numeric::VoxelGrid< typename > Class Template Reference

#include <VoxelGrid.hh>

Public Types
typedef T	t_DataType
typedef platform::Size	Size
typedef platform::Real	Real
typedef xyzVector< Real >	Vector
typedef std::pair< T const *, T const * >	t_DataTypeCOPtrPair
typedef std::pair< T const *, Vector const * >	t_DataTypeVectorCOPtrPair

Public Member Functions
	VoxelGrid (Real const &resolution=4.0, bool const &cache_edges=false)
	default constructor More...
virtual	~VoxelGrid ()
	destructor More...
virtual Vector const *	ExtractPosition (t_DataType const &input) const =0
	extract the 3D coordinates of a given t_DataType input. TO BE IMPLEMENTED BY DERIVED CLASSES. More...
virtual bool	IsSameItem (t_DataType const &item1, t_DataType const &item2) const =0
	check if two grid items are the same. TO BE IMPLEMENTED BY DERIVED CLASSES. More...
virtual bool	IsRelevantItem (t_DataType const &item) const =0
	is item relevant to consider as neighbor. TO BE IMPLEMENTED BY DERIVED CLASSES. More...
Size	GetNumberItems () const
	Get the number of items in the voxel grid. More...
Size	GetDimension () const
	Get the actual internally used dimension of the voxel grid. More...
Real	GetResolution () const
	Get the requested resolution by the user. More...
geometry::BoundingBox< Vector > const &	GetBoundingBox () const
	Get the bounding box of this grid. More...
utility::vector1 < utility::vector1 < t_DataTypeVectorCOPtrPair > > const &	GetGridItems () const
	Get the items of this grid. More...
utility::vector1< std::pair < t_DataType const *, Real > >	GetNeighbors (t_DataType const &input, Real const &neighborhood, bool check_relevance=false) const
	Find neighbors within a specified distance of a given DATA. More...
bool	HasNeighbors (t_DataType const &input, Real const &neighborhood, bool check_relevance=false) const
	Has given DATA a neighbor in the grid within a specified distance. More...
utility::vector1< std::pair < t_DataTypeCOPtrPair, Real > >	GetNeighborsIn (VoxelGrid const &grid, Real const &neighborhood, bool check_relevance=false) const
	Find all neighbor pairs within a specified distance. More...
utility::vector1< std::pair < t_DataTypeCOPtrPair, Real > >	GetNeighbors (Real const &neighborhood, bool check_relevance=false) const
	Find all neighbor pairs within a specified distance. More...
void	SetObjects (utility::vector1< t_DataType const * > const &new_data, bool check_relevance=false)
	Update the VoxelGrid with new data. More...
void	InsertObject (t_DataType const &new_item, bool check_relevance=false)
	insert a new t_DataType object into the manager More...
void	InsertObjects (utility::vector1< t_DataType const * > const &new_items, bool check_relevance=false)
	inserts multiple t_DataType objects into the manager More...
void	RemoveObject (t_DataType const &item_to_remove)
	remove a t_DataType object from the manager More...
void	RemoveObjects (utility::vector1< t_DataType const * > const &items_to_remove)
	remove multiple t_DataType objects from the manager More...
void	Clear ()
	Remove all objects from the voxel grid while keeping the grid itself intact. More...
void	Translate (Vector const &translation)
	Translate the grid. More...

Private Types
enum	BorderFlag {   e_None = 0, e_XMin = 1, e_XMax = 2, e_YMin = 4,   e_YMax = 8, e_ZMin = 16, e_ZMax = 32 }

Private Member Functions
Size	GetIndex (Real const &X, Real const &Y, Real const &Z) const
	Get the position for the given coordinate vector. Places out-of-bounds vector in the bin closest to where they belong. More...
Size	GetIndex (Vector const &pos) const
	Get the position for the given coordinate vector. Places out-of-bounds vector in the bin closest to where they belong. More...
void	SetupGrid (Vector const &min_vals, Vector const &max_vals, Size const &expected_n_elements)
	Try to allocate a grid of a given size. If this size would cause the object to definitely exceed the max memory allotment, the grid will be truncated to include only the core. It is assumed that Resolution_ has been setup prior to this. More...
Real	GetSqDistanceOutsideBoundingBox (Vector const &point) const
	Compute distance from this point to the nearest edge of the bounding box of all given points, provided the point is outside the box. More...
Real	GetSqDistanceOutsideBoundingBox (Vector const &min_box, Vector const &max_box) const
	Compute distance from another grid's bounding box to the nearest edge of this bounding box provided that the MIN and MAX is outside of this bounding box. More...
utility::vector1< std::pair < t_DataTypeCOPtrPair, Real > >	GetNeighborsMultiDimensional (Real const &neighborhood, bool check_relevance=false) const
	Find all neighbor pairs of this grid within a specified distance. More...
utility::vector1< std::pair < t_DataType const *, Real > >	GetNeighborsMultiDimensional (t_DataType const &obj, Real const &neighborhood, bool check_relevance=false) const
	Find all neighbors of this object within a specified distance. More...
utility::vector1< std::pair < t_DataTypeCOPtrPair, Real > >	GetNeighborsMultiDimensional (VoxelGrid< t_DataType > const &grid, Real const &neighborhood, bool check_relevance=false) const
	Find all neighbors between the input and this grid within a specified distance. More...
bool	HasNeighborsMultiDimensional (t_DataType const &obj, Real const &neighborhood, bool check_relevance=false) const
	Has given object a neighbor in the grid within a specified distance. More...
utility::vector1< std::pair < t_DataTypeCOPtrPair, Real > >	GetNeighbors1D (Real const &neighborhood, bool check_relevance=false) const
	Find all neighbor pairs of this 1D grid within a specified distance. More...
utility::vector1< std::pair < t_DataType const *, Real > >	GetNeighbors1D (t_DataType const &obj, Real const &neighborhood, bool check_relevance=false) const
	Find all neighbors of this object within a specified distance. More...
utility::vector1< std::pair < t_DataTypeCOPtrPair, Real > >	GetNeighbors1D (VoxelGrid< t_DataType > const &grid, Real const &neighborhood, bool check_relevance=false) const
	Find all neighbors between the input and this grid within a specified distance. More...
bool	HasNeighbors1D (t_DataType const &obj, Real const &neighborhood, bool check_relevance=false) const
	Has given object a neighbor in the grid within a specified distance. More...

Private Attributes
utility::vector1 < utility::vector1 < t_DataTypeVectorCOPtrPair > >	Assignments_
utility::vector1 < utility::vector1 < utility::vector1 < t_DataTypeVectorCOPtrPair > > >	Edges_
utility::vector1 < utility::vector1 < utility::vector1 < t_DataTypeVectorCOPtrPair > > >	EdgesComplete_
utility::vector1< Size >	BorderFlags_
Size	NBinsX_
Size	NBinsY_
Size	NBinsZ_
Real	Resolution_
bool	CacheEdges_
Real	ResolutionX_
Real	ResolutionY_
Real	ResolutionZ_
Real	MinResolution_
Real	MinX_
Real	MinY_
Real	MinZ_
geometry::BoundingBox< Vector >	Box_
Size	NDimensional_
Size	NItems_
Size	MinNumberElements_
Size	MaxNumberElements_

Member Typedef Documentation

template<typename >

typedef platform::Real numeric::VoxelGrid< typename >::Real

template<typename >

typedef platform::Size numeric::VoxelGrid< typename >::Size

template<typename >

typedef T numeric::VoxelGrid< typename >::t_DataType

template<typename >

typedef std::pair< T const *, T const * > numeric::VoxelGrid< typename >::t_DataTypeCOPtrPair

template<typename >

typedef std::pair< T const *, Vector const * > numeric::VoxelGrid< typename >::t_DataTypeVectorCOPtrPair

template<typename >

typedef xyzVector<Real> numeric::VoxelGrid< typename >::Vector

Member Enumeration Documentation

template<typename >

enum numeric::VoxelGrid::BorderFlag

private

Enumerator
e_None
e_XMin
e_XMax
e_YMin
e_YMax
e_ZMin
e_ZMax

Constructor & Destructor Documentation

template<typename T >

numeric::VoxelGrid< T >::VoxelGrid	(	Real const &	resolution = 4.0,
		bool const &	cache_edges = false
	)

default constructor

template<typename T >

numeric::VoxelGrid< T >::~VoxelGrid ( )

virtual

destructor

Member Function Documentation

template<typename T >

void numeric::VoxelGrid< T >::Clear

(

)

Remove all objects from the voxel grid while keeping the grid itself intact.

template<typename >

virtual Vector const* numeric::VoxelGrid< typename >::ExtractPosition ( t_DataType const &  input ) const

pure virtual

extract the 3D coordinates of a given t_DataType input. TO BE IMPLEMENTED BY DERIVED CLASSES.

Parameters

input

reference to object T

template<typename T >

geometry::BoundingBox< xyzVector< Real > > const & numeric::VoxelGrid< T >::GetBoundingBox

(

)

const

Get the bounding box of this grid.

Referenced by numeric::VoxelGrid< typename >::GetNeighbors1D(), and numeric::VoxelGrid< typename >::GetNeighborsMultiDimensional().

template<typename T >

Size numeric::VoxelGrid< T >::GetDimension

(

)

const

Get the actual internally used dimension of the voxel grid.

template<typename T >

utility::vector1< utility::vector1< std::pair< T const *, xyzVector< Real > const * > > > const & numeric::VoxelGrid< T >::GetGridItems

(

)

const

Get the items of this grid.

Referenced by numeric::VoxelGrid< typename >::GetNeighbors1D(), and numeric::VoxelGrid< typename >::GetNeighborsMultiDimensional().

template<typename T >

Size numeric::VoxelGrid< T >::GetIndex ( Real const &  X, Real const &  Y, Real const &  Z  ) const

private

Get the position for the given coordinate vector. Places out-of-bounds vector in the bin closest to where they belong.

Parameters

X,Y,Z

the position of interest

References max(), and min().

template<typename T >

Size numeric::VoxelGrid< T >::GetIndex ( Vector const &  pos ) const

private

Get the position for the given coordinate vector. Places out-of-bounds vector in the bin closest to where they belong.

Parameters

pos	the position of interest

References numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

template<typename T >

utility::vector1< std::pair< T const *, Real > > numeric::VoxelGrid< T >::GetNeighbors	(	t_DataType const &	input,
		Real const &	neighborhood,
		bool	check_relevance = false
	)		const

Find neighbors within a specified distance of a given DATA.

Parameters

input	datapoint of interest
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

template<typename T >

utility::vector1< std::pair< std::pair< T const *, T const * >, Real > > numeric::VoxelGrid< T >::GetNeighbors	(	Real const &	neighborhood,
		bool	check_relevance = false
	)		const

Find all neighbor pairs within a specified distance.

Parameters

neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

template<typename T >

utility::vector1< std::pair< std::pair< T const *, T const * >, Real > > numeric::VoxelGrid< T >::GetNeighbors1D ( Real const &  neighborhood, bool  check_relevance = false  ) const

private

Find all neighbor pairs of this 1D grid within a specified distance.

Parameters

neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

References numeric::xyzVector< typename >::distance_squared(), and runtime_assert_msg.

template<typename T >

utility::vector1< std::pair< T const *, Real > > numeric::VoxelGrid< T >::GetNeighbors1D ( t_DataType const &  obj, Real const &  neighborhood, bool  check_relevance = false  ) const

private

Find all neighbors of this object within a specified distance.

Parameters

obj	object to look for neighbors
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

References numeric::xyzVector< typename >::distance_squared(), make_symmdef_file_denovo::pos, and runtime_assert_msg.

template<typename T >

utility::vector1< std::pair< std::pair< T const *, T const * >, Real > > numeric::VoxelGrid< T >::GetNeighbors1D ( VoxelGrid< t_DataType > const &  grid, Real const &  neighborhood, bool  check_relevance = false  ) const

private

Find all neighbors between the input and this grid within a specified distance.

Parameters

grid	input grid in which to look for objects that are neighbors of this grid
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

References numeric::xyzVector< typename >::distance_squared(), numeric::VoxelGrid< typename >::GetBoundingBox(), numeric::VoxelGrid< typename >::GetGridItems(), numeric::geometry::BoundingBox< typename >::lower(), make_symmdef_file_denovo::pos, runtime_assert_msg, and numeric::geometry::BoundingBox< typename >::upper().

template<typename >

utility::vector1< std::pair< std::pair< T const *, T const * >, Real > > numeric::VoxelGrid< T >::GetNeighborsIn	(	VoxelGrid< typename > const &	grid,
		Real const &	neighborhood,
		bool	check_relevance = false
	)		const

Find all neighbor pairs within a specified distance.

Parameters

grid	other grid to search for neighbors with this grid
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

template<typename T >

utility::vector1< std::pair< std::pair< T const *, T const * >, Real > > numeric::VoxelGrid< T >::GetNeighborsMultiDimensional ( Real const &  neighborhood, bool  check_relevance = false  ) const

private

Find all neighbor pairs of this grid within a specified distance.

Parameters

neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

References numeric::xyzVector< typename >::distance_squared(), make_symmdef_file_denovo::pos, runtime_assert_msg, and numeric::crick_equations::z().

template<typename T >

utility::vector1< std::pair< T const *, Real > > numeric::VoxelGrid< T >::GetNeighborsMultiDimensional ( t_DataType const &  obj, Real const &  neighborhood, bool  check_relevance = false  ) const

private

Find all neighbors of this object within a specified distance.

Parameters

obj	object to look for neighbors
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

References begin, numeric::xyzVector< typename >::distance_squared(), basic::options::OptionKeys::cutoutdomain::end, make_symmdef_file_denovo::pos, runtime_assert_msg, and numeric::crick_equations::z().

template<typename T >

utility::vector1< std::pair< std::pair< T const *, T const * >, Real > > numeric::VoxelGrid< T >::GetNeighborsMultiDimensional ( VoxelGrid< t_DataType > const &  grid, Real const &  neighborhood, bool  check_relevance = false  ) const

private

Find all neighbors between the input and this grid within a specified distance.

Parameters

grid	input grid in which to look for objects that are neighbors of this grid
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return neighboring objects which are relevant

References begin, numeric::xyzVector< typename >::distance_squared(), basic::options::OptionKeys::cutoutdomain::end, numeric::VoxelGrid< typename >::GetBoundingBox(), numeric::VoxelGrid< typename >::GetGridItems(), numeric::geometry::BoundingBox< typename >::lower(), make_symmdef_file_denovo::pos, runtime_assert_msg, numeric::geometry::BoundingBox< typename >::upper(), and numeric::crick_equations::z().

template<typename T >

Size numeric::VoxelGrid< T >::GetNumberItems

(

)

const

Get the number of items in the voxel grid.

template<typename T >

Real numeric::VoxelGrid< T >::GetResolution

(

)

const

Get the requested resolution by the user.

template<typename T >

Real numeric::VoxelGrid< T >::GetSqDistanceOutsideBoundingBox ( Vector const &  point ) const

private

Compute distance from this point to the nearest edge of the bounding box of all given points, provided the point is outside the box.

Parameters

point

point of interest

References numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

template<typename T >

Real numeric::VoxelGrid< T >::GetSqDistanceOutsideBoundingBox ( Vector const &  min_box, Vector const &  max_box  ) const

private

Compute distance from another grid's bounding box to the nearest edge of this bounding box provided that the MIN and MAX is outside of this bounding box.

Parameters

min_box	min of the grid of interest
min_box	max of the grid of interest

References numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

template<typename T >

bool numeric::VoxelGrid< T >::HasNeighbors	(	t_DataType const &	input,
		Real const &	neighborhood,
		bool	check_relevance = false
	)		const

Has given DATA a neighbor in the grid within a specified distance.

Parameters

input	datapoint of interest
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return true if neighboring objects are relevant

template<typename T >

bool numeric::VoxelGrid< T >::HasNeighbors1D ( t_DataType const &  obj, Real const &  neighborhood, bool  check_relevance = false  ) const

private

Has given object a neighbor in the grid within a specified distance.

Parameters

obj	object to look for neighbors
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return true if neighboring objects are relevant

References numeric::xyzVector< typename >::distance_squared(), make_symmdef_file_denovo::pos, and runtime_assert_msg.

template<typename T >

bool numeric::VoxelGrid< T >::HasNeighborsMultiDimensional ( t_DataType const &  obj, Real const &  neighborhood, bool  check_relevance = false  ) const

private

Has given object a neighbor in the grid within a specified distance.

Parameters

obj	object to look for neighbors
neighborhood	range in which to search for neighbors; must be <= resolution
check_relevance	check and only return true if neighboring objects are relevant

References begin, numeric::xyzVector< typename >::distance_squared(), basic::options::OptionKeys::cutoutdomain::end, make_symmdef_file_denovo::pos, runtime_assert_msg, and numeric::crick_equations::z().

template<typename T >

void numeric::VoxelGrid< T >::InsertObject	(	t_DataType const &	new_item,
		bool	check_relevance = false
	)

insert a new t_DataType object into the manager

Parameters

new_item	reference to item to insert
check_relevance	check and only insert if object is relevant for neighbor calculation

References ObjexxFCL::index().

template<typename T >

void numeric::VoxelGrid< T >::InsertObjects	(	utility::vector1< t_DataType const * > const &	new_items,
		bool	check_relevance = false
	)

inserts multiple t_DataType objects into the manager

Parameters

new_items	vector of references to items to insert
check_relevance	check and only insert if objects are relevant for neighbor calculation

template<typename >

virtual bool numeric::VoxelGrid< typename >::IsRelevantItem ( t_DataType const &  item ) const

pure virtual

is item relevant to consider as neighbor. TO BE IMPLEMENTED BY DERIVED CLASSES.

Parameters

item	item to check

template<typename >

virtual bool numeric::VoxelGrid< typename >::IsSameItem ( t_DataType const &  item1, t_DataType const &  item2  ) const

pure virtual

check if two grid items are the same. TO BE IMPLEMENTED BY DERIVED CLASSES.

Parameters

item1	first comparison item
item2	second comparison item

template<typename T >

void numeric::VoxelGrid< T >::RemoveObject

(

t_DataType const &

item_to_remove

)

remove a t_DataType object from the manager

Parameters

item_to_remove

reference to the item to remove

References ObjexxFCL::index(), and make_symmdef_file_denovo::pos.

template<typename T >

void numeric::VoxelGrid< T >::RemoveObjects

(

utility::vector1< t_DataType const * > const &

items_to_remove

)

remove multiple t_DataType objects from the manager

Parameters

items_to_remove

vector of references to items to remove

template<typename T >

void numeric::VoxelGrid< T >::SetObjects	(	utility::vector1< t_DataType const * > const &	new_data,
		bool	check_relevance = false
	)

Update the VoxelGrid with new data.

Parameters

new_data	Vector of the new data
check_relevance	check if objects are relevant for neighbor calculation and only insert those

References ObjexxFCL::index(), max(), and min().

template<typename T >

void numeric::VoxelGrid< T >::SetupGrid ( Vector const &  min_vals, Vector const &  max_vals, Size const &  expected_n_elements  )

private

Try to allocate a grid of a given size. If this size would cause the object to definitely exceed the max memory allotment, the grid will be truncated to include only the core. It is assumed that Resolution_ has been setup prior to this.

Parameters

min_vals	dimension of bounding box
max_vals	dimension of bounding box

References erraser_analysis::diff, max(), min(), make_symmdef_file_denovo::pos, runtime_assert_msg, erraser_single_res_analysis::score, numeric::crick_equations::x(), numeric::xyzVector< typename >::x(), numeric::crick_equations::y(), numeric::xyzVector< typename >::y(), numeric::crick_equations::z(), and numeric::xyzVector< typename >::z().

template<typename T >

void numeric::VoxelGrid< T >::Translate

(

Vector const &

translation

)

Translate the grid.

Parameters

translation

amount to translate by

References basic::options::OptionKeys::rigid::translation, numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

Member Data Documentation

template<typename >

utility::vector1< utility::vector1< t_DataTypeVectorCOPtrPair> > numeric::VoxelGrid< typename >::Assignments_

private

template<typename >

utility::vector1< Size > numeric::VoxelGrid< typename >::BorderFlags_

private

template<typename >

geometry::BoundingBox< Vector > numeric::VoxelGrid< typename >::Box_

private

template<typename >

bool numeric::VoxelGrid< typename >::CacheEdges_

private

template<typename >

utility::vector1< utility::vector1< utility::vector1< t_DataTypeVectorCOPtrPair> > > numeric::VoxelGrid< typename >::Edges_

private

template<typename >

utility::vector1< utility::vector1< utility::vector1< t_DataTypeVectorCOPtrPair> > > numeric::VoxelGrid< typename >::EdgesComplete_

private

template<typename >

Size numeric::VoxelGrid< typename >::MaxNumberElements_

private

template<typename >

Size numeric::VoxelGrid< typename >::MinNumberElements_

private

template<typename >

Real numeric::VoxelGrid< typename >::MinResolution_

private

template<typename >

Real numeric::VoxelGrid< typename >::MinX_

private

template<typename >

Real numeric::VoxelGrid< typename >::MinY_

private

template<typename >

Real numeric::VoxelGrid< typename >::MinZ_

private

template<typename >

Size numeric::VoxelGrid< typename >::NBinsX_

private

template<typename >

Size numeric::VoxelGrid< typename >::NBinsY_

private

template<typename >

Size numeric::VoxelGrid< typename >::NBinsZ_

private

template<typename >

Size numeric::VoxelGrid< typename >::NDimensional_

private

template<typename >

Size numeric::VoxelGrid< typename >::NItems_

private

template<typename >

Real numeric::VoxelGrid< typename >::Resolution_

private

template<typename >

Real numeric::VoxelGrid< typename >::ResolutionX_

private

template<typename >

Real numeric::VoxelGrid< typename >::ResolutionY_

private

template<typename >

Real numeric::VoxelGrid< typename >::ResolutionZ_

private

---

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

• src/numeric/VoxelGrid.fwd.hh
• src/numeric/VoxelGrid.hh
• src/numeric/VoxelGrid.impl.hh