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ObjCryst::PowderPattern Class Reference

Powder pattern class, with an observed pattern and several calculated components to modelize the spectrum. More...

#include <PowderPattern.h>

Inheritance diagram for ObjCryst::PowderPattern::

ObjCryst::RefinableObj List of all members.

Public Methods

 PowderPattern ()
 PowderPattern (const PowderPattern &)
 ~PowderPattern ()
virtual const string & GetClassName () const
 Name for this class ("RefinableObj", "Crystal",...). This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry.

void AddPowderPatternComponent (PowderPatternComponent &)
 Add a component (phase, backround) to this spectrum. More...

unsigned int GetNbPowderPatternComponent () const
 Number of components.

const PowderPatternComponentGetPowderPatternComponent (const string &name) const
 Access to a component of the powder spectrum.

const PowderPatternComponentGetPowderPatternComponent (const int) const
 Access to a component of the powder spectrum.

PowderPatternComponentGetPowderPatternComponent (const string &name)
 Access to a component of the powder spectrum.

PowderPatternComponentGetPowderPatternComponent (const int)
 Access to a component of the powder spectrum.

void SetPowderPatternPar (const REAL tthetaMin, const REAL tthetaStep, unsigned long nbPoint)
 \briefSet the powder spectrum angular range & resolution parameter. More...

unsigned long GetNbPoint () const
 Number of points ?

void SetRadiation (const Radiation &radiation)
 Set the radiation.

const RadiationGetRadiation () const
 Neutron or x-ray experiment ?

void SetRadiationType (const RadiationType radiation)
 Set the radiation type.

RadiationType GetRadiationType () const
 Neutron or x-ray experiment ?

void SetWavelength (const REAL lambda)
 Set the wavelength of the experiment (in Angstroems).

void SetWavelength (const string &XRayTubeElementName, const REAL alpha12ratio=0.5)
 Set the wavelength of the experiment to that of an X-Ray tube. More...

void SetEnergy (const REAL energy)
 Set the energy of the experiment [in keV, lambda(A)=12398/E(keV)].

REAL GetWavelength () const
 wavelength of the experiment (in Angstroems).

const CrystVector_REAL & GetPowderPatternCalc () const
 Get the calculated powder spectrum.

const CrystVector_REAL & GetPowderPatternObs () const
 Get the observed powder spectrum.

const CrystVector_REAL & GetPowderPatternObsSigma () const
 Get the sigma for each point of the observed powder spectrum.

const CrystVector_REAL & GetPowderPatternWeight () const
 Get the weight for each point of the powder spectrum.

REAL Get2ThetaMin () const
 Get the Minimum 2theta.

REAL Get2ThetaStep () const
 Get the step in 2theta.

REAL Get2ThetaMax () const
 Get the maximum 2theta.

const RefinableObjClockGetClockPowderPatternCalc () const
 Last time the spectrum was calculated.

const RefinableObjClockGetClockPowderPatternPar () const
 When were the spectrum parameters (2theta range, step) changed ?

const RefinableObjClockGetClockPowderPatternRadiation () const
 When were the radiation parameter (radiation type, wavelength) changed ?

const RefinableObjClockGetClockPowderPattern2ThetaCorr () const
 When were the parameters for 2theta correction (zero, transparency, displacement) last changed ?

void Set2ThetaZero (const REAL newZero)
 Change Zero in 2Theta.

void Set2ThetaDisplacement (const REAL displacement)
 Change displacement correction .

void Set2ThetaTransparency (const REAL transparency)
 Change transparency correction .

REAL Get2ThetaCorr (const REAL ttheta) const
 Get the experimental 2theta from the theoretical value, taking into account all corrections (zero, transparency,..).
Parameters:
ttheta:  the theoretical 2theta value.
Returns:
the 2theta value as it appears on the spectrum.
More...


long Get2ThetaCorrPixel (const REAL ttheta) const
 Get the pixel number on the experimental spectrum, from the theoretical (uncorrected) value of 2theta, taking into account all corrections. (zero, transparency,..).
Parameters:
ttheta:  the theoretical 2theta value.
Returns:
the 2theta value as it appears on the spectrum.
More...


void ImportPowderPatternFullprof (const string &fullprofFileName)
 Import fullprof-style diffraction data. More...

void ImportPowderPatternPSI_DMC (const string &filename)
 Import powder spectrum, format DMC from PSI.

void ImportPowderPatternILL_D1A5 (const string &filename)
 Import powder spectrum, format from ILL D1A/D2B (format without counter info).

void ImportPowderPatternXdd (const string &fileName)
 Import *.xdd diffraction data (Topas,...). More...

void ImportPowderPatternSietronicsCPI (const string &fileName)
 Import *.cpi Sietronics diffraction data. More...

void ImportPowderPattern2ThetaObsSigma (const string &fileName, const int nbSkip=0)
 Import file with 3 columns 2Theta Iobs Sigma. More...

void ImportPowderPattern2ThetaObs (const string &fileName, const int nbSkip=0)
 Import file with 2 columns 2Theta Iobs. More...

void SetPowderPatternObs (const CrystVector_REAL &obs)
 Set observed powder spectrum from vector array. More...

void SavePowderPattern (const string &filename="powderPattern.out") const
 Save powder spectrum to one file, text format, 3 columns theta Iobs Icalc.If Iobs is missing, the column is omitted. position for all phases... More...

void PrintObsCalcData (ostream &os=cout) const
 Print to thee screen/console the observed and calculated spectrum (long, mostly useful for debugging).

REAL GetR () const
 Unweighted R-factor. More...

REAL GetIntegratedR () const
REAL GetRw () const
 Get the weighted R-factor. More...

REAL GetIntegratedRw () const
REAL GetChiSq () const
 Return conventionnal Chi^2. More...

void FitScaleFactorForR ()
 Fit the scale(s) factor of each component to minimize R.

void FitScaleFactorForIntegratedR ()
void FitScaleFactorForRw ()
 Fit the scale(s) factor of each component to minimize Rw.

void FitScaleFactorForIntegratedRw ()
void SetSigmaToSqrtIobs ()
 Set sigma=sqrt(Iobs).

void SetWeightToInvSigmaSq (const REAL minRelatSigma=1e-3)
 Set w = 1/sigma^2. To filter too small or null intensities :If sigma< minRelatSigma* max(sigma), then w=1/(minRelatSigma* max(sigma))^2.

void SetWeightToSinTheta (const REAL power=1.)
 Set w = sin(theta). Not really usful, huh ?

void SetWeightToUnit ()
 Set w = 1.

void SetWeightPolynomial (const REAL a, const REAL b, const REAL c, const REAL minRelatIobs=1e-3)
 Set w = 1/(a+ Iobs + b*Iobs^2+c*Iobs^3) To filter too small or null intensities: if Iobs < [minRelatIobs * max(Iobs)], then use Iobs=minRelatIobs * max(Iobs) to compute the weight. Typical values: a=2*min(Iobs) b=2/max(Iobs) c=0.

void Add2ThetaExcludedRegion (const REAL min2Theta, const REAL max2theta)
 Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be, as always, in radians. Does not work yet with integrated R factors. Note that the pattern is still computed in these regions. They are only ignored by statistics functions (R, Rws).

unsigned int GetNbCostFunction () const
 Number of Cost functions.

const string & GetCostFunctionName (const unsigned int) const
 Get a Cost function name from its id#.

const string & GetCostFunctionDescription (const unsigned int) const
 Get the (short) description of a cost function.

virtual REAL GetCostFunctionValue (const unsigned int)
 Get the current value of a cost function this should be 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 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...

void Prepare ()
 Prepare everything (if necessary) for an optimization/calculation. More...

virtual void GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
 Get the gene group assigned to each parameter. More...

virtual void SetMaxSinThetaOvLambda (const REAL max)
 Set the maximum value for sin(theta)/lambda. All data (reflections,..) still exist but are ignored for all calculations.

REAL GetMaxSinThetaOvLambda () const
 Get the maximum value for sin(theta)/lambda.


Protected Methods

void CalcPowderPattern () const
 Calc the powder spectrum.

virtual void Init ()
 Init parameters and options.

void PrepareIntegratedRfactor () const
 Prepare the calculation of the integrated R-factors.

void CalcNbPointUsed () const
 Calculate the number of points of the pattern actually used, from the maximum value of sin(theta)/lambda.


Protected Attributes

CrystVector_REAL mPowderPatternCalc
 The calculated powder spectrum. It is mutable since it is completely defined by other parameters (eg it is not an 'independent parameter').

CrystVector_REAL mPowderPatternBackgroundCalc
 The calculated powder spectrum part which corresponds to 'background' (eg non-scalable components). It is already included in mPowderPatternCalc.

CrystVector_REAL mPowderPatternObs
 The observed powder spectrum.

CrystVector_REAL mPowderPatternObsSigma
 The sigma of the observed spectrum.

CrystVector_REAL mPowderPatternWeight
 The weight for each point of the spectrum.

REAL m2ThetaMin
 2theta min and step for the spectrum.

REAL m2ThetaStep
 2theta min and step for the spectrum.

unsigned long mNbPoint
 Number of points in the spectrum.

REAL mWavelength
 The wavelength of the experiment, in Angstroems.
Warning:
This should be removed, as it is also available in mRadiation.


Radiation mRadiation
 The wavelength of the experiment, in Angstroems.

RefinableObjClock mClockPowderPatternPar
 When were the spectrum parameters (2theta range, step) changed ?

RefinableObjClock mClockPowderPatternRadiation
 When were the radiation parameter (radiation type, wavelength) changed ?

RefinableObjClock mClockPowderPatternCalc
 When was the powder spectrum last computed ?

RefinableObjClock mClockPowderPattern2ThetaCorr
 Corrections to 2Theta.

RefinableObjClock mClockScaleFactor
 Last modification of the scale factor.

CrystVector_REAL mExcludedRegionMin2Theta
 Min value for 2theta for all excluded regions.

CrystVector_REAL mExcludedRegionMax2Theta
 Max value for 2theta for all excluded regions.

REAL m2ThetaZero
 Zero correction : Thus mPowderPattern2ThetaMin=(mPowderPattern2ThetaMin-m2ThetaZero).

REAL m2ThetaDisplacement
 Displacement correction : .

REAL m2ThetaTransparency
 Transparency correction : .

ObjRegistry< PowderPatternComponentmPowderPatternComponentRegistry
 The components (crystalline phases, background,...) of the powder spectrum.

CrystVector_REAL mScaleFactor
 The scale factors for each component. For unscalable phases, this is set to 1 (constant).

bool mUseFastLessPreciseFunc
 Use faster, less precise functions ?

bool mStatisticsExcludeBackground
 Should Statistics (R, Rw,..) exclude the background ?

CrystVector_int mScalableComponentIndex
 To compute scale factors, which are the components (phases) that can be scaled ? More...

CrystMatrix_REAL mFitScaleFactorM
 Used to fit the components' scale factors. More...

CrystMatrix_REAL mFitScaleFactorB
 Used to fit the components' scale factors. More...

CrystMatrix_REAL mFitScaleFactorX
 Used to fit the components' scale factors. More...

CrystVector_long mIntegratedPatternMin
CrystVector_long mIntegratedPatternMax
CrystVector_REAL mIntegratedObs
CrystVector_REAL mIntegratedWeight
RefinableObjClock mClockIntegratedFactorsPrep
REAL mMaxSinThetaOvLambda
 Maximum sin(theta)/lambda for all calculations (10 by default). More...

unsigned long mNbPointUsed
 Number of points actually used, due to the maximum value of sin(theta)/lambda.

RefinableObjClock mClockNbPointUsed
 Clock recording the last time the number of points used (PowderPattern::mNbPointUsed) was changed.


Detailed Description

Powder pattern class, with an observed pattern and several calculated components to modelize the spectrum.

This can also be used for simulation, using a fake Iobs. Supports multiple phases.


Member Function Documentation

void ObjCryst::PowderPattern::AddPowderPatternComponent PowderPatternComponent  
 

Add a component (phase, backround) to this spectrum.

It must have been allocated in the heap. The spectrum parameters (2theta min, step, nbpoints, wavelength, radiation type) of the component are automatically changed to that of the PowderPattern object.

REAL ObjCryst::PowderPattern::Get2ThetaCorr const REAL    ttheta const
 

Get the experimental 2theta from the theoretical value, taking into account all corrections (zero, transparency,..).

Parameters:
ttheta:  the theoretical 2theta value.
Returns:
the 2theta value as it appears on the spectrum.

For internal use only.

long ObjCryst::PowderPattern::Get2ThetaCorrPixel const REAL    ttheta const
 

Get the pixel number on the experimental spectrum, from the theoretical (uncorrected) value of 2theta, taking into account all corrections. (zero, transparency,..).

Parameters:
ttheta:  the theoretical 2theta value.
Returns:
the 2theta value as it appears on the spectrum.

For internal use only.

REAL ObjCryst::PowderPattern::GetChiSq   const
 

Return conventionnal Chi^2.

Returns:

virtual void ObjCryst::PowderPattern::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 \RefinableObj, 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.

REAL ObjCryst::PowderPattern::GetR   const
 

Unweighted R-factor.

Returns:

REAL ObjCryst::PowderPattern::GetRw   const
 

Get the weighted R-factor.

Returns:

void ObjCryst::PowderPattern::ImportPowderPattern2ThetaObs const string &    fileName,
const int    nbSkip = 0
 

Import file with 2 columns 2Theta Iobs.

Warning:
the 2theta step is assumed to be constant !!!
Parameters:
fileName:  the filename (surprise!)
nbSkip:  the number of lines to skip at the beginning of the file (default=0)

void ObjCryst::PowderPattern::ImportPowderPattern2ThetaObsSigma const string &    fileName,
const int    nbSkip = 0
 

Import file with 3 columns 2Theta Iobs Sigma.

Warning:
the 2theta step is assumed to be constant !!!
Parameters:
fileName:  the filename (surprise!)
nbSkip:  the number of lines to skip at the beginning of the file (default=0)

void ObjCryst::PowderPattern::ImportPowderPatternFullprof const string &    fullprofFileName
 

Import fullprof-style diffraction data.

Parameters:
fullprofFileName:  filename

void ObjCryst::PowderPattern::ImportPowderPatternSietronicsCPI const string &    fileName
 

Import *.cpi Sietronics diffraction data.

Parameters:
fileName:  filename

void ObjCryst::PowderPattern::ImportPowderPatternXdd const string &    fileName
 

Import *.xdd diffraction data (Topas,...).

Parameters:
fileName:  filename

void ObjCryst::PowderPattern::Prepare   [virtual]
 

Prepare everything (if necessary) for an optimization/calculation.

For internal use only.

Reimplemented from ObjCryst::RefinableObj.

void ObjCryst::PowderPattern::SavePowderPattern const string &    filename = "powderPattern.out" const
 

Save powder spectrum to one file, text format, 3 columns theta Iobs Icalc.If Iobs is missing, the column is omitted. position for all phases...

Todo:
export in other formats (.prf,...), with a list of reflection

void ObjCryst::PowderPattern::SetPowderPatternObs const CrystVector_REAL &    obs
 

Set observed powder spectrum from vector array.

Note: powder spectrum parameters must have been set before calling this function, for example by calling DiffractionDataPowder::InitPowderPatternPar().

void ObjCryst::PowderPattern::SetPowderPatternPar const REAL    tthetaMin,
const REAL    tthetaStep,
unsigned long    nbPoint
 

\briefSet the powder spectrum angular range & resolution parameter.

this will affect all components (phases) of the spectrum.

Use this with caution, as the number of points must be correct with respect to the observed data (Iobs).

Parameters:
tthetaMin:  min 2theta value, in radians
tthetaStep:  step (assumed constant) in 2theta.
nbPoints:  number of points in the spectrum.

void ObjCryst::PowderPattern::SetWavelength const string &    XRayTubeElementName,
const REAL    alpha12ratio = 0.5
 

Set the wavelength of the experiment to that of an X-Ray tube.

Parameters:
XRayTubeElementName  : name of the anticathode element name. Known ones are Cr, Fe, Cu, Mo, Ag.
alpha2Alpha2ratio:  Kalpha2/Kalpha1 ratio (0.5 by default)
Alpha1 and alpha2 wavelength are taken from R. Grosse-Kunstleve package, and the average wavelength is calculated using the alpha2/alpha1 weight. All structure factors computation are made using the average wavelength, and for powder diffraction, profiles are output at the alpha1 and alpha2 ratio for the calculated pattern.

NOTE : if the name of the wavelength is generic (eg"Cu"), then the program considers that there are both Alpha1 and Alpha2, and thus automatically changes the WavelengthType to WAVELENGTH_ALPHA12. If instead either alpha1 or alpha2 (eg "CuA1") is asked for, the WavelengthType is set to WAVELENGTH_MONOCHROMATIC. In both cases, the radiation type is set to X-Ray.

virtual void ObjCryst::PowderPattern::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::PowderPattern::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.


Member Data Documentation

CrystMatrix_REAL ObjCryst::PowderPattern::mFitScaleFactorB [protected]
 

Used to fit the components' scale factors.

For internal use only.

CrystMatrix_REAL ObjCryst::PowderPattern::mFitScaleFactorM [protected]
 

Used to fit the components' scale factors.

For internal use only.

CrystMatrix_REAL ObjCryst::PowderPattern::mFitScaleFactorX [protected]
 

Used to fit the components' scale factors.

For internal use only.

REAL ObjCryst::PowderPattern::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.

CrystVector_int ObjCryst::PowderPattern::mScalableComponentIndex [protected]
 

To compute scale factors, which are the components (phases) that can be scaled ?

For internal use only.


The documentation for this class was generated from the following file:
Generated on Tue Feb 5 17:37:22 2002 for ObjCryst++ by doxygen1.2.13.1 written by Dimitri van Heesch, © 1997-2001