clipper::Xmap< T > Class Template Reference

Xmap<T>: actual crystallographic map class. More...

#include <xmap.h>

Inheritance diagram for clipper::Xmap< T >:

Public Member Functions
	Xmap ()
	Null constructor, for later initialisation.
	Xmap (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
	constructor: from spacegroup, cell, and grid
void	init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
	initialiser: from spacegroup, cell, and grid
const T &	operator[] (const Xmap_base::Map_reference_index &ix) const
	get data by Map_reference_index
T &	operator[] (const Xmap_base::Map_reference_index &ix)
	set data by Map_reference_index
const T &	operator[] (const Xmap_base::Map_reference_coord &ix) const
	get data by Map_reference_coord
T &	operator[] (const Xmap_base::Map_reference_coord &ix)
	set data by Map_reference_coord
const T &	get_data (const Coord_grid &pos) const
	get a density value for an arbitrary position
void	set_data (const Coord_grid &pos, const T &val)
	set a density value for an arbitrary position
const T &	get_data (const int &index) const
	get data by index (not recommended)
bool	set_data (const int &index, const T &val)
	set data by index (not recommended)
template<class I>
T	interp (const Coord_frac &pos) const
	get map value for fractional coord using supplied interpolator
template<class I>
void	interp_grad (const Coord_frac &pos, T &val, Grad_frac< T > &grad) const
	get map value and grad for fractional coord using supplied interpolator
template<class I>
void	interp_curv (const Coord_frac &pos, T &val, Grad_frac< T > &grad, Curv_frac< T > &curv) const
	get map value and curv for fractional coord using supplied interpolator
template<class I>
T	interp (const Coord_map &pos) const
	get map value for map coord using supplied interpolator
template<class I>
void	interp_grad (const Coord_map &pos, T &val, Grad_map< T > &grad) const
	get map value and grad for map coord using supplied interpolator
template<class I>
void	interp_curv (const Coord_map &pos, T &val, Grad_map< T > &grad, Curv_map< T > &curv) const
	get map value and curv for map coord using supplied interpolator
template<class H>
void	fft_from (const H &fphidata, const FFTtype type=Default)
	FFT from reflection list to map.
template<class H>
void	fft_to (H &fphidata, const FFTtype type=Default) const
	FFT from map to reflection list.
const Cell &	cell () const
const Spacegroup &	spacegroup () const
const Grid_sampling &	grid_sampling () const
const Grid_range &	grid_asu () const
Coord_grid	coord_of (const int &index) const
int	index_of (const Coord_grid &coord) const
const int	multiplicity (const Coord_grid &pos) const
const Coord_grid	to_map_unit (const Coord_grid &pos) const
const Map_reference_index	first () const
const Map_reference_coord	first_coord () const
const T &	operator= (const T &value)
	assignment operator: assigns a single value to the whole map
const Xmap< T > &	operator+= (const Xmap< T > &other)
	add another map to this one
const Xmap< T > &	operator-= (const Xmap< T > &other)
	subtract another map from this one
Public Member Functions inherited from clipper::Xmap_base
bool	is_null () const
	test if object has been initialised
const Cell &	cell () const
	get the cell
const Spacegroup &	spacegroup () const
	get the spacegroup
const Grid_sampling &	grid_sampling () const
	get the cell grid
const Grid_range &	grid_asu () const
	get the ASU grid
Coord_grid	coord_of (const int &index) const
	map coordinate from index
int	index_of (const Coord_grid &coord) const
	map index from coordinate
Coord_grid	to_map_unit (const Coord_grid &pos) const
	function to pick right cell repeat for any grid coord
const RTop &	operator_orth_grid () const
	return the orthogonal-to-grid coordinate operator (translation is zero)
const RTop &	operator_grid_orth () const
	return the grid-to-orthogonal coordinate operator (translation is zero)
Coord_orth	coord_orth (const Coord_map &cm) const
	convert map coordinate to orthogonal
Coord_map	coord_map (const Coord_orth &co) const
	convert orthogonal coordinate to map
bool	in_map (const Coord_grid &) const
	(This method is for compatibility with NXmap - it always returns true)
template<class I>
bool	in_map (const Coord_map &cm) const
	(This method is for compatibility with NXmap - it always returns true)
int	multiplicity (const Coord_grid &pos) const
	get multiplicity of a map grid point
Map_reference_index	first () const
	return a Map_reference_index for this map
Map_reference_coord	first_coord () const
	return a Map_reference_coord for this map

Additional Inherited Members
Public Types inherited from clipper::Xmap_base
enum	FFTtype { Default , Normal , Sparse }
Static Public Member Functions inherited from clipper::Xmap_base
static FFTtype &	default_type ()
	set/get default backend type
Protected Member Functions inherited from clipper::Xmap_base
	Xmap_base ()
	Null constructor, for later initialisation.
void	init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
	initialiser
void	find_sym (const Coord_grid &base, int &index, int &sym) const
void	asu_error (const Coord_grid &pos) const
Protected Attributes inherited from clipper::Xmap_base
ObjectCache< Xmap_cacheobj >::Reference	cacheref
	object cache reference
const unsigned char *	asu
	fast access ptr
const Isymop *	isymop
	fast access ptr
const int *	du
	fast access ptr
const int *	dv
	fast access ptr
const int *	dw
	fast access ptr
Grid_range	asu_grid
	fast access copy
Grid_range	map_grid
	fast access copy
int	nsym
	fast access copy
Cell	cell_
	unit cell
Spacegroup	spacegroup_
	spacegroup
Grid_sampling	grid_sam_
	grid for the whole cell
RTop	rt_orth_grid
	orth->grid operator
RTop	rt_grid_orth
	grid->orth operator
Static Protected Attributes inherited from clipper::Xmap_base
static FFTtype	default_type_ = Xmap_base::Sparse
	default backend type

Detailed Description

template<class T>
class clipper::Xmap< T >

Xmap<T>: actual crystallographic map class.

The crystallographic map class stores a map of arbitrary data type. Its main difference from a 3-d array is that the data extent appears to be infinite, and yet internally only a unique ASU is stored. Iterators provide efficient access to data.

This is derived from Xmap_base, and adds the templatised data itself and the methods which deal with it.

Note

The following methods are inherited from Xmap_base but are documented here for convenience: cell(), spacegroup(), grid_sampling(), grid_asu(), in_asu(), multiplicity(), to_map_unit(), first(), first_coord().

Member Function Documentation

get_data() [1/2]

template<class T>

const T & clipper::Xmap< T >::get_data

(

const Coord_grid &

pos

)

const

get a density value for an arbitrary position

Accessing the data by coordinate, rather than by Map_reference_index or Map_reference_coord, involves a symmetry lookup and is therefore slow. Avoid using these methods when you can.

set_data() [1/2]

template<class T>

void clipper::Xmap< T >::set_data	(	const Coord_grid &	pos,
		const T &	val )

set a density value for an arbitrary position

Accessing the data by coordinate, rather than by Map_reference_index or Map_reference_coord, involves a symmetry lookup and is therefore slow. Avoid using these methods when you can.

get_data() [2/2]

template<class T>

const T & clipper::Xmap< T >::get_data ( const int & index ) const

inline

get data by index (not recommended)

Accessing the data by index, rather than by Map_reference_index or Map_reference_coord, is generally to be avoided since the indices do not start at zero and do not increase contiguously. These methods are only useful when a large number of references into a map must be stored, e.g. for sorting into density order.

set_data() [2/2]

template<class T>

bool clipper::Xmap< T >::set_data	(	const int &	index,
		const T &	val )

set data by index (not recommended)

Accessing the data by index, rather than by Map_reference_index or Map_reference_coord, is generally to be avoided since the indices do not start at zero and do not increase contiguously. These methods are only useful when a large number of references into a map must be stored, e.g. for sorting into density order.

Returns

true if data was set, i.e. index is valid.

interp() [1/2]

template<class T>

template<class I>

T clipper::Xmap< T >::interp

(

const Coord_frac &

pos

)

const

get map value for fractional coord using supplied interpolator

The value of the map at the desired non-grid fractional coordinate are calculated using the supplied interpolator template.

Coord_frac f( u, v, w );
y = xmap.interp<Interp_cubic>( f );

Parameters

pos	The fractional coord at which the density is to be calcuated.

Returns

The value of the density at that point.

interp_grad() [1/2]

template<class T>

template<class I>

void clipper::Xmap< T >::interp_grad	(	const Coord_frac &	pos,
		T &	val,
		Grad_frac< T > &	grad ) const

get map value and grad for fractional coord using supplied interpolator

The value of the map at the desired non-grid fractional coordinate and its gradient are calculated using the supplied interpolator template.

Parameters

pos	The fractional coord at which the density is to be calcuated.
val	The value of the density at that point.
grad	The interpolated gradient vector with respect to the fractional coordinates (see Cell::coord_orth).

interp_curv() [1/2]

template<class T>

template<class I>

void clipper::Xmap< T >::interp_curv	(	const Coord_frac &	pos,
		T &	val,
		Grad_frac< T > &	grad,
		Curv_frac< T > &	curv ) const

get map value and curv for fractional coord using supplied interpolator

The value of the map at the desired non-grid fractional coordinate and its gradient and curvature are calculated using the supplied interpolator template. e.g.

Parameters

pos	The fractional coord at which the density is to be calcuated.
val	The value of the density at that point.
grad	The interpolated gradient vector with respect to the fractional coordinates (see Cell::coord_orth).
curv	The interpolated curvature matrix with respect to the fractional coordinates (see Cell::coord_orth).

interp() [2/2]

template<class T>

template<class I>

T clipper::Xmap< T >::interp

(

const Coord_map &

pos

)

const

get map value for map coord using supplied interpolator

The value of the map at the desired non-grid map coordinate are calculated using the supplied interpolator template.

Coord_map m( u, v, w );
y = xmap.interp<Interp_cubic>( m );

Parameters

pos	The map coord at which the density is to be calcuated.

Returns

The value of the density at that point.

interp_grad() [2/2]

template<class T>

template<class I>

void clipper::Xmap< T >::interp_grad	(	const Coord_map &	pos,
		T &	val,
		Grad_map< T > &	grad ) const

get map value and grad for map coord using supplied interpolator

The value of the map at the desired non-grid map coordinate and its gradient are calculated using the supplied interpolator template.

Parameters

pos	The map coord at which the density is to be calcuated.
val	The value of the density at that point.
grad	The interpolated gradient vector with respect to the map coordinates (see Cell::coord_orth).

interp_curv() [2/2]

template<class T>

template<class I>

void clipper::Xmap< T >::interp_curv	(	const Coord_map &	pos,
		T &	val,
		Grad_map< T > &	grad,
		Curv_map< T > &	curv ) const

get map value and curv for map coord using supplied interpolator

The value of the map at the desired non-grid map coordinate and its gradient and curvature are calculated using the supplied interpolator template. e.g.

Parameters

pos	The map coord at which the density is to be calcuated.
val	The value of the density at that point.
grad	The interpolated gradient vector with respect to the map coordinates (see Cell::coord_orth).
curv	The interpolated curvature matrix with respect to the map coordinates (see Cell::coord_orth).

fft_from()

template<class T>

template<class H>

void clipper::Xmap< T >::fft_from	(	const H &	fphidata,
		const FFTtype	type = Default )

FFT from reflection list to map.

An FFT is calculated using the provided reflection list of F_phi, and used to fill this map. The reflection list is unchanged.

Parameters

fphidata

The reflection data list to use

fft_to()

template<class T>

template<class H>

void clipper::Xmap< T >::fft_to	(	H &	fphidata,
		const FFTtype	type = Default ) const

FFT from map to reflection list.

The Fourier transform of this map is calculated and used to fill a reflection list of F_phi. The map is unchanged.

Arguably this should be part of hkl_data<F_phi<T>>. But that requires writing a specialisation of hkl_data for F_phi. This is simpler and imposes less demands on the compiler.

Parameters

fphidata

The reflection data list to set.

operator=()

template<class T>

const T & clipper::Xmap< T >::operator=

(

const T &

value

)

assignment operator: assigns a single value to the whole map

All values, including missing values, are overwritten by the value.

Parameters

value

The value to which the map is to be set.

operator+=()

template<class T>

const Xmap< T > & clipper::Xmap< T >::operator+=

(

const Xmap< T > &

other

)

add another map to this one

The map grids and spacegroups must match.

operator-=()

template<class T>

const Xmap< T > & clipper::Xmap< T >::operator-=

(

const Xmap< T > &

other

)

subtract another map from this one

The map grids and spacegroups must match.

---

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

• xmap.h