Computer Assited Medical Intervention Tool Kit  version 3.3
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PhysicalModel Class Reference

This is the main class of this project. More...

#include <PhysicalModel.h>

Public Member Functions

properties general manipulation
const std::string getName () const
 Return the name of the physical model. More...
 
void setName (const std::string)
 set the name of the physical model More...
 
PropertiesgetProperties ()
 get all properties (beware of what you do with them!): please consider calling setModified(). More...
 
bool isModified ()
 check if something have changed More...
 
void setModified ()
 tell the physical model something has changed (for example: a property was modified/added). More...
 
export to files
void xmlPrint (std::ostream &o, bool opt=false)
 print the physical model to an output stream in a XML format (see physicalmodel.xsd for detail about the XML format). More...
 
void exportPatran (std::string filename)
 Save the geometry (atoms/cells) of this PhysicalModel in the Patran format. More...
 
void exportAnsysMesh (std::string filename)
 Save the mesh (atoms/cells) of this PhysicalModel in the Ansys format. More...
 
component manipulations
unsigned int getNumberOfExclusiveComponents () const
 get the total number of exclusive components More...
 
unsigned int getNumberOfInformativeComponents () const
 get the total number of informative components More...
 
unsigned int getNumberOfAtoms () const
 get the number of atoms More...
 
unsigned int getNumberOfCells () const
 get the total nr of cell in the physical model (exclusive as well as informative) More...
 
ComponentgetExclusiveComponent (const unsigned int) const
 get an exclusive component by its index in the list More...
 
void setExclusiveComponents (MultiComponent *)
 set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent More...
 
MultiComponentgetExclusiveComponents () const
 get all the exclusive components More...
 
MultiComponentgetInformativeComponents () const
 get all the informative components More...
 
StructuralComponentgetAtoms () const
 get all the atoms More...
 
ComponentgetInformativeComponent (const unsigned int) const
 get an informative component by its index in the list More...
 
void setInformativeComponents (MultiComponent *)
 set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent More...
 
void setAtoms (StructuralComponent *, bool deleteOld=true)
 set the atom structural component. More...
 
bool addAtom (Atom *)
 Add a new atom to the atoms' structural component. More...
 
AtomgetAtom (const unsigned int id)
 Get the atom that has the global index given in parameters. More...
 
bool addGlobalIndexAtomPair (std::GlobalIndexStructurePair)
 add or update a pair to the atom map. More...
 
bool addGlobalIndexCellPair (std::GlobalIndexStructurePair)
 add or update a pair to the cell map. More...
 
CellgetCell (const unsigned int id)
 get the cell that has the global index given in parameters. More...
 
StructuregetStructureByName (const std::string n)
 get a cell using its name More...
 
ComponentgetComponentByName (const std::string n)
 get a structural or multi component by its name. More...
 
virtual void setProgress (const float donePercentage)
 this method is called during a long process everytime a little bit of the process is finished. More...
 
virtual void setAtomPosition (Atom *atom, const double pos[3])
 Set the new position of an atom. More...
 
double * getPositionPointer () const
 get the pointer to the memory space allocated for the atom's position. More...
 
double * getPositionPointer (const unsigned int index) const
 get the pointer to the memory space allocated for atom #index's position (using global index) More...
 
double * getPositionPointer (const Atom *a) const
 get the pointer to the memory space allocated for a given atom More...
 

Private Member Functions

void clear ()
 Clear everything. That allows to restart an allready instanciated object from scratch. More...
 
void init ()
 initialization method More...
 
void optimizeIndexes ()
 optimize atom and cell indexes so that each order number is equal to the index More...
 
void optimizeIndexes (MultiComponent *, unsigned int *)
 optimize the indexes for a given multi component (new indexing will start using the parameter) More...
 
bool parseAtoms (xmlNodePtr atomsRoot)
 read the atom list in the xml tree and build them. More...
 
bool parseComponents (xmlNodePtr exclusiveRoot, Component *father, bool isExclusive)
 read the exclusive components list in the xml tree and build them. More...
 
bool parseTree (xmlNodePtr root)
 read the xml tree and call other parse methods to biuld the physicalModel. More...
 
void xmlRead (const char *n)
 use the XML Parser/Reader to read an XML file conform to physicalmodel.dtd More...
 

Private Attributes

std::GlobalIndexStructureMap atomMap
 the association couple list, which contains the direct map between the atom's global index and the atom ptr More...
 
StructuralComponentatoms
 List of all the atoms : this is the basic stuff for a physicall model. More...
 
bool cellIndexOptimized
 tell if optimizedCellList can be used More...
 
std::GlobalIndexStructureMap cellMap
 the association couple list, which contains the direct map between the cell's global index and the cell ptr More...
 
MultiComponentexclusiveComponents
 Exclusive components are the non-overlaping components : they defined all the components of the physicalModel and the physicalModel could be defined by all this components. More...
 
MultiComponentinformativeComponents
 Informative components could be overlaping with other components : they are extra components that give information about group of cells. More...
 
bool isModifiedFlag
 is the current property state modified More...
 
std::vector< Cell * > optimizedCellList
 optimized consecutive cell vector (in here optimizedCellList[i]->getIndex() == i ) More...
 
double * positionPtr
 the big memory space where all the atom's position are stored (it is one big block, optimizing the memory cache management). Size = 3*nrOfAtoms*sizeof(double) More...
 
Propertiesproperties
 all physical model properties More...
 
PtrToSetProgressFunction setProgressFunction
 the progress function More...
 

constructors and destructors.

static const char * VERSION
 Current PML library version. More...
 
 PhysicalModel ()
 Default constructor : this one just initialize everything. More...
 
 PhysicalModel (const char *fileName, PtrToSetProgressFunction pspf=NULL) throw (PMLAbortException)
 Instanciate a physical model object using a XML native format file. More...
 
virtual ~PhysicalModel ()
 destructor More...
 

Detailed Description

This is the main class of this project.

Following a nice concept, a physical model is able to represent any kind of 3D physical model that appeared, appears or will appear on earth. This include FEM meshes, spring-mass networks, phymulob etc...

Constructor & Destructor Documentation

PhysicalModel::PhysicalModel ( )

Default constructor : this one just initialize everything.

Structures and atoms are empty.

PhysicalModel::PhysicalModel ( const char *  fileName,
PtrToSetProgressFunction  pspf = NULL 
)
throw (PMLAbortException
)

Instanciate a physical model object using a XML native format file.

Parameters
fileNamethe name of the xml file to use
pspfis a pointer to the method that will be called by the setProgress(...) method (default = NULL)
virtual PhysicalModel::~PhysicalModel ( )
virtual

destructor

Member Function Documentation

bool PhysicalModel::addAtom ( Atom )

Add a new atom to the atoms' structural component.

It does add the atom only if it has a unique index, otherwise nothing is done. (if index is correct, then it also call the addGlobalIndexAtomPair method).

Returns
true only if the atom was added
bool PhysicalModel::addGlobalIndexAtomPair ( std::GlobalIndexStructurePair  )

add or update a pair to the atom map.

It does nothing if the atom already exist in the map

Returns
true only if the atom was added
bool PhysicalModel::addGlobalIndexCellPair ( std::GlobalIndexStructurePair  )

add or update a pair to the cell map.

It does nothing if the cell already exist in the map

Returns
true only if the cell was added
void PhysicalModel::clear ( )
private

Clear everything. That allows to restart an allready instanciated object from scratch.

void PhysicalModel::exportAnsysMesh ( std::string  filename)

Save the mesh (atoms/cells) of this PhysicalModel in the Ansys format.

//@@ This method is usefull only for a FEM (?) mesh. Maybe it's better to put it in a femPM class that inherits PhysicalModel???

void PhysicalModel::exportPatran ( std::string  filename)

Save the geometry (atoms/cells) of this PhysicalModel in the Patran format.

%%% This method is usefull only for a FEM (?) mesh. Maybe it's better to put it in a femPM class that inherits PhysicalModel???

Atom * PhysicalModel::getAtom ( const unsigned int  id)
inline

Get the atom that has the global index given in parameters.

Parameters
idthe atom index in the physical model
Returns
the corresponding atom or NULL if non existant (i.e. no atoms have this index)

References atomMap, atoms, Structure::getIndex(), and StructuralComponent::getStructure().

StructuralComponent * PhysicalModel::getAtoms ( ) const
inline

get all the atoms

References atoms.

Cell * PhysicalModel::getCell ( const unsigned int  id)
inline

get the cell that has the global index given in parameters.

Parameters
idthe cell index in the physical model
Returns
the corresponding cell or NULL if non existant (i.e. no cels have this index)

References cellIndexOptimized, cellMap, and optimizedCellList.

Component* PhysicalModel::getComponentByName ( const std::string  n)

get a structural or multi component by its name.

Becareful: this method never returns a cell (only a structural component or a multiple component. To get a cell, use getStructureByName(..)

Component* PhysicalModel::getExclusiveComponent ( const unsigned  int) const

get an exclusive component by its index in the list

MultiComponent * PhysicalModel::getExclusiveComponents ( ) const
inline

get all the exclusive components

References exclusiveComponents.

Component* PhysicalModel::getInformativeComponent ( const unsigned  int) const

get an informative component by its index in the list

MultiComponent * PhysicalModel::getInformativeComponents ( ) const
inline

get all the informative components

References informativeComponents.

const std::string PhysicalModel::getName ( ) const
inline

Return the name of the physical model.

References Properties::getName(), and properties.

unsigned int PhysicalModel::getNumberOfAtoms ( ) const

get the number of atoms

unsigned int PhysicalModel::getNumberOfCells ( ) const

get the total nr of cell in the physical model (exclusive as well as informative)

unsigned int PhysicalModel::getNumberOfExclusiveComponents ( ) const

get the total number of exclusive components

unsigned int PhysicalModel::getNumberOfInformativeComponents ( ) const

get the total number of informative components

double* PhysicalModel::getPositionPointer ( ) const

get the pointer to the memory space allocated for the atom's position.

The memory is a big block of size getNumberOfAtoms()*3*sizeof(double). The atom positions are stored in the same order as in the atoms structural component

double* PhysicalModel::getPositionPointer ( const unsigned int  index) const

get the pointer to the memory space allocated for atom #index's position (using global index)

double* PhysicalModel::getPositionPointer ( const Atom a) const

get the pointer to the memory space allocated for a given atom

Properties * PhysicalModel::getProperties ( )
inline

get all properties (beware of what you do with them!): please consider calling setModified().

When you modify/add a property (or the physical model or any component/structure), you should always call setModified() in order to specify that something has changed.

References properties.

Structure * PhysicalModel::getStructureByName ( const std::string  n)
inline

get a cell using its name

References atomMap, and cellMap.

void PhysicalModel::init ( )
private

initialization method

bool PhysicalModel::isModified ( )
inline

check if something have changed

References isModifiedFlag.

void PhysicalModel::optimizeIndexes ( )
private

optimize atom and cell indexes so that each order number is equal to the index

void PhysicalModel::optimizeIndexes ( MultiComponent ,
unsigned int *   
)
private

optimize the indexes for a given multi component (new indexing will start using the parameter)

bool PhysicalModel::parseAtoms ( xmlNodePtr  atomsRoot)
private

read the atom list in the xml tree and build them.

bool PhysicalModel::parseComponents ( xmlNodePtr  exclusiveRoot,
Component father,
bool  isExclusive 
)
private

read the exclusive components list in the xml tree and build them.

bool PhysicalModel::parseTree ( xmlNodePtr  root)
private

read the xml tree and call other parse methods to biuld the physicalModel.

virtual void PhysicalModel::setAtomPosition ( Atom atom,
const double  pos[3] 
)
virtual

Set the new position of an atom.

void PhysicalModel::setAtoms ( StructuralComponent ,
bool  deleteOld = true 
)

set the atom structural component.

Becareful: the physical model takes control of this structural component

Parameters
scthe new atom structural component
deleteOldif true, then the old atoms SC is delete (thus deleting its atoms as well)
void PhysicalModel::setExclusiveComponents ( MultiComponent )

set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent

void PhysicalModel::setInformativeComponents ( MultiComponent )

set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent

void PhysicalModel::setModified ( )
inline

tell the physical model something has changed (for example: a property was modified/added).

This can be useful to check if something has changed since the PhysicalModel was created.

References isModifiedFlag.

void PhysicalModel::setName ( const std::string  n)
inline

set the name of the physical model

References properties, and Properties::setName().

virtual void PhysicalModel::setProgress ( const float  donePercentage)
virtual

this method is called during a long process everytime a little bit of the process is finished.

This method should be overloaded by the subclass to give a mean to produce a progress bar or equivalent gui/hmi stuff.

Parameters
donePercentagethe percentage (between 0 and 100) of the work already done
void PhysicalModel::xmlPrint ( std::ostream &  o,
bool  opt = false 
)

print the physical model to an output stream in a XML format (see physicalmodel.xsd for detail about the XML format).

By default the output is not optimized (optimized = faster loading). In order to optimize, the cell and atom indexes are renumbered to be consecutive, so access to celli or atomi is done in linear time. There are many reasons why you would not want to optimize the output, e.g. if you have a specific cell numbering that you are using somewhere else, in a different software or so.

Parameters
othe ostream to write to
opta boolean indicating if yes or no you want the pm to optimize the output
void PhysicalModel::xmlRead ( const char *  n)
private

use the XML Parser/Reader to read an XML file conform to physicalmodel.dtd

Parameters
nthe name of the XML file

Member Data Documentation

std::GlobalIndexStructureMap PhysicalModel::atomMap
private

the association couple list, which contains the direct map between the atom's global index and the atom ptr

Referenced by getAtom(), and getStructureByName().

StructuralComponent* PhysicalModel::atoms
private

List of all the atoms : this is the basic stuff for a physicall model.

The smallest entity here

Referenced by getAtom(), and getAtoms().

bool PhysicalModel::cellIndexOptimized
private

tell if optimizedCellList can be used

Referenced by getCell().

std::GlobalIndexStructureMap PhysicalModel::cellMap
private

the association couple list, which contains the direct map between the cell's global index and the cell ptr

Referenced by getCell(), and getStructureByName().

MultiComponent* PhysicalModel::exclusiveComponents
private

Exclusive components are the non-overlaping components : they defined all the components of the physicalModel and the physicalModel could be defined by all this components.

exclusiveComponents could only contains StructuralComponents...

Referenced by getExclusiveComponents().

MultiComponent* PhysicalModel::informativeComponents
private

Informative components could be overlaping with other components : they are extra components that give information about group of cells.

This components are not mandatory.

Referenced by getInformativeComponents().

bool PhysicalModel::isModifiedFlag
private

is the current property state modified

Referenced by isModified(), and setModified().

std::vector<Cell *> PhysicalModel::optimizedCellList
private

optimized consecutive cell vector (in here optimizedCellList[i]->getIndex() == i )

Referenced by getCell().

double* PhysicalModel::positionPtr
private

the big memory space where all the atom's position are stored (it is one big block, optimizing the memory cache management). Size = 3*nrOfAtoms*sizeof(double)

Properties* PhysicalModel::properties
private

all physical model properties

Referenced by getName(), getProperties(), and setName().

PtrToSetProgressFunction PhysicalModel::setProgressFunction
private

the progress function

const char* PhysicalModel::VERSION
static

Current PML library version.


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