ObjCryst::CellExplorer Class Reference

Algorithm class to find the correct indexing from observed peak positions. More...

Inheritance diagram for ObjCryst::CellExplorer:

Collaboration diagram for ObjCryst::CellExplorer:

Public Member Functions
	CellExplorer (const PeakList &dhkl, const CrystalSystem lattice, const unsigned int nbSpurious)
void	Evolution (unsigned int ng, const bool randomize=true, const float f=0.7, const float cr=0.5, unsigned int np=100)
void	SetLengthMinMax (const float min, const float max)
void	SetAngleMinMax (const float min, const float max)
void	SetVolumeMinMax (const float min, const float max)
void	SetNbSpurious (const unsigned int nb)
void	SetD2Error (const float err)
	Allowed error on 1/d (squared!), used for dicvol.
void	SetMinMaxZeroShift (const float min, const float max)
void	SetCrystalSystem (const CrystalSystem system)
void	SetCrystalCentering (const CrystalCentering cent)
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...
virtual const string &	GetName () const
	Name of the object.
virtual void	Print () const
virtual unsigned int	GetNbLSQFunction () const
	Number of LSQ functions.
virtual const CrystVector_REAL &	GetLSQCalc (const unsigned int) const
	Get the current calculated value for the LSQ function.
virtual const CrystVector_REAL &	GetLSQObs (const unsigned int) const
	Get the observed values for the LSQ function.
virtual const CrystVector_REAL &	GetLSQWeight (const unsigned int) const
	Get the weight values for the LSQ function.
virtual const CrystVector_REAL &	GetLSQDeriv (const unsigned int, RefinablePar &)
	Get the first derivative values for the LSQ function, for a given parameter. More...
virtual void	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization. More...
void	LSQRefine (int nbCycle=1, bool useLevenbergMarquardt=true, const bool silent=false)
void	DicVol (const float minScore=10, const unsigned int minDepth=3, const float stopOnScore=50.0, const unsigned int stopOnDepth=6)
	Run DicVOl algorithm, store only solutions with score >minScore or depth>=minDepth, stop at the end of one volume interval (~400 A^3) if best score>stopOnScore, or if one solution was found at depth>=stopOnDepth. More...
void	ReduceSolutions (const bool updateReportThreshold=false)
	Sort all solutions by score, remove duplicates. More...
float	GetBestScore () const
const std::list< std::pair < RecUnitCell, float > > &	GetSolutions () const
std::list< std::pair < RecUnitCell, float > > &	GetSolutions ()
Public Member Functions inherited from ObjCryst::RefinableObj
	RefinableObj ()
	Constructor.
	RefinableObj (const bool internalUseOnly)
	Constructor. More...
	RefinableObj (const RefinableObj &old)
	Defined not implemented... More...
virtual	~RefinableObj ()
	Destructor.
virtual void	SetName (const string &name)
	Name of the object.
void	operator= (const RefinableObj &old)
	Defined not implemented... More...
void	PrepareForRefinement () const
	Find which parameters are used and not fixed, for a refinement /optimization. More...
void	FixAllPar ()
	Fix All parameters.
void	UnFixAllPar ()
	UnFix All parameters.
void	SetParIsFixed (const long parIndex, const bool fix)
	Fix/un-fix one parameter from its #.
void	SetParIsFixed (const string &parName, const bool fix)
	Fix/un-fix one parameter from its name.
void	SetParIsFixed (const RefParType *type, const bool fix)
	Fix/un-fix one family of parameters.
void	SetParIsUsed (const string &parName, const bool use)
	Set whether a parameter is used.
void	SetParIsUsed (const RefParType *type, const bool use)
	Set whether a family of parameters is used.
long	GetNbPar () const
	Total number of refinable parameter in the object. More...
long	GetNbParNotFixed () const
	Total number of non-fixed parameters. Is initialized by PrepareForRefinement()
RefinablePar &	GetPar (const long i)
	Access all parameters in the order they were inputted.
const RefinablePar &	GetPar (const long i) const
	Access all parameters in the order they were inputted.
RefinablePar &	GetPar (const string &name)
	Access all parameters from their name.
const RefinablePar &	GetPar (const string &name) const
	Access all parameters from their name.
RefinablePar &	GetPar (const REAL *)
	Access parameter from its adress.
const RefinablePar &	GetPar (const REAL *) const
	Access parameter from its adress.
RefinablePar &	GetParNotFixed (const long i)
	Access all parameters in the order they were inputted, skipping fixed parameters. More...
const RefinablePar &	GetParNotFixed (const long i) const
	Access all parameters in the order they were inputed, skipping fixed parameters. More...
void	AddPar (const RefinablePar &newRefPar)
	Add a refinable parameter. More...
void	AddPar (RefinablePar *newRefPar)
	Add a refinable parameter. More...
void	AddPar (RefinableObj &newRefParList, const bool copyParam=false)
	Add all the parameters in another RefinableObj. More...
vector< RefinablePar * >::iterator	RemovePar (RefinablePar *refPar)
	Remove a refinable parameter. More...
unsigned long	CreateParamSet (const string name="") const
	Save the current set of refined values in a new set. More...
void	ClearParamSet (const unsigned long id) const
	Erase the param set with the given id, releasing memory.
void	SaveParamSet (const unsigned long id) const
	Save the current set of refined values over a previously-created set of saved values. More...
void	RestoreParamSet (const unsigned long id)
	Restore a saved set of values. More...
const CrystVector_REAL &	GetParamSet (const unsigned long setId) const
	Access one save refpar set. More...
CrystVector_REAL &	GetParamSet (const unsigned long setId)
	Access one save refpar set. More...
REAL	GetParamSet_ParNotFixedHumanValue (const unsigned long setId, const long parNumber) const
	Access the (human) value of one refined parameter in a saved set of parameters. More...
const void	EraseAllParamSet ()
	Erase all saved refpar sets. More...
const string &	GetParamSetName (const unsigned long setId) const
	Get the name associated to a refpar set. More...
void	SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving absolute new limits.
void	SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving absolute new limits.
void	SetLimitsRelative (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0. More...
void	SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). More...
void	SetLimitsProportional (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, proportionnaly to the current value. More...
void	SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, proportionnaly to their current value. More...
void	SetGlobalOptimStep (const RefParType *type, const REAL step)
	Change the maximum step to use during Global Optimization algorithms.
ObjRegistry< RefinableObj > &	GetSubObjRegistry ()
	Access to the registry of RefinableObj used by this object.
const ObjRegistry< RefinableObj > &	GetSubObjRegistry () const
	Access to the registry of RefinableObj used by this object.
virtual void	RegisterClient (RefinableObj &) const
	Register a new object using this object. More...
virtual void	DeRegisterClient (RefinableObj &) const
	Deregister an object (which not any more) using this object.
virtual const ObjRegistry < RefinableObj > &	GetClientRegistry () const
	Get the list of clients.
virtual ObjRegistry < RefinableObj > &	GetClientRegistry ()
	Get the list of clients.
bool	IsBeingRefined () const
	Is the object being refined ? (Can be refined by one algorithm at a time only.)
virtual void	EndOptimization ()
	This should be called by any optimization class at the end of an optimization. More...
virtual void	SetApproximationFlag (const bool allow)
	Enable or disable numerical approximations. More...
virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization). More...
virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration. More...
void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More...
virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object. More...
virtual std::map< RefinablePar *, CrystVector_REAL > &	GetLSQ_FullDeriv (const unsigned int, std::set< RefinablePar * > &vPar)
	Get the first derivative for the LSQ function for each parameter supplied in a list. More...
void	ResetParList ()
	Re-init the list of refinable parameters, removing all parameters. More...
virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML. More...
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream. More...
virtual void	UpdateDisplay () const
	If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. More...
unsigned int	GetNbOption () const
	Number of Options for this object.
RefObjOpt &	GetOption (const unsigned int i)
	Access to the options.
const RefObjOpt &	GetOption (const unsigned int i) const
	const access to the options
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. More...
void	SetDeleteRefParInDestructor (const bool b)
	Set this object not to delete its list of parameters when destroyed. More...
const RefinableObjClock &	GetRefParListClock () const
	What was the last time a RefinablePar was added/removed ? More...
virtual REAL	GetRestraintCost () const
	Get the restraint cost (overall penalty of all restraints) More...
void	AddRestraint (Restraint *pNewRestraint)
	Add a new restraint. More...
vector< Restraint * >::iterator	RemoveRestraint (Restraint *pRestraint)
	Remove a restraint from the list of known restraints. More...
virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config. More...
const RefinableObjClock &	GetClockMaster () const
	This clocks records any change in the object. See refinableObj::mClockMaster.

Private Member Functions
unsigned int	RDicVol (RecUnitCell uc0, RecUnitCell uc1, unsigned int depth, unsigned long &nbCalc, const float minV, const float maxV, vector< unsigned int > vdepth=vector< unsigned int >())
void	Init ()

Private Attributes
std::list< std::pair < RecUnitCell, float > >	mvSolution
	Max number of obs reflections to use.
unsigned int	mnpar
const PeakList *	mpPeakList
float	mLengthMin
float	mLengthMax
float	mAngleMin
float	mAngleMax
float	mVolumeMin
float	mVolumeMax
float	mZeroShiftMin
float	mZeroShiftMax
float	mMin [7]
	Min values for all parameters (7=unit cell +zero)
float	mAmp [7]
	Max amplitude (max=min+amplitude) for all parameters All parameters are treated as periodic for DE (??)
CrystalSystem	mlattice
	Lattice type for which we search.
CrystalCentering	mCentering
	Centering type.
unsigned int	mNbSpurious
float	mD2Error
LSQNumObj	mLSQObj
CrystVector_REAL	mObs
CrystVector_REAL	mCalc
CrystVector_REAL	mWeight
CrystVector_REAL	mDeriv
RecUnitCell	mRecUnitCell
	Reciprocal unit cell used for least squares refinement.
float	mBestScore
	Current best score.
std::vector< unsigned int >	mvNbSolutionDepth
	Number of solutions found during dicvol search, at each depth.
float	mMinScoreReport
unsigned int	mMaxDicVolDepth
unsigned int	mDicVolDepthReport
float	mCosAngMax
	Stored value of cos(max ang) for tricilinic search - we do not want to recompute the cos at every dicvol iteration.
unsigned int	mNbLSQExcept
	Number of exceptions caught during LSQ, in a given search - above 20 LSQ is disabled.

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::RefinableObj
long	FindPar (const string &name) const
	Find a refinable parameter with a given name.
long	FindPar (const REAL *) const
	Find a refinable parameter from the adress of its value.
void	AddSubRefObj (RefinableObj &)
void	RemoveSubRefObj (RefinableObj &)
void	AddOption (RefObjOpt *opt)
virtual void	Prepare ()
map< unsigned long, pair < CrystVector_REAL, string > >::iterator	FindParamSet (unsigned long id) const
	Find a parameter set with a given id (and check if it is there)
Protected Attributes inherited from ObjCryst::RefinableObj
string	mName
	Name for this RefinableObject. Should be unique, at least in the same scope.+.
vector< RefinablePar * >	mvpRefPar
	Vector of pointers to the refinable parameters.
vector< Restraint * >	mvpRestraint
	Vector of pointers to the restraints for this object. More...
map< unsigned long, pair < CrystVector_REAL, string > >	mvpSavedValuesSet
	Map of (index,pointers to arrays) used to save sets of values for all parameters. More...
long	mNbRefParNotFixed
	Total of not-fixed parameters.
CrystVector_long	mRefparNotFixedIndex
	Index of not-fixed parameters.
int	mOptimizationDepth
	Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place. More...
ObjRegistry< RefinableObj >	mSubObjRegistry
	Registry of RefinableObject needed for this object (owned by this object or not)
ObjRegistry< RefinableObj >	mClientObjRegistry
	Registry of RefinableObject using this object. More...
ObjRegistry< RefObjOpt >	mOptionRegistry
	List of options for this object. More...
bool	mDeleteRefParInDestructor
	If true (the default), then all RefinablePar will be deleted when the the object is deleted. More...
RefinableObjClock	mRefParListClock
	Last time the RefinableParList was modified (a parameter added or removed).
bool	mRandomMoveIsDone
CrystVector_REAL	mLSQDeriv
	Temporary array used to return derivative values of the LSQ function for given parameters. More...
std::map< unsigned int, std::map< RefinablePar *, CrystVector_REAL > >	mLSQ_FullDeriv
	Temporary map to return the derivative of the LSQ function versus a list of parameters. More...
RefinableObjClock	mClockMaster
	Master clock, which is changed whenever the object has been altered. More...

Detailed Description

Algorithm class to find the correct indexing from observed peak positions.

Definition at line 212 of file Indexing.h.

Member Function Documentation

void ObjCryst::CellExplorer::BeginOptimization ( const bool  allowApproximations = false, const bool  enableRestraints = false  )

virtual

This should be called by any optimization class at the begining of an optimization.

This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects.

Note

this may be called several time for some objects which are used by several other objects, or for nested optimizations (e.g. least-squares optimizations inside a global one).

EndOptimization() must be called at the end of the optimization, the same number of time BeginOptimization() was called !

Parameters

allowApproximations	if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives.
enableRestraints	xrefitem deprecated 28.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1481 of file Indexing.cpp.

void ObjCryst::CellExplorer::DicVol	(	const float	minScore = 10,
		const unsigned int	minDepth = 3,
		const float	stopOnScore = 50.0,
		const unsigned int	stopOnDepth = 6
	)

Run DicVOl algorithm, store only solutions with score >minScore or depth>=minDepth, stop at the end of one volume interval (~400 A^3) if best score>stopOnScore, or if one solution was found at depth>=stopOnDepth.

If stopOnDepth==0, do not stop for any depth

Definition at line 2126 of file Indexing.cpp.

const string & ObjCryst::CellExplorer::GetClassName ( ) const

virtual

Name for this class ("RefinableObj", "Crystal",...).

This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1410 of file Indexing.cpp.

const CrystVector_REAL & ObjCryst::CellExplorer::GetLSQDeriv ( const unsigned int  n, RefinablePar &  par  )

virtual

Get the first derivative values for the LSQ function, for a given parameter.

Note that the default method in the base RefinableObj class is to use numerical derivatives, so it should be overridden for better precision.

Todo:

This should be a const method, and the given RefPar should be const too...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1451 of file Indexing.cpp.

void ObjCryst::CellExplorer::ReduceSolutions

(

const bool

updateReportThreshold = false

)

Sort all solutions by score, remove duplicates.

Parameters

updateReportThreshold

if true, when too many solutions are produced, the threshold above which solutions are reported will be updated to get less solutions.

Definition at line 2628 of file Indexing.cpp.

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

• Indexing.h
• Indexing.cpp