Class for sampling a density map from particles.

#include <IMP/em/SampledDensityMap.h>

Inheritance diagram for IMP::em::SampledDensityMap:

Public Member Functions
	SampledDensityMap (KernelType kt=GAUSSIAN)
	Creates a new density map for sampled map. More...

	SampledDensityMap (const DensityHeader &header, KernelType kt=GAUSSIAN)
	The size of the map is determined by the header and the data is allocated.

	SampledDensityMap (const ParticlesTemp &ps, emreal resolution, emreal voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3, KernelType kt=GAUSSIAN)
	Generate a sampled density map from the particles. More...

KernelParameters *	get_kernel_params ()

float	get_minimum_resampled_value ()
	Get minimum density value between voxels that correspond to particles.

const Particles &	get_sampled_particles () const

FloatKey	get_weight_key () const

const core::XYZRs &	get_xyzr_particles () const

void	project (const ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key())
	Project particles on the grid by their mass value. More...

virtual void	resample ()
	Resample beads on an EM grid. More...

void	set_particles (const ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key())
	setting particles in case they were not set by the constructor

Public Member Functions inherited from IMP::em::DensityMap
	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
IMP::algebra::BoundingBoxD< 3 >	calculate_particles_bounding_box (const Particles &ps)
	Calculate the parameters of the particles bounding box. More...

void	determine_grid_size (emreal resolution, emreal voxel_size, int sig_cutoff)

void	set_header (const algebra::Vector3D &lower_bound, const algebra::Vector3D &upper_bound, emreal maxradius, emreal resolution, emreal voxel_size, int sig_offset)

void	set_neighbor_mask (float radius)

Protected Member Functions inherited from IMP::em::DensityMap
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
KernelParameters	kernel_params_
	kernel handling

KernelType	kt_

Particles	ps_

FloatKey	weight_key_

FloatKey	x_key_

core::XYZRs	xyzr_

FloatKey	y_key_

FloatKey	z_key_

Protected Attributes inherited from IMP::em::DensityMap
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_

Related Functions
(Note that these are not member functions.)
SampledDensityMap *	particles2binarized_density (const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())

SampledDensityMap *	particles2density (const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
	Resample a set of particles into a density grid. More...

SurfaceShellDensityMap *	particles2surface (const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
	Resample a set of particles into a density grid. More...

typedef IMP::base::Vector < IMP::base::WeakPointer < SampledDensityMap > >	SampledDensityMapsTemp

Related Functions inherited from IMP::em::DensityMap
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

Definition at line 29 of file SampledDensityMap.h.

Constructor & Destructor Documentation

IMP::em::SampledDensityMap::SampledDensityMap ( KernelType kt = GAUSSIAN )

The header of the map is not determined and no data is being allocated

Definition at line 38 of file SampledDensityMap.h.

IMP::em::SampledDensityMap::SampledDensityMap	(	const ParticlesTemp &	ps,
		emreal	resolution,
		emreal	voxel_size,
		IMP::FloatKey	mass_key = `IMP::atom::Mass::get_mass_key()`,
		int	sig_cuttoff = `3`,
		KernelType	kt = `GAUSSIAN`
	)

/param[in] ps particles with XYZ, radius and weight attributes /param[in] resolution half width the Gaussian /param[in] voxel_size /param[in] sig_cutoff Choose what should be the sigma cutoff for accurate sampling. It is used in two functions; (i) to determine the size of the grid dimensions (ii) to determine the voxels around the coords participating in the sampling procedure.

Member Function Documentation

IMP::algebra::BoundingBoxD<3> IMP::em::SampledDensityMap::calculate_particles_bounding_box ( const Particles & ps )

protected

Parameters

[in] ps particles with XYZ, radius and weight attributes

Returns: the particles bounding box

void IMP::em::SampledDensityMap::determine_grid_size	(	emreal	resolution,
		emreal	voxel_size,
		int	sig_cutoff
	)

protected

Determine the size of the grid as a function of the particles and the resolution.

void IMP::em::SampledDensityMap::project	(	const ParticlesTemp &	ps,
		int	x_margin,
		int	y_margin,
		int	z_margin,
		algebra::Vector3D	shift = `algebra::Vector3D(0., 0., 0.)`,
		FloatKey	mass_key = `atom::Mass::get_mass_key()`
	)

Parameters

	ps	the particles to project
[in]	x_margin	sampling is restricted to [x_margin,nx-x_margin]
[in]	y_margin	sampling is restricted to [y_margin,ny-y_margin]
[in]	z_margin	sampling is restricted to [z_margin,nz-z_margin]
[in]	shift	the positions of all particles are shifted by this value before projection
[in]	mass_key	key to obtain particle mass

virtual void IMP::em::SampledDensityMap::resample ( )

virtual

Note: The density of a particle p centered at pl at position gl is: \(\frac{{Z}e^{\frac{{-0.5}({p_l}-{g_l})}{\sigma}}}{\sqrt{{2}{\pi}\sigma}}\) , such that \({Z}\) is the weight of the particle and \({\sigma}\) is defined to be \({0.425}\) times the resolution, to follow the 'full width at half maxima' criterion. For more details please refer to Topf et al, Structure, 2008.

Reimplemented in IMP::em::SurfaceShellDensityMap.

Friends And Related Function Documentation

SampledDensityMap * particles2binarized_density	(	const ParticlesTemp &	ps,
		Float	resolution,
		Float	apix,
		int	sig_cutoff = `3`,
		const FloatKey &	weight_key = `IMP::atom::Mass::get_mass_key()`
	)

Parameters

[in]	ps	the particles to sample
[in]	resolution	the resolution of the new sampled map
[in]	apix	the voxel size of the sampled map
[in]	sig_cutoff	sigma cutoff used in sampling
[in]	weight_key	the weight attribute key of the particles

Returns: the sampled density grid

Definition at line 82 of file converters.h.

SampledDensityMap * particles2density	(	const ParticlesTemp &	ps,
		Float	resolution,
		Float	apix,
		int	sig_cutoff = `3`,
		const FloatKey &	weight_key = `IMP::atom::Mass::get_mass_key()`
	)

Parameters

[in]	ps	the particles to sample
[in]	resolution	the resolution of the new sampled map
[in]	apix	the voxel size of the sampled map
[in]	sig_cutoff	sigma cutoff used in sampling
[in]	weight_key	the weight attribute key of the particles

Returns: the sampled density grid

SurfaceShellDensityMap * particles2surface	(	const ParticlesTemp &	ps,
		Float	apix,
		const FloatKey &	weight_key = `IMP::atom::Mass::get_mass_key()`
	)

Parameters

[in]	ps	the particles to sample
[in]	apix	the voxel size of the surface map
[in]	weight_key	the weight attribute key of the particles

Returns: the surface grid

typedef IMP::base::Vector<IMP::base::WeakPointer< SampledDensityMap > > SampledDensityMapsTemp

Definition at line 132 of file SampledDensityMap.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Related Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation