/*
 * Copyright 2010-2015 Institut Pasteur.
 * 
 * This file is part of Icy.
 * 
 * Icy is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * Icy is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Icy. If not, see <http://www.gnu.org/licenses/>.
 */
package icy.roi;

import icy.canvas.IcyCanvas;
import icy.canvas.IcyCanvas2D;
import icy.canvas.IcyCanvas3D;
import icy.gui.util.FontUtil;
import icy.preferences.GeneralPreferences;
import icy.roi.edit.PositionROIEdit;
import icy.sequence.Sequence;
import icy.type.point.Point3D;
import icy.type.point.Point5D;
import icy.type.rectangle.Rectangle3D;
import icy.type.rectangle.Rectangle5D;
import icy.util.EventUtil;
import icy.util.GraphicsUtil;
import icy.util.XMLUtil;

import java.awt.Graphics2D;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.RenderingHints;
import java.awt.event.InputEvent;
import java.awt.event.MouseEvent;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.List;

import org.w3c.dom.Node;

/**
 * 3D ROI base class
 */
public abstract class ROI3D extends ROI
{
    /**
     * @deprecated Use {@link ROI3D#getROI3DList(List)} instead.
     */
    @Deprecated
    public static ArrayList<ROI3D> getROI3DList(ArrayList<ROI> rois)
    {
        final ArrayList<ROI3D> result = new ArrayList<ROI3D>();

        for (ROI roi : rois)
            if (roi instanceof ROI3D)
                result.add((ROI3D) roi);

        return result;
    }

    /**
     * Return all 3D ROI from the ROI list
     */
    public static List<ROI3D> getROI3DList(List<ROI> rois)
    {
        final List<ROI3D> result = new ArrayList<ROI3D>();

        for (ROI roi : rois)
            if (roi instanceof ROI3D)
                result.add((ROI3D) roi);

        return result;
    }

    public abstract class ROI3DPainter extends ROIPainter
    {
        protected Point3D startDragMousePosition;
        protected Point3D startDragROIPosition;

        public ROI3DPainter()
        {
            super();

            startDragMousePosition = null;
            startDragROIPosition = null;
        }

        @Override
        protected boolean updateFocus(InputEvent e, Point5D imagePoint, IcyCanvas canvas)
        {
            if (imagePoint == null)
                return false;

            // test on canvas has already be done, don't do it again
            final boolean focused = isOverEdge(canvas, imagePoint.getX(), imagePoint.getY(), imagePoint.getZ());

            setFocused(focused);

            return focused;
        }

        @Override
        protected boolean updateDrag(InputEvent e, Point5D imagePoint, IcyCanvas canvas)
        {
            // not dragging --> exit
            if (startDragMousePosition == null)
                return false;
            if (imagePoint == null)
                return false;
            if (!canSetPosition())
                return false;

            double dx = imagePoint.getX() - startDragMousePosition.getX();
            double dy = imagePoint.getY() - startDragMousePosition.getY();
            double dz = imagePoint.getZ() - startDragMousePosition.getZ();

            // shift action --> limit to one direction
            if (EventUtil.isShiftDown(e))
            {
                // X or Z drag
                if (Math.abs(dx) > Math.abs(dy))
                {
                    dy = 0d;

                    // Z drag
                    if (Math.abs(dz) > Math.abs(dx))
                        dx = 0d;
                    else
                        dz = 0d;
                }
                // Y or Z drag
                else
                {
                    dx = 0d;

                    // Z drag
                    if (Math.abs(dz) > Math.abs(dy))
                        dy = 0d;
                    else
                        dz = 0d;
                }
            }

            // needed for undo operation
            final Sequence sequence;
            final Point5D savePosition;

            // get canvas which modify the ROI --> get the sequence
            if (canvas != null)
                sequence = canvas.getSequence();
            else
                sequence = null;

            if (sequence != null)
                savePosition = getPosition5D();
            else
                savePosition = null;

            // set new position
            setPosition3D(new Point3D.Double(startDragROIPosition.getX() + dx, startDragROIPosition.getY() + dy,
                    startDragROIPosition.getZ() + dz));

            // allow undo as the ROI position has been modified from canvas
            if ((sequence != null) && (savePosition != null))
                // add position change to undo manager
                sequence.addUndoableEdit(new PositionROIEdit(ROI3D.this, savePosition));

            return true;
        }

        @Override
        public void mousePressed(MouseEvent e, Point5D.Double imagePoint, IcyCanvas canvas)
        {
            super.mousePressed(e, imagePoint, canvas);

            // ROI editable ? (don't check for consumption as selection can consume event)
            if (!isReadOnly())
            {
                // check we can do the action
                if (imagePoint != null)
                {
                    if (isActiveFor(canvas))
                    {
                        // left button action
                        if (EventUtil.isLeftMouseButton(e))
                        {
                            ROI3D.this.beginUpdate();
                            try
                            {
                                // roi focused ?
                                if (isFocused())
                                {
                                    startDragMousePosition = imagePoint.toPoint3D();
                                    startDragROIPosition = getPosition3D();
                                }
                            }
                            finally
                            {
                                ROI3D.this.endUpdate();
                            }
                        }
                    }
                }
            }
        }

        @Override
        public void mouseReleased(MouseEvent e, Point5D.Double imagePoint, IcyCanvas canvas)
        {
            // do parent stuff
            super.mouseReleased(e, imagePoint, canvas);

            startDragMousePosition = null;
        }

        @Override
        public void mouseDrag(MouseEvent e, Point5D.Double imagePoint, IcyCanvas canvas)
        {
            // do parent stuff
            super.mouseDrag(e, imagePoint, canvas);

            // not yet consumed and ROI editable...
            if (!e.isConsumed() && !isReadOnly())
            {
                // check we can do the action
                if (imagePoint != null)
                {
                    if (isActiveFor(canvas))
                    {
                        // left button action
                        if (EventUtil.isLeftMouseButton(e))
                        {
                            ROI3D.this.beginUpdate();
                            try
                            {
                                // roi focused ?
                                if (isFocused())
                                {
                                    // store drag start position if not yet done
                                    if (startDragMousePosition == null)
                                    {
                                        startDragMousePosition = imagePoint.toPoint3D();
                                        startDragROIPosition = getPosition3D();
                                    }

                                    updateDrag(e, imagePoint, canvas);

                                    // consume event
                                    e.consume();
                                }
                            }
                            finally
                            {
                                ROI3D.this.endUpdate();
                            }
                        }
                    }
                }
            }
        }

        @Override
        public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
        {
            super.paint(g, sequence, canvas);

            if (isActiveFor(canvas))
            {
                drawROI(g, sequence, canvas);
                // display name ?
                if (getShowName())
                    drawName(g, sequence, canvas);
            }
        }

        /**
         * Draw the ROI
         */
        public abstract void drawROI(Graphics2D g, Sequence sequence, IcyCanvas canvas);

        /**
         * Draw the ROI name
         */
        public void drawName(Graphics2D g, Sequence sequence, IcyCanvas canvas)
        {
            if (canvas instanceof IcyCanvas2D)
            {
                // not supported
                if (g == null)
                    return;

                final Rectangle3D bounds3d = getBounds3D();
                final int posZ = canvas.getPositionZ();

                // ROI is not visible on this Z position --> nothing to draw
                if ((posZ != -1) && (bounds3d.getMinZ() > posZ) || (bounds3d.getMaxZ() < posZ))
                    return;

                final Graphics2D g2 = (Graphics2D) g.create();
                final IcyCanvas2D cnv2d = (IcyCanvas2D) canvas;
                final Rectangle2D bounds = bounds3d.toRectangle2D();
                final Point pos = cnv2d.imageToCanvas(bounds.getCenterX(), bounds.getMinY());
                final double coef = Math.log(canvas.getScaleX() + 1);
                final double fontSize = (GeneralPreferences.getGuiFontSize() - 4) + (int) (coef * 10d);

                // go to absolute coordinates
                g2.transform(cnv2d.getInverseTransform());
                // set text anti alias
                g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
                // set font
                g2.setFont(FontUtil.setSize(g2.getFont(), (int) fontSize));
                // set color
                g2.setColor(getColor());

                // draw ROI name
                GraphicsUtil.drawHCenteredString(g2, getName(), pos.x, pos.y - (int) (2 * fontSize), true);

                g2.dispose();
            }

            if (canvas instanceof IcyCanvas3D)
            {
                // not yet supported

            }
        }
    }

    public static final String ID_T = "t";
    public static final String ID_C = "c";

    /**
     * t coordinate attachment
     */
    protected int t;
    /**
     * c coordinate attachment
     */
    protected int c;

    public ROI3D()
    {
        super();

        // by default we consider no specific T and C attachment
        t = -1;
        c = -1;
    }

    @Override
    public String getDefaultName()
    {
        return "ROI3D";
    }

    @Override
    final public int getDimension()
    {
        return 3;
    }

    /**
     * Returns true if specified ROI is on the same [T, C] position than current ROI.
     * 
     * @param shouldContain
     *        if <code>true</code> then current ROI should "contains" specified ROI position [T, C]
     */
    protected boolean onSamePos(ROI3D roi, boolean shouldContain)
    {
        final int t = getT();
        final int c = getC();
        final int roiT = roi.getT();
        final int roiC = roi.getC();

        // same position ?
        if (shouldContain)
        {
            if ((t != -1) && (t != roiT))
                return false;
            if ((c != -1) && (c != roiC))
                return false;
        }
        else
        {
            if ((t != -1) && (roiT != -1) && (t != roiT))
                return false;
            if ((c != -1) && (roiC != -1) && (c != roiC))
                return false;
        }

        return true;
    }

    /**
     * Tests if a specified {@link Point3D} is inside the ROI.
     * 
     * @param p
     *        the specified <code>Point3D</code> to be tested
     * @return <code>true</code> if the specified <code>Point3D</code> is inside the boundary of the <code>ROI</code>;
     *         <code>false</code> otherwise.
     */
    public boolean contains(Point3D p)
    {
        return contains(p.getX(), p.getY(), p.getZ());
    }

    /**
     * Tests if the interior of the <code>ROI</code> entirely contains the specified <code>Rectangle3D</code>. The
     * {@code ROI.contains()} method allows a implementation to
     * conservatively return {@code false} when:
     * <ul>
     * <li>the <code>intersect</code> method returns <code>true</code> and
     * <li>the calculations to determine whether or not the <code>ROI</code> entirely contains the
     * <code>Rectangle3D</code> are prohibitively expensive.
     * </ul>
     * This means that for some ROIs this method might return {@code false} even though the {@code ROI} contains the
     * {@code Rectangle3D}.
     * 
     * @param r
     *        The specified <code>Rectangle3D</code>
     * @return <code>true</code> if the interior of the <code>ROI</code> entirely contains the <code>Rectangle3D</code>;
     *         <code>false</code> otherwise or, if the <code>ROI</code> contains the <code>Rectangle3D</code> and the
     *         <code>intersects</code> method returns <code>true</code> and the containment calculations would be too
     *         expensive to perform.
     * @see #contains(double, double, double, double, double, double)
     */
    public boolean contains(Rectangle3D r)
    {
        return contains(r.getX(), r.getY(), r.getZ(), r.getSizeX(), r.getSizeY(), r.getSizeZ());
    }

    /**
     * Tests if the specified coordinates are inside the <code>ROI</code>.
     * 
     * @param x
     *        the specified X coordinate to be tested
     * @param y
     *        the specified Y coordinate to be tested
     * @param z
     *        the specified Z coordinate to be tested
     * @return <code>true</code> if the specified 3D coordinates are inside the <code>ROI</code> boundary;
     *         <code>false</code> otherwise.
     */
    public abstract boolean contains(double x, double y, double z);

    /**
     * Tests if the <code>ROI</code> entirely contains the specified 3D rectangular area. All
     * coordinates that lie inside the rectangular area must lie within the <code>ROI</code> for the
     * entire rectangular area to be considered contained within the <code>ROI</code>.
     * <p>
     * The {@code ROI.contains()} method allows a {@code ROI} implementation to conservatively return {@code false}
     * when:
     * <ul>
     * <li>the <code>intersect</code> method returns <code>true</code> and
     * <li>the calculations to determine whether or not the <code>ROI</code> entirely contains the rectangular area are
     * prohibitively expensive.
     * </ul>
     * This means that for some {@code ROIs} this method might return {@code false} even though the {@code ROI} contains
     * the rectangular area.
     * 
     * @param x
     *        the X coordinate of the minimum corner position of the specified rectangular area
     * @param y
     *        the Y coordinate of the minimum corner position of the specified rectangular area
     * @param z
     *        the Z coordinate of the minimum corner position of the specified rectangular area
     * @param sizeX
     *        size for X dimension of the specified rectangular area
     * @param sizeY
     *        size for Y dimension of the specified rectangular area
     * @param sizeZ
     *        size for Z dimension of the specified rectangular area
     * @return <code>true</code> if the interior of the <code>ROI</code> entirely contains the
     *         specified 3D rectangular area; <code>false</code> otherwise or, if the <code>ROI</code> contains the 3D
     *         rectangular area and the <code>intersects</code> method returns <code>true</code> and the containment
     *         calculations would be too
     *         expensive to perform.
     */
    public abstract boolean contains(double x, double y, double z, double sizeX, double sizeY, double sizeZ);

    @Override
    public boolean contains(double x, double y, double z, double t, double c)
    {
        final boolean tok;
        final boolean cok;

        if (getT() == -1)
            tok = true;
        else
            tok = (t >= getT()) && (t < (getT() + 1d));
        if (getC() == -1)
            cok = true;
        else
            cok = (c >= getC()) && (c < (getC() + 1d));

        return contains(x, y, z) && tok && cok;
    }

    @Override
    public boolean contains(double x, double y, double z, double t, double c, double sizeX, double sizeY, double sizeZ,
            double sizeT, double sizeC)
    {
        final boolean tok;
        final boolean cok;

        if (getT() == -1)
            tok = true;
        else
            tok = (t >= getT()) && ((t + sizeT) <= (getT() + 1d));
        if (getC() == -1)
            cok = true;
        else
            cok = (c >= getC()) && ((c + sizeC) <= (getC() + 1d));

        return contains(x, y, z, sizeX, sizeY, sizeZ) && tok && cok;
    }

    /*
     * Generic implementation using the BooleanMask which is not accurate and slow. Override this
     * for specific ROI type.
     */
    @Override
    public boolean contains(ROI roi)
    {
        if (roi instanceof ROI3D)
        {
            final ROI3D roi3d = (ROI3D) roi;

            if (onSamePos(roi3d, true))
            {
                // special case of ROI Point
                if (roi3d.isEmpty())
                    return contains(roi3d.getPosition3D());

                BooleanMask3D mask;
                BooleanMask3D roiMask;

                // take content first
                mask = getBooleanMask(false);
                roiMask = roi3d.getBooleanMask(false);

                // test first only on content
                if (!mask.contains(roiMask))
                    return false;

                // take content and edge
                mask = getBooleanMask(true);
                roiMask = roi3d.getBooleanMask(true);

                // then test on content and edge
                if (!mask.contains(roiMask))
                    return false;

                // contained
                return true;
            }

            return false;
        }

        // use default implementation
        return super.contains(roi);
    }

    /**
     * Tests if the interior of the <code>ROI</code> intersects the interior of a specified <code>Rectangle3D</code>.
     * The {@code ROI.intersects()} method allows a {@code ROI} implementation to conservatively return {@code true}
     * when:
     * <ul>
     * <li>there is a high probability that the <code>Rectangle3D</code> and the <code>ROI</code> intersect, but
     * <li>the calculations to accurately determine this intersection are prohibitively expensive.
     * </ul>
     * This means that for some {@code ROIs} this method might return {@code true} even though the {@code Rectangle3D}
     * does not intersect the {@code ROI}.
     * 
     * @param r
     *        the specified <code>Rectangle3D</code>
     * @return <code>true</code> if the interior of the <code>ROI</code> and the interior of the
     *         specified <code>Rectangle3D</code> intersect, or are both highly likely to intersect
     *         and intersection calculations would be too expensive to perform; <code>false</code> otherwise.
     * @see #intersects(double, double, double,double, double, double)
     */
    public boolean intersects(Rectangle3D r)
    {
        return intersects(r.getX(), r.getY(), r.getZ(), r.getSizeX(), r.getSizeY(), r.getSizeZ());
    }

    /**
     * Tests if the interior of the <code>ROI</code> intersects the interior of a specified
     * 3D rectangular area. The 3D rectangular area is considered to intersect the <code>ROI</code> if any point is
     * contained in both the interior of the <code>ROI</code> and the specified
     * rectangular area.
     * <p>
     * The {@code ROI.intersects()} method allows a {@code ROI} implementation to conservatively return {@code true}
     * when:
     * <ul>
     * <li>there is a high probability that the 3D rectangular area and the <code>ROI</code> intersect, but
     * <li>the calculations to accurately determine this intersection are prohibitively expensive.
     * </ul>
     * This means that for some {@code ROIs} this method might return {@code true} even though the 3D rectangular area
     * does not intersect the {@code ROI}.
     * 
     * @param x
     *        the X coordinate of the minimum corner position of the specified rectangular area
     * @param y
     *        the Y coordinate of the minimum corner position of the specified rectangular area
     * @param z
     *        the Z coordinate of the minimum corner position of the specified rectangular area
     * @param sizeX
     *        size for X dimension of the specified rectangular area
     * @param sizeY
     *        size for Y dimension of the specified rectangular area
     * @param sizeZ
     *        size for Z dimension of the specified rectangular area
     * @return <code>true</code> if the interior of the <code>ROI</code> and the interior of the
     *         rectangular area intersect, or are both highly likely to intersect and intersection
     *         calculations would be too expensive to perform; <code>false</code> otherwise.
     */
    public abstract boolean intersects(double x, double y, double z, double sizeX, double sizeY, double sizeZ);

    @Override
    public boolean intersects(double x, double y, double z, double t, double c, double sizeX, double sizeY,
            double sizeZ, double sizeT, double sizeC)
    {
        // easy discard
        if ((sizeX == 0d) || (sizeY == 0d) || (sizeZ == 0d) || (sizeT == 0d) || (sizeC == 0d))
            return false;

        final boolean tok;
        final boolean cok;

        if (getT() == -1)
            tok = true;
        else
            tok = ((t + sizeT) > getT()) && (t < (getT() + 1d));
        if (getC() == -1)
            cok = true;
        else
            cok = ((c + sizeC) > getC()) && (c < (getC() + 1d));

        return intersects(x, y, z, sizeX, sizeY, sizeZ) && tok && cok;
    }

    /*
     * Generic implementation using the BooleanMask which is not accurate and slow.
     * Override this for specific ROI type.
     */
    @Override
    public boolean intersects(ROI roi)
    {
        if (roi instanceof ROI3D)
        {
            final ROI3D roi3d = (ROI3D) roi;

            if (onSamePos(roi3d, false))
                return getBooleanMask(true).intersects(roi3d.getBooleanMask(true));
        }

        // use default implementation
        return super.intersects(roi);
    }

    /**
     * Calculate and returns the 3D bounding box of the <code>ROI</code>.<br>
     * This method is used by {@link #getBounds3D()} which should try to cache the result as the
     * bounding box calculation can take some computation time for complex ROI.
     */
    public abstract Rectangle3D computeBounds3D();

    @Override
    public Rectangle5D computeBounds5D()
    {
        final Rectangle3D bounds3D = computeBounds3D();
        if (bounds3D == null)
            return new Rectangle5D.Double();

        final Rectangle5D.Double result = new Rectangle5D.Double(bounds3D.getX(), bounds3D.getY(), bounds3D.getZ(), 0d,
                0d, bounds3D.getSizeX(), bounds3D.getSizeY(), bounds3D.getSizeZ(), 0d, 0d);

        if (getT() == -1)
        {
            result.t = Double.NEGATIVE_INFINITY;
            result.sizeT = Double.POSITIVE_INFINITY;
        }
        else
        {
            result.t = getT();
            result.sizeT = 1d;
        }
        if (getC() == -1)
        {
            result.c = Double.NEGATIVE_INFINITY;
            result.sizeC = Double.POSITIVE_INFINITY;
        }
        else
        {
            result.c = getC();
            result.sizeC = 1d;
        }

        return result;
    }

    /**
     * Returns an integer {@link Rectangle3D} that completely encloses the <code>ROI</code>. Note
     * that there is no guarantee that the returned <code>Rectangle3D</code> is the smallest
     * bounding box that encloses the <code>ROI</code>, only that the <code>ROI</code> lies entirely
     * within the indicated <code>Rectangle3D</code>. The returned <code>Rectangle3D</code> might
     * also fail to completely enclose the <code>ROI</code> if the <code>ROI</code> overflows the
     * limited range of the integer data type. The <code>getBounds3D</code> method generally returns
     * a tighter bounding box due to its greater flexibility in representation.
     * 
     * @return an integer <code>Rectangle3D</code> that completely encloses the <code>ROI</code>.
     */
    public Rectangle3D.Integer getBounds()
    {
        return getBounds3D().toInteger();
    }

    /**
     * Returns the bounding box of the <code>ROI</code>. Note that there is no guarantee that the
     * returned {@link Rectangle3D} is the smallest bounding box that encloses the <code>ROI</code>,
     * only that the <code>ROI</code> lies entirely within the indicated <code>Rectangle3D</code>.
     * 
     * @return an instance of <code>Rectangle3D</code> that is a bounding box of the <code>ROI</code>.
     */
    public Rectangle3D getBounds3D()
    {
        return getBounds5D().toRectangle3D();
    }

    /**
     * Returns the integer ROI position which normally correspond to the <i>minimum</i> point of the
     * ROI bounds.
     * 
     * @see #getBounds()
     */
    public Point3D.Integer getPosition()
    {
        final Rectangle3D.Integer bounds = getBounds();
        return new Point3D.Integer(bounds.x, bounds.y, bounds.z);
    }

    /**
     * Returns the high precision ROI position which normally correspond to the <i>minimum</i> point
     * of the ROI bounds.<br>
     * 
     * @see #getBounds3D()
     */
    public Point3D getPosition3D()
    {
        return getBounds3D().getPosition();
    }

    @Override
    public boolean canSetBounds()
    {
        // default
        return false;
    }

    /**
     * Set the <code>ROI</code> 3D bounds.<br>
     * Note that not all ROI supports bounds modification and you should call {@link #canSetBounds()} first to test if
     * the operation is supported.<br>
     * 
     * @param bounds
     *        new ROI 3D bounds
     */
    public void setBounds3D(Rectangle3D bounds)
    {
        // do nothing by default (not supported)
    }

    @Override
    public void setBounds5D(Rectangle5D bounds)
    {
        beginUpdate();
        try
        {
            // infinite T dim ?
            if (bounds.getSizeT() == Double.POSITIVE_INFINITY)
                setT(-1);
            else
                setT((int) bounds.getT());
            // infinite C dim ?
            if (bounds.getSizeC() == Double.POSITIVE_INFINITY)
                setC(-1);
            else
                setC((int) bounds.getC());

            setBounds3D(bounds.toRectangle3D());
        }
        finally
        {
            endUpdate();
        }
    }

    @Override
    public boolean canSetPosition()
    {
        // default implementation use translation if available
        return canTranslate();
    }

    /**
     * Set the <code>ROI</code> 3D position.<br>
     * Note that not all ROI supports position modification and you should call {@link #canSetPosition()} first to test
     * if the operation is supported.<br>
     * 
     * @param position
     *        new ROI 3D position
     */
    public void setPosition3D(Point3D position)
    {
        // use translation operation by default if supported
        if (canTranslate())
        {
            final Point3D oldPos = getPosition3D();
            translate(position.getX() - oldPos.getX(), position.getY() - oldPos.getY(),
                    position.getZ() - oldPos.getZ());
        }
    }

    @Override
    public void setPosition5D(Point5D position)
    {
        beginUpdate();
        try
        {
            setT((int) position.getT());
            setC((int) position.getC());
            setPosition3D(position.toPoint3D());
        }
        finally
        {
            endUpdate();
        }
    }

    /**
     * Returns <code>true</code> if the ROI support translate operation.
     * 
     * @see #translate(double, double, double)
     */
    public boolean canTranslate()
    {
        // by default
        return false;
    }

    /**
     * Translate the ROI position by the specified delta X/Y/Z.<br>
     * Note that not all ROI support this operation so you should test it by calling {@link #canTranslate()} first.
     * 
     * @param dx
     *        translation value to apply on X dimension
     * @param dy
     *        translation value to apply on Y dimension
     * @param dz
     *        translation value to apply on Z dimension
     * @see #canTranslate()
     * @see #setPosition3D(Point3D)
     */
    public void translate(double dx, double dy, double dz)
    {
        // need a default implementation to not break all overriding classes
    }

    @Override
    public boolean[] getBooleanMask2D(int x, int y, int width, int height, int z, int t, int c, boolean inclusive)
    {
        // not on the correct T, C position --> return empty mask
        if (!isActiveFor(t, c))
            return new boolean[Math.max(0, width) * Math.max(0, height)];

        return getBooleanMask2D(x, y, width, height, z, inclusive);
    }

    /**
     * Get the boolean bitmap mask for the specified rectangular area of the roi and for the
     * specified Z position.<br>
     * if the pixel (x,y) is contained in the roi Z position then result[(y * width) + x] = true<br>
     * if the pixel (x,y) is not contained in the roi Z position then result[(y * width) + x] =
     * false
     * 
     * @param x
     *        the X coordinate of the upper-left corner of the specified rectangular area
     * @param y
     *        the Y coordinate of the upper-left corner of the specified rectangular area
     * @param width
     *        the width of the specified rectangular area
     * @param height
     *        the height of the specified rectangular area
     * @param z
     *        Z position we want to retrieve the boolean mask
     * @param inclusive
     *        If true then all partially contained (intersected) pixels are included in the mask.
     * @return the boolean bitmap mask
     */
    public boolean[] getBooleanMask2D(int x, int y, int width, int height, int z, boolean inclusive)
    {
        final boolean[] result = new boolean[Math.max(0, width) * Math.max(0, height)];

        // simple and basic implementation, override it to have better performance
        int offset = 0;
        for (int j = 0; j < height; j++)
        {
            for (int i = 0; i < width; i++)
            {
                if (inclusive)
                    result[offset] = intersects(x + i, y + j, z, 1d, 1d, 1d);
                else
                    result[offset] = contains(x + i, y + j, z, 1d, 1d, 1d);
                offset++;
            }
        }

        return result;
    }

    /**
     * Get the boolean bitmap mask for the specified rectangular area of the roi and for the
     * specified Z position.<br>
     * if the pixel (x,y) is contained in the roi Z position then result[(y * width) + x] = true<br>
     * if the pixel (x,y) is not contained in the roi Z position then result[(y * width) + x] =
     * false
     * 
     * @param rect
     *        2D rectangular area we want to retrieve the boolean mask
     * @param z
     *        Z position we want to retrieve the boolean mask
     * @param inclusive
     *        If true then all partially contained (intersected) pixels are included in the mask.
     */
    public boolean[] getBooleanMask2D(Rectangle rect, int z, boolean inclusive)
    {
        return getBooleanMask2D(rect.x, rect.y, rect.width, rect.height, z, inclusive);
    }

    @Override
    public BooleanMask2D getBooleanMask2D(int z, int t, int c, boolean inclusive)
    {
        // not on the correct T, C position --> return empty mask
        if (!isActiveFor(t, c))
            return new BooleanMask2D(new Rectangle(), new boolean[0]);

        return getBooleanMask2D(z, inclusive);
    }

    /**
     * Get the {@link BooleanMask2D} object representing the roi for the specified Z position.<br>
     * It contains the rectangle mask bounds and the associated boolean array mask.<br>
     * if the pixel (x,y) is contained in the roi Z position then result.mask[(y * w) + x] = true<br>
     * if the pixel (x,y) is not contained in the roi Z position then result.mask[(y * w) + x] =
     * false
     * 
     * @param z
     *        Z position we want to retrieve the boolean mask
     * @param inclusive
     *        If true then all partially contained (intersected) pixels are included in the mask.
     */
    public BooleanMask2D getBooleanMask2D(int z, boolean inclusive)
    {
        final Rectangle bounds = getBounds3D().toRectangle2D().getBounds();

        // empty ROI --> return empty mask
        if (bounds.isEmpty())
            return new BooleanMask2D(new Rectangle(), new boolean[0]);

        final BooleanMask2D result = new BooleanMask2D(bounds, getBooleanMask2D(bounds, z, inclusive));

        // optimized bounds to optimize memory usage for this specific Z slice mask
        result.optimizeBounds();

        return result;
    }

    /**
     * Returns the {@link BooleanMask3D} object representing the XYZ volume content at specified Z,
     * T, C position.<br>
     * It contains the 3D rectangle mask bounds and the associated boolean array mask.
     * 
     * @param z
     *        Z position we want to retrieve the boolean mask or -1 to retrieve the whole Z
     *        dimension
     * @param t
     *        T position we want to retrieve the boolean mask.<br>
     *        Set it to -1 to retrieve the mask whatever is the T position of this ROI3D.
     * @param c
     *        C position we want to retrieve the boolean mask.<br>
     *        Set it to -1 to retrieve the mask whatever is the C position of this ROI3D.
     * @param inclusive
     *        If true then all partially contained (intersected) pixels are included in the mask.
     */
    public BooleanMask3D getBooleanMask3D(int z, int t, int c, boolean inclusive)
    {
        // not on the correct T, C position --> return empty mask
        if (!isActiveFor(t, c))
            return new BooleanMask3D();

        // whole Z dimension
        if (z == -1)
            return getBooleanMask(inclusive);

        // define bounds
        final Rectangle3D.Integer bounds = getBounds();
        bounds.setZ(z);
        bounds.setSizeZ(1);

        return new BooleanMask3D(bounds, new BooleanMask2D[] {getBooleanMask2D(z, inclusive)});
    }

    /**
     * Get the {@link BooleanMask3D} object representing the roi.<br>
     * It contains the 3D rectangle mask bounds and the associated boolean array mask.<br>
     * 
     * @param inclusive
     *        If true then all partially contained (intersected) pixels are included in the mask.
     */
    public BooleanMask3D getBooleanMask(boolean inclusive)
    {
        final Rectangle3D.Integer bounds = getBounds();
        final BooleanMask2D masks[] = new BooleanMask2D[bounds.sizeZ];

        for (int z = 0; z < masks.length; z++)
            masks[z] = getBooleanMask2D(bounds.z + z, inclusive);

        return new BooleanMask3D(bounds, masks);
    }

    /*
     * Generic implementation for ROI3D using the BooleanMask object so the result is just an
     * approximation. This method should be overridden whenever possible to provide more optimal
     * approximations.
     */
    @Override
    public double computeNumberOfContourPoints()
    {
        return getBooleanMask(true).getContourLength();
    }

    /*
     * Generic implementation for ROI3D using the BooleanMask object so the result is just an
     * approximation. Override to optimize for specific ROI.
     */
    @Override
    public double computeNumberOfPoints()
    {
        double numPoints = 0;

        // approximation by using number of point of boolean mask with and without border
        numPoints += getBooleanMask(true).getNumberOfPoints();
        numPoints += getBooleanMask(false).getNumberOfPoints();
        numPoints /= 2d;

        return numPoints;
    }

    /**
     * Compute the surface area in um2 given the pixel size informations from the specified Sequence.<br>
     * Generic implementation of surface area computation using the number of contour point (approximation).<br>
     * This method should be overridden whenever possible to provide faster and accurate calculation.
     */
    public double computeSurfaceArea(Sequence sequence)
    {
        return sequence.calculateSize(getNumberOfContourPoints(), 3, 2);
    }

    /**
     * Returns surface area of the 3D ROI in um2 given the pixel size informations from the specified Sequence.
     * 
     * @see #computeSurfaceArea(Sequence)
     * @see #getNumberOfContourPoints()
     */
    public double getSurfaceArea(Sequence sequence)
    {
        // we cannot cache surface area as result depends from sequence metadata
        return computeSurfaceArea(sequence);
    }

    @Override
    public double getLength(Sequence sequence) throws UnsupportedOperationException
    {
        // not supported on ROI3D by default
        throw new UnsupportedOperationException("getLength() not supported for " + getClassName() + ".");
    }

    /**
     * Return surface area of the 3D ROI in pixels.<br>
     * This is basically the number of pixel representing ROI edges.<br>
     * 
     * @deprecated Use {@link #getNumberOfContourPoints()} instead.
     * @see #getNumberOfContourPoints()
     * @see #computeNumberOfContourPoints()
     */
    @Deprecated
    public double getSurfaceArea()
    {
        return getNumberOfContourPoints();
    }

    /**
     * Return volume of the 3D ROI in pixels.<br>
     * This is basically the number of pixel contained in the ROI.<br>
     * 
     * @deprecated Use {@link #getNumberOfPoints()} instead.
     * @see #getNumberOfPoints()
     * @see #computeNumberOfPoints()
     */
    @Override
    @Deprecated
    public double getVolume()
    {
        return getNumberOfPoints();
    }

    /**
     * Returns the T position.<br>
     * <code>-1</code> is a special value meaning the ROI is set on all T frames (infinite T
     * dimension).
     */
    public int getT()
    {
        return t;
    }

    /**
     * Sets T position of this 3D ROI.<br>
     * You cannot set the ROI on a negative T position as <code>-1</code> is a special value meaning
     * the ROI is set on all T frames (infinite T dimension).
     */
    public void setT(int value)
    {
        final int v;

        // special value for infinite dimension --> change to -1
        if (value == Integer.MIN_VALUE)
            v = -1;
        else
            v = value;

        if (t != v)
        {
            t = v;
            roiChanged(false);
        }
    }

    /**
     * Returns the C position.<br>
     * <code>-1</code> is a special value meaning the ROI is set on all C channels (infinite C
     * dimension).
     */
    public int getC()
    {
        return c;
    }

    /**
     * Sets C position of this 3D ROI.<br>
     * You cannot set the ROI on a negative C position as <code>-1</code> is a special value meaning
     * the ROI is set on all C channels (infinite C dimension).
     */
    public void setC(int value)
    {
        final int v;

        // special value for infinite dimension --> change to -1
        if (value == Integer.MIN_VALUE)
            v = -1;
        else
            v = value;

        if (c != v)
        {
            c = v;
            roiChanged(false);
        }
    }

    @Override
    public boolean isActiveFor(IcyCanvas canvas)
    {
        return isActiveFor(canvas.getPositionT(), canvas.getPositionC());
    }

    /**
     * Return true if the ROI is active for the specified T, C coordinates
     */
    public boolean isActiveFor(int t, int c)
    {
        return ((getT() == -1) || (t == -1) || (getT() == t)) && ((getC() == -1) || (c == -1) || (getC() == c));
    }

    // @Override
    // public void onChanged(CollapsibleEvent object)
    // {
    // super.onChanged(object);
    //
    // final ROIEvent event = (ROIEvent) object;
    //
    // if (event.getType() == ROIEventType.ROI_CHANGED)
    // {
    // // need to recompute surface area
    // if (StringUtil.equals(event.getPropertyName(), ROI_CHANGED_ALL))
    // surfaceAreaInvalid = true;
    // }
    // }

    /**
     * Returns true if specified point coordinates overlap the ROI edge.<br>
     * Use {@link #contains(Point3D)} to test for content overlap instead.
     */
    public boolean isOverEdge(IcyCanvas canvas, Point3D p)
    {
        return isOverEdge(canvas, p.getX(), p.getY(), p.getZ());
    }

    /**
     * Returns true if specified point coordinates overlap the ROI edge.<br>
     * Use {@link #contains(double, double, double)} to test for content overlap instead.</br>
     * We provide a default implementation to not break compatibility.
     */
    public boolean isOverEdge(IcyCanvas canvas, double x, double y, double z)
    {
        // override it in children classes
        return false;
    }

    /**
     * Returns true if specified point coordinates overlap the ROI edge.<br>
     * Use {@link #contains(Point5D)} to test for content overlap instead.
     */
    public boolean isOverEdge(IcyCanvas canvas, Point5D p)
    {
        return isOverEdge(canvas, p.getX(), p.getY(), p.getZ(), p.getT(), p.getC());
    }

    /**
     * Returns true if specified point coordinates overlap the ROI edge.<br>
     * Use {@link #contains(double, double, double, double, double)} to test for content overlap
     * instead.
     */
    public boolean isOverEdge(IcyCanvas canvas, double x, double y, double z, double t, double c)
    {
        if (isActiveFor((int) t, (int) c))
            return isOverEdge(canvas, x, y, z);

        return false;
    }

    @Override
    public boolean loadFromXML(Node node)
    {
        beginUpdate();
        try
        {
            if (!super.loadFromXML(node))
                return false;

            setT(XMLUtil.getElementIntValue(node, ID_T, -1));
            setC(XMLUtil.getElementIntValue(node, ID_C, -1));
        }
        finally
        {
            endUpdate();
        }

        return true;
    }

    @Override
    public boolean saveToXML(Node node)
    {
        if (!super.saveToXML(node))
            return false;

        XMLUtil.setElementIntValue(node, ID_T, getT());
        XMLUtil.setElementIntValue(node, ID_C, getC());

        return true;
    }
}