matrix.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.
 */


/*
 *    Matrix.java
 *    Copyright (C) 1999 Yong Wang, Eibe Frank, Len Trigg, Gabi Schmidberger
 *
 *    The code contains some functions from the CERN Jet Java libraries
 *    for these the following copyright applies:
 *
 *    Copyright (C) 1999 CERN - European Organization for Nuclear Research.
 *    Permission to use, copy, modify, distribute and sell this software and
 *    its documentation for any purpose is hereby granted without fee, provided
 *    that the above copyright notice appear in all copies and that both that
 *    copyright notice and this permission notice appear in supporting documentation. 
 *    CERN and the University of Waikato make no representations about the
 *    suitability of this software for any purpose.
 *    It is provided "as is" without expressed or implied warranty.
 *
 */

package weka.core;

import java.io.Writer;
import java.io.Reader;
import java.io.LineNumberReader;
import java.io.Serializable;
import java.util.StringTokenizer;

/**
 * Class for performing operations on a matrix of floating-point values.
 *
 * @author Gabi Schmidberger ([e-mail])
 * @author Yong Wang ([e-mail])
 * @author Eibe Frank ([e-mail])
 * @author Len Trigg ([e-mail])
 * @version $Revision: 1.1.1.1 $
 */
public class Matrix implements Cloneable, Serializable {

  /**
   * The values of the matrix */
  protected double [][] m_Elements;

  /**
   * Constructs a matrix and initializes it with default values.
   *
   * @param nr the number of rows
   * @param nc the number of columns
   */
  public Matrix(int nr, int nc) {

    m_Elements = new double[nr][nc];
    initialize();
  }

  /**
   * Constructs a matrix using a given array.
   *
   * @param array the values of the matrix
   */
  public Matrix(double[][] array) throws Exception {
    
    m_Elements = new double[array.length][array[0].length];
    for (int i = 0; i < array.length; i++) {
      for (int j = 0; j < array[0].length; j++) {
	m_Elements[i][j] = array[i][j];
      }
    } 
  }

  /**
   * Reads a matrix from a reader. The first line in the file should
   * contain the number of rows and columns. Subsequent lines
   * contain elements of the matrix.
   *
   * @param r the reader containing the matrix
   * @exception Exception if an error occurs
   */
  public Matrix(Reader r) throws Exception {

    LineNumberReader lnr = new LineNumberReader(r);
    String line;
    int currentRow = -1;

    while ((line = lnr.readLine()) != null) {

      if (line.startsWith("%")) { // Comments
	continue;
      }
      StringTokenizer st = new StringTokenizer(line);
      if (!st.hasMoreTokens()) {  // Ignore blank lines
	continue;
      }

      if (currentRow < 0) {
	int rows = Integer.parseInt(st.nextToken());
	if (!st.hasMoreTokens()) {
	  throw new Exception("Line " + lnr.getLineNumber() 
			      + ": expected number of columns");
	}
	int cols = Integer.parseInt(st.nextToken());
	m_Elements = new double [rows][cols];
	initialize();
	currentRow ++;
	continue;

      } else {
	if (currentRow == numRows()) {
	  throw new Exception("Line " + lnr.getLineNumber() 
			      + ": too many rows provided");
	}
	for (int i = 0; i < numColumns(); i++) {
	  if (!st.hasMoreTokens()) {
	    throw new Exception("Line " + lnr.getLineNumber() 
				+ ": too few matrix elements provided");
	  }
	  m_Elements[currentRow][i] = Double.valueOf(st.nextToken())
	    .doubleValue();
	}
	currentRow ++;
      }
    }
    if (currentRow == -1) {
      throw new Exception("Line " + lnr.getLineNumber() 
			      + ": expected number of rows");
    } else if (currentRow != numRows()) {
      throw new Exception("Line " + lnr.getLineNumber() 
			  + ": too few rows provided");
    }
  }

  /**
   * Creates and returns a clone of this object.
   *
   * @return a clone of this instance.
   * @exception CloneNotSupportedException if an error occurs
   */
  public Object clone() throws CloneNotSupportedException {

    Matrix m = (Matrix)super.clone();
    m.m_Elements = new double[numRows()][numColumns()];
    for (int r = 0; r < numRows(); r++) {
      for (int c = 0; c < numColumns(); c++) {
        m.m_Elements[r][c] = m_Elements[r][c];
      }
    }
    return m;
  }

  /**
   * Writes out a matrix.
   *
   * @param w the output Writer
   * @exception Exception if an error occurs
   */
  public void write(Writer w) throws Exception {

    w.write("% Rows\tColumns\n");
    w.write("" + numRows() + "\t" + numColumns() + "\n");
    w.write("% Matrix elements\n");
    for(int i = 0; i < numRows(); i++) {
      for(int j = 0; j < numColumns(); j++) {
	w.write("" + m_Elements[i][j] + "\t");
      }
      w.write("\n");
    }
    w.flush();
  }

  /**
   * Resets the elements to default values (i.e. 0).
   */
  protected void initialize() {

    for (int i = 0; i < numRows(); i++) {
      for (int j = 0; j < numColumns(); j++) {
	m_Elements[i][j] = 0;
      }
    }
  }

  /**
   * Returns the value of a cell in the matrix.
   *
   * @param rowIndex the row's index
   * @param columnIndex the column's index
   * @return the value of the cell of the matrix
   */
  public final double getElement(int rowIndex, int columnIndex) {
    
    return m_Elements[rowIndex][columnIndex];
  }

  /**
   * Add a value to an element.
   *
   * @param rowIndex the row's index.
   * @param columnIndex the column's index.
   * @param value the value to add.
   */
  public final void addElement(int rowIndex, int columnIndex, double value) {

    m_Elements[rowIndex][columnIndex] += value;
  }

  /**
   * Returns the number of rows in the matrix.
   *
   * @return the number of rows
   */
  public final int numRows() {
  
    return m_Elements.length;
  }

  /**
   * Returns the number of columns in the matrix.
   *
   * @return the number of columns
   */
  public final int numColumns() {
  
    return m_Elements[0].length;
  }

  /**
   * Sets an element of the matrix to the given value.
   *
   * @param rowIndex the row's index
   * @param columnIndex the column's index
   * @param value the value
   */
  public final void setElement(int rowIndex, int columnIndex, double value) {
    
    m_Elements[rowIndex][columnIndex] = value;
  }

  /**
   * Sets a row of the matrix to the given row. Performs a deep copy.
   *
   * @param index the row's index
   * @param newRow an array of doubles
   */
  public final void setRow(int index, double[] newRow) {

    for (int i = 0; i < newRow.length; i++) {
      m_Elements[index][i] = newRow[i];
    }
  }
  
  /**
   * Gets a row of the matrix and returns it as double array.
   *
   * @param index the row's index
   * @return an array of doubles
   */
  public double[] getRow(int index) {

    double [] newRow = new double[this.numColumns()];
    for (int i = 0; i < newRow.length; i++) {
      newRow[i] = m_Elements[index][i];
    }
    return newRow;
  }

  /**
   * Gets a column of the matrix and returns it as a double array.
   *
   * @param index the column's index
   * @return an array of doubles
   */
  public double[] getColumn(int index) {

    double [] newColumn = new double[this.numRows()];
    for (int i = 0; i < newColumn.length; i++) {
      newColumn[i] = m_Elements[i][index];
    }
    return newColumn;
  }

  /**
   * Sets a column of the matrix to the given column. Performs a deep copy.
   *
   * @param index the column's index
   * @param newColumn an array of doubles
   */
  public final void setColumn(int index, double[] newColumn) {

    for (int i = 0; i < m_Elements.length; i++) {
      m_Elements[i][index] = newColumn[i];
    }
  }

  /** 
   * Converts a matrix to a string
   *
   * @return the converted string
   */
  public String toString() {

    // Determine the width required for the maximum element,
    // and check for fractional display requirement.
    double maxval = 0;
    boolean fractional = false;
    for(int i = 0; i < m_Elements.length; i++) {
      for(int j = 0; j < m_Elements[i].length; j++) {
	double current = m_Elements[i][j];
        if (current < 0) {
          current *= -10;
        }
	if (current > maxval) {
	  maxval = current;
	}
	double fract = current - Math.rint(current);
	if (!fractional
	    && ((Math.log(fract) / Math.log(10)) >= -2)) {
	  fractional = true;
	}
      }
    }
    int width = (int)(Math.log(maxval) / Math.log(10) 
                      + (fractional ? 4 : 1));

    StringBuffer text = new StringBuffer();   
    for(int i = 0; i < m_Elements.length; i++) {
      for(int j = 0; j < m_Elements[i].length; j++) {
        text.append(" ").append(Utils.doubleToString(m_Elements[i][j],
                                                     width,
                                                     (fractional ? 2 : 0)));
      }
      text.append("\n");
    }
    
    return text.toString();
  } 
    
  /**
   * Returns the sum of this matrix with another.
   *
   * @return a matrix containing the sum.
   */
  public final Matrix add(Matrix other) {

    int nr = m_Elements.length, nc = m_Elements[0].length;
    Matrix b;
    try {
      b = (Matrix)clone();
    } catch (CloneNotSupportedException ex) {
      b = new Matrix(nr, nc);
    }
    
    for(int i = 0;i < nc; i++) {
      for(int j = 0; j < nr; j++) {
        b.m_Elements[i][j] = m_Elements[j][i] + other.m_Elements[j][i];
      }
    }
    return b;
  }
  
  /**
   * Returns the transpose of a matrix.
   *
   * @return the transposition of this instance.
   */
  public final Matrix transpose() {

    int nr = m_Elements.length, nc = m_Elements[0].length;
    Matrix b = new Matrix(nc, nr);

    for(int i = 0;i < nc; i++) {
      for(int j = 0; j < nr; j++) {
	b.m_Elements[i][j] = m_Elements[j][i];
      }
    }

    return b;
  }