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The Waikato Environment for Knowledge Analysis (WEKA), a machine
learning workbench. This version represents the developer version, the
"bleeding edge" of development, you could say. New functionality gets added
to this version.
The newest version!
/*
* 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 3 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, see
*
* For more information about libsvm see:
*
* http://www.csie.ntu.edu.tw/~cjlin/libsvm/
*
*
*
* @author FracPete (fracpete at waikato dot ac dot nz)
* @version $Revision: 11360 $
* @see Loader
*/
public class LibSVMLoader
extends AbstractFileLoader
implements BatchConverter, URLSourcedLoader {
/** for serialization. */
private static final long serialVersionUID = 4988360125354664417L;
/** the file extension. */
public static String FILE_EXTENSION = ".libsvm";
/** 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 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 source that is in libsvm format.\n\n"
+ "For more information about libsvm see:\n\n"
+ "http://www.csie.ntu.edu.tw/~cjlin/libsvm/";
}
/**
* Get the file extension used for libsvm files.
*
* @return the file extension
*/
@Override
public String getFileExtension() {
return FILE_EXTENSION;
}
/**
* Gets all the file extensions used for this type of file.
*
* @return the file extensions
*/
@Override
public String[] getFileExtensions() {
return new String[] { getFileExtension() };
}
/**
* Returns a description of the file type.
*
* @return a short file description
*/
@Override
public String getFileDescription() {
return "libsvm data files";
}
/**
* Resets the Loader ready to read a new data set.
*
* @throws IOException if something goes wrong
*/
@Override
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.
*/
@Override
public void setURL(String url) throws IOException {
m_URL = url;
setSource(new URL(url));
}
/**
* Return the current url.
*
* @return the current url
*/
@Override
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.
*/
@Override
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));
}
/**
* turns a libsvm row into a double array with the class as the last entry.
*
* @param row the row to turn into a double array
* @return the corresponding double array
*/
protected double[] libsvmToArray(String row) {
double[] result;
StringTokenizer tok;
int index;
int max;
String col;
double value;
// determine max index
max = 0;
tok = new StringTokenizer(row, " \t");
tok.nextToken(); // skip class
while (tok.hasMoreTokens()) {
col = tok.nextToken();
index = Integer.parseInt(col.substring(0, col.indexOf(":")));
if (index > max) {
max = index;
}
}
// read values into array
tok = new StringTokenizer(row, " \t");
result = new double[max + 1];
// 1. class
result[result.length - 1] = Double.parseDouble(tok.nextToken());
// 2. attributes
while (tok.hasMoreTokens()) {
col = tok.nextToken();
index = Integer.parseInt(col.substring(0, col.indexOf(":")));
value = Double.parseDouble(col.substring(col.indexOf(":") + 1));
result[index - 1] = value;
}
return result;
}
/**
* determines the number of attributes, if the number of attributes in the
* given row is greater than the current amount then this number will be
* returned, otherwise the current number.
*
* @param row row to determine the number of attributes from
* @param num the current number of attributes
* @return the new number of attributes
*/
protected int determineNumAttributes(String row, int num) {
int result;
int count;
result = num;
count = libsvmToArray(row).length;
if (count > result) {
result = count;
}
return result;
}
/**
* 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
*/
@Override
public Instances getStructure() throws IOException {
String line;
int cInt;
char c;
int numAtt;
ArrayList atts;
int i;
String relName;
if (m_sourceReader == null) {
throw new IOException("No source has been specified");
}
if (m_structure == null) {
m_Buffer = new Vector();
try {
// determine number of attributes
numAtt = 0;
int len = 1024 * 1024 * 8; // 8 MB
char[] cbuf = new char[len];
int iter = 0;
String linesplitter = null;
String[] lines;
String oldLine = null;
String read = null;
while ((cInt = m_sourceReader.read(cbuf, 0, len)) != -1) {
read = String.valueOf(cbuf, 0, cInt);
if (oldLine != null) {
read = oldLine + read;
}
if (linesplitter == null) {
if (read.contains("\r\n")) {
linesplitter = "\r\n";
} else if (read.contains("\n")) {
linesplitter = "\n";
}
}
if (linesplitter != null) {
lines = read.split(linesplitter, -1);
} else {
lines = new String[] { read };
}
for (int j = 0; j < lines.length - 1; j++) {
line = lines[j];
m_Buffer.add(libsvmToArray(line));
numAtt = determineNumAttributes(line, numAtt);
}
oldLine = lines[lines.length - 1];
}
// last line?
if (oldLine != null && oldLine.length() != 0) {
m_Buffer.add(libsvmToArray(oldLine));
numAtt = determineNumAttributes(oldLine, numAtt);
}
// generate header
atts = new ArrayList(numAtt);
for (i = 0; i < numAtt - 1; i++) {
atts.add(new Attribute("att_" + (i + 1)));
}
atts.add(new Attribute("class"));
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 libsvm: " + 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
*/
@Override
public Instances getDataSet() throws IOException {
Instances result;
double[] sparse;
double[] data;
int i;
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 arrays
for (i = 0; i < m_Buffer.size(); i++) {
sparse = m_Buffer.get(i);
if (sparse.length != m_structure.numAttributes()) {
data = new double[m_structure.numAttributes()];
// attributes
System.arraycopy(sparse, 0, data, 0, sparse.length - 1);
// class
data[data.length - 1] = sparse[sparse.length - 1];
}
else {
data = sparse;
}
result.add(new SparseInstance(1, data));
}
try {
// close the stream
m_sourceReader.close();
} catch (Exception ex) {
}
return result;
}
/**
* LibSVmLoader is unable to process a data set incrementally.
*
* @param structure ignored
* @return never returns without throwing an exception
* @throws IOException always. LibSVMLoader is unable to process a data set
* incrementally.
*/
@Override
public Instance getNextInstance(Instances structure) throws IOException {
throw new IOException("LibSVMLoader can't read data sets incrementally.");
}
/**
* Returns the revision string.
*
* @return the revision
*/
@Override
public String getRevision() {
return RevisionUtils.extract("$Revision: 11360 $");
}
/**
* Main method.
*
* @param args should contain the name of an input file.
*/
public static void main(String[] args) {
runFileLoader(new LibSVMLoader(), args);
}
}