MergedSOMDataMapper.java

/*
 * Copyright 2004-2010 Information & Software Engineering Group (188/1)
 *                     Institute of Software Technology and Interactive Systems
 *                     Vienna University of Technology, Austria
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.ifs.tuwien.ac.at/dm/somtoolbox/license.html
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package at.tuwien.ifs.somtoolbox.apps;

import java.io.IOException;
import java.util.ArrayList;
import java.util.logging.Logger;

import com.martiansoftware.jsap.JSAPResult;
import com.martiansoftware.jsap.Parameter;

import at.tuwien.ifs.somtoolbox.SOMToolboxException;
import at.tuwien.ifs.somtoolbox.apps.config.OptionFactory;
import at.tuwien.ifs.somtoolbox.apps.helper.SOMMerger;
import at.tuwien.ifs.somtoolbox.data.InputData;
import at.tuwien.ifs.somtoolbox.data.InputDatum;
import at.tuwien.ifs.somtoolbox.data.SOMLibSparseInputData;
import at.tuwien.ifs.somtoolbox.input.SOMLibFormatInputReader;
import at.tuwien.ifs.somtoolbox.layers.GrowingLayer;
import at.tuwien.ifs.somtoolbox.layers.Unit;
import at.tuwien.ifs.somtoolbox.models.GrowingSOM;
import at.tuwien.ifs.somtoolbox.output.SOMLibMapOutputter;
import at.tuwien.ifs.somtoolbox.util.FileUtils;

/**
 * Maps inputs on a merged SOM. The merged SOM is trained from the weight vectors of two or more initial SOMs, e.g. by
 * using {@link SOMMerger}. The input vectors mapped to the initial SOMs will be put on the units in the merged SOM on
 * which the weight-vector initially representing them is merged.
 * 
 * @author Rudolf Mayer
 * @version $Id: MergedSOMDataMapper.java 3589 2010-05-21 10:42:01Z mayer $
 */
public class MergedSOMDataMapper {
    private static final Logger logger = Logger.getLogger("at.tuwien.ifs.somtoolbox");

    public static void main(String[] args) throws IOException, SOMToolboxException {
        new MergedSOMDataMapper(args);
    }

    public MergedSOMDataMapper(String[] args) throws IOException, SOMToolboxException {
        // register and parse all options
        // Labelling is an optional step, and requires input and template vectors
        JSAPResult config = OptionFactory.parseResults(args, new Parameter[] {
                OptionFactory.getOptWeightVectorFile(true), OptionFactory.getOptUnitDescriptionFile(true),
                OptionFactory.getOptInputVectorFile(false), OptionFactory.getOptNumberWinners(false),
                OptionFactory.getSwitchSkipDataWinnerMapping(), OptionFactory.getOptClassInformationFile(false),
                OptionFactory.getOptProperties(true), OptionFactory.getOptSOMLibMaps(true) });

        String unitDescFileName = config.getString("unitDescriptionFile");
        String weightVectorFileName = config.getString("weightVectorFile");
        String classInformationFile = config.getString("classInformationFile");
        String[] originalMaps = config.getStringArray("maps");

        boolean skipDataWinnerMapping = config.getBoolean("skipDataWinnerMapping", false);
        int numDataWinners = config.getInt("numberWinners");

        GrowingSOM som = null;
        /* restore SOM */
        try {
            som = new GrowingSOM(new SOMLibFormatInputReader(weightVectorFileName, unitDescFileName, null));
        } catch (Exception e) {
            logger.severe(e.getMessage() + " Aborting.");
            e.printStackTrace();
            System.exit(-1);
        }

        ArrayList<String> originalMappedUnitvectorNames = som.getLayer().getAllMappedDataNamesAsList();

        for (String originalMap2 : originalMaps) {
            String orignalMapPrefix = FileUtils.extractSOMLibInputPrefix(FileUtils.stripPathPrefix(originalMap2));
            GrowingSOM originalSOM = new GrowingSOM(new SOMLibFormatInputReader(null, originalMap2, null));
            final GrowingLayer originalMap = originalSOM.getLayer();
            for (Unit originalMapUnit : originalMap.getAllUnits()) {
                // find the unit where this weight vector is mapped to
                final String unitInputName = orignalMapPrefix + "_" + originalMapUnit.printCoordinates();
                final Unit unitForDatum = som.getLayer().getUnitForDatum(unitInputName);

                // replace the mapping of the unit's weight vector with the inputs it represents
                if (originalMapUnit.getNumberOfMappedInputs() > 0) {
                    for (String string : originalMapUnit.getMappedInputNames()) {
                        unitForDatum.addMappedInput(new InputDatum(string, new double[som.getLayer().getDim()]), false);
                    }
                }
                // remove this weight vector from the mapped unit files
                unitForDatum.removeMappedInput(unitInputName);
            }
        }

        ArrayList<String> finalMappedVectorNames = som.getLayer().getAllMappedDataNamesAsList();

        originalMappedUnitvectorNames.retainAll(finalMappedVectorNames);
        logger.info("New unit file contains " + finalMappedVectorNames.size() + " vectors.");
        if (originalMappedUnitvectorNames.size() > 0) {
            logger.warning("Could not replace " + originalMappedUnitvectorNames.size() + " unit weight vectors: "
                    + originalMappedUnitvectorNames);
        }

        final String outfilePrefix = FileUtils.extractSOMLibInputPrefix(FileUtils.stripPathPrefix(weightVectorFileName))
                + ".mergeMapped";
        try {
            SOMLibMapOutputter.writeUnitDescriptionFile(som, "", outfilePrefix, true);
        } catch (IOException e) { // TODO: create new exception type
            logger.severe("Could not open or write to output file " + outfilePrefix + ": " + e.getMessage());
            e.printStackTrace();
            System.exit(-1);
        }
        if (!skipDataWinnerMapping) {
            int numWinners = Math.min(numDataWinners, som.getLayer().getXSize() * som.getLayer().getYSize());
            try {
                InputData data = new SOMLibSparseInputData(config.getString("inputVectorFile"));
                SOMLibMapOutputter.writeDataWinnerMappingFile(som, data, numWinners, "", outfilePrefix, true);
            } catch (IOException e) {
                logger.severe("Could not open or write to output file " + outfilePrefix + ": " + e.getMessage());
                System.exit(-1);
            }
        } else {
            logger.info("Skipping writing data winner mapping file");
        }
        // just copy along the class information file, so we have a copy with the same name-prefix, eases SOMViewer
        // starting..
        if (classInformationFile != null) {
            String classInfoDestination = outfilePrefix + ".cls" + (classInformationFile.endsWith(".gz") ? ".gz" : "");
            FileUtils.copyFile(classInformationFile, classInfoDestination);
        }
    }
}