ijfx.core.overlay.DefaultPixelStatistics.java Source code

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Here is the source code for ijfx.core.overlay.DefaultPixelStatistics.java

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/*
This file is part of ImageJ FX.
    
ImageJ FX 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.
    
ImageJ FX 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 ImageJ FX.  If not, see <http://www.gnu.org/licenses/>. 
    
 Copyright 2015,2016 Cyril MONGIS, Michael Knop
       
 */
package ijfx.core.overlay;

import net.imagej.display.ImageDisplay;
import net.imagej.overlay.Overlay;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import org.scijava.Context;
import org.scijava.plugin.Parameter;

/**
 *
 * @author Pierre BONNEAU
 */
public class DefaultPixelStatistics implements PixelStatistics {

    @Parameter
    public OverlayStatService overlayStatService;

    private final int MEDIAN_PERCENTILE = 50;

    private final double mean;
    private final double max;
    private final double min;
    private final double standardDeviation;
    private final double variance;
    private final double median;
    private final long pixelCount;

    public DefaultPixelStatistics(ImageDisplay display, Overlay overlay, Context context) {

        context.inject(this);

        Double[] valueList = overlayStatService.getValueListFromImageDisplay(display, overlay);

        DescriptiveStatistics statistics = new DescriptiveStatistics(ArrayUtils.toPrimitive(valueList));

        this.mean = statistics.getMean();
        this.max = statistics.getMax();
        this.min = statistics.getMin();
        this.standardDeviation = statistics.getStandardDeviation();
        this.variance = statistics.getVariance();
        this.median = statistics.getPercentile(MEDIAN_PERCENTILE);
        this.pixelCount = valueList.length;
    }

    @Override
    public double getMean() {
        return this.mean;
    }

    @Override
    public double getMax() {
        return this.max;
    }

    @Override
    public double getMin() {
        return this.min;
    }

    @Override
    public double getStandardDeviation() {
        return this.standardDeviation;
    }

    @Override
    public double getVariance() {
        return this.variance;
    }

    @Override
    public double getMedian() {
        return this.median;
    }

    @Override
    public long getPixelCount() {
        return this.pixelCount;
    }

    public String toString() {
        return "\n Pixel Statistics : " + "\n\t Mean : " + this.mean + "\n\t Max : " + this.max + "\n\t Min : "
                + this.min + "\n\t SD : " + this.standardDeviation + "\n\t Variance : " + this.variance
                + "\n\t Median : " + this.median + "\n\t PixelCount : " + this.pixelCount;
    }
}