#include <CSensMethod.h>

Inheritance diagram for CSensMethod:

Collaboration diagram for CSensMethod:

Public Member Functions
	CSensMethod (const CSensMethod &src, const CCopasiContainer *pParent=NULL)

size_t	getNumberOfSubtaskCalculations ()

bool	initialize (CSensProblem *problem)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

bool	process (CProcessReport *handler)

bool	restore (const bool &updateModel)

	~CSensMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)

const CCopasiMethod::SubType &	getSubType () const

const CCopasiTask::Type &	getType () 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)

CCopasiParameterGroup *	assertGroup (const std::string &name)

template<class CType >
CCopasiParameter *	assertParameter (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

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (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 CObjectInterface *	getObject (const CCopasiObjectName &cn) const

CCopasiParameter *	getParameter (const std::string &name)

const CCopasiParameter *	getParameter (const std::string &name) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (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::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (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::Type &	getType () const

const Value &	getValue () const

Value &	getValue ()

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () 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

CCopasiParameter &	operator= (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 objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () 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 DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () 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 ()

Static Public Member Functions
static CSensMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::sensMethod)

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)

Protected Member Functions
void	calculate_difference (size_t level, const C_FLOAT64 &delta, CCopasiArray &result, CCopasiArray::index_type &resultindex)

bool	calculate_one_level (size_t level, CCopasiArray &result)

	CSensMethod (CCopasiMethod::SubType subType, const CCopasiContainer *pParent=NULL)

void	do_collapsing ()

C_FLOAT64	do_collapsing_innerloop (CCopasiArray::index_type &fullindex)

void	do_scaling ()

bool	do_target_calculation (CCopasiArray &result, bool first)

C_FLOAT64	do_variation (CCopasiObject *variable)

void	scaling_targetfunction (const C_FLOAT64 &factor, CCopasiArray::index_type &resultindex)

void	scaling_variables (size_t level, const C_FLOAT64 &factor, CCopasiArray::index_type &resultindex)

void	setValue (CCopasiObject *variable, C_FLOAT64 value)

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 >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (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
std::vector< Refresh * >	mInitialRefreshes

std::vector< CSensMethodLocalData >	mLocalData

C_FLOAT64 *	mpDeltaFactor

C_FLOAT64 *	mpMinDelta

CSensProblem *	mpProblem

CCopasiTask *	mpSubTask

bool	mStoreSubtasktUpdateFlag
	stores the update model flag of the subtask More...

std::vector< CCopasiObject * >	mTargetfunctionPointers

Protected Attributes inherited from CCopasiMethod
CProcessReport *	mpCallBack

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
	CSensMethod ()

Private Attributes
size_t	mCounter

size_t	mFailedCounter

unsigned C_INT32	mProgress

size_t	mProgressHandler

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 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 }

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 49 of file CSensMethod.h.

Constructor & Destructor Documentation

CSensMethod::CSensMethod ( )

private

Default constructor.

Referenced by createMethod().

CSensMethod::CSensMethod	(	CCopasiMethod::SubType	subType,
		const CCopasiContainer *	pParent = `NULL`
	)

explicitprotected

Specific constructor.

Parameters

CCopasiMethod::SubType	subType
const	CCopasiContainer * pParent (default: NULL)

Default constructor.

Definition at line 55 of file CSensMethod.cpp.

References CCopasiParameterGroup::addParameter(), C_FLOAT64, CONSTRUCTOR_TRACE, CCopasiParameter::getValue(), mpDeltaFactor, mpMinDelta, CCopasiParameter::Value::pUDOUBLE, and CCopasiParameter::UDOUBLE.

                                                           :
   CCopasiMethod(CCopasiTask::sens, subType, pParent),
   mpProblem(NULL),
   mLocalData(),
   mTargetfunctionPointers(),
   mpSubTask(NULL),
   mInitialRefreshes(),
   mpDeltaFactor(NULL),
   mpMinDelta(NULL),
   mStoreSubtasktUpdateFlag(false),
   mProgressHandler(C_INVALID_INDEX),
   mProgress(0),
   mCounter(0),
   mFailedCounter(0)
 {
   addParameter("Delta factor",
                CCopasiParameter::UDOUBLE, (C_FLOAT64) 1e-3);
   mpDeltaFactor = (C_FLOAT64*)getValue("Delta factor").pUDOUBLE;
 
   addParameter("Delta minimum",
                CCopasiParameter::UDOUBLE, (C_FLOAT64) 1e-12);
   mpMinDelta = (C_FLOAT64*)getValue("Delta minimum").pUDOUBLE;
 
   CONSTRUCTOR_TRACE;
 }

CSensMethod::CSensMethod	(	const CSensMethod &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor.

Parameters

const CTSSMethod &	src
const	CCopasiContainer * pParent (default: NULL)

Copy constructor.

Parameters

const CSensMethod & src

Definition at line 86 of file CSensMethod.cpp.

References CONSTRUCTOR_TRACE.

                                                           :
   CCopasiMethod(src, pParent),
   mpProblem(src.mpProblem),
   mLocalData(),
   mTargetfunctionPointers(),
   mpSubTask(NULL),
   mInitialRefreshes(),
   mpDeltaFactor(NULL),
   mpMinDelta(NULL),
   mStoreSubtasktUpdateFlag(false),
   mProgressHandler(C_INVALID_INDEX),
   mProgress(0),
   mCounter(0),
   mFailedCounter(0)
 {CONSTRUCTOR_TRACE;}

CSensMethod::~CSensMethod ( )

Destructor.

Definition at line 106 of file CSensMethod.cpp.

References DESTRUCTOR_TRACE.

107 {DESTRUCTOR_TRACE;}

DESTRUCTOR_TRACE

#define DESTRUCTOR_TRACE

Definition: copasi.h:206

Member Function Documentation

void CSensMethod::calculate_difference	(	size_t	level,
		const C_FLOAT64 &	delta,
		CCopasiArray &	result,
		CCopasiArray::index_type &	resultindex
	)

protected

Definition at line 213 of file CSensMethod.cpp.

References C_INVALID_INDEX, and mLocalData.

Referenced by calculate_one_level().

 {
   assert(delta != 0.0);
   assert(mLocalData[level].tmp1.size() == mLocalData[level].tmp2.size());
   size_t dim = mLocalData[level].tmp1.dimensionality();
   assert(resultindex.size() >= dim);
 
   CCopasiArray::index_type indexmax = mLocalData[level].tmp1.size();
 
   //init index with zero
   CCopasiArray::index_type indexit; indexit.resize(dim);
   size_t i;
 
   for (i = 0; i < dim; ++i)
     indexit[i] = 0;
 
   //handle scalars separately
   if (dim == 0)
     {
       result[resultindex] = (mLocalData[level].tmp2[indexit] - mLocalData[level].tmp1[indexit]) / delta;
       return;
     }
 
   //now for all higher dimensionalities
   for (;;)
     {
       //do difference calculation
       for (i = 0; i < dim; ++i)
         resultindex[i] = indexit[i];  //TODO: use stl algorithm
 
       result[resultindex] = (mLocalData[level].tmp2[indexit] - mLocalData[level].tmp1[indexit]) / delta;
 
       //increase index
       ++indexit[dim - 1];
 
       //check overflow
       size_t j;
 
       for (j = dim - 1; j != C_INVALID_INDEX; --j)
         {
           if (indexit[j] >= indexmax[j])
             {
               indexit[j] = 0;
 
               if (j > 0)
                 ++indexit[j - 1];
               else
                 return;
             }
           else
             break;
         }
     }
 }

bool CSensMethod::calculate_one_level	(	size_t	level,
		CCopasiArray &	result
	)

protected

Definition at line 269 of file CSensMethod.cpp.

References C_FLOAT64, calculate_difference(), do_target_calculation(), do_variation(), CCopasiParameter::getValuePointer(), mLocalData, CCopasiArray::resize(), and setValue().

Referenced by process().

 {
   //do first calculation
   if (level == 0)
     {
       if (!do_target_calculation(mLocalData[level].tmp1, true)) return false;
     }
   else
     {
       if (!calculate_one_level(level - 1, mLocalData[level].tmp1)) return false;
     }
 
   //resize results array
   CCopasiArray::index_type resultindex; resultindex = mLocalData[level].tmp1.size();
 
   if (mLocalData[level].variables.size() > 1)
     resultindex.push_back(mLocalData[level].variables.size());
 
   result.resize(resultindex);
 
   //loop over all variables
   size_t i, imax = mLocalData[level].variables.size();
 
   for (i = 0; i < imax; ++i)
     {
       //store variable value
       C_FLOAT64 store = *(C_FLOAT64 *)mLocalData[level].variables[i]->getValuePointer();
 
       //change variable
       C_FLOAT64 delta = do_variation(mLocalData[level].variables[i]);
 
       //do second calculation
       if (level == 0)
         {
           if (!do_target_calculation(mLocalData[level].tmp2, false)) return false;
         }
       else
         {
           if (!calculate_one_level(level - 1, mLocalData[level].tmp2)) return false;
         }
 
       //restore variable
       //mLocalData[level].variables[i]->setObjectValue(store);
       setValue(mLocalData[level].variables[i], store);
 
       //calculate derivative
       if (imax > 1)
         resultindex[resultindex.size() - 1] = i;
 
       calculate_difference(level, delta, result, resultindex);
     }
 
   return true;
 }

CSensMethod * CSensMethod::createMethod ( CCopasiMethod::SubType subType = CCopasiMethod::sensMethod )

static

Create a trajectory method. Note: the returned object has to be released after use with delete

CSensMethod class.

Definition at line 34 of file CSensMethod.cpp.

References CSensMethod(), fatalError, CCopasiMethod::sensMethod, and CCopasiMethod::unset.

Referenced by SensitivitiesWidget::createMethod(), and CSensTask::createMethod().

 {
   CSensMethod * pMethod = NULL;
 
   switch (subType)
     {
       case unset:
       case sensMethod:
         pMethod = new CSensMethod(subType);
         break;
 
       default:
         fatalError();
     }
 
   return pMethod;
 }

void CSensMethod::do_collapsing ( )

protected

collapse the first dimension of the scaled result (by calculating the 2-norm over the target functions)

Definition at line 437 of file CSensMethod.cpp.

References C_INVALID_INDEX, CSensProblem::collapsRequested(), do_collapsing_innerloop(), CSensProblem::getCollapsedResult(), CSensProblem::getScaledResult(), mpProblem, and CCopasiArray::size().

Referenced by process().

 {
   if (mpProblem->collapsRequested())
     {
       CCopasiArray::index_type fullresultindex = mpProblem->getScaledResult().size();
       CCopasiArray::index_type collapsedresultindex = mpProblem->getCollapsedResult().size();
 
       size_t shift = fullresultindex.size() - collapsedresultindex.size();
 
       if (shift != 1) return; //only supported if target functions list is 1D
 
       //***** skalar ********
       if (collapsedresultindex.size() == 0)
         {
           mpProblem->getCollapsedResult()[collapsedresultindex] =
             do_collapsing_innerloop(fullresultindex);
           return;
         }
 
       //***** higher dimensions *********
       size_t i, dim = collapsedresultindex.size();
       CCopasiArray::index_type indexmax = mpProblem->getCollapsedResult().size();
 
       //set index to zero
       for (i = 0; i < dim; ++i) collapsedresultindex[i] = 0;
 
       for (;;)
         {
           fullresultindex[0] = 0;
 
           for (i = 0; i < dim; ++i)
             fullresultindex[i + shift] = collapsedresultindex[i];
 
           mpProblem->getCollapsedResult()[collapsedresultindex] =
             do_collapsing_innerloop(fullresultindex);
 
           //increase index
           ++collapsedresultindex[dim - 1];
 
           //check overflow
           size_t j;
 
           for (j = dim - 1; j != C_INVALID_INDEX; --j)
             {
               if (collapsedresultindex[j] >= indexmax[j])
                 {
                   collapsedresultindex[j] = 0;
 
                   if (j > 0)
                     ++collapsedresultindex[j - 1];
                   else
                     return;
                 }
               else
                 break;
             }
         }
     }
   else
     {}
 }

C_FLOAT64 CSensMethod::do_collapsing_innerloop ( CCopasiArray::index_type & fullindex )

protected

Definition at line 413 of file CSensMethod.cpp.

References C_FLOAT64, CSensProblem::getScaledResult(), max, mpProblem, and CCopasiArray::size().

Referenced by do_collapsing().

 {
   //fullindex[0]=0;
   //return mpProblem->getScaledResult()[fullindex];
 
   //assumes the sum is to be taken over the first dim of the scaled result array
   C_FLOAT64 tmpFloat, tmpSum = 0;
   size_t i, imax = mpProblem->getScaledResult().size()[0];
 
   for (i = 0; i < imax; ++i)
     {
       fullindex[0] = i;
       tmpFloat = mpProblem->getScaledResult()[fullindex];
 
       if (tmpFloat != tmpFloat) continue;
 
       if (fabs(tmpFloat) >= std::numeric_limits< C_FLOAT64 >::max()) continue;
 
       tmpSum += tmpFloat * tmpFloat;
     }
 
   return sqrt(tmpSum);
 }

void CSensMethod::do_scaling ( )

protected

calculate the scaled sensitivities. Calls scaling_variables(). It is assumed that the scaled result array is already of the correct size (this is done in initialize()).

Definition at line 404 of file CSensMethod.cpp.

References CCopasiArray::dimensionality(), CSensProblem::getResult(), mLocalData, mpProblem, and scaling_variables().

Referenced by process().

 {
   CCopasiArray::index_type index;
   index.resize(mpProblem->getResult().dimensionality());
   scaling_variables(mLocalData.size() - 1, 1.0, index);
 }

bool CSensMethod::do_target_calculation	(	CCopasiArray &	result,
		bool	first
	)

protected

Definition at line 111 of file CSensMethod.cpp.

References C_FLOAT64, CCopasiProblem::getModel(), CCopasiParameter::getValuePointer(), mCounter, mFailedCounter, mInitialRefreshes, CCopasiMethod::mpCallBack, mpProblem, mProgress, mProgressHandler, mpSubTask, mTargetfunctionPointers, CCopasiTask::process(), CProcessReport::progressItem(), CCopasiArray::resize(), CModel::updateNonSimulatedValues(), and CModel::updateSimulatedValues().

Referenced by calculate_one_level().

 {
   bool success = false;
 
   //perform the necessary updates
   std::vector< Refresh * >::iterator it = mInitialRefreshes.begin();
   std::vector< Refresh * >::iterator end = mInitialRefreshes.end();
 
   while (it != end)
     (**it++)();
 
   //****** do subtask ******************
   if (mpSubTask != NULL)
     {
       success = mpSubTask->process(/*first*/true);
       mCounter++;
     }
   else
     {
       success = true; // doing nothing should never fail.
     }
 
   mpProblem->getModel()->updateSimulatedValues(true);
   mpProblem->getModel()->updateNonSimulatedValues();
 
   //****** retrieve results ************
 
   //resize results array
   CCopasiArray::index_type resultindex;
   size_t i, imax = mTargetfunctionPointers.size();
 
   if (imax > 1)
     resultindex.push_back(imax);
 
   result.resize(resultindex);
 
   //copy result
   if (success)
     {
       for (i = 0; i < imax; ++i)
         {
           if (imax > 1)
             resultindex[0] = i;
 
           result[resultindex] = *(C_FLOAT64 *)mTargetfunctionPointers[i]->getValuePointer();
         }
     }
   else
     {
       mFailedCounter++;
 
       for (i = 0; i < imax; ++i)
         {
           if (imax > 1)
             resultindex[0] = i;
 
           result[resultindex] = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
         }
     }
 
   //progress bar
   ++mProgress;
 
   if (mpCallBack)
     {
       bool tmp = mpCallBack->progressItem(mProgressHandler);
       return tmp;
     }
 
   return success;
 }

C_FLOAT64 CSensMethod::do_variation ( CCopasiObject * variable )

protected

Definition at line 183 of file CSensMethod.cpp.

References C_FLOAT64, CCopasiObject::getValuePointer(), mpDeltaFactor, mpMinDelta, and setValue().

Referenced by calculate_one_level().

 {
   C_FLOAT64 value;
   value = *(C_FLOAT64*)variable->getValuePointer();
   C_FLOAT64 delta;
   delta = fabs(value) * *mpDeltaFactor;
 
   if (delta < *mpMinDelta) delta = *mpMinDelta;
 
   setValue(variable, delta + value);
 
   return delta;
 }

size_t CSensMethod::getNumberOfSubtaskCalculations ( )

estimate how many calls to the subtask are necessary. Works only after initialize() was called.

Definition at line 686 of file CSensMethod.cpp.

References mLocalData.

Referenced by process().

 {
   size_t ret = 1;
   size_t i;
 
   for (i = 0; i < mLocalData.size(); ++i)
     {
       ret *= mLocalData[i].variables.size() + 1;
     }
 
   return ret;
 }

bool CSensMethod::initialize ( CSensProblem * problem )

initializes the subtask, creates the internal data structures of the method, resizes the result arrays and creates the array annotations

Definition at line 501 of file CSensMethod.cpp.

Referenced by CSensTask::updateMatrices().

 {
   bool success = true;
 
   mpProblem = problem;
   assert(mpProblem);
 
   //initialize the target calculation
   mpSubTask = NULL;
   CCopasiDataModel* pDataModel = getObjectDataModel();
   assert(pDataModel != NULL);
 
   switch (mpProblem->getSubTaskType())
     {
       case CSensProblem::Evaluation:
         mpSubTask = NULL;
         break;
 
       case CSensProblem::SteadyState:
         mpSubTask = dynamic_cast<CCopasiTask*>
                     ((*pDataModel->getTaskList())["Steady-State"]);
         break;
 
       case CSensProblem::TimeSeries:
         mpSubTask = dynamic_cast<CCopasiTask*>
                     ((*pDataModel->getTaskList())["Time-Course"]);
         break;
 
         /*    case CSensProblem::LyapunovExp:
               mpSubTask = dynamic_cast<CCopasiTask*>
                           ((*pDataModel->getTaskList())["Lyapunov Exponents"]);
               break;*/
 
       case CSensProblem::ParameterEstimation:
         mpSubTask = dynamic_cast<CCopasiTask*>
                     ((*pDataModel->getTaskList())["Parameter Estimation"]);
         break;
 
       case CSensProblem::Optimization:
         mpSubTask = dynamic_cast<CCopasiTask*>
                     ((*pDataModel->getTaskList())["Optimization"]);
         break;
 
       case CSensProblem::CrossSection:
         mpSubTask = dynamic_cast<CCopasiTask*>
                     ((*pDataModel->getTaskList())["Cross Section"]);
         break;
     }
 
   if (mpSubTask)
     {
       //the subtask should not change the initial state of the model
       mStoreSubtasktUpdateFlag = mpSubTask->isUpdateModel();
       mpSubTask->setUpdateModel(false);
       
       mpSubTask->getProblem()->setModel(mpProblem->getModel());
       mpSubTask->setCallBack(NULL);
       success &= mpSubTask->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
     }
 
   //initialize the variables pointers
   std::set< const CCopasiObject * > ObjectSet;
   size_t i, imax = mpProblem->getNumberOfVariables();
   mLocalData.resize(imax);
 
   for (i = 0; i < imax; ++i)
     {
       mLocalData[i].variables = mpProblem->getVariables(i).getVariablesPointerList(pDataModel);
 
       ObjectSet.insert(mLocalData[i].variables.begin(), mLocalData[i].variables.end());
     }
 
   //determine which refreshes need to be called when the variables are changed
   ObjectSet.erase(NULL);
   mInitialRefreshes.clear();
   mInitialRefreshes = mpProblem->getModel()->buildInitialRefreshSequence(ObjectSet);
 
   //initialize the target function pointers
   mTargetfunctionPointers = mpProblem->getTargetFunctions().getVariablesPointerList(pDataModel);
 
   //****** initialize result annotations ****************
 
   //determine dimensions of result
   CCopasiArray::index_type s;
   CCopasiArray::index_type sc; //size of collapsed result
 
   if (mTargetfunctionPointers.size() > 1)
     {
       s.push_back(mTargetfunctionPointers.size());
     }
 
   for (i = 0; i < imax; ++i)
     {
       if (mLocalData[i].variables.size() > 1)
         {
           mLocalData[i].index = s.size();
           s.push_back(mLocalData[i].variables.size());
           sc.push_back(mLocalData[i].variables.size());
         }
       else
         mLocalData[i].index = C_INVALID_INDEX;
     }
 
   //resize result & annotations
   mpProblem->getResult().resize(s);
   mpProblem->getResultAnnotated()->resize();
   //mpProblem->getResultAnnotated()->setMode(CArrayAnnotation::OBJECTS);
 
   mpProblem->getScaledResult().resize(s);
   mpProblem->getScaledResultAnnotated()->resize();
   //mpProblem->getScaledResultAnnotated()->setMode(CArrayAnnotation::OBJECTS);
 
   if (mpProblem->collapsRequested())
     {
       mpProblem->getCollapsedResult().resize(sc);
       mpProblem->getCollapsedResultAnnotated()->resize();
       //mpProblem->getCollapsedResultAnnotated()->setMode(CArrayAnnotation::OBJECTS);
     }
 
   size_t dim = 0;
   size_t j;
 
   //target function annotations //TODO: only implemented for scalar and vector
   if (mTargetfunctionPointers.size() > 1)
     {
       std::ostringstream tmp;
       tmp << "Target functions, " << mpProblem->getTargetFunctions().getListTypeDisplayName();
       mpProblem->getResultAnnotated()->setDimensionDescription(dim, tmp.str());
       mpProblem->getScaledResultAnnotated()->setDimensionDescription(dim, tmp.str());
 
       for (j = 0; j < mTargetfunctionPointers.size(); ++j)
         {
           mpProblem->getResultAnnotated()->setAnnotationCN(dim, j, mTargetfunctionPointers[j]->getCN());
           mpProblem->getScaledResultAnnotated()->setAnnotationCN(dim, j, mTargetfunctionPointers[j]->getCN());
         }
 
       ++dim;
     }
 
   //variables annotiation
   size_t dim2 = 0; //for collapsed result
 
   for (i = 0; i < imax; ++i)
     {
       if (mLocalData[i].variables.size() > 1)
         {
           std::ostringstream tmp;
           tmp << "Variables " << i + 1 << ", " << mpProblem->getVariables(i).getListTypeDisplayName();
           mpProblem->getResultAnnotated()->setDimensionDescription(dim, tmp.str());
           mpProblem->getScaledResultAnnotated()->setDimensionDescription(dim, tmp.str());
 
           if (mpProblem->collapsRequested())
             mpProblem->getCollapsedResultAnnotated()->setDimensionDescription(dim2, tmp.str());
 
           for (j = 0; j < mLocalData[i].variables.size(); ++j)
             {
               mpProblem->getResultAnnotated()->setAnnotationCN(dim, j, mLocalData[i].variables[j]->getCN());
               mpProblem->getScaledResultAnnotated()->setAnnotationCN(dim, j, mLocalData[i].variables[j]->getCN());
 
               if (mpProblem->collapsRequested())
                 mpProblem->getCollapsedResultAnnotated()->setAnnotationCN(dim2, j, mLocalData[i].variables[j]->getCN());
             }
 
           ++dim;
           ++dim2;
         }
     }
 
   return success;
 }

bool CSensMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CCopasiMethod.

Definition at line 738 of file CSensMethod.cpp.

References CCopasiMessage::EXCEPTION, and CCopasiMethod::isValidProblem().

 {
   if (!CCopasiMethod::isValidProblem(pProblem)) return false;
 
   const CSensProblem * pP = dynamic_cast<const CSensProblem *>(pProblem);
 
   if (!pP)
     {
       CCopasiMessage(CCopasiMessage::EXCEPTION, "Problem is not a sensitivities problem.");
       return false;
     }
 
   return true;
 
   //all sizes at least one
 
   //dimension of variables 0 or 1
 
   //if target is scan make sure the scan subtask is not sens.
 }

bool CSensMethod::process ( CProcessReport * handler )

Definition at line 699 of file CSensMethod.cpp.

References CProcessReport::addItem(), C_INT32, calculate_one_level(), do_collapsing(), do_scaling(), CProcessReport::finishItem(), getNumberOfSubtaskCalculations(), CSensProblem::getResult(), max, MCCopasiTask, mCounter, mFailedCounter, mLocalData, CCopasiMethod::mpCallBack, mpProblem, mProgress, mProgressHandler, mpSubTask, CCopasiTask::setCallBack(), CProcessReport::setName(), and CCopasiMessage::WARNING.

Referenced by CSensTask::process().

 {
   // Reset the evaluation counter
   mCounter = 0;
   mFailedCounter = 0;
 
   if (!mLocalData.size()) return false;
 
   //initialize progress bar
   mpCallBack = handler;
 
   if (mpCallBack)
     {
       mpCallBack->setName("performing sensitivities calculation...");
       unsigned C_INT32 max = (unsigned C_INT32) getNumberOfSubtaskCalculations();
       mProgress = 0;
       mProgressHandler = mpCallBack->addItem("Completion",
                                              mProgress,
                                              &max);
 
       if (mpSubTask)
         mpSubTask->setCallBack(mpCallBack);
     }
 
   if (!calculate_one_level(mLocalData.size() - 1, mpProblem->getResult())) return false;
 
   do_scaling();
 
   do_collapsing();
 
   if (mpCallBack) mpCallBack->finishItem(mProgressHandler);
 
   if (mFailedCounter * 20 > mCounter) // > 5% failure rate
     CCopasiMessage(CCopasiMessage::WARNING, MCCopasiTask + 8, mFailedCounter, mCounter);
 
   return true;
 }

bool CSensMethod::restore ( const bool & updateModel )

Do all necessary restore procedures so that the model is in the same state as before

Parameters

const bool & updateModel

Returns: bool success

Definition at line 672 of file CSensMethod.cpp.

References mpSubTask, mStoreSubtasktUpdateFlag, CCopasiTask::restore(), and CCopasiTask::setUpdateModel().

Referenced by CSensTask::restore().

 {
   bool success = true;
 
   if (mpSubTask != NULL)
   {
     success &= mpSubTask->restore();
 
     //restore the update model flag
     mpSubTask->setUpdateModel(mStoreSubtasktUpdateFlag);
   }
   return success;
 }

void CSensMethod::scaling_targetfunction	(	const C_FLOAT64 &	factor,
		CCopasiArray::index_type &	resultindex
	)

protected

This contains the loop over the target functions for scaling the sensitivities

Definition at line 326 of file CSensMethod.cpp.

References C_INVALID_INDEX, CSensProblem::getResult(), CSensProblem::getScaledResult(), mLocalData, and mpProblem.

Referenced by scaling_variables().

 {
   size_t dim = mLocalData[0].tmp1.dimensionality();
   assert(resultindex.size() >= dim);
 
   CCopasiArray::index_type indexmax = mLocalData[0].tmp1.size();
   //init index with zero
   CCopasiArray::index_type indexit; indexit.resize(dim);
   size_t i;
 
   for (i = 0; i < dim; ++i)
     indexit[i] = 0;
 
   //handle scalars separately
   if (dim == 0)
     {
       mpProblem->getScaledResult()[resultindex] = mpProblem->getResult()[resultindex] * factor / mLocalData[0].tmp1[indexit];
       return;
     }
 
   //now for all higher dimensionalities
   for (;;)
     {
       for (i = 0; i < dim; ++i)
         resultindex[i] = indexit[i];  //TODO: use stl algorithm
 
       mpProblem->getScaledResult()[resultindex] = mpProblem->getResult()[resultindex] * factor / mLocalData[0].tmp1[indexit];
 
       //increase index
       ++indexit[dim - 1];
 
       //check overflow
       size_t j;
 
       for (j = dim - 1; j != C_INVALID_INDEX; --j)
         {
           if (indexit[j] >= indexmax[j])
             {
               indexit[j] = 0;
 
               if (j > 0)
                 ++indexit[j - 1];
               else
                 return;
             }
           else
             break;
         }
     }
 }

void CSensMethod::scaling_variables	(	size_t	level,
		const C_FLOAT64 &	factor,
		CCopasiArray::index_type &	resultindex
	)

protected

This contains the loop over the variables for scaling the sensitivities. Works recursively and calls scaling_targetfunction() in the end.

Definition at line 378 of file CSensMethod.cpp.

References C_FLOAT64, CCopasiParameter::getValuePointer(), mLocalData, and scaling_targetfunction().

Referenced by do_scaling().

 {
   //loop over all variables
   size_t i, imax = mLocalData[level].variables.size();
 
   for (i = 0; i < imax; ++i)
     {
       //get Value
       C_FLOAT64 value = *(C_FLOAT64 *)mLocalData[level].variables[i]->getValuePointer() * factor;
 
       //do recursive calculation
       if (imax > 1)
         resultindex[mLocalData[level].index] = i;
 
       if (level == 0)
         {
           scaling_targetfunction(value, resultindex);
         }
       else
         {
           scaling_variables(level - 1, value, resultindex);
         }
     }
 }

void CSensMethod::setValue	(	CCopasiObject *	variable,
		C_FLOAT64	value
	)

protected

wraps the CCopasiObject::setObjectValue() method so we can add special treatment of concentrations

Definition at line 197 of file CSensMethod.cpp.

References CCopasiObject::getObjectAncestor(), CCopasiObject::getObjectName(), CMetab::refreshNumber(), CMetab::setConcentration(), and CCopasiObject::setObjectValue().

Referenced by calculate_one_level(), and do_variation().

 {
   variable->setObjectValue(value);
 
   if (variable->getObjectName() == "Concentration")
     {
       CMetab* pMetab = dynamic_cast<CMetab*>(variable->getObjectAncestor("Metabolite"));
 
       if (pMetab)
         {
           pMetab->setConcentration(value);
           pMetab->refreshNumber();
         }
     }
 }