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From "Mark R. Diggory" <mdigg...@apache.org>
Subject Re: cvs commit: jakarta-commons/math/src/test/org/apache/commons/math/linear RealMatrixImplTest.java
Date Mon, 11 Oct 2004 16:34:02 GMT
Hey Phil,

Thanks for working on the RealMatrixImpl, it really gets things rolling. 
I was working on some things offline to support it further. One point of 
concern I have is that I thought we were going to make RealMatrixImpl 
"immutable" and allow the submatrix accessors return implementations 
that reference the internal matrix structure.

So, currently I would recommend our using an implementation of 
RealMatrix that maintains a reference to the original data[][] array and 
the submatix dimensions it is working within on that matrix. I have been 
working on such an implementation upto this point. Your adding the 
methods to the interface is good and I'll start working on 
implementations that use this strategy.

I also notice in the implementations there a great degree of "copying" 
by using the "getData() method" going on during the processing of 
methods such as add,subtract etc.

getData()
http://jakarta.apache.org/commons/math/xref/org/apache/commons/math/linear/RealMatrixImpl.html#256

which calls copyOut(), copying the internal array just to access its 
contents
http://jakarta.apache.org/commons/math/xref/org/apache/commons/math/linear/RealMatrixImpl.html#821

add()
http://jakarta.apache.org/commons/math/xref/org/apache/commons/math/linear/RealMatrixImpl.html#141

This seems unnecessary, I think using methods to access the array 
contents of the operand matrix would alleviate this unneeded copying. 
For instance:

> for (int row = 0; row < rowCount; row++) {
>    for (int col = 0; col < columnCount; col++) {
>       outData[row][col] = data[row][col] + m.getEntry(row,col);
>    }
> }

The modifications I am working on include these fixes and produce a 
separate abstract class "AbstractRealMatrix" which supports "storage 
independent" versions of these methods. I'm working to use this Abstract 
implementation to form the basis for RealMatrixImpl and any 
"internalized" versions used to support the column, Row and Submatrices.

-Mark


psteitz@apache.org wrote:
> psteitz     2004/10/09 14:15:56
> 
>   Modified:    math/src/java/org/apache/commons/math/linear RealMatrix.java
>                         RealMatrixImpl.java
>                math/src/test/org/apache/commons/math/linear
>                         RealMatrixImplTest.java
>   Log:
>   Added submatrix accessors.
>   Pr #30897
>   Submitted by: Kim van der Linde
>   Reviewed by: Phil Steitz
>   
>   Revision  Changes    Path
>   1.23      +30 -2     jakarta-commons/math/src/java/org/apache/commons/math/linear/RealMatrix.java
>   
>   Index: RealMatrix.java
>   ===================================================================
>   RCS file: /home/cvs/jakarta-commons/math/src/java/org/apache/commons/math/linear/RealMatrix.java,v
>   retrieving revision 1.22
>   retrieving revision 1.23
>   diff -u -r1.22 -r1.23
>   --- RealMatrix.java	5 Sep 2004 01:19:23 -0000	1.22
>   +++ RealMatrix.java	9 Oct 2004 21:15:56 -0000	1.23
>   @@ -108,7 +108,35 @@
>         * @return norm
>         */
>        double getNorm();
>   -
>   +    
>   +    /**
>   +     * Gets a submatrix. Rows and columns are indicated
>   +     * counting from 0 to n-1.
>   +     *
>   +     * @param startRow Initial row index
>   +     * @param endRow Final row index
>   +     * @param startColumn Initial column index
>   +     * @param endColumn Final column index
>   +     * @return The subMatrix containing the data of the
>   +     *         specified rows and columns
>   +     * @exception MatrixIndexException  if the indices are not valid
>   +     */
>   +   RealMatrix getSubMatrix(int startRow, int endRow, int startColumn,
>   +            int endColumn) throws MatrixIndexException;
>   +   
>   +   /**
>   +    * Gets a submatrix. Rows and columns are indicated
>   +    * counting from 0 to n-1.
>   +    *
>   +    * @param rows Array of row indices.
>   +    * @param columns Array of column indices.
>   +    * @return The subMatrix containing the data in the
>   +    *         specified rows and columns
>   +    * @exception MatrixIndexException if row or column selections are not valid
>   +    */
>   +   RealMatrix getSubMatrix(int[] selectedRows, int[] selectedColumns)
>   +   throws MatrixIndexException;
>   +             
>        /**
>         * Returns the entries in row number <code>row</code> as an array.
>         * <p>
>   
>   
>   
>   1.29      +65 -1     jakarta-commons/math/src/java/org/apache/commons/math/linear/RealMatrixImpl.java
>   
>   Index: RealMatrixImpl.java
>   ===================================================================
>   RCS file: /home/cvs/jakarta-commons/math/src/java/org/apache/commons/math/linear/RealMatrixImpl.java,v
>   retrieving revision 1.28
>   retrieving revision 1.29
>   diff -u -r1.28 -r1.29
>   --- RealMatrixImpl.java	5 Sep 2004 01:19:23 -0000	1.28
>   +++ RealMatrixImpl.java	9 Oct 2004 21:15:56 -0000	1.29
>   @@ -307,6 +307,70 @@
>            }
>            return maxColSum;
>        }
>   +    
>   +    /**
>   +     * Gets a submatrix. Rows and columns are indicated
>   +     * counting from 0 to n-1.
>   +     *
>   +     * @param startRow Initial row index
>   +     * @param endRow Final row index
>   +     * @param startColumn Initial column index
>   +     * @param endColumn Final column index
>   +     * @return The subMatrix containing the data of the
>   +     *         specified rows and columns
>   +     * @exception MatrixIndexException if row or column selections are not valid
>   +     */
>   +    public RealMatrix getSubMatrix(int startRow, int endRow, int startColumn,
>   +            int endColumn) throws MatrixIndexException {
>   +        if (startRow < 0 || startRow > endRow || endRow > data.length
>   +             || startColumn < 0 || startColumn > endColumn
>   +             || endColumn > data[0].length ) {
>   +            throw new MatrixIndexException(
>   +                    "invalid row or column index selection");
>   +        }
>   +        RealMatrixImpl subMatrix = new RealMatrixImpl(endRow - startRow+1,
>   +                endColumn - startColumn+1);
>   +        double[][] subMatrixData = subMatrix.getDataRef();
>   +        for (int i = startRow; i <= endRow; i++) {
>   +            for (int j = startColumn; j <= endColumn; j++) {
>   +                    subMatrixData[i - startRow][j - startColumn] = data[i][j];
>   +                }
>   +            }
>   +        return subMatrix;
>   +    }
>   +    
>   +    /**
>   +     * Gets a submatrix. Rows and columns are indicated
>   +     * counting from 0 to n-1.
>   +     *
>   +     * @param rows Array of row indices must be non-empty
>   +     * @param columns Array of column indices must be non-empty
>   +     * @return The subMatrix containing the data in the
>   +     *     specified rows and columns
>   +     * @exception MatrixIndexException  if supplied row or column index arrays
>   +     *     are not valid
>   +     */
>   +    public RealMatrix getSubMatrix(int[] selectedRows, int[] selectedColumns)
>   +    throws MatrixIndexException {
>   +        if (selectedRows.length * selectedColumns.length == 0) {
>   +            throw new MatrixIndexException(
>   +                    "selected row and column index arrays must be non-empty");
>   +        }
>   +        RealMatrixImpl subMatrix = new RealMatrixImpl(selectedRows.length,
>   +                selectedColumns.length);
>   +        double[][] subMatrixData = subMatrix.getDataRef();
>   +        try  {
>   +            for (int i = 0; i < selectedRows.length; i++) {
>   +                for (int j = 0; j < selectedColumns.length; j++) {
>   +                    subMatrixData[i][j] = data[selectedRows[i]][selectedColumns[j]];
>   +                }
>   +            }
>   +        }
>   +        catch (ArrayIndexOutOfBoundsException e) {
>   +            throw new MatrixIndexException("matrix dimension mismatch");
>   +        }
>   +        return subMatrix;
>   +    } 
>    
>         /**
>         * Returns the entries in row number <code>row</code> as an array.
>   
>   
>   
>   1.16      +115 -23   jakarta-commons/math/src/test/org/apache/commons/math/linear/RealMatrixImplTest.java
>   
>   Index: RealMatrixImplTest.java
>   ===================================================================
>   RCS file: /home/cvs/jakarta-commons/math/src/test/org/apache/commons/math/linear/RealMatrixImplTest.java,v
>   retrieving revision 1.15
>   retrieving revision 1.16
>   diff -u -r1.15 -r1.16
>   --- RealMatrixImplTest.java	5 Sep 2004 01:19:23 -0000	1.15
>   +++ RealMatrixImplTest.java	9 Oct 2004 21:15:56 -0000	1.16
>   @@ -27,32 +27,59 @@
>    
>    public final class RealMatrixImplTest extends TestCase {
>        
>   -    private double[][] testData = { {1d,2d,3d}, {2d,5d,3d}, {1d,0d,8d} };
>   -    private double[][] testDataLU = {{2d, 5d, 3d}, {.5d, -2.5d, 6.5d}, {0.5d, 0.2d,
.2d}};
>   -    private double[][] testDataPlus2 = { {3d,4d,5d}, {4d,7d,5d}, {3d,2d,10d} };
>   -    private double[][] testDataMinus = { {-1d,-2d,-3d}, {-2d,-5d,-3d}, 
>   +    // 3 x 3 identity matrix
>   +    protected double[][] id = { {1d,0d,0d}, {0d,1d,0d}, {0d,0d,1d} };
>   +    
>   +    // Test data for group operations
>   +    protected double[][] testData = { {1d,2d,3d}, {2d,5d,3d}, {1d,0d,8d} };
>   +    protected double[][] testDataLU = {{2d, 5d, 3d}, {.5d, -2.5d, 6.5d}, {0.5d, 0.2d,
.2d}};
>   +    protected double[][] testDataPlus2 = { {3d,4d,5d}, {4d,7d,5d}, {3d,2d,10d} };
>   +    protected double[][] testDataMinus = { {-1d,-2d,-3d}, {-2d,-5d,-3d}, 
>           {-1d,0d,-8d} };
>   -    private double[] testDataRow1 = {1d,2d,3d};
>   -    private double[] testDataCol3 = {3d,3d,8d};
>   -    private double[][] testDataInv = 
>   +    protected double[] testDataRow1 = {1d,2d,3d};
>   +    protected double[] testDataCol3 = {3d,3d,8d};
>   +    protected double[][] testDataInv = 
>            { {-40d,16d,9d}, {13d,-5d,-3d}, {5d,-2d,-1d} };
>   -    private double[] preMultTest = {8,12,33};
>   -    private double[][] testData2 ={ {1d,2d,3d}, {2d,5d,3d}};
>   -    private double[][] testData2T = { {1d,2d}, {2d,5d}, {3d,3d}};
>   -    private double[][] testDataPlusInv = 
>   +    protected double[] preMultTest = {8,12,33};
>   +    protected double[][] testData2 ={ {1d,2d,3d}, {2d,5d,3d}};
>   +    protected double[][] testData2T = { {1d,2d}, {2d,5d}, {3d,3d}};
>   +    protected double[][] testDataPlusInv = 
>            { {-39d,18d,12d}, {15d,0d,0d}, {6d,-2d,7d} };
>   -    private double[][] id = { {1d,0d,0d}, {0d,1d,0d}, {0d,0d,1d} };
>   -    private double[][] luData = { {2d,3d,3d}, {0d,5d,7d}, {6d,9d,8d} };
>   -    private double[][] luDataLUDecomposition = { {6d,9d,8d}, {0d,5d,7d}, {0.33333333333333,0d,0.33333333333333}
};
>   -    private double[][] singular = { {2d,3d}, {2d,3d} };
>   -    private double[][] bigSingular = {{1d,2d,3d,4d}, {2d,5d,3d,4d},
>   +    
>   +    // lu decomposition tests
>   +    protected double[][] luData = { {2d,3d,3d}, {0d,5d,7d}, {6d,9d,8d} };
>   +    protected double[][] luDataLUDecomposition = { {6d,9d,8d}, {0d,5d,7d},
>   +            {0.33333333333333,0d,0.33333333333333} };
>   +    
>   +    // singular matrices
>   +    protected double[][] singular = { {2d,3d}, {2d,3d} };
>   +    protected double[][] bigSingular = {{1d,2d,3d,4d}, {2d,5d,3d,4d},
>            {7d,3d,256d,1930d}, {3d,7d,6d,8d}}; // 4th row = 1st + 2nd
>   -    private double[][] detData = { {1d,2d,3d}, {4d,5d,6d}, {7d,8d,10d} };
>   -    private double[][] detData2 = { {1d, 3d}, {2d, 4d}};
>   -    private double[] testVector = {1,2,3};
>   -    private double[] testVector2 = {1,2,3,4};
>   -    private double entryTolerance = 10E-16;
>   -    private double normTolerance = 10E-14;
>   +    protected double[][] detData = { {1d,2d,3d}, {4d,5d,6d}, {7d,8d,10d} };
>   +    protected double[][] detData2 = { {1d, 3d}, {2d, 4d}};
>   +    
>   +    // vectors
>   +    protected double[] testVector = {1,2,3};
>   +    protected double[] testVector2 = {1,2,3,4};
>   +    
>   +    // submatrix accessor tests
>   +    protected double[][] subTestData = {{1, 2, 3, 4}, {1.5, 2.5, 3.5, 4.5},
>   +            {2, 4, 6, 8}, {4, 5, 6, 7}}; 
>   +    // array selections
>   +    protected double[][] subRows02Cols13 = { {2, 4}, {4, 8}};
>   +    protected double[][] subRows03Cols12 = { {2, 3}, {5, 6}};
>   +    protected double[][] subRows03Cols123 = { {2, 3, 4} , {5, 6, 7}};
>   +    // effective permutations
>   +    protected double[][] subRows20Cols123 = { {4, 6, 8} , {2, 3, 4}};
>   +    protected double[][] subRows31Cols31 = {{7, 5}, {4.5, 2.5}};
>   +    // contiguous ranges
>   +    protected double[][] subRows01Cols23 = {{3,4} , {3.5, 4.5}};
>   +    protected double[][] subRows23Cols00 = {{2} , {4}};
>   +    protected double[][] subRows00Cols33 = {{4}};
>   +    
>   +    // tolerances
>   +    protected double entryTolerance = 10E-16;
>   +    protected double normTolerance = 10E-14;
>        
>        public RealMatrixImplTest(String name) {
>            super(name);
>   @@ -462,6 +489,71 @@
>            assertEquals(-1 * solution[0] + 7 * solution[1] + 6 * solution[2], constants[1],
1E-12);
>            assertEquals(4 * solution[0] - 3 * solution[1] -5 * solution[2], constants[2],
1E-12);   
>            
>   +    }
>   +    
>   +    // test submatrix accessors
>   +    public void testSubMatrix() {
>   +        RealMatrix m = new RealMatrixImpl(subTestData);
>   +        RealMatrix mRows23Cols00 = new RealMatrixImpl(subRows23Cols00);
>   +        RealMatrix mRows00Cols33 = new RealMatrixImpl(subRows00Cols33);
>   +        RealMatrix mRows01Cols23 = new RealMatrixImpl(subRows01Cols23);
>   +        RealMatrix mRows02Cols13 = new RealMatrixImpl(subRows02Cols13);
>   +        RealMatrix mRows03Cols12 = new RealMatrixImpl(subRows03Cols12);
>   +        RealMatrix mRows03Cols123 = new RealMatrixImpl(subRows03Cols123);
>   +        RealMatrix mRows20Cols123 = new RealMatrixImpl(subRows20Cols123);
>   +        RealMatrix mRows31Cols31 = new RealMatrixImpl(subRows31Cols31);
>   +        assertClose("Rows23Cols00", mRows23Cols00, 
>   +                m.getSubMatrix(2 , 3 , 0, 0), normTolerance );
>   +        assertClose("Rows00Cols33", mRows00Cols33, 
>   +                m.getSubMatrix(0 , 0 , 3, 3), normTolerance );
>   +        assertClose("Rows01Cols23", mRows01Cols23,
>   +                m.getSubMatrix(0 , 1 , 2, 3), normTolerance );   
>   +        assertClose("Rows02Cols13", mRows02Cols13,
>   +                m.getSubMatrix(new int[] {0,2}, new int[] {1,3}), normTolerance);
 
>   +        assertClose("Rows03Cols12", mRows03Cols12,
>   +                m.getSubMatrix(new int[] {0,3}, new int[] {1,2}), normTolerance);
 
>   +        assertClose("Rows03Cols123", mRows03Cols123,
>   +                m.getSubMatrix(new int[] {0,3}, new int[] {1,2,3}), normTolerance);

>   +        assertClose("Rows20Cols123", mRows20Cols123,
>   +                m.getSubMatrix(new int[] {2,0}, new int[] {1,2,3}), normTolerance);

>   +        assertClose("Rows31Cols31", mRows31Cols31,
>   +                m.getSubMatrix(new int[] {3,1}, new int[] {3,1}), normTolerance);

>   +        try {
>   +            m.getSubMatrix(1,0,2,4);
>   +            fail("Expecting MatrixIndexException");
>   +        } catch (MatrixIndexException ex) {
>   +            // expected
>   +        }
>   +        try {
>   +            m.getSubMatrix(-1,1,2,2);
>   +            fail("Expecting MatrixIndexException");
>   +        } catch (MatrixIndexException ex) {
>   +            // expected
>   +        }
>   +        try {
>   +            m.getSubMatrix(1,0,2,2);
>   +            fail("Expecting MatrixIndexException");
>   +        } catch (MatrixIndexException ex) {
>   +            // expected
>   +        }
>   +        try {
>   +            m.getSubMatrix(1,0,2,4);
>   +            fail("Expecting MatrixIndexException");
>   +        } catch (MatrixIndexException ex) {
>   +            // expected
>   +        }
>   +        try {
>   +            m.getSubMatrix(new int[] {}, new int[] {0});
>   +            fail("Expecting MatrixIndexException");
>   +        } catch (MatrixIndexException ex) {
>   +            // expected
>   +        }
>   +        try {
>   +            m.getSubMatrix(new int[] {0}, new int[] {4});
>   +            fail("Expecting MatrixIndexException");
>   +        } catch (MatrixIndexException ex) {
>   +            // expected
>   +        }
>        }
>        
>        //--------------- -----------------Protected methods
>   
>   
>   
> 
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> 

-- 
Mark Diggory
Open Source Software Developer
Apache Jakarta Project
http://jakarta.apache.org

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