IMP::em::DensityMap Class Reference

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 95 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)
	Sums two grids; the result is kept in the map. More...
void	add (Float d)
	Add a number to every voxel in the map. More...
void	calc_all_voxel2loc ()
	Calculates the coordinates that correspond to all voxels. More...
double	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 (double threshold=0.0) const
	Get the centroid of all voxels with density above a given threshold. More...
DensityMap *	get_cropped (float threshold)
	Create and return a new cropped map. More...
DensityMap *	get_cropped (Particles ps, double distance, bool inverse=false, bool keep_map_dimensions=false)
	Create and return a new cropped map based on particles. More...
DensityMap *	get_cropped (const algebra::BoundingBox3D &bb)
	Create and return a new cropped map with the given 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
	Returns a read-only pointer to the header of the map. More...
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)
	Print the locations of all voxels with value above a given threshold. More...
double	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...
double	get_min_value () const
	Returns the value of the voxel with the lowest density. More...
long	get_number_of_voxels () const
	Get the number of map voxels. More...
algebra::Vector3D	get_origin () const
bool	get_rms_calculated () const
Float	get_spacing () const
	Get the voxel size of the map. More...
algebra::Vector3D	get_top () const
virtual std::string	get_type_name () const override
double	get_value (float x, float y, float z) const
	Gets the value of the voxel located at (x,y,z) More...
double	get_value (const algebra::Vector3D &point) const
double	get_value (long index) const
	Gets the value of the voxel at a given index. More...
virtual ::IMP::VersionInfo	get_version_info () const override
	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. More...
bool	is_part_of_volume (const algebra::Vector3D &v) const
	Checks whether a given point is in the grid. More...
bool	is_xyz_ind_part_of_volume (int ix, int iy, int iz) const
int	lower_voxel_shift (double loc, double kdist, double orig, int ndim) const
void	multiply (float factor)
	Multiply in place each voxel in the map by the input factor. More...
void	pad (int nx, int ny, int nz, float val=0.0)
	Increase the dimension of the map. More...
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)
	Pick the max value between two corresponding voxels between two maps. More...
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, double value)
	Set the value of the voxel at a given index. More...
void	set_value (float x, float y, float z, double value)
	Set the value of the voxel at given coordinates. 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)
	Update the voxel size of the map. More...
int	upper_voxel_shift (double loc, double kdist, double orig, int ndim) const
long	xyz_ind2voxel (int x, int y, int z) const
	Calculate the voxel of a given xyz index. 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< double > &r_data)
void	real2float (double *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< double >	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)
void	write_map (DensityMap *m, std::string filename, MapReaderWriter *writer)

Related Functions
(Note that these are not member functions.)
void	add_to_map (DensityMap *dm, const Particles &pis)
	Rasterize the particles into an existing density map. More...
DensityMap *	create_density_map (algebra::DenseGrid3D< float > &grid)
	Return a density map with the values taken from the grid. More...
DensityMap *	create_density_map (algebra::DenseGrid3D< double > &grid)
	Return a density map with the values taken from the grid. More...
DensityMap *	get_binarized_interior (DensityMap *dmap)
	Return a binarized map with 1 for voxels that are internal in the input map. More...
double	get_density (const DensityMap *m, const algebra::Vector3D &v)
	Get density value at point v, interpolating linearly from the sample values. More...
DensityMap *	get_resampled (DensityMap *input, double scaling)
	Get a resampled version of the map. More...
DensityMap *	get_transformed (const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
	Return a new density map containing a rotated version of the old one. More...
DensityMap *	get_transformed (DensityMap *input, const algebra::Transformation3D &tr)
	Return a new density map containing a rotated version of the old one. More...
void	get_transformed_into (const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)
	Rotate a density map into another map. More...
DensityMap *	read_map (std::string filename, MapReaderWriter *reader)
	Read a density map from a file (using the given reader) and return it. More...
DensityMap *	read_map (std::string filename)
	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 using the given writer. More...
void	write_map (DensityMap *m, std::string filename)
	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::add

(

Float

d

)

Add a number to every voxel in the map.

Parameters

[in]

d

Value to add

void IMP::em::DensityMap::calc_all_voxel2loc

(

)

Calculates the coordinates that correspond to all voxels.

double IMP::em::DensityMap::calcRMS

(

)

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

The header stores whether the map is normalized.

void IMP::em::DensityMap::copy_map

(

const DensityMap *

other

)

Copy map into this map.

algebra::Vector3D IMP::em::DensityMap::get_centroid

(

double

threshold = 0.0

)

const

Get the centroid of all voxels with density above a given threshold.

Parameters

[in]

threshold

the input threshold

DensityMap* IMP::em::DensityMap::get_cropped

(

float

threshold

)

Create and return 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

Returns

the new cropped map.

DensityMap* IMP::em::DensityMap::get_cropped	(	Particles	ps,
		double	distance,
		bool	inverse = false,
		bool	keep_map_dimensions = false
	)

Create and return a new cropped map based on particles.

The map is cropped based on voxel proximity to a set of particles. All voxel centers farther than [distance] away from any particle center in [ps] will have their density value set to 0.0, unless inverse is set to true in which case all voxel centers within [distance] of a particle will be set to 0.0.

Parameters

[in]	ps	List of particles used to crop map
[in]	distance	Distance from particles at which to crop map
[in]	inverse	If true, remove nearby density rather than distant density
[in]	keep_map_dimensions	If false, crop the map to remove as many voxels set to 0.0 as possible; otherwise, return a map the same size as the input.

Returns

the new cropped map.

DensityMap* IMP::em::DensityMap::get_cropped

(

const algebra::BoundingBox3D &

bb

)

Create and return a new cropped map with the given bounding box extent.

Parameters

[in]

bb

the bounding box

Returns

the new cropped map.

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)

const DensityHeader* IMP::em::DensityMap::get_header

(

)

const

Returns a read-only pointer to the header of the map.

Definition at line 245 of file DensityMap.h.

DensityHeader* IMP::em::DensityMap::get_header_writable

(

)

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

Definition at line 248 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

)

Print the locations of all voxels with value above a given threshold.

double 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.

double 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

Get the number of map voxels.

Definition at line 330 of file DensityMap.h.

Float IMP::em::DensityMap::get_spacing

(

)

const

Get the voxel size of the map.

Note

Use update_voxel_size() to set the spacing value.

Definition at line 430 of file DensityMap.h.

double 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().

double 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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 435 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.

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.

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 in place 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 zeroes 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

UsageException

if the input numbers of x/y/z voxels are smaller than those 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, with a 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

Returns

the new padded map.

Exceptions

UsageException

if the input numbers of x/y/z voxels are smaller than those 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,
		double	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,
		double	value
	)

Set the value of the voxel at given coordinates.

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

)

Update 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 index.

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

void add_to_map ( DensityMap *  dm, const Particles &  pis  )

related

Rasterize the particles into an existing density map.

DensityMap * create_density_map ( algebra::DenseGrid3D< float > &  grid )

related

Return a density map with the values taken from the grid.

DensityMap * create_density_map ( algebra::DenseGrid3D< double > &  grid )

related

Return a density map with the values taken from the grid.

DensityMap * get_binarized_interior ( DensityMap *  dmap )

related

Return a binarized map with 1 for voxels that are internal in the input map.

double get_density ( const DensityMap *  m, const algebra::Vector3D &  v  )

related

Get density value at point v, interpolating linearly from the sample values.

The resulting function is C0 over R3.

DensityMap * get_resampled ( DensityMap *  input, double  scaling  )

related

Get a resampled version of the map.

The spacing is multiplied by scaling, i.e. scaling values greater than 1 increase the voxel size.

DensityMap * get_transformed ( const DensityMap *  input, const algebra::Transformation3D &  tr, double  threshold  )

related

Return a new density map containing a rotated version of the old one.

Only voxels whose value is above threshold are considered when computing the bounding box of the new map (set IMP::em::get_bounding_box()).

DensityMap * get_transformed ( DensityMap *  input, const algebra::Transformation3D &  tr  )

related

Return a new density map containing a rotated version of the old one.

The dimension of the new map is the same as the old one.

void get_transformed_into ( const DensityMap *  source, const algebra::Transformation3D &  tr, DensityMap *  into, bool  calc_rms = true  )

related

Rotate a density map into another map.

Parameters

[in]	source	the map to transform
[in]	tr	transform the from density map by this transformation
[out]	into	the map to transform into
[in]	calc_rms	if true RMS is calculated on the transformed map

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

related

Read a density map from a file (using the given reader) and return it.

DensityMap * read_map ( std::string  filename )

related

Read a density map from a file and return it.

Guess the file type from the file name. The file formats supported are:

• .mrc/.map
• .em
• .vol
• .xplor

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

related

Write a density map to a file using the given writer.

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

related

Write a density map to a file.

Guess the file type from the file name. The file formats supported are:

• .mrc/.map
• .em
• .vol
• .xplor

Member Data Documentation

bool IMP::em::DensityMap::loc_calculated_

protected

true if the locations have already been computed

Definition at line 481 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 479 of file DensityMap.h.

---

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

• DensityMap.h