Generic class to compute components (eg the contribution of a given phase, or background) of a powder pattern. More...

Inheritance diagram for ObjCryst::PowderPatternComponent:

Collaboration diagram for ObjCryst::PowderPatternComponent:

Public Member Functions
	PowderPatternComponent (const PowderPatternComponent &)

virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...

const PowderPattern &	GetParentPowderPattern () const
	Get the PowderPattern object which uses this component. More...

PowderPattern &	GetParentPowderPattern ()
	Get the PowderPattern object which uses this component. More...

virtual void	SetParentPowderPattern (PowderPattern &)=0
	Set the PowderPattern object which uses this component. More...

virtual const CrystVector_REAL &	GetPowderPatternCalc () const =0
	Get the calculated powder pattern for this component. More...

virtual std::map< RefinablePar *, CrystVector_REAL > &	GetPowderPattern_FullDeriv (std::set< RefinablePar * > &vPar)

virtual pair< const CrystVector_REAL , const RefinableObjClock >	GetPowderPatternIntegratedCalc () const =0
	Get the integrated values of the powder pattern. More...

virtual std::map< RefinablePar *, CrystVector_REAL > &	GetPowderPatternIntegrated_FullDeriv (std::set< RefinablePar * > &vPar)

bool	IsScalable () const
	Is this component scalable ? More...

virtual const CrystVector_REAL &	GetPowderPatternCalcVariance () const =0
	Get the variance associated to each point of the calculated powder pattern, for this component. More...

virtual pair< const CrystVector_REAL , const RefinableObjClock >	GetPowderPatternIntegratedCalcVariance () const =0
	Get the variance associated to each point of the calculated powder pattern, for this component (integrated version). More...

virtual bool	HasPowderPatternCalcVariance () const =0
	Does this component have a variance associated with each calculated point ? i.e., do we use maximum likelihood to take into account incomplete models ?

const RefinableObjClock &	GetClockPowderPatternCalc () const
	Last time the powder pattern was calculated.

const list< pair< const REAL,const string > > &	GetPatternLabelList () const
	Get a list of labels for the pattern (usually reflection indexes). More...

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 const string &	GetName () const
	Name of the object.

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...

virtual void	Print () const

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	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization. More...

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 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 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.

Protected Member Functions
const RefinableObjClock &	GetClockPowderPatternCalcVariance () const
	Last time the variance on the pattern was actually calculated.

virtual void	CalcPowderPattern () const =0
	Calc the powder pattern. More...

virtual void	CalcPowderPattern_FullDeriv (std::set< RefinablePar * > &vPar)

virtual void	CalcPowderPatternIntegrated_FullDeriv (std::set< RefinablePar * > &vPar)
	Calc the integrated powder pattern. More...

virtual const CrystVector_long &	GetBraggLimits () const =0
	Get the pixel positions separating the integration intervals around reflections. More...

const RefinableObjClock &	GetClockBraggLimits () const
	Get last time the Bragg Limits were changed.

virtual void	SetMaxSinThetaOvLambda (const REAL max)=0
	Set the maximum value for sin(theta)/lambda. More...

virtual void	Prepare ()=0

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)

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
CrystVector_REAL	mPowderPatternCalc
	The calculated component of a powder pattern. More...

CrystVector_REAL	mPowderPatternIntegratedCalc
	The calculated powder pattern, integrated.

CrystVector_REAL	mPowderPatternCalcVariance
	The variance associated to each point of the calculated powder pattern.

CrystVector_REAL	mPowderPatternIntegratedCalcVariance
	The variance associated to each point of the calculated powder pattern, integrated.

CrystVector_long	mIntegratedReflLimits
	Interval limits around each reflection, for integrated R-factors.

bool	mIsScalable
	Scalable ? (crystal phase = scalable, background= not scalable)

RefinableObjClock	mClockPowderPatternCalc
	When was the powder pattern last computed ?

RefinableObjClock	mClockPowderPatternIntegratedCalc
	When was the 'integrated' powder pattern last computed ?

RefinableObjClock	mClockPowderPatternVarianceCalc
	When was the powder pattern variance last computed ?

RefinableObjClock	mClockPowderPatternIntegratedVarianceCalc
	When was the 'integrated' powder pattern variance last computed ?

PowderPattern *	mpParentPowderPattern
	The PowderPattern object in which this component is included.

RefinableObjClock	mClockBraggLimits
	Get last time the Bragg Limits were changed.

list< pair< const REAL,const string > >	mvLabel
	The labels associated to different points of the pattern.

std::map< RefinablePar *, CrystVector_REAL >	mPowderPattern_FullDeriv

std::map< RefinablePar *, CrystVector_REAL >	mPowderPatternIntegrated_FullDeriv

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...

Friends
class	PowderPattern

Detailed Description

Generic class to compute components (eg the contribution of a given phase, or background) of a powder pattern.

This is an abstract base class.

Most functions are protected, only to be accessed, internally or from the friend class PowderPattern.

Definition at line 48 of file PowderPattern.h.

Member Function Documentation

virtual void ObjCryst::PowderPatternComponent::CalcPowderPattern ( ) const

protectedpure virtual

Calc the powder pattern.

As always, recomputation is only done if necessary (ie if a parameter has changed since the last computation)

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

void ObjCryst::PowderPatternComponent::CalcPowderPatternIntegrated_FullDeriv ( std::set< RefinablePar * > & vPar )

protectedvirtual

Calc the integrated powder pattern.

This should be optimized so that the full powder pattern is not explicitely computed.

Reimplemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

Definition at line 155 of file PowderPattern.cpp.

virtual const CrystVector_long& ObjCryst::PowderPatternComponent::GetBraggLimits ( ) const

protectedpure virtual

Get the pixel positions separating the integration intervals around reflections.

Returns: : an array with the pixel positions, empty if this component has no peaks. The positions should be in increasing order, but could go beyond the pattern limits.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

const string & ObjCryst::PowderPatternComponent::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.

Reimplemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

Definition at line 88 of file PowderPattern.cpp.

const PowderPattern & ObjCryst::PowderPatternComponent::GetParentPowderPattern ( ) const

Get the PowderPattern object which uses this component.

This allows to know the observed powder pattern to evaluate the background.

Definition at line 94 of file PowderPattern.cpp.

PowderPattern & ObjCryst::PowderPatternComponent::GetParentPowderPattern ( )

Get the PowderPattern object which uses this component.

This allows to know the observed powder pattern to evaluate the background.

Definition at line 111 of file PowderPattern.cpp.

const list< pair< const REAL, const string > > & ObjCryst::PowderPatternComponent::GetPatternLabelList ( ) const

Get a list of labels for the pattern (usually reflection indexes).

This returns the list generated during the last computation of the powder pattern.

Definition at line 127 of file PowderPattern.cpp.

virtual const CrystVector_REAL& ObjCryst::PowderPatternComponent::GetPowderPatternCalc ( ) const

pure virtual

Get the calculated powder pattern for this component.

Note that the pattern is not scaled.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

virtual const CrystVector_REAL& ObjCryst::PowderPatternComponent::GetPowderPatternCalcVariance ( ) const

pure virtual

Get the variance associated to each point of the calculated powder pattern, for this component.

Warning: : this is experimental, with the aim of using Maximum Likelihood to improve structure determination.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

virtual pair<const CrystVector_REAL*,const RefinableObjClock*> ObjCryst::PowderPatternComponent::GetPowderPatternIntegratedCalc ( ) const

pure virtual

Get the integrated values of the powder pattern.

Note: : the integration intervals are those given by the parent PowderPattern, so that all PowderPatternComponent's intervals are taken into account

This avoids explicitely calculating the full profile powder pattern.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

virtual pair<const CrystVector_REAL*,const RefinableObjClock*> ObjCryst::PowderPatternComponent::GetPowderPatternIntegratedCalcVariance ( ) const

pure virtual

Get the variance associated to each point of the calculated powder pattern, for this component (integrated version).

Warning: : this is experimental, with the aim of using Maximum Likelihood to improve structure determination.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

bool ObjCryst::PowderPatternComponent::IsScalable ( ) const

Is this component scalable ?

This is used by the PowderPattern class, which fits all pattern components using scale factors. Some components may not need to be scaled: background components, which are assumed to be absolute.

Definition at line 116 of file PowderPattern.cpp.

virtual void ObjCryst::PowderPatternComponent::Prepare ( )

protectedpure virtual

This will be called by the parent PowderPattern object, before calculating the first powder pattern. Or maybe it should be called automatically by the object itself...

Reimplemented from ObjCryst::RefinableObj.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

virtual void ObjCryst::PowderPatternComponent::SetMaxSinThetaOvLambda ( const REAL max )

protectedpure virtual

Set the maximum value for sin(theta)/lambda.

All data above still exist but are ignored for all calculations.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

virtual void ObjCryst::PowderPatternComponent::SetParentPowderPattern ( PowderPattern & )

pure virtual

Set the PowderPattern object which uses this component.

This sets all necessary pattern parameters (2theta/tof range, wavelength, radiation type...) accordingly.

Implemented in ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPatternBackground.

Member Data Documentation

CrystVector_REAL ObjCryst::PowderPatternComponent::mPowderPatternCalc

mutableprotected

The calculated component of a powder pattern.

It is mutable since it is completely defined by other parameters (eg it is not an 'independent parameter')

Definition at line 145 of file PowderPattern.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Function Documentation

Member Data Documentation