/*
*------------------------------------------------------------------------------
* Copyright (C) 2006-2015 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.env.rnd.roi;
import java.awt.Point;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.commons.collections.CollectionUtils;
import omero.gateway.Gateway;
import omero.gateway.SecurityContext;
import omero.gateway.exception.DataSourceException;
import org.openmicroscopy.shoola.util.roi.model.ROIShape;
import org.openmicroscopy.shoola.util.roi.model.util.Coord3D;
import omero.gateway.model.PixelsData;
/**
* Does some basic statistic analysis on a collection of {@link ROIShape}
* which all refer to the same pixels set.
*
* @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>
* @version 3.0
* @since OME3.0
*/
public class ROIAnalyser
{
/**
* Iterates an {@link ROIShape} over our pixels set.
* Observers compute the statistics as the iteration moves forward.
*/
private PointIterator runner;
/** The number of z-sections. */
private int sizeZ;
/** The number of time-points. */
private int sizeT;
/** The number of channels. */
private int sizeC;
/**
* Controls if the specified coordinates are valid.
* Returns <code>true</code> if the passed values are in the correct ranges,
* <code>false</code> otherwise.
*
* @param z The z coordinate. Must be in the range <code>[0, sizeZ)</code>.
* @param t The t coordinate. Must be in the range <code>[0, sizeT)</code>.
* @return See above.
*/
private boolean checkPlane(int z, int t)
{
if (z < 0 || sizeZ <= z) return false;
if (t < 0 || sizeT <= t) return false;
return true;
}
/**
* Checks if z and t match the given plane.
*
* @param z
* The z plane to check
* @param t
* The t plane to check
* @param plane
* The plane to check against
* @return See above
*/
private boolean matchesPlane(int z, int t, Coord3D plane) {
return (z == plane.getZSection() || plane.getZSection() < 0)
&& (t == plane.getTimePoint() || plane.getTimePoint() < 0);
}
/**
* Controls if the specified channel is valid.
* Returns <code>true</code> if the passed value is in the correct range,
* <code>false</code> otherwise.
*
* @param w The w coordinate. Must be in the range <code>[0, sizeW)</code>.
* @return See above.
*/
private boolean checkChannel(int w)
{
return !(w < 0 || sizeC <= w);
}
/**
* Creates a new instance to analyze the pixels set accessible through
* <code>source</code>.
*
* @param gateway Gateway to the raw data of the pixels set this iterator
* will work on. Mustn't be <code>null</code>.
* @param pixels The pixels to analyze.
*/
public ROIAnalyser(Gateway gateway, PixelsData pixels)
{
//Constructor will check source and dims.
runner = new PointIterator(gateway, pixels);
this.sizeZ = pixels.getSizeZ();
this.sizeT = pixels.getSizeT();
this.sizeC = pixels.getSizeC();
}
/**
* Computes an {@link ROIShapeStats} object for each {@link ROIShape}
* specified
*
* @param ctx The security context.
* @param shapes The shapes to analyze.
* @param channels Collection of selected channels.
* @param plane The plane to analyze the shapes for, can be <code>null</code>
* @return A map whose keys are the {@link ROIShape} objects specified
* and whose values are a map (keys: channel index, value
* the corresponding {@link AbstractROIShapeStats} objects computed by
* this method).
* @throws DataSourceException If an error occurs while retrieving plane
* data from the pixels source.
*/
public Map<ROIShape, Map<Integer, AbstractROIShapeStats>> analyze(
SecurityContext ctx, ROIShape[] shapes,
Collection<Integer> channels, Coord3D plane)
throws DataSourceException
{
if (shapes == null) throw new NullPointerException("No shapes.");
if (shapes.length == 0)
throw new IllegalArgumentException("No shapes defined.");
if (CollectionUtils.isEmpty(channels))
throw new IllegalArgumentException("No channels defined.");
Map<ROIShape, Map<Integer, AbstractROIShapeStats>>
r = new HashMap<ROIShape, Map<Integer, AbstractROIShapeStats>>();
AbstractROIShapeStats computer;
Map<Integer, AbstractROIShapeStats> stats;
Iterator<Integer> j;
int n = channels.size();
Integer w;
ROIShape shape;
boolean close = false;
for (int i = 0; i < shapes.length; ++i) {
shape = shapes[i];
close = i == shapes.length-1;
if (checkPlane(shape.getZ(), shape.getT())) {
stats = new HashMap<Integer, AbstractROIShapeStats>(n);
if (plane == null || matchesPlane(shape.getZ(), shape.getT(), plane)) {
j = channels.iterator();
List<Point> points = shape.getFigure().getPoints();
int count = 0;
boolean last = false;
while (j.hasNext()) {
w = j.next();
if (checkChannel(w.intValue())) {
computer = new ROIShapeStatsSimple();
runner.register(computer);
if (close) {
last = count == channels.size()-1;
}
runner.iterate(ctx, shape, points, w.intValue(), last);
runner.remove(computer);
stats.put(w, computer);
}
count++;
}
}
r.put(shape, stats);
}
}
return r;
}
}