Source Code Cross Referenced for LibSVMLoader.java in  » Science » weka » weka » core » converters » Java Source Code / Java DocumentationJava Source Code and Java Documentation

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Java Source Code / Java Documentation » Science » weka » weka.core.converters 
Source Cross Referenced  Class Diagram Java Document (Java Doc) 


001:        /*
002:         *    This program is free software; you can redistribute it and/or modify
003:         *    it under the terms of the GNU General Public License as published by
004:         *    the Free Software Foundation; either version 2 of the License, or
005:         *    (at your option) any later version.
006:         *
007:         *    This program is distributed in the hope that it will be useful,
008:         *    but WITHOUT ANY WARRANTY; without even the implied warranty of
009:         *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
010:         *    GNU General Public License for more details.
011:         *
012:         *    You should have received a copy of the GNU General Public License
013:         *    along with this program; if not, write to the Free Software
014:         *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
015:         */
016:
017:        /*
018:         * LibSVMLoader.java
019:         * Copyright (C) 2006 University of Waikato, Hamilton, NZ
020:         *
021:         */
022:
023:        package weka.core.converters;
024:
025:        import weka.core.Attribute;
026:        import weka.core.FastVector;
027:        import weka.core.Instance;
028:        import weka.core.Instances;
029:
030:        import java.io.BufferedReader;
031:        import java.io.File;
032:        import java.io.IOException;
033:        import java.io.InputStream;
034:        import java.io.InputStreamReader;
035:        import java.io.Reader;
036:        import java.net.URL;
037:        import java.util.StringTokenizer;
038:        import java.util.Vector;
039:
040:        /**
041:         <!-- globalinfo-start -->
042:         * Reads a source that is in libsvm format.<br/>
043:         * <br/>
044:         * For more information about libsvm see:<br/>
045:         * <br/>
046:         * http://www.csie.ntu.edu.tw/~cjlin/libsvm/
047:         * <p/>
048:         <!-- globalinfo-end -->
049:         *
050:         * @author FracPete (fracpete at waikato dot ac dot nz)
051:         * @version $Revision: 1.3 $
052:         * @see Loader
053:         */
054:        public class LibSVMLoader extends AbstractFileLoader implements 
055:                BatchConverter, URLSourcedLoader {
056:
057:            /** for serialization */
058:            private static final long serialVersionUID = 4988360125354664417L;
059:
060:            /** the file extension */
061:            public static String FILE_EXTENSION = ".libsvm";
062:
063:            /** the url */
064:            protected String m_URL = "http://";
065:
066:            /** The reader for the source file. */
067:            protected transient Reader m_sourceReader = null;
068:
069:            /** the buffer of the rows read so far */
070:            protected Vector m_Buffer = null;
071:
072:            /**
073:             * Returns a string describing this Loader
074:             * 
075:             * @return 		a description of the Loader suitable for
076:             * 			displaying in the explorer/experimenter gui
077:             */
078:            public String globalInfo() {
079:                return "Reads a source that is in libsvm format.\n\n"
080:                        + "For more information about libsvm see:\n\n"
081:                        + "http://www.csie.ntu.edu.tw/~cjlin/libsvm/";
082:            }
083:
084:            /**
085:             * Get the file extension used for libsvm files
086:             *
087:             * @return 		the file extension
088:             */
089:            public String getFileExtension() {
090:                return FILE_EXTENSION;
091:            }
092:
093:            /**
094:             * Gets all the file extensions used for this type of file
095:             *
096:             * @return the file extensions
097:             */
098:            public String[] getFileExtensions() {
099:                return new String[] { getFileExtension() };
100:            }
101:
102:            /**
103:             * Returns a description of the file type.
104:             *
105:             * @return 		a short file description
106:             */
107:            public String getFileDescription() {
108:                return "libsvm data files";
109:            }
110:
111:            /**
112:             * Resets the Loader ready to read a new data set
113:             * 
114:             * @throws IOException 	if something goes wrong
115:             */
116:            public void reset() throws IOException {
117:                m_structure = null;
118:                m_Buffer = null;
119:
120:                setRetrieval(NONE);
121:
122:                if ((m_File != null) && (new File(m_File)).isFile()) {
123:                    setFile(new File(m_File));
124:                } else if ((m_URL != null) && !m_URL.equals("http://")) {
125:                    setURL(m_URL);
126:                }
127:            }
128:
129:            /**
130:             * Resets the Loader object and sets the source of the data set to be 
131:             * the supplied url.
132:             *
133:             * @param url 	the source url.
134:             * @throws IOException 	if an error occurs
135:             */
136:            public void setSource(URL url) throws IOException {
137:                m_structure = null;
138:                m_Buffer = null;
139:
140:                setRetrieval(NONE);
141:
142:                setSource(url.openStream());
143:
144:                m_URL = url.toString();
145:            }
146:
147:            /**
148:             * Set the url to load from
149:             *
150:             * @param url 		the url to load from
151:             * @throws IOException 		if the url can't be set.
152:             */
153:            public void setURL(String url) throws IOException {
154:                m_URL = url;
155:                setSource(new URL(url));
156:            }
157:
158:            /**
159:             * Return the current url
160:             *
161:             * @return the current url
162:             */
163:            public String retrieveURL() {
164:                return m_URL;
165:            }
166:
167:            /**
168:             * Resets the Loader object and sets the source of the data set to be 
169:             * the supplied InputStream.
170:             *
171:             * @param in 			the source InputStream.
172:             * @throws IOException 	if initialization of reader fails.
173:             */
174:            public void setSource(InputStream in) throws IOException {
175:                m_File = (new File(System.getProperty("user.dir")))
176:                        .getAbsolutePath();
177:                m_URL = "http://";
178:
179:                m_sourceReader = new BufferedReader(new InputStreamReader(in));
180:            }
181:
182:            /**
183:             * turns a libsvm row into a double array with the class as the last
184:             * entry
185:             * 
186:             * @param row		the row to turn into a double array
187:             * @return		the corresponding double array
188:             */
189:            protected double[] libsvmToArray(String row) {
190:                double[] result;
191:                StringTokenizer tok;
192:                int index;
193:                int max;
194:                String col;
195:                double value;
196:
197:                // determine max index
198:                max = 0;
199:                tok = new StringTokenizer(row, " \t");
200:                tok.nextToken(); // skip class
201:                while (tok.hasMoreTokens()) {
202:                    col = tok.nextToken();
203:                    index = Integer
204:                            .parseInt(col.substring(0, col.indexOf(":")));
205:                    if (index > max)
206:                        max = index;
207:                }
208:
209:                // read values into array
210:                tok = new StringTokenizer(row, " \t");
211:                result = new double[max + 1];
212:
213:                // 1. class
214:                result[result.length - 1] = Double.parseDouble(tok.nextToken());
215:
216:                // 2. attributes
217:                while (tok.hasMoreTokens()) {
218:                    col = tok.nextToken();
219:                    index = Integer
220:                            .parseInt(col.substring(0, col.indexOf(":")));
221:                    value = Double.parseDouble(col
222:                            .substring(col.indexOf(":") + 1));
223:                    result[index - 1] = value;
224:                }
225:
226:                return result;
227:            }
228:
229:            /**
230:             * determines the number of attributes, if the number of attributes in the
231:             * given row is greater than the current amount then this number will be
232:             * returned, otherwise the current number
233:             * 
234:             * @param row		row to determine the number of attributes from
235:             * @param num		the current number of attributes
236:             * @return 		the new number of attributes
237:             */
238:            protected int determineNumAttributes(String row, int num) {
239:                int result;
240:                int count;
241:
242:                result = num;
243:
244:                count = libsvmToArray(row).length;
245:                if (count > result)
246:                    result = count;
247:
248:                return result;
249:            }
250:
251:            /**
252:             * Determines and returns (if possible) the structure (internally the 
253:             * header) of the data set as an empty set of instances.
254:             *
255:             * @return 			the structure of the data set as an empty set 
256:             * 				of Instances
257:             * @throws IOException 	if an error occurs
258:             */
259:            public Instances getStructure() throws IOException {
260:                StringBuffer line;
261:                int cInt;
262:                char c;
263:                int numAtt;
264:                FastVector atts;
265:                int i;
266:                String relName;
267:
268:                if (m_sourceReader == null)
269:                    throw new IOException("No source has been specified");
270:
271:                if (m_structure == null) {
272:                    m_Buffer = new Vector();
273:                    try {
274:                        // determine number of attributes
275:                        numAtt = 0;
276:                        line = new StringBuffer();
277:                        while ((cInt = m_sourceReader.read()) != -1) {
278:                            c = (char) cInt;
279:                            if ((c == '\n') || (c == '\r')) {
280:                                if (line.length() > 0) {
281:                                    m_Buffer
282:                                            .add(libsvmToArray(line.toString()));
283:                                    numAtt = determineNumAttributes(line
284:                                            .toString(), numAtt);
285:                                }
286:                                line = new StringBuffer();
287:                            } else {
288:                                line.append(c);
289:                            }
290:                        }
291:
292:                        // last line?
293:                        if (line.length() != 0) {
294:                            m_Buffer.add(libsvmToArray(line.toString()));
295:                            numAtt = determineNumAttributes(line.toString(),
296:                                    numAtt);
297:                        }
298:
299:                        // generate header
300:                        atts = new FastVector(numAtt);
301:                        for (i = 0; i < numAtt - 1; i++)
302:                            atts.addElement(new Attribute("att_" + (i + 1)));
303:                        atts.addElement(new Attribute("class"));
304:
305:                        if (!m_URL.equals("http://"))
306:                            relName = m_URL;
307:                        else
308:                            relName = m_File;
309:
310:                        m_structure = new Instances(relName, atts, 0);
311:                        m_structure
312:                                .setClassIndex(m_structure.numAttributes() - 1);
313:                    } catch (Exception ex) {
314:                        throw new IOException(
315:                                "Unable to determine structure as libsvm.");
316:                    }
317:                }
318:
319:                return new Instances(m_structure, 0);
320:            }
321:
322:            /**
323:             * Return the full data set. If the structure hasn't yet been determined
324:             * by a call to getStructure then method should do so before processing
325:             * the rest of the data set.
326:             *
327:             * @return 			the structure of the data set as an empty 
328:             * 				set of Instances
329:             * @throws IOException 	if there is no source or parsing fails
330:             */
331:            public Instances getDataSet() throws IOException {
332:                Instances result;
333:                double[] sparse;
334:                double[] data;
335:                int i;
336:
337:                if (m_sourceReader == null)
338:                    throw new IOException("No source has been specified");
339:
340:                if (getRetrieval() == INCREMENTAL)
341:                    throw new IOException(
342:                            "Cannot mix getting Instances in both incremental and batch modes");
343:
344:                setRetrieval(BATCH);
345:                if (m_structure == null)
346:                    getStructure();
347:
348:                result = new Instances(m_structure, 0);
349:
350:                // create instances from buffered arrays
351:                for (i = 0; i < m_Buffer.size(); i++) {
352:                    sparse = (double[]) m_Buffer.get(i);
353:
354:                    if (sparse.length != m_structure.numAttributes()) {
355:                        data = new double[m_structure.numAttributes()];
356:                        // attributes
357:                        System.arraycopy(sparse, 0, data, 0, sparse.length - 1);
358:                        // class
359:                        data[data.length - 1] = sparse[sparse.length - 1];
360:                    } else {
361:                        data = sparse;
362:                    }
363:
364:                    result.add(new Instance(1, data));
365:                }
366:
367:                return result;
368:            }
369:
370:            /**
371:             * LibSVmLoader is unable to process a data set incrementally.
372:             *
373:             * @param structure 		ignored
374:             * @return 			never returns without throwing an exception
375:             * @throws IOException 	always. LibSVMLoader is unable to process a 
376:             * 				data set incrementally.
377:             */
378:            public Instance getNextInstance(Instances structure)
379:                    throws IOException {
380:                throw new IOException(
381:                        "LibSVMLoader can't read data sets incrementally.");
382:            }
383:
384:            /**
385:             * Main method.
386:             *
387:             * @param args 	should contain the name of an input file.
388:             */
389:            public static void main(String[] args) {
390:                runFileLoader(new LibSVMLoader(), args);
391:            }
392:        }
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