Conjugate Gradient Algorithm object. More...

Inheritance diagram for ObjCryst::SimplexObj:

Collaboration diagram for ObjCryst::SimplexObj:

Public Member Functions
	SimplexObj (const string name="Unnamed Simplex Object")
	Constructor.

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

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

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

Public Member Functions inherited from ObjCryst::OptimizationObj
	OptimizationObj (const string name="")
	Constructor.

virtual	~OptimizationObj ()
	Destructor.

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

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.

Private Member Functions
REAL	GenerateNewSimplexConfiguration (CrystVector_REAL &vLLK, CrystVector_long &vIndex, unsigned long worst, REAL f)
	Try a new configuration by expanding the worst vertex from the center by a factor f. More...

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::OptimizationObj
void	PrepareRefParList ()

virtual void	InitOptions ()
	Initialization of options.

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

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

Protected Attributes inherited from ObjCryst::OptimizationObj
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
	Number of trials so far.

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.

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. More...

Detailed Description

Conjugate Gradient Algorithm object.

currently does not handle parameters hitting limits, and is not very efficient (uses numerical derivatives)

Definition at line 36 of file Simplex.h.

Member Function Documentation

REAL ObjCryst::SimplexObj::GenerateNewSimplexConfiguration	(	CrystVector_REAL &	vLLK,
		CrystVector_long &	vIndex,
		unsigned long	worst,
		REAL	f
	)

private

Try a new configuration by expanding the worst vertex from the center by a factor f.

If it is better, store it as new worst. Return the new obtained llk

Definition at line 145 of file Simplex.cpp.

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

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).

Implements ObjCryst::OptimizationObj.

Definition at line 127 of file Simplex.cpp.

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

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).

Implements ObjCryst::OptimizationObj.

Definition at line 32 of file Simplex.cpp.

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

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.

Implements ObjCryst::OptimizationObj.

Definition at line 142 of file Simplex.cpp.

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

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).

Implements ObjCryst::OptimizationObj.

Definition at line 139 of file Simplex.cpp.

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

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation