath.lib.objects.PathObjectTools) ROI(qupath.lib.roi.interfaces.ROI) QP(qupath.lib.scripting.QP) GridLines(qupath.lib.gui.viewer.GridLines) PathPrefs(qupath.lib.gui.prefs.PathPrefs) RenderedImageServer(qupath.lib.gui.images.servers.RenderedImageServer) PaneTools(qupath.lib.gui.tools.PaneTools) PathIO(qupath.lib.io.PathIO) Button(javafx.scene.control.Button) Pos(javafx.geometry.Pos) ImageServer(qupath.lib.images.servers.ImageServer) CombineOp(qupath.lib.roi.RoiTools.CombineOp) LoggerFactory(org.slf4j.LoggerFactory) ObservableDoubleValue(javafx.beans.value.ObservableDoubleValue) ComboBox(javafx.scene.control.ComboBox) ImageServers(qupath.lib.images.servers.ImageServers) PolygonROI(qupath.lib.roi.PolygonROI) QuPathGUI(qupath.lib.gui.QuPathGUI) Pane(javafx.scene.layout.Pane) TextField(javafx.scene.control.TextField) BufferedImage(java.awt.image.BufferedImage) Collection(java.util.Collection) Collectors(java.util.stream.Collectors) PathDetectionObject(qupath.lib.objects.PathDetectionObject) PathObject(qupath.lib.objects.PathObject) QuPathViewer(qupath.lib.gui.viewer.QuPathViewer) Priority(javafx.scene.layout.Priority) List(java.util.List) DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) ProjectIO(qupath.lib.projects.ProjectIO) GuiTools(qupath.lib.gui.tools.GuiTools) TMASummaryViewer(qupath.lib.gui.tma.TMASummaryViewer) ImagePlane(qupath.lib.regions.ImagePlane) PathCellObject(qupath.lib.objects.PathCellObject) Scene(javafx.scene.Scene) WorkflowCommandLogView(qupath.lib.gui.panes.WorkflowCommandLogView) TextArea(javafx.scene.control.TextArea) ButtonType(javafx.scene.control.ButtonType) Action(org.controlsfx.control.action.Action) HashMap(java.util.HashMap) DoubleProperty(javafx.beans.property.DoubleProperty) Function(java.util.function.Function) Dialogs(qupath.lib.gui.dialogs.Dialogs) Insets(javafx.geometry.Insets) ActionTools(qupath.lib.gui.ActionTools) Tooltip(javafx.scene.control.Tooltip) WeakHashMap(java.util.WeakHashMap) ImageData(qupath.lib.images.ImageData) RoiTools(qupath.lib.roi.RoiTools) Modality(javafx.stage.Modality) Logger(org.slf4j.Logger) Label(javafx.scene.control.Label) Iterator(java.util.Iterator) ImageWriterTools(qupath.lib.images.writers.ImageWriterTools) TMACoreObject(qupath.lib.objects.TMACoreObject) Stage(javafx.stage.Stage) Collections(java.util.Collections) ContentDisplay(javafx.scene.control.ContentDisplay) DialogButton(qupath.lib.gui.dialogs.Dialogs.DialogButton) DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) PathObject(qupath.lib.objects.PathObject)

Example 3 with DefaultScriptableWorkflowStep

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

the class Commands method resetClassifications.

/**
 * Select objects that are instances of a specified class, logging an appropriate method in the workflow.
 *
 * @param imageData
 * @param cls
 */
public static void resetClassifications(final ImageData<?> imageData, final Class<? extends PathObject> cls) {
    if (imageData == null) {
        logger.warn("No classifications to reset!");
        return;
    }
    // Do the reset
    QP.resetClassifications(imageData.getHierarchy(), cls);
    // Log the appropriate command
    Map<String, String> params = Collections.singletonMap("Type", PathObjectTools.getSuitableName(cls, false));
    String method;
    if (cls == PathDetectionObject.class)
        method = "resetDetectionClassifications();";
    else
        // TODO: Get a suitable name to disguise Java classes
        method = "resetClassifications(" + cls.getName() + ");";
    WorkflowStep newStep = new DefaultScriptableWorkflowStep("Reset classifications", params, method);
    WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
    if (newStep.equals(lastStep))
        imageData.getHistoryWorkflow().replaceLastStep(newStep);
    else
        imageData.getHistoryWorkflow().addStep(newStep);
}
Also used : DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) WorkflowStep(qupath.lib.plugins.workflow.WorkflowStep) DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep)

Example 4 with DefaultScriptableWorkflowStep

use of qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep 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()"));
}
Also used : DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) PathObjectHierarchy(qupath.lib.objects.hierarchy.PathObjectHierarchy)

Example 5 with DefaultScriptableWorkflowStep

use of qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep 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;
}
Also used : Arrays(java.util.Arrays) GeneralTools(qupath.lib.common.GeneralTools) GeoJsonExportOptions(qupath.lib.io.PathIO.GeoJsonExportOptions) Collection(java.util.Collection) IOException(java.io.IOException) PathObjectHierarchy(qupath.lib.objects.hierarchy.PathObjectHierarchy) Collectors(java.util.stream.Collectors) File(java.io.File) ArrayList(java.util.ArrayList) PathObject(qupath.lib.objects.PathObject) LinkedHashMap(java.util.LinkedHashMap) Dialogs(qupath.lib.gui.dialogs.Dialogs) List(java.util.List) ParameterList(qupath.lib.plugins.parameters.ParameterList) DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) Map(java.util.Map) QP(qupath.lib.scripting.QP) QuPathGUI(qupath.lib.gui.QuPathGUI) PathObjectHierarchy(qupath.lib.objects.hierarchy.PathObjectHierarchy) ArrayList(java.util.ArrayList) LinkedHashMap(java.util.LinkedHashMap) DefaultScriptableWorkflowStep(qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep) PathObject(qupath.lib.objects.PathObject) ParameterList(qupath.lib.plugins.parameters.ParameterList) GeoJsonExportOptions(qupath.lib.io.PathIO.GeoJsonExportOptions) File(java.io.File)

Aggregations

DefaultScriptableWorkflowStep (qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep)31 PathObject (qupath.lib.objects.PathObject)12 PathObjectHierarchy (qupath.lib.objects.hierarchy.PathObjectHierarchy)12 WorkflowStep (qupath.lib.plugins.workflow.WorkflowStep)12 ArrayList (java.util.ArrayList)10 List (java.util.List)10 Map (java.util.Map)10 Dialogs (qupath.lib.gui.dialogs.Dialogs)10 Collectors (java.util.stream.Collectors)9 QuPathGUI (qupath.lib.gui.QuPathGUI)9 BufferedImage (java.awt.image.BufferedImage)8 IOException (java.io.IOException)8 Arrays (java.util.Arrays)8 ImageData (qupath.lib.images.ImageData)8 File (java.io.File)7 StringProperty (javafx.beans.property.StringProperty)7 Logger (org.slf4j.Logger)7 LoggerFactory (org.slf4j.LoggerFactory)7 GeneralTools (qupath.lib.common.GeneralTools)7 Collections (java.util.Collections)6