Examples with EllipseROI qupath.lib.roi.EllipseROI used on opensource projects

Example 1 with EllipseROI

use of qupath.lib.roi.EllipseROI in project qupath by qupath.

the class IconFactory method createROIIcon.

/**
 * Create an icon depicting a ROI.
 * @param roi the region of interest
 * @param width the preferred icon width
 * @param height the preferred icon height
 * @param color the icon (line) color
 * @return a node that may be used as an icon resembling the shape of the ROI
 */
public static Node createROIIcon(ROI roi, int width, int height, Color color) {
    double scale = Math.min(width / roi.getBoundsWidth(), height / roi.getBoundsHeight());
    if (roi instanceof RectangleROI) {
        Rectangle rect = new Rectangle(0, 0, roi.getBoundsWidth() * scale, roi.getBoundsHeight() * scale);
        rect.setStroke(color);
        rect.setFill(null);
        return rect;
    } else if (roi instanceof EllipseROI) {
        double w = roi.getBoundsWidth() * scale;
        double h = roi.getBoundsHeight() * scale;
        Ellipse ellipse = new Ellipse(w / 2, height / 2, w / 2, h / 2);
        ellipse.setStroke(color);
        ellipse.setFill(null);
        return ellipse;
    } else if (roi instanceof LineROI) {
        LineROI l = (LineROI) roi;
        double xMin = Math.min(l.getX1(), l.getX2());
        double yMin = Math.min(l.getY1(), l.getY2());
        Line line = new Line((l.getX1() - xMin) * scale, (l.getY1() - yMin) * scale, (l.getX2() - xMin) * scale, (l.getY2() - yMin) * scale);
        line.setStroke(color);
        line.setFill(null);
        return line;
    } else if (roi.isPoint()) {
        // Just show generic points
        Node node = IconFactory.createNode(Math.min(width, height), Math.min(width, height), IconFactory.PathIcons.POINTS_TOOL);
        if (node instanceof Glyph) {
            var glyph = (Glyph) node;
            glyph.textFillProperty().unbind();
            glyph.setColor(color);
        }
        return node;
    } else {
        var path = pathCache.getOrDefault(roi, null);
        if (path == null) {
            var shape = roi.isArea() ? RoiTools.getArea(roi) : RoiTools.getShape(roi);
            if (shape != null) {
                var transform = new AffineTransform();
                transform.translate(-roi.getBoundsX(), -roi.getBoundsY());
                transform.scale(scale, scale);
                PathIterator iterator = shape.getPathIterator(transform, Math.max(0.5, 1.0 / scale));
                path = createShapeIcon(iterator, color);
                pathCache.put(roi, path);
            }
        } else {
            path = new Path(path.getElements());
            path.setStroke(color);
        }
        if (path != null)
            return path;
    }
    logger.warn("Unable to create icon for ROI: {}", roi);
    return null;
}

Example 2 with EllipseROI

use of qupath.lib.roi.EllipseROI in project qupath by qupath.

the class IJTools method convertToIJRoi.

/**
 * Convert a QuPath ROI to an ImageJ Roi.
 * @param <T>
 * @param pathROI
 * @param xOrigin x-origin indicating relationship of ImagePlus to the original image, as stored in ImageJ Calibration object
 * @param yOrigin y-origin indicating relationship of ImagePlus to the original image, as stored in ImageJ Calibration object
 * @param downsampleFactor downsample factor at which the ImagePlus was extracted from the full-resolution image
 * @return
 */
public static <T extends PathImage<ImagePlus>> Roi convertToIJRoi(ROI pathROI, double xOrigin, double yOrigin, double downsampleFactor) {
    if (pathROI instanceof PolygonROI)
        return ROIConverterIJ.convertToPolygonROI((PolygonROI) pathROI, xOrigin, yOrigin, downsampleFactor);
    if (pathROI instanceof RectangleROI)
        return ROIConverterIJ.getRectangleROI((RectangleROI) pathROI, xOrigin, yOrigin, downsampleFactor);
    if (pathROI instanceof EllipseROI)
        return ROIConverterIJ.convertToOvalROI((EllipseROI) pathROI, xOrigin, yOrigin, downsampleFactor);
    if (pathROI instanceof LineROI)
        return ROIConverterIJ.convertToLineROI((LineROI) pathROI, xOrigin, yOrigin, downsampleFactor);
    if (pathROI instanceof PolylineROI)
        return ROIConverterIJ.convertToPolygonROI((PolylineROI) pathROI, xOrigin, yOrigin, downsampleFactor);
    if (pathROI instanceof PointsROI)
        return ROIConverterIJ.convertToPointROI((PointsROI) pathROI, xOrigin, yOrigin, downsampleFactor);
    // If we have any other kind of shape, create a general shape roi
    if (pathROI != null && pathROI.isArea()) {
        // TODO: Deal with non-AWT area ROIs!
        Shape shape = RoiTools.getArea(pathROI);
        // "scaleX", "shearY", "shearX", "scaleY", "translateX", "translateY"
        shape = new AffineTransform(1.0 / downsampleFactor, 0, 0, 1.0 / downsampleFactor, xOrigin, yOrigin).createTransformedShape(shape);
        return ROIConverterIJ.setIJRoiProperties(new ShapeRoi(shape), pathROI);
    }
    // TODO: Integrate ROI not supported exception...?
    return null;
}

Example 3 with EllipseROI

use of qupath.lib.roi.EllipseROI in project qupath by qupath.

the class PathObjectTools method transformObject.

/**
 * Create a(n optionally) transformed version of a {@link PathObject}.
 * <p>
 * Note: only detections (including tiles and cells) and annotations are fully supported by this method.
 * Root objects are duplicated.
 * TMA core objects are transformed only if the resulting transform creates an ellipse ROI, since this is
 * currently the only ROI type supported for a TMA core (this behavior may change).
 * Any other object types result in an {@link UnsupportedOperationException} being thrown.
 *
 * @param pathObject the object to transform; this will be unchanged
 * @param transform optional affine transform; if {@code null}, this effectively acts to duplicate the object
 * @param copyMeasurements if true, the measurement list of the new object will be populated with the measurements of pathObject
 *
 * @return a duplicate of pathObject, with affine transform applied to the object's ROI(s) if required
 */
public static PathObject transformObject(PathObject pathObject, AffineTransform transform, boolean copyMeasurements) {
    ROI roi = maybeTransformROI(pathObject.getROI(), transform);
    PathClass pathClass = pathObject.getPathClass();
    PathObject newObject;
    if (pathObject instanceof PathCellObject) {
        ROI roiNucleus = maybeTransformROI(((PathCellObject) pathObject).getNucleusROI(), transform);
        newObject = PathObjects.createCellObject(roi, roiNucleus, pathClass, null);
    } else if (pathObject instanceof PathTileObject) {
        newObject = PathObjects.createTileObject(roi, pathClass, null);
    } else if (pathObject instanceof PathDetectionObject) {
        newObject = PathObjects.createDetectionObject(roi, pathClass, null);
    } else if (pathObject instanceof PathAnnotationObject) {
        newObject = PathObjects.createAnnotationObject(roi, pathClass, null);
    } else if (pathObject instanceof PathRootObject) {
        newObject = new PathRootObject();
    } else if (pathObject instanceof TMACoreObject && roi instanceof EllipseROI) {
        var core = (TMACoreObject) pathObject;
        newObject = PathObjects.createTMACoreObject(roi.getBoundsX(), roi.getBoundsY(), roi.getBoundsWidth(), roi.getBoundsHeight(), core.isMissing());
    } else
        throw new UnsupportedOperationException("Unable to transform object " + pathObject);
    if (copyMeasurements && !pathObject.getMeasurementList().isEmpty()) {
        MeasurementList measurements = pathObject.getMeasurementList();
        for (int i = 0; i < measurements.size(); i++) {
            String name = measurements.getMeasurementName(i);
            double value = measurements.getMeasurementValue(i);
            newObject.getMeasurementList().addMeasurement(name, value);
        }
        newObject.getMeasurementList().close();
    }
    return newObject;
}