SparseRCDoubleMatrix2D (Parallel Colt 0.10.1

java.lang.Object
- cern.colt.PersistentObject
- - cern.colt.matrix.AbstractMatrix
  - - cern.colt.matrix.AbstractMatrix2D
    - - cern.colt.matrix.tdouble.DoubleMatrix2D
      - cern.colt.matrix.tdouble.impl.WrapperDoubleMatrix2D
        
        cern.colt.matrix.tdouble.impl.SparseRCDoubleMatrix2D

All Implemented Interfaces:: Serializable, Cloneable

public class SparseRCDoubleMatrix2D
extends WrapperDoubleMatrix2D

Sparse row-compressed 2-d matrix holding double elements. First see the package summary and javadoc tree view to get the broad picture.

Implementation:

Internally uses the standard sparse row-compressed format
Note that this implementation is not synchronized.

Memory requirements:

Cells that

are never set to non-zero values do not use any memory.
switch from zero to non-zero state do use memory.
switch back from non-zero to zero state also do use memory. Their memory is not automatically reclaimed (because of the lists vs. arrays). Reclamation can be triggered via trimToSize().

memory [bytes] = 4*rows + 12 * nonZeros.
Where nonZeros = cardinality() is the number of non-zero cells. Thus, a 1000 x 1000 matrix with 1000000 non-zero cells consumes 11.5 MB. The same 1000 x 1000 matrix with 1000 non-zero cells consumes 15 KB.

Time complexity:

Getting a cell value takes time O(log nzr) where nzr is the number of non-zeros of the touched row. This is usually quick, because typically there are only few nonzeros per row. So, in practice, get has expected constant time. Setting a cell value takes worst-case time O(nz) where nzr is the total number of non-zeros in the matrix. This can be extremely slow, but if you traverse coordinates properly (i.e. upwards), each write is done much quicker:

 // rather quick
 matrix.assign(0);
 for (int row = 0; row < rows; row++) {
     for (int column = 0; column < columns; column++) {
         if (someCondition)
             matrix.setQuick(row, column, someValue);
     }
 }
 
 // poor
 matrix.assign(0);
 for (int row = rows; --row >= 0;) {
     for (int column = columns; --column >= 0;) {
         if (someCondition)
             matrix.setQuick(row, column, someValue);
     }
 }

If for whatever reasons you can't iterate properly, consider to create an empty dense matrix, store your non-zeros in it, then call sparse.assign(dense). Under the circumstances, this is still rather quick.

Fast iteration over non-zeros can be done via forEachNonZero(cern.colt.function.tdouble.IntIntDoubleFunction), which supplies your function with row, column and value of each nonzero. Although the internally implemented version is a bit more sophisticated, here is how a quite efficient user-level matrix-vector multiplication could look like:

 // Linear algebraic y = A * x
 A.forEachNonZero(new cern.colt.function.IntIntDoubleFunction() {
     public double apply(int row, int column, double value) {
         y.setQuick(row, y.getQuick(row) + value * x.getQuick(column));
         return value;
     }
 });

Here is how a a quite efficient user-level combined scaling operation could look like:

 // Elementwise A = A + alpha*B
 B.forEachNonZero(new cern.colt.function.IntIntDoubleFunction() {
     public double apply(int row, int column, double value) {
         A.setQuick(row, column, A.getQuick(row, column) + alpha * value);
         return value;
     }
 });

Method assign(DoubleMatrix2D,cern.colt.function.tdouble.DoubleDoubleFunction) does just that if you supply DoubleFunctions.plusMultSecond(double) as argument.

Version:: 0.9, 04/14/2000
Author:: wolfgang.hoschek@cern.ch
See Also:: Serialized Form

Constructor Summary

Constructors
Constructor and Description
`SparseRCDoubleMatrix2D(double[][] values)` Constructs a matrix with a copy of the given values.
`SparseRCDoubleMatrix2D(int rows, int columns)` Constructs a matrix with a given number of rows and columns.
`SparseRCDoubleMatrix2D(int rows, int columns, int nzmax)` Constructs a matrix with a given number of rows and columns.
`SparseRCDoubleMatrix2D(int rows, int columns, int[] rowPointers, int[] columnIndexes, double[] values)` Constructs a matrix with given parameters.
`SparseRCDoubleMatrix2D(int rows, int columns, int[] rowIndexes, int[] columnIndexes, double[] values, boolean removeDuplicates, boolean removeZeroes, boolean sortColumnIndexes)` Constructs a matrix with indexes and values given in the coordinate format.
`SparseRCDoubleMatrix2D(int rows, int columns, int[] rowIndexes, int[] columnIndexes, double value, boolean removeDuplicates, boolean sortColumnIndexes)` Constructs a matrix with indexes given in the coordinate format and single value.

Method Summary

Methods
Modifier and Type	Method and Description
`DoubleMatrix2D`	`assign(double value)` Sets all cells to the state specified by `value`.
`DoubleMatrix2D`	`assign(DoubleFunction function)` Assigns the result of a function to each cell; `x[row,col] = function(x[row,col])`.
`DoubleMatrix2D`	`assign(DoubleMatrix2D source)` Replaces all cell values of the receiver with the values of another matrix.
`DoubleMatrix2D`	`assign(DoubleMatrix2D y, DoubleDoubleFunction function)` Assigns the result of a function to each cell; `x[row,col] = function(x[row,col],y[row,col])`.
`int`	`cardinality()` Returns the number of cells having non-zero values; ignores tolerance.
`DoubleMatrix2D`	`forEachNonZero(IntIntDoubleFunction function)` Assigns the result of a function to each non-zero cell; `x[row,col] = function(x[row,col])`.
`SparseCCDoubleMatrix2D`	`getColumnCompressed()` Returns a new matrix that has the same elements as this matrix, but is in a column-compressed form.
`int[]`	`getColumnIndexes()` Returns column indexes
`DenseDoubleMatrix2D`	`getDense()` Returns a new matrix that has the same elements as this matrix, but is in a dense form.
`double`	`getQuick(int row, int column)` Returns the matrix cell value at coordinate `[row,column]`.
`int[]`	`getRowPointers()` Returns row pointers
`SparseRCDoubleMatrix2D`	`getTranspose()` Returns a new matrix that is the transpose of this matrix.
`double[]`	`getValues()` Returns numerical values
`boolean`	`hasColumnIndexesSorted()` Returns true if column indexes are sorted, false otherwise
`DoubleMatrix2D`	`like(int rows, int columns)` Construct and returns a new empty matrix of the same dynamic type as the receiver, having the specified number of rows and columns.
`DoubleMatrix1D`	`like1D(int size)` Construct and returns a new 1-d matrix of the corresponding dynamic type, entirelly independent of the receiver.
`void`	`removeDuplicates()` Removes (sums) duplicate entries (if any}
`void`	`removeZeroes()` Removes zero entries (if any)
`void`	`setQuick(int row, int column, double value)` Sets the matrix cell at coordinate `[row,column]` to the specified value.
`void`	`sortColumnIndexes()` Sorts column indexes
`String`	`toString()` Returns a string representation using default formatting.
`void`	`trimToSize()` Releases any superfluous internal memory.
`DoubleMatrix1D`	`zMult(DoubleMatrix1D y, DoubleMatrix1D z, double alpha, double beta, boolean transposeA)` Linear algebraic matrix-vector multiplication; `z = alpha * A * y + beta*z`.
`DoubleMatrix2D`	`zMult(DoubleMatrix2D B, DoubleMatrix2D C, double alpha, double beta, boolean transposeA, boolean transposeB)` Linear algebraic matrix-matrix multiplication; `C = alpha * A x B + beta*C`.

Methods inherited from class cern.colt.matrix.tdouble.impl.WrapperDoubleMatrix2D
assign, assign, dct2, dctColumns, dctRows, dht2, dhtColumns, dhtRows, dst2, dstColumns, dstRows, elements, equals, equals, fft2, getFft2, getFftColumns, getFftRows, getIfft2, getIfftColumns, getIfftRows, idct2, idctColumns, idctRows, idht2, idhtColumns, idhtRows, idst2, idstColumns, idstRows, ifft2, vectorize, viewColumn, viewColumnFlip, viewDice, viewPart, viewRow, viewRowFlip, viewSelection, viewStrides

Methods inherited from class cern.colt.matrix.tdouble.DoubleMatrix2D
aggregate, aggregate, aggregate, aggregate, assign, assign, assign, assign, copy, get, getMaxLocation, getMinLocation, getNegativeValues, getNonZeros, getPositiveValues, like, normalize, set, toArray, viewSelection, viewSelection, viewSorted, zAssign8Neighbors, zMult, zMult, zSum

Methods inherited from class cern.colt.matrix.AbstractMatrix2D
checkShape, checkShape, columns, columnStride, index, rows, rowStride, size, toStringShort

Methods inherited from class cern.colt.matrix.AbstractMatrix
ensureCapacity, isView

Methods inherited from class cern.colt.PersistentObject
clone

Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - SparseRCDoubleMatrix2D
```
public SparseRCDoubleMatrix2D(double[][] values)
```
    Constructs a matrix with a copy of the given values. values is required to have the form values[row][column] and have exactly the same number of columns in every row.
    The values are copied. So subsequent changes in values are not reflected in the matrix, and vice-versa.
    
    Parameters:
    values - The values to be filled into the new matrix.
    
    Throws:
    
    IllegalArgumentException - if for any 1 <= row < values.length: values[row].length != values[row-1].length .
  - SparseRCDoubleMatrix2D
```
public SparseRCDoubleMatrix2D(int rows,
                      int columns)
```
    Constructs a matrix with a given number of rows and columns. All entries are initially 0.
    
    Parameters:
    rows - the number of rows the matrix shall have.
    columns - the number of columns the matrix shall have.
    
    Throws:
    
    IllegalArgumentException - if rows<0 || columns<0 || (double)columns*rows > Integer.MAX_VALUE .
  - SparseRCDoubleMatrix2D
```
public SparseRCDoubleMatrix2D(int rows,
                      int columns,
                      int nzmax)
```
    Constructs a matrix with a given number of rows and columns. All entries are initially 0.
    
    Parameters:
    rows - the number of rows the matrix shall have.
    columns - the number of columns the matrix shall have.
    nzmax - maximum number of nonzero elements
    
    Throws:
    
    IllegalArgumentException - if rows<0 || columns<0 || (double)columns*rows > Integer.MAX_VALUE .
  - SparseRCDoubleMatrix2D
```
public SparseRCDoubleMatrix2D(int rows,
                      int columns,
                      int[] rowIndexes,
                      int[] columnIndexes,
                      double value,
                      boolean removeDuplicates,
                      boolean sortColumnIndexes)
```
    Constructs a matrix with indexes given in the coordinate format and single value.
    
    Parameters:
    rows - the number of rows the matrix shall have.
    columns - the number of columns the matrix shall have.
    rowIndexes - row indexes
    columnIndexes - column indexes
    value - numerical value, cannot be zero
    removeDuplicates - if true, then duplicates (if any) are removed
    sortColumnIndexes - if true, then column indexes are sorted
  - SparseRCDoubleMatrix2D
```
public SparseRCDoubleMatrix2D(int rows,
                      int columns,
                      int[] rowIndexes,
                      int[] columnIndexes,
                      double[] values,
                      boolean removeDuplicates,
                      boolean removeZeroes,
                      boolean sortColumnIndexes)
```
    Constructs a matrix with indexes and values given in the coordinate format.
    
    Parameters:
    rows - the number of rows the matrix shall have.
    columns - the number of columns the matrix shall have.
    rowIndexes - row indexes
    columnIndexes - column indexes
    values - numerical values
    removeDuplicates - if true, then duplicates (if any) are removed
    removeZeroes - if true, then zeroes (if any) are removed
    sortColumnIndexes - if true, then column indexes are sorted
  - SparseRCDoubleMatrix2D
```
public SparseRCDoubleMatrix2D(int rows,
                      int columns,
                      int[] rowPointers,
                      int[] columnIndexes,
                      double[] values)
```
    Constructs a matrix with given parameters. The arrays are not copied.
    
    Parameters:
    rows - the number of rows the matrix shall have.
    columns - the number of columns the matrix shall have.
    rowPointers - row pointers
    columnIndexes - column indexes
    values - numerical values
- Method Detail
  - assign
```
public DoubleMatrix2D assign(DoubleFunction function)
```
    Description copied from class: DoubleMatrix2D
    Assigns the result of a function to each cell; x[row,col] = function(x[row,col]).
    Example:
```
         matrix = 2 x 2 matrix 
         0.5 1.5      
         2.5 3.5
 
         // change each cell to its sine
         matrix.assign(cern.jet.math.Functions.sin);
         -->
         2 x 2 matrix
         0.479426  0.997495 
         0.598472 -0.350783
 
 
```
    For further examples, see the package doc.
    Overrides:
    
    assign in class DoubleMatrix2D
    
    Parameters:
    function - a function object taking as argument the current cell's value.
    
    Returns:
    this (for convenience only).
    See Also:
    DoubleFunctions
  - assign
```
public DoubleMatrix2D assign(double value)
```
    Description copied from class: DoubleMatrix2D
    
    Sets all cells to the state specified by value.
    
    Overrides:
    
    assign in class DoubleMatrix2D
    
    Parameters:
    value - the value to be filled into the cells.
    
    Returns:
    this (for convenience only).
  - assign
```
public DoubleMatrix2D assign(DoubleMatrix2D source)
```
    Description copied from class: DoubleMatrix2D
    
    Replaces all cell values of the receiver with the values of another matrix. Both matrices must have the same number of rows and columns. If both matrices share the same cells (as is the case if they are views derived from the same matrix) and intersect in an ambiguous way, then replaces as if using an intermediate auxiliary deep copy of other.
    
    Overrides:
    
    assign in class DoubleMatrix2D
    
    Parameters:
    source - the source matrix to copy from (may be identical to the receiver).
    
    Returns:
    this (for convenience only).
  - assign
```
public DoubleMatrix2D assign(DoubleMatrix2D y,
                    DoubleDoubleFunction function)
```
    Description copied from class: DoubleMatrix2D
    Assigns the result of a function to each cell; x[row,col] = function(x[row,col],y[row,col]).
    Example:
```
         // assign x[row,col] = x[row,col]<sup>y[row,col]</sup>
         m1 = 2 x 2 matrix 
         0 1 
         2 3
 
         m2 = 2 x 2 matrix 
         0 2 
         4 6
 
         m1.assign(m2, cern.jet.math.Functions.pow);
         -->
         m1 == 2 x 2 matrix
         1   1 
         16 729
 
 
```
    For further examples, see the package doc.
    Overrides:
    
    assign in class WrapperDoubleMatrix2D
    
    Parameters:
    y - the secondary matrix to operate on.
    function - a function object taking as first argument the current cell's value of this, and as second argument the current cell's value of y,
    
    Returns:
    this (for convenience only).
    See Also:
    DoubleFunctions
  - cardinality
```
public int cardinality()
```
    Description copied from class: DoubleMatrix2D
    
    Returns the number of cells having non-zero values; ignores tolerance.
    
    Overrides:
    
    cardinality in class DoubleMatrix2D
    
    Returns:
    cardinality
  - forEachNonZero
```
public DoubleMatrix2D forEachNonZero(IntIntDoubleFunction function)
```
    Description copied from class: DoubleMatrix2D
    
    Assigns the result of a function to each non-zero cell; x[row,col] = function(x[row,col]). Use this method for fast special-purpose iteration. If you want to modify another matrix instead of this (i.e. work in read-only mode), simply return the input value unchanged. Parameters to function are as follows: first==row, second==column, third==nonZeroValue.
    
    Overrides:
    
    forEachNonZero in class DoubleMatrix2D
    
    Parameters:
    function - a function object taking as argument the current non-zero cell's row, column and value.
    
    Returns:
    this (for convenience only).
  - getColumnCompressed
```
public SparseCCDoubleMatrix2D getColumnCompressed()
```
    Returns a new matrix that has the same elements as this matrix, but is in a column-compressed form. This method creates a new object (not a view), so changes in the returned matrix are NOT reflected in this matrix.
    
    Returns:
    this matrix in a column-compressed form
  - getColumnIndexes
```
public int[] getColumnIndexes()
```
    Returns column indexes
    
    Returns:
    column indexes
  - getDense
```
public DenseDoubleMatrix2D getDense()
```
    Returns a new matrix that has the same elements as this matrix, but is in a dense form. This method creates a new object (not a view), so changes in the returned matrix are NOT reflected in this matrix.
    
    Returns:
    this matrix in a dense form
  - getQuick
```
public double getQuick(int row,
              int column)
```
    Description copied from class: DoubleMatrix2D
    
    Returns the matrix cell value at coordinate [row,column].
    Provided with invalid parameters this method may return invalid objects without throwing any exception. You should only use this method when you are absolutely sure that the coordinate is within bounds. Precondition (unchecked): 0 <= column < columns() && 0 <= row < rows().
    
    Overrides:
    
    getQuick in class WrapperDoubleMatrix2D
    
    Parameters:
    row - the index of the row-coordinate.
    column - the index of the column-coordinate.
    
    Returns:
    the value at the specified coordinate.
  - getRowPointers
```
public int[] getRowPointers()
```
    Returns row pointers
    
    Returns:
    row pointers
  - getTranspose
```
public SparseRCDoubleMatrix2D getTranspose()
```
    Returns a new matrix that is the transpose of this matrix. This method creates a new object (not a view), so changes in the returned matrix are NOT reflected in this matrix.
    
    Returns:
    the transpose of this matrix
  - getValues
```
public double[] getValues()
```
    Returns numerical values
    
    Returns:
    numerical values
  - hasColumnIndexesSorted
```
public boolean hasColumnIndexesSorted()
```
    Returns true if column indexes are sorted, false otherwise
    
    Returns:
    true if column indexes are sorted, false otherwise
  - like
```
public DoubleMatrix2D like(int rows,
                  int columns)
```
    Description copied from class: DoubleMatrix2D
    
    Construct and returns a new empty matrix of the same dynamic type as the receiver, having the specified number of rows and columns. For example, if the receiver is an instance of type DenseDoubleMatrix2D the new matrix must also be of type DenseDoubleMatrix2D, if the receiver is an instance of type SparseDoubleMatrix2D the new matrix must also be of type SparseDoubleMatrix2D, etc. In general, the new matrix should have internal parametrization as similar as possible.
    
    Overrides:
    
    like in class WrapperDoubleMatrix2D
    
    Parameters:
    rows - the number of rows the matrix shall have.
    columns - the number of columns the matrix shall have.
    
    Returns:
    a new empty matrix of the same dynamic type.
  - like1D
```
public DoubleMatrix1D like1D(int size)
```
    Description copied from class: DoubleMatrix2D
    
    Construct and returns a new 1-d matrix of the corresponding dynamic type, entirelly independent of the receiver. For example, if the receiver is an instance of type DenseDoubleMatrix2D the new matrix must be of type DenseDoubleMatrix1D, if the receiver is an instance of type SparseDoubleMatrix2D the new matrix must be of type SparseDoubleMatrix1D, etc.
    
    Overrides:
    
    like1D in class WrapperDoubleMatrix2D
    
    Parameters:
    size - the number of cells the matrix shall have.
    
    Returns:
    a new matrix of the corresponding dynamic type.
  - removeDuplicates
```
public void removeDuplicates()
```
    Removes (sums) duplicate entries (if any}
  - removeZeroes
```
public void removeZeroes()
```
    Removes zero entries (if any)
  - setQuick
```
public void setQuick(int row,
            int column,
            double value)
```
    Description copied from class: DoubleMatrix2D
    
    Sets the matrix cell at coordinate [row,column] to the specified value.
    Provided with invalid parameters this method may access illegal indexes without throwing any exception. You should only use this method when you are absolutely sure that the coordinate is within bounds. Precondition (unchecked): 0 <= column < columns() && 0 <= row < rows().
    
    Overrides:
    
    setQuick in class WrapperDoubleMatrix2D
    
    Parameters:
    row - the index of the row-coordinate.
    column - the index of the column-coordinate.
    value - the value to be filled into the specified cell.
  - sortColumnIndexes
```
public void sortColumnIndexes()
```
    Sorts column indexes
  - toString
```
public String toString()
```
    Description copied from class: DoubleMatrix2D
    
    Returns a string representation using default formatting.
    
    Overrides:
    
    toString in class DoubleMatrix2D
    
    See Also:
    DoubleFormatter
  - trimToSize
```
public void trimToSize()
```
    Description copied from class: AbstractMatrix
    
    Releases any superfluous internal memory. An application can use this operation to minimize the storage of the receiver.
    This default implementation does nothing. Override this method if necessary.
    
    Overrides:
    
    trimToSize in class AbstractMatrix
  - zMult
```
public DoubleMatrix1D zMult(DoubleMatrix1D y,
                   DoubleMatrix1D z,
                   double alpha,
                   double beta,
                   boolean transposeA)
```
    Description copied from class: DoubleMatrix2D
    
    Linear algebraic matrix-vector multiplication; z = alpha * A * y + beta*z. z[i] = alpha*Sum(A[i,j] * y[j]) + beta*z[i], i=0..A.rows()-1, j=0..y.size()-1 . Where A == this.
    Note: Matrix shape conformance is checked after potential transpositions.
    
    Overrides:
    
    zMult in class DoubleMatrix2D
    
    Parameters:
    y - the source vector.
    z - the vector where results are to be stored. Set this parameter to null to indicate that a new result vector shall be constructed.
    
    Returns:
    z (for convenience only).
  - zMult
```
public DoubleMatrix2D zMult(DoubleMatrix2D B,
                   DoubleMatrix2D C,
                   double alpha,
                   double beta,
                   boolean transposeA,
                   boolean transposeB)
```
    Description copied from class: DoubleMatrix2D
    
    Linear algebraic matrix-matrix multiplication; C = alpha * A x B + beta*C. C[i,j] = alpha*Sum(A[i,k] * B[k,j]) + beta*C[i,j], k=0..n-1.
    Matrix shapes: A(m x n), B(n x p), C(m x p).
    Note: Matrix shape conformance is checked after potential transpositions.
    
    Overrides:
    
    zMult in class DoubleMatrix2D
    
    Parameters:
    B - the second source matrix.
    C - the matrix where results are to be stored. Set this parameter to null to indicate that a new result matrix shall be constructed.
    
    Returns:
    C (for convenience only).

Class SparseRCDoubleMatrix2D

Constructor Summary

Method Summary

Methods inherited from class cern.colt.matrix.tdouble.impl.WrapperDoubleMatrix2D

Methods inherited from class cern.colt.matrix.tdouble.DoubleMatrix2D

Methods inherited from class cern.colt.matrix.AbstractMatrix2D

Methods inherited from class cern.colt.matrix.AbstractMatrix

Methods inherited from class cern.colt.PersistentObject

Methods inherited from class java.lang.Object

Constructor Detail

SparseRCDoubleMatrix2D

SparseRCDoubleMatrix2D

SparseRCDoubleMatrix2D

SparseRCDoubleMatrix2D

SparseRCDoubleMatrix2D

SparseRCDoubleMatrix2D

Method Detail

assign

assign

assign

assign

cardinality

forEachNonZero

getColumnCompressed

getColumnIndexes

getDense

getQuick

getRowPointers

getTranspose

getValues

hasColumnIndexesSorted

like

like1D

removeDuplicates

removeZeroes

setQuick

sortColumnIndexes

toString

trimToSize

zMult

zMult