/*
* org.openmicroscopy.shoola.util.image.roi.ROI5D
*
*------------------------------------------------------------------------------
* Copyright (C) 2006 University of Dundee. All rights reserved.
*
*
* This program 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 2 of the License, or
* (at your option) any later version.
* This program 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 this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
*------------------------------------------------------------------------------
*/
package org.openmicroscopy.shoola.util.image.roi;
//Java imports
//Third-party libraries
//Application-internal dependencies
import org.openmicroscopy.shoola.util.math.geom2D.PlaneArea;
import org.openmicroscopy.shoola.util.mem.Copiable;
import org.openmicroscopy.shoola.util.mem.CopiableArray;
/**
* This <i>stateless</i> class extends {@link CopiableArray}.
* This class is the top container of the ROI selection algorithm.
* The {@link #set(Copiable, int)} and {@link #get(int)} methods defined
* by {@link CopiableArray} are overridden for type-safety.
* It also provides two utility methods to access directly the
* {@link PlaneArea elements} positioned at the bottom of the hierarchy.
* <p>
* A {@link ROI5D} object can be seen as a collection of
* <code>stack of ROIs across time</code> {@link ROI4D objects}.
* </p>
* <p>
* A {@link ROI5D} object is an array of {@link ROI4D} elements.
* In turn, a {@link ROI4D} object is an array of {@link ROI3D} elements.
* A {@link ROI3D} is an array of {@link PlaneArea} objects (leaf).
* </p>
*
* @author Jean-Marie Burel
* <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @author <br>Andrea Falconi
* <a href="mailto:a.falconi@dundee.ac.uk">
* a.falconi@dundee.ac.uk</a>
* @version 2.2
* <small>
* (<b>Internal version:</b> $Revision$ $Date$)
* </small>
* @since OME2.2
*/
public class ROI5D
extends CopiableArray
{
/**
* Creates a new instance.
*
* @param size The size of the array.
*/
public ROI5D(int size)
{
super(size);
}
/**
* Constructs a new {@link CopiableArray} of the specified size.
*
* @param size number of elements in the array.
* @return See above.
*/
protected CopiableArray makeNew(int size) { return new ROI5D(size); }
/**
* Overrides the {@link #set(Copiable, int)} method of
* {@link CopiableArray}. Check if the element is an instance of
* the excepted type i.e. {@link ROI4D}.
* Note that a {@link ROI4D} object cannot be set to <code>null</code>.
*/
public void set(Copiable roi4D, int channel)
{
if (!(roi4D instanceof ROI4D))
throw new IllegalArgumentException();
super.set(roi4D, channel);
}
/**
* Set an element of the correct type i.e. {@link ROI4D}
* at the specified channel.
*
* @param stackAcrossTimeROI The {@link ROI4D} objet to set.
* @param channel The specified channel.
* */
public void setChannel(ROI4D stackAcrossTimeROI, int channel)
{
set(stackAcrossTimeROI, channel);
}
/**
* Returns an {@link ROI4D} for the specified channel.
*
* @param channel The specified channel.
* @return See above.
*/
public ROI4D getChannel(int channel) { return (ROI4D) get(channel); }
/**
* Returns the {@link PlaneArea leaf} at the specified position in the
* hierarchy.
*
* @param z The specified z-section.
* @param t The speficied timepoint.
* @param channel The specified channel.
* @return See above.
*/
public PlaneArea getPlaneArea(int z, int t, int channel)
{
ROI4D stackAcrossTimeROI = (ROI4D) get(channel);
if (stackAcrossTimeROI == null) return null;
ROI3D stackROI = (ROI3D) stackAcrossTimeROI.get(t);
if (stackROI == null) return null;
return stackROI.getPlaneArea(z);
}
/**
* Replaces the {@link PlaneArea leaf} at the specified positioned with
* the specified element.
*
* @param pa The {@link PlaneArea} to set.
* @param z The specified z-section.
* @param t The speficied timepoint.
* @param channel The specified channel.
*/
public void setPlaneArea(PlaneArea pa, int z, int t, int channel)
{
ROI4D stackAcrossTimeROI = (ROI4D) get(channel);
if (stackAcrossTimeROI != null) {
ROI3D stackROI = (ROI3D) stackAcrossTimeROI.get(t);
if (stackROI != null)
stackROI.setPlaneArea(pa, z);
}
}
}