utils.java

wekaUT是 university texas austin 开发的基于weka的半指导学习(semi supervised learning)的分类器

/*
 *    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.
 */

/*
 *    Utils.java
 *    Copyright (C) 1999 Eibe Frank,Len Trigg,Yong Wang
 *
 */

package weka.core;

import java.lang.Math;
import java.util.StringTokenizer;
import java.util.Properties;
import java.io.File;
import java.io.FileInputStream;

/**
 * Class implementing some simple utility methods.
 *
 * @author Eibe Frank ([e-mail])
 * @author Yong Wang ([e-mail])
 * @author Len Trigg ([e-mail])
 * @version $Revision: 1.2 $
 */
public final class Utils {

  /** The natural logarithm of 2. */
  public static double log2 = Math.log(2);

  /** The small deviation allowed in double comparisons */
  public static double SMALL = 1e-6;
    
    /* Begin Edit - Melville */
    //Print the elements of a double array
    public static void printArray(double []array){
	for(int i=0; i<array.length; i++)
	    System.out.print(array[i]+" ");
	System.out.println();
    }
    /* End Edit - Melville */

  /**
   * Reads properties that inherit from three locations. Properties
   * are first defined in the system resource location (i.e. in the
   * CLASSPATH).  These default properties must exist. Properties
   * defined in the users home directory (optional) override default
   * settings. Properties defined in the current directory (optional)
   * override all these settings.
   *
   * @param resourceName the location of the resource that should be
   * loaded.  e.g.: "weka/core/Utils.props". (The use of hardcoded
   * forward slashes here is OK - see
   * jdk1.1/docs/guide/misc/resources.html) This routine will also
   * look for the file (in this case) "Utils.props" in the users home
   * directory and the current directory.
   * @return the Properties
   * @exception Exception if no default properties are defined, or if
   * an error occurs reading the properties files.  
   */
  public static Properties readProperties(String resourceName)
    throws Exception {

    Properties defaultProps = new Properties();
    try {
      // Apparently hardcoded slashes are OK here
      // jdk1.1/docs/guide/misc/resources.html
      defaultProps.load(ClassLoader.getSystemResourceAsStream(resourceName));
    } catch (Exception ex) {
/*      throw new Exception("Problem reading default properties: "
	+ ex.getMessage()); */
      System.err.println("Warning, unable to load properties file from "
			 +"system resource (Utils.java)");
    }

    // Hardcoded slash is OK here
    // eg: see jdk1.1/docs/guide/misc/resources.html
    int slInd = resourceName.lastIndexOf('/');
    if (slInd != -1) {
      resourceName = resourceName.substring(slInd + 1);
    }

    // Allow a properties file in the home directory to override
    Properties userProps = new Properties(defaultProps);    
    File propFile = new File(System.getProperties().getProperty("user.home")
                             + File.separatorChar
                             + resourceName);
    if (propFile.exists()) {
      try {
        userProps.load(new FileInputStream(propFile));
      } catch (Exception ex) {
        throw new Exception("Problem reading user properties: " + propFile);
      }
    }

    // Allow a properties file in the current directory to override
    Properties localProps = new Properties(userProps);
    propFile = new File(resourceName);
    if (propFile.exists()) {
      try {
        localProps.load(new FileInputStream(propFile));
      } catch (Exception ex) {
        throw new Exception("Problem reading local properties: " + propFile);
      }
    }
    
    return localProps;
  }

  /**
   * Returns the correlation coefficient of two double vectors.
   *
   * @param y1 double vector 1
   * @param y2 double vector 2
   * @param n the length of two double vectors
   * @return the correlation coefficient
   */
  public static final double correlation(double y1[],double y2[],int n) {

    int i;
    double av1 = 0.0, av2 = 0.0, y11 = 0.0, y22 = 0.0, y12 = 0.0, c;
    
    if (n <= 1) {
      return 1.0;
    }
    for (i = 0; i < n; i++) {
      av1 += y1[i];
      av2 += y2[i];
    }
    av1 /= (double) n;
    av2 /= (double) n;
    for (i = 0; i < n; i++) {
      y11 += (y1[i] - av1) * (y1[i] - av1);
      y22 += (y2[i] - av2) * (y2[i] - av2);
      y12 += (y1[i] - av1) * (y2[i] - av2);
    }
    if (y11 * y22 == 0.0) {
      c=1.0;
    } else {
      c = y12 / Math.sqrt(Math.abs(y11 * y22));
    }
    
    return c;
  }

  /**
   * Removes all occurrences of a string from another string.
   *
   * @param inString the string to remove substrings from.
   * @param substring the substring to remove.
   * @return the input string with occurrences of substring removed.
   */
  public static String removeSubstring(String inString, String substring) {

    StringBuffer result = new StringBuffer();
    int oldLoc = 0, loc = 0;
    while ((loc = inString.indexOf(substring, oldLoc))!= -1) {
      result.append(inString.substring(oldLoc, loc));
      oldLoc = loc + substring.length();
    }
    result.append(inString.substring(oldLoc));
    return result.toString();
  }

  /**
   * Replaces with a new string, all occurrences of a string from 
   * another string.
   *
   * @param inString the string to replace substrings in.
   * @param substring the substring to replace.
   * @param replaceString the replacement substring
   * @return the input string with occurrences of substring replaced.
   */
  public static String replaceSubstring(String inString, String subString,
					String replaceString) {

    StringBuffer result = new StringBuffer();
    int oldLoc = 0, loc = 0;
    while ((loc = inString.indexOf(subString, oldLoc))!= -1) {
      result.append(inString.substring(oldLoc, loc));
      result.append(replaceString);
      oldLoc = loc + subString.length();
    }
    result.append(inString.substring(oldLoc));
    return result.toString();
  }


  /**
   * Pads a string to a specified length, inserting spaces on the left
   * as required. If the string is too long, characters are removed (from
   * the right).
   *
   * @param inString the input string
   * @param length the desired length of the output string
   * @return the output string
   */
  public static String padLeft(String inString, int length) {

    return fixStringLength(inString, length, false);
  }
  
  /**
   * Pads a string to a specified length, inserting spaces on the right
   * as required. If the string is too long, characters are removed (from
   * the right).
   *
   * @param inString the input string
   * @param length the desired length of the output string
   * @return the output string
   */
  public static String padRight(String inString, int length) {

    return fixStringLength(inString, length, true);
  }
  
  /**
   * Pads a string to a specified length, inserting spaces as
   * required. If the string is too long, characters are removed (from
   * the right).
   *
   * @param inString the input string
   * @param length the desired length of the output string
   * @param right true if inserted spaces should be added to the right
   * @return the output string
   */
  private static String fixStringLength(String inString, int length,
					boolean right) {

    if (inString.length() < length) {
      while (inString.length() < length) {
	inString = (right ? inString.concat(" ") : " ".concat(inString));
      }
    } else if (inString.length() > length) {
      inString = inString.substring(0, length);
    }
    return inString;
  }
 
  /**
   * Rounds a double and converts it into String.
   *
   * @param value the double value
   * @param afterDecimalPoint the (maximum) number of digits permitted
   * after the decimal point
   * @return the double as a formatted string
   */
  public static String doubleToString(double value, int afterDecimalPoint) {
    
    StringBuffer stringBuffer;
    double temp;
    int i,dotPosition;
    long precisionValue;
    
    temp = value * Math.pow(10.0, afterDecimalPoint);
    if (Math.abs(temp) < Long.MAX_VALUE) {
      precisionValue = 	(temp > 0) ? (long)(temp + 0.5) 
                                   : -(long)(Math.abs(temp) + 0.5);
      if (precisionValue == 0) {
	stringBuffer = new StringBuffer(String.valueOf(0));
      } else {
	stringBuffer = new StringBuffer(String.valueOf(precisionValue));
      }
      if (afterDecimalPoint == 0) {
	return stringBuffer.toString();
      }
      dotPosition = stringBuffer.length() - afterDecimalPoint;
      while (((precisionValue < 0) && (dotPosition < 1)) ||
	     (dotPosition < 0)) {
	if (precisionValue < 0) {
	  stringBuffer.insert(1, '0');
	} else {
	  stringBuffer.insert(0, '0');
	}
	dotPosition++;
      }
      stringBuffer.insert(dotPosition, '.');
      if ((precisionValue < 0) && (stringBuffer.charAt(1) == '.')) {
	stringBuffer.insert(1, '0');
      } else if (stringBuffer.charAt(0) == '.') {
	stringBuffer.insert(0, '0');
      }
      int currentPos = stringBuffer.length() - 1;
      while ((currentPos > dotPosition) &&
	     (stringBuffer.charAt(currentPos) == '0')) {
	stringBuffer.setCharAt(currentPos--, ' ');
      }
      if (stringBuffer.charAt(currentPos) == '.') {
	stringBuffer.setCharAt(currentPos, ' ');
      }
      
      return stringBuffer.toString().trim();
    }
    return new String("" + value);
  }

  /**
   * Rounds a double and converts it into a formatted decimal-justified String.
   * Trailing 0's are replaced with spaces.
   *
   * @param value the double value
   * @param width the width of the string
   * @param afterDecimalPoint the number of digits after the decimal point
   * @return the double as a formatted string
   */
  public static String doubleToString(double value, int width,
				      int afterDecimalPoint) {
    
    String tempString = doubleToString(value, afterDecimalPoint);
    char[] result;
    int dotPosition;

    if ((afterDecimalPoint >= width) 
        || (tempString.indexOf('E') != -1)) { // Protects sci notation
      return tempString;
    }

    // Initialize result
    result = new char[width];
    for (int i = 0; i < result.length; i++) {
      result[i] = ' ';
    }

    if (afterDecimalPoint > 0) {
      // Get position of decimal point and insert decimal point
      dotPosition = tempString.indexOf('.');
      if (dotPosition == -1) {
	dotPosition = tempString.length();
      } else {
	result[width - afterDecimalPoint - 1] = '.';
      }
    } else {
      dotPosition = tempString.length();
    }
    

    int offset = width - afterDecimalPoint - dotPosition;
    if (afterDecimalPoint > 0) {
      offset--;
    }

    // Not enough room to decimal align within the supplied width
    if (offset < 0) {
      return tempString;
    }

    // Copy characters before decimal point
    for (int i = 0; i < dotPosition; i++) {
      result[offset + i] = tempString.charAt(i);
    }

    // Copy characters after decimal point
    for (int i = dotPosition + 1; i < tempString.length(); i++) {
      result[offset + i] = tempString.charAt(i);
    }

    return new String(result);
  }

  /**
   * Tests if a is equal to b.
   *
   * @param a a double
   * @param b a double
   */
  public static boolean eq(double a, double b){
    
    return (a - b < SMALL) && (b - a < SMALL); 
  }

  /**
   * Checks if the given array contains any non-empty options.
   *
   * @param strings an array of strings
   * @exception Exception if there are any non-empty options
   */
  public static void checkForRemainingOptions(String [] options) 
    throws Exception {
    
    int illegalOptionsFound = 0;
    StringBuffer text = new StringBuffer();

    if (options == null) {
      return;
    }
    for (int i = 0; i < options.length; i++) {
      if (options[i].length() > 0) {
	illegalOptionsFound++;
	text.append(options[i] + ' ');
      }
    }
    if (illegalOptionsFound > 0) {
      throw new Exception("Illegal options: " + text);
    }
  }
  
  /**
   * Checks if the given array contains the flag "-Char". Stops
   * searching at the first marker "--". If the flag is found,
   * it is replaced with the empty string.
   *
   * @param flag the character indicating the flag.
   * @param strings the array of strings containing all the options.
   * @return true if the flag was found
   * @exception Exception if an illegal option was found
   */

  public static boolean getFlag(char flag, String [] options) 
    throws Exception {

    if (options == null) {
      return false;
    }
    for (int i = 0; i < options.length; i++) {
      if ((options[i].length() > 1) && (options[i].charAt(0) == '-')) {
	try {
	  Double dummy = Double.valueOf(options[i]);
	} catch (NumberFormatException e) {
	  if (options[i].length() > 2) {
	    throw new Exception("Illegal option: " + options[i]);
	  }
	  if (options[i].charAt(1) == flag) {
	    options[i] = "";
	    return true;
	  }
	  if (options[i].charAt(1) == '-') {
	    return false;
	  }
	}
      }
    }
    return false;
  }

  /**
   * Gets an option indicated by a flag "-Char" from the given array
   * of strings. Stops searching at the first marker "--". Replaces 
   * flag and option with empty strings.
   *
   * @param flag the character indicating the option.
   * @param options the array of strings containing all the options.
   * @return the indicated option or an empty string
   * @exception Exception if the option indicated by the flag can't be found
   */
  public static String getOption(char flag, String [] options) 
    throws Exception {

    String newString;

    if (options == null)
      return "";
    for (int i = 0; i < options.length; i++) {
      if ((options[i].length() > 0) && (options[i].charAt(0) == '-')) {
	
	// Check if it is a negative number
	try {
	  Double dummy = Double.valueOf(options[i]);
	} catch (NumberFormatException e) {
	  if (options[i].length() != 2) {
	    throw new Exception("Illegal option: " + options[i]);
	  }
	  if (options[i].charAt(1) == flag) {