Detailed Description

template<typename T, int D>
class IMP::algebra::MultiArray< T, D >

Template class for managing multidimensional arrays. This class is based on boost multi_array. This classes is primarily aimed to implement generic 2D and 3D bitmaps. See GridD if you want a more general purpose spatial grid.

The class adds new functionality to the boost class: 1) Operators + - * and / to deal with other multiarrays and scalars 2) Computation of maximum, minimum, and statistical properties of the array. 3) Read/Write both in text and binary modes (taking into account the endianess).

Inheritance diagram for IMP::algebra::MultiArray< T, D >:

List of all members.

Public Types
typedef boost::multi_array< T, D >	BMA
typedef boost::multi_array_types::index	index
typedef boost::multi_array_types::size_type	size_type
typedef MultiArray< T, D >	This

Public Member Functions
	MultiArray ()
	Empty constructor.
bool	almost_equal (const double a, const double b, const double epsilon)
void	centered_start ()
double	compute_avg () const
	Average of the values in the array.
T	compute_max () const
	Maximum of the values in the array.
template<typename T1 >
T	compute_max (T1 &max_idx) const
	Maximum of the values in the array.
T	compute_min () const
	Minimum of the values in the array.
template<typename T1 >
T	compute_min (T1 &min_idx) const
	Minimum of the values in the array.
void	compute_stats (double &avg, double &stddev, T &minval, T &maxval) const
	Compute average, standard deviation, minimum and maximum values.
double	compute_stddev () const
	Standard deviation of the values in the array.
void	copy (This &v)
template<typename U >
void	copy_with_casting (MultiArray< U, D > &v)
	Copy with casting. Use with care!
double	cross_correlation_coefficient (const This &v, bool apply_threshold=false, double threshold=0.0, bool divide_by_stddev=true, bool force_recalc_stats=true, double avg=0.0, double stddev=0.0, double avg_v=0.0, double stddev_v=0.0)
	Computes the cross correlation coeffcient between two MultiArrays.
void	fill_with_value (T val=0)
	Fill all the voxels of the array with a given value.
bool	first_element () const
	Returns the first element.
int	get_finish (const int dim) const
int	get_size (const int dim) const
int	get_start (const int dim) const
void	init_zeros ()
	All the values of the array are set to zero.
template<typename T1 >
bool	is_logical_element (T1 &v) const
	Returns true if the LOGICAL index belongs to those of the matrix.
template<typename T1 >
bool	is_physical_element (T1 &v) const
	Returns true if the PHYSICAL index belongs to those of the matrix.
bool	is_void () const
	Check if the array has some dimensionality or is just empty.
void	normalize ()
This	operator* (const This &v) const
	Multiplication operator.
This	operator* (const T &v) const
	Multiplication operator for an array and a scalar.
void	operator*= (const This &v) const
	Multiplication operator.
void	operator*= (const T &v) const
	Multiplication operator for an array and a scalar.
This	operator+ (const This &v) const
	Sum operator.
This	operator+ (const T &v) const
	Sum operator for an array and a scalar.
void	operator+= (const This &v) const
	Addition operator.
void	operator+= (const T &v) const
	Addition operator for an array and a scalar.
This	operator- (const This &v) const
	Minus operator.
This	operator- (const T &v) const
	Minus operator for an array and a scalar.
void	operator-= (const This &v) const
	Substraction operator.
void	operator-= (const T &v) const
	Substraction operator for an array and a scalar.
This	operator/ (const This &v) const
	Division operator.
This	operator/ (const T &v) const
	Division operator for an array and a scalar.
void	operator/= (const This &v) const
	Division operator.
void	operator/= (const T &v) const
	Division operator for an array and a scalar.
void	print_shape (std::ostream &out=std::cout) const
	Print shape of multidimensional array.
void	read (const std::string &filename)
	Read from an ASCII file.
void	read_binary (const std::string &filename, bool reversed=false)
	Read from a binary file.
void	read_binary (std::ifstream &input, bool reversed=false)
	Read from a input stream in binary mode.
template<typename T1 >
bool	same_shape (const MultiArray< T1, D > &b) const
	Compares the shape of two multidimensional arrays.
template<typename T1 >
bool	same_size (const MultiArray< T1, D > &b) const
	Compares the size of two multidimensional arrays.
template<typename T1 >
bool	same_start (const MultiArray< T1, D > &b) const
	Compares the origin of two multidimensional arrays.
void	set_start (const int dim, const int value)
template<typename T1 >
void	set_start (const T1 &v)
T	squared_difference (const This &v) const
T	sum_elements () const
	Computes the sum of all the array elements.
T	sum_squared_elements () const
void	write (const std::string &filename) const
	Write to an ASCII file.
void	write_binary (const std::string &filename, bool reversed=false)
	Write to a binary file.
void	write_binary (std::ofstream &out, bool reversed=false)
	Write to a output stream in binary mode.

Friends
std::istream &	operator>> (std::istream &input, This &v)

Related Functions
(Note that these are not member functions.)
template<class T , int D>
MultiArray< T, D >	operator* (const T &X, const MultiArray< T, D > &a1)
	Multiplication operator for a scalar and an array.
template<class T , int D>
MultiArray< T, D >	operator+ (const T &X, const MultiArray< T, D > &a1)
	Sum operator for a scalar and an array.
template<class T , int D>
MultiArray< T, D >	operator- (const T &X, const MultiArray< T, D > &a1)
	Minus operator for a scalar and an array.
template<class T , int D>
MultiArray< T, D >	operator/ (const T &X, const MultiArray< T, D > &a1)
	Division operator for a scalar and an array.

Constructor & Destructor Documentation

template<typename T, int D>

IMP::algebra::MultiArray< T, D >::MultiArray ( )

Empty constructor.

Member Function Documentation

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::centered_start ( )

Sets the zero (0,0,0,...) of the logical coordinates at the center of the center of the matrix. Some examples:

m.centered_start(); // if m is a 5x4 matrix, the origin will be (-2,-2)

m.centered_start(); // if m is a 16x3 matrix, the origin will be (-8,-1)

template<typename T, int D>

double IMP::algebra::MultiArray< T, D >::compute_avg ( ) const

Average of the values in the array.

The returned value is always double, independently of the type of the array.

template<typename T, int D>

T IMP::algebra::MultiArray< T, D >::compute_max ( ) const

Maximum of the values in the array.

template<typename T, int D>

template<typename T1 >

T IMP::algebra::MultiArray< T, D >::compute_max ( T1 & max_idx ) const

Maximum of the values in the array.

Parameters:

[out] max_idx index containing the maximum value

template<typename T, int D>

T IMP::algebra::MultiArray< T, D >::compute_min ( ) const

Minimum of the values in the array.

template<typename T, int D>

template<typename T1 >

T IMP::algebra::MultiArray< T, D >::compute_min ( T1 & min_idx ) const

Minimum of the values in the array.

Parameters:

[out] min_idx index containing the minimum value

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::compute_stats	(	double &	avg,
		double &	stddev,
		T &	minval,
		T &	maxval
	)		const

Compute average, standard deviation, minimum and maximum values.

template<typename T, int D>

double IMP::algebra::MultiArray< T, D >::compute_stddev ( ) const

Standard deviation of the values in the array.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::copy ( This & v )

Copies the contents of a MultiArray to this one (no resizing is done). For copying with resizing use operator=

Parameters:

[in] v MultiArray whose contents to copy

template<typename T, int D>

template<typename U >

void IMP::algebra::MultiArray< T, D >::copy_with_casting ( MultiArray< U, D > & v )

Copy with casting. Use with care!

template<typename T, int D>

double IMP::algebra::MultiArray< T, D >::cross_correlation_coefficient	(	const This &	v,
		bool	apply_threshold = `false`,
		double	threshold = `0.0`,
		bool	divide_by_stddev = `true`,
		bool	force_recalc_stats = `true`,
		double	avg = `0.0`,
		double	stddev = `0.0`,
		double	avg_v = `0.0`,
		double	stddev_v = `0.0`
	)

Computes the cross correlation coeffcient between two MultiArrays.

Note:: Both MultiArrays are required to have the same size, but not the same origin

Parameters:

[in]	v	array to compute the cross_correlation with.
[in]	apply_threshold	true if a threshold is applied to the elements of v .
[in]	threshold	minimum value for an element v to consider it in the computation .
[in]	divide_by_stddev	true if the cross correlation term is divided by the standard deviation to get the cross correlation coefficient (0 <= ccc <= 1).
[in]	force_recalc_stats	true if the statistics (mean, stddev) for the Multiarrays must be recalculated (default). If the statistics are known from previous computations, you can speed up the next computations setting this variable to false and directly providing the parameters.
[in]	avg	average of this Multiarray.
[in]	stddev	standard deviation of this Multiarray.
[in]	avg_v	average of Multiarray v.
[in]	stddev_v	standard deviation of Multiarray v.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::fill_with_value ( T val = 0 )

Fill all the voxels of the array with a given value.

template<typename T, int D>

bool IMP::algebra::MultiArray< T, D >::first_element ( ) const

Returns the first element.

template<typename T, int D>

int IMP::algebra::MultiArray< T, D >::get_finish ( const int dim ) const

Another way of asking for the final value (logical) for the index of the dimension

template<typename T, int D>

int IMP::algebra::MultiArray< T, D >::get_size ( const int dim ) const

Another way of asking for the size of a given dimension. You can always use x.shape()[i] too.

template<typename T, int D>

int IMP::algebra::MultiArray< T, D >::get_start ( const int dim ) const

Another way of asking for the initial value (logical) for the index of the dimension. You can always use index_bases()[dim]

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::init_zeros ( )

All the values of the array are set to zero.

template<typename T, int D>

template<typename T1 >

bool IMP::algebra::MultiArray< T, D >::is_logical_element ( T1 & v ) const

Returns true if the LOGICAL index belongs to those of the matrix.

Parameters:

[in] v Any class able to be accessed with []

template<typename T, int D>

template<typename T1 >

bool IMP::algebra::MultiArray< T, D >::is_physical_element ( T1 & v ) const

Returns true if the PHYSICAL index belongs to those of the matrix.

Parameters:

[in] v Any class able to be accessed with []

template<typename T, int D>

bool IMP::algebra::MultiArray< T, D >::is_void ( ) const

Check if the array has some dimensionality or is just empty.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::normalize ( )

Normalize the values of the MultiArray to mean value 0 and standard deviation 1.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator* ( const This & v ) const

Multiplication operator.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator* ( const T & v ) const

Multiplication operator for an array and a scalar.

Reimplemented in IMP::algebra::Matrix2D< T >, and IMP::algebra::Matrix3D< T >.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator*= ( const This & v ) const

Multiplication operator.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator*= ( const T & v ) const

Multiplication operator for an array and a scalar.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator+ ( const This & v ) const

Sum operator.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator+ ( const T & v ) const

Sum operator for an array and a scalar.

Reimplemented in IMP::algebra::Matrix2D< T >, and IMP::algebra::Matrix3D< T >.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator+= ( const This & v ) const

Addition operator.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator+= ( const T & v ) const

Addition operator for an array and a scalar.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator- ( const This & v ) const

Minus operator.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator- ( const T & v ) const

Minus operator for an array and a scalar.

Reimplemented in IMP::algebra::Matrix2D< T >, and IMP::algebra::Matrix3D< T >.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator-= ( const This & v ) const

Substraction operator.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator-= ( const T & v ) const

Substraction operator for an array and a scalar.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator/ ( const This & v ) const

Division operator.

template<typename T, int D>

This IMP::algebra::MultiArray< T, D >::operator/ ( const T & v ) const

Division operator for an array and a scalar.

Reimplemented in IMP::algebra::Matrix2D< T >, and IMP::algebra::Matrix3D< T >.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator/= ( const This & v ) const

Division operator.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::operator/= ( const T & v ) const

Division operator for an array and a scalar.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::print_shape ( std::ostream & out = std::cout ) const

Print shape of multidimensional array.

This function shows the size, starting and finishing indexes of the given array. No end of line is printed neither at the beginning nor the end.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::read ( const std::string & filename )

Read from an ASCII file.

The array must be previously resized to the correct size.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::read_binary	(	const std::string &	filename,
		bool	reversed = `false`
	)

Read from a binary file.

The array must be previously resized to the correct size.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::read_binary	(	std::ifstream &	input,
		bool	reversed = `false`
	)

Read from a input stream in binary mode.

The array must be previously resized to the correct size.

template<typename T, int D>

template<typename T1 >

bool IMP::algebra::MultiArray< T, D >::same_shape ( const MultiArray< T1, D > & b ) const

Compares the shape of two multidimensional arrays.

Returns:: true if both arrays have the same size and origin

template<typename T, int D>

template<typename T1 >

bool IMP::algebra::MultiArray< T, D >::same_size ( const MultiArray< T1, D > & b ) const

Compares the size of two multidimensional arrays.

Returns:: true if both arrays have the same size

template<typename T, int D>

template<typename T1 >

bool IMP::algebra::MultiArray< T, D >::same_start ( const MultiArray< T1, D > & b ) const

Compares the origin of two multidimensional arrays.

Returns:: true if both arrays have the same origin

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::set_start	(	const int	dim,
		const int	value
	)

Another way setting the initial value (logical) for the index of the dimension. You can always use reindex()

template<typename T, int D>

template<typename T1 >

void IMP::algebra::MultiArray< T, D >::set_start ( const T1 & v )

Another way setting the initial value (logical) for the index of the dimension.

Parameters:

[in] v Any class able to be accessed with []

template<typename T, int D>

T IMP::algebra::MultiArray< T, D >::squared_difference ( const This & v ) const

Computes the sum of the squared elements of the difference MultiArray obtained from substracting v.

Note:: Both MultiArrays are required to have the same shape (size and origin)

template<typename T, int D>

T IMP::algebra::MultiArray< T, D >::sum_elements ( ) const

Computes the sum of all the array elements.

template<typename T, int D>

T IMP::algebra::MultiArray< T, D >::sum_squared_elements ( ) const

Computes the sum of all the squared elements of the array. (Frobenius norm)

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::write ( const std::string & filename ) const

Write to an ASCII file.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::write_binary	(	const std::string &	filename,
		bool	reversed = `false`
	)

Write to a binary file.

template<typename T, int D>

void IMP::algebra::MultiArray< T, D >::write_binary	(	std::ofstream &	out,
		bool	reversed = `false`
	)

Write to a output stream in binary mode.

Friends And Related Function Documentation

template<class T , int D>

MultiArray< T, D > operator*	(	const T &	X,
		const MultiArray< T, D > &	a1
	)

template<class T , int D>

MultiArray< T, D > operator+	(	const T &	X,
		const MultiArray< T, D > &	a1
	)

template<class T , int D>

MultiArray< T, D > operator-	(	const T &	X,
		const MultiArray< T, D > &	a1
	)

template<class T , int D>

MultiArray< T, D > operator/	(	const T &	X,
		const MultiArray< T, D > &	a1
	)

The documentation for this class was generated from the following file:

MultiArray.h

Detailed Description

template<typename T, int D> class IMP::algebra::MultiArray< T, D >

Public Types

Public Member Functions

Friends

Related Functions

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<typename T, int D>
class IMP::algebra::MultiArray< T, D >