/*
* 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);
}
}