Class to search path on grids. More...

#include <IMP/bff/PathMap.h>

Inheritance diagram for IMP::bff::PathMap:

Detailed Description

Class to search path on grids.

Definition at line 45 of file PathMap.h.

Public Member Functions
	PathMap (PathMapHeader &header, std::string name="PathMap%1%", IMP::em::KernelType kt=IMP::em::BINARIZED_SPHERE, float resolution=-1.0)
	Constructs a PathMap object. More...

void	fill_sphere (IMP::algebra::Vector3D r0, double radius, double value, bool inverse=true)
	Change the value of a density inside or outside of a sphere. More...

void	find_path (long path_begin_idx, long path_end_idx=-1, int heuristic_mode=0)
	Finds a path between two indices in the path map. More...

void	find_path_astar (long path_begin_idx, long path_end_idx=-1)
	Finds the shortest path between two indices using the A* algorithm. More...

void	find_path_dijkstra (long path_begin_idx, long path_end_idx=-1)
	Finds the shortest path between two nodes using Dijkstra's algorithm. More...

int	get_dim_index_by_voxel (long index, int dim)
	Get index of voxel in an axis. More...

std::vector< int >	get_neighbor_idx_offsets (double neighbor_radius=-1)

const PathMapHeader *	get_path_map_header () const
	Returns a read-only pointer to the header of the map. More...

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

void	get_tile_values (float *output, int nx, int ny, int nz, int value_type=PM_TILE_COST, std::pair< float, float > bounds=std::pair< float, float >({std::numeric_limits< float >::min(), std::numeric_limits< float >::max()}), const std::string &feature_name="")
	Retrieves the values of the tiles in the path map. More...

std::vector< PathMapTile > &	get_tiles ()

std::vector < IMP::algebra::Vector4D >	get_xyz_density ()
	Get the XYZ density of the path map. This function returns a vector of IMP::algebra::Vector4D objects representing the XYZ density of the path map. More...

void	get_xyz_density (double *output, int n_output1, int *n_output2)
	Get the XYZ density of the path map. This function returns the XYZ density of the path map as a 2D array. More...

void	resize (unsigned int nvox)
	Resizes the PathMap object. More...

void	sample_obstacles (double extra_radius=0.0)
	Resamples the obstacles in the path map. More...

void	set_data (double *input, int n_input, float obstacle_threshold=-1, bool binarize=true, float obstacle_penalty=TILE_PENALTY_DEFAULT)
	Sets the data for the path map. More...

void	set_path_map_header (PathMapHeader &path_map_header, float resolution=-1.0)
	Set the path map header. More...

void	update_tiles (float obstacle_threshold=-1.0, bool binarize=true, float obstacle_penalty=TILE_PENALTY_DEFAULT, bool reset_tile_edges=true)
	Updates the tiles in the path map. More...

Public Member Functions inherited from IMP::em::SampledDensityMap
	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. More...

	SampledDensityMap (const ParticlesTemp &ps, double resolution, double voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cutoff=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. More...

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 More...

void	update_resolution (Float res)
	Update the simulation resolution. More...

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 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
std::vector< PathMapTileEdge > &	get_edges (int tile_idx)

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

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

void	set_header (const algebra::Vector3D &lower_bound, const algebra::Vector3D &upper_bound, double maxradius, double resolution, double 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< 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
std::vector< int >	offsets_

PathMapHeader	pathMapHeader_

std::vector< PathMapTile >	tiles

Protected Attributes inherited from IMP::em::SampledDensityMap
KernelParameters	kernel_params_
	kernel handling More...

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< 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_

Related Functions
(Note that these are not member functions.)
std::vector< float >	get_tile_values (int value_type=PM_TILE_COST, std::pair< float, float > bounds=std::pair< float, float >({std::numeric_limits< float >::min(), std::numeric_limits< float >::max()}), const std::string &feature_name="")
	Get the values of all tiles. More...

Related Functions inherited from IMP::em::DensityMap
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::bff::PathMap::PathMap	(	PathMapHeader &	header,
		std::string	name = `"PathMap%1%"`,
		IMP::em::KernelType	kt = `IMP::em::BINARIZED_SPHERE`,
		float	resolution = `-1.0`
	)

explicit

Constructs a PathMap object.

Parameters

header	The PathMapHeader object.
name	The name of the PathMap.
kt	The kernel type.
resolution	The resolution of the PathMap.

Member Function Documentation

void IMP::bff::PathMap::fill_sphere	(	IMP::algebra::Vector3D	r0,
		double	radius,
		double	value,
		bool	inverse = `true`
	)

Change the value of a density inside or outside of a sphere.

Changes the value of the density inside or outside of a sphere. The density is used in the path-search (i.e., the accessible volume calculation

Parameters

r0	location of the sphere
radius	radius of the sphere
value	value inside or outside of the sphere
inverse	if set to true (default) the values outside of the sphere are modified. If false the values inside of the sphere are modified.

void IMP::bff::PathMap::find_path	(	long	path_begin_idx,
		long	path_end_idx = `-1`,
		int	heuristic_mode = `0`
	)

Finds a path between two indices in the path map.

This function finds a path between the specified path begin index and path end index in the path map. If the path end index is not specified, the function will find a path from the path begin index to the last index in the path map. The heuristic mode parameter determines the heuristic function to be used for path finding.

Parameters

path_begin_idx	The index of the path begin point in the path map.
path_end_idx	The index of the path end point in the path map. Default value is -1, which means the last index in the path map.
heuristic_mode	The mode of the heuristic function to be used for path finding. Default value is 0.

Returns: void

void IMP::bff::PathMap::find_path_astar	(	long	path_begin_idx,
		long	path_end_idx = `-1`
	)

Finds the shortest path between two indices using the A* algorithm.

This function uses the A* algorithm to find the shortest path between two indices in the path map. The path is stored in the path member variable.

Parameters

path_begin_idx	The index of the starting point of the path.
path_end_idx	The index of the ending point of the path. If not provided, the function will use the last index in the path map.

void IMP::bff::PathMap::find_path_dijkstra	(	long	path_begin_idx,
		long	path_end_idx = `-1`
	)

Finds the shortest path between two nodes using Dijkstra's algorithm.

This function finds the shortest path between two nodes in the path map using Dijkstra's algorithm. The path is calculated from the node at index path_begin_idx to the node at index path_end_idx. If path_end_idx is not provided, the function will calculate the path to the last node in the map.

Parameters

path_begin_idx	The index of the starting node.
path_end_idx	The index of the ending node (optional).

int IMP::bff::PathMap::get_dim_index_by_voxel	(	long	index,
		int	dim
	)

Get index of voxel in an axis.

Returns the index of a voxel on a grid in a certain dimension.

Parameters

index	voxel index
dim	dimension

Returns: index of voxel in axis of dimension

std::vector<int> IMP::bff::PathMap::get_neighbor_idx_offsets ( double neighbor_radius = -1 )

Returns a vector of neighbor index offsets within a given radius.

Parameters

neighbor_radius The radius within which to find neighbors. If negative, the radius is obtained from the path map header.

Returns: A vector of neighbor index offsets, where each offset consists of three integers (z, y, x) representing the relative position of the neighbor, and one integer representing the tile offset. The vector also includes the edge cost between the current tile and the neighbor.

Definition at line 121 of file PathMap.h.

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const PathMapHeader* IMP::bff::PathMap::get_path_map_header ( ) const

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

Returns: const PathMapHeader* A read-only pointer to the header of the map.

Definition at line 177 of file PathMap.h.

PathMapHeader* IMP::bff::PathMap::get_path_map_header_writable ( )

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

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

Definition at line 186 of file PathMap.h.

void IMP::bff::PathMap::get_tile_values	(	float **	output,
		int *	nx,
		int *	ny,
		int *	nz,
		int	value_type = `PM_TILE_COST`,
		std::pair< float, float >	bounds = `std::pair< float, float >({std::numeric_limits< float >::min(), std::numeric_limits< float >::max()})`,
		const std::string &	feature_name = `""`
	)

Retrieves the values of the tiles in the path map.

This function retrieves the values of the tiles in the path map and stores them in the output array.

Parameters

output	A pointer to a 2D array of floats where the tile values will be stored.
nx	A pointer to an integer that will store the number of tiles in the x-direction.
ny	A pointer to an integer that will store the number of tiles in the y-direction.
nz	A pointer to an integer that will store the number of tiles in the z-direction.
value_type	The type of value to retrieve for each tile. Defaults to PM_TILE_COST.
bounds	A pair of floats representing the lower and upper bounds for the tile values. Defaults to the minimum and maximum float values.
feature_name	The name of the feature for which to retrieve the tile values. Defaults to an empty string.

std::vector<PathMapTile>& IMP::bff::PathMap::get_tiles ( )

Values of tiles

Returns: vector of all tiles in the accessible volume

std::vector<IMP::algebra::Vector4D> IMP::bff::PathMap::get_xyz_density ( )

Get the XYZ density of the path map. This function returns a vector of IMP::algebra::Vector4D objects representing the XYZ density of the path map.

Returns: std::vector The XYZ density of the path map.

void IMP::bff::PathMap::get_xyz_density	(	double **	output,
		int *	n_output1,
		int *	n_output2
	)

Get the XYZ density of the path map. This function returns the XYZ density of the path map as a 2D array.

Parameters

output	A pointer to a 2D array to store the XYZ density.
n_output1	A pointer to an integer to store the number of rows in the output array.
n_output2	A pointer to an integer to store the number of columns in the output array.

void IMP::bff::PathMap::resize ( unsigned int nvox )

Resizes the PathMap object.

This function resizes the PathMap object to accommodate the specified number of voxels.

Parameters

nvox	The number of voxels to resize the PathMap to.

void IMP::bff::PathMap::sample_obstacles ( double extra_radius = 0.0 )

Resamples the obstacles in the path map.

This function resamples the obstacles in the path map, updating their positions and sizes.

Parameters

extra_radius The extra radius to add to the obstacles (optional, default is 0.0).

void IMP::bff::PathMap::set_data	(	double *	input,
		int	n_input,
		float	obstacle_threshold = `-1`,
		bool	binarize = `true`,
		float	obstacle_penalty = `TILE_PENALTY_DEFAULT`
	)

Sets the data for the path map.

This function sets the input data for the path map. The input data is a 1D array of doubles representing the map.

Parameters

input	Pointer to the input data array.
n_input	Number of elements in the input data array.
obstacle_threshold	The threshold value for considering a cell as an obstacle. Default value is -1.
binarize	Flag indicating whether to binarize the input data. Default value is true.
obstacle_penalty	The penalty value for obstacle cells. Default value is TILE_PENALTY_DEFAULT.

Note: The input data array should be of size n_input.; If binarize is set to true, the input data will be converted to binary values based on the obstacle_threshold.; The obstacle_penalty is used to assign penalty values to obstacle cells in the path map.

void IMP::bff::PathMap::set_path_map_header	(	PathMapHeader &	path_map_header,
		float	resolution = `-1.0`
	)

Set the path map header.

This function sets the path map header for the path map.

Parameters

path_map_header	The path map header to set.
resolution	The resolution of the path map. Default value is -1.0.

void IMP::bff::PathMap::update_tiles	(	float	obstacle_threshold = `-1.0`,
		bool	binarize = `true`,
		float	obstacle_penalty = `TILE_PENALTY_DEFAULT`,
		bool	reset_tile_edges = `true`
	)

Updates the tiles in the path map.

This function updates the tiles in the path map based on the given parameters.

Parameters

obstacle_threshold	The threshold value for considering a cell as an obstacle. Default value is -1.0.
binarize	A flag indicating whether to binarize the path map. Default value is true.
obstacle_penalty	The penalty value for obstacle cells. Default value is TILE_PENALTY_DEFAULT.
reset_tile_edges	A flag indicating whether to reset the edges of the tiles. Default value is true.

Friends And Related Function Documentation

std::vector<float> get_tile_values	(	int	value_type = `PM_TILE_COST`,
		std::pair< float, float >	bounds = `std::pair< float, float >({std::numeric_limits< float >::min(), std::numeric_limits< float >::max()})`,
		const std::string &	feature_name = `""`
	)

A tile in a path map contains information on the penalty for visiting a tile, the cost of a path from the origin of a path search to the tile, the density of the tile, and other user-defined information.

When getting information from a tile, the returned values can be cropped to a specified range.

Parameters

value_type	Specifies the type of the returned information (see: PathMapTileOutputs). Depending on the value type, the output can be the penalty for visiting the tile, the total cost of a path to the tile, or the density of the tile. Additional user-defined content can also be accessed.
bounds	Bound for cropping the output values.
feature_name	Name of a feature when accessing additional information.

Returns: A vector of values for the specified parameters.

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

PathMap.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Related Functions

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation