SparseRCDoubleMatrix2D
cern.colt.matrix.tdouble.impl

Class SparseRCDoubleMatrix2D

  • All Implemented Interfaces:
    Serializable, Cloneable


    public class SparseRCDoubleMatrix2Dextends 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.
    See Also:
    Serialized Form
    • 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
      • 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).

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