Examples with PathObject qupath.lib.objects.PathObject used on opensource projects

Example 11 with PathObject

use of qupath.lib.objects.PathObject 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 12 with PathObject

use of qupath.lib.objects.PathObject 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");
    }
}

Example 13 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class CountingPanelCommand method makeButtonPanel.

@SuppressWarnings("deprecation")
private Pane makeButtonPanel() {
    if (qupath == null)
        return null;
    VBox panel = new VBox();
    panel.setSpacing(10);
    // TilePane panel = new TilePane(Orientation.VERTICAL);
    // panel.setBorder(BorderFactory.createEmptyBorder(5, 10, 10, 10));
    sliderRadius = new Slider(1, 100, PathPrefs.pointRadiusProperty().get());
    sliderRadius.valueProperty().addListener(event -> {
        PathPrefs.pointRadiusProperty().set((int) sliderRadius.getValue());
        // PathPrefs.setMinPointSeparation(sliderRadius.getValue());
        qupath.getViewer().repaint();
    });
    // panel.setSpacing(10);
    BorderPane sliderPane = new BorderPane();
    sliderPane.setLeft(new Label("Point size"));
    sliderPane.setCenter(sliderRadius);
    // Add load/save buttons
    btnLoad = new Button("Load points");
    btnLoad.setOnAction(event -> {
        if (hierarchy == null)
            return;
        File file = Dialogs.promptForFile(null, null, "TSV (Tab delimited)", new String[] { "tsv" });
        if (file == null)
            return;
        try {
            List<PathObject> pointsList = null;
            if (file.toPath().toString().endsWith(".zip"))
                pointsList = PointIO.readPointsObjectList(file);
            else if (file.toPath().toString().endsWith(".tsv"))
                pointsList = PointIO.readPoints(file);
            if (pointsList != null) {
                for (PathObject points : pointsList) hierarchy.addPathObject(points);
            }
        } catch (IOException e) {
            Dialogs.showErrorMessage("Load points error", e);
        }
    });
    btnSave = new Button("Save points");
    btnSave.setOnAction(event -> {
        if (countingPanel == null)
            return;
        // Prompt the user with choice over which annotations to save
        ListView<PathObject> listView = countingPanel.getListView();
        var selection = listView.getSelectionModel().getSelectedItems();
        List<PathObject> pointsList = countingPanel.getPathObjects();
        if (!selection.isEmpty()) {
            ArrayList<String> choiceList = new ArrayList<>();
            choiceList.addAll(Arrays.asList("All point annotations", "Selected objects"));
            var choice = Dialogs.showChoiceDialog("Save points", "Choose point annotations to save", Arrays.asList("All points", "Selected points"), savingOption);
            if (choice == null)
                return;
            if (choice.equals("Selected points"))
                pointsList = selection;
            savingOption = choice;
        }
        if (pointsList.isEmpty()) {
            Dialogs.showErrorMessage("Save points", "No points available!");
            return;
        }
        String defaultName = null;
        try {
            // Sorry, this is lazy...
            defaultName = ServerTools.getDisplayableImageName(qupath.getViewer().getServer()) + "-points.tsv";
        } catch (Exception e) {
        // Ignore...
        }
        ;
        File file = Dialogs.promptToSaveFile(null, null, defaultName, "TSV (Tab delimited)", "tsv");
        if (file == null)
            return;
        try {
            PointIO.writePoints(file, pointsList);
        } catch (IOException e) {
            Dialogs.showErrorMessage("Save points error", e);
        }
    });
    GridPane panelLoadSave = PaneTools.createColumnGridControls(btnLoad, btnSave);
    var actionConvexPoints = ActionTools.createSelectableAction(PathPrefs.showPointHullsProperty(), "Show point convex hull");
    var actionSelectedColor = ActionTools.createSelectableAction(PathPrefs.useSelectedColorProperty(), "Highlight selected objects by color");
    var actionDetectionsToPoints = qupath.createImageDataAction(imageData -> Commands.convertDetectionsToPoints(imageData, true));
    actionDetectionsToPoints.setText("Convert detections to points");
    var btnConvert = ActionTools.createButton(actionDetectionsToPoints, false);
    var convertPane = new Pane(btnConvert);
    btnConvert.prefWidthProperty().bind(convertPane.widthProperty());
    var cbConvex = ActionTools.createCheckBox(actionConvexPoints);
    var cbSelected = ActionTools.createCheckBox(actionSelectedColor);
    // panel.setSpacing(5);
    panel.getChildren().addAll(cbConvex, cbSelected, sliderPane, convertPane, panelLoadSave);
    return panel;
}

Example 14 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class CountingPanelCommand method attemptToSelectPoints.

private void attemptToSelectPoints() {
    if (hierarchy == null || countingPanel == null)
        return;
    logger.trace("Attempting to select");
    PathObject pathObjectSelected = hierarchy.getSelectionModel().getSelectedObject();
    // Try to set selected object to be a Point object
    if (pathObjectSelected == null || !PathObjectTools.hasPointROI(pathObjectSelected)) {
        List<PathObject> pointObjects = countingPanel.getPathObjects();
        if (pointObjects.isEmpty())
            hierarchy.getSelectionModel().setSelectedObject(null);
        else
            // Use the first point object
            hierarchy.getSelectionModel().setSelectedObject(pointObjects.get(0));
    }
}

Example 15 with PathObject

use of qupath.lib.objects.PathObject 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;
}