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weka.classifiers.evaluation.output.prediction.AbstractOutput Maven / Gradle / Ivy

/*
 *   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 .
 */

/*
 * AbstractOutput.java
 * Copyright (C) 2009-2012 University of Waikato, Hamilton, New Zealand
 */

package weka.classifiers.evaluation.output.prediction;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.Serializable;
import java.util.Enumeration;
import java.util.Vector;

import weka.classifiers.Classifier;
import weka.core.BatchPredictor;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.Utils;
import weka.core.WekaException;
import weka.core.converters.ConverterUtils.DataSource;

/**
 * A superclass for outputting the classifications of a classifier.
 * 

 * Basic use with a classifier and a test set:
 * 
 * 
 * Classifier classifier = ... // trained classifier
 * Instances testset = ... // the test set to output the predictions for
 * StringBuffer buffer = ... // the string buffer to add the output to
 * AbstractOutput output = new FunkyOutput();
 * output.setHeader(...);
 * output.printClassifications(classifier, testset);
 * 
 * 
 * Basic use with a classifier and a data source:
 * 
 * 
 * Classifier classifier = ... // trained classifier
 * DataSource testset = ... // the data source to obtain the test set from to output the predictions for
 * StringBuffer buffer = ... // the string buffer to add the output to
 * AbstractOutput output = new FunkyOutput();
 * output.setHeader(...);
 * output.printClassifications(classifier, testset);
 * 
 * 
 * In order to make the output generation easily integrate into GUI components,
 * one can output the header, classifications and footer separately:
 * 
 * 
 * Classifier classifier = ... // trained classifier
 * Instances testset = ... // the test set to output the predictions for
 * StringBuffer buffer = ... // the string buffer to add the output to
 * AbstractOutput output = new FunkyOutput();
 * output.setHeader(...);
 * // print the header
 * output.printHeader();
 * // print the classifications one-by-one
 * for (int i = 0; i < testset.numInstances(); i++) {
 *   output.printClassification(classifier, testset.instance(i), i);
 *   // output progress information
 *   if ((i+1) % 100 == 0)
 *     System.out.println((i+1) + "/" + testset.numInstances());
 * }
 * // print the footer
 * output.printFooter();
 * 
 * 
 * @author fracpete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 10169 $
 */
public abstract class AbstractOutput implements Serializable, OptionHandler {

  /** for serialization. */
  private static final long serialVersionUID = 752696986017306241L;

  /** the header of the dataset. */
  protected Instances m_Header;

  /** the buffer to write to. */
  protected StringBuffer m_Buffer;

  /** the file buffer to write to. */
  protected StringBuffer m_FileBuffer;

  /** whether to output the class distribution. */
  protected boolean m_OutputDistribution;

  /** the range of attributes to output. */
  protected Range m_Attributes;

  /** the number of decimals after the decimal point. */
  protected int m_NumDecimals;

  /** the file to store the output in. */
  protected File m_OutputFile;

  /** whether to suppress the regular output and only store in file. */
  protected boolean m_SuppressOutput;

  /**
   * Initializes the output class.
   */
  public AbstractOutput() {
    m_Header = null;
    m_OutputDistribution = false;
    m_Attributes = null;
    m_Buffer = null;
    m_NumDecimals = 3;
    m_OutputFile = new File(".");
    m_FileBuffer = new StringBuffer();
    m_SuppressOutput = false;
  }

  /**
   * Returns a string describing the output generator.
   * 
   * @return a description suitable for displaying in the GUI
   */
  public abstract String globalInfo();

  /**
   * Returns a short display text, to be used in comboboxes.
   * 
   * @return a short display text
   */
  public abstract String getDisplay();

  /**
   * Returns an enumeration of all the available options..
   * 
   * @return an enumeration of all available options.
   */
  @Override
  public Enumeration listOptions() {
    Vector result;

    result = new Vector();

    result.addElement(new Option(
      "\tThe range of attributes to print in addition to the classification.\n"
        + "\t(default: none)", "p", 1, "-p "));

    result.addElement(new Option(
      "\tWhether to turn on the output of the class distribution.\n"
        + "\tOnly for nominal class attributes.\n" + "\t(default: off)",
      "distribution", 0, "-distribution"));

    result.addElement(new Option(
      "\tThe number of digits after the decimal point.\n" + "\t(default: "
        + getDefaultNumDecimals() + ")", "decimals", 1, "-decimals "));

    result.addElement(new Option(
      "\tThe file to store the output in, instead of outputting it on stdout.\n"
        + "\tGets ignored if the supplied path is a directory.\n"
        + "\t(default: .)", "file", 1, "-file "));

    result
      .addElement(new Option(
        "\tIn case the data gets stored in a file, then this flag can be used\n"
          + "\tto suppress the regular output.\n"
          + "\t(default: not suppressed)", "suppress", 0, "-suppress"));

    return result.elements();
  }

  /**
   * Sets the OptionHandler's options using the given list. All options will be
   * set (or reset) during this call (i.e. incremental setting of options is not
   * possible).
   * 
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {
    String tmpStr;

    setAttributes(Utils.getOption("p", options));
    setOutputDistribution(Utils.getFlag("distribution", options));

    tmpStr = Utils.getOption("decimals", options);
    if (tmpStr.length() > 0) {
      setNumDecimals(Integer.parseInt(tmpStr));
    } else {
      setNumDecimals(getDefaultNumDecimals());
    }

    tmpStr = Utils.getOption("file", options);
    if (tmpStr.length() > 0) {
      setOutputFile(new File(tmpStr));
    } else {
      setOutputFile(new File("."));
    }

    setSuppressOutput(Utils.getFlag("suppress", options));
  }

  /**
   * Gets the current option settings for the OptionHandler.
   * 
   * @return the list of current option settings as an array of strings
   */
  @Override
  public String[] getOptions() {
    Vector result;

    result = new Vector();

    if (getAttributes().length() > 0) {
      result.add("-p");
      result.add(getAttributes());
    }

    if (getOutputDistribution()) {
      result.add("-distribution");
    }

    if (getNumDecimals() != getDefaultNumDecimals()) {
      result.add("-decimals");
      result.add("" + getNumDecimals());
    }

    if (!getOutputFile().isDirectory()) {
      result.add("-file");
      result.add(getOutputFile().getAbsolutePath());
      if (getSuppressOutput()) {
        result.add("-suppress");
      }
    }

    return result.toArray(new String[result.size()]);
  }

  /**
   * Sets the header of the dataset.
   * 
   * @param value the header
   */
  public void setHeader(Instances value) {
    m_Header = new Instances(value, 0);
  }

  /**
   * Returns the header of the dataset.
   * 
   * @return the header
   */
  public Instances getHeader() {
    return m_Header;
  }

  /**
   * Sets the buffer to use.
   * 
   * @param value the buffer
   */
  public void setBuffer(StringBuffer value) {
    m_Buffer = value;
  }

  /**
   * Returns the current buffer.
   * 
   * @return the buffer, can be null
   */
  public StringBuffer getBuffer() {
    return m_Buffer;
  }

  /**
   * Sets the range of attributes to output.
   * 
   * @param value the range
   */
  public void setAttributes(String value) {
    if (value.length() == 0) {
      m_Attributes = null;
    } else {
      m_Attributes = new Range(value);
    }
  }

  /**
   * Returns the range of attributes to output.
   * 
   * @return the range
   */
  public String getAttributes() {
    if (m_Attributes == null) {
      return "";
    } else {
      return m_Attributes.getRanges();
    }
  }

  /**
   * Returns the tip text for this property.
   * 
   * @return tip text for this property suitable for displaying in the GUI
   */
  public String attributesTipText() {
    return "The indices of the attributes to print in addition.";
  }

  /**
   * Sets whether to output the class distribution or not.
   * 
   * @param value true if the class distribution is to be output as well
   */
  public void setOutputDistribution(boolean value) {
    m_OutputDistribution = value;
  }

  /**
   * Returns whether to output the class distribution as well.
   * 
   * @return true if the class distribution is output as well
   */
  public boolean getOutputDistribution() {
    return m_OutputDistribution;
  }

  /**
   * Returns the tip text for this property.
   * 
   * @return tip text for this property suitable for displaying in the GUI
   */
  public String outputDistributionTipText() {
    return "Whether to ouput the class distribution as well (only nominal class attributes).";
  }

  /**
   * Returns the default number of digits to output after the decimal point.
   * 
   * @return the default number of digits
   */
  public int getDefaultNumDecimals() {
    return 3;
  }

  /**
   * Sets the number of digits to output after the decimal point.
   * 
   * @param value the number of digits
   */
  public void setNumDecimals(int value) {
    if (value >= 0) {
      m_NumDecimals = value;
    } else {
      System.err.println("Number of decimals cannot be negative (provided: "
        + value + ")!");
    }
  }

  /**
   * Returns the number of digits to output after the decimal point.
   * 
   * @return the number of digits
   */
  public int getNumDecimals() {
    return m_NumDecimals;
  }

  /**
   * Returns the tip text for this property.
   * 
   * @return tip text for this property suitable for displaying in the GUI
   */
  public String numDecimalsTipText() {
    return "The number of digits to output after the decimal point.";
  }

  /**
   * Sets the output file to write to. A directory disables this feature.
   * 
   * @param value the file to write to or a directory
   */
  public void setOutputFile(File value) {
    m_OutputFile = value;
  }

  /**
   * Returns the output file to write to. A directory if turned off.
   * 
   * @return the file to write to or a directory
   */
  public File getOutputFile() {
    return m_OutputFile;
  }

  /**
   * Returns the tip text for this property.
   * 
   * @return tip text for this property suitable for displaying in the GUI
   */
  public String outputFileTipText() {
    return "The file to write the generated output to (disabled if path is a directory).";
  }

  /**
   * Sets whether to the regular output is suppressed in case the output is
   * stored in a file.
   * 
   * @param value true if the regular output is to be suppressed
   */
  public void setSuppressOutput(boolean value) {
    m_SuppressOutput = value;
  }

  /**
   * Returns whether to the regular output is suppressed in case the output is
   * stored in a file.
   * 
   * @return true if the regular output is to be suppressed
   */
  public boolean getSuppressOutput() {
    return m_SuppressOutput;
  }

  /**
   * Returns the tip text for this property.
   * 
   * @return tip text for this property suitable for displaying in the GUI
   */
  public String suppressOutputTipText() {
    return "Whether to suppress the regular output when storing the output in a file.";
  }

  /**
   * Performs basic checks.
   * 
   * @return null if everything is in order, otherwise the error message
   */
  protected String checkBasic() {
    if (m_Buffer == null) {
      return "Buffer is null!";
    }

    if (m_Header == null) {
      return "No dataset structure provided!";
    }

    if (m_Attributes != null) {
      m_Attributes.setUpper(m_Header.numAttributes() - 1);
    }

    return null;
  }

  /**
   * Returns whether regular output is generated or not.
   * 
   * @return true if regular output is generated
   */
  public boolean generatesOutput() {
    return m_OutputFile.isDirectory()
      || (!m_OutputFile.isDirectory() && !m_SuppressOutput);
  }

  /**
   * If an output file was defined, then the string gets added to the file
   * buffer, otherwise to the actual buffer.
   * 
   * @param s the string to append
   * @see #m_Buffer
   * @see #m_FileBuffer
   */
  protected void append(String s) {
    if (generatesOutput()) {
      m_Buffer.append(s);
    }
    if (!m_OutputFile.isDirectory()) {
      m_FileBuffer.append(s);
    }
  }

  /**
   * Performs checks whether everything is correctly setup for the header.
   * 
   * @return null if everything is in order, otherwise the error message
   */
  protected String checkHeader() {
    return checkBasic();
  }

  /**
   * Performs the actual printing of the header.
   */
  protected abstract void doPrintHeader();

  /**
   * Prints the header to the buffer.
   */
  public void printHeader() {
    String error;

    if ((error = checkHeader()) != null) {
      throw new IllegalStateException(error);
    }

    doPrintHeader();
  }

  /**
   * Performs the actual printing of the classification.
   * 
   * @param classifier the classifier to use for printing the classification
   * @param inst the instance to print
   * @param index the index of the instance
   * @throws Exception if printing of classification fails
   */
  protected abstract void doPrintClassification(Classifier classifier,
    Instance inst, int index) throws Exception;

  /**
   * Performs the actual printing of the classification.
   * 
   * @param dist the distribution to use for printing the classification
   * @param inst the instance to print
   * @param index the index of the instance
   * @throws Exception if printing of classification fails
   */
  protected abstract void doPrintClassification(double[] dist, Instance inst,
    int index) throws Exception;

  /**
   * Preprocesses an input instance and its copy (that will get its class value
   * set to missing for prediction purposes). Basically this only does something
   * special in the case when the classifier is an InputMappedClassifier.
   * 
   * @param inst the original instance to predict
   * @param withMissing a copy of the instance to predict
   * @param classifier the classifier that will be used to make the prediction
   * @return the original instance unchanged or mapped (in the case of an
   *         InputMappedClassifier) and the withMissing copy with the class
   *         attribute set to missing value.
   * @throws Exception if a problem occurs.
   */
  protected Instance preProcessInstance(Instance inst, Instance withMissing,
    Classifier classifier) throws Exception {

    if (classifier instanceof weka.classifiers.misc.InputMappedClassifier) {
      inst = (Instance) inst.copy();
      inst = ((weka.classifiers.misc.InputMappedClassifier) classifier)
        .constructMappedInstance(inst);
      int mappedClass = ((weka.classifiers.misc.InputMappedClassifier) classifier)
        .getMappedClassIndex();
      withMissing.setMissing(mappedClass);
    } else {
      withMissing.setMissing(withMissing.classIndex());
    }

    return inst;
  }

  /**
   * Prints the classification to the buffer.
   * 
   * @param classifier the classifier to use for printing the classification
   * @param inst the instance to print
   * @param index the index of the instance
   * @throws Exception if check fails or error occurs during printing of
   *           classification
   */
  public void printClassification(Classifier classifier, Instance inst,
    int index) throws Exception {
    String error;

    if ((error = checkBasic()) != null) {
      throw new WekaException(error);
    }

    doPrintClassification(classifier, inst, index);
  }

  /**
   * Prints the classification to the buffer.
   * 
   * @param dist the distribution from classifier for the supplied instance
   * @param inst the instance to print
   * @param index the index of the instance
   * @throws Exception if check fails or error occurs during printing of
   *           classification
   */
  public void printClassification(double[] dist, Instance inst, int index)
    throws Exception {
    String error;

    if ((error = checkBasic()) != null) {
      throw new WekaException(error);
    }

    doPrintClassification(dist, inst, index);
  }

  /**
   * Prints the classifications to the buffer.
   * 
   * @param classifier the classifier to use for printing the classifications
   * @param testset the data source to obtain the test instances from
   * @throws Exception if check fails or error occurs during printing of
   *           classifications
   */
  public void printClassifications(Classifier classifier, DataSource testset)
    throws Exception {
    int i;
    Instances test;
    Instance inst;

    i = 0;
    testset.reset();

    if (classifier instanceof BatchPredictor) {
      test = testset.getDataSet(m_Header.classIndex());
      double[][] predictions = ((BatchPredictor) classifier)
        .distributionsForInstances(test);
      for (i = 0; i < test.numInstances(); i++) {
        printClassification(predictions[i], test.instance(i), i);
      }
    } else {
      test = testset.getStructure(m_Header.classIndex());
      while (testset.hasMoreElements(test)) {
        inst = testset.nextElement(test);
        doPrintClassification(classifier, inst, i);
        i++;
      }
    }
  }

  /**
   * Prints the classifications to the buffer.
   * 
   * @param classifier the classifier to use for printing the classifications
   * @param testset the test instances
   * @throws Exception if check fails or error occurs during printing of
   *           classifications
   */
  public void printClassifications(Classifier classifier, Instances testset)
    throws Exception {
    int i;

    if (classifier instanceof BatchPredictor) {
      double[][] predictions = ((BatchPredictor) classifier)
        .distributionsForInstances(testset);
      for (i = 0; i < testset.numInstances(); i++) {
        printClassification(predictions[i], testset.instance(i), i);
      }
    } else {
      for (i = 0; i < testset.numInstances(); i++) {
        doPrintClassification(classifier, testset.instance(i), i);
      }
    }
  }

  /**
   * Performs the actual printing of the footer.
   */
  protected abstract void doPrintFooter();

  /**
   * Prints the footer to the buffer. This will also store the generated output
   * in a file if an output file was specified.
   * 
   * @throws Exception if check fails
   */
  public void printFooter() throws Exception {
    String error;
    BufferedWriter writer;

    if ((error = checkBasic()) != null) {
      throw new WekaException(error);
    }

    doPrintFooter();

    // write output to file
    if (!m_OutputFile.isDirectory()) {
      try {
        writer = new BufferedWriter(new FileWriter(m_OutputFile));
        writer.write(m_FileBuffer.toString());
        writer.newLine();
        writer.flush();
        writer.close();
      } catch (Exception e) {
        e.printStackTrace();
      }
    }
  }

  /**
   * Prints the header, classifications and footer to the buffer.
   * 
   * @param classifier the classifier to use for printing the classifications
   * @param testset the data source to obtain the test instances from
   * @throws Exception if check fails or error occurs during printing of
   *           classifications
   */
  public void print(Classifier classifier, DataSource testset) throws Exception {
    printHeader();
    printClassifications(classifier, testset);
    printFooter();
  }

  /**
   * Prints the header, classifications and footer to the buffer.
   * 
   * @param classifier the classifier to use for printing the classifications
   * @param testset the test instances
   * @throws Exception if check fails or error occurs during printing of
   *           classifications
   */
  public void print(Classifier classifier, Instances testset) throws Exception {
    printHeader();
    printClassifications(classifier, testset);
    printFooter();
  }

  /**
   * Returns a fully configured object from the given commandline.
   * 
   * @param cmdline the commandline to turn into an object
   * @return the object or null in case of an error
   */
  public static AbstractOutput fromCommandline(String cmdline) {
    AbstractOutput result;
    String[] options;
    String classname;

    try {
      options = Utils.splitOptions(cmdline);
      classname = options[0];
      options[0] = "";
      result = (AbstractOutput) Utils.forName(AbstractOutput.class, classname,
        options);
    } catch (Exception e) {
      result = null;
    }

    return result;
  }
}