cern.colt.matrix.tdouble.impl
Class SparseCCDoubleMatrix2D

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.SparseCCDoubleMatrix2D

All Implemented Interfaces:

Serializable, Cloneable

public class SparseCCDoubleMatrix2D
extends WrapperDoubleMatrix2D

Sparse column-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 column-compressed format.
Note that this implementation is not synchronized.

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. Reclamation can be triggered via trimToSize().

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

Author:

Piotr Wendykier

See Also:

Serialized Form

Constructor Summary

SparseCCDoubleMatrix2D(edu.emory.mathcs.csparsej.tdouble.Dcs_common.Dcs dcs)
Constructs a matrix with a given internal storage.

SparseCCDoubleMatrix2D(double[][] values)
Constructs a matrix with a copy of the given values.

SparseCCDoubleMatrix2D(int rows, int columns)
Constructs a matrix with a given number of rows and columns.

SparseCCDoubleMatrix2D(int rows, int columns, int nzmax)
Constructs a matrix with a given number of rows and columns.

SparseCCDoubleMatrix2D(int rows, int columns, int[] rowIndexes, int[] columnIndexes, double[] values, boolean removeDuplicates, boolean removeZeroes, boolean sortRowIndexes)
Constructs a matrix with indexes and values given in the coordinate format.

SparseCCDoubleMatrix2D(int rows, int columns, int[] rowIndexes, int[] columnIndexes, double value, boolean removeDuplicates, boolean sortRowIndexes)
Constructs a matrix with indexes given in the coordinate format and a single value.

Method Summary

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.
edu.emory.mathcs.csparsej.tdouble.Dcs_common.Dcs	elements() Returns the elements of this matrix.
DoubleMatrix2D	forEachNonZero(IntIntDoubleFunction function) Assigns the result of a function to each non-zero cell; x[row,col] = function(x[row,col]).
int[]	getColumnPointers() Returns column pointers
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].
SparseRCDoubleMatrix2D	getRowCompressed() Returns a new matrix that has the same elements as this matrix, but is in a row-compressed form.
int[]	getRowIndexes() Returns row indexes;
SparseCCDoubleMatrix2D	getTranspose() Returns a new matrix that is the transpose of this matrix.
double[]	getValues() Returns numerical values
boolean	hasRowIndexesSorted() Returns true if row 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	sortRowIndexes() Sorts row 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, 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

SparseCCDoubleMatrix2D

public SparseCCDoubleMatrix2D(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 .

SparseCCDoubleMatrix2D

public SparseCCDoubleMatrix2D(edu.emory.mathcs.csparsej.tdouble.Dcs_common.Dcs dcs)

Constructs a matrix with a given internal storage.

Parameters:

dcs - internal storage.

SparseCCDoubleMatrix2D

public SparseCCDoubleMatrix2D(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 .

SparseCCDoubleMatrix2D

public SparseCCDoubleMatrix2D(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 .

SparseCCDoubleMatrix2D

public SparseCCDoubleMatrix2D(int rows,
                              int columns,
                              int[] rowIndexes,
                              int[] columnIndexes,
                              double value,
                              boolean removeDuplicates,
                              boolean sortRowIndexes)

Constructs a matrix with indexes given in the coordinate format and a 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

removeDuplicates - if true, then duplicates (if any) are removed

sortRowIndexes - if true, then row indexes are sorted

SparseCCDoubleMatrix2D

public SparseCCDoubleMatrix2D(int rows,
                              int columns,
                              int[] rowIndexes,
                              int[] columnIndexes,
                              double[] values,
                              boolean removeDuplicates,
                              boolean removeZeroes,
                              boolean sortRowIndexes)

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

sortRowIndexes - if true, then row indexes are sorted

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

elements

public edu.emory.mathcs.csparsej.tdouble.Dcs_common.Dcs elements()

Description copied from class: DoubleMatrix2D

Returns the elements of this matrix.

Overrides:

elements in class WrapperDoubleMatrix2D

Returns:

the elements

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).

getColumnPointers

public int[] getColumnPointers()

Returns column pointers

Returns:

column pointers

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.

getRowCompressed

public SparseRCDoubleMatrix2D getRowCompressed()

Returns a new matrix that has the same elements as this matrix, but is in a row-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 row-compressed form

getRowIndexes

public int[] getRowIndexes()

Returns row indexes;

Returns:

row indexes

getTranspose

public SparseCCDoubleMatrix2D 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

hasRowIndexesSorted

public boolean hasRowIndexesSorted()

Returns true if row indexes are sorted, false otherwise

Returns:

true if row 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.

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.

sortRowIndexes

public void sortRowIndexes()

Sorts row indexes

removeDuplicates

public void removeDuplicates()

Removes (sums) duplicate entries (if any}

removeZeroes

public void removeZeroes()

Removes zero entries (if any)

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

toString

public String toString()

Description copied from class: DoubleMatrix2D

Returns a string representation using default formatting.

Overrides:

toString in class DoubleMatrix2D

See Also:

DoubleFormatter

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).