An Alterneria hypha modeled as a cylinder. More...

#include <hypha.h>

Inheritance diagram for Apical_hypha:

Collaboration diagram for Apical_hypha:

Public Member Functions
	Apical_hypha (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 Apical_hypha_density *density) throw (jwscxx::base::Arg_error)
	Creates a parent-less Apical_hypha positioned w.r.t. a centroid.
	Apical_hypha (Structure parent, float length, float width, float base_theta, float base_psi, float theta, float psi, float opacity, const class Apical_hypha_density density) throw (jwscxx::base::Arg_error, Apical_error)
	Creates an Apical_hypha and attaches it to a parent.
	Apical_hypha (const Apical_hypha &h)
	Constructs a Apical_hypha by copying another.
	Apical_hypha (const class Spore &s, float width, const Apical_hypha_density *density) throw (jwscxx::base::Arg_error)
	Constructs an Apical_hypha by copying a Spore.
Apical_hypha *	clone () const
	Clones this Apical_hypha.
Apical_hypha &	operator= (const Apical_hypha &h)
	Copies a Apical_hypha into this Apical_hypha.
class Apical_hypha_density *	get_density () const
	Returns the density parameters used by this Structure.
Apical_hypha *	split_into_apical (const Apical_hypha rvals_1, const Apical_hypha rvals_2) throw (jwscxx::base::Arg_error)
	Stochastically splits this Apical_hypha into this and another Apical_hypha.
Apical_hypha *	merge_with_apical (const Apical_hypha *rvals) throw (jwscxx::base::Arg_error)
	Stochastically merges this Apical_hypha with its Apical_hypha::apical.
Apical_hypha *	merge_with_apical (class Spore *spore_out, const class Spore rvals) throw (jwscxx::base::Arg_error)
	Stochastically merges this Apical_hypha with its Apical_hypha::apical into a Spore.
class Lateral_hypha *	split_into_lateral (const Apical_hypha rvals_1, const class Lateral_hypha rvals_2) throw (jwscxx::base::Arg_error)
	Stochastically splits this Apical_hypha into this and another Lateral_hypha.
class Lateral_hypha *	merge_with_lateral (class Lateral_hypha lateral, const Apical_hypha rvals) throw (jwscxx::base::Arg_error)
	Stochastically merges this Apical_hypha with one of its Apical_hypha::laterals.
void	replace (class Spore *spore) throw (jwscxx::base::Arg_error)
	Replaces this Apical_hypha with a Spore.
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 Apical_hypha 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 Apical_hypha 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	update_log_prob ()
	Updates Structure::log_prob.
Protected Attributes
class Apical_hypha_density *	density
	Parameters for density functions over an Apical_hypha.

Detailed Description

An Alterneria hypha modeled as a cylinder.

Definition at line 77 of file hypha.h.

Constructor & Destructor Documentation

Apical_hypha::Apical_hypha	(	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 Apical_hypha_density *	density
	)		throw (jwscxx::base::Arg_error)

Creates a parent-less Apical_hypha 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 Apical_hypha.
level	Level of the hypha.
density	Apical_hypha_density parameters for probabilities.

Exceptions:

jwscxx::base::Arg_error Apical_hypha values are not in the density parameter ranges.

Definition at line 612 of file hypha.cpp.

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

Creates an Apical_hypha and attaches it to a parent.

Parameters:

parent	Parent Structure to add this Apical_hypha 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 Apical_hypha.
density	Apical_hypha_density parameters for probabilities.

Exceptions:

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

Definition at line 652 of file hypha.cpp.

Apical_hypha::Apical_hypha ( const Apical_hypha & h )

Constructs a Apical_hypha by copying another.

Parameters:

h	Apical_hypha to construct a new one from.

Definition at line 674 of file hypha.cpp.

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

Constructs an Apical_hypha by copying a Spore.

Parameters:

s	Spore to construct a new Apical_hypha from.

Definition at line 682 of file hypha.cpp.

Member Function Documentation

Apical_hypha * Apical_hypha::clone ( ) const [virtual]

Clones this Apical_hypha.

Returns:: A pointer to a cloned Apical_hypha.

Implements Apical_structure.

Definition at line 716 of file hypha.cpp.

Apical_hypha & Apical_hypha::operator= ( const Apical_hypha & h )

Copies a Apical_hypha into this Apical_hypha.

Parameters:

h	Apical_hypha to copy.

Returns:: A reference to this Apical_hypha with h copied into it.

Definition at line 727 of file hypha.cpp.

class Apical_hypha_density* Apical_hypha::get_density ( ) const [inline]

Returns the density parameters used by this Structure.

Reimplemented from Structure.

Definition at line 142 of file hypha.h.

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

Stochastically splits this Apical_hypha into this and another 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 Apical_hypha that was split into this Apical_hypha::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 748 of file hypha.cpp.

Apical_hypha * Apical_hypha::merge_with_apical ( const Apical_hypha * rvals ) throw (jwscxx::base::Arg_error)

Stochastically merges this Apical_hypha with its Apical_hypha::apical.

Parameters:

rvals Random values to use for the stochastic merge.

Returns:: The Apical_hypha::apical that was merged with this Apical_hypha.

Note:: The apical and laterals from this Apical_hypha::apical are removed and merged into this Apical_hypha. So the returned Apical_hypha 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 773 of file hypha.cpp.

Apical_hypha * Apical_hypha::merge_with_apical	(	class Spore **	spore_out,
		const class Spore *	rvals
	)		throw (jwscxx::base::Arg_error)

Stochastically merges this Apical_hypha with its Apical_hypha::apical into a Spore.

Parameters:

spore_out	Result parameter. The merged Spore on return.
rvals	Random values to use for the stochastic merge.

Returns:: The Apical_hypha::apical that was merged with this Apical_hypha.

Note:: The apical and laterals from this and its Apical_hypha::apical are removed and put in the merged Spore. So this and the returned Apical_hypha are 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 808 of file hypha.cpp.

Lateral_hypha * Apical_hypha::split_into_lateral	(	const Apical_hypha *	rvals_1,
		const class Lateral_hypha *	rvals_2
	)		throw (jwscxx::base::Arg_error)

Stochastically splits this Apical_hypha into this and another Lateral_hypha.

Parameters:

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

Returns:: The Lateral_hypha that was split into this Apical_hypha::laterals.

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 859 of file hypha.cpp.

Lateral_hypha * Apical_hypha::merge_with_lateral	(	class Lateral_hypha *	lateral,
		const Apical_hypha *	rvals
	)		throw (jwscxx::base::Arg_error)

Stochastically merges this Apical_hypha with one of its Apical_hypha::laterals.

Parameters:

lateral	Lateral_hypha to merge with this Apical_hypha.
rvals	Random values to use for the stochastic merge.

Returns:: The Lateral_hypha that was merged with this Apical_hypha.

Note:: The apical and laterals from lateral are removed and merged into this Apical_hypha. So the returned Lateral_hypha 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.

Warning:: This Apical_hypha must not have an apical and lateral must be found in this Apical_hypha::laterals.

Definition at line 887 of file hypha.cpp.

void Apical_hypha::replace ( class Spore * spore ) throw (jwscxx::base::Arg_error)

Replaces this Apical_hypha with a Spore.

Parameters:

spore Spore to use for replacement.

Note:: This Apical_hypha is safe to delete after upon return.

Definition at line 902 of file hypha.cpp.

bool Apical_hypha::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 Apical_hypha 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 M_blk->elts[0][0][0] in the hypha coordinate system. Increasing indices of M_blk 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 is

      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 the Hypha in.
x	Position of the first M_blk column index in the hypha coordinate system.
y	Position of the first M_blk row index in the hypha coordinate system.
z	Position of the first M_blk matrix index in the hypha coordinate system.
x_scale	Number of hypha coordinate system units per column.
y_scale	Number of hypha coordinate system units per row.
z_scale	Number of hypha coordinate system units per matrix.
fill	Set to 1 if the hypha is to be filled; 0 otherwise.

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

Implements Structure.

Definition at line 950 of file hypha.cpp.

float Apical_hypha::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 Apical_hypha in an OpenGL environment.

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

Parameters:

quad	GLUquadric to use for drawing.
scale	Number of GL units per hypha 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 1116 of file hypha.cpp.

const char* Apical_hypha::get_type_str ( ) const [inline, virtual]

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

Implements Structure.

Definition at line 244 of file hypha.h.

static const char* Apical_hypha::type_str ( ) [inline, static]

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

Definition at line 250 of file hypha.h.

void Apical_hypha::update_log_prob ( ) [protected, virtual]

Updates Structure::log_prob.

Calls the base virtual update_log_prob members.

Reimplemented from Apical_structure.

Definition at line 1227 of file hypha.cpp.

Member Data Documentation

class Apical_hypha_density* Apical_hypha::density [protected]

Parameters for density functions over an Apical_hypha.

Reimplemented from Apical_structure.

Definition at line 262 of file hypha.h.

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation