/*
* org.openmicroscopy.shoola.env.rnd.roi.ROIShapeStats
*
*------------------------------------------------------------------------------
* 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.
*
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*/
package org.openmicroscopy.shoola.env.rnd.roi;
//Java imports
import java.awt.Point;
import java.util.LinkedHashMap;
import java.util.Map;
//Third-party libraries
//Application-internal dependencies
/**
* Stores the results of some basic statistic analysis run on a given
* 2D-selection within an XY-plane.
* Some of the fields are also used as accumulators during the computation.
*
*
* @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 ROIShapeStats extends AbstractROIShapeStats
{
//NOTE: fields have package visibility so they can easily be accessed
//during the computation. However, we only supply getters to outside
//clients b/c these fields are read-only after the computation is done.
/**
* Map whose keys are the point on the plane and the values are
* the corresponding pixels value.
*/
private Map<Point, Double> pixelsValue;
/**
* Returns the map storing the pixel coordinates and the corresponding
* pixel value.
*
* @return See above.
*/
public Map<Point, Double> getPixelsValue() { return pixelsValue; }
/**
* Calculates the mean and standard deviation for the current
* {@link ROIShapeStats}.
* @see PointIteratorObserver#onEndPlane(int, int, int, int)
*/
public void onEndPlane(int z, int c, int t, int pointsCount)
{
if (pointsCount <= 0) return;
mean = sum/pointsCount;
this.pointsCount = pointsCount;
if (0 < pointsCount-1) {
double sigmaSquare =
(sumOfSquares-sum*sum/pointsCount)/(pointsCount-1);
if (sigmaSquare > 0)
standardDeviation = Math.sqrt(sigmaSquare);
}
}
/**
* Updates the min, max, and sum values of the current
* {@link ROIShapeStats}.
* @see PointIteratorObserver#update(double, int, int, int, Point)
*/
public void update(double pixelValue, int z, int w, int t, Point loc)
{
min = Math.min(pixelValue,min);
max = Math.max(pixelValue,max);
sum += pixelValue;
sumOfSquares += pixelValue*pixelValue;
pixelsValue.put(loc, new Double(pixelValue));
}
/**
* Creates a new map to store the pixel values.
* @see PointIteratorObserver#onStartPlane(int, int, int, int)
*/
public void onStartPlane(int z, int w, int t, int pointsCount)
{
pixelsValue = new LinkedHashMap<Point, Double>(pointsCount);
}
/**
* Required by {@link PointIteratorObserver} interface, but no-operation
* implementation in our case.
* @see PointIteratorObserver#iterationStarted()
*/
public void iterationStarted() {}
/**
* Required by {@link PointIteratorObserver} interface, but no-operation
* implementation in our case.
* @see PointIteratorObserver#iterationFinished()
*/
public void iterationFinished() {}
}