IMP::em::DensityMap Class Reference

Class for handling density maps. More...

#include <IMP/em/DensityMap.h>

Inheritance diagram for IMP::em::DensityMap:

Public Member Functions
	DensityMap (std::string name="DensityMap%1%")
	DensityMap (const DensityHeader &header, std::string name="DensityMap%1%")
	Construct a density map as intructed in the input header.
void	add (const DensityMap *other)
void	calc_all_voxel2loc ()
	Calculates the coordinates that correspond to all voxels.
emreal	calcRMS ()
	Calculates RMSD and mean of a map values are stored in the header. More...
void	copy_map (const DensityMap *other)
	copy map into this map
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.
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 the value of the voxel with the highest density.
float	get_maximum_value_in_xy_plane (int z_ind)
	Get the maximum value in a XY plane indicated by a Z index.
float	get_maximum_value_in_xz_plane (int y_ind)
	Get the maximum value in a XZ plane indicated by a Y index.
float	get_maximum_value_in_yz_plane (int x_ind)
	Get the maximum value in a YZ plane indicated by a X index.
emreal	get_min_value () const
	Returns the the value of the voxel with the lowest density.
long	get_number_of_voxels () const
	number of map voxels
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
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...
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	release ()
void	reset_data (float value=0.0)
	Set the density voxels to some calue and reset the managment 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 ()
	Normailze the density voxles according to standard deviation (stdv). More...
void	update_voxel_size (float new_apix)
	Updated the voxel size of the map.
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::base::Object
virtual void	clear_caches ()
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
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
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

Protected Attributes
boost::scoped_array< emreal >	data_
bool	data_allocated_
DensityHeader	header_
bool	loc_calculated_
	true if the locations have already been computed
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.)
typedef IMP::base::Vector < IMP::base::WeakPointer < DensityMap > >	DensityMapsTemp
double	get_density (const DensityMap *m, const algebra::Vector3D &v)
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)
DensityMap *	get_transformed (DensityMap *input, const algebra::Transformation3D &tr)
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)
DensityMap *	read_map (std::string filename)
void	write_map (DensityMap *m, std::string filename, MapReaderWriter *writer)
void	write_map (DensityMap *m, std::string filename)
Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

Detailed Description

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 98 of file DensityMap.h.

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 sumed

The two maps should have the same voxelsize and other should be contained within this map

emreal IMP::em::DensityMap::calcRMS

(

)

The header stores whether map is normalized.

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

)

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

)

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

Parameters

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

algebra::Vector3D IMP::em::DensityMap::get_location_by_voxel

(

long

index

)

const

Parameters

[in]

index

The voxel index

Returns

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

Definition at line 188 of file DensityMap.h.

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

Parameters

[in]	index	The voxel index
[in]	dim	The dimesion of intereset (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.

Float IMP::em::DensityMap::get_spacing

(

)

const

Note

Use update_voxel_size() to set the spacing value.

Definition at line 429 of file DensityMap.h.

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

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.

emreal IMP::em::DensityMap::get_value

(

long

index

)

const

Parameters

[in]

index

voxel number in physical sense, NOT logical

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

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

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 175 of file DensityMap.h.

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

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

Parameters

[in]

v

The position ( in angstroms)

Returns

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

Definition at line 209 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
	)

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

)

Parameters

[in]

value

all of the density voxels will have this value

bool IMP::em::DensityMap::same_dimensions

(

const DensityMap *

other

)

const

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

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

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
	)

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
	)

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
	)

index voxel number in physical sense, NOT logical

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

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

(

)

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

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

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 155 of file DensityMap.h.

Friends And Related Function Documentation

typedef IMP::base::Vector<IMP::base::WeakPointer< DensityMap > > DensityMapsTemp

related

Pass a set of objects.

Definition at line 537 of file DensityMap.h.

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

related

Return the value for the density map, m, at point v, interpolating linearly from the sample values. The resulting function is C0 over R3.

DensityMap * get_resampled ( DensityMap *  input, double  scaling  )

related

The spacing is multiplied by scaling. That means, 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

Parameters

[in]	source	the map to transform
[in]	tr	transform the from density map by this transformation
[out]	into	the map to tranform 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 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
• .em
• .vol
• .xplor

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

friend

Read a density map from a file and return it.

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

related

Write a density map to a file.

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
• .em
• .vol
• .xplor

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

friend

Write a density map to a file.

Member Data Documentation

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

protected

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