Biomechanical Joint Model  Author: Anderson Maciel

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COME_BioStructure Class Reference

#include <comebiostructure.h>

Inherits COME.

Inherited by COME_Bone, COME_Cartilage, COME_Clamp, and COME_Container.

Inheritance diagram for COME_BioStructure:

[legend]Collaboration diagram for COME_BioStructure:

[legend]List of all members.

Public Member Functions
void	setSystem (int systemN)
void	setSurface (COME_Mesh *surfaceN)
void	setFixed (bool flag)
void	setLIM (const COME_Matrix &limN)
void	setGIM (const COME_Matrix &gimN)
void	setGlobalHooke (double hookN)
void	setCollisionRadius (double rad)
void	setType (int nType)
int	getSystem () const
COME_Mesh *	getSurface ()
COME_Mesh *	getPointerToSurface ()
double	getGlobalHooke () const
double	getCollisionRadius () const
double	getTopStress ()
void	scale (double factorx, double factory, double factorz)
void	translate (double px, double py, double pz)
void	translate (const COME_Vector3D &disp)
void	rotate (double rx, double ry, double rz)
void	scaleNominals (double factor)
bool	isFixed () const
double	getMass () const
const COME_Matrix &	getLIM () const
const COME_Matrix &	getGIM () const
virtual bool	update (double timestep, double simClock)=0
virtual void	updateSkin ()=0
virtual void	updateSurface (bool regenerate)=0
virtual void	getEnvelop (COME_Point3D &mins, COME_Point3D &maxs)=0
virtual COME_MoleculesTissue *	getTissue ()=0
virtual void	respondCollision ()=0
void	initializeHashStructure ()
void	initializeHashStructureRayCasting ()
COME_HashElement	getHashElement (COME_Point2D p)
	returns the element in the hash table corresponding to the spherical coordinates given by p
int	fillHashHoles ()
void	globalToLocal (COME_Matrix M, COME_Matrix MP)
Public Attributes
int	hashSize
COME_HashElement *	hashTable
vector< COME_BioStructure * >	internals
vector< string >	internalsDesc
COME_Vector3D	sUnit
COME_Point2D	sSpherical
Protected Attributes
int	system
double	volume
double	collisionRadius
COME_Mesh *	surface
	Radius of the enclosing sphere defining collision volume.
bool	fixed
int	type
double	globalHooke
COME_Matrix	localInstanceMatrix
COME_Matrix	globalInstanceMatrix

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Detailed Description

An abstract class to represent one organ (biological structure) of a patient. It must be implemented by adding specific features and behavior for each organ in the subclass.

Definition at line 64 of file comebiostructure.h.

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Member Function Documentation

int COME_BioStructure::fillHashHoles (   )

Definition at line 413 of file comebiostructure.cpp. References HashElement::distance, elem, HashElement::face, hashTable, and INFINITE.

double COME_BioStructure::getCollisionRadius (   )  const

Definition at line 145 of file comebiostructure.cpp. References collisionRadius.

virtual void COME_BioStructure::getEnvelop (  COME_Point3D &  mins, COME_Point3D &  maxs )  [pure virtual]

Implemented in COME_Cartilage, COME_Clamp, COME_MoleculesBone, and COME_MoleculesCartilage.

const COME_Matrix & COME_BioStructure::getGIM (   )  const

Definition at line 132 of file comebiostructure.cpp. References globalInstanceMatrix.

double COME_BioStructure::getGlobalHooke (   )  const

Definition at line 139 of file comebiostructure.cpp. References globalHooke. Referenced by COME_Mechatester::clickedStartSim(), and COME_Mechatester::updateEquation().

COME_HashElement COME_BioStructure::getHashElement (  COME_Point2D  p  )

returns the element in the hash table corresponding to the spherical coordinates given by p Definition at line 403 of file comebiostructure.cpp. References elem, COME_Point2D::getX(), COME_Point2D::getY(), hashTable, and M_PI. Here is the call graph for this function:

const COME_Matrix & COME_BioStructure::getLIM (   )  const

Definition at line 126 of file comebiostructure.cpp. References localInstanceMatrix.

double COME_BioStructure::getMass (   )  const

COME_Mesh * COME_BioStructure::getPointerToSurface (   )

Definition at line 114 of file comebiostructure.cpp. References surface. Referenced by COME_Clamp::initializeSkinning().

COME_Mesh * COME_BioStructure::getSurface (   )

Definition at line 108 of file comebiostructure.cpp. References surface. Referenced by COME_Collision::calculatePenetration(), COME_Collision::calculatePenetrationGlobalPosition(), COME_Collision::COME_Collision(), COME_Collide::detectContacts(), COME_Collide::detectContactsDisplacement(), COME_Discretizer::fileOpen(), COME_MoleculesCartilage::initializeSkinning(), COME_MoleculesBone::initializeSkinning(), and COME_Mechatester::updateClampIntersections().

int COME_BioStructure::getSystem (   )  const

Getting Definition at line 102 of file comebiostructure.cpp. References system.

virtual COME_MoleculesTissue* COME_BioStructure::getTissue (   )  [pure virtual]

Implemented in COME_Bone, COME_Cartilage, COME_Clamp, COME_MoleculesBone, and COME_MoleculesCartilage. Referenced by COME_Mechatester::clickedAssociate(), COME_Mechatester::clickedStartSim(), COME_Collide::detectContactsHybrid(), getTopStress(), globalToLocal(), rotate(), scale(), scaleNominals(), and translate().

double COME_BioStructure::getTopStress (   )

Definition at line 151 of file comebiostructure.cpp. References getTissue(), and COME_MoleculesTissue::getTopStress(). Here is the call graph for this function:

void COME_BioStructure::globalToLocal (  COME_Matrix  M, COME_Matrix  MP )

Definition at line 218 of file comebiostructure.cpp. References getTissue(), LIGAMENT, COME_MoleculesTissue::transform(), and type. Here is the call graph for this function:

void COME_BioStructure::initializeHashStructure (   )

define base vector initialize S unit vector with j for first test. allocate memory for hashMatrix Initialize Hash tabel with NULLs Definition at line 232 of file comebiostructure.cpp. References HashElement::distance, elem, hashSize, hashTable, INFINITE, sSpherical, sUnit, COME_Point3D::x, COME_Point3D::y, and COME_Point3D::z.

void COME_BioStructure::initializeHashStructureRayCasting (   )

define base vector initialize S unit vector with j for first test. allocate memory for hashMatrix Initialize Hash tabel with NULLs fill matrix by ray casting Definition at line 309 of file comebiostructure.cpp. References HashElement::distance, elem, hashTable, INFINITE, sSpherical, sUnit, COME_Point3D::x, COME_Point3D::y, and COME_Point3D::z. Referenced by COME_Scenario::initializeAllHashs().

bool COME_BioStructure::isFixed (   )  const

Definition at line 120 of file comebiostructure.cpp. References fixed. Referenced by COME_MoleculesBone::derivs(), rotate(), scale(), scaleNominals(), and translate().

virtual void COME_BioStructure::respondCollision (   )  [pure virtual]

Implemented in COME_Clamp, COME_MoleculesBone, and COME_MoleculesCartilage.

void COME_BioStructure::rotate (  double  rx, double  ry, double  rz )

Definition at line 194 of file comebiostructure.cpp. References getTissue(), isFixed(), COME_MoleculesTissue::makeAllLocalFrames(), COME_Mesh::rotate(), COME_MoleculesTissue::rotate(), surface, and COME_Mesh::updateSkin(). Referenced by COME_ModelJoint::rotateSelected(), and COME_Mechatester::rotateSelected(). Here is the call graph for this function:

void COME_BioStructure::scale (  double  factorx, double  factory, double  factorz )

Definition at line 157 of file comebiostructure.cpp. References getTissue(), isFixed(), COME_MoleculesTissue::makeAllLocalFrames(), COME_Mesh::scale(), COME_MoleculesTissue::scale(), surface, and COME_Mesh::updateSkin(). Referenced by COME_Mechatester::COME_Mechatester(), COME_ModelJoint::scaleSelected(), and COME_Mechatester::scaleSelected(). Here is the call graph for this function:

void COME_BioStructure::scaleNominals (  double  factor  )

Definition at line 210 of file comebiostructure.cpp. References getTissue(), isFixed(), and COME_MoleculesTissue::scaleNominals(). Referenced by COME_ModelJoint::sliderNominalReleased(). Here is the call graph for this function:

void COME_BioStructure::setCollisionRadius (  double  rad  )

Definition at line 86 of file comebiostructure.cpp. References collisionRadius. Referenced by COME_Xml::loadShapes().

void COME_BioStructure::setFixed (  bool  flag  )

Definition at line 62 of file comebiostructure.cpp. References fixed. Referenced by COME_Xml::loadMoleculeOrgan(), and COME_Scenario::loadOrganMesh().

void COME_BioStructure::setGIM (  const COME_Matrix &  gimN  )

Definition at line 74 of file comebiostructure.cpp. References globalInstanceMatrix.

void COME_BioStructure::setGlobalHooke (  double  hookN  )

Definition at line 80 of file comebiostructure.cpp. References globalHooke. Referenced by COME_Mechatester::clickedStartSim(), and COME_Xml::loadMoleculeOrgan().

void COME_BioStructure::setLIM (  const COME_Matrix &  limN  )

Definition at line 68 of file comebiostructure.cpp. References localInstanceMatrix.

void COME_BioStructure::setSurface (  COME_Mesh *  surfaceN  )

Definition at line 54 of file comebiostructure.cpp. References COME_Mesh::setCollisionDetectableFaces(), COME::setParent(), and surface. Here is the call graph for this function:

void COME_BioStructure::setSystem (  int  systemN  )

Setting Definition at line 48 of file comebiostructure.cpp. References system.

void COME_BioStructure::setType (  int  nType  )

Definition at line 92 of file comebiostructure.cpp. References type. Referenced by COME_Xml::loadMoleculeOrgan().

void COME_BioStructure::translate (  const COME_Vector3D &  disp  )

Definition at line 188 of file comebiostructure.cpp. References COME_Point3D::getX(), COME_Point3D::getY(), COME_Point3D::getZ(), and translate(). Here is the call graph for this function:

void COME_BioStructure::translate (  double  px, double  py, double  pz )

Definition at line 173 of file comebiostructure.cpp. References getTissue(), isFixed(), COME_MoleculesTissue::makeAllLocalFrames(), surface, COME_Mesh::translate(), COME_MoleculesTissue::translate(), and COME_Mesh::updateSkin(). Referenced by COME_Mechatester::COME_Mechatester(), translate(), COME_ModelJoint::translateSelected(), and COME_Mechatester::translateSelected(). Here is the call graph for this function:

virtual bool COME_BioStructure::update (  double  timestep, double  simClock )  [pure virtual]

Implemented in COME_Bone, COME_Cartilage, COME_Clamp, COME_MoleculesBone, and COME_MoleculesCartilage.

virtual void COME_BioStructure::updateSkin (   )  [pure virtual]

Implemented in COME_Clamp, COME_MoleculesBone, and COME_MoleculesCartilage. Referenced by COME_Mechatester::COME_Mechatester().

virtual void COME_BioStructure::updateSurface (  bool  regenerate  )  [pure virtual]

Implemented in COME_Bone, COME_Cartilage, COME_Clamp, COME_MoleculesBone, and COME_MoleculesCartilage.

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Member Data Documentation

double COME_BioStructure::collisionRadius [protected]

Definition at line 69 of file comebiostructure.h. Referenced by COME_MoleculesBone::COME_MoleculesBone(), COME_MoleculesCartilage::COME_MoleculesCartilage(), getCollisionRadius(), and setCollisionRadius().

bool COME_BioStructure::fixed [protected]

Definition at line 71 of file comebiostructure.h. Referenced by isFixed(), and setFixed().

double COME_BioStructure::globalHooke [protected]

Definition at line 73 of file comebiostructure.h. Referenced by COME_MoleculesBone::COME_MoleculesBone(), COME_MoleculesCartilage::COME_MoleculesCartilage(), getGlobalHooke(), and setGlobalHooke().

COME_Matrix COME_BioStructure::globalInstanceMatrix [protected]

Definition at line 75 of file comebiostructure.h. Referenced by getGIM(), and setGIM().

int COME_BioStructure::hashSize

Definition at line 121 of file comebiostructure.h. Referenced by initializeHashStructure().

COME_HashElement* COME_BioStructure::hashTable

Definition at line 122 of file comebiostructure.h. Referenced by COME_MoleculesBone::COME_MoleculesBone(), COME_MoleculesCartilage::COME_MoleculesCartilage(), fillHashHoles(), getHashElement(), initializeHashStructure(), and initializeHashStructureRayCasting().

vector<COME_BioStructure*> COME_BioStructure::internals

Definition at line 123 of file comebiostructure.h.

vector<string> COME_BioStructure::internalsDesc

Definition at line 124 of file comebiostructure.h. Referenced by COME_Xml::loadShapes().

COME_Matrix COME_BioStructure::localInstanceMatrix [protected]

Definition at line 74 of file comebiostructure.h. Referenced by getLIM(), and setLIM().

COME_Point2D COME_BioStructure::sSpherical

Definition at line 127 of file comebiostructure.h. Referenced by initializeHashStructure(), and initializeHashStructureRayCasting().

COME_Vector3D COME_BioStructure::sUnit

Definition at line 126 of file comebiostructure.h. Referenced by initializeHashStructure(), and initializeHashStructureRayCasting().

COME_Mesh* COME_BioStructure::surface [protected]

Radius of the enclosing sphere defining collision volume. Definition at line 70 of file comebiostructure.h. Referenced by COME_Clamp::COME_Clamp(), COME_MoleculesBone::COME_MoleculesBone(), COME_MoleculesCartilage::COME_MoleculesCartilage(), COME_MoleculesCartilage::discretize(), COME_MoleculesBone::generateEnvelopSurface(), COME_Clamp::getEnvelop(), getPointerToSurface(), getSurface(), COME_MoleculesCartilage::initializeJacobian(), COME_MoleculesCartilage::initializeSkinning(), COME_MoleculesBone::initializeSkinning(), rotate(), scale(), setSurface(), translate(), COME_MoleculesBone::updateInertiaTensor(), COME_MoleculesCartilage::updateSkin(), COME_MoleculesBone::updateSkin(), COME_Clamp::updateSkin(), COME_MoleculesCartilage::updateSurface(), and COME_MoleculesBone::updateSurface().

int COME_BioStructure::system [protected]

Definition at line 67 of file comebiostructure.h. Referenced by getSystem(), and setSystem().

int COME_BioStructure::type [protected]

Definition at line 72 of file comebiostructure.h. Referenced by globalToLocal(), and setType().

double COME_BioStructure::volume [protected]

Definition at line 68 of file comebiostructure.h. Referenced by COME_MoleculesCartilage::updateSurface(), and COME_MoleculesBone::updateSurface().

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

• comebiostructure.h
• comebiostructure.cpp

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