IMP::em::DensityMap Class Reference

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 voxel2loc.

Inheritance diagram for IMP::em::DensityMap:

[legend]


Public Member Functions
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.
void	CreateVoidMap (const int &nx, const int &ny, const int &nz)
	Creates a new map with the given dimension.
	DensityMap (const DensityMap &other)
algebra::VectorD< 3 >	get_centroid (emreal threshold=0.0) const
emreal *	get_data () const
const DensityHeader *	get_header () const
DensityHeader *	get_header_writable ()
	Returns a pointer to the header of the map in a writable version.
std::string	get_locations_string (float t)
emreal	get_max_value () const
	Returns the the value of the voxel with the highest density.
emreal	get_min_value () const
	Returns the the value of the voxel with the lowest density.
long	get_number_of_voxels () const
algebra::VectorD< 3 >	get_origin () const
Float	get_spacing () const
	Updated the voxel size of the map.
algebra::VectorD< 3 >	get_top () const
virtual std::string	get_type_name () const
emreal	get_value (long index) const
	Gets the value of the voxel at a given index.
emreal	get_value (const algebra::VectorD< 3 > &point) const
emreal	get_value (float x, float y, float z) const
	Gets the value of the voxel located at (x,y,z).
virtual ::IMP::VersionInfo	get_version_info () const
float *	get_x_loc () const
	Returns the x-location of the map.
float *	get_y_loc () const
	Returns the y-location of the map.
float *	get_z_loc () const
	Returns the z-location of the map.
bool	is_normalized () const
bool	is_part_of_volume (const algebra::VectorD< 3 > &v) const
	Checks whether a given point is in the grid the voxel of a given location.
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.
bool	is_xyz_ind_part_of_volume (int ix, int iy, int iz) const
long	loc2voxel (const algebra::VectorD< 3 > &v) const
long	loc2voxel (float x, float y, float z) const
	Calculate the voxel of a given location.
void	multiply (float factor)
DensityMap &	operator= (const DensityMap &other)
void	pad (int nx, int ny, int nz, float val=0.0)
void	reset_data (float value=0.0)
	Set the density voxels to some calue and reset the managment flags.
bool	same_dimensions (const DensityMap &other) const
	Checks if two maps have the same dimensions.
bool	same_origin (const DensityMap &other) const
	Checks if two maps have the same origin.
bool	same_voxel_size (const DensityMap &other) const
	Checks if two maps have the same voxel size.
void	set_origin (const IMP::algebra::VectorD< 3 > &v)
void	set_origin (float x, float y, float z)
	Sets the origin of the header.
void	set_value (float x, float y, float z, emreal value)
	Set the value of the voxel at a given index.
void	set_value (long index, emreal value)
	Set the value of the voxel at a given index.
void	std_normalize ()
	Normailze the density voxles according to standard deviation (stdv).
void	update_voxel_size (float new_apix)
	Updated the voxel size of the map.
float	voxel2loc (const int &index, int dim) const
	Calculate the location of a given voxel.
long	xyz_ind2voxel (int x, int y, int z) const
	Calculate the voxel of a given xyz indexes.
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_voxel2loc ()
void	update_header ()
	update the header values -- still in work
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 (const char *filename, MapReaderWriter &reader)
void	write_map (DensityMap m, const char filename, MapReaderWriter &writer)
Related Functions
(Note that these are not member functions.)
double	get_density (DensityMap *m, const algebra::VectorD< 3 > &v)
DensityMap *	get_transformed (DensityMap *in, const algebra::Transformation3D &tr)
DensityMap *	get_transformed (DensityMap *in, const algebra::Transformation3D &tr, double threshold)
DensityMap *	read_map (const char *filename)

Member Function Documentation

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

Sums two grids. The result is kept in the map. The two maps should have the same dimensions and the same voxelsize

Parameters:

[in] other the other map

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

Calculates the coordinates that correspond to all voxels.

Can be precomputed to make corr faster.

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

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

The header stores whether map is normalized.

void IMP::em::DensityMap::CreateVoidMap	(	const int &	nx,
		const int &	ny,
		const int &	nz
	)

Creates a new map with the given dimension.

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

algebra::VectorD<3> 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

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

Updated the voxel size of the map.

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

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

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.

float* IMP::em::DensityMap::get_x_loc ( ) const

Returns the x-location of the map.

Exceptions:

InvalidStateException

The locations have not been calculated.

float* IMP::em::DensityMap::get_y_loc ( ) const

Returns the y-location of the map.

Exceptions:

InvalidStateException

The locations have not been calculated.

float* IMP::em::DensityMap::get_z_loc ( ) const

Returns the z-location of the map.

Exceptions:

InvalidStateException

The locations have not been calculated.

bool IMP::em::DensityMap::is_part_of_volume ( const algebra::VectorD< 3 > & 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.

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.

long IMP::em::DensityMap::loc2voxel	(	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

Exceptions:

IndexException

The point is not covered by the grid.

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

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

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

Set the density voxels to some calue and reset the managment 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	(	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_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::std_normalize ( )

Normailze the density voxles 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

float IMP::em::DensityMap::voxel2loc	(	const int &	index,
		int	dim
	)			const

Calculate the location of a given voxel.

Parameters:

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

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.

Friends And Related Function Documentation

double get_density	(	DensityMap *	m,
		const algebra::VectorD< 3 > &	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_transformed	(	DensityMap *	in,
		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.

DensityMap * get_transformed	(	DensityMap *	in,
		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 * read_map ( const char * 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 for MRC files

DensityMap * read_map	(	const char *	filename,
		MapReaderWriter &	reader
	)			`[friend]`

Read a density map from a file and return it.

void write_map	(	DensityMap *	m,
		const char *	filename,
		MapReaderWriter &	writer
	)			`[friend]`

Write a density map to a file.

Field 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)

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

DensityMap.h
em/__init__.py

IMP::em::DensityMap Class Reference

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Related Functions

Member Function Documentation

Friends And Related Function Documentation

Field Documentation