#include <PathMap.h>

Inheritance diagram for PathMap:

Collaboration diagram for PathMap:

Public Member Functions
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.

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

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.

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

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

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

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

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

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.

std::vector< PathMapTile > &	get_tiles ()

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.

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.

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

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

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.

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.

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

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

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

Protected Attributes
std::vector< PathMapTile >	tiles

PathMapHeader	pathMapHeader_

std::vector< int >	offsets_

Related Symbols
(Note that these are not member symbols.)
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.

Constructor & Destructor Documentation

◆ PathMap()

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

◆ fill_sphere()

void 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.

◆ find_path()

void 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

◆ find_path_astar()

void 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.

◆ find_path_dijkstra()

void 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).

◆ get_dim_index_by_voxel()

int 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

◆ get_edges()

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

protected

◆ get_neighbor_idx_offsets()

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

inline

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.

◆ get_path_map_header()

const PathMapHeader * PathMap::get_path_map_header ( ) const

inline

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

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

◆ get_path_map_header_writable()

PathMapHeader * PathMap::get_path_map_header_writable ( )

inline

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.

◆ get_tile_values()

void 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.

◆ get_tiles()

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

Values of tiles

Returns: vector of all tiles in the accessible volume

◆ get_xyz_density() [1/2]

std::vector< IMP::algebra::Vector4D > 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.

◆ get_xyz_density() [2/2]

void 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.

◆ resize()

void 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.

◆ sample_obstacles()

void 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).

◆ set_data()

void 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.

◆ set_path_map_header()

void 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.

◆ update_tiles()

void 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 Symbol Documentation

◆ get_tile_values()

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.

Member Data Documentation

◆ offsets_

std::vector<int> PathMap::offsets_

protected

◆ pathMapHeader_

PathMapHeader PathMap::pathMapHeader_

protected

◆ tiles

std::vector<PathMapTile> PathMap::tiles

protected

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

/Users/tpeulen/dev/imp.bff/include/PathMap.h

Public Member Functions

Protected Member Functions

Protected Attributes

Related Symbols

Constructor & Destructor Documentation

◆ PathMap()

Member Function Documentation

◆ fill_sphere()

◆ find_path()

◆ find_path_astar()

◆ find_path_dijkstra()

◆ get_dim_index_by_voxel()

◆ get_edges()

◆ get_neighbor_idx_offsets()

◆ get_path_map_header()

◆ get_path_map_header_writable()

◆ get_tile_values()

◆ get_tiles()

◆ get_xyz_density() [1/2]

◆ get_xyz_density() [2/2]

◆ resize()

◆ sample_obstacles()

◆ set_data()

◆ set_path_map_header()

◆ update_tiles()

Friends And Related Symbol Documentation

◆ get_tile_values()

Member Data Documentation

◆ offsets_

◆ pathMapHeader_

◆ tiles