/*
* org.openmicroscopy.shoola.util.roi.model.ROIMap
*
*------------------------------------------------------------------------------
* Copyright (C) 2006-2007 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.roi.model;
import java.util.ArrayList;
import java.util.List;
import java.util.TreeMap;
import org.openmicroscopy.shoola.util.roi.exception.NoSuchROIException;
import org.openmicroscopy.shoola.util.roi.exception.ROICreationException;
import org.openmicroscopy.shoola.util.roi.model.util.Coord3D;
/**
*
*
* @author Jean-Marie Burel
* <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @author Donald MacDonald
* <a href="mailto:donald@lifesci.dundee.ac.uk">donald@lifesci.dundee.ac.uk</a>
* @since OME3.0
*/
public class ROIMap
{
/** The class to map the Coord3D to the list of ROI on that Coord. */
private ROICoordMap roiCoordMap;
/** The class to map the ROI ID to a particular ROI. */
private ROIIDMap roiIDMap;
/**
* This is the general class to map ROI ID's to ROI, Coord3D to lists
* of ROIs and manage them.
*/
public ROIMap()
{
roiCoordMap = new ROICoordMap();
roiIDMap = new ROIIDMap();
}
/**
* Returns true if the roiIDMap contains the roi with id.
* @param id see above.
* @return see above.
*/
public boolean containsROI(long id)
{
return roiIDMap.containsKey(id);
}
/**
* Add an ROI with id to the maps. This maps the ROI to id in the ROIIDMap,
* and adds the ROIshapes of that ROI to the list of ROIShapes at Coord3D
* in the ROICoordMap.
* @param id The id of the ROI.
* @param roi The ROI to add.
*/
public void add(Long id, ROI roi)
{
roiIDMap.add(id, roi);
roiCoordMap.add(roi);
}
/**
* Get the ROIID map of the ROIIDMap class. This is used to
* @return see above.
*/
public TreeMap<Long, ROI> getROIMap()
{
return roiIDMap.getROIMap();
}
/**
* Return the roi with id
* @param id the id of the ROI you wish returned.
* @return see above.
* @throws NoSuchROIException
*/
public ROI getROI(long id)
throws NoSuchROIException
{
return roiIDMap.getROI(id);
}
/**
* Returns the ROIShape within ROI with id on plane coord.
*
* @param id the id of the ROI you wish returned.
* @param coord the plane on which the ROIShape resides.
* @return see above.
* @throws NoSuchROIException
*/
public ROIShape getShape(long id, Coord3D coord)
throws NoSuchROIException
{
return roiIDMap.getShape(id, coord);
}
/**
* Gets the Shapelist for the coord plane.
*
* @param coord see above.
* @return see above.
* @throws NoSuchROIException
*/
public ShapeList getShapeList(Coord3D coord)
throws NoSuchROIException
{
return roiCoordMap.getShapeList(coord);
}
/**
* Delete the ROI and all associated ROIShapes on the ROI.
* @param id The id of the ROI to delete.
* @throws NoSuchROIException
*/
public void deleteROI(long id) throws NoSuchROIException
{
ROI roi = roiIDMap.getROI(id);
roiCoordMap.deleteROI(roi);
roiIDMap.deleteROI(id);
}
/**
* Delete the ROIShape of ROI id on plane coord.
* @param id The id of the ROI containing the ROIShape to delete.
* @param coord The plane of the ROIShape to delete.
* @throws NoSuchROIException
*/
public void deleteShape(long id, Coord3D coord)
throws NoSuchROIException
{
roiCoordMap.deleteShape(id, coord);
roiIDMap.deleteShape(id, coord);
}
/**
* Add ROIShape to ROI id on plane coord. If an ROIShape already exists on
* the plane coord, replace it.
* @param id The id of the ROI containing the ROI Shape.
* @param coord The coord of the plane.
* @param shape The shape to add.
* @throws ROICreationException
* @throws NoSuchROIException
*/
public void addShape(long id, Coord3D coord, ROIShape shape)
throws ROICreationException,
NoSuchROIException
{
roiIDMap.addShape(id, coord, shape);
roiCoordMap.addShape(id, coord, shape);
}
/**
* Propagate the Shape identified on coord selectedShape contained within
* ROI id, from the start coord to the end coord, iterating through all
* planes. If an ROIShape exists on a plane between start and end it will
* be replaced by the new ROIShape.
* @param id The id of the ROI containing the ROI Shape.
* @param selectedShape The coord of the plane containing the shape to
* propagate.
* @param start The start coord to propagate from.
* @param end The end coord to propagate to.
* @throws ROICreationException
* @throws NoSuchROIException
*/
public List<ROIShape> propagateShape(long id, Coord3D selectedShape,
Coord3D start, Coord3D end)
throws ROICreationException,
NoSuchROIException
{
List<ROIShape> addedList = new ArrayList<ROIShape>();
if (!roiIDMap.containsKey(id))
throw new NoSuchROIException("No ROI with id : "+ id);
ROI roi = roiIDMap.getROI(id);
int mint = Math.min(start.getTimePoint(), end.getTimePoint());
int maxt = Math.max(start.getTimePoint(), end.getTimePoint());
int minz = Math.min(start.getZSection(), end.getZSection());
int maxz = Math.max(start.getZSection(), end.getZSection());
maxt = maxt+1;
maxz = maxz+1;
ROIShape shape = roi.getShape(selectedShape);
ROIShape newShape;
Coord3D newCoord;
//for(int c = start.c; c < end.c ; c++)
for (int t = mint; t < maxt ; t++)
for (int z = minz; z < maxz ; z++)
{
newCoord = new Coord3D(z, t);
if (selectedShape.equals(newCoord))
continue;
if (roi.containsShape(newCoord))
continue;
//deleteShape(id, newCoord);
newShape = new ROIShape(roi, newCoord, shape);
newShape.getFigure().setClientObject(true);
newShape.getFigure().setObjectDirty(true);
addShape(id, newCoord, newShape);
addedList.add(newShape);
}
return addedList;
}
/**
* Delete the Shape contained within ROI id, from the start coord to the
* end coord, iterating through all planes.
* If an ROIShape does not exist on the plane it will be skipped, it will
* not throw an exception.
* @param id The id of the ROI containing the ROI Shape.
* @param start The start coord to propagate from.
* @param end The end coord to propagate to.
* @throws NoSuchROIException
*/
public void deleteShape(long id, Coord3D start, Coord3D end)
throws NoSuchROIException
{
if(!roiIDMap.containsKey(id))
throw new NoSuchROIException("No ROI with id : "+ id);
ROI roi = roiIDMap.getROI(id);
int mint = Math.min(start.getTimePoint(), end.getTimePoint());
int maxt = Math.max(start.getTimePoint(), end.getTimePoint());
int minz = Math.min(start.getZSection(), end.getZSection());
int maxz = Math.max(start.getZSection(), end.getZSection());
maxt = maxt+1;
maxz = maxz+1;
Coord3D newCoord;
//for(int c = start.c; c < end.c ; c++)
for (int t = mint; t < maxt ; t++)
for (int z = minz; z < maxz ; z++)
{
newCoord = new Coord3D(z, t);
if (roi.containsShape(newCoord))
this.deleteShape(id, newCoord);
}
}
}