Data type holding regularly spaced data in a cube. More...

#include <avogadro/cube.h>

Inheritance diagram for Avogadro::Cube:

Public Types
enum	Type { VdW, ESP, ElectronDensity, MO, FromFile, None }
Public Member Functions
	Cube (QObject *parent=0)
Eigen::Vector3d	min () const
Eigen::Vector3d	max () const
Eigen::Vector3d	spacing () const
Eigen::Vector3i	dimensions () const
bool	setLimits (const Eigen::Vector3d &min, const Eigen::Vector3d &max, const Eigen::Vector3i &points)
bool	setLimits (const Eigen::Vector3d &min, const Eigen::Vector3d &max, double spacing)
bool	setLimits (const Eigen::Vector3d &min, const Eigen::Vector3i &dim, double spacing)
bool	setLimits (const Cube &cube)
bool	setLimits (const Molecule *mol, double spacing, double padding)
std::vector< double > *	data ()
bool	setData (const std::vector< double > &values)
bool	addData (const std::vector< double > &values)
unsigned int	closestIndex (const Eigen::Vector3d &pos) const
Eigen::Vector3i	indexVector (const Eigen::Vector3d &pos) const
Eigen::Vector3d	position (unsigned int index) const
double	value (int i, int j, int k) const
double	value (const Eigen::Vector3i &pos) const
float	valuef (const Eigen::Vector3f &pos) const
double	value (const Eigen::Vector3d &pos) const
bool	setValue (int i, int j, int k, double value)
bool	setValue (unsigned int i, double value)
double	minValue () const
double	maxValue () const
void	setName (QString name)
QString	name () const
void	setCubeType (Type type)
Type	cubeType ()
QReadWriteLock *	lock () const
Protected Attributes
std::vector< double >	m_data
Eigen::Vector3d	m_min
Eigen::Vector3d	m_max
Eigen::Vector3d	m_spacing
Eigen::Vector3i	m_points
double	m_minValue
double	m_maxValue
QString	m_name
Type	m_cubeType
QReadWriteLock *	m_lock

Detailed Description

Data type holding regularly spaced data in a cube.

Author:: Marcus D. Hanwell

The Cube class is a Primitive subclass that provides storage for scalar values on a regularly spaced grid in three dimensions. This is typically used for things such as molecular orbital values, which can be rendered using other techniques.

Member Enumeration Documentation

enum Avogadro::Cube::Type

This enum allows us to iterate through the various types of primitives.

Holds the primitive type

Reimplemented from Avogadro::Primitive.

Member Function Documentation

bool Avogadro::Cube::addData ( const std::vector< double > & values )

Adds the values in the cube to those passed in the vector.

unsigned int Avogadro::Cube::closestIndex ( const Eigen::Vector3d & pos ) const

Returns:: Index of the point closest to the position supplied.

Parameters:

pos	Position to get closest index for.

std::vector< double > * Avogadro::Cube::data ( )

Returns:: Vector containing all the data in a one-dimensional array.

Eigen::Vector3i Avogadro::Cube::dimensions ( ) const [inline]

Returns:: The x, y and z dimensions of the cube.

Referenced by Avogadro::MeshGenerator::initialize(), and Avogadro::Molecule::OBMol().

Vector3i Avogadro::Cube::indexVector ( const Eigen::Vector3d & pos ) const

Returns:: Index vector of the point closest to the position supplied, in the form of i, j, k.

Parameters:

pos	Position to get closest index for.

Returns:: The i, j, k index closest to the position supplied.

QReadWriteLock * Avogadro::Cube::lock ( ) const

Provides locking.

Referenced by Avogadro::MeshGenerator::initialize(), and Avogadro::MeshGenerator::run().

Eigen::Vector3d Avogadro::Cube::max ( ) const [inline]

Returns:: The maximum point in the cube.

Referenced by setLimits().

double Avogadro::Cube::maxValue ( ) const [inline]

Returns:: The minimum value at any point in the Cube.

Eigen::Vector3d Avogadro::Cube::min ( ) const [inline]

Returns:: The minimum point in the cube.

Referenced by Avogadro::MeshGenerator::initialize(), Avogadro::Molecule::OBMol(), and setLimits().

double Avogadro::Cube::minValue ( ) const [inline]

Returns:: The minimum value at any point in the Cube.

Vector3d Avogadro::Cube::position ( unsigned int index ) const

Parameters:

index Index to be translated to a position.

Returns:: Position of the given index.

bool Avogadro::Cube::setData ( const std::vector< double > & values )

Set the values in the cube to those passed in the vector.

Referenced by Avogadro::Molecule::setOBMol().

bool Avogadro::Cube::setLimits	(	const Eigen::Vector3d &	min,
		const Eigen::Vector3d &	max,
		const Eigen::Vector3i &	points
	)

Set the limits of the cube.

Parameters:

min	The minimum point in the cube.
max	The maximum point in the cube.
points	The number of (integer) points in the cube.

Referenced by setLimits(), and Avogadro::Molecule::setOBMol().

bool Avogadro::Cube::setLimits	(	const Eigen::Vector3d &	min,
		const Eigen::Vector3d &	max,
		double	spacing
	)

Set the limits of the cube.

Parameters:

min	The minimum point in the cube.
max	The maximum point in the cube.
spacing	The interval between points in the cube.

bool Avogadro::Cube::setLimits	(	const Eigen::Vector3d &	min,
		const Eigen::Vector3i &	dim,
		double	spacing
	)

Set the limits of the cube.

Parameters:

min	The minimum point in the cube.
dim	The integer dimensions of the cube in x, y and z.
spacing	The interval between points in the cube.

bool Avogadro::Cube::setLimits ( const Cube & cube )

Set the limits of the cube - copy the limits of an existing Cube.

Parameters:

cube	Existing Cube to copy the limits from.

bool Avogadro::Cube::setLimits	(	const Molecule *	mol,
		double	spacing,
		double	padding
	)

Set the limits of the cube by the molecule supplied with padding.

Parameters:

mol	The molecule to use when finding bounds.
spacing	The interval between points in the cube.
padding	The padding to use around the extents of the molecule.

References QList::at(), Avogadro::Molecule::atoms(), max(), min(), Avogadro::Atom::pos(), setLimits(), and QList::size().

bool Avogadro::Cube::setValue	(	int	i,
		int	j,
		int	k,
		double	value
	)

Sets the value at the specified point in the cube.

Parameters:

i	x compenent of the position.
j	y compenent of the position.
k	z compenent of the position.
value	Value at the specified position.

References Avogadro::Primitive::index(), and value().

bool Avogadro::Cube::setValue	(	unsigned int	i,
		double	value
	)		`[inline]`

Sets the value at the specified index in the cube.

Parameters:

i	1-dimenional index of the point to set in the cube.

References value().

Eigen::Vector3d Avogadro::Cube::spacing ( ) const [inline]

Returns:: The spacing of the grid.

Referenced by Avogadro::MeshGenerator::initialize(), and Avogadro::Molecule::OBMol().

double Avogadro::Cube::value	(	int	i,
		int	j,
		int	k
	)		const

This function is very quick as it just returns the value at the point.

Returns:: Cube value at the integer point i, j, k.

References Avogadro::Primitive::index().

Referenced by Avogadro::MeshGenerator::marchingCube(), setValue(), and valuef().

double Avogadro::Cube::value ( const Eigen::Vector3i & pos ) const

This function is very quick as it just returns the value at the point.

Returns:: Cube value at the integer point pos.

double Avogadro::Cube::value ( const Eigen::Vector3d & pos ) const

This function uses trilinear interpolation to find the value at points between those specified in the cube.

Returns:: Cube value at the specified position.

Warning:: This function is quite computationally expensive and should be avoided where possible.

float Avogadro::Cube::valuef ( const Eigen::Vector3f & pos ) const

This function uses trilinear interpolation to find the value at points between those specified in the cube.

Returns:: Cube value at the specified position.

Warning:: This function is quite computationally expensive and should be avoided where possible.

References value().

Referenced by Avogadro::MeshGenerator::normal().

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

/home/kitware/dashboards/avogadro/libavogadro/src/cube.h
/home/kitware/dashboards/avogadro/libavogadro/src/cube.cpp

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Member Function Documentation