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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.
/*
* 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 hasMoreElements,
* nextElement). Before the data can be read again, one has to
* call the reset method. The data source can also be initialized
* with an Instances object, in order to provide a unified interface to files
* and already loaded datasets.
*
* @author FracPete (fracpete at waikato dot ac dot nz)
* @version $Revision: 14285 $
* @see #hasMoreElements(Instances)
* @see #nextElement(Instances)
* @see #reset()
* @see DataSink
*/
public static class DataSource implements Serializable, RevisionHandler {
/** for serialization. */
private static final long serialVersionUID = -613122395928757332L;
/** the file to load. */
protected File m_File;
/** the URL to load. */
protected URL m_URL;
/** the loader. */
protected Loader m_Loader;
/** whether the loader is incremental. */
protected boolean m_Incremental;
/** the instance counter for the batch case. */
protected int m_BatchCounter;
/** the last internally read instance. */
protected Instance m_IncrementalBuffer;
/** the batch buffer. */
protected Instances m_BatchBuffer;
/**
* Tries to load the data from the file. Can be either a regular file or a
* web location (http://, https://, ftp:// or file://).
*
* @param location the name of the file to load
* @throws Exception if initialization fails
*/
public DataSource(String location) throws Exception {
super();
// file or URL?
if (location.startsWith("http://") || location.startsWith("https://")
|| location.startsWith("ftp://") || location.startsWith("file://")) {
m_URL = new URL(location);
} else {
m_File = new File(location);
}
// quick check: is it ARFF?
if (isArff(location)) {
m_Loader = new ArffLoader();
} else {
if (m_File != null) {
m_Loader = ConverterUtils.getLoaderForFile(location);
} else {
m_Loader = ConverterUtils.getURLLoaderForFile(location);
}
// do we have a converter?
if (m_Loader == null) {
throw new IllegalArgumentException(
"No suitable converter found for '" + location + "'!");
}
}
// incremental loader?
m_Incremental = (m_Loader instanceof IncrementalConverter);
reset();
}
/**
* Initializes the datasource with the given dataset.
*
* @param inst the dataset to use
*/
public DataSource(Instances inst) {
super();
m_BatchBuffer = inst;
m_Loader = null;
m_File = null;
m_URL = null;
m_Incremental = false;
}
/**
* Initializes the datasource with the given Loader.
*
* @param loader the Loader to use
*/
public DataSource(Loader loader) {
super();
m_BatchBuffer = null;
m_Loader = loader;
m_File = null;
m_URL = null;
m_Incremental = (m_Loader instanceof IncrementalConverter);
initBatchBuffer();
}
/**
* Initializes the datasource with the given input stream. This stream is
* always interpreted as ARFF.
*
* @param stream the stream to use
*/
public DataSource(InputStream stream) {
super();
m_BatchBuffer = null;
m_Loader = new ArffLoader();
try {
m_Loader.setSource(stream);
} catch (Exception e) {
m_Loader = null;
}
m_File = null;
m_URL = null;
m_Incremental = (m_Loader instanceof IncrementalConverter);
initBatchBuffer();
}
/**
* initializes the batch buffer if necessary, i.e., for non-incremental
* loaders.
*/
protected void initBatchBuffer() {
try {
if (!isIncremental()) {
m_BatchBuffer = m_Loader.getDataSet();
} else {
m_BatchBuffer = null;
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* returns whether the extension of the location is likely to be of ARFF
* format, i.e., ending in ".arff" or ".arff.gz" (case-insensitive).
*
* @param location the file location to check
* @return true if the location seems to be of ARFF format
*/
public static boolean isArff(String location) {
if (location.toLowerCase().endsWith(
ArffLoader.FILE_EXTENSION.toLowerCase())
|| location.toLowerCase().endsWith(
ArffLoader.FILE_EXTENSION_COMPRESSED.toLowerCase())) {
return true;
} else {
return false;
}
}
/**
* returns whether the loader is an incremental one.
*
* @return true if the loader is a true incremental one
*/
public boolean isIncremental() {
return m_Incremental;
}
/**
* returns the determined loader, null if the DataSource was initialized
* with data alone and not a file/URL.
*
* @return the loader used for retrieving the data
*/
public Loader getLoader() {
return m_Loader;
}
/**
* returns the full dataset, can be null in case of an error.
*
* @return the full dataset
* @throws Exception if resetting of loader fails
*/
public Instances getDataSet() throws Exception {
Instances result;
result = null;
// reset the loader
reset();
try {
if (m_BatchBuffer == null) {
result = m_Loader.getDataSet();
} else {
result = m_BatchBuffer;
}
} catch (Exception e) {
e.printStackTrace();
result = null;
}
return result;
}
/**
* returns the full dataset with the specified class index set, can be null
* in case of an error.
*
* @param classIndex the class index for the dataset
* @return the full dataset
* @throws Exception if resetting of loader fails
*/
public Instances getDataSet(int classIndex) throws Exception {
Instances result;
result = getDataSet();
if (result != null) {
result.setClassIndex(classIndex);
}
return result;
}
/**
* resets the loader.
*
* @throws Exception if resetting fails
*/
public void reset() throws Exception {
if (m_File != null) {
((AbstractFileLoader) m_Loader).setFile(m_File);
} else if (m_URL != null) {
((URLSourcedLoader) m_Loader).setURL(m_URL.toString());
} else if (m_Loader != null) {
m_Loader.reset();
}
m_BatchCounter = 0;
m_IncrementalBuffer = null;
if (m_Loader != null) {
if (!isIncremental()) {
m_BatchBuffer = m_Loader.getDataSet();
} else {
m_BatchBuffer = null;
}
}
}
/**
* returns the structure of the data.
*
* @return the structure of the data
* @throws Exception if something goes wrong
*/
public Instances getStructure() throws Exception {
if (m_BatchBuffer == null) {
return m_Loader.getStructure();
} else {
return new Instances(m_BatchBuffer, 0);
}
}
/**
* returns the structure of the data, with the defined class index.
*
* @param classIndex the class index for the dataset
* @return the structure of the data
* @throws Exception if something goes wrong
*/
public Instances getStructure(int classIndex) throws Exception {
Instances result;
result = getStructure();
if (result != null) {
result.setClassIndex(classIndex);
}
return result;
}
/**
* returns whether there are more Instance objects in the data.
*
* @param structure the structure of the dataset
* @return true if there are more Instance objects available
* @see #nextElement(Instances)
*/
public boolean hasMoreElements(Instances structure) {
boolean result;
result = false;
if (isIncremental()) {
// user still hasn't collected the last one?
if (m_IncrementalBuffer != null) {
result = true;
} else {
try {
m_IncrementalBuffer = m_Loader.getNextInstance(structure);
result = (m_IncrementalBuffer != null);
} catch (Exception e) {
e.printStackTrace();
result = false;
}
}
} else {
result = (m_BatchCounter < m_BatchBuffer.numInstances());
}
return result;
}
/**
* returns the next element and sets the specified dataset, null if none
* available.
*
* @param dataset the dataset to set for the instance
* @return the next Instance
*/
public Instance nextElement(Instances dataset) {
Instance result;
result = null;
if (isIncremental()) {
// is there still an instance in the buffer?
if (m_IncrementalBuffer != null) {
result = m_IncrementalBuffer;
m_IncrementalBuffer = null;
} else {
try {
result = m_Loader.getNextInstance(dataset);
} catch (Exception e) {
e.printStackTrace();
result = null;
}
}
} else {
if (m_BatchCounter < m_BatchBuffer.numInstances()) {
result = m_BatchBuffer.instance(m_BatchCounter);
m_BatchCounter++;
}
}
if (result != null) {
result.setDataset(dataset);
}
return result;
}
/**
* convencience method for loading a dataset in batch mode.
*
* @param location the dataset to load
* @return the dataset
* @throws Exception if loading fails
*/
public static Instances read(String location) throws Exception {
DataSource source;
Instances result;
source = new DataSource(location);
result = source.getDataSet();
return result;
}
/**
* convencience method for loading a dataset in batch mode from a stream.
*
* @param stream the stream to load the dataset from
* @return the dataset
* @throws Exception if loading fails
*/
public static Instances read(InputStream stream) throws Exception {
DataSource source;
Instances result;
source = new DataSource(stream);
result = source.getDataSet();
return result;
}
/**
* convencience method for loading a dataset in batch mode.
*
* @param loader the loader to get the dataset from
* @return the dataset
* @throws Exception if loading fails
*/
public static Instances read(Loader loader) throws Exception {
DataSource source;
Instances result;
source = new DataSource(loader);
result = source.getDataSet();
return result;
}
/**
* for testing only - takes a data file as input.
*
* @param args the commandline arguments
* @throws Exception if something goes wrong
*/
public static void main(String[] args) throws Exception {
if (args.length != 1) {
System.out.println("\nUsage: " + DataSource.class.getName()
+ " \n");
System.exit(1);
}
DataSource loader = new DataSource(args[0]);
System.out.println("Incremental? " + loader.isIncremental());
System.out.println("Loader: " + loader.getLoader().getClass().getName());
System.out.println("Data:\n");
Instances structure = loader.getStructure();
System.out.println(structure);
while (loader.hasMoreElements(structure)) {
System.out.println(loader.nextElement(structure));
}
Instances inst = loader.getDataSet();
loader = new DataSource(inst);
System.out.println("\n\nProxy-Data:\n");
System.out.println(loader.getStructure());
while (loader.hasMoreElements(structure)) {
System.out.println(loader.nextElement(inst));
}
}
/**
* Returns the revision string.
*
* @return the revision
*/
@Override
public String getRevision() {
return RevisionUtils.extract("$Revision: 14285 $");
}
}
/**
* Helper class for saving data to files. Via the ConverterUtils class it
* determines which converter to use for saving the data. It is the logical
* counterpart to DataSource.
*
* @author FracPete (fracpete at waikato dot ac dot nz)
* @version $Revision: 14285 $
* @see DataSource
*/
public static class DataSink implements Serializable, RevisionHandler {
/** for serialization. */
private static final long serialVersionUID = -1504966891136411204L;
/** the saver to use for storing the data. */
protected Saver m_Saver = null;
/** the stream to store the data in (always in ARFF format). */
protected OutputStream m_Stream = null;
/**
* initializes the sink to save the data to the given file.
*
* @param filename the file to save data to
* @throws Exception if set of saver fails
*/
public DataSink(String filename) throws Exception {
m_Stream = null;
if (DataSource.isArff(filename)) {
m_Saver = new ArffSaver();
} else {
m_Saver = getSaverForFile(filename);
}
((AbstractFileSaver) m_Saver).setFile(new File(filename));
}
/**
* initializes the sink to save the data to the given Saver (expected to be
* fully configured).
*
* @param saver the saver to use for saving the data
*/
public DataSink(Saver saver) {
m_Saver = saver;
m_Stream = null;
}
/**
* initializes the sink to save the data in the stream (always in ARFF
* format).
*
* @param stream the output stream to use for storing the data in ARFF
* format
*/
public DataSink(OutputStream stream) {
m_Saver = null;
m_Stream = stream;
}
/**
* writes the given data either via the saver or to the defined output
* stream (depending on the constructor). In case of the stream, the stream
* is only flushed, but not closed.
*
* @param data the data to save
* @throws Exception if saving fails
*/
public void write(Instances data) throws Exception {
if (m_Saver != null) {
m_Saver.setInstances(data);
m_Saver.writeBatch();
} else {
m_Stream.write(data.toString().getBytes());
m_Stream.flush();
}
}
/**
* writes the data to the given file.
*
* @param filename the file to write the data to
* @param data the data to store
* @throws Exception if writing fails
*/
public static void write(String filename, Instances data) throws Exception {
DataSink sink;
sink = new DataSink(filename);
sink.write(data);
}
/**
* writes the data via the given saver.
*
* @param saver the saver to use for writing the data
* @param data the data to store
* @throws Exception if writing fails
*/
public static void write(Saver saver, Instances data) throws Exception {
DataSink sink;
sink = new DataSink(saver);
sink.write(data);
}
/**
* writes the data to the given stream (always in ARFF format).
*
* @param stream the stream to write the data to (ARFF format)
* @param data the data to store
* @throws Exception if writing fails
*/
public static void write(OutputStream stream, Instances data)
throws Exception {
DataSink sink;
sink = new DataSink(stream);
sink.write(data);
}
/**
* for testing only - takes a data file as input and a data file for the
* output.
*
* @param args the commandline arguments
* @throws Exception if something goes wrong
*/
public static void main(String[] args) throws Exception {
if (args.length != 2) {
System.out.println("\nUsage: " + DataSource.class.getName()
+ " \n");
System.exit(1);
}
// load data
Instances data = DataSource.read(args[0]);
// save data
DataSink.write(args[1], data);
}
/**
* Returns the revision string.
*
* @return the revision
*/
@Override
public String getRevision() {
return RevisionUtils.extract("$Revision: 14285 $");
}
}
/** all available loaders (extension <-> classname). */
protected static Hashtable m_FileLoaders;
/** all available URL loaders (extension <-> classname). */
protected static Hashtable m_URLFileLoaders;
/** all available savers (extension <-> classname). */
protected static Hashtable m_FileSavers;
// determine all loaders/savers
static {
initialize();
}
public static void initialize() {
ConverterResources.initialize();
m_FileLoaders = ConverterResources.getFileLoaders();
m_URLFileLoaders = ConverterResources.getURLFileLoaders();
m_FileSavers = ConverterResources.getFileSavers();
}
/**
* Gets token, skipping empty lines.
*
* @param tokenizer the stream tokenizer
* @throws IOException if reading the next token fails
*/
public static void getFirstToken(StreamTokenizer tokenizer)
throws IOException {
StreamTokenizerUtils.getFirstToken(tokenizer);
}
/**
* Gets token.
*
* @param tokenizer the stream tokenizer
* @throws IOException if reading the next token fails
*/
public static void getToken(StreamTokenizer tokenizer) throws IOException {
StreamTokenizerUtils.getToken(tokenizer);
}
/**
* Throws error message with line number and last token read.
*
* @param theMsg the error message to be thrown
* @param tokenizer the stream tokenizer
* @throws IOException containing the error message
*/
public static void errms(StreamTokenizer tokenizer, String theMsg)
throws IOException {
throw new IOException(theMsg + ", read " + tokenizer.toString());
}
/**
* returns a vector with the classnames of all the loaders from the given
* hashtable.
*
* @param ht the hashtable with the extension/converter relation
* @return the classnames of the loaders
*/
protected static Vector getConverters(Hashtable ht) {
Vector result;
Enumeration enm;
String converter;
result = new Vector();
// get all classnames
enm = ht.elements();
while (enm.hasMoreElements()) {
converter = enm.nextElement();
if (!result.contains(converter)) {
result.add(converter);
}
}
// sort names
Collections.sort(result);
return result;
}
/**
* tries to determine the converter to use for this kind of file, returns null
* if none can be found in the given hashtable.
*
* @param filename the file to return a converter for
* @param ht the hashtable with the relation extension/converter
* @return the converter if one was found, null otherwise
*/
protected static Object getConverterForFile(String filename,
Hashtable ht) {
Object result;
String extension;
int index;
result = null;
index = filename.lastIndexOf('.');
if (index > -1) {
extension = filename.substring(index).toLowerCase();
result = getConverterForExtension(extension, ht);
// is it a compressed format?
if (extension.equals(".gz") && result == null) {
index = filename.lastIndexOf('.', index - 1);
extension = filename.substring(index).toLowerCase();
result = getConverterForExtension(extension, ht);
}
}
return result;
}
/**
* tries to determine the loader to use for this kind of extension, returns
* null if none can be found.
*
* @param extension the file extension to return a converter for
* @param ht the hashtable with the relation extension/converter
* @return the converter if one was found, null otherwise
*/
protected static Object getConverterForExtension(String extension,
Hashtable ht) {
Object result;
String classname;
result = null;
classname = ht.get(extension);
if (classname != null) {
try {
result = WekaPackageClassLoaderManager.forName(classname).newInstance();
} catch (Exception e) {
result = null;
e.printStackTrace();
}
}
return result;
}
/**
* returns a vector with the classnames of all the file loaders.
*
* @return the classnames of the loaders
*/
public static Vector getFileLoaders() {
return getConverters(m_FileLoaders);
}
/**
* tries to determine the loader to use for this kind of file, returns null if
* none can be found.
*
* @param filename the file to return a converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileLoader getLoaderForFile(String filename) {
return (AbstractFileLoader) getConverterForFile(filename, m_FileLoaders);
}
/**
* tries to determine the loader to use for this kind of file, returns null if
* none can be found.
*
* @param file the file to return a converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileLoader getLoaderForFile(File file) {
return getLoaderForFile(file.getAbsolutePath());
}
/**
* tries to determine the loader to use for this kind of extension, returns
* null if none can be found.
*
* @param extension the file extension to return a converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileLoader getLoaderForExtension(String extension) {
return (AbstractFileLoader) getConverterForExtension(extension,
m_FileLoaders);
}
/**
* returns a vector with the classnames of all the URL file loaders.
*
* @return the classnames of the loaders
*/
public static Vector getURLFileLoaders() {
return getConverters(m_URLFileLoaders);
}
/**
* tries to determine the URL loader to use for this kind of file, returns
* null if none can be found.
*
* @param filename the file to return a URL converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileLoader getURLLoaderForFile(String filename) {
return (AbstractFileLoader) getConverterForFile(filename, m_URLFileLoaders);
}
/**
* tries to determine the URL loader to use for this kind of file, returns
* null if none can be found.
*
* @param file the file to return a URL converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileLoader getURLLoaderForFile(File file) {
return getURLLoaderForFile(file.getAbsolutePath());
}
/**
* tries to determine the URL loader to use for this kind of extension,
* returns null if none can be found.
*
* @param extension the file extension to return a URL converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileLoader getURLLoaderForExtension(String extension) {
return (AbstractFileLoader) getConverterForExtension(extension,
m_URLFileLoaders);
}
/**
* returns a vector with the classnames of all the file savers.
*
* @return the classnames of the savers
*/
public static Vector getFileSavers() {
return getConverters(m_FileSavers);
}
/**
* tries to determine the saver to use for this kind of file, returns null if
* none can be found.
*
* @param filename the file to return a converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileSaver getSaverForFile(String filename) {
return (AbstractFileSaver) getConverterForFile(filename, m_FileSavers);
}
/**
* tries to determine the saver to use for this kind of file, returns null if
* none can be found.
*
* @param file the file to return a converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileSaver getSaverForFile(File file) {
return getSaverForFile(file.getAbsolutePath());
}
/**
* tries to determine the saver to use for this kind of extension, returns
* null if none can be found.
*
* @param extension the file extension to return a converter for
* @return the converter if one was found, null otherwise
*/
public static AbstractFileSaver getSaverForExtension(String extension) {
return (AbstractFileSaver) getConverterForExtension(extension, m_FileSavers);
}
/**
* Returns the revision string.
*
* @return the revision
*/
@Override
public String getRevision() {
return RevisionUtils.extract("$Revision: 14285 $");
}
}
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