The PeaksStatistics class is a small helper class that is used in SortHKL. More...

#include <PeakStatisticsTools.h>

Public Member Functions
	PeaksStatistics (const UniqueReflectionCollection &reflections)

	PeaksStatistics (const UniqueReflectionCollection &reflections, std::string &equivalentIntensities, double &sigmaCritical, bool &weightedZ)

Public Attributes
double	m_chiSquared

double	m_completeness
	Fraction of observed unique reflections in the resolution range defined by d_min and d_max. More...

double	m_dspacingMax
	Upper d-spacing limit in the data set. More...

double	m_dspacingMin
	Lower d-spacing limit in the data set, sometimes referred to as upper resolution limit. More...

double	m_meanIOverSigma
	Average signal to noise ratio in the reflections. More...

int	m_measuredReflections
	Total number of observed reflections - no symmetry is taken into account for this. More...

std::vector< DataObjects::Peak >	m_peaks

double	m_redundancy
	Average number of observations for a unique reflection. More...

double	m_rMerge
	Merging R-factor, R_merge, sometimes also called R_sym. More...

double	m_rPim
	Precision indicating R-factor (R_{p.i.m}). More...

int	m_uniqueReflections
	Number of unique reflections. More...

Private Member Functions
void	calculatePeaksStatistics (const std::map< Kernel::V3D, UniqueReflection > &uniqueReflections, std::string &equivalentIntensities, double &sigmaCritical, bool &weightedZ)
	PeaksStatistics::calculatePeaksStatistics. More...

std::pair< double, double >	getDSpacingLimits (const std::vector< DataObjects::Peak > &peaks) const
	Returns the lowest and hights wavelength in the peak list. More...

double	getIOverSigmaSum (const std::vector< double > &sigmas, const std::vector< double > &intensities) const
	Returns the sum of all I/sigma-ratios defined by the two vectors using std::inner_product. More...

double	getRMS (const std::vector< double > &data) const
	Returns the Root mean square of the supplied vector. More...

Detailed Description

The PeaksStatistics class is a small helper class that is used in SortHKL.

It takes a UniqueReflectionCollection and calculates a few data set quality indicators such as Rmerge and Rpim.

Do not rely on this class to exist forever, parts of it may change or the entire class may disappear over time.

Definition at line 109 of file PeakStatisticsTools.h.

Constructor & Destructor Documentation

◆ PeaksStatistics() [1/2]

Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::PeaksStatistics ( const UniqueReflectionCollection & reflections )

inlineexplicit

Definition at line 111 of file PeakStatisticsTools.h.

References Mantid::Crystal::PeakStatisticsTools::UniqueReflectionCollection::getObservedReflectionCount(), and Mantid::Crystal::PeakStatisticsTools::UniqueReflectionCollection::getReflections().

◆ PeaksStatistics() [2/2]

Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::PeaksStatistics	(	const UniqueReflectionCollection &	reflections,
		std::string &	equivalentIntensities,
		double &	sigmaCritical,
		bool &	weightedZ
	)

inlineexplicit

Definition at line 120 of file PeakStatisticsTools.h.

References Mantid::Crystal::PeakStatisticsTools::UniqueReflectionCollection::getObservedReflectionCount(), and Mantid::Crystal::PeakStatisticsTools::UniqueReflectionCollection::getReflections().

Member Function Documentation

◆ calculatePeaksStatistics()

void Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::calculatePeaksStatistics	(	const std::map< Kernel::V3D, UniqueReflection > &	uniqueReflections,
		std::string &	equivalentIntensities,
		double &	sigmaCritical,
		bool &	weightedZ
	)

private

PeaksStatistics::calculatePeaksStatistics.

This function iterates through the unique reflections map and computes statistics for the reflections/peaks. It calls UniqueReflection::removeOutliers, so outliers are removed before the statistical quantities are calculated.

Furthermore it sets the intensities of each peak to the mean of the group of equivalent reflections.

Parameters

uniqueReflections	:: Map of unique reflections and peaks.
equivalentIntensities	:: Mean or median for statistics of equivalent peaks.
sigmaCritical	:: Number of standard deviations for outliers.
weightedZ	:: True for weighted Zscore

Definition at line 206 of file PeakStatisticsTools.cpp.

References getDSpacingLimits(), getIOverSigmaSum(), Mantid::Kernel::getStatistics(), m_chiSquared, m_completeness, m_dspacingMax, m_dspacingMin, m_meanIOverSigma, m_measuredReflections, m_peaks, m_redundancy, m_rMerge, m_rPim, m_uniqueReflections, Mantid::Kernel::StatOptions::Mean, Mantid::Kernel::StatOptions::Median, and Mantid::Kernel::StatOptions::UncorrectedStdDev.

◆ getDSpacingLimits()

std::pair< double, double > Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::getDSpacingLimits ( const std::vector< DataObjects::Peak > & peaks ) const

private

Returns the lowest and hights wavelength in the peak list.

Definition at line 307 of file PeakStatisticsTools.cpp.

References rhs.

Referenced by calculatePeaksStatistics().

◆ getIOverSigmaSum()

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::getIOverSigmaSum	(	const std::vector< double > &	sigmas,
		const std::vector< double > &	intensities
	)		const

private

Returns the sum of all I/sigma-ratios defined by the two vectors using std::inner_product.

Definition at line 293 of file PeakStatisticsTools.cpp.

Referenced by calculatePeaksStatistics().

◆ getRMS()

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::getRMS ( const std::vector< double > & data ) const

private

Returns the Root mean square of the supplied vector.

Definition at line 300 of file PeakStatisticsTools.cpp.

Member Data Documentation

◆ m_chiSquared

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_chiSquared

Definition at line 163 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::exec().

◆ m_completeness

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_completeness

Fraction of observed unique reflections in the resolution range defined by d_min and d_max.

Definition at line 138 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_dspacingMax

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_dspacingMax

Upper d-spacing limit in the data set.

Definition at line 161 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_dspacingMin

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_dspacingMin

Lower d-spacing limit in the data set, sometimes referred to as upper resolution limit.

Definition at line 158 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_meanIOverSigma

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_meanIOverSigma

Average signal to noise ratio in the reflections.

Definition at line 154 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_measuredReflections

int Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_measuredReflections

Total number of observed reflections - no symmetry is taken into account for this.

Definition at line 130 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics().

◆ m_peaks

std::vector<DataObjects::Peak> Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_peaks

Definition at line 164 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::exec().

◆ m_redundancy

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_redundancy

Average number of observations for a unique reflection.

Definition at line 141 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_rMerge

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_rMerge

Merging R-factor, R_merge, sometimes also called R_sym.

This is a basic measure for how well the intensities of symmetry equivalent reflections agree with each other.

Definition at line 146 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_rPim

double Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_rPim

Precision indicating R-factor (R_{p.i.m}).

Also a measurement of agreement between equivalent reflections, but without some of the weeknesses of R_merge.

Definition at line 151 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

◆ m_uniqueReflections

int Mantid::Crystal::PeakStatisticsTools::PeaksStatistics::m_uniqueReflections

Number of unique reflections.

This counts each reflection family once, according to the point group.

Definition at line 134 of file PeakStatisticsTools.h.

Referenced by calculatePeaksStatistics(), and Mantid::Crystal::SortHKL::insertStatisticsIntoTable().

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

Framework/Crystal/inc/MantidCrystal/PeakStatisticsTools.h
Framework/Crystal/src/PeakStatisticsTools.cpp

Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ PeaksStatistics() [1/2]

◆ PeaksStatistics() [2/2]

Member Function Documentation

◆ calculatePeaksStatistics()

◆ getDSpacingLimits()

◆ getIOverSigmaSum()

◆ getRMS()

Member Data Documentation

◆ m_chiSquared

◆ m_completeness

◆ m_dspacingMax

◆ m_dspacingMin

◆ m_meanIOverSigma

◆ m_measuredReflections

◆ m_peaks

◆ m_redundancy

◆ m_rMerge

◆ m_rPim

◆ m_uniqueReflections