clusterAnalysis.cpp File Reference

#include "clusterAnalysis.h"
#include "filterCommon.h"
#include <queue>
#include <algorithm>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_eigen.h>
#include "../../common/gsl_helper.h"
#include "backend/plot.h"

Include dependency graph for clusterAnalysis.cpp:

Enumerations
enum	{   KEY_CLUSTERANALYSIS_ALGORITHM, KEY_CORECLASSIFY_ENABLE, KEY_CORECLASSIFYDIST, KEY_CORECLASSIFYKNN,   KEY_LINKDIST, KEY_BULKLINK_ENABLE, KEY_BULKLINK, KEY_ERODE_ENABLE,   KEY_ERODEDIST, KEY_WANT_CLUSTERSIZEDIST, KEY_WANT_LOGSIZEDIST, KEY_WANT_COMPOSITIONDIST,   KEY_WANT_CLUSTERMORPHOLOGY, KEY_WANT_CLUSTERID, KEY_NORMALISE_COMPOSITION, KEY_CROP_SIZE,   KEY_SIZE_COUNT_BULK, KEY_CROP_NMIN, KEY_CROP_NMAX, KEY_BULK_ALL,   KEY_CORE_OFFSET =100000, KEY_BULK_OFFSET =200000 }
enum	{ NOCORE_ERR =1, NOBULK_ERR, CLUSTER_ERR_ENUM_END }
enum	{ CLUSTER_LINK_ERODE, CLUSTER_ALGORITHM_ENUM_END }
enum	{ COMPOSITION_NONE, COMPOSITION_UNNORMALISED, COMPOSITION_NORMALISED }

Functions
void	makeFrequencyTable (const IonStreamData *i, const RangeFile *r, std::vector< std::pair< string, size_t > > &freqTable)
void	makeCompositionTable (const IonStreamData *i, const RangeFile *r, std::vector< std::pair< string, float > > &compTable)
void	computeEigenValues (gsl_matrix *m, size_t numRows, size_t numCols, vector< float > &resultValues, vector< Point3D > &resultVectors)
void	computeMatrixEntries (const vector< IonHit > &atoms, const Point3D &clusterCentre, gsl_matrix *m)

Variables
const char	SIZE_DIST_DATALABEL [] =NTRANS("Size Distribution")
const char	CHEM_DIST_DATALABEL [] =NTRANS("Chemistry Distribution")
const float	SPHERE_PRESEARCH_CUTOFF = 75
const bool	WANT_COUNT_BULK_FORCROP =false

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
KEY_CLUSTERANALYSIS_ALGORITHM
KEY_CORECLASSIFY_ENABLE
KEY_CORECLASSIFYDIST
KEY_CORECLASSIFYKNN
KEY_LINKDIST
KEY_BULKLINK_ENABLE
KEY_BULKLINK
KEY_ERODE_ENABLE
KEY_ERODEDIST
KEY_WANT_CLUSTERSIZEDIST
KEY_WANT_LOGSIZEDIST
KEY_WANT_COMPOSITIONDIST
KEY_WANT_CLUSTERMORPHOLOGY
KEY_WANT_CLUSTERID
KEY_NORMALISE_COMPOSITION
KEY_CROP_SIZE
KEY_SIZE_COUNT_BULK
KEY_CROP_NMIN
KEY_CROP_NMAX
KEY_BULK_ALL
KEY_CORE_OFFSET
KEY_BULK_OFFSET

anonymous enum

anonymous enum

Enumerator
NOCORE_ERR
NOBULK_ERR
CLUSTER_ERR_ENUM_END

anonymous enum

anonymous enum

Enumerator
CLUSTER_LINK_ERODE
CLUSTER_ALGORITHM_ENUM_END

anonymous enum

anonymous enum

Enumerator
COMPOSITION_NONE
COMPOSITION_UNNORMALISED
COMPOSITION_NORMALISED

Function Documentation

computeEigenValues()

void computeEigenValues	(	gsl_matrix *	m,
		size_t	numRows,
		size_t	numCols,
		vector< float > &	resultValues,
		vector< Point3D > &	resultVectors
	)

References ASSERT, RangeStreamData::enabledIons, RangeFile::getNumIons(), and RangeStreamData::rangeFile.

Referenced by computeMatrixEntries().

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computeMatrixEntries()

void computeMatrixEntries	(	const vector< IonHit > &	atoms,
		const Point3D &	clusterCentre,
		gsl_matrix *	m
	)

References RangeFile::addIon(), RangeFile::addRange(), ASSERT, RGBf::blue, ClusterAnalysisFilter::ClusterAnalysisFilter(), computeEigenValues(), IonStreamData::data, RangeStreamData::enabledIons, RangeStreamData::enabledRanges, EQ_TOL, RandNumGen::genUniformDev(), IonHit::getCentroid(), RangeFile::getIonID(), RangeFile::getNumIons(), RangeFile::getNumRanges(), RGBf::green, ClusterAnalysisFilter::initFilter(), RandNumGen::initTimer(), KEY_BULKLINK, KEY_CORE_OFFSET, KEY_CORECLASSIFY_ENABLE, KEY_CORECLASSIFYDIST, KEY_CORECLASSIFYKNN, KEY_ERODEDIST, KEY_LINKDIST, KEY_WANT_CLUSTERSIZEDIST, KEY_WANT_COMPOSITIONDIST, IonHit::makePos(), FilterStreamData::parent, RangeStreamData::rangeFile, RGBf::red, ClusterAnalysisFilter::refresh(), Filter::setCaching(), IonHit::setMassToCharge(), IonHit::setPos(), ClusterAnalysisFilter::setProperty(), Point3D::sqrMag(), STREAM_TYPE_IONS, TEST, and WARN.

makeCompositionTable()

void makeCompositionTable	(	const IonStreamData *	i,
		const RangeFile *	r,
		std::vector< std::pair< string, float > > &	compTable
	)

References makeFrequencyTable().

Referenced by ClusterAnalysisFilter::refresh().

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makeFrequencyTable()

void makeFrequencyTable	(	const IonStreamData *	i,
		const RangeFile *	r,
		std::vector< std::pair< string, size_t > > &	freqTable
	)

References ASSERT, IonStreamData::data, RangeFile::getIonID(), RangeFile::getName(), and RangeFile::getNumIons().

Referenced by makeCompositionTable(), and ClusterAnalysisFilter::refresh().

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Variable Documentation

CHEM_DIST_DATALABEL

const char CHEM_DIST_DATALABEL[] =NTRANS("Chemistry Distribution")

Referenced by ClusterAnalysisFilter::setProperty(), and ClusterAnalysisFilter::setPropFromBinding().

SIZE_DIST_DATALABEL

const char SIZE_DIST_DATALABEL[] =NTRANS("Size Distribution")

Referenced by ClusterAnalysisFilter::setProperty(), and ClusterAnalysisFilter::setPropFromBinding().

SPHERE_PRESEARCH_CUTOFF

const float SPHERE_PRESEARCH_CUTOFF = 75

WANT_COUNT_BULK_FORCROP

const bool WANT_COUNT_BULK_FORCROP =false

Referenced by ClusterAnalysisFilter::refresh(), and ClusterAnalysisFilter::setPropFromBinding().