inflor.core.singlets.SingletsModel.java Source code

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Here is the source code for inflor.core.singlets.SingletsModel.java

Source

/*
 * ------------------------------------------------------------------------ Copyright 2016 by Aaron
 * Hart Email: Aaron.Hart@gmail.com
 *
 * This program is free software; you can redistribute it and/or modify it under the terms of the
 * GNU General Public License, Version 3, as published by the Free Software Foundation.
 *
 * 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, see <http://www.gnu.org/licenses>.
 * ---------------------------------------------------------------------
 *
 * Created on December 14, 2016 by Aaron Hart
 */
package inflor.core.singlets;

import java.util.ArrayList;
import java.util.BitSet;

import org.apache.commons.math3.stat.StatUtils;

public class SingletsModel {

    String[] initialColumns = null;
    ArrayList<String> areaColumnNames = null;
    ArrayList<String> heightColumnNames = null;
    ArrayList<String> widthColumnNames = null;

    double ratioThreshold;

    public SingletsModel(String[] columnNames) {
        initialColumns = columnNames;
        areaColumnNames = findColumns(columnNames, PuleProperties.AREA);
        heightColumnNames = findColumns(columnNames, PuleProperties.HEIGHT);
        widthColumnNames = findColumns(columnNames, PuleProperties.WIDTH);
    }

    public double[] buildModel(double[] area, double[] height) {
        final double[] ratioAH = ratio(area, height);
        final double minimum = StatUtils.percentile(ratioAH, 1);
        final double median = StatUtils.percentile(ratioAH, 50);
        ratioThreshold = (median - minimum) + median;
        return ratioAH;
    }

    public ArrayList<String> findColumns(String[] columnNames, PuleProperties type) {
        /**
         * Applies the regular expressions from the PulseProperties Enum.
         */
        final String[] expressions = type.regi();
        ArrayList<String> foundColumns = new ArrayList<String>();
        for (final String s : columnNames) {
            for (final String regex : expressions) {
                if (s.matches(regex)) {
                    foundColumns.add(s);
                }
            }
        }
        if (foundColumns.size() == 0) {
            foundColumns = new ArrayList<String>();
            foundColumns.add("None");
        }
        return foundColumns;
    }

    private double[] ratio(double[] a, double[] b) {
        final double[] ratio = new double[a.length];
        for (int i = 0; i < a.length; i++) {
            ratio[i] = a[i] / b[i];
        }
        return ratio;
    }

    public BitSet scoreModel(double[] ratio) {
        final BitSet mask = new BitSet(ratio.length);
        for (int i = 0; i < mask.size(); i++) {
            if (ratio[i] <= ratioThreshold) {
                mask.set(i);
            }
        }
        return mask;
    }
}