All Implemented Interfaces:

java.io.Serializable
```
public abstract class DenseMatrix
extends BaseMatrix
                    
```
Base class for dense matrix implementations, containing the core data structure and methods that directly manipulate the underlying dense matrix representation.
This class encapsulates all interactions with EJML's DMatrixRMaj and CommonOps_DDRM classes, providing a clean abstraction layer for dense matrix operations. It serves as the foundation for concrete dense matrix implementations.
The class provides:
- Basic matrix operations (get, set, dimensions)
- Encapsulated CommonOps_DDRM method calls
- Memory management for dense matrix data structures
- Utility methods for matrix manipulation
Dense matrices store all elements (including zeros) explicitly, making them suitable for matrices with a high percentage of non-zero elements or when dense linear algebra operations are required.
Since:

1.0

Author:

QORE Lab, Imperial College London

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`protected DMatrixRMaj`	`data`

Constructor Summary

Constructors
Constructor	Description
`DenseMatrix(int numRows, int numCols)`	Constructs a dense matrix with specified dimensions.
`DenseMatrix(DMatrixRMaj matrix)`	Constructs a dense matrix by copying an existing EJML dense matrix.
`DenseMatrix(DMatrix matrix)`	Constructs a dense matrix by copying an existing DMatrix.
`DenseMatrix(DenseMatrix matrix)`	Copy constructor for creating a new dense matrix from an existing one.
`DenseMatrix()`	Protected constructor for delayed initialization.

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DMatrixRMaj`	`getData()`	Returns the underlying EJML dense matrix data structure.
`void`	`setData(DMatrixRMaj newData)`	Sets the underlying EJML dense matrix data structure.
`static void`	`addMatricesInPlaceStatic(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)`
`static DMatrixRMaj`	`addMatricesStatic(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)`
`static DMatrixRMaj`	`addStatic(DMatrixRMaj A, DMatrixRMaj B, DMatrixRMaj output)`	Performs element-wise addition of two dense matrices: output = A + B.
`static void`	`changeSignStatic(DMatrix input, DMatrix output)`
`static double`	`determinantStatic(DMatrix matrix)`
`static DMatrixRMaj`	`elementMultStatic(DMatrix A, DMatrix B, DMatrix output)`
`static void`	`extractMatrixStatic(DMatrix src, int srcX0, int srcX1, int srcY0, int srcY1, DMatrix dst, int dstY0, int dstX0)`
`static void`	`fillMatrixStatic(DMatrix matrix, double value)`
`static DMatrixRMaj`	`identityStatic(int size)`	Creates an identity matrix of the specified size.
`static void`	`invertStatic(DMatrix input, DMatrix output)`
`static DMatrixRMaj`	`kronStatic(DMatrixRMaj A, DMatrixRMaj B, DMatrixRMaj output)`	Computes the Kronecker product of two dense matrices: A ⊗ B.
`static DMatrixRMaj`	`multMatrixStatic(DMatrix A, DMatrix B, DMatrix output)`
`static void`	`scaleMatrixStatic(double scalar, DMatrix input, DMatrix output)`
`static void`	`transposeMatrixStatic(DMatrix input, DMatrix output)`
`void`	`absEq()`	Replaces each value in the matrix with its absolute value, in-place.
`void`	`add(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)`	Performs the operation: output = alphaA + betaB.
`DMatrix`	`addMatrices(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)`	Performs the operation: output = alphaA + betaB.
`void`	`addMatricesInPlace(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)`
`boolean`	`any()`	Checks if the current matrix contains any non-zero elements.
`void`	`applyConditionalTransform(double source, double target, double tol, String operation)`	Applies a transformation to matrix elements based on conditions.
`void`	`changeSign()`
`abstract BaseMatrix`	`copy()`	Creates and returns a deep copy of this dense matrix.
`void`	`colIncrease(int col, double a)`	Adds a scalar value to each element in the specified column.
`void`	`concatColumnsInPlace(DMatrix left, DMatrix right, DMatrix output)`	Concatenates matrices column-wise.
`void`	`concatRowsInPlace(DMatrix top, DMatrix bottom, DMatrix output)`	Concatenates matrices row-wise.
`BaseMatrix`	`countEachRow(double val)`	Counts occurrences of each unique value in each row.
`abstract BaseMatrix`	`createNewInstance(int rows, int cols, int nzLength)`	Creates a new instance of the concrete dense matrix implementation.
`double`	`determinant()`
`void`	`divideInPlace(double scalar)`
`void`	`divideMatrix(double scalar, DMatrix output)`
`void`	`divideRowsByArray(Array<double> diag, int offset)`
`void`	`divideScalarByMatrix(double scalar, DMatrix output)`
`double`	`elementMax()`
`double`	`elementMaxAbs()`
`double`	`elementMin()`
`DMatrix`	`elementMult(DMatrix A, DMatrix B, DMatrix output)`
`double`	`elementSum()`
`abstract boolean`	`equals(Object obj)`	Indicates whether some other object is "equal to" this dense matrix.
`void`	`extractMatrix(DMatrix src, int srcX0, int srcX1, int srcY0, int srcY1, DMatrix dst, int dstY0, int dstX0)`
`void`	`fillMatrix(double value)`	Fills the matrix with the specified value.
`BaseMatrix`	`findNonNegative()`	Returns a matrix containing indices of all non-negative elements.
`double`	`get(int row, int col)`	Returns the value at the specified matrix position.
`int`	`getColumnIndex(int col)`
`Array<int>`	`getColumnIndicesArray()`
`void`	`setData(DMatrix newData)`	Sets the underlying EJML dense matrix data structure.
`void`	`setData(Object newData)`	Sets the underlying data structure.
`int`	`getNonZeroLength()`	Returns the number of stored non-zero elements.
`void`	`setNonZeroLength(int length)`
`int`	`getNonZeroRow(int index)`
`Array<int>`	`getNonZeroRows()`	Returns array of row indices of non-zero entries.
`double`	`getNonZeroValue(int index)`
`Array<double>`	`getNonZeroValues()`	Returns array of non-zero values.
`int`	`getNonZeros()`	Returns the number of non-zero elements in the matrix.
`int`	`getNumCols()`	Returns the number of columns in the matrix.
`int`	`getNumRows()`	Returns the number of rows in the matrix.
`boolean`	`hasDuplicates()`	Checks if the matrix contains duplicate values.
`boolean`	`hasFinite()`	Checks if the matrix contains any finite (non-infinite, non-NaN) values.
`boolean`	`hasInfinite()`	Checks if the matrix contains any infinite values.
`boolean`	`hasMultipleFinite()`	Checks if more than one finite value exists.
`boolean`	`hasNaN()`	Checks if the matrix contains any NaN values.
`void`	`mult(DMatrix A, DMatrix B, DMatrix output)`	Performs matrix multiplication: output = A * B.
`DMatrix`	`multMatrix(DMatrix B, DMatrix output)`	Performs matrix multiplication with sparse matrices.
`void`	`removeZeros()`	Removes zero-valued elements from the matrix with default tolerance.
`void`	`removeZerosWithTol(double tolerance)`	Removes zero-valued elements from the matrix with specified tolerance.
`void`	`reshape(int numRows, int numCols)`	Reshapes the matrix to the specified dimensions.
`void`	`scaleInPlace(double alpha)`	Scales the matrix in-place by the specified factor.
`void`	`scaleMatrix(double scalar, DMatrix output)`
`void`	`set(int row, int col, double value)`	Sets the value at the specified matrix position.
`void`	`setColumnIndex(int col, int value)`
`void`	`setNonZeroRow(int index, int row)`
`void`	`setNonZeroValue(int index, double value)`
`void`	`shrinkNumCols(int newmax)`	Reduce the maximum number of columns by setting the internal column count.
`void`	`shrinkNumRows(int newmax)`	Reduce the maximum number of rows by setting the internal row count.
`DMatrix`	`sumColsRaw()`
`DMatrix`	`sumRowsRaw()`
`String`	`toString()`	Returns a string representation of the matrix.
`void`	`transpose(DMatrix input, DMatrix output)`	Computes the transpose of the input matrix.
`void`	`transposeMatrix(DMatrix output)`	Computes the transpose of this matrix.
`void`	`zero()`	Sets all elements in the matrix to zero.

Methods inherited from class jline.util.matrix.BaseMatrix
getData, getNumNonZeros
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - DenseMatrix
```
DenseMatrix(int numRows, int numCols)
```
    Constructs a dense matrix with specified dimensions.
    
    Parameters:
    
    numRows - the number of rows in the matrix
    
    numCols - the number of columns in the matrix
  - DenseMatrix
```
DenseMatrix(DMatrixRMaj matrix)
```
    Constructs a dense matrix by copying an existing EJML dense matrix.
    
    Parameters:
    
    matrix - the EJML dense matrix to copy
  - DenseMatrix
```
DenseMatrix(DMatrix matrix)
```
    Constructs a dense matrix by copying an existing DMatrix.
    
    Parameters:
    
    matrix - the DMatrix to copy
  - DenseMatrix
```
DenseMatrix(DenseMatrix matrix)
```
    Copy constructor for creating a new dense matrix from an existing one.
    
    Parameters:
    
    matrix - the dense matrix to copy
  - DenseMatrix
```
DenseMatrix()
```
    Protected constructor for delayed initialization.
- Method Detail
  - getData
```
 DMatrixRMaj getData()
```
    Returns the underlying EJML dense matrix data structure. This method provides direct access to the internal data for subclasses.
    
    Returns:
    
    the underlying DMatrixRMaj instance
  - setData
```
 void setData(DMatrixRMaj newData)
```
    Sets the underlying EJML dense matrix data structure. This method allows subclasses to replace the internal data.
    
    Parameters:
    
    newData - the new DMatrixRMaj instance to use
  - addMatricesInPlaceStatic
```
 static void addMatricesInPlaceStatic(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)
```
  - addMatricesStatic
```
 static DMatrixRMaj addMatricesStatic(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)
```
  - addStatic
```
 static DMatrixRMaj addStatic(DMatrixRMaj A, DMatrixRMaj B, DMatrixRMaj output)
```
    Performs element-wise addition of two dense matrices: output = A + B.
    
    Parameters:
    
    A - the first matrix
    
    B - the second matrix
    
    output - the result matrix (can be null to create a new matrix)
    
    Returns:
    
    the sum matrix
  - changeSignStatic
```
 static void changeSignStatic(DMatrix input, DMatrix output)
```
  - determinantStatic
```
 static double determinantStatic(DMatrix matrix)
```
  - elementMultStatic
```
 static DMatrixRMaj elementMultStatic(DMatrix A, DMatrix B, DMatrix output)
```
  - extractMatrixStatic
```
 static void extractMatrixStatic(DMatrix src, int srcX0, int srcX1, int srcY0, int srcY1, DMatrix dst, int dstY0, int dstX0)
```
  - fillMatrixStatic
```
 static void fillMatrixStatic(DMatrix matrix, double value)
```
  - identityStatic
```
 static DMatrixRMaj identityStatic(int size)
```
    Creates an identity matrix of the specified size. An identity matrix has ones on the main diagonal and zeros elsewhere.
    
    Parameters:
    
    size - the number of rows and columns in the identity matrix
    
    Returns:
    
    a new identity matrix
  - invertStatic
```
 static void invertStatic(DMatrix input, DMatrix output)
```
  - kronStatic
```
 static DMatrixRMaj kronStatic(DMatrixRMaj A, DMatrixRMaj B, DMatrixRMaj output)
```
    Computes the Kronecker product of two dense matrices: A ⊗ B. The Kronecker product creates a larger matrix where each element of A is multiplied by the entire matrix B.
    
    Parameters:
    
    A - the left matrix
    
    B - the right matrix
    
    output - the result matrix (can be null to create a new matrix)
    
    Returns:
    
    the Kronecker product matrix
  - multMatrixStatic
```
 static DMatrixRMaj multMatrixStatic(DMatrix A, DMatrix B, DMatrix output)
```
  - scaleMatrixStatic
```
 static void scaleMatrixStatic(double scalar, DMatrix input, DMatrix output)
```
  - transposeMatrixStatic
```
 static void transposeMatrixStatic(DMatrix input, DMatrix output)
```
  - absEq
```
 void absEq()
```
    Replaces each value in the matrix with its absolute value, in-place.
  - add
```
 void add(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)
```
    Performs the operation: output = alpha*A + beta*B.
    
    Parameters:
    
    alpha - scalar coefficient for matrix A
    
    A - first input matrix
    
    beta - scalar coefficient for matrix B
    
    B - second input matrix
    
    output - the result matrix
  - addMatrices
```
 DMatrix addMatrices(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)
```
    Performs the operation: output = alpha*A + beta*B.
    
    Parameters:
    
    alpha - scalar coefficient for matrix A
    
    A - first input matrix
    
    beta - scalar coefficient for matrix B
    
    B - second input matrix
    
    output - the result matrix
  - addMatricesInPlace
```
 void addMatricesInPlace(double alpha, DMatrix A, double beta, DMatrix B, DMatrix output)
```
  - any
```
 boolean any()
```
    Checks if the current matrix contains any non-zero elements.
    
    Returns:
    
    true if at least one non-zero element exists; false otherwise.
  - applyConditionalTransform
```
 void applyConditionalTransform(double source, double target, double tol, String operation)
```
    Applies a transformation to matrix elements based on conditions. Replaces elements matching the condition with the target value.
  - changeSign
```
 void changeSign()
```
  - copy
```
 abstract BaseMatrix copy()
```
    Creates and returns a deep copy of this dense matrix.
    
    Returns:
    
    a new dense matrix that is a copy of this instance
  - colIncrease
```
 void colIncrease(int col, double a)
```
    Adds a scalar value to each element in the specified column.
    
    Parameters:
    
    col - Column index to update.
    
    a - Scalar value to add to each element in the column.
  - concatColumnsInPlace
```
 void concatColumnsInPlace(DMatrix left, DMatrix right, DMatrix output)
```
    Concatenates matrices column-wise.
    
    Parameters:
    
    left - the left matrix
    
    right - the right matrix
    
    output - the result matrix
  - concatRowsInPlace
```
 void concatRowsInPlace(DMatrix top, DMatrix bottom, DMatrix output)
```
    Concatenates matrices row-wise.
    
    Parameters:
    
    top - the top matrix
    
    bottom - the bottom matrix
    
    output - the result matrix
  - countEachRow
```
 BaseMatrix countEachRow(double val)
```
    Counts occurrences of each unique value in each row.
  - createNewInstance
```
 abstract BaseMatrix createNewInstance(int rows, int cols, int nzLength)
```
    Creates a new instance of the concrete dense matrix implementation. This factory method allows the base class to create instances of the correct subtype.
    
    Parameters:
    
    rows - the number of rows for the new matrix
    
    cols - the number of columns for the new matrix
    
    Returns:
    
    a new instance of the concrete dense matrix type
  - determinant
```
 double determinant()
```
  - divideInPlace
```
 void divideInPlace(double scalar)
```
  - divideMatrix
```
 void divideMatrix(double scalar, DMatrix output)
```
  - divideRowsByArray
```
 void divideRowsByArray(Array<double> diag, int offset)
```
  - divideScalarByMatrix
```
 void divideScalarByMatrix(double scalar, DMatrix output)
```
  - elementMax
```
 double elementMax()
```
  - elementMaxAbs
```
 double elementMaxAbs()
```
  - elementMin
```
 double elementMin()
```
  - elementMult
```
 DMatrix elementMult(DMatrix A, DMatrix B, DMatrix output)
```
  - elementSum
```
 double elementSum()
```
  - equals
```
 abstract boolean equals(Object obj)
```
    Indicates whether some other object is "equal to" this dense matrix.
    
    Parameters:
    
    obj - the reference object with which to compare
    
    Returns:
    
    true if this object is the same as the obj argument; false otherwise
  - extractMatrix
```
 void extractMatrix(DMatrix src, int srcX0, int srcX1, int srcY0, int srcY1, DMatrix dst, int dstY0, int dstX0)
```
  - fillMatrix
```
 void fillMatrix(double value)
```
    Fills the matrix with the specified value.
    
    Parameters:
    
    value - the value to fill the matrix with
  - findNonNegative
```
 BaseMatrix findNonNegative()
```
    Returns a matrix containing indices of all non-negative elements.
  - get
```
 double get(int row, int col)
```
    Returns the value at the specified matrix position.
    
    Parameters:
    
    row - the row index
    
    col - the column index
    
    Returns:
    
    the value at position (row, col)
  - getColumnIndex
```
 int getColumnIndex(int col)
```
  - getColumnIndicesArray
```
 Array<int> getColumnIndicesArray()
```
  - setData
```
 void setData(DMatrix newData)
```
    Sets the underlying EJML dense matrix data structure. This method allows subclasses to replace the internal data.
    
    Parameters:
    
    newData - the new DMatrix instance to use
  - setData
```
 void setData(Object newData)
```
    Sets the underlying data structure. Implementation depends on the concrete matrix type.
    
    Parameters:
    
    newData - the new data structure
  - getNonZeroLength
```
 int getNonZeroLength()
```
    Returns the number of stored non-zero elements. This may be different from actual non-zero count for dense matrices.
    
    Returns:
    
    number of stored non-zero elements
  - setNonZeroLength
```
 void setNonZeroLength(int length)
```
  - getNonZeroRow
```
 int getNonZeroRow(int index)
```
  - getNonZeroRows
```
 Array<int> getNonZeroRows()
```
    Returns array of row indices of non-zero entries. For dense matrices, this may compute row indices dynamically. For sparse matrices, this returns the compressed row index array.
    
    Returns:
    
    array of row indices
  - getNonZeroValue
```
 double getNonZeroValue(int index)
```
  - getNonZeroValues
```
 Array<double> getNonZeroValues()
```
    Returns array of non-zero values. For dense matrices, this may return all values or only actual non-zeros. For sparse matrices, this returns the compressed storage array.
    
    Returns:
    
    array of non-zero values
  - getNonZeros
```
 int getNonZeros()
```
    Returns the number of non-zero elements in the matrix. For dense matrices, this counts actual non-zero values. For sparse matrices, this returns the stored non-zero count.
    
    Returns:
    
    the number of non-zero elements
  - getNumCols
```
 int getNumCols()
```
    Returns the number of columns in the matrix.
    
    Returns:
    
    the number of columns
  - getNumRows
```
 int getNumRows()
```
    Returns the number of rows in the matrix.
    
    Returns:
    
    the number of rows
  - hasDuplicates
```
 boolean hasDuplicates()
```
    Checks if the matrix contains duplicate values.
    
    Returns:
    
    true if duplicates exist
  - hasFinite
```
 boolean hasFinite()
```
    Checks if the matrix contains any finite (non-infinite, non-NaN) values.
    
    Returns:
    
    true if at least one finite value exists
  - hasInfinite
```
 boolean hasInfinite()
```
    Checks if the matrix contains any infinite values.
    
    Returns:
    
    true if at least one infinite value exists
  - hasMultipleFinite
```
 boolean hasMultipleFinite()
```
    Checks if more than one finite value exists.
    
    Returns:
    
    true if more than one finite value exists
  - hasNaN
```
 boolean hasNaN()
```
    Checks if the matrix contains any NaN values.
    
    Returns:
    
    true if at least one NaN exists
  - mult
```
 void mult(DMatrix A, DMatrix B, DMatrix output)
```
    Performs matrix multiplication: output = A * B.
    
    Parameters:
    
    A - the left matrix
    
    B - the right matrix
    
    output - the result matrix
  - multMatrix
```
 DMatrix multMatrix(DMatrix B, DMatrix output)
```
    Performs matrix multiplication with sparse matrices.
    
    Parameters:
    
    B - the right matrix
    
    output - the result matrix
  - removeZeros
```
 void removeZeros()
```
    Removes zero-valued elements from the matrix with default tolerance. For dense matrices, this may be a no-op or convert to sparse representation.
  - removeZerosWithTol
```
 void removeZerosWithTol(double tolerance)
```
    Removes zero-valued elements from the matrix with specified tolerance.
    
    Parameters:
    
    tolerance - the tolerance for considering values as zero
  - reshape
```
 void reshape(int numRows, int numCols)
```
    Reshapes the matrix to the specified dimensions.
    
    Parameters:
    
    numRows - the new number of rows
    
    numCols - the new number of columns
  - scaleInPlace
```
 void scaleInPlace(double alpha)
```
    Scales the matrix in-place by the specified factor.
    
    Parameters:
    
    alpha - the scaling factor
  - scaleMatrix
```
 void scaleMatrix(double scalar, DMatrix output)
```
  - set
```
 void set(int row, int col, double value)
```
    Sets the value at the specified matrix position.
    
    Parameters:
    
    row - the row index
    
    col - the column index
    
    value - the value to set
  - setColumnIndex
```
 void setColumnIndex(int col, int value)
```
  - setNonZeroRow
```
 void setNonZeroRow(int index, int row)
```
  - setNonZeroValue
```
 void setNonZeroValue(int index, double value)
```
  - shrinkNumCols
```
 void shrinkNumCols(int newmax)
```
    Reduce the maximum number of columns by setting the internal column count.
    
    Parameters:
    
    newmax - the new maximum number of columns
  - shrinkNumRows
```
 void shrinkNumRows(int newmax)
```
    Reduce the maximum number of rows by setting the internal row count.
    
    Parameters:
    
    newmax - the new maximum number of rows
  - sumColsRaw
```
 DMatrix sumColsRaw()
```
  - sumRowsRaw
```
 DMatrix sumRowsRaw()
```
  - toString
```
 String toString()
```
    Returns a string representation of the matrix. Elements are formatted to 4 decimal places in a grid layout.
    
    Returns:
    
    a formatted string representation of the matrix
  - transpose
```
 void transpose(DMatrix input, DMatrix output)
```
    Computes the transpose of the input matrix.
    
    Parameters:
    
    input - the matrix to transpose
    
    output - the transposed matrix
  - transposeMatrix
```
 void transposeMatrix(DMatrix output)
```
    Computes the transpose of this matrix.
    
    Parameters:
    
    output - the transposed matrix
  - zero
```
 void zero()
```
    Sets all elements in the matrix to zero.

Class DenseMatrix

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class jline.util.matrix.BaseMatrix

Methods inherited from class java.lang.Object

Constructor Detail

DenseMatrix

DenseMatrix

DenseMatrix

DenseMatrix

DenseMatrix

Method Detail

getData

setData

addMatricesInPlaceStatic

addMatricesStatic

addStatic

changeSignStatic

determinantStatic

elementMultStatic

extractMatrixStatic

fillMatrixStatic

identityStatic

invertStatic

kronStatic

multMatrixStatic

scaleMatrixStatic

transposeMatrixStatic

absEq

add

addMatrices

addMatricesInPlace

any

applyConditionalTransform

changeSign

copy

colIncrease

concatColumnsInPlace

concatRowsInPlace

countEachRow

createNewInstance

determinant

divideInPlace

divideMatrix

divideRowsByArray

divideScalarByMatrix

elementMax

elementMaxAbs

elementMin

elementMult

elementSum

equals

extractMatrix

fillMatrix

findNonNegative

get

getColumnIndex

getColumnIndicesArray

setData

setData

getNonZeroLength

setNonZeroLength

getNonZeroRow

getNonZeroRows

getNonZeroValue

getNonZeroValues

getNonZeros

getNumCols

getNumRows

hasDuplicates

hasFinite

hasInfinite

hasMultipleFinite

hasNaN

mult

multMatrix

removeZeros