Matrix< Value > Class Template Reference

A 2D matrix class with efficient buffer access for NumPy interoperability. More...

#include <OpenMS/DATASTRUCTURES/Matrix.h>

Inheritance diagram for Matrix< Value >:

Collaboration diagram for Matrix< Value >:

Public Types
Type definitions
using	value_type = Value
using	iterator = typename std::vector< Value >::iterator
using	const_iterator = typename std::vector< Value >::const_iterator

Public Member Functions
Constructors and assignment
	Matrix ()
	Default constructor creates empty matrix.
	Matrix (Size rows, Size cols, Value value=Value())
	Constructor to create a matrix with specified dimensions and fill value.
	Matrix (const Matrix &)=default
	Copy constructor.
	Matrix (Matrix &&) noexcept=default
	Move constructor.
Matrix &	operator= (const Matrix &)=default
	Copy assignment operator.
Matrix &	operator= (Matrix &&) noexcept=default
	Move assignment operator.
	~Matrix ()=default
	Destructor.
Dimension accessors
Size	rows () const
	Number of rows.
Size	cols () const
	Number of columns.
Size	size () const
	Total number of elements.
bool	empty () const
	Check if matrix is empty.
Element access
const Value &	getValue (size_t const row, size_t const col) const
	Get element at (row, col)
Value &	getValue (size_t const row, size_t const col)
	Get mutable element at (row, col)
void	setValue (size_t const row, size_t const col, const Value &value)
	Set element at (row, col)
Value &	operator() (size_t row, size_t col)
	Unchecked element access (row, col)
const Value &	operator() (size_t row, size_t col) const
	Unchecked const element access (row, col)
Modifiers
void	resize (size_t rows, size_t cols)
	Resize matrix (contents become undefined after resize)
void	fill (Value value)
	Fill all elements with value.
void	clear ()
	Clear matrix (set to 0x0)
template<typename T , long int ROWS, long int COLS>
void	setMatrix (T const (&array)[ROWS][COLS])
	Sets the matrix values using a 2D array.
Iterators
iterator	begin ()
iterator	end ()
const_iterator	begin () const
const_iterator	end () const
const_iterator	cbegin () const
const_iterator	cend () const
Reduction operations
Value	maxValue () const
	Returns the maximum value in the matrix.
Value	minValue () const
	Returns the minimum value in the matrix.
Comparison
bool	operator== (const Matrix &rhs) const
	Equality operator. Compares two matrices for equality.
bool	operator!= (const Matrix &rhs) const

Private Attributes
std::vector< Value >	data_
	Column-major storage.
Size	rows_
	Number of rows.
Size	cols_
	Number of columns.

Friends
std::ostream &	operator<< (std::ostream &os, const Matrix< Value > &matrix)
	Friend function to output the matrix to an output stream.

Buffer access (for NumPy/Cython interoperability)
Value *	data ()
	Pointer to raw data buffer (column-major storage)
const Value *	data () const
	Const pointer to raw data buffer.
int	innerStride () const
	Stride between consecutive elements in same column (always 1 for column-major)
int	outerStride () const
	Stride between consecutive columns.
static constexpr bool	rowMajor ()
	Returns false (column-major storage, not row-major)

Detailed Description

template<typename Value>
class OpenMS::Matrix< Value >

A 2D matrix class with efficient buffer access for NumPy interoperability.

Data is stored in column-major order (Fortran style) for compatibility with Eigen and most numerical libraries. Internal OpenMS code can obtain zero-copy Eigen views via the eigenView() function in MatrixEigen.h (internal header).

Template Parameters

Value

The element type (typically double or float)

Member Typedef Documentation

const_iterator

template<typename Value >

using const_iterator = typename std::vector<Value>::const_iterator

iterator

template<typename Value >

using iterator = typename std::vector<Value>::iterator

value_type

template<typename Value >

using value_type = Value

Constructor & Destructor Documentation

Matrix() [1/4]

template<typename Value >

Matrix ( )

inline

Default constructor creates empty matrix.

Matrix() [2/4]

template<typename Value >

Matrix ( Size  rows, Size  cols, Value  value = Value()  )

inline

Constructor to create a matrix with specified dimensions and fill value.

Parameters

rows	Number of rows in the matrix.
cols	Number of columns in the matrix.
value	Initial value to fill the matrix.

Matrix() [3/4]

template<typename Value >

Matrix ( const Matrix< Value > &  )

default

Copy constructor.

Matrix() [4/4]

template<typename Value >

Matrix ( Matrix< Value > &&  )

defaultnoexcept

Move constructor.

~Matrix()

template<typename Value >

~Matrix ( )

default

Destructor.

Member Function Documentation

begin() [1/2]

template<typename Value >

iterator begin ( )

inline

References Matrix< Value >::data_.

begin() [2/2]

template<typename Value >

const_iterator begin ( ) const

inline

References Matrix< Value >::data_.

cbegin()

template<typename Value >

const_iterator cbegin ( ) const

inline

References Matrix< Value >::data_.

cend()

template<typename Value >

const_iterator cend ( ) const

inline

References Matrix< Value >::data_.

clear()

template<typename Value >

void clear ( )

inline

Clear matrix (set to 0x0)

References Matrix< Value >::cols_, Matrix< Value >::data_, and Matrix< Value >::rows_.

cols()

template<typename Value >

Size cols ( ) const

inline

Number of columns.

References Matrix< Value >::cols_.

Referenced by BilinearInterpolation< Key, Value >::addValue(), MSExperiment::aggregateFromMatrix(), OpenMS::eigenView(), OpenMS::eigenView(), MSExperiment::extractXICsFromMatrix(), Matrix< Value >::resize(), BilinearInterpolation< Key, Value >::supportMax_1(), and BilinearInterpolation< Key, Value >::value().

data() [1/2]

template<typename Value >

Value * data ( )

inline

Pointer to raw data buffer (column-major storage)

References Matrix< Value >::data_.

Referenced by OpenMS::eigenView(), and OpenMS::eigenView().

data() [2/2]

template<typename Value >

const Value * data ( ) const

inline

Const pointer to raw data buffer.

References Matrix< Value >::data_.

empty()

template<typename Value >

bool empty ( ) const

inline

Check if matrix is empty.

References Matrix< Value >::data_.

Referenced by BilinearInterpolation< Key, Value >::empty().

end() [1/2]

template<typename Value >

iterator end ( )

inline

References Matrix< Value >::data_.

end() [2/2]

template<typename Value >

const_iterator end ( ) const

inline

References Matrix< Value >::data_.

fill()

template<typename Value >

void fill ( Value  value )

inline

Fill all elements with value.

References Matrix< Value >::data_.

getValue() [1/2]

template<typename Value >

Value & getValue ( size_t const  row, size_t const  col  )

inline

Get mutable element at (row, col)

Note: pyOpenMS can't easily wrap operator() so we provide additional getter.

Parameters

[in]	row	Zero-based row index.
[in]	col	Zero-based column index.

Returns

Mutable reference to the value at the given position.

References Matrix< Value >::data_, and Matrix< Value >::rows_.

getValue() [2/2]

template<typename Value >

const Value & getValue ( size_t const  row, size_t const  col  ) const

inline

Get element at (row, col)

Note: pyOpenMS can't easily wrap operator() so we provide additional getter.

Parameters

[in]	row	Zero-based row index.
[in]	col	Zero-based column index.

Returns

Const reference to the value at the given position.

References Matrix< Value >::data_, and Matrix< Value >::rows_.

innerStride()

template<typename Value >

int innerStride ( ) const

inline

Stride between consecutive elements in same column (always 1 for column-major)

maxValue()

template<typename Value >

Value maxValue ( ) const

inline

Returns the maximum value in the matrix.

Returns

The maximum value. For empty matrices, returns Value() (default-constructed value).

References Matrix< Value >::data_.

minValue()

template<typename Value >

Value minValue ( ) const

inline

Returns the minimum value in the matrix.

Returns

The minimum value. For empty matrices, returns Value() (default-constructed value).

References Matrix< Value >::data_.

operator!=()

template<typename Value >

bool operator!= ( const Matrix< Value > &  rhs ) const

inline

operator()() [1/2]

template<typename Value >

Value & operator() ( size_t  row, size_t  col  )

inline

Unchecked element access (row, col)

References Matrix< Value >::data_, and Matrix< Value >::rows_.

operator()() [2/2]

template<typename Value >

const Value & operator() ( size_t  row, size_t  col  ) const

inline

Unchecked const element access (row, col)

References Matrix< Value >::data_, and Matrix< Value >::rows_.

operator=() [1/2]

template<typename Value >

Matrix & operator= ( const Matrix< Value > &  )

default

Copy assignment operator.

operator=() [2/2]

template<typename Value >

Matrix & operator= ( Matrix< Value > &&  )

defaultnoexcept

Move assignment operator.

operator==()

template<typename Value >

bool operator== ( const Matrix< Value > &  rhs ) const

inline

Equality operator. Compares two matrices for equality.

Parameters

[in]

rhs

The matrix to be compared.

Returns

True if matrices are equal, false otherwise.

Exceptions

Exception::Precondition

if matrices have different dimensions (Debug mode only)

References Matrix< Value >::cols_, Matrix< Value >::data_, OPENMS_PRECONDITION, and Matrix< Value >::rows_.

outerStride()

template<typename Value >

int outerStride ( ) const

inline

Stride between consecutive columns.

References Matrix< Value >::rows_.

resize()

template<typename Value >

void resize ( size_t  rows, size_t  cols  )

inline

Resize matrix (contents become undefined after resize)

References Matrix< Value >::cols(), Matrix< Value >::cols_, Matrix< Value >::data_, Matrix< Value >::rows(), and Matrix< Value >::rows_.

Referenced by Matrix< Value >::setMatrix().

rowMajor()

template<typename Value >

static constexpr bool rowMajor ( )

inlinestaticconstexpr

Returns false (column-major storage, not row-major)

rows()

template<typename Value >

Size rows ( ) const

inline

Number of rows.

References Matrix< Value >::rows_.

Referenced by BilinearInterpolation< Key, Value >::addValue(), MSExperiment::aggregateFromMatrix(), OpenMS::eigenView(), OpenMS::eigenView(), MSExperiment::extractXICsFromMatrix(), Matrix< Value >::resize(), BilinearInterpolation< Key, Value >::supportMax_0(), and BilinearInterpolation< Key, Value >::value().

setMatrix()

template<typename Value >

template<typename T , long int ROWS, long int COLS>

void setMatrix ( T const (&)  array[ROWS][COLS] )

inline

Sets the matrix values using a 2D array.

This function resizes the matrix to the specified number of rows and columns, and then assigns the values from the 2D array to the corresponding elements in the matrix.

Template Parameters

T	The type of the matrix elements.
ROWS	The number of rows in the matrix.
COLS	The number of columns in the matrix.

Parameters

[in]

array

The 2D array containing the values to be assigned to the matrix.

References Matrix< Value >::resize().

setValue()

template<typename Value >

void setValue ( size_t const  row, size_t const  col, const Value &  value  )

inline

Set element at (row, col)

Note: pyOpenMS can't easily wrap operator() so we provide additional setter.

Parameters

[in]	row	Zero-based row index.
[in]	col	Zero-based column index.
[in]	value	Value to set at the given position.

References Matrix< Value >::data_, and Matrix< Value >::rows_.

size()

template<typename Value >

Size size ( ) const

inline

Total number of elements.

References Matrix< Value >::data_.

Friends And Related Symbol Documentation

operator<<

template<typename Value >

std::ostream & operator<< ( std::ostream &  os, const Matrix< Value > &  matrix  )

friend

Friend function to output the matrix to an output stream.

Parameters

[in,out]	os	Output stream.
[in]	matrix	Matrix to be output.

Returns

Reference to the output stream.

Member Data Documentation

cols_

template<typename Value >

Size cols_

private

Number of columns.

Referenced by Matrix< Value >::clear(), Matrix< Value >::cols(), Matrix< Value >::operator==(), and Matrix< Value >::resize().

data_

template<typename Value >

std::vector<Value> data_

private

Column-major storage.

Referenced by Matrix< Value >::begin(), Matrix< Value >::begin(), Matrix< Value >::cbegin(), Matrix< Value >::cend(), Matrix< Value >::clear(), Matrix< Value >::data(), Matrix< Value >::data(), Matrix< Value >::empty(), Matrix< Value >::end(), Matrix< Value >::end(), Matrix< Value >::fill(), Matrix< Value >::getValue(), Matrix< Value >::getValue(), Matrix< Value >::maxValue(), Matrix< Value >::minValue(), Matrix< Value >::operator()(), Matrix< Value >::operator()(), Matrix< Value >::operator==(), Matrix< Value >::resize(), Matrix< Value >::setValue(), and Matrix< Value >::size().

rows_

template<typename Value >

Size rows_

private

Number of rows.

Referenced by Matrix< Value >::clear(), Matrix< Value >::getValue(), Matrix< Value >::getValue(), Matrix< Value >::operator()(), Matrix< Value >::operator()(), Matrix< Value >::operator==(), Matrix< Value >::outerStride(), Matrix< Value >::resize(), Matrix< Value >::rows(), and Matrix< Value >::setValue().