/*
* 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.
*/
/*
* CSVLoader.java
* Copyright (C) 2000 University of Waikato, Hamilton, New Zealand
*
*/
package weka.core.converters;
import weka.core.Attribute;
import weka.core.FastVector;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.RevisionUtils;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StreamTokenizer;
import java.io.StringReader;
import java.util.Enumeration;
import java.util.Hashtable;
/**
<!-- globalinfo-start -->
* Reads a source that is in comma separated or tab separated format. Assumes that the first row in the file determines the number of and names of the attributes.
* <p/>
<!-- globalinfo-end -->
*
* @author Mark Hall (mhall@cs.waikato.ac.nz)
* @version $Revision: 1.19 $
* @see Loader
*/
public class CSVLoader
extends AbstractFileLoader
implements BatchConverter {
/** for serialization */
static final long serialVersionUID = 5607529739745491340L;
/** the file extension */
public static String FILE_EXTENSION = ".csv";
/**
* A list of hash tables for accumulating nominal values during parsing.
*/
private FastVector m_cumulativeStructure;
/**
* Holds instances accumulated so far
*/
private FastVector m_cumulativeInstances;
/** the data collected from an InputStream */
private StringBuffer m_StreamBuffer;
/**
* default constructor
*/
public CSVLoader() {
// No instances retrieved yet
setRetrieval(NONE);
}
/**
* Get the file extension used for arff files
*
* @return the file extension
*/
public String getFileExtension() {
return FILE_EXTENSION;
}
/**
* Returns a description of the file type.
*
* @return a short file description
*/
public String getFileDescription() {
return "CSV data files";
}
/**
* Gets all the file extensions used for this type of file
*
* @return the file extensions
*/
public String[] getFileExtensions() {
return new String[]{getFileExtension()};
}
/**
* Returns a string describing this attribute evaluator
* @return a description of the evaluator suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "Reads a source that is in comma separated or tab separated format. "
+"Assumes that the first row in the file determines the number of "
+"and names of the attributes.";
}
/**
* Resets the Loader object and sets the source of the data set to be
* the supplied Stream object.
*
* @param input the input stream
* @exception IOException if an error occurs
*/
public void setSource(InputStream input) throws IOException {
BufferedReader reader;
String line;
m_structure = null;
m_sourceFile = null;
m_File = null;
m_StreamBuffer = new StringBuffer();
reader = new BufferedReader(new InputStreamReader(input));
while ((line = reader.readLine()) != null) {
m_StreamBuffer.append(line + "\n");
}
}
/**
* Resets the Loader object and sets the source of the data set to be
* the supplied File object.
*
* @param file the source file.
* @exception IOException if an error occurs
*/
public void setSource(File file) throws IOException {
super.setSource(file);
}
/**
* 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
* @exception IOException if an error occurs
*/
public Instances getStructure() throws IOException {
if ((m_sourceFile == null) && (m_StreamBuffer == null)) {
throw new IOException("No source has been specified");
}
if (m_structure == null) {
try {
BufferedReader br;
if (m_StreamBuffer != null)
br = new BufferedReader(new StringReader(m_StreamBuffer.toString()));
else
br = new BufferedReader(new FileReader(m_sourceFile));
StreamTokenizer st = new StreamTokenizer(br);
initTokenizer(st);
readStructure(st);
} catch (FileNotFoundException ex) {
}
}
return m_structure;
}
/**
* reads the structure
*
* @param st the stream tokenizer to read from
* @throws IOException if reading fails
*/
private void readStructure(StreamTokenizer st) throws IOException {
readHeader(st);
}
/**
* 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
* @exception IOException if there is no source or parsing fails
*/
public Instances getDataSet() throws IOException {
if ((m_sourceFile == null) && (m_StreamBuffer == null)) {
throw new IOException("No source has been specified");
}
BufferedReader br;
/* if (m_sourceFile != null) {
setSource(m_sourceFile);
br = new BufferedReader(new FileReader(m_sourceFile));
}
else { */
br = new BufferedReader(new StringReader(m_StreamBuffer.toString()));
StreamTokenizer st = new StreamTokenizer(br);
initTokenizer(st);
readStructure(st);
st.ordinaryChar(',');
st.ordinaryChar('\t');
m_cumulativeStructure = new FastVector(m_structure.numAttributes());
for (int i = 0; i < m_structure.numAttributes(); i++) {
m_cumulativeStructure.addElement(new Hashtable());
}
// Instances result = new Instances(m_structure);
m_cumulativeInstances = new FastVector();
FastVector current;
while ((current = getInstance(st)) != null) {
m_cumulativeInstances.addElement(current);
}
br.close();
// now determine the true structure of the data set
FastVector atts = new FastVector(m_structure.numAttributes());
for (int i = 0; i < m_structure.numAttributes(); i++) {
String attname = m_structure.attribute(i).name();
Hashtable tempHash = ((Hashtable)m_cumulativeStructure.elementAt(i));
if (tempHash.size() == 0) {
atts.addElement(new Attribute(attname));
} else {
FastVector values = new FastVector(tempHash.size());
// add dummy objects in order to make the FastVector's size == capacity
for (int z = 0; z < tempHash.size(); z++) {
values.addElement("dummy");
}
Enumeration e = tempHash.keys();
while (e.hasMoreElements()) {
Object ob = e.nextElement();
// if (ob instanceof Double) {
int index = ((Integer)tempHash.get(ob)).intValue();
values.setElementAt(new String(ob.toString()), index);
// }
}
atts.addElement(new Attribute(attname, values));
}
}
// make the instances
String relationName;
if (m_sourceFile != null)
relationName = (m_sourceFile.getName()).replaceAll("\\.[cC][sS][vV]$","");
else
relationName = "stream";
Instances dataSet = new Instances(relationName,
atts,
m_cumulativeInstances.size());
for (int i = 0; i < m_cumulativeInstances.size(); i++) {
current = ((FastVector)m_cumulativeInstances.elementAt(i));
double [] vals = new double[dataSet.numAttributes()];
for (int j = 0; j < current.size(); j++) {
Object cval = current.elementAt(j);
if (cval instanceof String) {
if (((String)cval).compareTo("'?'") == 0) {
vals[j] = Instance.missingValue();
} else {
if (!dataSet.attribute(j).isNominal()) {
System.err.println("Wrong attribute type!!!");
System.exit(1);
}
// find correct index
Hashtable lookup = (Hashtable)m_cumulativeStructure.elementAt(j);
int index = ((Integer)lookup.get(cval)).intValue();
vals[j] = (double)index;
}
} else if (dataSet.attribute(j).isNominal()) {
// find correct index
Hashtable lookup = (Hashtable)m_cumulativeStructure.elementAt(j);
int index = ((Integer)lookup.get(cval)).intValue();
vals[j] = (double)index;
} else {
vals[j] = ((Double)cval).doubleValue();
}
}
dataSet.add(new Instance(1.0, vals));
}
m_structure = new Instances(dataSet, 0);
setRetrieval(BATCH);
m_cumulativeStructure = null; // conserve memory
return dataSet;
}
/**
* CSVLoader is unable to process a data set incrementally.
*
* @param structure ignored
* @return never returns without throwing an exception
* @exception IOException always. CSVLoader is unable to process a data
* set incrementally.
*/
public Instance getNextInstance(Instances structure) throws IOException {
throw new IOException("CSVLoader can't read data sets incrementally.");
}
/**
* Attempts to parse a line of the data set.
*
* @param tokenizer the tokenizer
* @return a FastVector containg String and Double objects representing
* the values of the instance.
* @exception IOException if an error occurs
*
* <pre><jml>
* private_normal_behavior
* requires: tokenizer != null;
* ensures: \result != null;
* also
* private_exceptional_behavior
* requires: tokenizer == null
* || (* unsucessful parse *);
* signals: (IOException);
* </jml></pre>
*/
private FastVector getInstance(StreamTokenizer tokenizer)
throws IOException {
FastVector current = new FastVector();
// Check if end of file reached.
ConverterUtils.getFirstToken(tokenizer);
if (tokenizer.ttype == StreamTokenizer.TT_EOF) {
return null;
}
boolean first = true;
boolean wasSep;
while (tokenizer.ttype != StreamTokenizer.TT_EOL &&
tokenizer.ttype != StreamTokenizer.TT_EOF) {
// Get next token
if (!first) {
ConverterUtils.getToken(tokenizer);
}
if (tokenizer.ttype == ',' || tokenizer.ttype == '\t' ||
tokenizer.ttype == StreamTokenizer.TT_EOL) {
current.addElement("'?'");
wasSep = true;
} else if (tokenizer.ttype == '?') {
wasSep = false;
current.addElement(new String("'?'"));
} else {
wasSep = false;
// try to parse as a number
try {
double val = Double.valueOf(tokenizer.sval).doubleValue();
current.addElement(new Double(val));
} catch (NumberFormatException e) {
// otherwise assume its an enumerated value
current.addElement(new String(tokenizer.sval));
}
}
if (!wasSep) {
ConverterUtils.getToken(tokenizer);
}
first = false;
}
// check number of values read
if (current.size() != m_structure.numAttributes()) {
ConverterUtils.errms(tokenizer,
"wrong number of values. Read "+current.size()
+", expected "+m_structure.numAttributes());
}
// check for structure update
try {
checkStructure(current);
} catch (Exception ex) {
ex.printStackTrace();
}
return current;
}
/**
* Checks the current instance against what is known about the structure
* of the data set so far. If there is a nominal value for an attribute
* that was beleived to be numeric then all previously seen values for this
* attribute are stored in a Hashtable.
*
* @param current a <code>FastVector</code> value
* @exception Exception if an error occurs
*
* <pre><jml>
* private_normal_behavior
* requires: current != null;
* also
* private_exceptional_behavior
* requires: current == null
* || (* unrecognized object type in current *);
* signals: (Exception);
* </jml></pre>
*/
private void checkStructure(FastVector current) throws Exception {
if (current == null) {
throw new Exception("current shouldn't be null in checkStructure");
}
for (int i = 0; i < current.size(); i++) {
Object ob = current.elementAt(i);
if (ob instanceof String) {
if (((String)ob).compareTo("'?'") == 0) {
} else {
Hashtable tempHash = (Hashtable)m_cumulativeStructure.elementAt(i);
if (!tempHash.containsKey(ob)) {
// may have found a nominal value in what was previously thought to
// be a numeric variable.
if (tempHash.size() == 0) {
for (int j = 0; j < m_cumulativeInstances.size(); j++) {
FastVector tempUpdate =
((FastVector)m_cumulativeInstances.elementAt(j));
Object tempO = tempUpdate.elementAt(i);
if (tempO instanceof String) {
// must have been a missing value
} else {
if (!tempHash.containsKey(tempO)) {
tempHash.put(new Double(((Double)tempO).doubleValue()),
new Integer(tempHash.size()));
}
}
}
}
int newIndex = tempHash.size();
tempHash.put(ob, new Integer(newIndex));
}
}
} else if (ob instanceof Double) {
Hashtable tempHash = (Hashtable)m_cumulativeStructure.elementAt(i);
if (tempHash.size() != 0) {
if (!tempHash.containsKey(ob)) {
int newIndex = tempHash.size();
tempHash.put(new Double(((Double)ob).doubleValue()),
new Integer(newIndex));
}
}
} else {
throw new Exception("Wrong object type in checkStructure!");
}
}
}
/**
* Assumes the first line of the file contains the attribute names.
* Assumes all attributes are real (Reading the full data set with
* getDataSet will establish the true structure).
*
* @param tokenizer a <code>StreamTokenizer</code> value
* @exception IOException if an error occurs
*
* <pre><jml>
* private_normal_behavior
* requires: tokenizer != null;
* modifiable: m_structure;
* ensures: m_structure != null;
* also
* private_exceptional_behavior
* requires: tokenizer == null
* || (* unsucessful parse *);
* signals: (IOException);
* </jml></pre>
*/
private void readHeader(StreamTokenizer tokenizer) throws IOException {
FastVector attribNames = new FastVector();
ConverterUtils.getFirstToken(tokenizer);
if (tokenizer.ttype == StreamTokenizer.TT_EOF) {
ConverterUtils.errms(tokenizer,"premature end of file");
}
while (tokenizer.ttype != StreamTokenizer.TT_EOL) {
attribNames.addElement(new Attribute(tokenizer.sval));
ConverterUtils.getToken(tokenizer);
}
String relationName;
if (m_sourceFile != null)
relationName = (m_sourceFile.getName()).replaceAll("\\.[cC][sS][vV]$","");
else
relationName = "stream";
m_structure = new Instances(relationName, attribNames, 0);
}
/**
* Initializes the stream tokenizer
*
* @param tokenizer the tokenizer to initialize
*/
private void initTokenizer(StreamTokenizer tokenizer) {
tokenizer.resetSyntax();
tokenizer.whitespaceChars(0, (' '-1));
tokenizer.wordChars(' ','\u00FF');
tokenizer.whitespaceChars(',',',');
tokenizer.whitespaceChars('\t','\t');
tokenizer.commentChar('%');
tokenizer.quoteChar('"');
tokenizer.quoteChar('\'');
tokenizer.eolIsSignificant(true);
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.19 $");
}
/**
* Main method.
*
* @param args should contain the name of an input file.
*/
public static void main(String [] args) {
runFileLoader(new CSVLoader(), args);
}
}