Class for handling density maps. More...

#include <IMP/em/DensityMap.h>

Inheritance diagram for IMP::em::DensityMap:

Detailed Description

Class for handling density maps.

Note: The location of a voxel is its center. That is important for sampling function as well as for functions like get_location_in_dim_by_voxel.

Definition at line 94 of file DensityMap.h.

Public Member Functions
	DensityMap (std::string name="DensityMap%1%")

	DensityMap (const DensityHeader &header, std::string name="DensityMap%1%")
	Construct a density map as instructed in the input header. More...

void	add (const DensityMap *other)

void	calc_all_voxel2loc ()
	Calculates the coordinates that correspond to all voxels. More...

emreal	calcRMS ()
	Calculates RMSD and mean of a map values as stored in the header. More...

void	copy_map (const DensityMap *other)
	copy map into this map More...

algebra::Vector3D	get_centroid (emreal threshold=0.0) const

DensityMap *	get_cropped (float threshold)
	Create a new cropped map. More...

DensityMap *	get_cropped (const algebra::BoundingBox3D &bb)
	Create a new cropped map with the bounding box extent. More...

int	get_dim_index_by_location (const algebra::Vector3D &v, int ind) const
	Calculate dimension index of a given location. More...

int	get_dim_index_by_location (float loc_val, int ind) const

const DensityHeader *	get_header () const

DensityHeader *	get_header_writable ()
	Returns a pointer to the header of the map in a writable version. More...

algebra::Vector3D	get_location_by_voxel (long index) const
	Calculate the location of a given voxel. More...

float	get_location_in_dim_by_voxel (long index, int dim) const
	Calculate the location of a given voxel in a given dimension. More...

std::string	get_locations_string (float t)

emreal	get_max_value () const
	Returns the value of the voxel with the highest density. More...

float	get_maximum_value_in_xy_plane (int z_ind)
	Get the maximum value in a XY plane indicated by a Z index. More...

float	get_maximum_value_in_xz_plane (int y_ind)
	Get the maximum value in a XZ plane indicated by a Y index. More...

float	get_maximum_value_in_yz_plane (int x_ind)
	Get the maximum value in a YZ plane indicated by a X index. More...

emreal	get_min_value () const
	Returns the value of the voxel with the lowest density. More...

long	get_number_of_voxels () const
	number of map voxels More...

algebra::Vector3D	get_origin () const

bool	get_rms_calculated () const

Float	get_spacing () const
	Updated the voxel size of the map. More...

algebra::Vector3D	get_top () const

virtual std::string	get_type_name () const

emreal	get_value (float x, float y, float z) const
	Gets the value of the voxel located at (x,y,z) More...

emreal	get_value (const algebra::Vector3D &point) const

emreal	get_value (long index) const
	Gets the value of the voxel at a given index. More...

virtual ::IMP::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

long	get_voxel_by_location (float x, float y, float z) const
	Calculate the voxel of a given location. More...

long	get_voxel_by_location (const algebra::Vector3D &v) const
	Calculate the voxel of a given location. More...

bool	is_normalized () const

bool	is_part_of_volume (float x, float y, float z) const
	Checks whether a given point is in the grid the voxel of a given location. More...

bool	is_part_of_volume (const algebra::Vector3D &v) const
	Checks whether a given point is in the grid the voxel of a given location. More...

bool	is_xyz_ind_part_of_volume (int ix, int iy, int iz) const

int	lower_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const

void	multiply (float factor)

void	pad (int nx, int ny, int nz, float val=0.0)

DensityMap *	pad_margin (int mrg_x, int mrg_y, int mrg_z, float val=0.0)
	Create a new padded map. More...

void	pick_max (const DensityMap *other)

void	reset_data (float value=0.0)
	Set the density voxels to some value and reset the management flags. More...

bool	same_dimensions (const DensityMap *other) const
	Checks if two maps have the same dimensions. More...

bool	same_origin (const DensityMap *other) const
	Checks if two maps have the same origin. More...

bool	same_voxel_size (const DensityMap *other) const
	Checks if two maps have the same voxel size. More...

void	set_origin (float x, float y, float z)
	Sets the origin of the header. More...

void	set_origin (const IMP::algebra::Vector3D &v)

void	set_value (long index, emreal value)
	Set the value of the voxel at a given index. More...

void	set_value (float x, float y, float z, emreal value)
	Set the value of the voxel at a given index. More...

void	set_void_map (int nx, int ny, int nz)
	Set the map dimension and reset all voxels to 0. More...

void	std_normalize ()
	Normalize the density voxels according to standard deviation (stdv). More...

void	update_voxel_size (float new_apix)
	Updated the voxel size of the map. More...

int	upper_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const

long	xyz_ind2voxel (int x, int y, int z) const
	Calculate the voxel of a given xyz indexes. More...

Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Protected Member Functions
void	allocated_data ()

void	float2real (float *f_data, boost::scoped_array< emreal > &r_data)

void	real2float (emreal *r_data, boost::scoped_array< float > &f_data)

void	reset_all_voxel2loc ()

void	update_header ()
	update the header values – still in work More...

Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Protected Attributes
boost::scoped_array< emreal >	data_

bool	data_allocated_

DensityHeader	header_

bool	loc_calculated_
	true if the locations have already been computed More...

bool	normalized_

bool	rms_calculated_

boost::scoped_array< float >	x_loc_

boost::scoped_array< float >	y_loc_

boost::scoped_array< float >	z_loc_

Friends
DensityMap *	read_map (std::string filename, MapReaderWriter *reader)
	Read a density map from a file and return it. More...

void	write_map (DensityMap m, std::string filename, MapReaderWriter writer)
	Write a density map to a file. More...

Constructor & Destructor Documentation

IMP::em::DensityMap::DensityMap	(	const DensityHeader &	header,
		std::string	name = `"DensityMap%1%"`
	)

Construct a density map as instructed in the input header.

Member Function Documentation

void IMP::em::DensityMap::add ( const DensityMap * other )

Sums two grids. The result is kept in the map.

Parameters

[in] other the other map

Note: The shared extend is summed; The two maps should have the same voxelsize and other should be contained within this map

void IMP::em::DensityMap::calc_all_voxel2loc ( )

Calculates the coordinates that correspond to all voxels.

emreal IMP::em::DensityMap::calcRMS ( )

Calculates RMSD and mean of a map values as stored in the header.

The header stores whether map is normalized.

void IMP::em::DensityMap::copy_map ( const DensityMap * other )

copy map into this map

algebra::Vector3D IMP::em::DensityMap::get_centroid ( emreal threshold = 0.0 ) const

Calculates the centroid of all the voxels with density above a given threshold

Parameters

[in] threshold the input threshold

DensityMap* IMP::em::DensityMap::get_cropped ( float threshold )

Create a new cropped map.

The margins are determined to be the bounding box with density values below the input

Parameters

[in] threshold used for cropping

DensityMap* IMP::em::DensityMap::get_cropped ( const algebra::BoundingBox3D & bb )

Create a new cropped map with the bounding box extent.

Parameters

[in] bb the bounding box

Note: If the input bounding box is larger than the density box, it is snapped to the right size.

int IMP::em::DensityMap::get_dim_index_by_location	(	const algebra::Vector3D &	v,
		int	ind
	)		const

Calculate dimension index of a given location.

Parameters

[in]	v	The position (in angstroms)
[in]	ind	dimension index (X:0,Y:1 or Z:2)

DensityHeader* IMP::em::DensityMap::get_header_writable ( )

Returns a pointer to the header of the map in a writable version.

Definition at line 253 of file DensityMap.h.

algebra::Vector3D IMP::em::DensityMap::get_location_by_voxel ( long index ) const

Calculate the location of a given voxel.

Parameters

[in] index The voxel index

Returns: the location (x,y,z) (in angstroms) of a given voxel.

Definition at line 170 of file DensityMap.h.

float IMP::em::DensityMap::get_location_in_dim_by_voxel	(	long	index,
		int	dim
	)		const

Calculate the location of a given voxel in a given dimension.

Parameters

[in]	index	The voxel index
[in]	dim	The dimension of interest (x:=0,y:=1,z:=2)

Returns: the location (x,y,z) (in angstroms) of a given voxel. If the index is not part of the map, the function returns -1.

std::string IMP::em::DensityMap::get_locations_string ( float t )

Prints the locations of all of the voxels with value above a given threshold into the input stream.

emreal IMP::em::DensityMap::get_max_value ( ) const

Returns the value of the voxel with the highest density.

float IMP::em::DensityMap::get_maximum_value_in_xy_plane ( int z_ind )

Get the maximum value in a XY plane indicated by a Z index.

float IMP::em::DensityMap::get_maximum_value_in_xz_plane ( int y_ind )

Get the maximum value in a XZ plane indicated by a Y index.

float IMP::em::DensityMap::get_maximum_value_in_yz_plane ( int x_ind )

Get the maximum value in a YZ plane indicated by a X index.

emreal IMP::em::DensityMap::get_min_value ( ) const

Returns the value of the voxel with the lowest density.

long IMP::em::DensityMap::get_number_of_voxels ( ) const

number of map voxels

Float IMP::em::DensityMap::get_spacing ( ) const

Updated the voxel size of the map.

Note: Use update_voxel_size() to set the spacing value.

Definition at line 407 of file DensityMap.h.

emreal IMP::em::DensityMap::get_value	(	float	x,
		float	y,
		float	z
	)		const

Gets the value of the voxel located at (x,y,z)

Parameters

[in]	x	The position ( in angstroms) of the x coordinate
[in]	y	The position ( in angstroms) of the y coordinate
[in]	z	The position ( in angstroms) of the z coordinate

Returns: the value of the voxel located at (x,y,z)

Exceptions

IndexException The point is not covered by the grid.

Note: the value is not interpolated between this and neighboring voxels. For that, see get_density().

emreal IMP::em::DensityMap::get_value ( long index ) const

Gets the value of the voxel at a given index.

Parameters

[in] index voxel number in physical sense, NOT logical

virtual ::IMP::VersionInfo IMP::em::DensityMap::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 412 of file DensityMap.h.

long IMP::em::DensityMap::get_voxel_by_location	(	float	x,
		float	y,
		float	z
	)		const

Calculate the voxel of a given location.

Parameters

[in]	x	The position (in angstroms) of the x coordinate
[in]	y	The position (in angstroms) of the y coordinate
[in]	z	The position (in angstroms) of the z coordinate

Returns: the voxel index of a given position. If the position is out of the boundaries of the map, the function returns -1.

long IMP::em::DensityMap::get_voxel_by_location ( const algebra::Vector3D & v ) const

Calculate the voxel of a given location.

Parameters

[in] v The position (in angstroms)

Returns: the voxel index of a given position. If the position is out of the boundaries of the map, the function returns -1.

Definition at line 157 of file DensityMap.h.

bool IMP::em::DensityMap::is_part_of_volume	(	float	x,
		float	y,
		float	z
	)		const

Checks whether a given point is in the grid the voxel of a given location.

Parameters

[in]	x	The position ( in angstroms) of the x coordinate
[in]	y	The position ( in angstroms) of the y coordinate
[in]	z	The position ( in angstroms) of the z coordinate

Returns: true if the point is part of the grid, false otherwise.

bool IMP::em::DensityMap::is_part_of_volume ( const algebra::Vector3D & v ) const

Checks whether a given point is in the grid the voxel of a given location.

Parameters

[in] v The position ( in angstroms)

Returns: true if the point is part of the grid, false otherwise.

Definition at line 192 of file DensityMap.h.

void IMP::em::DensityMap::multiply ( float factor )

Multiply each voxel in the map by the input factor The result is kept in the map.

Parameters

[in] factor the multiplication factor

void IMP::em::DensityMap::pad	(	int	nx,
		int	ny,
		int	nz,
		float	val = `0.0`
	)

Increase the dimension of the map The function pads zeros to the right-upper section on the map. The original content of the map will be in the lower XYZ part of the map

Parameters

[in]	nx	the number of voxels on the X axis
[in]	ny	the number of voxels on the Y axis
[in]	nz	the number of voxels on the Z axis
[in]	val	all additional voxels will have this value

Exceptions

if	the input x/y/z voxels is smaller than the one currently in the map

DensityMap* IMP::em::DensityMap::pad_margin	(	int	mrg_x,
		int	mrg_y,
		int	mrg_z,
		float	val = `0.0`
	)

Create a new padded map.

Given this map of size [nx,ny,nz], the new map is of size [2*mrg_x+nx,2*mrg_y+ny,2*mrg_z+nz]. The new map will consist of the values of the old map, padded margin on all sides.

Parameters

[in]	mrg_x	number of margin voxels to add on both right and left on the X axis
[in]	mrg_y	number of margin voxels to add on both right and left on the Y axis
[in]	mrg_z	number of margin voxels to add on both right and left on the Z axis
[in]	val	ignored

Exceptions

if	the input x/y/z voxels is smaller than the one currently in the map

void IMP::em::DensityMap::pick_max ( const DensityMap * other )

Pick the max value between two corresponding voxels between two maps The result is kept in the map.

Parameters

[in] other the other map

Note: The two maps should have the same voxelsize and the same dimensions

void IMP::em::DensityMap::reset_data ( float value = 0.0 )

Set the density voxels to some value and reset the management flags.

Parameters

[in] value all of the density voxels will have this value

bool IMP::em::DensityMap::same_dimensions ( const DensityMap * other ) const

Checks if two maps have the same dimensions.

Parameters

[in] other the map to compare with

Returns: true if the two maps have the same dimensions

bool IMP::em::DensityMap::same_origin ( const DensityMap * other ) const

Checks if two maps have the same origin.

Parameters

[in] other the map to compare with

Returns: true if the two maps have the same origin

bool IMP::em::DensityMap::same_voxel_size ( const DensityMap * other ) const

Checks if two maps have the same voxel size.

Parameters

[in] other the map to compare with

Returns: true if the two maps have the same voxel size

void IMP::em::DensityMap::set_origin	(	float	x,
		float	y,
		float	z
	)

Sets the origin of the header.

Parameters

x	the new x (angstroms)
y	the new y (angstroms)
z	the new z (angstroms)

void IMP::em::DensityMap::set_value	(	long	index,
		emreal	value
	)

Set the value of the voxel at a given index.

Parameters

[in]	index	voxel number in physical sense, NOT logical
[in]	value	value

void IMP::em::DensityMap::set_value	(	float	x,
		float	y,
		float	z,
		emreal	value
	)

Set the value of the voxel at a given index.

index voxel number in physical sense, NOT logical

void IMP::em::DensityMap::set_void_map	(	int	nx,
		int	ny,
		int	nz
	)

Set the map dimension and reset all voxels to 0.

Parameters

[in]	nx	x-dimension (voxels)
[in]	ny	y-dimension (voxels)
[in]	nz	z-dimension (voxels)

Note: the origin and spacing remain unchanged

void IMP::em::DensityMap::std_normalize ( )

Normalize the density voxels according to standard deviation (stdv).

The mean is subtracted from the map, which is then divided by the stdv. The normalization flag is set to avoid repeated computation

void IMP::em::DensityMap::update_header ( )

protected

update the header values – still in work

void IMP::em::DensityMap::update_voxel_size ( float new_apix )

Updated the voxel size of the map.

long IMP::em::DensityMap::xyz_ind2voxel	(	int	x,
		int	y,
		int	z
	)		const

Calculate the voxel of a given xyz indexes.

Parameters

[in]	x	The voxel index on the x axis of the grid
[in]	y	The voxel index on the y axis of the grid
[in]	z	The voxel index on the z axis of the grid

Returns: the voxel index.

Definition at line 139 of file DensityMap.h.

Friends And Related Function Documentation

DensityMap* read_map	(	std::string	filename,
		MapReaderWriter *	reader
	)

friend

Read a density map from a file and return it.

See Also: DensityMap

void write_map	(	DensityMap *	m,
		std::string	filename,
		MapReaderWriter *	writer
	)

friend

Write a density map to a file.

See Also: DensityMap

Member Data Documentation

bool IMP::em::DensityMap::loc_calculated_

protected

true if the locations have already been computed

Definition at line 458 of file DensityMap.h.

boost::scoped_array<float> IMP::em::DensityMap::x_loc_

protected

Locations (centers) for each of the voxels of the map (they are precomputed and each one is of size nvox, where nvox is the size of the map)

Definition at line 456 of file DensityMap.h.

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

DensityMap.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation