#include <marchingcubes.h>

Inheritance diagram for EMAN::MarchingCubes:

Collaboration diagram for EMAN::MarchingCubes:

[legend]

Public Member Functions
	MarchingCubes ()
	Default constructor. More...

	MarchingCubes (EMData *em)
	Most commonly used constructor calls set_data(em) More...

virtual	~MarchingCubes ()

void	set_data (EMData *data)
	Sets Voxel data for Isosurface implementation Calls calculate_min_max_vals which generates the tree of data. More...

void	set_surface_value (const float value)
	Set Isosurface value. More...

float	get_surface_value () const
	Get the current isosurface value being used. More...

void	set_sampling (const int rate)
	Set sampling rates A smaller value means a finer sampling. More...

int	get_sampling () const
	Current the current sampling rate Finest sampling is -1. More...

int	get_sampling_range ()
	Get the range of feasible sampling rates. More...

void	color_vertices ()
	Color the vertices. More...

Dict	get_isosurface ()
	Get the isosurface as dictionary Traverses the tree and marches the cubes. More...

void	surface_face_z ()

void	setRGBorigin (int x, int y, int z)
	Functions to control colroing mode. More...

void	setRGBscale (float i, float o)

void	setRGBmode (int mode)

int	getRGBmode ()
	Return RGB mode. More...

void	setCmapData (EMData *data)
	Sets the colormap. More...

void	setCmapMinMax (float min, float max)
	Sets the colormap mix max range. More...

Public Member Functions inherited from EMAN::Isosurface
	Isosurface ()

virtual	~Isosurface ()

Private Member Functions
bool	calculate_min_max_vals ()
	Calculate the min and max value trees Stores minimum and maximum cube neighborhood values in a tree structure. More...

void	clear_min_max_vals ()
	Clear the minimum and maximum value search trees Frees memory in the minvals and maxvals. More...

void	draw_cube (const int x, const int y, const int z, const int cur_level)
	The main cube drawing function To start the process of generate triangles call with draw_cube(0,0,0,minvals.size()-1) Once cur_level becomes drawing_level marching_cube is called. More...

void	marching_cube (int fX, int fY, int fZ, const int cur_level)
	Function for managing cases where a triangles can potentially be rendered Called by draw_cube. More...

void	calculate_surface ()
	Calculate and generate the entire set of vertices and normals using current states Calls draw_cube(0,0,0,minvals.size()-1) More...

float	get_offset (float fValue1, float fValue2, float fValueDesired)
	Find the approximate point of intersection of the surface between two points with the values fValue1 and fValue2. More...

int	get_edge_num (int x, int y, int z, int edge)
	Get edge num needs better commenting. More...

void	get_normal (Vector3 &normal, int fX, int fY, int fZ)
	Find the gradient of the scalar field at a point. More...

Private Attributes
map< int, int >	point_map

unsigned long	_isodl

GLuint	buffer [4]

vector< EMData * >	minvals
	Vectors for storing the search trees. More...

vector< EMData * >	maxvals

int	drawing_level
	The "sampling rate". More...

CustomVector< float >	pp
	.Custom vectors for storing points, normals and faces More...

CustomVector< float >	cc

CustomVector< int >	vv

CustomVector< float >	nn

CustomVector< unsigned int >	ff

ColorRGBGenerator	rgbgenerator
	Color by radius generator. More...

bool	needtobind

Friends
class	GLUtil

Additional Inherited Members
Protected Attributes inherited from EMAN::Isosurface
EMData *	_emdata

float	_surf_value

Detailed Description

Definition at line 271 of file marchingcubes.h.

Constructor & Destructor Documentation

◆ MarchingCubes() [1/2]

EMAN::MarchingCubes::MarchingCubes ( )

Default constructor.

◆ MarchingCubes() [2/2]

EMAN::MarchingCubes::MarchingCubes ( EMData * em )

Most commonly used constructor calls set_data(em)

Parameters

em	the EMData object to generate triangles and normals for

◆ ~MarchingCubes()

virtual EMAN::MarchingCubes::~MarchingCubes ( )

virtual

Member Function Documentation

◆ calculate_min_max_vals()

bool EMAN::MarchingCubes::calculate_min_max_vals ( )

private

Calculate the min and max value trees Stores minimum and maximum cube neighborhood values in a tree structure.

Exceptions

NullPointerException if _emdata is null... this should not happen but is left for clarity for programmers

◆ calculate_surface()

void EMAN::MarchingCubes::calculate_surface ( )

private

Calculate and generate the entire set of vertices and normals using current states Calls draw_cube(0,0,0,minvals.size()-1)

◆ clear_min_max_vals()

void EMAN::MarchingCubes::clear_min_max_vals ( )

private

Clear the minimum and maximum value search trees Frees memory in the minvals and maxvals.

◆ color_vertices()

void EMAN::MarchingCubes::color_vertices ( )

Color the vertices.

◆ draw_cube()

void EMAN::MarchingCubes::draw_cube	(	const int	x,
		const int	y,
		const int	z,
		const int	cur_level
	)

private

The main cube drawing function To start the process of generate triangles call with draw_cube(0,0,0,minvals.size()-1) Once cur_level becomes drawing_level marching_cube is called.

Parameters

x	the current x value, relative to cur_level
y	the current y value, relative to cur_level
z	the current z value, relative to cur_level
cur_level	the current tree traversal level

◆ get_edge_num()

int EMAN::MarchingCubes::get_edge_num	(	int	x,
		int	y,
		int	z,
		int	edge
	)

private

Get edge num needs better commenting.

◆ get_isosurface()

Dict EMAN::MarchingCubes::get_isosurface ( )

virtual

Get the isosurface as dictionary Traverses the tree and marches the cubes.

Returns: a dictionary object containing to float pointers (to vertex and normal data), and an int pointer (to face data)

Implements EMAN::Isosurface.

◆ get_normal()

void EMAN::MarchingCubes::get_normal	(	Vector3 &	normal,
		int	fX,
		int	fY,
		int	fZ
	)

private

Find the gradient of the scalar field at a point.

This gradient can be used as a very accurate vertx normal for lighting calculations.

THIS FUNCTION IS NO LONGER CALLED - d.woolford but is retained because it may be useful, perhaps even for saving time

Parameters

normal	where to store the normal
fX
fY
fZ

◆ get_offset()

float EMAN::MarchingCubes::get_offset	(	float	fValue1,
		float	fValue2,
		float	fValueDesired
	)

private

Find the approximate point of intersection of the surface between two points with the values fValue1 and fValue2.

Parameters

fValue1
fValue2
fValueDesired

Returns: offset

◆ get_sampling()

int EMAN::MarchingCubes::get_sampling ( ) const

inlinevirtual

Current the current sampling rate Finest sampling is -1.

Implements EMAN::Isosurface.

Definition at line 315 of file marchingcubes.h.

315{ return drawing_level; }

EMAN::MarchingCubes::drawing_level

int drawing_level

The "sampling rate".

Definition: marchingcubes.h:390

References drawing_level.

◆ get_sampling_range()

int EMAN::MarchingCubes::get_sampling_range ( )

inlinevirtual

Get the range of feasible sampling rates.

Implements EMAN::Isosurface.

Definition at line 319 of file marchingcubes.h.

319{ return minvals.size()-1; }

EMAN::MarchingCubes::minvals

vector< EMData * > minvals

Vectors for storing the search trees.

Definition: marchingcubes.h:387

References minvals.

◆ get_surface_value()

float EMAN::MarchingCubes::get_surface_value ( ) const

inlinevirtual

Get the current isosurface value being used.

Returns: the current isosurface value

Implements EMAN::Isosurface.

Definition at line 300 of file marchingcubes.h.

300{ return _surf_value; }

EMAN::Isosurface::_surf_value

float _surf_value

Definition: isosurface.h:86

References EMAN::Isosurface::_surf_value.

◆ getRGBmode()

int EMAN::MarchingCubes::getRGBmode ( )

inline

Return RGB mode.

Definition at line 351 of file marchingcubes.h.

                {
                        return rgbgenerator.getRGBmode();
                }

References EMAN::ColorRGBGenerator::getRGBmode(), and rgbgenerator.

◆ marching_cube()

void EMAN::MarchingCubes::marching_cube	(	int	fX,
		int	fY,
		int	fZ,
		const int	cur_level
	)

private

Function for managing cases where a triangles can potentially be rendered Called by draw_cube.

Generates vertices, normals, and keeps track of common points

Parameters

fX	the current x coordinate, relative to cur_level
fY	the current y coordinate, relative to cur_level
fZ	the current z coordinate, relative to cur_level
cur_level

◆ set_data()

void EMAN::MarchingCubes::set_data ( EMData * data )

virtual

Sets Voxel data for Isosurface implementation Calls calculate_min_max_vals which generates the tree of data.

Parameters

data	the emdata object to be rendered in 3D

Exceptions

ImageDimensionException if the image z dimension is 1

Reimplemented from EMAN::Isosurface.

◆ set_sampling()

void EMAN::MarchingCubes::set_sampling ( const int rate )

inlinevirtual

Set sampling rates A smaller value means a finer sampling.

The finest sampling level is -1 Sampling values increment in steps of 1, and a single increment is interpreted as one step up or down the tree stored in minvals and maxvals

Parameters

rate	the tree level to render

Implements EMAN::Isosurface.

Definition at line 310 of file marchingcubes.h.

310{ drawing_level = rate; }

References drawing_level.

◆ set_surface_value()

void EMAN::MarchingCubes::set_surface_value ( const float value )

virtual

Set Isosurface value.

Parameters

value the new isosurface value

Implements EMAN::Isosurface.

◆ setCmapData()

void EMAN::MarchingCubes::setCmapData ( EMData * data )

inlinevirtual

Sets the colormap.

Implements EMAN::Isosurface.

Definition at line 357 of file marchingcubes.h.

                {
                        rgbgenerator.set_cmap_data(data);
                }

References rgbgenerator, and EMAN::ColorRGBGenerator::set_cmap_data().

◆ setCmapMinMax()

void EMAN::MarchingCubes::setCmapMinMax	(	float	min,
		float	max
	)

inlinevirtual

Sets the colormap mix max range.

Implements EMAN::Isosurface.

Definition at line 363 of file marchingcubes.h.

                {
                        rgbgenerator.setMinMax(min, max);
                }

References rgbgenerator, and EMAN::ColorRGBGenerator::setMinMax().

◆ setRGBmode()

void EMAN::MarchingCubes::setRGBmode ( int mode )

inlinevirtual

Implements EMAN::Isosurface.

Definition at line 345 of file marchingcubes.h.

                {
                        rgbgenerator.setRGBmode(mode);
                }

References rgbgenerator, and EMAN::ColorRGBGenerator::setRGBmode().

◆ setRGBorigin()

void EMAN::MarchingCubes::setRGBorigin	(	int	x,
		int	y,
		int	z
	)

inlinevirtual

Functions to control colroing mode.

Implements EMAN::Isosurface.

Definition at line 335 of file marchingcubes.h.

                {
                        rgbgenerator.setOrigin(x, y, z);
                }

References rgbgenerator, EMAN::ColorRGBGenerator::setOrigin(), x, and y.

◆ setRGBscale()

void EMAN::MarchingCubes::setRGBscale	(	float	i,
		float	o
	)

inlinevirtual

Implements EMAN::Isosurface.

Definition at line 340 of file marchingcubes.h.

                {
                        rgbgenerator.setScale(i, o);
                }

References rgbgenerator, and EMAN::ColorRGBGenerator::setScale().

◆ surface_face_z()

void EMAN::MarchingCubes::surface_face_z ( )

Friends And Related Function Documentation

◆ GLUtil

friend class GLUtil

friend

Definition at line 272 of file marchingcubes.h.

Member Data Documentation

◆ _isodl

unsigned long EMAN::MarchingCubes::_isodl

private

Definition at line 370 of file marchingcubes.h.

◆ buffer

GLuint EMAN::MarchingCubes::buffer[4]

private

Definition at line 371 of file marchingcubes.h.

◆ cc

CustomVector<float> EMAN::MarchingCubes::cc

private

Definition at line 447 of file marchingcubes.h.

◆ drawing_level

int EMAN::MarchingCubes::drawing_level

private

The "sampling rate".

Definition at line 390 of file marchingcubes.h.

Referenced by get_sampling(), and set_sampling().

◆ ff

CustomVector<unsigned int> EMAN::MarchingCubes::ff

private

Definition at line 450 of file marchingcubes.h.

◆ maxvals

vector<EMData*> EMAN::MarchingCubes::maxvals

private

Definition at line 387 of file marchingcubes.h.

◆ minvals

vector<EMData*> EMAN::MarchingCubes::minvals

private

Vectors for storing the search trees.

Definition at line 387 of file marchingcubes.h.

Referenced by get_sampling_range().

◆ needtobind

bool EMAN::MarchingCubes::needtobind

private

Definition at line 455 of file marchingcubes.h.

◆ nn

CustomVector<float> EMAN::MarchingCubes::nn

private

Definition at line 449 of file marchingcubes.h.

◆ point_map

map<int, int> EMAN::MarchingCubes::point_map

private

Definition at line 369 of file marchingcubes.h.

◆ pp

CustomVector<float> EMAN::MarchingCubes::pp

private

.Custom vectors for storing points, normals and faces

Definition at line 446 of file marchingcubes.h.

◆ rgbgenerator

ColorRGBGenerator EMAN::MarchingCubes::rgbgenerator

private

Color by radius generator.

Definition at line 453 of file marchingcubes.h.

Referenced by getRGBmode(), setCmapData(), setCmapMinMax(), setRGBmode(), setRGBorigin(), and setRGBscale().

◆ vv

CustomVector<int> EMAN::MarchingCubes::vv

private

Definition at line 448 of file marchingcubes.h.

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

marchingcubes.h

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MarchingCubes() [1/2]

◆ MarchingCubes() [2/2]

◆ ~MarchingCubes()

Member Function Documentation

◆ calculate_min_max_vals()

◆ calculate_surface()

◆ clear_min_max_vals()

◆ color_vertices()

◆ draw_cube()

◆ get_edge_num()

◆ get_isosurface()

◆ get_normal()

◆ get_offset()

◆ get_sampling()

◆ get_sampling_range()

◆ get_surface_value()

◆ getRGBmode()

◆ marching_cube()

◆ set_data()

◆ set_sampling()

◆ set_surface_value()

◆ setCmapData()

◆ setCmapMinMax()

◆ setRGBmode()

◆ setRGBorigin()

◆ setRGBscale()

◆ surface_face_z()

Friends And Related Function Documentation

◆ GLUtil

Member Data Documentation

◆ _isodl

◆ buffer

◆ cc

◆ drawing_level

◆ ff

◆ maxvals

◆ minvals

◆ needtobind

◆ nn

◆ point_map

◆ pp

◆ rgbgenerator

◆ vv