Base object for Optimization methods. More...

Inheritance diagram for ObjCryst::OptimizationObj:

Collaboration diagram for ObjCryst::OptimizationObj:

Classes
struct	DynamicObjWeight

struct	LogLikelihoodStats
	Statistics about each object contributing to the overall Log(likelihood) More...

Public Member Functions
	OptimizationObj ()
	Default constructor.

	OptimizationObj (const string name)
	Constructor.

	OptimizationObj (const OptimizationObj &old)
	Copy constructor.

virtual	~OptimizationObj ()
	Destructor.

virtual void	RandomizeStartingConfig ()
	Randomize starting configuration. More...

virtual void	Optimize (long &nbSteps, const bool silent=false, const REAL finalcost=0, const REAL maxTime=-1)=0
	Launch optimization (a single run) for N steps. More...

virtual void	MultiRunOptimize (long &nbCycle, long &nbSteps, const bool silent=false, const REAL finalcost=0, const REAL maxTime=-1)=0
	Launch optimization for multiple runs of N steps. More...

void	FixAllPar ()
	Fix all parameters.

void	SetParIsFixed (const string &parName, const bool fix)
	Fix one parameter.

void	SetParIsFixed (const RefParType *type, const bool fix)
	Fix one family of parameters.

void	UnFixAllPar ()
	UnFix All parameters.

void	SetParIsUsed (const string &parName, const bool use)
	Set a parameter to be used.

void	SetParIsUsed (const RefParType *type, const bool use)
	Set a family of parameters to be used.

void	SetLimitsRelative (const string &parName, const REAL min, const REAL max)
	Change the relative limits for a parameter from its name.

void	SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
	Change the relative limits for a family of parameter.

void	SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
	Change the absolute limits for a parameter from its name.

void	SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
	Change the absolute limits for a family of parameter.

virtual REAL	GetLogLikelihood () const
	The optimized (minimized, actually) function. More...

void	StopAfterCycle ()
	Stop after the current cycle. USed for interactive refinement.

virtual void	DisplayReport ()
	Show report to the user during refinement. Used for GUI update.

void	AddRefinableObj (RefinableObj &)
	Add a refined object. All sub-objects are also added.

RefinableObj &	GetFullRefinableObj (const bool rebuild=true)
	Get the RefinableObj with all the parameters from all refined objects. More...

virtual void	XMLOutput (ostream &os, int indent=0) const =0
	Output a description of the object in XML format to a stream. More...

virtual void	XMLInput (istream &is, const XMLCrystTag &tag)=0
	Input in XML format from a stream, restoring the set of refined objects and the associated cost functions. More...

const string &	GetName () const
	Get the name for this object.

void	SetName (const string &)
	Set the name for this object.

virtual const string	GetClassName () const
	Get the name for this class type.

virtual void	Print () const
	Print some information about this object.

void	RestoreBestConfiguration ()
	Restore the Best configuration.

bool	IsOptimizing () const
	Are we busy optimizing ?

void	TagNewBestConfig ()
	During a global optimization, tell all objects that the current config is the latest "best" config.

REAL	GetLastOptimElapsedTime () const
	Get the elapsed time (in seconds) during the last optimization.

MainTracker &	GetMainTracker ()
	Get the MainTracker.

const MainTracker &	GetMainTracker () const
	Get the MainTracker.

RefObjOpt &	GetXMLAutoSaveOption ()

const RefObjOpt &	GetXMLAutoSaveOption () const

const REAL &	GetBestCost () const
	Access to current best cost.

REAL &	GetBestCost ()
	Access to current best cost.

virtual void	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	Begin optimization for all objects.

virtual void	EndOptimization ()
	End optimization for all objects.

virtual long &	NbTrialPerRun ()
	Number of trial per run.

virtual const long &	NbTrialPerRun () const
	Number of trial per run.

long	GetTrial () const
	Current trial number (updated during a run)

long	GetRun () const
	Current run number (updated during a run)

ObjRegistry< RefObjOpt > &	GetOptionList ()
	Access to the options registry.

unsigned int	GetNbOption () const
	Number of Options for this object.

RefObjOpt &	GetOption (const unsigned int i)
	Access to the options.

RefObjOpt &	GetOption (const string &name)
	Access to the options by name.

const RefObjOpt &	GetOption (const unsigned int i) const
	const access to the options

const RefObjOpt &	GetOption (const string &name) const
	const access to the options by name

const ObjRegistry< RefinableObj > &	GetRefinedObjList () const
	Access the list of refined object.

virtual void	UpdateDisplay () const
	Update Display (if any display is available), when a new 'relevant' configuration is reached. More...

unsigned int	GetNbParamSet () const
	Get the number of saved parameters set.

long	GetParamSetIndex (const unsigned int i) const
	Get the index of a saved parameters set in the compiled RefinableObj. More...

long	GetParamSetCost (const unsigned int i) const
	Get the cost (log-likelihood) of a saved parameters set.

void	RestoreParamSet (const unsigned int i, const bool update_display=true)
	Restore a given saved parameter set. More...

Protected Member Functions
void	PrepareRefParList ()

virtual void	InitOptions ()
	Initialization of options.

void	BuildRecursiveRefObjList ()
	(Re)build OptimizationObj::mRecursiveRefinedObjList, if an object has been added or modified. More...

void	AddOption (RefObjOpt *opt)

Protected Attributes
RefinableObj	mRefParList
	The refinable par list used during refinement. More...

string	mName
	Name of the GlobalOptimization object.

string	mSaveFileName
	File name where refinement info is saved (NOT USED so far...)

long	mNbTrialPerRun
	Number of trial per run, to be saved/restored in XML output.

long	mNbTrial
	Current trial number.

long	mRun
	Current run number (during multiple runs)

REAL	mBestCost
	Best value of the cost function so far.

long	mBestParSavedSetIndex
	Index of the 'best' saved parameter set.

unsigned long	mContext
	The current 'context', in the case the optimization is run in different parallel contexts.

map< unsigned long, map< const RefinableObj *, LogLikelihoodStats > >	mvContextObjStats
	Statistics for each context (mutable for dynamic update during optimization)

map< const RefinableObj *, DynamicObjWeight >	mvObjWeight
	Weights for each objects in each context (mutable for dynamic update during optimization)

std::vector< pair< long, REAL > >	mvSavedParamSet
	List of saved parameter sets. More...

bool	mIsOptimizing
	True if a refinement is being done. For multi-threaded environment.

bool	mStopAfterCycle
	If true, then stop at the end of the cycle. Used in multi-threaded environment.

ObjRegistry< RefinableObj >	mRefinedObjList
	The refined objects. More...

ObjRegistry< RefinableObj >	mRecursiveRefinedObjList
	The refined objects, recursively including all sub-objects. More...

RefObjOpt	mXMLAutoSave
	Periodic save of complete environment as an xml file.

REAL	mLastOptimTime
	The time elapsed after the last optimization, in seconds.

MainTracker	mMainTracker
	MainTracker object to track the evolution of cost functions, likelihood, and individual parameters.

ObjRegistry< RefObjOpt >	mOptionRegistry
	List of options for this object. More...

Detailed Description

Base object for Optimization methods.

This is an abstract base class, derived for Monte-Cralo type algorithms (Simulated Annealing & Parallel Tempering), and hopefully soon for Genetic Algorithms.

Remarks: Instead of keeping a copy of the list of parameters here, maybe it would be better to delegate all parameter handling to the refined objects (they would also have to keep in memory the saved parameter sets, so that could be difficult to administrate...).

Definition at line 102 of file GlobalOptimObj.h.

Member Function Documentation

◆ AddOption()

void ObjCryst::OptimizationObj::AddOption ( RefObjOpt * opt )

protected

Add an option for this parameter

Definition at line 549 of file GlobalOptimObj.cpp.

◆ BuildRecursiveRefObjList()

void ObjCryst::OptimizationObj::BuildRecursiveRefObjList ( )

protected

(Re)build OptimizationObj::mRecursiveRefinedObjList, if an object has been added or modified.

If no object has been added and no sub-object has been added/removed, then nothing is done.

Definition at line 533 of file GlobalOptimObj.cpp.

◆ GetFullRefinableObj()

RefinableObj & ObjCryst::OptimizationObj::GetFullRefinableObj ( const bool rebuild = true )

Get the RefinableObj with all the parameters from all refined objects.

If rebuild=true, prepare again the list of objects/parameters.

Definition at line 296 of file GlobalOptimObj.cpp.

◆ GetLogLikelihood()

REAL ObjCryst::OptimizationObj::GetLogLikelihood ( ) const

virtual

The optimized (minimized, actually) function.

This function is the weighted sum of the chosen Cost Functions for the refined objects.

Definition at line 246 of file GlobalOptimObj.cpp.

◆ GetParamSetIndex()

long ObjCryst::OptimizationObj::GetParamSetIndex ( const unsigned int i ) const

Get the index of a saved parameters set in the compiled RefinableObj.

The parameters can then be accessed using GetRefinedObjList().GetParamSet(idx)

Definition at line 420 of file GlobalOptimObj.cpp.

◆ MultiRunOptimize()

virtual void ObjCryst::OptimizationObj::MultiRunOptimize	(	long &	nbCycle,
		long &	nbSteps,
		const bool	silent = `false`,
		const REAL	finalcost = `0`,
		const REAL	maxTime = `-1`
	)

pure virtual

Launch optimization for multiple runs of N steps.

Parameters

nbCycle	the number of runs (cycles) to perform. The structure is randomized at the beginning of each cycle. If nbCycle==-1, this will run indefinitely. The nbCycle parameter is decreased after each run.
nbSteps	the number of steps to go. This number is modified (decreases!) as the refinement goes on.
silent	: if true, absolutely no message should be printed (except debugging)
finalcost	the optimization will stop if overall cost fallse below this value
maxTime	the optimization will stop after the given number of seconds has been spent optimizing (ignored if <0).

Implemented in ObjCryst::SimplexObj, and ObjCryst::MonteCarloObj.

◆ Optimize()

virtual void ObjCryst::OptimizationObj::Optimize	(	long &	nbSteps,
		const bool	silent = `false`,
		const REAL	finalcost = `0`,
		const REAL	maxTime = `-1`
	)

pure virtual

Launch optimization (a single run) for N steps.

Parameters

nbSteps	the number of steps to go. This number is modified (decreases!) as the refinement goes on.
silent	: if true, absolutely no message should be printed (except debugging)
finalcost	the optimization will stop if overall cost fallse below this value
maxTime	the optimization will stop after the given number of seconds has been spent optimizing (ignored if <0).

Implemented in ObjCryst::SimplexObj, and ObjCryst::MonteCarloObj.

◆ PrepareRefParList()

void ObjCryst::OptimizationObj::PrepareRefParList ( )

protected

Prepare mRefParList for the refinement

Definition at line 441 of file GlobalOptimObj.cpp.

◆ RandomizeStartingConfig()

void ObjCryst::OptimizationObj::RandomizeStartingConfig ( )

virtual

Randomize starting configuration.

Only affects limited and periodic parameters.

Definition at line 157 of file GlobalOptimObj.cpp.

◆ RestoreParamSet()

void ObjCryst::OptimizationObj::RestoreParamSet	(	const unsigned int	i,
		const bool	update_display = `true`
	)

Restore a given saved parameter set.

This is equivalent to GetRefinedObjList().RestoreParamSet(GetSavedParamSetIndex(i))

Parameters

i	the order of the saved parameter set

Definition at line 435 of file GlobalOptimObj.cpp.

◆ UpdateDisplay()

void ObjCryst::OptimizationObj::UpdateDisplay ( ) const

virtual

Update Display (if any display is available), when a new 'relevant' configuration is reached.

This calls all RefinableObj::UpdateDisplay()

Reimplemented in ObjCryst::MonteCarloObj.

Definition at line 525 of file GlobalOptimObj.cpp.

◆ XMLInput()

virtual void ObjCryst::OptimizationObj::XMLInput	(	istream &	is,
		const XMLCrystTag &	tag
	)

pure virtual

Input in XML format from a stream, restoring the set of refined objects and the associated cost functions.

Note that the corresponding objects must have been loaded in memory before, else shit happens.

Implemented in ObjCryst::SimplexObj, and ObjCryst::MonteCarloObj.

◆ XMLOutput()

virtual void ObjCryst::OptimizationObj::XMLOutput	(	ostream &	os,
		int	indent = `0`
	)		const

pure virtual

Output a description of the object in XML format to a stream.

This saves the list of refined object and the cost functions, as well as options for the refinement. The refined objects are not saved, so this must be done somewhere else (they must be reloaded before this object).

Implemented in ObjCryst::SimplexObj, and ObjCryst::MonteCarloObj.

Member Data Documentation

◆ mOptionRegistry

ObjRegistry<RefObjOpt> ObjCryst::OptimizationObj::mOptionRegistry

protected

List of options for this object.

Note that these are just references, to options allocated by the object, to have a simple global access to all options

Definition at line 354 of file GlobalOptimObj.h.

◆ mRecursiveRefinedObjList

ObjRegistry<RefinableObj> ObjCryst::OptimizationObj::mRecursiveRefinedObjList

mutableprotected

The refined objects, recursively including all sub-objects.

This is mutable, since it is a function of mRefinedObjList only.

Definition at line 341 of file GlobalOptimObj.h.

◆ mRefinedObjList

ObjRegistry<RefinableObj> ObjCryst::OptimizationObj::mRefinedObjList

mutableprotected

The refined objects.

This is mutable to allow a copy constructor for the OptimizationObj, and because the objects are not owned but rather referenced here.

Definition at line 338 of file GlobalOptimObj.h.

◆ mRefParList

RefinableObj ObjCryst::OptimizationObj::mRefParList

mutableprotected

The refinable par list used during refinement.

Only a condensed version of all objects. This is useful to keep an history of modifications, and to restore previous values.

Remarks: maybe this should be completely delegated to the refined objetcs.

Definition at line 278 of file GlobalOptimObj.h.

◆ mvSavedParamSet

std::vector<pair<long,REAL> > ObjCryst::OptimizationObj::mvSavedParamSet

protected

List of saved parameter sets.

This is used to save possible solutions during the optimization, so that the user can check them afterwards.

The first member of each pair is the index of the parameter set, and the second is the overall cost for that set.

Definition at line 327 of file GlobalOptimObj.h.

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ AddOption()

◆ BuildRecursiveRefObjList()

◆ GetFullRefinableObj()

◆ GetLogLikelihood()

◆ GetParamSetIndex()

◆ MultiRunOptimize()

◆ Optimize()

◆ PrepareRefParList()

◆ RandomizeStartingConfig()

◆ RestoreParamSet()

◆ UpdateDisplay()

◆ XMLInput()

◆ XMLOutput()

Member Data Documentation

◆ mOptionRegistry

◆ mRecursiveRefinedObjList

◆ mRefinedObjList

◆ mRefParList

◆ mvSavedParamSet