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• VectorSOM.java

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com.actelion.research.calc.VectorSOM Maven / Gradle / Ivy

/*
 * Copyright (c) 1997 - 2016
 * Actelion Pharmaceuticals Ltd.
 * Gewerbestrasse 16
 * CH-4123 Allschwil, Switzerland
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 3. Neither the name of the the copyright holder nor the
 *    names of its contributors may be used to endorse or promote products
 *    derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * @author Thomas Sander
 */

package com.actelion.research.calc;

import com.actelion.research.util.DoubleFormat;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.util.Random;

public class VectorSOM extends SelfOrganizedMap {
	private double[]	mMeanParameter,mStandardDeviation;
	private int			mParameterCount;

	public VectorSOM() {}
			// constructor to be used if SOM interna are read from a SOM file with read()

	public VectorSOM(int nx, int ny, int mode) {
		super(nx, ny, mode);
		}

	public void setParameterCount(int parameterCount) {
	    	// needs to be called before organize()
		mParameterCount = parameterCount;
		}

	@Override
	protected void initializeNormalization() {
			// must be overridden if input vectors aren't double arrays
		startProgress("Calculating mean parameters...", 0, mController.getInputVectorCount());

			// don't normalize input vectors if they are random vectors
		if (mController.getInputVectorCount() == -1) {
			mMeanParameter = new double[mParameterCount];
			mStandardDeviation = new double[mParameterCount];
			for (int i=0; i");
		writer.newLine();

		writer.write("");
		writer.newLine();
		}

	@Override
	public void read(BufferedReader reader) throws Exception {
		super.read(reader);

		String theLine = reader.readLine();
		boolean error = !theLine.startsWith("