package ij.gui;
import java.awt.*;
import java.awt.image.*;
import java.awt.geom.*;
import java.awt.event.KeyEvent;
import java.util.*;
import ij.*;
import ij.process.*;
import ij.measure.*;
import ij.plugin.filter.Analyzer;
import ij.util.Tools;

/**A subclass of <code>ij.gui.Roi</code> (2D Regions Of Interest) implemented in terms of java.awt.Shape.
 * A ShapeRoi is constructed from a <code>ij.gui.Roi</code> object, or as a result of logical operators
 * (i.e., union, intersection, exclusive or, and subtraction) provided by this class. These operators use the package
 * <code>java.awt.geom</code> as a backend. <br>
 * This code is in the public domain.
 * @author Cezar M.Tigaret <c.tigaret@ucl.ac.uk>
 */
public class ShapeRoi extends Roi {

    /***/
    static final int NO_TYPE = 128;
    
    /**The maximum tolerance allowed in calculating the length of the curve segments of this ROI's shape.*/
    static final double MAXERROR = 1.0e-3;
    
    /**Coefficient used to obtain a flattened version of this ROI's shape. A flattened shape is the
    * closest approximation of the original shape's curve segments with line segments.*/
    static final double FLATNESS = 0.1;
    
    /**Parsing a shape composed of linear segments less than this value will result in Roi objects of type
     * {@link ij.gui.Roi#POLYLINE} and {@link ij.gui.Roi#POLYGON} for open and closed shapes, respectively.
     * Conversion of shapes open and closed with more than MAXPOLY line segments will result,
     * respectively, in {@link ij.gui.Roi#FREELINE} and {@link ij.gui.Roi#FREEROI} (or
     * {@link ij.gui.Roi#TRACED_ROI} if {@link #forceTrace} flag is <strong><code>true</code></strong>.
     */
    private static final int MAXPOLY = 10; // I hate arbitrary values !!!!

    private static final int OR=0, AND=1, XOR=2, NOT=3;
    
    private static final double SHAPE_TO_ROI=-1.0;

    /**The <code>java.awt.Shape</code> encapsulated by this object.*/
    private Shape shape;
    
    /**The instance value of the maximum tolerance (MAXERROR) allowed in calculating the 
     * length of the curve segments of this ROI's shape.
     */
    private double maxerror = ShapeRoi.MAXERROR;
    
    /**The instance value of the coefficient (FLATNESS) used to 
     * obtain a flattened version of this ROI's shape.
     */
    private double flatness = ShapeRoi.FLATNESS;
    
    /**The instance value of MAXPOLY.*/
    private int maxPoly = ShapeRoi.MAXPOLY;
    
    /**If <strong></code>true</code></strong> then methods that manipulate this ROI's shape will work on
     * a flattened version of the shape. */
    private boolean flatten;
    
    /**Flag which specifies how Roi objects will be constructed from closed (sub)paths having more than
     * <code>MAXPOLY</code> and composed exclusively of line segments.
     * If <strong><code>true</code></strong> then (sub)path will be parsed into a
     * {@link ij.gui.Roi#TRACED_ROI}; else, into a {@link ij.gui.Roi#FREEROI}. */
    private boolean forceTrace = false;

    /**Flag which specifies if Roi objects constructed from open (sub)paths composed of only two line segments
     * will be of type {@link ij.gui.Roi#ANGLE}.
     * If <strong><code>true</code></strong> then (sub)path will be parsed into a {@link ij.gui.Roi#ANGLE};
     * else, into a {@link ij.gui.Roi#POLYLINE}. */
    private boolean forceAngle = false;
    
    private Vector savedRois;
    private static Stroke defaultStroke = new BasicStroke();


    /** Constructs a ShapeRoi from an Roi. */
    public ShapeRoi(Roi r) {
        this(r, ShapeRoi.FLATNESS, ShapeRoi.MAXERROR, false, false, false, ShapeRoi.MAXPOLY);
    }

    /** Constructs a ShapeRoi from a Shape. */
    public ShapeRoi(Shape s) {
        super(s.getBounds());
        AffineTransform at = new AffineTransform();
        at.translate(-x, -y);
        shape = new GeneralPath(at.createTransformedShape(s));
        type = COMPOSITE;
    }

    /** Constructs a ShapeRoi from a Shape. */
    public ShapeRoi(int x, int y, Shape s) {
        super(x, y, s.getBounds().width, s.getBounds().height);
        shape = new GeneralPath(s);
        type = COMPOSITE;
    }

    /**Creates a ShapeRoi object from a "classical" ImageJ ROI.
     * @param r An ij.gui.Roi object
     * @param flatness The flatness factor used in convertion of curve segments into line segments.
     * @param maxerror Error correction for calculating length of Bezeir curves.
     * @param forceAngle flag used in the conversion of Shape objects to Roi objects (see {@link #shapeToRois()}.
     * @param forceTrace flag for conversion of Shape objects to Roi objects (see {@link #shapeToRois()}.
     * @param flatten if <strong><code>true</code></strong> then the shape of this ROI will be flattened
     * (i.e., curve segments will be aproximated by line segments).
     * @param maxPoly Roi objects constructed from shapes composed of linear segments fewer than this
     * value will be of type {@link ij.gui.Roi#POLYLINE} or {@link ij.gui.Roi#POLYGON}; conversion of
     * shapes with linear segments more than this value will result in Roi objects of type
     * {@link ij.gui.Roi#FREELINE} or {@link ij.gui.Roi#FREEROI} (see {@link #shapeToRois()}).
     */
    ShapeRoi(Roi r, double flatness, double maxerror, boolean forceAngle, boolean forceTrace, boolean flatten, int maxPoly) {
        super(r.startX, r.startY, r.width, r.height);
        this.type = COMPOSITE;
        this.flatness = flatness;
        this.maxerror = maxerror;
        this.forceAngle = forceAngle;
        this.forceTrace = forceTrace;
        this.maxPoly= maxPoly;
        this.flatten = flatten;
        shape = roiToShape((Roi)r.clone());
    }

    /** Constructs a ShapeRoi from an array of variable length path segments. Each
        segment consists of the segment type followed by 0-3 end points and control
        points. Depending on the type, a segment uses from 1 to 7 elements of the array. */
    public ShapeRoi(float[] shapeArray) {
        super(0,0,null);
        shape = makeShapeFromArray(shapeArray);
        Rectangle r = shape.getBounds();
        x = r.x;
        y = r.y;
        width = r.width;
        height = r.height;
        
        state = NORMAL;
        oldX=x; oldY=y; oldWidth=width; oldHeight=height;
                
        AffineTransform at = new AffineTransform();
        at.translate(-x, -y);
        shape = new GeneralPath(at.createTransformedShape(shape));
        flatness = ShapeRoi.FLATNESS;
        maxerror = ShapeRoi.MAXERROR;
        maxPoly = ShapeRoi.MAXPOLY;
        flatten = false;
        type = COMPOSITE;
    }
    
    /**Returns a deep copy of this. */
    public synchronized Object clone() { // the equivalent of "operator=" ?
        ShapeRoi sr = (ShapeRoi)super.clone();
        sr.type = COMPOSITE;
        sr.flatness = flatness;
        sr.maxerror = maxerror;
        sr.forceAngle = forceAngle;
        sr.forceTrace = forceTrace;
        //sr.setImage(imp); //wsr
        sr.setShape(ShapeRoi.cloneShape(shape));
        return sr;
    }
    
    /**Returns a deep copy of the argument. */
    static Shape cloneShape(Shape rhs) {
        if(rhs==null) return null;
        if(rhs instanceof Rectangle2D.Double) { return (Rectangle2D.Double)((Rectangle2D.Double)rhs).clone(); }
        else if(rhs instanceof Ellipse2D.Double) { return (Ellipse2D.Double)((Ellipse2D.Double)rhs).clone(); }
        else if(rhs instanceof Line2D.Double) { return (Line2D.Double)((Line2D.Double)rhs).clone(); }
        else if(rhs instanceof Polygon) { return new Polygon(((Polygon)rhs).xpoints, ((Polygon)rhs).ypoints, ((Polygon)rhs).npoints); }
        else if(rhs instanceof GeneralPath) { return (GeneralPath)((GeneralPath)rhs).clone(); }
        return new GeneralPath(); // dodgy !!!
    }

    /**********************************************************************************/
    /***                  Logical operations on shaped rois                        ****/
    /**********************************************************************************/

    /**Unary union operator.
     * The caller is set to its union with the argument.
     * @return the union of <strong><code>this</code></strong> and <code>sr</code>
     */
    public ShapeRoi or(ShapeRoi sr) {return unaryOp(sr, OR);}

    /**Unary intersection operator.
     * The caller is set to its intersection with the argument (i.e., the overlapping regions between the
     * operands).
     * @return the overlapping regions between <strong><code>this</code></strong> and <code>sr</code>
     */
    public ShapeRoi and(ShapeRoi sr) {return unaryOp(sr, AND);}

    /**Unary exclusive or operator.
     * The caller is set to the non-overlapping regions between the operands.
     * @return the union of the non-overlapping regions of <strong><code>this</code></strong> and <code>sr</code>
     */
    public ShapeRoi xor(ShapeRoi sr) {return unaryOp(sr, XOR);}

    /**Unary subtraction operator.
     * The caller is set to the result of the operation between the operands.
     * @return <strong><code>this</code></strong> subtracted from <code>sr</code>
     */
    public ShapeRoi not(ShapeRoi sr) {return unaryOp(sr, NOT);}

    ShapeRoi unaryOp(ShapeRoi sr, int op) {
        AffineTransform at = new AffineTransform();
        at.translate(x, y);
        Area a1 = new Area(at.createTransformedShape(getShape()));
        at = new AffineTransform();
        at.translate(sr.x, sr.y);
        Area a2 = new Area(at.createTransformedShape(sr.getShape()));
        try {
            switch (op) {
                case OR: a1.add(a2); break;
                case AND: a1.intersect(a2); break;
                case XOR: a1.exclusiveOr(a2); break;
                case NOT: a1.subtract(a2); break;
            }
        } catch(Exception e) {}
        Rectangle r = a1.getBounds();
        at = new AffineTransform();
        at.translate(-r.x, -r.y);
        setShape(new GeneralPath(at.createTransformedShape(a1)));
        x = r.x;
        y = r.y;
        cachedMask = null;
        return this;
    }

    /**********************************************************************************/
    /***         Interconversions between "regular" rois and shaped rois           ****/
    /**********************************************************************************/

    /**Converts the Roi argument to an instance of java.awt.Shape.
     * Currently, the following conversions are supported:<br>
        <table><col><col><col><col><col><col><col>
            <thead>
                <tr><th scope=col> Roi class </th><th scope=col> Roi type </th><th scope=col> Shape </th><th scope=col> Winding<br> rule </th><th scope=col> Flag<br> forceAngle </th><th scope=col> Flag<br> forceTrace </th><th scope=col> Flag<br> complexShape </th></tr>
            </thead>
            <tbody>
                <tr><td> ij.gui.Roi </td><td> Roi.RECTANGLE </td><td> java.awt.geom.Rectangle2D.Double </td><td></td><td> false </td><td> false </td><td> false </td>   </tr>
                <tr><td> ij.gui.OvalRoi </td><td> Roi.OVAL </td><td> java.awt.geom.Ellipse2D.Double </td><td></td>  <td> false </td><td> false </td><td> false </td></tr>
                <tr><td> ij.gui.Line </td><td> Roi.LINE </td><td> java.awt.geom.Line2D.Double </td><td></td><td> false </td><td> false </td><td> false </td></tr>
                <tr>    <td> ij.gui.PolygonRoi </td>    <td> Roi.POLYGON </td>  <td> java.awt.Polygon </td> <td></td><td> false </td>   <td> false </td><td> false </td></tr>
                <tr><td> ij.gui.PolygonRoi </td>    <td> Roi.FREEROI </td>  <td> closed java.awt.geom.GeneralPath </td> <td> GeneralPath.WIND_EVEN_ODD </td><td> false </td><td> false </td>    <td> false </td>    </tr>
                <tr><td> ij.gui.PolygonRoi </td><td> Roi.TRACED_ROI </td><td> closed java.awt.geom.GeneralPath  </td>   <td> GeneralPath.WIND_EVEN_ODD </td>    <td> false </td>    <td> true </td> <td> false </td></tr>
                <tr><td> ij.gui.PolygonRoi </td>    <td> Roi.POLYLINE </td> <td> open java.awt.geom.GeneralPath  </td>  <td> GeneralPath.WIND_NON_ZERO </td>    <td> false </td>    <td> false </td><td> false </td></tr>
                <tr><td> ij.gui.PolygonRoi </td>    <td> Roi.FREELINE </td> <td> open java.awt.geom.GeneralPath  </td>  <td> GeneralPath.WIND_NON_ZERO </td>    <td> false </td>    <td> false </td>    <td> false </td>    </tr>
                <tr>    <td> ij.gui.PolygonRoi </td>    <td> Roi.ANGLE </td>    <td> open java.awt.geom.GeneralPath  </td>  <td> GeneralPath.WIND_NON_ZERO </td>    <td> true </td> <td> false </td>    <td> false </td>    </tr>
                <tr>    <td> ij.gui.ShapeRoi </td>  <td> Roi.COMPOSITE </td>    <td> shape of argument  </td>   <td> winding rule of<br> argument </td><td> flag of<br> argument </td>  <td> flag of<br> argument </td> <td> flag of<br> argument </td> </tr>
                <tr><td> ij.gui.ShapeRoi </td>  <td> ShapeRoi.NO_TYPE </td> <td> null </td> <td>  </td> <td> false </td>    <td> false </td>    <td> false </td>    </tr>
            </tbody>
        </table>
     *
     * @return A java.awt.geom.* object that inherits from java.awt.Shape interface.
     *
     */
    private Shape roiToShape(Roi roi) {
        Shape shape = null;
        Rectangle r = roi.getBounds();
        int[] xCoords = null;
        int[] yCoords = null;
        int nCoords = 0;
        switch(roi.getType()) {
            case Roi.LINE:
                Line line = (Line)roi;              
                shape = new Line2D.Double ((double)(line.x1-r.x), (double)(line.y1-r.y), (double)(line.x2-r.x), (double)(line.y2-r.y) );
                break;
            case Roi.RECTANGLE:
                int arcSize = roi.getCornerDiameter();
                if (arcSize>0)
                    shape = new RoundRectangle2D.Float(0, 0, r.width, r.height, arcSize, arcSize);
                else
                    shape = new Rectangle2D.Double(0.0, 0.0, (double)r.width, (double)r.height);
                break;
            case Roi.OVAL:
                Polygon p = roi.getPolygon();
                for (int i=0; i<p.npoints; i++) {
                    p.xpoints[i] -= r.x;
                    p.ypoints[i] -= r.y;
                }
                shape = new Polygon(p.xpoints, p.ypoints, p.npoints);
                break;
            case Roi.POLYGON:
                nCoords =((PolygonRoi)roi).getNCoordinates();
                xCoords = ((PolygonRoi)roi).getXCoordinates();
                yCoords = ((PolygonRoi)roi).getYCoordinates();
                shape = new Polygon(xCoords,yCoords,nCoords);
                break;
            case Roi.FREEROI: case Roi.TRACED_ROI:
                nCoords =((PolygonRoi)roi).getNCoordinates();
                xCoords = ((PolygonRoi)roi).getXCoordinates();
                yCoords = ((PolygonRoi)roi).getYCoordinates();
                shape = new GeneralPath(GeneralPath.WIND_EVEN_ODD,nCoords);
                ((GeneralPath)shape).moveTo((float)xCoords[0], (float)yCoords[0]);
                for (int i=1; i<nCoords; i++)
                    ((GeneralPath)shape).lineTo((float)xCoords[i],(float)yCoords[i]);
                ((GeneralPath)shape).closePath();
                break;
            case Roi.POLYLINE: case Roi.FREELINE: case Roi.ANGLE:
                nCoords =((PolygonRoi)roi).getNCoordinates();
                xCoords = ((PolygonRoi)roi).getXCoordinates();
                yCoords = ((PolygonRoi)roi).getYCoordinates();
                shape = new GeneralPath(GeneralPath.WIND_NON_ZERO,nCoords);
                ((GeneralPath)shape).moveTo((float)xCoords[0], (float)yCoords[0]);
                for (int i=1; i<nCoords; i++)
                    ((GeneralPath)shape).lineTo((float)xCoords[i],(float)yCoords[i]);
                break;
            case Roi.POINT:
                ImageProcessor mask = roi.getMask();
                byte[] maskPixels = (byte[])mask.getPixels();
                Rectangle maskBounds = roi.getBounds();
                int maskWidth = mask.getWidth();
                Area area = new Area();
                for (int y=0; y<mask.getHeight(); y++) {
                    int yOffset = y*maskWidth;
                    for (int x=0; x<maskWidth; x++) {
                        if (maskPixels[x+yOffset]!=0)
                            area.add(new Area(new Rectangle(x+maskBounds.x, y+maskBounds.y, 1, 1)));
                    }
                }
                shape = area;
                break;
            case Roi.COMPOSITE: shape = ShapeRoi.cloneShape(((ShapeRoi)roi).getShape());
                break;
            default:
                throw new IllegalArgumentException("Roi type not supported");
        }

        if(shape!=null) {
            this.x = roi.x;
            this.y = roi.y;
            Rectangle bounds = shape.getBounds();
            this.width = bounds.width;
            this.height = bounds.height;
            this.startX = x;
            this.startY = y;
            //IJ.log("RoiToShape: "+x+" "+y+" "+width+" "+height+" "+bounds);
        }
        return shape;
    }

    /**Constructs a Shape from a float array. */
    Shape makeShapeFromArray(float[] array) {
        if(array==null) return null;
        Shape s = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
        int index=0, type, len;
        float[] seg = new float[7];
        while (true) {
            len = getSegment(array, seg, index);
            if (len<0) break;
            index += len;
            type = (int)seg[0];
            switch(type) {
                case PathIterator.SEG_MOVETO:
                    ((GeneralPath)s).moveTo(seg[1], seg[2]);
                    break;
                case PathIterator.SEG_LINETO:
                    ((GeneralPath)s).lineTo(seg[1], seg[2]);
                    break;
                case PathIterator.SEG_QUADTO:
                    ((GeneralPath)s).quadTo(seg[1], seg[2],seg[3], seg[4]);
                    break;
                case PathIterator.SEG_CUBICTO:
                    ((GeneralPath)s).curveTo(seg[1], seg[2], seg[3], seg[4], seg[5], seg[6]);
                    break;
                case PathIterator.SEG_CLOSE:
                    ((GeneralPath)s).closePath();
                    break;
                default: break;
            }
        }
        return s;
    }
    
    private int getSegment(float[] array, float[] seg, int index) {
        int len = array.length;
        if (index>=len) return -1; seg[0]=array[index++];
        int type = (int)seg[0];
        if (type==PathIterator.SEG_CLOSE) return 1;
        if (index>=len) return -1; seg[1]=array[index++];
        if (index>=len) return -1; seg[2]=array[index++];
        if (type==PathIterator.SEG_MOVETO||type==PathIterator.SEG_LINETO) return 3;
        if (index>=len) return -1; seg[3]=array[index++];
        if (index>=len) return -1; seg[4]=array[index++];
        if (type==PathIterator.SEG_QUADTO) return 5;
        if (index>=len) return -1; seg[5]=array[index++];
        if (index>=len) return -1; seg[6]=array[index++];
        if (type==PathIterator.SEG_CUBICTO) return 7;
        return -1;
    }

    /** Saves an Roi so it can be retrieved later using getRois(). */
    void saveRoi(Roi roi) {
        if (savedRois==null)
            savedRois = new Vector();
        savedRois.addElement(roi);
    }

    /**Converts a Shape into Roi object(s).
     * <br>This method parses the shape into (possibly more than one) Roi objects 
     * and returns them in an array.
     * <br>A simple, &quot;regular&quot; path results in a single Roi following these simple rules:
        <table><col><col><col>
            <thead><tr><th scope=col> Shape type </th><th scope=col> Roi class </th><th scope=col> Roi type </th></tr></thead>
            <tbody>
                <tr><td> java.awt.geom.Rectangle2D.Double </td><td> ij.gui.Roi </td><td> Roi.RECTANGLE </td></tr>
                <tr><td> java.awt.geom.Ellipse2D.Double </td><td> ij.gui.OvalRoi</td><td> Roi.OVAL </td></tr>
                <tr><td> java.awt.geom.Line2D.Double </td><td> ij.gui.Line </td><td> Roi.LINE </td></tr>
                <tr><td> java.awt.Polygon </td> <td> ij.gui.PolygonRoi </td><td> Roi.POLYGON </td></tr>
            </tbody>
        </table>
     * <br><br>Each subpath of a <code>java.awt.geom.GeneralPath</code> is converted following these rules:
        <table frame="border"><col><col><col><col><col><col>
            <thead>
                <tr><th rowspan="2" scope=col> Segment<br> types </th><th rowspan="2" scope=col> Number of<br> segments </th>
                    <th rowspan="2" scope=col> Closed<br> path </th><th rowspan="2" scope=col> Value of<br> forceAngle </th>
                    <th rowspan="2" scope=col> Value of<br> forceTrace </th><th rowspan="2" scope=col> Roi type </th></tr>
            </thead>
            <tbody>
                <tr><td> lines only: </td><td align="center"> 0 </td><td>  </td><td>  </td><td>  </td><td> ShapeRoi.NO_TYPE </td></tr>
                <tr><td>  </td><td align="center"> 1 </td><td>  </td><td>  </td><td>  </td> <td> ShapeRoi.NO_TYPE </td></tr>
                <tr><td>  </td><td align="center"> 2 </td><td align="center"> Y </td><td>  </td><td>  </td><td> ShapeRoi.NO_TYPE </td></tr>
                <tr><td>  </td><td>  </td><td align="center"> N </td><td>  </td><td>  </td><td> Roi.LINE </td></tr>
                <tr><td>  </td><td align="center"> 3 </td><td align="center"> Y </td><td align="center"> N </td><td>  </td><td> Roi.POLYGON </td></tr>
                <tr><td>  </td><td>  </td><td align="center"> N </td><td align="center"> Y </td><td>  </td><td> Roi.ANGLE </td></tr>
                <tr><td>  </td><td>  </td><td align="center"> N </td><td align="center"> N </td><td>  </td><td> Roi.POLYLINE </td></tr>
                <tr><td>  </td><td align="center"> 4 </td><td align="center"> Y </td><td>  </td<td>  </td><td> Roi.RECTANGLE </td></tr>
                <tr><td>  </td><td>  </td><td align="center"> N </td><td>  </td><td>  </td><td> Roi.POLYLINE </td></tr>
                <tr><td>  </td><td align="center"> &lt;= MAXPOLY </td>  <td align="center"> Y </td><td>  </td><td>  </td><td> Roi.POLYGON </td></tr>
                <tr><td>  </td><td>  </td><td align="center"> N </td><td>  </td><td>  </td><td> Roi.POLYLINE </td></tr>
                <tr><td>  </td><td align="center"> &gt; MAXPOLY </td><td align="center"> Y </td><td>  </td> <td align="center"> Y </td><td> Roi.TRACED_ROI </td></tr>
                <tr><td>  </td><td>  </td><td>  </td><td>  </td><td align="center"> N </td><td> Roi.FREEROI </td></tr>
                <tr><td>  </td><td>  </td><td align="center"> N </td><td>  </td><td>  </td><td> Roi.FREELINE </td></tr>
                <tr><td> anything<br>else: </td><td align="center"> &lt;= 2 </td><td>  </td><td>  </td><td>  </td><td> ShapeRoi.NO_TYPE </td></tr>
                <tr><td>  </td><td align="center"> &gt; 2 </td><td>  </td><td>  </td><td>  </td><td> ShapeRoi.SHAPE_ROI </td></tr>
            </tbody>
        </table>
     * @return an array of ij.gui.Roi objects.
     */
    public Roi[] getRois () {
        if (shape==null)
            return new Roi[0];
        if (savedRois!=null)
            return getSavedRois();
        Vector rois = new Vector();
        if (shape instanceof Rectangle2D.Double) {
            Roi r = new Roi((int)((Rectangle2D.Double)shape).getX(), (int)((Rectangle2D.Double)shape).getY(), (int)((Rectangle2D.Double)shape).getWidth(), (int)((Rectangle2D.Double)shape).getHeight());
            rois.addElement(r);
        } else if (shape instanceof Ellipse2D.Double) {
            Roi r = new OvalRoi((int)((Ellipse2D.Double)shape).getX(), (int)((Ellipse2D.Double)shape).getY(), (int)((Ellipse2D.Double)shape).getWidth(), (int)((Ellipse2D.Double)shape).getHeight());
            rois.addElement(r);
        } else if (shape instanceof Line2D.Double) {
            Roi r = new ij.gui.Line((int)((Line2D.Double)shape).getX1(), (int)((Line2D.Double)shape).getY1(), (int)((Line2D.Double)shape).getX2(), (int)((Line2D.Double)shape).getY2());
            rois.addElement(r);
        } else if (shape instanceof Polygon) {
            Roi r = new PolygonRoi(((Polygon)shape).xpoints, ((Polygon)shape).ypoints, ((Polygon)shape).npoints, Roi.POLYGON);
            rois.addElement(r);
        } else if (shape instanceof GeneralPath) {
            PathIterator pIter;
            if (flatten)
                pIter = getFlatteningPathIterator(shape,flatness);
            else
                pIter = shape.getPathIterator(new AffineTransform());
            parsePath(pIter, null, null, rois, null);
        }
        Roi[] array = new Roi[rois.size()];
        rois.copyInto((Roi[])array);
        return array;
    }
    
    Roi[] getSavedRois () {
        Roi[] array = new Roi[savedRois.size()];
        savedRois.copyInto((Roi[])array);
        return array;
    }

    /**Attempts to convert this ShapeRoi into a non-composite Roi.
     * @return an ij.gui.Roi object or null
     */
    public Roi shapeToRoi() {
        if (shape==null || !(shape instanceof GeneralPath))
            return null;
        PathIterator pIter = shape.getPathIterator(new AffineTransform());
        Vector rois = new Vector();
        double[] params = {SHAPE_TO_ROI};
        if (!parsePath(pIter, params, null, rois, null))
            return null;
        if (rois.size()==1)
            return (Roi)rois.elementAt(0);
        else
            return null;
    }
    
    /**Implements the rules of conversion from <code>java.awt.geom.GeneralPath</code> to <code>ij.gui.Roi</code>.
     * @param segments The number of segments that compose the path
     * @param linesOnly Indicates wether the GeneralPath object is composed only of SEG_LINETO segments
     * @param curvesOnly Indicates wether the GeneralPath object is composed only of SEG_CUBICTO and SEG_QUADTO segments
     * @param closed Indicates a closed GeneralPath
     * @see #shapeToRois()
     * @return a type flag
     */
    private int guessType(int segments, boolean linesOnly, boolean curvesOnly, boolean closed) {
        //IJ.log("guessType: "+segments+" "+linesOnly+" "+curvesOnly+" "+closed);
        closed = true; // lines currently not supported
        int roiType = Roi.RECTANGLE;
        if (linesOnly) {
            switch(segments) {
                case 0: roiType = NO_TYPE; break;
                case 1: roiType = NO_TYPE; break;
                case 2: roiType = (closed ? NO_TYPE : Roi.LINE); break;
                case 3: roiType = (closed ? Roi.POLYGON : (forceAngle ? Roi.ANGLE: Roi.POLYLINE)); break;
                case 4: roiType = (closed ? Roi.RECTANGLE : Roi.POLYLINE); break;
                default:
                    if (segments <= MAXPOLY) 
                        roiType = closed ? Roi.POLYGON : Roi.POLYLINE;
                    else 
                        roiType = closed ? (forceTrace ? Roi.TRACED_ROI: Roi.FREEROI): Roi.FREELINE;
                    break;
            }
        }
        else roiType = segments >=2 ? Roi.COMPOSITE : NO_TYPE;
        return roiType;
    }

    /**Creates a Roi object based on the arguments.
     * @see #shapeToRois()
     * @param xCoords the x coordinates
     * @param yCoords the y coordinates
     * @param type the type flag
     * @return a ij.gui.Roi object
     */
    private Roi createRoi(Vector xCoords, Vector yCoords, int roiType) {
        if (roiType==NO_TYPE) return null;
        Roi roi = null;
        if(xCoords.size() != yCoords.size() || xCoords.size()==0) { return null; }

        int[] xPoints = new int[xCoords.size()];
        int[] yPoints = new int[yCoords.size()];

        for (int i=0; i<xPoints.length; i++) {
            xPoints[i] = ((Integer)xCoords.elementAt(i)).intValue() + x;
            yPoints[i] = ((Integer)yCoords.elementAt(i)).intValue() + y;
        }

        int startX = 0;
        int startY = 0;
        int width = 0;
        int height = 0;
        switch(roiType) {
            //case NO_TYPE: roi = this; break;
            case Roi.COMPOSITE: roi = this; break; // hmmm.....!!!???
            case Roi.OVAL:
                startX = xPoints[xPoints.length-4];
                startY = yPoints[yPoints.length-3];
                width = max(xPoints)-min(xPoints);
                height = max(yPoints)-min(yPoints);
                roi = new OvalRoi(startX, startY, width, height);
                break;
            case Roi.RECTANGLE:
                startX = xPoints[0];
                startY = yPoints[0];
                width = max(xPoints)-min(xPoints);
                height = max(yPoints)-min(yPoints);
                roi = new Roi(startX, startY, width, height);
                break;
            case Roi.LINE: roi = new ij.gui.Line(xPoints[0],yPoints[0],xPoints[1],yPoints[1]); break;
            default:
                int n = xPoints.length;
                roi = new PolygonRoi(xPoints, yPoints, n, roiType);
                if (roiType==FREEROI) {
                    double length = roi.getLength();
                    double mag = ic!=null?ic.getMagnification():1.0;
                    length *= mag;
                    //IJ.log("createRoi: "+length/n+" "+mag);
                    if (length/n>=15.0) {
                        roi = new PolygonRoi(xPoints, yPoints, n, POLYGON);
                    }
                }
                break;
        }
        //if(roi!=null && imp!=null) roi.setImage(imp);
        return roi;
    }

    /**********************************************************************************/
    /***                                   Geometry                                ****/
    /**********************************************************************************/

    /**Checks whether the specified coordinates are inside a on this ROI's shape boundaries.*/
    public boolean contains(int x, int y) {
        if(shape==null) return false;
        return shape.contains(x-this.x, y-this.y);
    }

    /** Caculates "Feret" (maximum caliper width) and "MinFeret" (minimum caliper width). */    
    public double[] getFeretValues() {
        Roi[] rois = getRois();
        if (rois!=null && rois.length==1) {
            rois[0].setImage(imp);
            return rois[0].getFeretValues();
        }
        double min=Double.MAX_VALUE, diameter=0.0, angle=0.0;
        int p1=0, p2=0;
        double pw=1.0, ph=1.0;
        if (imp!=null) {
            Calibration cal = imp.getCalibration();
            pw = cal.pixelWidth;
            ph = cal.pixelHeight;
        }
        Shape shape = getShape();
        Shape s = null;
        Rectangle2D r = shape.getBounds2D();
        double cx = r.getX() + r.getWidth()/2;
        double cy = r.getY() + r.getHeight()/2;
        AffineTransform at = new AffineTransform();
        at.translate(cx, cy);
        for (int i=0; i<181; i++) {
            at.rotate(Math.PI/180.0);
            s = at.createTransformedShape(shape);
            r = s.getBounds2D();
            double max2 = Math.max(r.getWidth(), r.getHeight());
            if (max2>diameter) {
                diameter = max2*pw;
                //angle = i;
            }
            double min2 = Math.min(r.getWidth(), r.getHeight());
            min = Math.min(min, min2);
        }
        if (pw!=ph) {
            diameter = 0.0;
            angle = 0.0;
        }
        if (pw==ph)
            min *= pw;
        else {
            min = 0.0;
            angle = 0.0;
        }
        double[] a = new double[5];
        a[0] = diameter;
        a[1] = angle;
        a[2] = min;
        a[3] = 0.0; // FeretX
        a[4] = 0.0; // FeretY
        return a;
    }

    /**Returns the perimeter if this ShapeRoi can be decomposed 
        into simple ROIs, otherwise returns zero. */
    public double getLength() {
        if (width==0 && height==0)
            return 0.0;
        double length = 0.0;
        Roi[] rois = getRois();
        ImagePlus imp2 = getImage();
        if (rois!=null) {
            for (int i=0; i<rois.length; i++) {
                Roi roi = rois[i];
                if (roi instanceof ShapeRoi)
                    return 0.0;
                roi.setImage(imp2);
                length += roi.getLength();
                roi.setImage(null);
            }
        }
        return length;
    }

    /**Returns a flattened version of the path iterator for this ROi's shape*/
    FlatteningPathIterator getFlatteningPathIterator(Shape s, double fl) {
        return (FlatteningPathIterator)s.getPathIterator(new AffineTransform(),fl);
    }

    /**Length of the control polygon of the cubic B&eacute;zier curve argument, in double precision.*/
    double cplength(CubicCurve2D.Double c) {
        double result = Math.sqrt(Math.pow((c.ctrlx1-c.x1),2.0)+Math.pow((c.ctrly1-c.y1),2.0));
        result += Math.sqrt(Math.pow((c.ctrlx2-c.ctrlx1),2.0)+Math.pow((c.ctrly2-c.ctrly1),2.0));
        result += Math.sqrt(Math.pow((c.x2-c.ctrlx2),2.0)+Math.pow((c.y2-c.ctrly2),2.0));
        return result;
    }

    /**Length of the control polygon of the quadratic B&eacute;zier curve argument, in double precision.*/
    double qplength(QuadCurve2D.Double c) {
        double result = Math.sqrt(Math.pow((c.ctrlx-c.x1),2.0)+Math.pow((c.ctrly-c.y1),2.0));
        result += Math.sqrt(Math.pow((c.x2-c.ctrlx),2.0)+Math.pow((c.y2-c.ctrly),2.0));
        return result;
    }

    /**Length of the chord of the arc of the cubic B&eacute;zier curve argument, in double precision.*/
    double cclength(CubicCurve2D.Double c)
    { return Math.sqrt(Math.pow((c.x2-c.x1),2.0) + Math.pow((c.y2-c.y1),2.0)); }

    /**Length of the chord of the arc of the quadratic B&eacute;zier curve argument, in double precision.*/
    double qclength(QuadCurve2D.Double c)
    { return Math.sqrt(Math.pow((c.x2-c.x1),2.0) + Math.pow((c.y2-c.y1),2.0)); }

    /**Calculates the length of a cubic B&eacute;zier curve specified in double precision.
     * The algorithm is based on the theory presented in paper <br>
     * &quot;Jens Gravesen. Adaptive subdivision and the length and energy of B&eacute;zier curves. Computational Geometry <strong>8:</strong><em>13-31</em> (1997)&quot;
     * implemented using <code>java.awt.geom.CubicCurve2D.Double</code>.
     * Please visit {@link <a href="http://www.graphicsgems.org/gems.html#gemsiv">Graphics Gems IV</a>} for
     * examples of other possible implementations in C and C++.
     */
    double cBezLength(CubicCurve2D.Double c) {
        double l = 0.0;
        double cl = cclength(c);
        double pl = cplength(c);
        if((pl-cl)/2.0 > maxerror)
        {
            CubicCurve2D.Double[] cc = cBezSplit(c);
            for(int i=0; i<2; i++) l+=cBezLength(cc[i]);
            return l;
        }
        l = 0.5*pl+0.5*cl;
        return l;
    }

    /**Calculates the length of a quadratic B&eacute;zier curve specified in double precision.
     * The algorithm is based on the theory presented in paper <br>
     * &quot;Jens Gravesen. Adaptive subdivision and the length and energy of B&eacute;zier curves. Computational Geometry <strong>8:</strong><em>13-31</em> (1997)&quot;
     * implemented using <code>java.awt.geom.CubicCurve2D.Double</code>.
     * Please visit {@link <a href="http://www.graphicsgems.org/gems.html#gemsiv">Graphics Gems IV</a>} for
     * examples of other possible implementations in C and C++.
     */
    double qBezLength(QuadCurve2D.Double c) {
        double l = 0.0;
        double cl = qclength(c);
        double pl = qplength(c);
        if((pl-cl)/2.0 > maxerror)
        {
            QuadCurve2D.Double[] cc = qBezSplit(c);
            for(int i=0; i<2; i++) l+=qBezLength(cc[i]);
            return l;
        }
        l = (2.0*pl+cl)/3.0;
        return l;
    }

 /**Splits a cubic B&eacute;zier curve in half.
  * @param c A cubic B&eacute;zier curve to be divided
  * @return an array with the left and right cubic B&eacute;zier subcurves
  *
    */
    CubicCurve2D.Double[] cBezSplit(CubicCurve2D.Double c) {
        CubicCurve2D.Double[] cc = new CubicCurve2D.Double[2];
        for (int i=0; i<2 ; i++) cc[i] = new CubicCurve2D.Double();
        c.subdivide(cc[0],cc[1]);
        return cc;
    }

 /**Splits a quadratic B&eacute;zier curve in half.
  * @param c A quadratic B&eacute;zier curve to be divided
  * @return an array with the left and right quadratic B&eacute;zier subcurves
  *
    */
    QuadCurve2D.Double[] qBezSplit(QuadCurve2D.Double c) {
        QuadCurve2D.Double[] cc = new QuadCurve2D.Double[2];
        for(int i=0; i<2; i++) cc[i] = new QuadCurve2D.Double();
        c.subdivide(cc[0],cc[1]);
        return cc;
    }

    // c is an array of even length with x0, y0, x1, y1, ... ,xn, yn coordinate pairs
    /**Scales a coordinate array with the size calibration of a 2D image.
     * The array is modified in place.
     * @param c Array of coordinates in double precision with a <strong>fixed</strong> structure:<br>
     * <code>x0,y0,x1,y1,....,xn,yn</code> and with even length of <code>2*(n+1)</code>.
     * @param pw The x-scale of the image.
     * @param ph The y-scale of the image.
     *
     */
    void scaleCoords(double[] c, double pw, double ph) {
        int k = c.length/2;
        if (2*k!=c.length) return; // bail out if array has odd length
        for(int i=0; i<c.length; i+=2)
        {
            c[i]*=pw;
            c[i+1]*=ph;
        }
    }

    Vector parseSegments(PathIterator pI) {
        Vector v = new Vector();
        if (parsePath(pI, null, v, null, null)) return v;
        return null;
    }

    /** Retrieves the end points and control points of the path as a float array. The array 
        contains a sequence of variable length segments that use from from one to seven elements.
        The first element of a segment is the type as defined in the PathIterator interface. SEG_MOVETO 
        and SEG_LINETO segments also include two coordinates, SEG_QUADTO segments include four 
        coordinates and SEG_CUBICTO segments include six coordinates. */
    public float[] getShapeAsArray() {
        if(shape==null) return null;
        //if (savedRois!=null)
        //  return getSavedRoisAsArray();
        PathIterator pIt = shape.getPathIterator(new AffineTransform());
        Vector h = new Vector(); // handles
        Vector s = new Vector(); // segment types
        if (!(parsePath(pIt, null, s, null, h))) return null;
        float[] result = new float[7*s.size()];
        Point2D.Double p;
        int segType;
        int k=0, j=0;
        int index = 0;
        for (int i=0; i<s.size(); i++) {
            segType = ((Integer)s.elementAt(i)).intValue();
            switch(segType) {
                case PathIterator.SEG_MOVETO: case PathIterator.SEG_LINETO:
                    result[index++] = segType;
                    p = (Point2D.Double)h.elementAt(j++);
                    result[index++]=(float)p.getX()+x; result[index++]=(float)p.getY()+y;
                    break;
                case PathIterator.SEG_QUADTO:
                    result[index++] = segType;
                    p = (Point2D.Double)h.elementAt(j++);
                    result[index++]=(float)p.getX()+x; result[index++]=(float)p.getY()+y;
                    p = (Point2D.Double)h.elementAt(j++);
                    result[index++]=(float)p.getX()+x; result[index++]=(float)p.getY()+y;
                    break;
                case PathIterator.SEG_CUBICTO:
                    result[index++] = segType;
                    p = (Point2D.Double)h.elementAt(j++);
                    result[index++]=(float)p.getX()+x; result[index++]=(float)p.getY()+y;
                    p = (Point2D.Double)h.elementAt(j++);
                    result[index++]=(float)p.getX()+x; result[index++]=(float)p.getY()+y;
                    p = (Point2D.Double)h.elementAt(j++);
                    result[index++]=(float)p.getX()+x; result[index++]=(float)p.getY()+y;
                    break;
                case PathIterator.SEG_CLOSE:
                    result[index++] = segType;
                    break;
                default: break;
            }
        }
        float[] result2 = new float[index];
        System.arraycopy(result, 0, result2, 0, result2.length);
        return result2;
    }

    /**Parses the geometry of this ROI's shape by means of the shape's PathIterator 
     * and returns several convenience parameters in the arguments.
     * Iterates through the PathIterator argument and as a byproduct sets the values of
     * the other arguments passed to the method. To retrieve, for example, the length 
     * (or perimeter) of a shape (or path), call this method as<br>
     * <code> parsePath(pIter, par, null, null) <code>,
     * <br> where <code>par</code> is a double array of length one, then get the length as <code>par[0]</code>
     * @param pIter the PathIterator to be parsed.
     * @param params an array with one elemet that will hold the calculated length of path;
     * @param segments a Vector of Integer objects that will hold the types of the segments composing the shape's path
     * @param rois a Vector that will hold ij.gui.Roi objects constructed from elements of this path
     * (see @link #shapeToRois()} for details;
     * @param handles a Vector of Point2D.Double objects representing vertices (segment joinings) and 
     * control points of the curves segments in the iteration order;
     * @return <strong><code>true</code></strong> if successful.*/
    boolean parsePath(PathIterator pIter, double[] params, Vector segments, Vector rois, Vector handles) {
        if (pIter==null || pIter.isDone())
            return false;
        boolean result = true;
        double pw = 1.0, ph = 1.0;
        if (imp!=null) {
            Calibration cal = imp.getCalibration();
            pw = cal.pixelWidth;
            ph = cal.pixelHeight;
        }
        Vector xCoords = new Vector();
        Vector yCoords = new Vector();
        if (segments==null) segments = new Vector();
        if (handles==null) handles = new Vector();
        //if(rois==null) rois = new Vector();
        if (params == null) params = new double[1];
        boolean shapeToRoi = params[0]==SHAPE_TO_ROI;
        int subPaths = 0; // the number of subpaths
        int count = 0;// the number of segments in each subpath w/o SEG_CLOSE; resets to one after each SEG_MOVETO
        int roiType = Roi.RECTANGLE;
        int segType;
        boolean closed = false;
        boolean linesOnly = true;
        boolean curvesOnly = true;
        //boolean success = false;
        double[] coords; // scaled coordinates of the path segment
        double[] ucoords; // unscaled coordinates of the path segment
        double sX = Double.NaN; // start x of subpath (scaled)
        double sY = Double.NaN; // start y of subpath (scaled)
        double x0 = Double.NaN; // last x in the subpath (scaled)
        double y0 = Double.NaN; // last y in the subpath (scaled)
        double usX = Double.NaN;// unscaled versions of the above
        double usY = Double.NaN;
        double ux0 = Double.NaN;
        double uy0 = Double.NaN;
        double pathLength = 0.0;
        Shape curve; // temporary reference to a curve segment of the path
        boolean done = false;
        while (!done) {
            coords = new double[6];
            ucoords = new double[6];
            segType = pIter.currentSegment(coords);
            segments.add(new Integer(segType));
            count++;
            System.arraycopy(coords,0,ucoords,0,coords.length);
            scaleCoords(coords,pw,ph);
            switch(segType) {
                case PathIterator.SEG_MOVETO:
                    if (subPaths>0) {
                        closed = ((int)ux0==(int)usX && (int)uy0==(int)usY);
                        if (closed && (int)ux0!=(int)usX && (int)uy0!=(int)usY) { // this may only happen after a SEG_CLOSE
                            xCoords.add(new Integer(((Integer)xCoords.elementAt(0)).intValue()));
                            yCoords.add(new Integer(((Integer)yCoords.elementAt(0)).intValue()));
                        }
                        if (rois!=null) {
                            roiType = guessType(count, linesOnly, curvesOnly, closed);
                            Roi r = createRoi(xCoords, yCoords, roiType);
                            if (r!=null)
                                rois.addElement(r);
                        }
                        xCoords = new Vector();
                        yCoords = new Vector();
                        count = 1;
                    }
                    subPaths++;
                    usX = ucoords[0];
                    usY = ucoords[1];
                    ux0 = ucoords[0];
                    uy0 = ucoords[1];
                    sX = coords[0];
                    sY = coords[1];
                    x0 = coords[0];
                    y0 = coords[1];
                    handles.add(new Point2D.Double(ucoords[0],ucoords[1]));
                    xCoords.add(new Integer((int)ucoords[0]));
                    yCoords.add(new Integer((int)ucoords[1]));
                    closed = false;
                    break;
                case PathIterator.SEG_LINETO:
                    linesOnly = linesOnly & true;
                    curvesOnly = curvesOnly & false;
                    pathLength += Math.sqrt(Math.pow((y0-coords[1]),2.0)+Math.pow((x0-coords[0]),2.0));
                    ux0 = ucoords[0];
                    uy0 = ucoords[1];
                    x0 = coords[0];
                    y0 = coords[1];
                    handles.add(new Point2D.Double(ucoords[0],ucoords[1]));
                    xCoords.add(new Integer((int)ucoords[0]));
                    yCoords.add(new Integer((int)ucoords[1]));
                    closed = ((int)ux0==(int)usX && (int)uy0==(int)usY);
                    break;
                case PathIterator.SEG_QUADTO:
                    linesOnly = linesOnly & false;
                    curvesOnly = curvesOnly & true;
                    curve = new QuadCurve2D.Double(x0,y0,coords[0],coords[2],coords[2],coords[3]);
                    pathLength += qBezLength((QuadCurve2D.Double)curve);
                    ux0 = ucoords[2];
                    uy0 = ucoords[3];
                    x0 = coords[2];
                    y0 = coords[3];
                    handles.add(new Point2D.Double(ucoords[0],ucoords[1]));
                    handles.add(new Point2D.Double(ucoords[2],ucoords[3]));
                    xCoords.add(new Integer((int)ucoords[2]));
                    yCoords.add(new Integer((int)ucoords[3]));
                    closed = ((int)ux0==(int)usX && (int)uy0==(int)usY);
                    break;
                case PathIterator.SEG_CUBICTO:
                    linesOnly = linesOnly & false;
                    curvesOnly  = curvesOnly & true;
                    curve = new CubicCurve2D.Double(x0,y0,coords[0],coords[1],coords[2],coords[3],coords[4],coords[5]);
                    pathLength += cBezLength((CubicCurve2D.Double)curve);
                    ux0 = ucoords[4];
                    uy0 = ucoords[5];
                    x0 = coords[4];
                    y0 = coords[5];
                    handles.add(new Point2D.Double(ucoords[0],ucoords[1]));
                    handles.add(new Point2D.Double(ucoords[2],ucoords[3]));
                    handles.add(new Point2D.Double(ucoords[4],ucoords[5]));
                    xCoords.add(new Integer((int)ucoords[4]));
                    yCoords.add(new Integer((int)ucoords[5]));
                    closed = ((int)ux0==(int)usX && (int)uy0==(int)usY);
                    break;
                case PathIterator.SEG_CLOSE:
                    if((int)ux0 != (int)usX && (int)uy0 != (int)usY) pathLength += Math.sqrt(Math.pow((x0-sX),2.0) + Math.pow((y0-sY),2.0));
                    closed = true;
                    break;
                default:
                    break;
            }
            pIter.next();
            done = pIter.isDone() || (shapeToRoi&&rois!=null&&rois.size()==1);
            if (done) {
                if(closed && (int)x0!=(int)sX && (int)y0!=(int)sY) { // this may only happen after a SEG_CLOSE
                    xCoords.add(new Integer(((Integer)xCoords.elementAt(0)).intValue()));
                    yCoords.add(new Integer(((Integer)yCoords.elementAt(0)).intValue()));
                }
                if (rois!=null) {
                    roiType = shapeToRoi?TRACED_ROI:guessType(count+1, linesOnly, curvesOnly, closed);
                    Roi r = createRoi(xCoords, yCoords, roiType);
                    if (r!=null)
                        rois.addElement(r);
                }
            }
        }
        params[0] = pathLength;
        return result;
    }

    /** Non-destructively draws the shape of this object on the associated ImagePlus. */
    public void draw(Graphics g) {
        Color color =  strokeColor!=null? strokeColor:ROIColor;
        boolean isActiveOverlayRoi = !overlay && isActiveOverlayRoi();
        //IJ.log("draw: "+overlay+"  "+isActiveOverlayRoi);
        if (isActiveOverlayRoi)
            color = Color.cyan;
        if (fillColor!=null) color = fillColor;
        g.setColor(color);
        AffineTransform aTx = (((Graphics2D)g).getDeviceConfiguration()).getDefaultTransform();
        Graphics2D g2d = (Graphics2D)g;
        if (stroke!=null && !isActiveOverlayRoi)
            g2d.setStroke((ic!=null&&ic.getCustomRoi())||isCursor()?stroke:getScaledStroke());
        mag = getMagnification();
        int basex=0, basey=0;
        if (ic!=null) {
            Rectangle r = ic.getSrcRect();
            basex=r.x; basey=r.y;
        }
        aTx.setTransform(mag, 0.0, 0.0, mag, -basex*mag, -basey*mag);
        aTx.translate(x, y);
        if (fillColor!=null) {
            if (isActiveOverlayRoi) {
                g2d.setColor(Color.cyan);
                g2d.draw(aTx.createTransformedShape(shape));
            } else
                g2d.fill(aTx.createTransformedShape(shape));
        } else
            g2d.draw(aTx.createTransformedShape(shape));
        if (stroke!=null) g2d.setStroke(defaultStroke);
        if (Toolbar.getToolId()==Toolbar.OVAL)
            drawRoiBrush(g);
        if (state!=NORMAL && imp!=null && imp.getRoi()!=null)
            showStatus();
        if (updateFullWindow) 
            {updateFullWindow = false; imp.draw();}
    }

    public void drawRoiBrush(Graphics g) {
        g.setColor(ROIColor);
        int size = Toolbar.getBrushSize();
        if (size==0 || ic==null)
            return;
        int flags = ic.getModifiers();
        if ((flags&16)==0) return; // exit if mouse button up
        size = (int)(size*mag);
        Point p = ic.getCursorLoc();
        int sx = ic.screenX(p.x);
        int sy = ic.screenY(p.y);
        g.drawOval(sx-size/2, sy-size/2, size, size);
    }
    
    /**Draws the shape of this object onto the specified ImageProcessor.
     * <br> This method will always draw a flattened version of the actual shape
     * (i.e., all curve segments will be approximated by line segments).
     */
    public void drawPixels(ImageProcessor ip) {
        PathIterator pIter = shape.getPathIterator(new AffineTransform(), flatness);
        float[] coords = new float[6];
        float sx=0f, sy=0f;
        while (!pIter.isDone()) {
            int segType = pIter.currentSegment(coords);
            switch(segType) {
                case PathIterator.SEG_MOVETO:
                    sx = coords[0];
                    sy = coords[1];
                    ip.moveTo(x+(int)sx, y+(int)sy);
                    break;
                case PathIterator.SEG_LINETO:
                    ip.lineTo(x+(int)coords[0], y+(int)coords[1]);
                    break;
                case PathIterator.SEG_CLOSE:
                    ip.lineTo(x+(int)sx, y+(int)sy);
                    break;
                default: break;
            }
            pIter.next();
        }
    }

    /** Returns this ROI's mask pixels as a ByteProcessor with pixels "in" the mask
        set to white (255) and pixels "outside" the mask set to black (0). */
    public ImageProcessor getMask() {
        if (shape==null)
            return null;
        if (cachedMask!=null && cachedMask.getPixels()!=null)
            return cachedMask;
        BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_GRAY);
        Graphics2D g2d = bi.createGraphics();
        g2d.setColor(Color.white);
        g2d.fill(shape);
        Raster raster = bi.getRaster();
        DataBufferByte buffer = (DataBufferByte)raster.getDataBuffer();     
        byte[] mask = buffer.getData();
        cachedMask = new ByteProcessor(width, height, mask, null);
        cachedMask.setThreshold(255,255,ImageProcessor.NO_LUT_UPDATE);
        return cachedMask;
    }

    /**Returns a reference to the Shape object encapsulated by this ShapeRoi. */
    public Shape getShape() {
        return shape;
    }

    /**Sets the <code>java.awt.Shape</code> object encapsulated by <strong><code>this</code></strong>
     * to the argument.
     * <br>This object will hold a (shallow) copy of the shape argument. If a deep copy
     * of the shape argumnt is required, then a clone of the argument should be passed
     * in; a possible example is <code>setShape(ShapeRoi.cloneShape(shape))</code>.
     * @return <strong><code>false</code></strong> if the argument is null.
     */
    boolean setShape(Shape rhs) {
        boolean result = true;
        if (rhs==null) return false;
        if (shape.equals(rhs)) return false;
        shape = rhs;
        type = Roi.COMPOSITE;
        Rectangle rect = shape.getBounds();
        width = rect.width;
        height = rect.height;
        return true;
    }

    /**Returns the element with the smallest value in the array argument.*/
    private int min(int[] array) {
        int val = array[0];
        for (int i=1; i<array.length; i++) val = Math.min(val,array[i]);
        return val;
    }

    /**Returns the element with the largest value in the array argument.*/
    private int max(int[] array) {
        int val = array[0];
        for (int i=1; i<array.length; i++) val = Math.max(val,array[i]);
        return val;
    }
    
    static ShapeRoi getCircularRoi(int x, int y, int width) {
        return new ShapeRoi(new OvalRoi(x - width / 2, y - width / 2, width, width));
    }

    /** Always returns -1 since ShapeRois do not have handles. */
    public int isHandle(int sx, int sy) {
           return -1;
    }
    
    public Polygon getConvexHull() {
        Roi[] rois = getRois();
        if (rois!=null && rois.length==1)
            return rois[0].getConvexHull();
        else
            return null;
    }
    
    public Polygon getPolygon() {
        Roi[] rois = getRois();
        if (rois!=null && rois.length==1)
            return rois[0].getPolygon();
        else
            return super.getPolygon();
    }

    public FloatPolygon getFloatPolygon() {
        Roi[] rois = getRois();
        if (rois!=null && rois.length==1)
            return rois[0].getFloatPolygon();
        else
            return super.getFloatPolygon();
    }

}