COPASI API  4.16.103
Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
COptMethodStatistics Class Reference

#include <COptMethodStatistics.h>

Inheritance diagram for COptMethodStatistics:
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Collaboration diagram for COptMethodStatistics:
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Public Member Functions

 COptMethodStatistics (const COptMethodStatistics &src)
 
virtual bool optimise ()
 
virtual ~COptMethodStatistics ()
 
- Public Member Functions inherited from COptMethod
 COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL)
 
bool isBounded (void)
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
void setProblem (COptProblem *problem)
 
virtual ~COptMethod ()
 
- Public Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)
 
const CCopasiMethod::SubTypegetSubType () const
 
const CCopasiTask::TypegetType () const
 
virtual void load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
 
virtual void print (std::ostream *ostream) const
 
virtual void printResult (std::ostream *ostream) const
 
virtual bool setCallBack (CProcessReport *pCallBack)
 
virtual ~CCopasiMethod ()
 
- Public Member Functions inherited from CCopasiParameterGroup
bool addGroup (const std::string &name)
 
bool addParameter (const CCopasiParameter &parameter)
 
bool addParameter (const std::string &name, const CCopasiParameter::Type type)
 
template<class CType >
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)
 
void addParameter (CCopasiParameter *pParameter)
 
CCopasiParameterGroupassertGroup (const std::string &name)
 
template<class CType >
CCopasiParameterassertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)
 
index_iterator beginIndex () const
 
name_iterator beginName () const
 
 CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)
 
 CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")
 
void clear ()
 
virtual bool elevateChildren ()
 
index_iterator endIndex () const
 
name_iterator endName () const
 
CCopasiParameterGroupgetGroup (const std::string &name)
 
const CCopasiParameterGroupgetGroup (const std::string &name) const
 
CCopasiParameterGroupgetGroup (const size_t &index)
 
const CCopasiParameterGroupgetGroup (const size_t &index) const
 
size_t getIndex (const std::string &name) const
 
std::string getKey (const std::string &name) const
 
std::string getKey (const size_t &index) const
 
virtual const std::string & getName (const size_t &index) const
 
virtual const CObjectInterfacegetObject (const CCopasiObjectName &cn) const
 
CCopasiParametergetParameter (const std::string &name)
 
const CCopasiParametergetParameter (const std::string &name) const
 
CCopasiParametergetParameter (const size_t &index)
 
const CCopasiParametergetParameter (const size_t &index) const
 
CCopasiParameter::Type getType (const std::string &name) const
 
CCopasiParameter::Type getType (const size_t &index) const
 
std::string getUniqueParameterName (const CCopasiParameter *pParameter) const
 
const CCopasiParameter::ValuegetValue (const std::string &name) const
 
const CCopasiParameter::ValuegetValue (const size_t &index) const
 
CCopasiParameter::ValuegetValue (const std::string &name)
 
CCopasiParameter::ValuegetValue (const size_t &index)
 
CCopasiParameterGroupoperator= (const CCopasiParameterGroup &rhs)
 
bool removeParameter (const std::string &name)
 
bool removeParameter (const size_t &index)
 
template<class CType >
bool setValue (const std::string &name, const CType &value)
 
template<class CType >
bool setValue (const size_t &index, const CType &value)
 
size_t size () const
 
bool swap (const size_t &iFrom, const size_t &iTo)
 
bool swap (index_iterator &from, index_iterator &to)
 
virtual ~CCopasiParameterGroup ()
 
- Public Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)
 
 CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter")
 
virtual CCopasiObjectName getCN () const
 
virtual const std::string & getKey () const
 
virtual std::string getObjectDisplayName (bool regular=true, bool richtext=false) const
 
const CCopasiParameter::TypegetType () const
 
const ValuegetValue () const
 
ValuegetValue ()
 
virtual voidgetValuePointer () const
 
CCopasiObjectgetValueReference () const
 
bool isValidValue (const C_FLOAT64 &value) const
 
bool isValidValue (const C_INT32 &value) const
 
bool isValidValue (const unsigned C_INT32 &value) const
 
bool isValidValue (const bool &value) const
 
bool isValidValue (const std::string &value) const
 
bool isValidValue (const CCopasiObjectName &value) const
 
bool isValidValue (const std::vector< CCopasiParameter * > &value) const
 
CCopasiParameteroperator= (const CCopasiParameter &rhs)
 
template<class CType >
bool setValue (const CType &value)
 
bool setValue (const std::vector< CCopasiParameter * > &value)
 
virtual ~CCopasiParameter ()
 
- Public Member Functions inherited from CCopasiContainer
virtual bool add (CCopasiObject *pObject, const bool &adopt=true)
 
 CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)
 
 CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)
 
virtual std::string getChildObjectUnits (const CCopasiObject *pObject) const
 
virtual const objectMapgetObjects () const
 
virtual std::string getUnits () const
 
virtual const CCopasiObjectgetValueObject () const
 
virtual bool remove (CCopasiObject *pObject)
 
virtual ~CCopasiContainer ()
 
- Public Member Functions inherited from CCopasiObject
void addDirectDependency (const CCopasiObject *pObject)
 
 CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)
 
void clearDirectDependencies ()
 
void clearRefresh ()
 
bool dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const
 
void getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const
 
virtual const DataObjectSetgetDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
 
CCopasiContainergetObjectAncestor (const std::string &type) const
 
CCopasiDataModelgetObjectDataModel ()
 
const CCopasiDataModelgetObjectDataModel () const
 
const std::string & getObjectName () const
 
CCopasiContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const
CObjectInterface::ObjectSet
getPrerequisites () const
 
virtual RefreshgetRefresh () const
 
UpdateMethodgetUpdateMethod () const
 
bool hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
 
bool hasUpdateMethod () const
 
bool isArray () const
 
bool isContainer () const
 
bool isDataModel () const
 
bool isMatrix () const
 
bool isNameVector () const
 
bool isNonUniqueName () const
 
virtual bool isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
 
bool isReference () const
 
bool isRoot () const
 
bool isSeparator () const
 
bool isStaticString () const
 
bool isValueBool () const
 
bool isValueDbl () const
 
bool isValueInt () const
 
bool isValueInt64 () const
 
bool isValueString () const
 
bool isVector () const
 
virtual bool mustBeDeleted (const DataObjectSet &deletedObjects) const
 
void removeDirectDependency (const CCopasiObject *pObject)
 
void setDirectDependencies (const DataObjectSet &directDependencies)
 
bool setObjectName (const std::string &name)
 
virtual bool setObjectParent (const CCopasiContainer *pParent)
 
void setObjectValue (const C_FLOAT64 &value)
 
void setObjectValue (const C_INT32 &value)
 
void setObjectValue (const bool &value)
 
template<class CType >
void setRefresh (CType *pType, void(CType::*method)(void))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
 
virtual ~CCopasiObject ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
virtual ~CObjectInterface ()
 

Private Member Functions

 COptMethodStatistics ()
 
bool evaluate (const CVector< C_FLOAT64 > &individual)
 
virtual bool initialize ()
 

Private Attributes

C_FLOAT64 mBestValue
 
CVector< C_FLOAT64mIndividual
 
C_FLOAT64 mValue
 
size_t mVariableSize
 

Friends

COptMethodCOptMethod::createMethod (CCopasiMethod::SubType subType)
 

Additional Inherited Members

- Public Types inherited from CCopasiMethod
enum  SubType {
  unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing,
  CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm,
  EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR,
  HookeJeeves, LevenbergMarquardt, NelderMead, SRES,
  Statistics, ParticleSwarm, Praxis, TruncatedNewton,
  Newton, deterministic, LSODAR, directMethod,
  stochastic, tauLeap, adaptiveSA, hybrid,
  hybridLSODA, hybridODE45, DsaLsodar, tssILDM,
  tssILDMModified, tssCSP, mcaMethodReder, scanMethod,
  lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm,
  EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation
}
 
- Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator index_iterator
 
typedef
CCopasiContainer::objectMap::iterator 
name_iterator
 
typedef std::vector
< CCopasiParameter * > 
parameterGroup
 
- Public Types inherited from CCopasiParameter
enum  Type {
  DOUBLE = 0, UDOUBLE, INT, UINT,
  BOOL, GROUP, STRING, CN,
  KEY, FILE, EXPRESSION, INVALID
}
 
- Public Types inherited from CCopasiContainer
typedef std::multimap
< std::string, CCopasiObject * > 
objectMap
 
- Public Types inherited from CCopasiObject
typedef std::set< const
CCopasiObject * > 
DataObjectSet
 
typedef std::vector< Refresh * > DataUpdateSequence
 
- Public Types inherited from CObjectInterface
typedef std::set< const
CObjectInterface * > 
ObjectSet
 
typedef std::vector
< CObjectInterface * > 
UpdateSequence
 
- Static Public Member Functions inherited from COptMethod
static COptMethodcreateMethod (CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch)
 
- Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * > buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
 
static void setRenameHandler (CRenameHandler *rh)
 
- Static Public Attributes inherited from CCopasiMethod
static const std::string SubTypeName []
 
static const char * XMLSubType []
 
- Static Public Attributes inherited from CCopasiParameter
static const std::string TypeName []
 
static const char * XMLType []
 
- Static Public Attributes inherited from CCopasiContainer
static const std::vector
< CCopasiContainer * > 
EmptyList
 
- Protected Types inherited from CCopasiObject
enum  Flag {
  Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8,
  Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80,
  ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800,
  Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000,
  Root = 0x10000, Gui = 0x20000
}
 
- Protected Member Functions inherited from COptMethod
virtual bool cleanup ()
 
 COptMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObjectaddMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
void initObjects ()
 
- Protected Member Functions inherited from CCopasiObject
 CCopasiObject ()
 
 CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
 
- Protected Attributes inherited from COptMethod
const bool mBounds
 
const std::vector< COptItem * > * mpOptContraints
 
const std::vector< COptItem * > * mpOptItem
 
COptProblemmpOptProblem
 
COptTaskmpParentTask
 
const std::vector
< UpdateMethod * > * 
mpSetCalculateVariable
 
- Protected Attributes inherited from CCopasiMethod
CProcessReportmpCallBack
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
CCopasiObjectmpValueReference
 
size_t mSize
 
Value mValue
 
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
 
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL
 

Detailed Description

Definition at line 36 of file COptMethodStatistics.h.

Constructor & Destructor Documentation

COptMethodStatistics::COptMethodStatistics ( )
private
COptMethodStatistics::COptMethodStatistics ( const COptMethodStatistics src)

Copy Constructor

Parameters
constCOptMethodStatistics & src

Definition at line 41 of file COptMethodStatistics.cpp.

References CCopasiContainer::initObjects().

41  :
42  COptMethod(src)
43 {initObjects();}
COptMethodStatistics::~COptMethodStatistics ( )
virtual

Destructor

Definition at line 48 of file COptMethodStatistics.cpp.

References COptMethod::cleanup().

49 {//*** added similar to coptga
50  cleanup();
51 }
virtual bool cleanup()
Definition: COptMethod.cpp:215

Member Function Documentation

bool COptMethodStatistics::evaluate ( const CVector< C_FLOAT64 > &  individual)
private

Evaluate the fitness of one individual

Parameters
constCVector< C_FLOAT64 > & individual
Returns
bool continue

Definition at line 124 of file COptMethodStatistics.cpp.

References COptProblem::calculate(), COptProblem::checkFunctionalConstraints(), COptProblem::getCalculateValue(), max, COptMethod::mpOptProblem, and mValue.

Referenced by optimise().

125 {
126  bool Continue = true;
127 
128  // We do not need to check whether the parametric constraints are fulfilled
129  // since the parameters are created within the bounds.
130 
131  // evaluate the fitness
132  Continue = mpOptProblem->calculate();
133 
134  // check whether the functional constraints are fulfilled
137  else
139 
140  return Continue;
141 }
COptProblem * mpOptProblem
Definition: COptMethod.h:56
virtual bool calculate()
virtual bool checkFunctionalConstraints()
const C_FLOAT64 & getCalculateValue() const
#define max(a, b)
Definition: f2c.h:176
bool COptMethodStatistics::initialize ( )
privatevirtual

Initialize arrays and pointer.

Returns
bool success

Optimizer Function Returns: true if properly initialized should return a boolean

Reimplemented from COptMethod.

Definition at line 58 of file COptMethodStatistics.cpp.

References COptMethod::cleanup(), COptMethod::initialize(), mBestValue, mIndividual, COptMethod::mpOptItem, mVariableSize, and CVector< CType >::resize().

Referenced by optimise().

59 {
60  cleanup();
61 
62  if (!COptMethod::initialize()) return false;
63 
64  mBestValue = std::numeric_limits< C_FLOAT64 >::infinity();
65 
66  mVariableSize = mpOptItem->size();
68 
69  return true;
70 }
virtual bool initialize()
Definition: COptMethod.cpp:189
CVector< C_FLOAT64 > mIndividual
void resize(size_t size, const bool &copy=false)
Definition: CVector.h:301
virtual bool cleanup()
Definition: COptMethod.cpp:215
const std::vector< COptItem * > * mpOptItem
Definition: COptMethod.h:70
bool COptMethodStatistics::optimise ( void  )
virtual

Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback.

Optimizer Function Returns: nothing should return a boolean

Reimplemented from COptMethod.

Definition at line 77 of file COptMethodStatistics.cpp.

References C_FLOAT64, COptItem::checkConstraint(), COutputInterface::DURING, evaluate(), COptItem::getLowerBoundValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), initialize(), mBestValue, mIndividual, COptMethod::mpOptProblem, COptMethod::mpParentTask, mValue, mVariableSize, CCopasiTask::output(), and COptProblem::setSolution().

78 {
79  bool Continue = true;
80 
81  if (!initialize()) return false;
82 
83  size_t j;
84 
85  // Initialize the population
86  // first individual is the initial guess
87  for (j = 0; j < mVariableSize; j++)
88  {
89  C_FLOAT64 & mut = mIndividual[j];
90  COptItem & OptItem = *(*mpOptItem)[j];
91 
92  mut = OptItem.getStartValue();
93 
94  // force it to be within the bounds
95  switch (OptItem.checkConstraint(mut))
96  {
97  case - 1:
98  mut = *OptItem.getLowerBoundValue();
99  break;
100 
101  case 1:
102  mut = *OptItem.getUpperBoundValue();
103  break;
104  }
105 
106  // We need to set the value here so that further checks take
107  // account of the value.
108  (*(*mpSetCalculateVariable)[j])(mut);
109  }
110 
111  Continue = evaluate(mIndividual);
112 
113  mBestValue = mValue;
115 
116  // We found a new best value lets report it.
117  //if (mpReport) mpReport->printBody();
119 
120  return true;
121 }
virtual C_INT32 checkConstraint() const
Definition: COptItem.cpp:401
COptTask * mpParentTask
Definition: COptMethod.h:58
CVector< C_FLOAT64 > mIndividual
bool evaluate(const CVector< C_FLOAT64 > &individual)
COptProblem * mpOptProblem
Definition: COptMethod.h:56
virtual void output(const COutputInterface::Activity &activity)
const C_FLOAT64 * getLowerBoundValue() const
Definition: COptItem.h:191
virtual bool setSolution(const C_FLOAT64 &value, const CVector< C_FLOAT64 > &variables)
const C_FLOAT64 & getStartValue() const
Definition: COptItem.cpp:199
#define C_FLOAT64
Definition: copasi.h:92
const C_FLOAT64 * getUpperBoundValue() const
Definition: COptItem.h:198

Friends And Related Function Documentation

Member Data Documentation

C_FLOAT64 COptMethodStatistics::mBestValue
private

The best value found so far.

Definition at line 78 of file COptMethodStatistics.h.

Referenced by initialize(), and optimise().

CVector<C_FLOAT64> COptMethodStatistics::mIndividual
private

a vector of the number of individuals.

Definition at line 63 of file COptMethodStatistics.h.

Referenced by initialize(), and optimise().

C_FLOAT64 COptMethodStatistics::mValue
private

array of values of objective function f/ individuals

Definition at line 68 of file COptMethodStatistics.h.

Referenced by evaluate(), and optimise().

size_t COptMethodStatistics::mVariableSize
private

*** Perhaps this is actually not needed ****number of parameters

Definition at line 73 of file COptMethodStatistics.h.

Referenced by initialize(), and optimise().


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