PeakAna Class Reference

Inheritance diagram for PeakAna:

Public Member Functions
	PeakAna ()
	Default constructor that always creates a new TGraph.
	PeakAna (int size, double *xvals, double *yvals)
	Constructor using array of x and y values with known size.
	PeakAna (TGraph *Sig)
	Constructor with a known TGraph.
	PeakAna (TH1 *hist)
	Constructor with a histogram, histogram gets converted to graph object.
	PeakAna (const PeakAna &OldAna, TGraph *graph=0)
	Copy constructor can be called with a new graph.
PeakAna &	operator= (const PeakAna &rhs)
	Assignment operator doesn't clone graph.
virtual	~PeakAna ()
	Destructor.
virtual void	Copy (TObject &obj) const
	Internal method use Clone instead.
virtual TObject *	Clone (const char *newname) const
	Clones internal graph as opposed to just copying the pointer.
virtual void	AddPeakStats (TPaveText *pave, const char *opt="")
	Add peak information to a "statistics" box. More...
void	ConvertPeaksToGraph ()
	same as ConvertPeaksToGraph() but creates a new graph that replaces old one
PeakAna	ConvertPeaksToAna ()
	same as ConvertPeaksToAna() but returns new PeakAna with same settings without modifying current one
virtual void	GetPossiblePeaks ()
	Finds all possible Peaks in signal with some criteria. More...
virtual Int_t	SearchForPeak (const std::vector< PeakWindow > &PossiblePeaks)
	searches a vector of PeakWindow's for a specific peak based on input search criteria More...
Int_t	SearchForPeak (const std::vector< PeakWindow > &PossiblePeaks, const PeakWindow &search)
	same as SearchForPeak() but and set search criteria using PeakWindow
Int_t	SearchForPeak (const std::vector< PeakWindow > &PossiblePeaks, Double_t peak, Double_t width)
	same as SearchForPeak() and set search window by peak location and width
virtual Int_t	AnalyzeForPeak ()
	Main analysis method for finding peaks. More...
virtual Int_t	AnalyzeForPeak (Double_t peak, Double_t width)
virtual Int_t	AnalyzeForNoisyPeak ()
virtual void	MergeByProbability (std::vector< PeakWindow > &newpeaks) const
	Merges peaks in mPeaks using peak probability parameters. More...
virtual void	MergeByChirality (std::vector< PeakWindow > &newpeaks) const
virtual short	MergeLeftOrRight (UInt_t index) const
Double_t	Baseline () const
Double_t	BaselineSigma () const
Double_t	BaselineSigmaScale () const
Double_t	MinX () const
Double_t	MinY () const
Double_t	MaxX () const
Double_t	MaxY () const
Double_t	SearchPeak () const
Double_t	SearchWidth () const
Double_t	TunnelScale () const
Double_t	TunnelSigma () const
Double_t	TunnelThreshold () const
virtual void	Draw (Option_t *opt="")
	Draw method for PeakAna. More...
virtual void	Paint (Option_t *opt="")
PeakAnaPainter *	GetPainter (Option_t *opt="")
void	ForceInternal ()
PeakAna *	GausFilter (Int_t sizeavgs=0, bool copy=true)
	Apply a Gaussian filter to the data. More...
bool	GoodWindow ()
	Check if found peak is inside mXRangeMin, mYRangeMin, mXRangeMax, mYRangeMax and has logical values.
virtual TGraph *	GetData () const
UInt_t	GetDebug () const
const PeakWindow &	GetPeak (UInt_t peakidx) const
PeakWindow &	GetPeak (UInt_t peakidx)
UInt_t	GetFilter () const
Int_t	GetFilterScale () const
Int_t	FoundPeakIndex () const
virtual void	GetXYMax (Double_t xmin, Double_t xmax)
	Finds and sets mMaxX and mMaxY.
Double_t	MaxXval ()
Double_t	MaxYval ()
PeakAna *	MeanFilter (Int_t sizeavgs=0, bool copy=true)
	Apply a Mean filter to the data. More...
int	NPeaks () const
bool	ValidPeakIdx () const
Double_t	PeakStart ()
	Found Signal starting x-value.
Double_t	PeakEnd ()
	Found Signal ending x-value.
Double_t	PeakX ()
	x-value of found signal peak
Double_t	PeakY ()
	y-value of found signal peak
void	PeakXY (Double_t &xval, Double_t &yval)
	get peak x, and y value directly by reference
bool	PeakTunnel (const PeakWindow &window) const
	test whether a given peak satisifies peak tunnel parameters More...
Double_t	PeakProb (const PeakWindow &window, Double_t scale, Double_t sigma) const
	compute a given PeakWindow probability using internal graph More...
virtual void	Print (Option_t *opt="") const
	Print peak information.
void	ResetPeak ()
	Resets values associated with peak finding.
void	SetDebug (UInt_t level)
virtual void	SetData (TGraph *graph)
	sets new data for PeakAna More...
virtual void	SetData (TH1 *hist, UInt_t numavgs=1)
	sets new data for PeakAna using histogram object More...
void	SetBaseline (Double_t base, Double_t sigma)
void	SetBaselineSigmaScale (Double_t scale)
void	SetContinuity (Double_t val)
void	SetFilter (UInt_t filter, Int_t scale, Double_t sigma=0)
	Set the filter to use when peak finding. More...
void	SetRange (Double_t xmin, Double_t ymin, Double_t xmax, Double_t ymax)
	Sets the absolute range of the data. More...
void	SetSearchWindow (Double_t peak, Double_t width)
	Sets peak search parameters. More...
void	SetTunnelScale (Double_t value)
void	SetTunnelSigma (Double_t value)
void	SetTunnelPars (Double_t scale, Double_t sigma)
void	SetTunnelThreshold (Double_t value)
Double_t	ChiralityPeakScale () const
Double_t	ChiralityScale () const
Double_t	ChiralityProbScale () const
Double_t	ChiralityThreshold () const
void	SetChiralityPeakScale (Double_t v)
void	SetChiralityScale (Double_t v)
void	SetChiralityProbScale (Double_t v)
void	SetChiralityThreshold (Double_t v)
void	SetPeak (const Int_t peakpoint, const Double_t peakx)
	Overwrite peak location in #mFoundpeak. WARNING doesn't set start and end values nor overwrite mComputedIndex.
void	SetWindow (const Int_t start, const Int_t end)
	Overwrite peak start and end values in mFoundPeak. WARNING doesn't set peak values nor overwrite mComputedIndex.
void	SetWindow (PeakWindow window)
	Overwrite mFoundPeak with a different PeakWindow. WARNING doesn't overwrite mComputedIndex.
Color_t	GetLineColor () const
Style_t	GetLineStyle () const
Width_t	GetLineWidth () const
Color_t	GetFillColor () const
Style_t	GetFillStyle () const
Color_t	GetMarkerColor () const
Size_t	GetMarkerSize () const
Style_t	GetMarkerStyle () const
void	SetLineColor (Color_t color)
void	SetLineColorAlpha (Color_t color, Float_t alpha)
void	SetLineStyle (Style_t style)
void	SetLineWidth (Width_t width)
void	SetFillColor (Color_t color)
void	SetFillColorAlpha (Color_t color, Float_t alpha)
void	SetFillStyle (Style_t style)
void	SetMarkerColor (Color_t color=1)
void	SetMarkerColorAlpha (Color_t color, Float_t alpha)
void	SetMarkerSize (Size_t size=1)
void	SetMarkerStyle (Style_t style=1)
Color_t	GetBaseLineColor () const
Style_t	GetBaseLineStyle () const
Width_t	GetBaseLineWidth () const
Color_t	GetHitLineColor () const
Style_t	GetHitLineStyle () const
Width_t	GetHitLineWidth () const
void	SetBaseLineColor (Color_t color)
void	SetBaseLineColorAlpha (Color_t color, Float_t alpha)
void	SetBaseLineStyle (Style_t style)
void	SetBaseLineWidth (Width_t width)
void	SetHitLineColor (Color_t color)
void	SetHitLineColorAlpha (Color_t color, Float_t alpha)
void	SetHitLineStyle (Style_t style)
void	SetHitLineWidth (Width_t width)
Color_t	GetPeakLineColorS (UInt_t peakidx) const
Color_t	GetPeakLineColorE (UInt_t peakidx) const
Style_t	GetPeakStyleS (UInt_t peakidx) const
Style_t	GetPeakStyleE (UInt_t peakidx) const
Width_t	GetPeakWidthS (UInt_t peakidx) const
Width_t	GetPeakWidthE (UInt_t peakidx) const
Color_t	GetFoundPeakLineColorS () const
Color_t	GetFoundPeakLineColorE () const
Style_t	GetFoundPeakStyleS () const
Style_t	GetFoundPeakStyleE () const
Width_t	GetFoundPeakWidthS () const
Width_t	GetFoundPeakWidthE () const
void	SetFoundPeakLineColorS (Color_t s_color)
void	SetFoundPeakLineColorE (Color_t e_color)
void	SetFoundPeakLineColor (Color_t s_color, Color_t e_color)
void	SetFoundPeakStyleS (Style_t s_style)
void	SetFoundPeakStyleE (Style_t e_style)
void	SetFoundPeakStyle (Style_t s_style, Style_t e_style)
void	SetFoundPeakWidthS (Width_t s_width)
void	SetFoundPeakWidthE (Width_t e_width)
void	SetFoundPeakWidth (Width_t s_width, Width_t e_width)
void	SetPeakLineColorS (UInt_t peakidx, Color_t s_color)
void	SetPeakLineColorE (UInt_t peakidx, Color_t e_color)
void	SetPeakLineColor (UInt_t peakidx, Color_t s_color, Color_t e_color)
void	SetPeakLineColorAlphaS (UInt_t peakidx, Color_t s_color, Float_t s_alpha)
void	SetPeakLineColorAlphaE (UInt_t peakidx, Color_t e_color, Float_t e_alpha)
void	SetPeakLineColorAlpha (UInt_t peakidx, Color_t s_color, Float_t s_alpha, Color_t e_color, Float_t e_alpha)
void	SetPeakLineStyleS (UInt_t peakidx, Style_t s_style)
void	SetPeakLineStyleE (UInt_t peakidx, Style_t e_style)
void	SetPeakLineStyle (UInt_t peakidx, Style_t s_style, Style_t e_style)
void	SetPeakLineWidthS (UInt_t peakidx, Width_t s_width)
void	SetPeakLineWidthE (UInt_t peakidx, Width_t e_width)
void	SetPeakLineWidth (UInt_t peakidx, Width_t s_width, Width_t e_width)
void	SetAllPeakLineColor (Color_t s_color, Color_t e_color)
void	SetAllPeakLineStyle (Style_t s_style, Color_t e_style)
void	SetAllPeakLineWidth (Width_t s_width, Width_t e_width)

Static Public Member Functions
static TGraph *	ConvertHistToGraph (TH1 *graph, UInt_t numavgs=1)
	Converts a histogram to a graph. More...
static TGraph *	ConvertPeaksToGraph (const std::vector< PeakWindow > &Peaks)
	Convert each peak position into a TGraph. More...
static PeakAna	ConvertPeaksToAna (const PeakAna &Ana)
	same as ConvertPeaksToGraph() but returns a new PeakAna with same settings without modifying old one

Protected Member Functions
void	Init ()
	Initialize internal varaibles.
virtual bool	MergeLeft (Double_t leftchir, Double_t thischir, Double_t rightchir) const
virtual std::vector< std::pair < int, int > >	MergeIndices (std::vector< short > &vec) const

Static Protected Member Functions
static double *	GaussianMatrix2D (int rx, double sx=0, int ry=0, double sy=0, bool kNorm=true)
	Generates up to a 2D matrix of Gaussian weights. More...

Protected Attributes
Int_t	mComputedIndex
	Index in mPeaks where a peak was found. More...
std::vector< PeakWindow >	mPeaks
	vector that stores all the found peaks in the data
PeakWindow	mFoundPeak
	Copy of found peak in mPeaks. More...
PeakWindow	mSearch
	Variable that defines peak search parameters. More...
Double_t	mBaseline
	Minimum threshold to search for a peak. More...
Double_t	mBaselineSigma
	Error on PeakAna::mBaseline. More...
Double_t	mBaselineSigmaScale
	scale on PeakAna::mBaselineSigma to determine final threshold More...
Double_t	mMaxX
	x-value where global maximum occurs
Double_t	mMaxY
	y-value of global maximum
Double_t	mDeltaX
	graph known delta-x More...
TGraph *	mG_Data
	TGraph that stores the x,y data. More...
Double_t	mXRangeMin
	Absolute possible x-value minimum of data.
Double_t	mXRangeMax
	Absolute possible x-value maximum of data.
Double_t	mYRangeMin
	Absolute possible y-value minimum of data.
Double_t	mYRangeMax
	Absolute possible y-value maximum of data.
Double_t	mTunnelScale
	Scale on exponential for determining tunneling probability (default is 1) see #PeakWindow::PeakTunelProb()
Double_t	mTunnelSigma
	Sigma for Gaussian for determining tunneling probability (default is 1) see #PeakWindow::PeakTunelProb()
Double_t	mTunnelThreshold
	Cutoff probability for peak tunneling method. If threshold less than 0 (default) then skip peak tunnel method, see PeakTunnel()
Double_t	mChiralityPeakScale
Double_t	mChiralityScale
Double_t	mChiralityProbScale
Double_t	mChiralityThreshold
UInt_t	mFilter
	Filter to use in AnalyzeForPeak() More...
Double_t *	mFilterWeights
	Array of weights to use in filtering, size is 2*mFilterScale+1.
Int_t	mFilterScale
	How many points to group together when applying filter.
PeakAnaPainter *	mPainter
	Painter for this class.
TString	mOption
	Drawing option.

Detailed Description

Definition at line 94 of file PeakAna.h.

Member Function Documentation

void PeakAna::AddPeakStats ( TPaveText *  pave, const char *  opt = ""  )

virtual

Add peak information to a "statistics" box.

"statistics" box can be a TPaveText or a TPaveStats since the latter inherits from the former.

Parameters

pave	TPaveText to write peak information
opt	options for what information to add to stats box "" (No option) means just show found peak "a" means show all found peaks "d" means show all detail information for the peak

Definition at line 1010 of file PeakAna.cxx.

References AnalyzeForPeak(), GetData(), GetPeak(), mComputedIndex, mPeaks, NPeaks(), TunnelScale(), and TunnelSigma().

Referenced by PeakAnaPainter::PaintStats().

Int_t PeakAna::AnalyzeForPeak ( )

virtual

Main analysis method for finding peaks.

First filters the data if the mFilter is set, then calls GetPossiblePeaks(), then calls SearchForPeak().

Returns

index of found peak, if no found peak then returns size of mPeaks

Reimplemented in StFcsPulseAna.

Definition at line 153 of file PeakAna.cxx.

References GausFilter(), GetPossiblePeaks(), mComputedIndex, MeanFilter(), mFilter, mFilterScale, mFoundPeak, mPeaks, mXRangeMax, ResetPeak(), SearchForPeak(), and PeakWindow::SetWindow().

Referenced by AddPeakStats(), StFcsPulseAna::AnalyzeForPeak(), GoodWindow(), PeakAnaPainter::PaintFoundMarker(), PeakAnaPainter::PaintFoundPeakRange(), PeakAnaPainter::PaintPeakMarkers(), PeakAnaPainter::PaintPeakRanges(), PeakEnd(), PeakStart(), PeakX(), PeakXY(), and PeakY().

Double_t PeakAna::Baseline ( ) const

inline

Returns

mBaseline

Definition at line 178 of file PeakAna.h.

References mBaseline.

Referenced by GausFilter(), StFcsPulseAna::GausFit(), GetPossiblePeaks(), StFcsPulseAna::MBFit(), MeanFilter(), PeakAnaPainter::PaintBaselines(), PeakAnaPainter::PaintPeakRanges(), StFcsWaveformFitMaker::PedFitPulseFit(), StFcsPulseAna::PulseFit(), StFcsWaveformFitMaker::PulseFitAll(), StFcsPulseAna::SetFitPars(), StFcsPulseAna::SignalMBPars(), and StFcsPulseAna::Sum().

Double_t PeakAna::BaselineSigma ( ) const

inline

Returns

fabs(mBaselineSigma)

Definition at line 179 of file PeakAna.h.

References mBaselineSigma.

Referenced by GetPossiblePeaks(), PeakAnaPainter::PaintBaselines(), PeakAnaPainter::PaintPeakRanges(), StFcsWaveformFitMaker::PedFitPulseFit(), and StFcsWaveformFitMaker::PulseFitAll().

Double_t PeakAna::BaselineSigmaScale ( ) const

inline

Returns

mBaselineSigmaScale

Definition at line 180 of file PeakAna.h.

References mBaselineSigmaScale.

Referenced by GetPossiblePeaks(), PeakAnaPainter::PaintBaselines(), PeakAnaPainter::PaintPeakRanges(), and StFcsWaveformFitMaker::PulseFitAll().

TGraph * PeakAna::ConvertHistToGraph ( TH1 *  graph, UInt_t  numavgs = 1  )

static

Converts a histogram to a graph.

Treats each bin in the histogram as a point in a TGraph and the bin content as the y-value. Also, can be used to do a running average over "numavgs" bins

Parameters

graph	histogram to be converted to a graph
numavgs	number of bins to average over when creating the graph (running average), 1 means no running average

Returns

TGraph with bin data as points

Definition at line 382 of file PeakAna.cxx.

Referenced by PeakAna(), and SetData().

TGraph * PeakAna::ConvertPeaksToGraph ( const std::vector< PeakWindow > &  Peaks )

static

Convert each peak position into a TGraph.

The purpose of this function is to help with really noisy data where the "peaks" are really just noise. Essentially the idea is that each "peak" should actually be a point on a kind of "running average" in this way you capture the overall shape of the data without noise.

Parameters

Peaks

vector of PeakWindows to convert to a TGraph

Returns

TGraph with each peak in "Peaks" as a point

Definition at line 401 of file PeakAna.cxx.

void PeakAna::Draw ( Option_t *  opt = "" )

virtual

Draw method for PeakAna.

Options are semicolon seperated list with graph options first then the peak qa drawing options and finally the stats box drawing option.
peak qa drawing options(case insensitive):

• "R" for range
  
• "B" for baselines
  
• "F" found peak window
  
• "P" for all peak windows
  
• "M" for found peak marker
  
• "W" for all peak markers (upside down M)
  
• "E" combines "P" and "W"
  
• "A" for all, which combines "B", "P", and "W"
  stats drawing options(case insensitive):
  
• "S" is to show just the found peak
  
• "A" is to show for all peaks
  
• "D" is whether to show detailed printout or not (works with option "S" or "A")
  

Example1: "APL;FB;S" means draw graph using option "APL", draw only found peak qa and baselines, and create a stats box showing only basic information about the found peak. Example2: ";A;AD" means don't draw graph but draw all peaks and put detailed information of all peaks in a stats box Example3: "PL;A" means draw graph with option "PL" and draw all peaks but don't draw a stats box

Definition at line 984 of file PeakAna.cxx.

Referenced by StFcsWaveformFitMaker::drawFitter().

Int_t PeakAna::FoundPeakIndex ( ) const

inline

Returns

mComputedIndex

Definition at line 233 of file PeakAna.h.

References mComputedIndex.

Referenced by StFcsPulseAna::Clone(), Clone(), StFcsWaveformFitMaker::drawDualFit(), StFcsWaveformFitMaker::gausFit(), PeakAnaPainter::PaintFoundMarker(), PeakAnaPainter::PaintFoundPeakRange(), PeakAnaPainter::PaintPeakMarkers(), PeakAnaPainter::PaintPeakRanges(), StFcsWaveformFitMaker::PulseFit1(), StFcsWaveformFitMaker::PulseFit2(), StFcsWaveformFitMaker::PulseFitAll(), and StFcsPulseAna::SetFitPars().

PeakAna * PeakAna::GausFilter	(	Int_t	sizeavgs = 0,
		bool	copy = true
	)

Apply a Gaussian filter to the data.

Applies a Gaussian filter by sampling "sizeavgs" and Gaussian weights stored in mFilterWeights.

Parameters

sizeavgs	number of points to sample during filtering
copy	if copy is true returns a new PeakAna with Gaussian filtered data, if false modifies "this" object

Returns

new PeakAna object if copy=true or "this" object if false

Definition at line 518 of file PeakAna.cxx.

References Baseline(), GetData(), GetDebug(), mDeltaX, mFilterWeights, PeakAna(), ResetPeak(), and SetData().

Referenced by AnalyzeForPeak().

double * PeakAna::GaussianMatrix2D ( int  rx, double  sx = 0, int  ry = 0, double  sy = 0, bool  kNorm = true  )

staticprotected

Generates up to a 2D matrix of Gaussian weights.

Generates Gaussian weights to use in Gaussian filtering in a flattened 2D matrix.

Parameters

rx	number of columns to generate weights
sx	sigma of Gaussian to use in column weights
ry	number of rows to generate weights
sy	sigma of Gaussian to use in row weights
kNorm	if true use a normalized Gaussian i.e. sum of all weights=1

Returns

1D array containing weights

Definition at line 1248 of file PeakAna.cxx.

Referenced by SetFilter().

virtual TGraph* PeakAna::GetData ( ) const

inlinevirtual

Returns

mG_Data

Reimplemented in StFcsPulseAna.

Definition at line 226 of file PeakAna.h.

References mG_Data.

Referenced by AddPeakStats(), Clone(), GausFilter(), MeanFilter(), operator=(), PeakAnaPainter::PaintFoundPeak(), PeakAnaPainter::PaintRawData(), PeakAna(), and PeakAnaPainter::ValidGraph().

UInt_t PeakAna::GetDebug ( ) const

inline

Returns

#mDEBUG

Definition at line 227 of file PeakAna.h.

Referenced by StFcsPulseAna::AnalyzeForPedestal(), StFcsPulseAna::FindBaseline(), GausFilter(), StFcsPulseAna::GausFit(), GetPossiblePeaks(), StFcsPulseAna::MBFit(), MeanFilter(), PeakAnaPainter::PaintPeakRanges(), PeakTunnel(), StFcsPulseAna::PulseFit(), SearchForPeak(), and StFcsPulseAna::Sum().

UInt_t PeakAna::GetFilter ( ) const

inline

Returns

mFilter

Definition at line 230 of file PeakAna.h.

References mFilter.

Int_t PeakAna::GetFilterScale ( ) const

inline

Returns

mFilterScale

Definition at line 231 of file PeakAna.h.

References mFilterScale.

const PeakWindow& PeakAna::GetPeak ( UInt_t  peakidx ) const

inline

Returns

peak at index peakidx

Definition at line 228 of file PeakAna.h.

References mPeaks.

Referenced by AddPeakStats(), ConvertPeaksToAna(), StFcsWaveformFitMaker::drawDualFit(), StFcsWaveformFitMaker::gausFit(), StFcsWaveformFitMaker::NPeaksPrePost(), PeakAnaPainter::PaintFoundMarker(), PeakAnaPainter::PaintFoundPeakRange(), PeakAnaPainter::PaintPeakMarkers(), PeakAnaPainter::PaintPeakRanges(), StFcsWaveformFitMaker::PulseFit1(), StFcsWaveformFitMaker::PulseFit2(), StFcsWaveformFitMaker::PulseFitAll(), and StFcsPulseAna::SetFitPars().

PeakWindow& PeakAna::GetPeak ( UInt_t  peakidx )

inline

Returns

peak at index peakidx

Definition at line 229 of file PeakAna.h.

References mPeaks.

void PeakAna::GetPossiblePeaks ( )

virtual

Finds all possible Peaks in signal with some criteria.

Uses a second derivative test to find all peaks in the data. Found peaks must be above the baseline, and the slope must change by mBaseline+mBaselineSigma*mBaselineSigmaScale. These values can be set with the appropriate function calls. Also, checks each peak's probability and merges peaks below some threshold if set.
Called by AnalyzeForPeak();

Definition at line 640 of file PeakAna.cxx.

References Baseline(), BaselineSigma(), BaselineSigmaScale(), PeakWindow::Combine(), GetDebug(), mDeltaX, PeakWindow::mEndX, PeakWindow::mEndY, mG_Data, PeakWindow::mP_Peak, mPeaks, PeakWindow::mPeakX, PeakWindow::mPeakY, PeakWindow::mStartX, PeakWindow::mStartY, mTunnelScale, mTunnelSigma, mXRangeMax, mXRangeMin, mYRangeMax, mYRangeMin, PeakTunnel(), PeakWindow::PeakTunnelProb(), PeakWindow::Print(), PeakWindow::Reset(), and PeakWindow::SetPeak().

Referenced by AnalyzeForPeak().

Double_t PeakAna::MaxX ( ) const

inline

Returns

mXRangeMax

Definition at line 183 of file PeakAna.h.

References mXRangeMax.

Referenced by StFcsPulseAna::GausFit(), PeakAnaPainter::PaintBaselines(), and PeakAnaPainter::PaintFoundPeak().

Double_t PeakAna::MaxXval ( )

inline

Returns

mMaxX

Definition at line 235 of file PeakAna.h.

References GetXYMax(), mMaxX, mXRangeMax, and mXRangeMin.

Double_t PeakAna::MaxY ( ) const

inline

Returns

mYRangeMax

Definition at line 184 of file PeakAna.h.

References mYRangeMax.

Referenced by StFcsPulseAna::GausFit(), PeakAnaPainter::PaintFoundPeakRange(), and PeakAnaPainter::PaintPeakRanges().

Double_t PeakAna::MaxYval ( )

inline

Returns

mMaxY

Definition at line 236 of file PeakAna.h.

References GetXYMax(), mMaxY, mXRangeMax, mXRangeMin, and mYRangeMin.

PeakAna * PeakAna::MeanFilter	(	Int_t	sizeavgs = 0,
		bool	copy = true
	)

Apply a Mean filter to the data.

Applies a Mean filter by sampling "sizeavgs"

Parameters

sizeavgs	number of points to sample during filtering
copy	if copy is true returns a new PeakAna with Mean filtered data, if false modifies "this" object

Returns

new PeakAna object if copy=true or "this" object if false

Definition at line 435 of file PeakAna.cxx.

References Baseline(), GetData(), GetDebug(), mDeltaX, mFilterWeights, PeakAna(), ResetPeak(), and SetData().

Referenced by AnalyzeForPeak().

void PeakAna::MergeByProbability ( std::vector< PeakWindow > &  newpeaks ) const

virtual

Merges peaks in mPeaks using peak probability parameters.

It is intended to be used after calling AnalyzeForPeak() since it doesn't do this by itself.

Parameters

newpeaks

vector to store merged peaks

Reimplemented in StFcsPulseAna.

Definition at line 792 of file PeakAna.cxx.

References mG_Data, mPeaks, mTunnelScale, mTunnelSigma, and PeakTunnel().

Double_t PeakAna::MinX ( ) const

inline

Returns

mXRangeMin

Definition at line 181 of file PeakAna.h.

References mXRangeMin.

Referenced by PeakAnaPainter::PaintBaselines().

Double_t PeakAna::MinY ( ) const

inline

Returns

mYRangeMin

Definition at line 182 of file PeakAna.h.

References mYRangeMin.

Referenced by PeakAnaPainter::PaintFoundPeakRange(), and PeakAnaPainter::PaintPeakRanges().

int PeakAna::NPeaks ( ) const

inline

Returns

size of mPeaks

Definition at line 246 of file PeakAna.h.

References mPeaks.

Referenced by AddPeakStats(), ConvertPeaksToAna(), StFcsWaveformFitMaker::drawDualFit(), StFcsWaveformFitMaker::gausFit(), StFcsWaveformFitMaker::NPeaksPrePost(), PeakAnaPainter::PaintFoundMarker(), PeakAnaPainter::PaintFoundPeakRange(), PeakAnaPainter::PaintPeakMarkers(), PeakAnaPainter::PaintPeakRanges(), StFcsWaveformFitMaker::PulseFit1(), StFcsWaveformFitMaker::PulseFit2(), StFcsWaveformFitMaker::PulseFitAll(), and StFcsPulseAna::SetFitPars().

Double_t PeakAna::PeakProb	(	const PeakWindow &	window,
		Double_t	scale,
		Double_t	sigma
	)		const

compute a given PeakWindow probability using internal graph

Evaluates a given PeakWindow's prbability using internal graph and external parameters for the probability function

Parameters

window	PeakWindow to compute probability
scale	x-value scale for probability, see mTunnelScale
sigma	y-value scale for probability, see mTunnelSigma

Returns

computed probability

Definition at line 635 of file PeakAna.cxx.

References mG_Data, and PeakWindow::PeakTunnelProb().

bool PeakAna::PeakTunnel

(

const PeakWindow &

window

)

const

test whether a given peak satisifies peak tunnel parameters

Evaluates a PeakWindow's probability with function parameters stored in this class, and the internal graph object.

Parameters

window

PeakWindow to be evaluated

Returns

true if peak probability>mTunnelThreshold, false otherwise

Definition at line 619 of file PeakAna.cxx.

References GetDebug(), mG_Data, mTunnelScale, mTunnelSigma, mTunnelThreshold, and PeakWindow::PeakTunnelProb().

Referenced by GetPossiblePeaks(), StFcsPulseAna::MergeByProbability(), and MergeByProbability().

Int_t PeakAna::SearchForPeak ( const std::vector< PeakWindow > &  PossiblePeaks )

virtual

searches a vector of PeakWindow's for a specific peak based on input search criteria

Search criteria is stored in mSearch where the #mStartX is the peak location to search for and #mEndX is the tolerance (width) around which the peak should be found.
Called by AnalyzeForPeak() on mPeaks

Parameters

PossiblePeaks

vector of peaks to search

Returns

index in mPeaks of found peak that matched search criteria

Definition at line 741 of file PeakAna.cxx.

References GetDebug(), PeakWindow::mEndX, mSearch, and PeakWindow::mStartX.

Referenced by StFcsPulseAna::AnalyzeForPeak(), AnalyzeForPeak(), and SearchForPeak().

Double_t PeakAna::SearchPeak ( ) const

inline

Returns

expected peak location for searching

Definition at line 185 of file PeakAna.h.

References mSearch, and PeakWindow::mStartX.

Referenced by Copy().

Double_t PeakAna::SearchWidth ( ) const

inline

Returns

width from expected peak location to search

Definition at line 186 of file PeakAna.h.

References PeakWindow::mEndX, and mSearch.

Referenced by Copy().

void PeakAna::SetBaseline	(	Double_t	base,
		Double_t	sigma
	)

Parameters

base	sets mBaseline
sigma	sets mBaselineSigma

Definition at line 330 of file PeakAna.cxx.

References mBaseline, and mBaselineSigma.

Referenced by StFcsWaveformFitMaker::InitFitter(), StFcsWaveformFitMaker::PulseFit1(), StFcsWaveformFitMaker::PulseFit2(), StFcsWaveformFitMaker::PulseFitAll(), and StFcsPulseAna::SetZS().

void PeakAna::SetBaselineSigmaScale

(

Double_t

scale

)

Parameters

scale

sets mBaselineSigmaScale

Definition at line 337 of file PeakAna.cxx.

References mBaselineSigmaScale.

Referenced by StFcsWaveformFitMaker::InitFitter().

void PeakAna::SetContinuity ( Double_t  val )

inline

Parameters

val	sets mDeltaX

Definition at line 293 of file PeakAna.h.

References mDeltaX.

Referenced by StFcsWaveformFitMaker::InitFitter().

void PeakAna::SetData ( TGraph *  graph )

virtual

sets new data for PeakAna

This will change mG_Data to the graph object passed in and calls ResetPeak(). Since graph is passed as external parameter this means this object should not delete it in the future so #mInternalSignal is set to false. If you want to change this behavior so this class deletes mG_Data call #ForceInternal()

Parameters

graph

sets mG_Data

Definition at line 302 of file PeakAna.cxx.

References mG_Data, and ResetPeak().

Referenced by ConvertPeaksToGraph(), GausFilter(), StFcsWaveformFitMaker::gausFit(), MeanFilter(), StFcsWaveformFitMaker::PedFitPulseFit(), StFcsWaveformFitMaker::PulseFit1(), StFcsWaveformFitMaker::PulseFit2(), StFcsWaveformFitMaker::PulseFitAll(), and StFcsPulseAna::ResetFinder().

void PeakAna::SetData ( TH1 *  hist, UInt_t  numavgs = 1  )

virtual

sets new data for PeakAna using histogram object

Works like SetData() but first calls ConvertHistToGraph() to convert a histogram to a graph. Since it creates a new graph #mInternalSignal is set to true so that the new graph gets deleted properly. The second argument can be used to do a running average over 'numavgs' number of bins.

Parameters

hist	histogram to use as graph data
numavgs	controls how many bins you want to average over when creating graph (1 means no average)

Definition at line 311 of file PeakAna.cxx.

References ConvertHistToGraph(), mG_Data, and ResetPeak().

void PeakAna::SetDebug ( UInt_t  level )

inline

Parameters

level

sets debug level #mDEBUG

Definition at line 275 of file PeakAna.h.

Referenced by StFcsWaveformFitMaker::PedFitPulseFit(), StFcsWaveformFitMaker::PulseFit1(), StFcsWaveformFitMaker::PulseFit2(), and StFcsWaveformFitMaker::PulseFitAll().

void PeakAna::SetFilter	(	UInt_t	filter,
		Int_t	scale,
		Double_t	sigma = 0
	)

Set the filter to use when peak finding.

There are two filters that can be used: a Mean filter which just averages over small samples of the data at a time, and a Gaussian filter which does a weighted average over the data samples, where the weights resemble a Gaussian function see GaussianMatrix2D(). The data sample averaging size is determined by mFilterScale. Note that a filter does not alter the size of the data.

Parameters

filter	sets mFilter (0=none, 1=Mean, 2=Gaussian)
scale	sets mFilterScale (number of points to group together when filtering)
sigma	sigma of Gaussian to use to compute mFilterWeights (0 means sigma=mFilterScale/2)

Definition at line 320 of file PeakAna.cxx.

References GaussianMatrix2D(), mFilter, mFilterScale, and mFilterWeights.

void PeakAna::SetRange	(	Double_t	xmin,
		Double_t	ymin,
		Double_t	xmax,
		Double_t	ymax
	)

Sets the absolute range of the data.

This sets the varaibles that tell the finder the range of x,y values possible for the data. This kind of range is needed for the algorithm to work properly since it only checks for peaks inside that range.

Parameters

xmin	sets mXRangeMin
ymin	sets mYRangeMin
xmax	sets mXRangeMax
ymax	sets mYRangeMax

Definition at line 342 of file PeakAna.cxx.

References mXRangeMax, mXRangeMin, mYRangeMax, and mYRangeMin.

Referenced by StFcsWaveformFitMaker::InitFitter().

void PeakAna::SetSearchWindow	(	Double_t	peak,
		Double_t	width
	)

Sets peak search parameters.

This function is needed if you want to pick/check out a particular peak in the vector of #PeakWindows. It allows you to set the x-value of where you expect or want a peak and how far from that ideal position (width) you would like to check for a peak.

Parameters

peak	x-location where you expect or want a peak
width	how far in x you expect or want a peak from the ideal position of "peak"

Definition at line 349 of file PeakAna.cxx.

References mSearch, ResetPeak(), and PeakWindow::SetWindow().

Referenced by StFcsWaveformFitMaker::InitFitter(), and SearchForPeak().

void PeakAna::SetTunnelPars	(	Double_t	scale,
		Double_t	sigma
	)

Parameters

scale	sets mTunnelScale
sigma	sets mTunnelSigma

Definition at line 371 of file PeakAna.cxx.

References SetTunnelScale(), and SetTunnelSigma().

void PeakAna::SetTunnelScale

(

Double_t

value

)

Parameters

value

sets mTunnelScale

Definition at line 363 of file PeakAna.cxx.

References mTunnelScale.

Referenced by SetTunnelPars(), and StFcsWaveformFitMaker::SetupDavidFitterMay2022().

void PeakAna::SetTunnelSigma

(

Double_t

value

)

Parameters

value

sets mTunnelSigma

Definition at line 367 of file PeakAna.cxx.

References mTunnelSigma.

Referenced by SetTunnelPars(), and StFcsWaveformFitMaker::SetupDavidFitterMay2022().

void PeakAna::SetTunnelThreshold

(

Double_t

value

)

Parameters

value

sets mTunnelThreshold

Definition at line 376 of file PeakAna.cxx.

References mTunnelThreshold.

Referenced by StFcsWaveformFitMaker::SetupDavidFitterMay2022().

Double_t PeakAna::TunnelScale ( ) const

inline

Returns

mTunnelScale

Definition at line 187 of file PeakAna.h.

References mTunnelScale.

Referenced by AddPeakStats().

Double_t PeakAna::TunnelSigma ( ) const

inline

Returns

mTunnelSigma

Definition at line 188 of file PeakAna.h.

References mTunnelSigma.

Referenced by AddPeakStats().

Double_t PeakAna::TunnelThreshold ( ) const

inline

Returns

mTunnelThreshold

Definition at line 189 of file PeakAna.h.

References mTunnelThreshold.

bool PeakAna::ValidPeakIdx

(

)

const

Returns

true if 0<= mComputedIndex < mPeaks.size(), false otherwise

Definition at line 204 of file PeakAna.cxx.

References mComputedIndex, and mPeaks.

Referenced by StFcsWaveformFitMaker::gausFit().

Member Data Documentation

Double_t PeakAna::mBaseline

protected

Minimum threshold to search for a peak.

Threshold for peak start and end values meaning y-value must exceed this variable to even check if it contains a peak. y-values below this variable will be ignored. This defines the noise level

Definition at line 456 of file PeakAna.h.

Referenced by StFcsPulseAna::AnalyzeForPedestal(), Baseline(), Copy(), StFcsPulseAna::FindBaseline(), Init(), StFcsPulseAna::Print(), Print(), StFcsPulseAna::ResetBaseline(), and SetBaseline().

Double_t PeakAna::mBaselineSigma

protected

Error on PeakAna::mBaseline.

This is used to characterize how much noise there is. It will be used with PeakAna::mBaseline to determine the threshold y-value for the data. It effectively sets the resolution of the finder. This is the standard deviation (sigma) around the baseline for ADCs (Also used as a threshold for the hit) error in baseline (fabs in case sigma is negative), //The sigma will determine the threshold value above baseline('value') i.e. the resolution of the finder

Definition at line 463 of file PeakAna.h.

Referenced by StFcsPulseAna::AnalyzeForPedestal(), BaselineSigma(), Copy(), StFcsPulseAna::FindBaseline(), Init(), StFcsPulseAna::Print(), Print(), StFcsPulseAna::ResetBaseline(), and SetBaseline().

Double_t PeakAna::mBaselineSigmaScale

protected

scale on PeakAna::mBaselineSigma to determine final threshold

This is a multiplicative factor on PeakAna::mBaselineSigma that is used to determine the final thresholds on the y-value and slope to start the second derivative test in GetPossiblePeaks(). This "hit" threshold is PeakAna::mBaseline + PeakAna::mBaselineSigma * PeakAna::mBaselineSigmaScale. The default is 4. This threshold also applies to the first positive slope to prevent finding data with small changes as potential peaks.

Definition at line 469 of file PeakAna.h.

Referenced by BaselineSigmaScale(), Copy(), Init(), and SetBaselineSigmaScale().

Int_t PeakAna::mComputedIndex

protected

Index in mPeaks where a peak was found.

This variables is negative if AnalyzeForPeak() was not called.
It is equal to size of mPeaks if AnalyzeForPeak() was called but no peak was found.
All other times it equals the index in mPeaks where the peak was found. The found peak is also stored in mFoundPeak.
This makes it easy to tell whether AnalyzeForPeak() was called and whether or not a peak was found.

Definition at line 436 of file PeakAna.h.

Referenced by AddPeakStats(), StFcsPulseAna::AnalyzeForPeak(), AnalyzeForPeak(), StFcsPulseAna::Clone(), Clone(), FoundPeakIndex(), GoodWindow(), Init(), PeakEnd(), PeakStart(), PeakX(), PeakXY(), PeakY(), ResetPeak(), and ValidPeakIdx().

Double_t PeakAna::mDeltaX

protected

graph known delta-x

Set this value if you know how far apart each x point in the data/graph needs to be. This way the finder can handle discontinuities (i.e. each adjacent point is not a fixed x-distance) in the actual data. Default is -1, which means don't check continuity.

Definition at line 478 of file PeakAna.h.

Referenced by Copy(), GausFilter(), GetPossiblePeaks(), Init(), MeanFilter(), and SetContinuity().

UInt_t PeakAna::mFilter

protected

Filter to use in AnalyzeForPeak()

see SetFilter(). Note that filters do not change the size of the data

• 0 = No Filter (default)
  
• 1 = Mean Filter
  
• 2 = Gauss Filter/Blur
  

Definition at line 509 of file PeakAna.h.

Referenced by AnalyzeForPeak(), Copy(), GetFilter(), Init(), and SetFilter().

PeakWindow PeakAna::mFoundPeak

protected

Copy of found peak in mPeaks.

This gets set after SearchForPeak() is called and finds a peak with given search parameters. It is separate for ease of access and so it can be overwritten for testing and debugging purposes

Definition at line 444 of file PeakAna.h.

Referenced by StFcsPulseAna::AnalyzeForPeak(), AnalyzeForPeak(), StFcsPulseAna::Clone(), Clone(), GoodWindow(), Init(), StFcsPulseAna::MBFit(), PeakEnd(), PeakStart(), PeakX(), PeakXY(), PeakY(), StFcsPulseAna::Print(), Print(), ResetPeak(), SetPeak(), SetWindow(), and StFcsPulseAna::SignalMBPars().

TGraph* PeakAna::mG_Data

protected

TGraph that stores the x,y data.

This graph object will not be deleted by this class unless #PeakAna::mInternalSiganl=true A TGraph is used because it is easier to process but may want to change to dynamic arrays for speed??

Definition at line 485 of file PeakAna.h.

Referenced by StFcsPulseAna::GausFit(), StFcsPulseAna::GetData(), GetData(), GetPossiblePeaks(), GetXYMax(), Init(), StFcsPulseAna::MBFit(), StFcsPulseAna::MergeByProbability(), MergeByProbability(), operator=(), PeakAna(), PeakProb(), PeakTunnel(), PeakX(), PeakXY(), PeakY(), Print(), StFcsPulseAna::PulseFit(), SetData(), StFcsPulseAna::Sum(), and ~PeakAna().

PeakWindow PeakAna::mSearch

protected

Variable that defines peak search parameters.

The values are stored in a PeakWindow object but only PeakWindow::mStartX is used for the peak location and PeakWindow::mEndX is used for the width. The width represents the +- window from PeakWindow::mStartX to look for a peak. This is used by SearchForPeak(). Default is peak at 0 with a width of 1.

Definition at line 450 of file PeakAna.h.

Referenced by Init(), StFcsPulseAna::Print(), Print(), SearchForPeak(), SearchPeak(), SearchWidth(), and SetSearchWindow().

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

• StFcsWaveformFitMaker/PeakAna.h
• StFcsWaveformFitMaker/PeakAna.cxx