Spore Class Reference

An Alterneria spore modeled as a symmetric ellipsoid. More...

#include <spore.h>

Inheritance diagram for Spore:

Collaboration diagram for Spore:

List of all members.

Public Member Functions
	Spore (float centroid_x, float centroid_y, float centroid_z, float length, float width, float base_theta, float base_psi, float theta, float psi, float opacity, size_t level, const class Spore_density *density) throw (jwscxx::base::Arg_error)
	Constructs a parent-less Spore positioned w.r.t. a centroid.
	Spore (Structure *parent, float length, float width, float base_theta, float base_psi, float theta, float psi, float opacity, const class Spore_density *density) throw (jwscxx::base::Arg_error, Apical_error)
	Constructs a Spore and attaches it to a parent.
	Spore (Structure *parent, float centroid_x, float centroid_y, float centroid_z, float length, float width, float base_theta, float base_psi, float opacity, const class Spore_density *density) throw (jwscxx::base::Arg_error, Apical_error)
	Constructs a Spore and attaches it to a parent.
	Spore (const Spore &s)
	Constructs a Spore by copying another.
	Spore (const class Apical_hypha &h, float width, const Spore_density *density) throw (jwscxx::base::Arg_error)
	Constructs a Spore by copying another.
Spore *	clone () const
	Clones this Spore.
Spore &	operator= (const Spore &s)
	Copies a Spore into this Spore.
class Spore_density *	get_density () const
	Returns the density parameters used by this Structure.
Spore *	split_into_apical (const Spore *rvals_1, const Spore *rvals_2) throw (jwscxx::base::Arg_error)
	Stochastically splits this Spore into this and another Spore.
Spore *	merge_with_apical (const Spore *rvals) throw (jwscxx::base::Arg_error)
	Stochastically merges this Spore with its Spore::apical.
class Apical_hypha *	split_into_apical (const Apical_hypha *rvals_1, const Apical_hypha *rvals_2) throw (jwscxx::base::Arg_error)
	Splits a Spore into 2 Apical_hypha.
void	replace (class Apical_hypha *hypha) throw (jwscxx::base::Arg_error)
	Replaces this Spore with an Apical_hypha.
bool	draw_in_matrix_f (jwsc::Matrix_f *M, float x, float y, float z, float x_scale, float y_scale, float z_scale, bool fill=true) const
	Draws this Spore in a matrix.
bool	draw_in_matblock_f (jwsc::Matblock_f *M_blk, float x, float y, float z, float x_scale, float y_scale, float z_scale, bool fill=true) const
	Draws this Spore in a matrix block.
float	get_intersection (jwsc::Vector_f **isect_out, uint32_t n, const jwsc::Vector_f *p1_in, const jwsc::Vector_f *p2_in) throw (jwscxx::base::Arg_error)
	Draws this Spore in an OpenGL environment.
const char *	get_type_str () const
	Returns the type of this Structure in the form of a string.
Static Public Member Functions
static const char *	type_str ()
	Returns the type of this Structure in the form of a string.
Protected Member Functions
void	draw_in_zeroed_matrix_f (jwsc::Matrix_f *M, float x, float y, float z, float x_scale, float y_scale, float z_scale, bool fill=true) const
	Draws this Spore in a zeroed matrix.
void	update_log_prob ()
	Updates Structure::log_prob.
Protected Attributes
class Spore_density *	density
	Parameters for density functions over a Spore.

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Detailed Description

An Alterneria spore modeled as a symmetric ellipsoid.

The ellipsoid is symmetric with respect to two of its minor axis.

Definition at line 79 of file spore.h.

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Constructor & Destructor Documentation

Spore::Spore	(	float	centroid_x,
		float	centroid_y,
		float	centroid_z,
		float	length,
		float	width,
		float	base_theta,
		float	base_psi,
		float	theta,
		float	psi,
		float	opacity,
		size_t	level,
		const class Spore_density *	density
	)		throw (jwscxx::base::Arg_error)

Constructs a parent-less Spore positioned w.r.t. a centroid.

Parameters:

centroid_x	X-coord of the Structure::centroid.
centroid_y	Y-coord of the Structure::centroid.
centroid_z	Z-coord of the Structure::centroid.
length	Length from the Structure::begin_pt to Structure::end_pt.
width	Width of the Structure.
base_theta	Euler angle: base rotation about the x-axis.
base_psi	Euler angle: base rotation about the z-axis.
theta	Euler angle: rotation about the x-axis.
psi	Euler angle: rotation about the z-axis.
opacity	Opacity of the Spore.
level	Level of the Spore.
density	Spore_density parameters for probabilities.

Exceptions:

jwscxx::base::Arg_error

Spore values are not in the density parameter ranges.

Definition at line 341 of file spore.cpp.

Spore::Spore	(	Structure *	parent,
		float	length,
		float	width,
		float	base_theta,
		float	base_psi,
		float	theta,
		float	psi,
		float	opacity,
		const class Spore_density *	density
	)		throw (jwscxx::base::Arg_error, Apical_error)

Constructs a Spore and attaches it to a parent.

Parameters:

parent	Parent Structure to add this Spore to.
length	Length from the Structure::begin_pt to Structure::end_pt.
width	Width of the Structure.
base_theta	Euler angle: base rotation about the x-axis.
base_psi	Euler angle: base rotation about the z-axis.
theta	Euler angle: rotation about the x-axis.
psi	Euler angle: rotation about the z-axis.
opacity	Opacity of the Spore.
density	Spore_density parameters for probabilities.

Exceptions:

jwscxx::base::Arg_error	Spore values are not in the density parameter range.
Apical_error	The parent already has an apical growth.

Definition at line 381 of file spore.cpp.

Spore::Spore	(	Structure *	parent,
		float	centroid_x,
		float	centroid_y,
		float	centroid_z,
		float	length,
		float	width,
		float	base_theta,
		float	base_psi,
		float	opacity,
		const class Spore_density *	density
	)		throw (jwscxx::base::Arg_error, Apical_error)

Constructs a Spore and attaches it to a parent.

Parameters:

parent	Parent Structure to add this Spore to.
centroid_x	X-coord of the Structure::centroid.
centroid_y	Y-coord of the Structure::centroid.
centroid_z	Z-coord of the Structure::centroid.
length	Length from the Structure::begin_pt to Structure::end_pt.
width	Width of the Structure.
base_theta	Euler angle: base rotation about the x-axis.
base_psi	Euler angle: base rotation about the z-axis.
opacity	Opacity of the Spore.
density	Spore_density parameters for probabilities.

Exceptions:

jwscxx::base::Arg_error	Spore values are not in the density parameter range.
Apical_error	The parent already has an apical growth.

Definition at line 419 of file spore.cpp.

Spore::Spore

(

const Spore &

s

)

Constructs a Spore by copying another.

Parameters:

s	Spore to construct a new one from.

Definition at line 442 of file spore.cpp.

Spore::Spore	(	const class Apical_hypha &	h,
		float	width,
		const Spore_density *	density
	)		throw (jwscxx::base::Arg_error)

Constructs a Spore by copying another.

Parameters:

h	Apical_hypha to construct a new Spore from.

Definition at line 450 of file spore.cpp.

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Member Function Documentation

Spore * Spore::clone

(

)

const [virtual]

Clones this Spore.

Returns:

A pointer to a cloned Spore.

Implements Apical_structure.

Definition at line 483 of file spore.cpp.

Spore & Spore::operator=

(

const Spore &

s

)

Copies a Spore into this Spore.

Parameters:

s	Spore to copy.

Returns:

A reference to this Spore with s copied into it.

Definition at line 494 of file spore.cpp.

class Spore_density* Spore::get_density

(

)

const [inline]

Returns the density parameters used by this Structure.

Reimplemented from Structure.

Definition at line 161 of file spore.h.

Spore * Spore::split_into_apical	(	const Spore *	rvals_1,
		const Spore *	rvals_2
	)		throw (jwscxx::base::Arg_error)

Stochastically splits this Spore into this and another Spore.

Parameters:

rvals_1	Random values to use for the stochastic split.
rvals_2	Random values to use for the stochastic split.

Returns:

The Spore that was split into this Spore::apical.

Exceptions:

jwscxx::base::Arg_error

The change would result in a Structure parameter that is not consistent with the parameter density functions.

Definition at line 515 of file spore.cpp.

Spore * Spore::merge_with_apical

(

const Spore *

rvals

)

throw (jwscxx::base::Arg_error)

Stochastically merges this Spore with its Spore::apical.

Parameters:

rvals

Random values to use for the stochastic merge.

Returns:

The Spore::apical that was merged with this Spore.

Note:

The apical and laterals from this Spore::apical are removed and merged into this Spore. So the returned Spore is safe to delete.

Exceptions:

jwscxx::base::Arg_error

The change would result in a Structure parameter that is not consistent with the parameter density functions or there is no apical to merge with.

Definition at line 540 of file spore.cpp.

class Apical_hypha * Spore::split_into_apical	(	const Apical_hypha *	rvals_1,
		const Apical_hypha *	rvals_2
	)		throw (jwscxx::base::Arg_error)

Splits a Spore into 2 Apical_hypha.

Parameters:

rvals_1	Random values to use for the stochastic split.
rvals_2	Random values to use for the stochastic split.

Returns:

The first Apical_hypha that this Spore was split into. Its apical is set to the other.

Note:

The apical and laterals from this Spore are removed and split into the Apical_hypha. So this Spore can be safely deleted upon return.

Exceptions:

jwscxx::base::Arg_error

The change would result in a Structure parameter that is not consistent with the parameter density functions.

Definition at line 574 of file spore.cpp.

void Spore::replace

(

class Apical_hypha *

hypha

)

throw (jwscxx::base::Arg_error)

Replaces this Spore with an Apical_hypha.

Parameters:

hypha

Apical_hypha to use for replacement.

Note:

This Spore is safe to delete upon return.

Definition at line 613 of file spore.cpp.

bool Spore::draw_in_matrix_f	(	jwsc::Matrix_f *	M,
		float	x,
		float	y,
		float	z,
		float	x_scale,
		float	y_scale,
		float	z_scale,
		bool	fill = true
	)		const

Draws this Spore in a matrix.

The drawing plane (M) has normal vector <x,y,z> = <0,0,1> in 3-space, i.e., it is parallel to the xy-plane. The parameter z specifies the distance of the drawing plane from the origin (0,0,1).

The parameters x and y specify the location of M->elts[0][0] in the spore coordinate system. Increasing indices of m correspond to increasing values of x and y scaled by x_scale and y_scale, respectively.

Formally, the center of the (i,j)th element of M in spore coordinates will be

      x_0 = x + x_scale*(i + 0.5); 
      y_0 = y + y_scale*(j + 0.5); 
      z_0 = z + z_scale*0.5;

The position of (x_0,y_0,z_0) in m is given by

      i = floor((x_0 - x) / x_scale + 0.5);
      j = floor((y_0 - y) / y_scale + 0.5);

Parameters:

M	Matrix to draw spore in.
x	Position of the first m column index in the spore coordinate system.
y	Position of the first m row index in the spore coordinate system.
z	Position of m in the spore coordinate system.
x_scale	Number of spore coordinate system units per column in m.
y_scale	Number of spore coordinate system units per row in m.
z_scale	Number of spore coordinate system units per matrix.
fill	Set to true if the spore is to be filled; false otherwise.

Returns:

True if any of the structures intersect with something other than one of its children.

Definition at line 660 of file spore.cpp.

bool Spore::draw_in_matblock_f	(	jwsc::Matblock_f *	M_blk,
		float	x,
		float	y,
		float	z,
		float	x_scale,
		float	y_scale,
		float	z_scale,
		bool	fill = true
	)		const [virtual]

Draws this Spore in a matrix block.

The drawing planes (M_blk) have normal vectors <x,y,z> = <0,0,1> in 3-space, i.e., parallel to the xy-plane. The parameter z specifies the distance of the drawing plane from the origin (0,0,1).

The parameters x, y, and z specify the location of mb->elts[0][0][0] in the spore coordinate system. Increasing indices of mb correspond to increasing values of x, y, and z scaled by x_scale, y_scale and z_scale, respectively.

Formally, the center of the (i,j,k)th element of M_blk in spore coordinates will be

      x_0 = x + x_scale*(i + 0.5); 
      y_0 = y + y_scale*(j + 0.5); 
      z_0 = z + z_scale*(k + 0.5);

The position of (x_0,y_0,z_0) in M_blk is given by

      i = floor((x_0 - x) / x_scale + 0.5);
      j = floor((y_0 - y) / y_scale + 0.5);
      k = floor((z_0 - z) / z_scale + 0.5);

Parameters:

M_blk	Matrix block to draw spore in.
x	Position of the first mb column index in the spore coordinate system.
y	Position of the first mb row index in the spore coordinate system.
z	Position of the first mb matrix in the spore coordinate system.
x_scale	Number of spore coordinate system units per column in mb.
y_scale	Number of spore coordinate system units per row in mb.
z_scale	Number of spore coordinate system units per matrix in mb.
fill	Set to true if the spore is to be filled; false otherwise.

Returns:

True if any of the structures intersect with something other than one of its children.

Implements Structure.

Definition at line 806 of file spore.cpp.

float Spore::get_intersection	(	jwsc::Vector_f **	isect_out,
		uint32_t	n,
		const jwsc::Vector_f *	p1_in,
		const jwsc::Vector_f *	p2_in
	)		throw (jwscxx::base::Arg_error) [virtual]

Draws this Spore in an OpenGL environment.

Calculates an intersection point between a line and this Spore, if it exists.

Parameters:

quad	GLUquadric to use for drawing.
scale	Number of GL units per spore coordinate system units.
isect_out	Result parameter. If *isect_out is NULL, an vector in R^3 is allocated; otherwise its space is re-used.
n	The number of the intersection to return, counting begins at points going from p1 to p2.
p1_in	End point of the line to intersect.
p2_in	End point of the line to intersect.

Returns:

If the n^th intersection point is found, its parametric distance along the line from p1_in to p2_in is returned in the range [0,1]. Otherwise a value < 0 is returned.

Exceptions:

jwscxx::base::Arg_error

The line end-points p1 and p2 must be in R^3. The intersection number to return n must be 1 or 2.

Implements Structure.

Definition at line 1158 of file spore.cpp.

const char* Spore::get_type_str

(

)

const [inline, virtual]

Returns the type of this Structure in the form of a string.

Implements Structure.

Definition at line 250 of file spore.h.

static const char* Spore::type_str

(

)

[inline, static]

Returns the type of this Structure in the form of a string.

Definition at line 256 of file spore.h.

void Spore::draw_in_zeroed_matrix_f	(	jwsc::Matrix_f *	M,
		float	x,
		float	y,
		float	z,
		float	x_scale,
		float	y_scale,
		float	z_scale,
		bool	fill = true
	)		const [protected]

Draws this Spore in a zeroed matrix.

The drawing plane (M) has normal vector <x,y,z> = <0,0,1> in 3-space, i.e., it is parallel to the xy-plane. The parameter z specifies the distance of the drawing plane from the origin (0,0,1).

The parameters x and y specify the location of M->elts[0][0] in the spore coordinate system. Increasing indices of m correspond to increasing values of x and y scaled by x_scale and y_scale, respectively.

Formally, the center of the (i,j)th element of m in spore coordinates will be

      x_0 = x + x_scale*(i + 0.5); 
      y_0 = y + y_scale*(j + 0.5); 
      z_0 = z + z_scale*0.5;

The position of (x_0,y_0,z_0) in m is given by

      i = floor((x_0 - x) / x_scale + 0.5);
      j = floor((y_0 - y) / y_scale + 0.5);

Parameters:

M	Matrix to draw spore in.
x	Position of the first m column index in the spore coordinate system.
y	Position of the first m row index in the spore coordinate system.
z	Position of m in the spore coordinate system.
x_scale	Number of spore coordinate system units per column in m.
y_scale	Number of spore coordinate system units per row in m.
z_scale	Number of spore coordinate system units per matrix.
fill	Set to true if the spore is to be filled; false otherwise.

Warning:

In order to do proper filling of the spore, the matrix M must be empty (zero) prior to calling this function.

Definition at line 889 of file spore.cpp.

void Spore::update_log_prob

(

)

[protected, virtual]

Updates Structure::log_prob.

Calls the base virtual update_log_prob members.

Reimplemented from Apical_structure.

Definition at line 1262 of file spore.cpp.

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Member Data Documentation

class Spore_density* Spore::density [protected]

Parameters for density functions over a Spore.

Reimplemented from Apical_structure.

Definition at line 282 of file spore.h.

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

• spore.h
• spore.cpp