weka.classifiers

## Class CostMatrix

- java.lang.Object
- - weka.classifiers.CostMatrix

- All Implemented Interfaces:
    java.io.Serializable, RevisionHandler

      public class CostMatrix
      extends java.lang.Object
      implements java.io.Serializable, RevisionHandler

  Class for storing and manipulating a misclassification cost matrix. The element at position i,j in the matrix is the penalty for classifying an instance of class j as class i. Cost values can be fixed or computed on a per-instance basis (cost sensitive evaluation only) from the value of an attribute or a mathematical expression involving attribute(s).
  Values in an instance are accessed in an expression by prefixing their index (starting at 1) with the character 'a'. E.g.
  a1 ˆ 2 * a5 / log(a7 * 4.0)
  Supported opperators: +, -, *, /, ^, log, abs, cos, exp, sqrt, floor, ceil, rint, tan, sin, (, ).
  Version:
    $Revision: 11868 $
  Author:
    Mark Hall, Richard Kirkby (rkirkby@cs.waikato.ac.nz)
  See Also:
    `UnsupportedAttributeTypeException`, Serialized Form

- - ### Field Summary

    Fields
    Modifier and Type | Field and Description
    --- | ---
    `static java.lang.String` | `FILE_EXTENSION` The deafult file extension for cost matrix files

  - ### Constructor Summary

    Constructors
    Constructor and Description
    `CostMatrix(CostMatrix toCopy)` Creates a cost matrix that is a copy of another.
    `CostMatrix(int numOfClasses)` Creates a default cost matrix of a particular size.
    `CostMatrix(java.io.Reader reader)` Reads a matrix from a reader.

  - ### Method Summary

    All Methods Static Methods Instance Methods Concrete Methods
    Modifier and Type | Method and Description
    --- | ---
    `Instances` | `applyCostMatrix(Instances data, java.util.Random random)` Applies the cost matrix to a set of instances.
    `double[]` | `expectedCosts(double[] classProbs)` Calculates the expected misclassification cost for each possible class value, given class probability estimates.
    `double[]` | `expectedCosts(double[] classProbs, Instance inst)` Calculates the expected misclassification cost for each possible class value, given class probability estimates.
    `java.lang.Object` | `getCell(int rowIndex, int columnIndex)` Return the contents of a particular cell.
    `double` | `getElement(int rowIndex, int columnIndex)` Return the value of a cell as a double (for legacy code)
    `double` | `getElement(int rowIndex, int columnIndex, Instance inst)` Return the value of a cell as a double.
    `double` | `getMaxCost(int classVal)` Gets the maximum cost for a particular class value.
    `double` | `getMaxCost(int classVal, Instance inst)` Gets the maximum cost for a particular class value.
    `java.lang.String` | `getRevision()` Returns the revision string.
    `void` | `initialize()` Initializes the matrix
    `void` | `normalize()` Normalizes the matrix so that the diagonal contains zeros.
    `int` | `numColumns()` Same as size
    `int` | `numRows()` Same as size
    `static CostMatrix` | `parseMatlab(java.lang.String matlab)` creates a matrix from the given Matlab string.
    `void` | `readOldFormat(java.io.Reader reader)` Loads a cost matrix in the old format from a reader.
    `void` | `setCell(int rowIndex, int columnIndex, java.lang.Object value)` Set the value of a particular cell in the matrix
    `void` | `setElement(int rowIndex, int columnIndex, double value)` Set the value of a cell as a double
    `int` | `size()` The number of rows (and columns)
    `java.lang.String` | `toMatlab()` converts the Matrix into a single line Matlab string: matrix is enclosed by parentheses, rows are separated by semicolon and single cells by blanks, e.g., [1 2; 3 4].
    `java.lang.String` | `toString()` Converts a matrix to a string.
    `void` | `write(java.io.Writer w)` Writes out a matrix.

    - ### Methods inherited from class java.lang.Object

      `equals, getClass, hashCode, notify, notifyAll, wait, wait, wait`

- - ### Field Detail

    - #### FILE_EXTENSION

          public static java.lang.String FILE_EXTENSION

      The deafult file extension for cost matrix files

  - ### Constructor Detail

    - #### CostMatrix

          public CostMatrix(int numOfClasses)

      Creates a default cost matrix of a particular size. All diagonal values will be 0 and all non-diagonal values 1.
      Parameters:
        `numOfClasses` - the number of classes that the cost matrix holds.

    - #### CostMatrix

          public CostMatrix(CostMatrix toCopy)

      Creates a cost matrix that is a copy of another.
      Parameters:
        `toCopy` - the matrix to copy.

    - #### CostMatrix

          public CostMatrix(java.io.Reader reader)
                     throws java.lang.Exception

      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. (FracPete: taken from old weka.core.Matrix class)
      Parameters:
        `reader` - the reader containing the matrix
      Throws:
        `java.lang.Exception` - if an error occurs
      See Also:
        `write(Writer)`

  - ### Method Detail

    - #### initialize

          public void initialize()

      Initializes the matrix

    - #### size

          public int size()

      The number of rows (and columns)
      Returns:
        the size of the matrix

    - #### numColumns

          public int numColumns()

      Same as size
      Returns:
        the number of columns

    - #### numRows

          public int numRows()

      Same as size
      Returns:
        the number of rows

    - #### applyCostMatrix

          public Instances applyCostMatrix(Instances data,
                                           java.util.Random random)
                                    throws java.lang.Exception

      Applies the cost matrix to a set of instances. If a random number generator is supplied the instances will be resampled, otherwise they will be rewighted. Adapted from code once sitting in Instances.java
      Parameters:
        `data` - the instances to reweight.
        `random` - a random number generator for resampling, if null then instances are rewighted.
      Returns:
        a new dataset reflecting the cost of misclassification.
      Throws:
        `java.lang.Exception` - if the data has no class or the matrix in inappropriate.

    - #### expectedCosts

          public double[] expectedCosts(double[] classProbs)
                                 throws java.lang.Exception

      Calculates the expected misclassification cost for each possible class value, given class probability estimates.
      Parameters:
        `classProbs` - the class probability estimates.
      Returns:
        the expected costs.
      Throws:
        `java.lang.Exception` - if the wrong number of class probabilities is supplied.

    - #### expectedCosts

          public double[] expectedCosts(double[] classProbs,
                                        Instance inst)
                                 throws java.lang.Exception

      Calculates the expected misclassification cost for each possible class value, given class probability estimates.
      Parameters:
        `classProbs` - the class probability estimates.
        `inst` - the current instance for which the class probabilites apply. Is used for computing any non-fixed cost values.
      Returns:
        the expected costs.
      Throws:
        `java.lang.Exception` - if something goes wrong

    - #### getMaxCost

          public double getMaxCost(int classVal)
                            throws java.lang.Exception

      Gets the maximum cost for a particular class value.
      Parameters:
        `classVal` - the class value.
      Returns:
        the maximum cost.
      Throws:
        `java.lang.Exception` - if cost matrix contains non-fixed costs

    - #### getMaxCost

          public double getMaxCost(int classVal,
                                   Instance inst)
                            throws java.lang.Exception

      Gets the maximum cost for a particular class value.
      Parameters:
        `classVal` - the class value.
      Returns:
        the maximum cost.
      Throws:
        `java.lang.Exception` - if cost matrix contains non-fixed costs

    - #### normalize

          public void normalize()

      Normalizes the matrix so that the diagonal contains zeros.

    - #### readOldFormat

          public void readOldFormat(java.io.Reader reader)
                             throws java.lang.Exception

      Loads a cost matrix in the old format from a reader. Adapted from code once sitting in Instances.java
      Parameters:
        `reader` - the reader to get the values from.
      Throws:
        `java.lang.Exception` - if the matrix cannot be read correctly.

    - #### write

          public void write(java.io.Writer w)
                     throws java.lang.Exception

      Writes out a matrix. The format can be read via the CostMatrix(Reader) constructor. (FracPete: taken from old weka.core.Matrix class)
      Parameters:
        `w` - the output Writer
      Throws:
        `java.lang.Exception` - if an error occurs

    - #### toMatlab

          public java.lang.String toMatlab()

      converts the Matrix into a single line Matlab string: matrix is enclosed by parentheses, rows are separated by semicolon and single cells by blanks, e.g., [1 2; 3 4].
      Returns:
        the matrix in Matlab single line format

    - #### parseMatlab

          public static CostMatrix parseMatlab(java.lang.String matlab)
                                        throws java.lang.Exception

      creates a matrix from the given Matlab string.
      Parameters:
        `matlab` - the matrix in matlab format
      Returns:
        the matrix represented by the given string
      Throws:
        `java.lang.Exception`
      See Also:
        `toMatlab()`

    - #### setCell

          public final void setCell(int rowIndex,
                                    int columnIndex,
                                    java.lang.Object value)

      Set the value of a particular cell in the matrix
      Parameters:
        `rowIndex` - the row
        `columnIndex` - the column
        `value` - the value to set

    - #### getCell

          public final java.lang.Object getCell(int rowIndex,
                                                int columnIndex)

      Return the contents of a particular cell. Note: this method returns the Object stored at a particular cell.
      Parameters:
        `rowIndex` - the row
        `columnIndex` - the column
      Returns:
        the value at the cell

    - #### getElement

          public final double getElement(int rowIndex,
                                         int columnIndex)
                                  throws java.lang.Exception

      Return the value of a cell as a double (for legacy code)
      Parameters:
        `rowIndex` - the row
        `columnIndex` - the column
      Returns:
        the value at a particular cell as a double
      Throws:
        `java.lang.Exception` - if the value is not a double

    - #### getElement

          public final double getElement(int rowIndex,
                                         int columnIndex,
                                         Instance inst)
                                  throws java.lang.Exception

      Return the value of a cell as a double. Computes the value for non-fixed costs using the supplied Instance
      Parameters:
        `rowIndex` - the row
        `columnIndex` - the column
      Returns:
        the value from a particular cell
      Throws:
        `java.lang.Exception` - if something goes wrong

    - #### setElement

          public final void setElement(int rowIndex,
                                       int columnIndex,
                                       double value)

      Set the value of a cell as a double
      Parameters:
        `rowIndex` - the row
        `columnIndex` - the column
        `value` - the value (double) to set

    - #### toString

          public java.lang.String toString()

      Converts a matrix to a string. (FracPete: taken from old weka.core.Matrix class)
      Overrides:
        `toString` in class `java.lang.Object`
      Returns:
        the converted string

    - #### getRevision

          public java.lang.String getRevision()

      Returns the revision string.
      Specified by:
        `getRevision` in interface `RevisionHandler`
      Returns:
        the revision