content: /*
   *    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., 675 Mass Ave, Cambridge, MA 02139, USA.
   */
  
  /*
   * MatlabLoader.java
   * Copyright (C) 2009 University of Waikato, Hamilton, NZ
   *
   */
  
  package weka.core.converters;
  
  import weka.core.Attribute;
  import weka.core.Instance;
  import weka.core.DenseInstance;
  import weka.core.Instances;
  import weka.core.RevisionUtils;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.InputStreamReader;
  import java.io.Reader;
  import java.net.URL;
  import java.util.Vector;
  import java.util.ArrayList;
  
  /**
   <!-- globalinfo-start -->
   * Reads a Matlab file containing a single matrix in ASCII format.
   * <p/>
   <!-- globalinfo-end -->
   *
   * @author FracPete (fracpete at waikato dot ac dot nz)
   * @version $Revision: 5987 $
   * @see Loader
   */
  public class MatlabLoader 
    extends AbstractFileLoader 
    implements BatchConverter, URLSourcedLoader {
  
    /** for serialization. */
    private static final long serialVersionUID = -8861142318612875251L;
  
    /** the file extension. */
    public static String FILE_EXTENSION = ".m";
  
    /** the url. */
    protected String m_URL = "http://";
  
    /** The reader for the source file. */
    protected transient Reader m_sourceReader = null;
  
    /** the buffer of the rows read so far. */
    protected Vector<Vector<Double>> m_Buffer = null;
    
    /**
     * Returns a string describing this Loader.
     * 
     * @return 		a description of the Loader suitable for
     * 			displaying in the explorer/experimenter gui
     */
    public String globalInfo() {
      return "Reads a Matlab file containing a single matrix in ASCII format.";
    }
  
    /**
     * Get the file extension used for libsvm files.
     *
     * @return 		the file extension
     */
    public String getFileExtension() {
      return FILE_EXTENSION;
    }
  
    /**
     * Gets all the file extensions used for this type of file.
     *
     * @return the file extensions
     */
    public String[] getFileExtensions() {
      return new String[]{getFileExtension()};
    }
  
    /**
     * Returns a description of the file type.
     *
     * @return 		a short file description
     */
    public String getFileDescription() {
      return "Matlab ASCII files";
    }
  
    /**
     * Resets the Loader ready to read a new data set.
     * 
     * @throws IOException 	if something goes wrong
     */
    public void reset() throws IOException {
      m_structure = null;
      m_Buffer    = null;
      
      setRetrieval(NONE);
      
      if ((m_File != null) && (new File(m_File)).isFile()) {
        setFile(new File(m_File));
      }
      else if ((m_URL != null) && !m_URL.equals("http://")) {
        setURL(m_URL);
      }
    }
  
    /**
     * Resets the Loader object and sets the source of the data set to be 
     * the supplied url.
     *
     * @param url 	the source url.
     * @throws IOException 	if an error occurs
     */
    public void setSource(URL url) throws IOException {
      m_structure = null;
      m_Buffer    = null;
      
      setRetrieval(NONE);
      
      setSource(url.openStream());
  
      m_URL = url.toString();
    }
  
    /**
     * Set the url to load from.
     *
     * @param url 		the url to load from
     * @throws IOException 		if the url can't be set.
     */
    public void setURL(String url) throws IOException {
      m_URL = url;
      setSource(new URL(url));
    }
  
    /**
     * Return the current url.
     *
     * @return the current url
     */
    public String retrieveURL() {
      return m_URL;
    }
  
    /**
     * Resets the Loader object and sets the source of the data set to be 
     * the supplied InputStream.
     *
     * @param in 			the source InputStream.
     * @throws IOException 	if initialization of reader fails.
     */
    public void setSource(InputStream in) throws IOException {
      m_File = (new File(System.getProperty("user.dir"))).getAbsolutePath();
      m_URL  = "http://";
  
      m_sourceReader = new BufferedReader(new InputStreamReader(in));
    }
    
    /**
     * Determines and returns (if possible) the structure (internally the 
     * header) of the data set as an empty set of instances.
     *
     * @return 			the structure of the data set as an empty set 
     * 				of Instances
     * @throws IOException 	if an error occurs
     */
    public Instances getStructure() throws IOException {
      int			numAtt;
      ArrayList<Attribute>		atts;
      int			i;
      String		relName;
      Vector<Double>	row;
      int			c;
      char		chr;
      StringBuffer	str;
      boolean		isComment;
      
      if (m_sourceReader == null)
        throw new IOException("No source has been specified");
  
      if (m_structure == null) {
        numAtt    = 0;
        m_Buffer  = new Vector<Vector<Double>>();
        row       = new Vector<Double>();
        str       = new StringBuffer();
        isComment = false;
        m_Buffer.add(row);
        try {
  	// determine number of attributes
  	while ((c = m_sourceReader.read()) != -1) {
  	  chr = (char) c;
  	  
  	  // comment found?
  	  if (chr == '%')
  	    isComment = true;
  	  
  	  // end of line reached
  	  if ((chr == '\n') || (chr == '\r')) {
  	    isComment = false;
  	    if (str.length() > 0)
  	      row.add(new Double(str.toString()));
  	    if (numAtt == 0)
  	      numAtt = row.size();
  	    if (row.size() > 0) {
  	      row = new Vector<Double>();
  	      m_Buffer.add(row);
  	    }
  	    str = new StringBuffer();
  	    continue;
  	  }
  
  	  // skip till end of comment line
  	  if (isComment)
  	    continue;
  	  
  	  // separator found?
  	  if ((chr == '\t') || (chr == ' ')) {
  	    if (str.length() > 0) {
  	      row.add(new Double(str.toString()));
  	      str = new StringBuffer();
  	    }
  	  }
  	  else {
  	    str.append(chr);
  	  }
  	}
  	
  	// last number?
  	if (str.length() > 0)
  	  row.add(new Double(str.toString()));
  	
  	// generate header
  	atts = new ArrayList<Attribute>(numAtt);
  	for (i = 0; i < numAtt; i++)
  	  atts.add(new Attribute("att_" + (i+1)));
  	
  	if (!m_URL.equals("http://"))
  	  relName = m_URL;
  	else
  	  relName = m_File;
  	
  	m_structure = new Instances(relName, atts, 0);
  	m_structure.setClassIndex(m_structure.numAttributes() - 1);
        }
        catch (Exception ex) {
  	ex.printStackTrace();
  	throw new IOException("Unable to determine structure as Matlab ASCII file: " + ex);
        }
      }
  
      return new Instances(m_structure, 0);
    }
    
    /**
     * Return the full data set. If the structure hasn't yet been determined
     * by a call to getStructure then method should do so before processing
     * the rest of the data set.
     *
     * @return 			the structure of the data set as an empty 
     * 				set of Instances
     * @throws IOException 	if there is no source or parsing fails
     */
    public Instances getDataSet() throws IOException {
      Instances 		result;
      Vector<Double>	row;
      double[]		data;
      int			i;
      int			n;
  
      if (m_sourceReader == null)
        throw new IOException("No source has been specified");
      
      if (getRetrieval() == INCREMENTAL)
        throw new IOException("Cannot mix getting Instances in both incremental and batch modes");
  
      setRetrieval(BATCH);
      if (m_structure == null)
        getStructure();
  
      result = new Instances(m_structure, 0);
  
      // create instances from buffered data
      for (i = 0; i < m_Buffer.size(); i++) {
        row = m_Buffer.get(i);
        if (row.size() == 0)
  	continue;
        data = new double[row.size()];
        for (n = 0; n < row.size(); n++)
  	data[n] = row.get(n);
        
        result.add(new DenseInstance(1.0, data));
      }
  
      // close the stream
      try {
        m_sourceReader.close();
      }
      catch (Exception ex) {
        // ignored
      }
      
      return result;
    }
  
    /**
     * MatlabLoader is unable to process a data set incrementally.
     *
     * @param structure 		ignored
     * @return 			never returns without throwing an exception
     * @throws IOException 	always. MatlabLoader is unable to process a 
     * 				data set incrementally.
     */
    public Instance getNextInstance(Instances structure) throws IOException {
      throw new IOException("MatlabLoader can't read data sets incrementally.");
    }
    
    /**
     * Returns the revision string.
     * 
     * @return		the revision
     */
    public String getRevision() {
      return RevisionUtils.extract("$Revision: 5987 $");
    }
  
    /**
     * Main method.
     *
     * @param args 	should contain the name of an input file.
     */
    public static void main(String[] args) {
      runFileLoader(new MatlabLoader(), args);
    }
  }
  