binomial.cpp File Reference

#include "binomial.h"
#include "common/basics.h"
#include <gsl/gsl_randist.h>
#include <gsl/gsl_cdf.h>
#include <map>
#include <vector>
#include <utility>
#include <numeric>

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Classes
class	CompareMagFloating< T >

Functions
int	rowMajorOffset (unsigned int x, unsigned int y, unsigned int nY)
void	rowMajorIndicies (unsigned int idx, unsigned int nY, unsigned int &x, unsigned int &y)
void	setGridABCoords (unsigned int binIdx, unsigned int *direction, unsigned int *nBins, float *binLen, const BoundCube &totalBound, GRID_ENTRY &gridEntry)
int	countBinnedIons (const std::vector< IonHit > &ions, const RangeFile *rng, const std::vector< size_t > &selectedIons, const SEGMENT_OPTION &segmentOptions, vector< GRID_ENTRY > &completedGridEntries)
void	genBinomialHistogram (const vector< GRID_ENTRY > &completedGridEntries, unsigned int nSelected, BINOMIAL_HIST &binHist)
void	computeBinomialStats (const vector< GRID_ENTRY > &gridEntries, BINOMIAL_HIST &binHist, unsigned int nSelected, BINOMIAL_STATS &stats)

Variables
const unsigned int	BINOMIAL_LOWCOUNT_SKEW_THRESHOLD =5

Function Documentation

computeBinomialStats()

void computeBinomialStats	(	const vector< GRID_ENTRY > &	gridEntries,
		BINOMIAL_HIST &	binHist,
		unsigned int	nSelected,
		BINOMIAL_STATS &	stats
	)

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References BINOMIAL_LOWCOUNT_SKEW_THRESHOLD, BINOMIAL_STATS::chiSquare, BINOMIAL_STATS::comparisonCoeff, BINOMIAL_HIST::mapIonFrequencies, BINOMIAL_STATS::mean, BINOMIAL_STATS::nBlocks, BINOMIAL_STATS::nIons, BINOMIAL_STATS::pValue, BINOMIAL_STATS::pValueOK, BINOMIAL_HIST::theoreticFrequencies, and BINOMIAL_HIST::theoreticNormalisedFrequencies.

Referenced by setGridABCoords(), and SpatialAnalysisFilter::setPropFromBinding().

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countBinnedIons()

int countBinnedIons	(	const std::vector< IonHit > &	ions,
		const RangeFile *	rng,
		const std::vector< size_t > &	selectedIons,
		const SEGMENT_OPTION &	segmentOptions,
		vector< GRID_ENTRY > &	completedGridEntries
	)

References ASSERT, BINOMIAL_NO_MEM, BINOMIAL_SEGMENT_AUTO_BRICK, GRID_ENTRY::endPt, BoundCube::expand(), SEGMENT_OPTION::extrudeMaxRatio, SEGMENT_OPTION::extrusionDirection, BoundCube::getBound(), IonHit::getBoundCube(), RangeFile::getIonID(), RangeFile::getNumIons(), BoundCube::getSize(), SEGMENT_OPTION::nIons, GRID_ENTRY::nIons, RangeFile::range(), rowMajorOffset(), setGridABCoords(), Point3D::setValue(), GRID_ENTRY::startPt, SEGMENT_OPTION::strategy, GRID_ENTRY::totalIons, vectorMultiErase(), and BoundCube::volume().

Referenced by setGridABCoords(), and SpatialAnalysisFilter::setPropFromBinding().

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genBinomialHistogram()

void genBinomialHistogram	(	const vector< GRID_ENTRY > &	completedGridEntries,
		unsigned int	nSelected,
		BINOMIAL_HIST &	binHist
	)

References ASSERT, BINOMIAL_HIST::mapIonFrequencies, and BINOMIAL_HIST::normalisedFrequencies.

Referenced by setGridABCoords(), and SpatialAnalysisFilter::setPropFromBinding().

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rowMajorIndicies()

void rowMajorIndicies	(	unsigned int	idx,
		unsigned int	nY,
		unsigned int &	x,
		unsigned int &	y
	)

Referenced by setGridABCoords().

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rowMajorOffset()

int rowMajorOffset	(	unsigned int	x,
		unsigned int	y,
		unsigned int	nY
	)

References ASSERT.

Referenced by countBinnedIons().

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setGridABCoords()

void setGridABCoords	(	unsigned int	binIdx,
		unsigned int *	direction,
		unsigned int *	nBins,
		float *	binLen,
		const BoundCube &	totalBound,
		GRID_ENTRY &	gridEntry
	)

References RangeFile::addIon(), RangeFile::addRange(), BINOMIAL_LOWCOUNT_SKEW_THRESHOLD, BINOMIAL_SEGMENT_AUTO_BRICK, RGBf::blue, computeBinomialStats(), countBinnedIons(), GRID_ENTRY::endPt, SEGMENT_OPTION::extrudeMaxRatio, SEGMENT_OPTION::extrusionDirection, genBinomialHistogram(), RandNumGen::genUniformDev(), BoundCube::getBound(), RangeFile::getIonID(), RGBf::green, RandNumGen::initTimer(), BINOMIAL_HIST::mapIonFrequencies, SEGMENT_OPTION::nIons, BINOMIAL_STATS::pValue, BINOMIAL_STATS::pValueOK, RGBf::red, rowMajorIndicies(), GRID_ENTRY::startPt, SEGMENT_OPTION::strategy, TEST, and WARN.

Referenced by countBinnedIons().

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Variable Documentation

BINOMIAL_LOWCOUNT_SKEW_THRESHOLD

const unsigned int BINOMIAL_LOWCOUNT_SKEW_THRESHOLD =5

Referenced by computeBinomialStats(), and setGridABCoords().