#include <PowderPattern.h>
Inheritance diagram for ObjCryst::PowderPattern::
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 PowderPatternComponent & | GetPowderPatternComponent (const string &name) const | ||
Access to a component of the powder spectrum. | |||
const PowderPatternComponent & | GetPowderPatternComponent (const int) const | ||
Access to a component of the powder spectrum. | |||
PowderPatternComponent & | GetPowderPatternComponent (const string &name) | ||
Access to a component of the powder spectrum. | |||
PowderPatternComponent & | GetPowderPatternComponent (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 Radiation & | GetRadiation () 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 RefinableObjClock & | GetClockPowderPatternCalc () const | ||
Last time the spectrum was calculated. | |||
const RefinableObjClock & | GetClockPowderPatternPar () const | ||
When were the spectrum parameters (2theta range, step) changed ? | |||
const RefinableObjClock & | GetClockPowderPatternRadiation () const | ||
When were the radiation parameter (radiation type, wavelength) changed ? | |||
const RefinableObjClock & | GetClockPowderPattern2ThetaCorr () 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,..).
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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,..).
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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.
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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 : ![]() | |||
REAL | m2ThetaDisplacement | ||
Displacement correction :![]() | |||
REAL | m2ThetaTransparency | ||
Transparency correction : ![]() | |||
ObjRegistry< PowderPatternComponent > | mPowderPatternComponentRegistry | ||
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. |
This can also be used for simulation, using a fake Iobs. Supports multiple phases.
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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. |
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Get the experimental 2theta from the theoretical value, taking into account all corrections (zero, transparency,..).
For internal use only.
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Get the pixel number on the experimental spectrum, from the theoretical (uncorrected) value of 2theta, taking into account all corrections. (zero, transparency,..).
For internal use only.
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Return conventionnal Chi^2.
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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.
Reimplemented from ObjCryst::RefinableObj. |
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Unweighted R-factor.
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Get the weighted R-factor.
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Import file with 2 columns 2Theta Iobs.
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Import file with 3 columns 2Theta Iobs Sigma.
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Import fullprof-style diffraction data.
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Import *.cpi Sietronics diffraction data.
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Import *.xdd diffraction data (Topas,...).
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Prepare everything (if necessary) for an optimization/calculation.
For internal use only.
Reimplemented from ObjCryst::RefinableObj. |
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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...
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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(). |
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\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).
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Set the wavelength of the experiment to that of an X-Ray tube.
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. |
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Input From stream.
Reimplemented from ObjCryst::RefinableObj. |
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Output to stream in well-formed XML.
Reimplemented from ObjCryst::RefinableObj. |
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Used to fit the components' scale factors.
For internal use only.
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Used to fit the components' scale factors.
For internal use only.
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Used to fit the components' scale factors.
For internal use only.
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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. |
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To compute scale factors, which are the components (phases) that can be scaled ?
For internal use only.
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