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

Example 26 with DefaultScriptableWorkflowStep

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

the class ImageDetailsPane method promptToSetPixelSize.

static boolean promptToSetPixelSize(ImageData<BufferedImage> imageData, boolean requestZSpacing) {
    var server = imageData.getServer();
    var hierarchy = imageData.getHierarchy();
    var selected = hierarchy.getSelectionModel().getSelectedObject();
    var roi = selected == null ? null : selected.getROI();
    PixelCalibration cal = server.getPixelCalibration();
    double pixelWidthMicrons = cal.getPixelWidthMicrons();
    double pixelHeightMicrons = cal.getPixelHeightMicrons();
    double zSpacingMicrons = cal.getZSpacingMicrons();
    // Use line or area ROI if possible
    if (!requestZSpacing && roi != null && !roi.isEmpty() && (roi.isArea() || roi.isLine())) {
        boolean setPixelHeight = true;
        boolean setPixelWidth = true;
        String message;
        String units = GeneralTools.micrometerSymbol();
        double pixelWidth = cal.getPixelWidthMicrons();
        double pixelHeight = cal.getPixelHeightMicrons();
        if (!Double.isFinite(pixelWidth))
            pixelWidth = 1;
        if (!Double.isFinite(pixelHeight))
            pixelHeight = 1;
        Double defaultValue = null;
        if (roi.isLine()) {
            setPixelHeight = roi.getBoundsHeight() != 0;
            setPixelWidth = roi.getBoundsWidth() != 0;
            message = "Enter selected line length";
            defaultValue = roi.getScaledLength(pixelWidth, pixelHeight);
        } else {
            message = "Enter selected ROI area";
            units = units + "^2";
            defaultValue = roi.getScaledArea(pixelWidth, pixelHeight);
        }
        // }
        if (Double.isNaN(defaultValue))
            defaultValue = 1.0;
        var params = new ParameterList().addDoubleParameter("inputValue", message, defaultValue, units, "Enter calibrated value in " + units + " for the selected ROI to calculate the pixel size").addBooleanParameter("squarePixels", "Assume square pixels", true, "Set the pixel width to match the pixel height");
        params.setHiddenParameters(setPixelHeight && setPixelWidth, "squarePixels");
        if (!Dialogs.showParameterDialog("Set pixel size", params))
            return false;
        Double result = params.getDoubleParameterValue("inputValue");
        setPixelHeight = setPixelHeight || params.getBooleanParameterValue("squarePixels");
        setPixelWidth = setPixelWidth || params.getBooleanParameterValue("squarePixels");
        // Double result = Dialogs.showInputDialog("Set pixel size", message, defaultValue);
        // if (result == null)
        // return false;
        double sizeMicrons;
        if (roi.isLine())
            sizeMicrons = result.doubleValue() / roi.getLength();
        else
            sizeMicrons = Math.sqrt(result.doubleValue() / roi.getArea());
        if (setPixelHeight)
            pixelHeightMicrons = sizeMicrons;
        if (setPixelWidth)
            pixelWidthMicrons = sizeMicrons;
    } else {
        // Prompt for all required values
        ParameterList params = new ParameterList().addDoubleParameter("pixelWidth", "Pixel width", pixelWidthMicrons, GeneralTools.micrometerSymbol(), "Enter the pixel width").addDoubleParameter("pixelHeight", "Pixel height", pixelHeightMicrons, GeneralTools.micrometerSymbol(), "Entry the pixel height").addDoubleParameter("zSpacing", "Z-spacing", zSpacingMicrons, GeneralTools.micrometerSymbol(), "Enter the spacing between slices of a z-stack");
        params.setHiddenParameters(server.nZSlices() == 1, "zSpacing");
        if (!Dialogs.showParameterDialog("Set pixel size", params))
            return false;
        if (server.nZSlices() != 1) {
            zSpacingMicrons = params.getDoubleParameterValue("zSpacing");
        }
        pixelWidthMicrons = params.getDoubleParameterValue("pixelWidth");
        pixelHeightMicrons = params.getDoubleParameterValue("pixelHeight");
    }
    if ((pixelWidthMicrons <= 0 || pixelHeightMicrons <= 0) || (server.nZSlices() > 1 && zSpacingMicrons <= 0)) {
        if (!Dialogs.showConfirmDialog("Set pixel size", "You entered values <= 0, do you really want to remove this pixel calibration information?")) {
            return false;
        }
        zSpacingMicrons = server.nZSlices() > 1 && zSpacingMicrons > 0 ? zSpacingMicrons : Double.NaN;
        if (pixelWidthMicrons <= 0 || pixelHeightMicrons <= 0) {
            pixelWidthMicrons = Double.NaN;
            pixelHeightMicrons = Double.NaN;
        }
    }
    if (QP.setPixelSizeMicrons(imageData, pixelWidthMicrons, pixelHeightMicrons, zSpacingMicrons)) {
        // Log for scripts
        WorkflowStep step;
        if (server.nZSlices() == 1) {
            var map = Map.of("pixelWidthMicrons", pixelWidthMicrons, "pixelHeightMicrons", pixelHeightMicrons);
            String script = String.format("setPixelSizeMicrons(%f, %f)", pixelWidthMicrons, pixelHeightMicrons);
            step = new DefaultScriptableWorkflowStep("Set pixel size " + GeneralTools.micrometerSymbol(), map, script);
        } else {
            var map = Map.of("pixelWidthMicrons", pixelWidthMicrons, "pixelHeightMicrons", pixelHeightMicrons, "zSpacingMicrons", zSpacingMicrons);
            String script = String.format("setPixelSizeMicrons(%f, %f, %f)", pixelWidthMicrons, pixelHeightMicrons, zSpacingMicrons);
            step = new DefaultScriptableWorkflowStep("Set pixel size " + GeneralTools.micrometerSymbol(), map, script);
        }
        imageData.getHistoryWorkflow().addStep(step);
        return true;
    } else
        return false;
}

Example 27 with DefaultScriptableWorkflowStep

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

the class Commands method selectObjectsByClass.

/**
 * Select objects that are instances of a specified class, logging an appropriate method in the workflow.
 *
 * @param imageData
 * @param cls
 */
public static void selectObjectsByClass(final ImageData<?> imageData, final Class<? extends PathObject> cls) {
    if (cls == TMACoreObject.class)
        QP.selectTMACores(imageData.getHierarchy());
    else
        QP.selectObjectsByClass(imageData.getHierarchy(), cls);
    Map<String, String> params = Collections.singletonMap("Type", PathObjectTools.getSuitableName(cls, false));
    String method;
    if (cls == PathAnnotationObject.class)
        method = "selectAnnotations();";
    else if (cls == PathDetectionObject.class)
        method = "selectDetections();";
    else if (cls == TMACoreObject.class)
        method = "selectTMACores();";
    else if (cls == PathCellObject.class)
        method = "selectCells();";
    else if (cls == PathTileObject.class)
        method = "selectTiles();";
    else
        // TODO: Get a suitable name to disguise Java classes
        method = "selectObjectsByClass(" + cls.getName() + ");";
    WorkflowStep newStep = new DefaultScriptableWorkflowStep("Select objects by class", params, method);
    WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
    if (newStep.equals(lastStep))
        imageData.getHistoryWorkflow().replaceLastStep(newStep);
    else
        imageData.getHistoryWorkflow().addStep(newStep);
}

Example 28 with DefaultScriptableWorkflowStep

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

the class Commands method selectAllObjects.

/**
 * Select all objects (excluding the root object) in the imageData.
 *
 * @param imageData
 */
public static void selectAllObjects(final ImageData<?> imageData) {
    // Select all objects
    QP.selectAllObjects(imageData.getHierarchy(), false);
    // Add this step to the history workflow
    Map<String, String> map = new HashMap<>();
    map.put("includeRootObject", "false");
    WorkflowStep newStep = new DefaultScriptableWorkflowStep("Select all objects", map, "selectAllObjects(false)");
    imageData.getHistoryWorkflow().addStep(newStep);
}

Example 29 with DefaultScriptableWorkflowStep

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

the class PixelClassifierUI method promptToClassifyDetectionsByCentroid.

private static boolean promptToClassifyDetectionsByCentroid(ImageData<BufferedImage> imageData, PixelClassifier classifier, String classifierName) {
    Objects.requireNonNull(imageData);
    Objects.requireNonNull(classifier);
    PixelClassifierTools.classifyDetectionsByCentroid(imageData, classifier);
    if (classifierName != null) {
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Classify detections by centroid", String.format("classifyDetectionsByCentroid(\"%s\")", classifierName)));
    }
    return true;
}

Example 30 with DefaultScriptableWorkflowStep

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

the class PixelClassifierUI method promptToAddMeasurements.

private static boolean promptToAddMeasurements(ImageData<BufferedImage> imageData, PixelClassifier classifier, String classifierName) {
    if (imageData == null) {
        Dialogs.showNoImageError("Pixel classifier");
        return false;
    }
    var hierarchy = imageData.getHierarchy();
    List<SelectionChoice> choices = buildChoiceList(imageData.getHierarchy(), SelectionChoice.values());
    SelectionChoice defaultChoice;
    if (choices.contains(SelectionChoice.CURRENT_SELECTION))
        defaultChoice = SelectionChoice.CURRENT_SELECTION;
    else if (choices.contains(SelectionChoice.ANNOTATIONS))
        defaultChoice = SelectionChoice.ANNOTATIONS;
    else
        defaultChoice = choices.get(0);
    var params = new ParameterList().addStringParameter("id", "Measurement name", classifierName == null ? "Classifier" : classifierName, "Choose a base name for measurements - this helps distinguish between measurements from different classifiers").addChoiceParameter("choice", "Select objects", defaultChoice, choices, "Select the objects");
    if (!Dialogs.showParameterDialog("Pixel classifier", params))
        return false;
    var measurementID = params.getStringParameterValue("id");
    var selectionChoice = (SelectionChoice) params.getChoiceParameterValue("choice");
    selectionChoice.handleSelection(imageData);
    var objectsToMeasure = hierarchy.getSelectionModel().getSelectedObjects();
    int n = objectsToMeasure.size();
    if (objectsToMeasure.isEmpty()) {
        objectsToMeasure = Collections.singleton(hierarchy.getRootObject());
        logger.info("Requesting measurements for image");
    } else if (n == 1)
        logger.info("Requesting measurements for one object");
    else
        logger.info("Requesting measurements for {} objects", n);
    if (PixelClassifierTools.addMeasurementsToSelectedObjects(imageData, classifier, measurementID)) {
        if (classifierName != null) {
            String idString = measurementID == null ? "null" : "\"" + measurementID + "\"";
            imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Pixel classifier measurements", String.format("addPixelClassifierMeasurements(\"%s\", %s)", classifierName, idString)));
        }
        return true;
    }
    return false;
}