ObjCryst::PowderPatternBackground Class Reference

Phase to compute a background contribution to a powder pattern using an interpolation. Currently only linear interpolation is available. (in the works: cubic spline interpolation background). More...

Inheritance diagram for ObjCryst::PowderPatternBackground:

[legend]Collaboration diagram for ObjCryst::PowderPatternBackground:

[legend]List of all members.

Public Member Functions
	PowderPatternBackground ()
	PowderPatternBackground (const PowderPatternBackground &)
virtual	~PowderPatternBackground ()
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...).
virtual void	SetParentPowderPattern (const PowderPattern &)
	Set the PowderPattern object which uses this component.
virtual const CrystVector_REAL &	GetPowderPatternCalc () const
	Get the calculated powder pattern for this component.
virtual pair< const CrystVector_REAL *, const RefinableObjClock * >	GetPowderPatternIntegratedCalc () const
	Get the integrated values of the powder pattern.
void	ImportUserBackground (const string &filename)
	Import background points from a file (with two columns 2theta (or tof), intensity).
void	SetInterpPoints (const CrystVector_REAL tth, const CrystVector_REAL backgd)
const std::pair< const CrystVector_REAL *, const CrystVector_REAL * >	GetInterpPoints () const
virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML.
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream.
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter.
virtual const CrystVector_REAL &	GetPowderPatternCalcVariance () const
	Get the variance associated to each point of the calculated powder pattern, for this component.
virtual pair< const CrystVector_REAL *, const RefinableObjClock * >	GetPowderPatternIntegratedCalcVariance () const
	Get the variance associated to each point of the calculated powder pattern, for this component (integrated version).
virtual bool	HasPowderPatternCalcVariance () const
	Does this component have a variance associated with each calculated point ? i.e., do we use maximum likelihood to take into account incomplete models ?
virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config.
void	OptimizeBayesianBackground ()
	Optimize the background using a Bayesian approach.
Protected Member Functions
virtual void	CalcPowderPattern () const
	Calc the powder pattern.
virtual void	CalcPowderPatternIntegrated () const
	Calc the integrated powder pattern.
virtual void	Prepare ()
virtual void	GetBraggLimits (CrystVector_long *&min, CrystVector_long *&max) const
	Get the integration limits (first and last pixels) around each reflection, if this component has Bragg reflections.
virtual void	SetMaxSinThetaOvLambda (const REAL max)
	exist but are ignored for all calculations.
void	InitRefParList ()
void	InitOptions ()
void	InitSpline () const
Protected Attributes
int	mBackgroundNbPoint
	Number of fitting points for background.
CrystVector_REAL	mBackgroundInterpPointX
	Vector of 2theta values for the fitting points of the background.
CrystVector_REAL	mBackgroundInterpPointIntensity
	Values of background at interpolating points.
CrystVector_long	mPointOrder
	Subscript of the points, sorted the correct order, taking into account the type of radiation (monochromatic/TOF).
CrystVector_REAL	mvSplinePixel
	Vector of pixel values between each interval, for faster CubicSpline calculations.
CubicSpline	mvSpline
	Spline used for interpolation.
RefinableObjClock	mClockBackgroundPoint
	Modification of the interpolated points.
RefinableObjClock	mClockSpline
	Initialization of the spline.
REAL	mMaxSinThetaOvLambda
	Maximum sin(theta)/lambda for all calculations (10 by default).
REAL	mModelVariance
	Constant error (sigma) on the calculated pattern, due to an incomplete model.
RefObjOpt	mInterpolationModel
	Type of interpolation performed: linear or cubic spline.
Friends
class	PowderPattern

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Detailed Description

Phase to compute a background contribution to a powder pattern using an interpolation. Currently only linear interpolation is available. (in the works: cubic spline interpolation background).

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Constructor & Destructor Documentation

ObjCryst::PowderPatternBackground::PowderPatternBackground (   )

ObjCryst::PowderPatternBackground::PowderPatternBackground (  const PowderPatternBackground &   )

virtual ObjCryst::PowderPatternBackground::~PowderPatternBackground (   )  [virtual]

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Member Function Documentation

virtual void ObjCryst::PowderPatternBackground::CalcPowderPattern (   )  const [protected, virtual]

Calc the powder pattern. As always, recomputation is only done if necessary (ie if a parameter has changed since the last computation) Implements ObjCryst::PowderPatternComponent.

virtual void ObjCryst::PowderPatternBackground::CalcPowderPatternIntegrated (   )  const [protected, virtual]

Calc the integrated powder pattern. This should be optimized so that the full powder pattern is not explicitely computed. Implements ObjCryst::PowderPatternComponent.

virtual void ObjCryst::PowderPatternBackground::GetBraggLimits (  CrystVector_long *&  min, CrystVector_long *&  max )  const [protected, virtual]

Get the integration limits (first and last pixels) around each reflection, if this component has Bragg reflections. Used for integrated R(w) factors. The limits currently go from -2*FWHM to +2*FWHM. returns a pointer to the min and max pixels arrays (null pointers if no reflection for this phase). Implements ObjCryst::PowderPatternComponent.

virtual const string& ObjCryst::PowderPatternBackground::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::PowderPatternComponent.

virtual void ObjCryst::PowderPatternBackground::GetGeneGroup (  const RefinableObj &  obj, CrystVector_uint &  groupIndex, unsigned int &  firstGroup )  const [virtual]

Get the gene group assigned to each parameter. Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life. The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique. Parameters: obj  the , supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object. groupIndex  a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned). firstGroup  this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group. Note: this function is not optimized, and should only be called at the beginning of a refinement. Reimplemented from ObjCryst::RefinableObj.

const std::pair<const CrystVector_REAL*,const CrystVector_REAL*> ObjCryst::PowderPatternBackground::GetInterpPoints (   )  const

virtual const CrystVector_REAL& ObjCryst::PowderPatternBackground::GetPowderPatternCalc (   )  const [virtual]

Get the calculated powder pattern for this component. Note that the pattern is not scaled. Implements ObjCryst::PowderPatternComponent.

virtual const CrystVector_REAL& ObjCryst::PowderPatternBackground::GetPowderPatternCalcVariance (   )  const [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. Implements ObjCryst::PowderPatternComponent.

virtual pair<const CrystVector_REAL*,const RefinableObjClock*> ObjCryst::PowderPatternBackground::GetPowderPatternIntegratedCalc (   )  const [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. Implements ObjCryst::PowderPatternComponent.

virtual pair<const CrystVector_REAL*,const RefinableObjClock*> ObjCryst::PowderPatternBackground::GetPowderPatternIntegratedCalcVariance (   )  const [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. Implements ObjCryst::PowderPatternComponent.

virtual bool ObjCryst::PowderPatternBackground::HasPowderPatternCalcVariance (   )  const [virtual]

Does this component have a variance associated with each calculated point ? i.e., do we use maximum likelihood to take into account incomplete models ? Implements ObjCryst::PowderPatternComponent.

void ObjCryst::PowderPatternBackground::ImportUserBackground (  const string &  filename  )

Import background points from a file (with two columns 2theta (or tof), intensity).

void ObjCryst::PowderPatternBackground::InitOptions (   )  [protected]

void ObjCryst::PowderPatternBackground::InitRefParList (   )  [protected]

void ObjCryst::PowderPatternBackground::InitSpline (   )  const [protected]

void ObjCryst::PowderPatternBackground::OptimizeBayesianBackground (   )

Optimize the background using a Bayesian approach. The background parameters must be un-fixed before. The minimization will a maximum of 50 Simplex runs (see the SimplexObj documentation), each with 200 cycles. See the class documentation for PowderPatternBackgroundBayesianMinimiser.

virtual void ObjCryst::PowderPatternBackground::Prepare (   )  [protected, virtual]

For internal use only. 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... Implements ObjCryst::PowderPatternComponent.

void ObjCryst::PowderPatternBackground::SetInterpPoints (  const CrystVector_REAL  tth, const CrystVector_REAL  backgd )

virtual void ObjCryst::PowderPatternBackground::SetMaxSinThetaOvLambda (  const REAL  max  )  [protected, virtual]

exist but are ignored for all calculations. All data above still Implements ObjCryst::PowderPatternComponent.

virtual void ObjCryst::PowderPatternBackground::SetParentPowderPattern (  const PowderPattern &   )  [virtual]

Set the PowderPattern object which uses this component. This sets all necessary pattern parameters (2theta/tof range, wavelength, radiation type...) accordingly. Implements ObjCryst::PowderPatternComponent.

virtual void ObjCryst::PowderPatternBackground::TagNewBestConfig (   )  const [virtual]

During a global optimization, tells the object that the current config is the latest "best" config. This can be used by the object to make more intellingent random moves (use with caution: highly experimental !). Reimplemented from ObjCryst::RefinableObj.

virtual void ObjCryst::PowderPatternBackground::XMLInput (  istream &  is, const XMLCrystTag &  tag )  [virtual]

Input From stream. Todo: Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc... Reimplemented from ObjCryst::RefinableObj.

virtual void ObjCryst::PowderPatternBackground::XMLOutput (  ostream &  os, int  indent = 0 )  const [virtual]

Output to stream in well-formed XML. Todo: Use inheritance.. as for XMLInputTag()... Reimplemented from ObjCryst::RefinableObj.

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Friends And Related Function Documentation

friend class PowderPattern [friend]

Reimplemented from ObjCryst::PowderPatternComponent.

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Member Data Documentation

CrystVector_REAL ObjCryst::PowderPatternBackground::mBackgroundInterpPointIntensity [protected]

Values of background at interpolating points.

CrystVector_REAL ObjCryst::PowderPatternBackground::mBackgroundInterpPointX [protected]

Vector of 2theta values for the fitting points of the background.

int ObjCryst::PowderPatternBackground::mBackgroundNbPoint [protected]

Number of fitting points for background.

RefinableObjClock ObjCryst::PowderPatternBackground::mClockBackgroundPoint [protected]

Modification of the interpolated points.

RefinableObjClock ObjCryst::PowderPatternBackground::mClockSpline [mutable, protected]

Initialization of the spline.

RefObjOpt ObjCryst::PowderPatternBackground::mInterpolationModel [protected]

Type of interpolation performed: linear or cubic spline.

REAL ObjCryst::PowderPatternBackground::mMaxSinThetaOvLambda [protected]

Maximum sin(theta)/lambda for all calculations (10 by default). This keeps all data in memory, but only the part which is below the max is calculated.

REAL ObjCryst::PowderPatternBackground::mModelVariance [protected]

Constant error (sigma) on the calculated pattern, due to an incomplete model.

CrystVector_long ObjCryst::PowderPatternBackground::mPointOrder [mutable, protected]

Subscript of the points, sorted the correct order, taking into account the type of radiation (monochromatic/TOF).

CubicSpline ObjCryst::PowderPatternBackground::mvSpline [mutable, protected]

Spline used for interpolation. Mutable since it copies information from mBackgroundInterpPointX and mBackgroundInterpPointIntensity.

CrystVector_REAL ObjCryst::PowderPatternBackground::mvSplinePixel [mutable, protected]

Vector of pixel values between each interval, for faster CubicSpline calculations. Mutable since it copies information from mBackgroundInterpPointX.

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

• PowderPattern.h

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