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Computer Assited Medical Intervention Tool Kit
version 3.3
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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... | |
Properties * | getProperties () |
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... | |
Component * | getExclusiveComponent (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... | |
MultiComponent * | getExclusiveComponents () const |
get all the exclusive components More... | |
MultiComponent * | getInformativeComponents () const |
get all the informative components More... | |
StructuralComponent * | getAtoms () const |
get all the atoms More... | |
Component * | getInformativeComponent (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... | |
Atom * | getAtom (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... | |
Cell * | getCell (const unsigned int id) |
get the cell that has the global index given in parameters. More... | |
Structure * | getStructureByName (const std::string n) |
get a cell using its name More... | |
Component * | getComponentByName (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... | |
StructuralComponent * | atoms |
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... | |
MultiComponent * | exclusiveComponents |
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... | |
MultiComponent * | informativeComponents |
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... | |
Properties * | properties |
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... | |
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...
PhysicalModel::PhysicalModel | ( | ) |
Default constructor : this one just initialize everything.
Structures and atoms are empty.
PhysicalModel::PhysicalModel | ( | const char * | fileName, |
PtrToSetProgressFunction | pspf = NULL |
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throw | ( | PMLAbortException | |
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Instanciate a physical model object using a XML native format file.
fileName | the name of the xml file to use |
pspf | is a pointer to the method that will be called by the setProgress(...) method (default = NULL) |
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virtual |
destructor
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).
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
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
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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???
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Get the atom that has the global index given in parameters.
id | the atom index in the physical model |
References atomMap, atoms, Structure::getIndex(), and StructuralComponent::getStructure().
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get all the atoms
References atoms.
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get the cell that has the global index given in parameters.
id | the cell index in the physical model |
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
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get all the exclusive components
References exclusiveComponents.
Component* PhysicalModel::getInformativeComponent | ( | const unsigned | int | ) | const |
get an informative component by its index in the list
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get all the informative components
References informativeComponents.
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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
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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.
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inline |
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initialization method
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check if something have changed
References isModifiedFlag.
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optimize atom and cell indexes so that each order number is equal to the index
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private |
optimize the indexes for a given multi component (new indexing will start using the parameter)
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read the atom list in the xml tree and build them.
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read the exclusive components list in the xml tree and build them.
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read the xml tree and call other parse methods to biuld the physicalModel.
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virtual |
Set the new position of an atom.
void PhysicalModel::setAtoms | ( | StructuralComponent * | , |
bool | deleteOld = true |
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set the atom structural component.
Becareful: the physical model takes control of this structural component
sc | the new atom structural component |
deleteOld | if 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
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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.
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set the name of the physical model
References properties, and Properties::setName().
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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.
donePercentage | the percentage (between 0 and 100) of the work already done |
void PhysicalModel::xmlPrint | ( | std::ostream & | o, |
bool | opt = false |
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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.
o | the ostream to write to |
opt | a boolean indicating if yes or no you want the pm to optimize the output |
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use the XML Parser/Reader to read an XML file conform to physicalmodel.dtd
n | the name of the XML file |
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the association couple list, which contains the direct map between the atom's global index and the atom ptr
Referenced by getAtom(), and getStructureByName().
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List of all the atoms : this is the basic stuff for a physicall model.
The smallest entity here
Referenced by getAtom(), and getAtoms().
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tell if optimizedCellList can be used
Referenced by getCell().
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the association couple list, which contains the direct map between the cell's global index and the cell ptr
Referenced by getCell(), and getStructureByName().
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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().
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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().
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is the current property state modified
Referenced by isModified(), and setModified().
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optimized consecutive cell vector (in here optimizedCellList[i]->getIndex() == i
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Referenced by getCell().
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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)
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all physical model properties
Referenced by getName(), getProperties(), and setName().
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the progress function
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static |
Current PML library version.