#include <ReadRun.h>

Inheritance diagram for ReadRun:

[legend]

Public Member Functions
TH1F *	BaselineCorrectionResults (int, int, float=-5, float=5, int=200)
	Histograms of the contents of baseline_correction_result.

void	ChargeCorrelation (float, float, float, float, float, float, int, int, int, bool=false)
	Plot correlation of integrals/amplitudes between two channels.

float *	ChargeList (int, float=20, float=80, float=0, float=300, bool=1)
	Returns array with the individual "charge"/amplitude for all events of one channel.

TH1F *	ChargeSpectrum (int, float, float, float=0, float=300, float=-50, float=600, int=750)
	Histogram of the "charge" spectrum for one channel.

void	CorrectBaseline (float, float=-999)
	Baseline correction constant window.

void	CorrectBaseline_function (TH1F *, float, float, int)
	Helper function called by CorrectBaseline()

void	CorrectBaselineMin (int=100, double=0.5, int=0, int=0, int=2)
	Baseline correction using minimum sum ( \(\propto\) mean) in range for correction.

void	CorrectBaselineMin (vector< float >, double=0, int=2, int=2)
	Baseline correction using minimum sum ( \(\propto\) mean) in range for correction.

void	CorrectBaselineMinSlopeRMS (int=100, bool=false, double=0.5, int=0, int=0, int=2)
	Baseline correction method searching for non-monotonic, rather constant regions.

void	CorrectBaselineMinSlopeRMS (vector< float >, double=0, int=2, int=3)
	Baseline correction method searching for non-monotonic, rather constant regions.

void	FilterAll (double=.3, double=.9, double=.2)
	Filter all waveforms.

void	FractionEventsAboveThreshold (float=4, bool=true, bool=true, double=0., double=0., bool=false)
	Find events with max/min above/below a certain threshold.

int	GetChannelIndex (int)
	Match channel number (wavecatcher input channel) to channel index.

int	GetCurrentChannel (int)
	Get the current channel index for a certain waveform index.

int	GetCurrentEvent (int)
	Get the current event index for a certain waveform index.

int	GetEventIndex (unsigned int)
	Returns index of a certain event number (if data files are read in parallel threads)

int *	GetIntWindow (TH1F *, float, float, float, float, int=0)
	Determine indices for integration window for peaks.

float	GetPeakIntegral (TH1F *, float, float, float, float, int=0)
	Calculate the integral around a peak with several options explained in GetIntWindow().

void	GetTimingCFD (float=.3, float=100, float=140, double=0., bool=true, int=2, bool=false)
	Determine the timing of the maximum peak with constant fraction discrimination.

TH1F *	Getwf (int)
	Helper that returns the waveform histogram for a certain waveform number number.

TH1F *	Getwf (int, int, int=1)
	Helper that returns the waveform histogram for a certain channel number and a certain event number.

double *	getx (double=0.)
	Get array of x axis (time) for standard wavecatcher settings.

double *	gety (int)
	Get array of y values for a certain waveform.

double *	gety (int, int)
	Get array of y values for a certain waveform.

TH1F *	His_GetTimingCFD (int, float, float, int=-999)
	Plot results of GetTimingCFD()

TH1F *	His_GetTimingCFD_diff (vector< int >, vector< int >, float, float, int=-999)
	Plot timing difference between the mean timings of two channel ranges.

void	IntegralFilter (vector< float >, vector< bool >, float, float, float=50, float=250, bool=false, bool=false)
	Skip events with threshold on integral.

TGraph2D *	MaxDist (int, float=0, float=300)
	Finds maximum amplitude for a given channel in time window ["from", "to"] and creates 3d map of waveforms ordered by maxima.

int	Nevents_good ()
	Number of good events that are not skipped.

bool	PlotChannel (int)
	Check if a channel index should be plotted according to ReadRun::plot_active_channels.

void	PlotChannelAverages (bool=false)
	Plot averages only of the good, corrected waveforms for each channel.

void	PlotChannelSums (bool=false, bool=false, double=0., double=0., int=2)
	Plot sums of all raw waveforms for each channel.

void	PlotWFHeatmaps (float=-20, float=200, int=880, string="", float=0, EColorPalette=kGistEarth)
	Plot stacks of all non-skipped waveforms for all active channels.

void	Print_GetTimingCFD (float=100, float=140, int=0, int=-999, string="S", bool=true)
	Plot results of GetTimingCFD()

void	Print_GetTimingCFD_diff (vector< int >, vector< int >, float=100, float=140, int=0, int=-999, float=-999, float=-999, string="RS", bool=true)
	Plot timing difference between the mean timings of two channel ranges.

void	PrintBaselineCorrectionResults (float=-5, float=5, int=200)
	Print histogram of the baseline correction values for all channels.

void	PrintChargeSpectrum (float, float, float=0, float=300, float=-50, float=600, int=750, float=0., float=0., int=99, int=0, bool=false)
	Plots the "charge" spectrums of all channels.

void	PrintChargeSpectrumWF (float, float, float=0, float=300, int=1, float=0., float=0., float=0., float=0.)
	Plot waveforms of all channels for a given event number and add the determined integration windows to the plot.

void	PrintDCR (float=15, float=85, float=0, float=300, double=3)
	Calculate (SiPM) dark count rate.

void	PrintMaxDist (float=0, float=300)
	Finds maximum amplitude for a given channel in time window ["from", "to"] and creates 3d map of waveforms ordered by maxima.

void	PrintSkippedEvents ()
	Prints a list of all skipped events into the terminal for diagnostics.

void	PrintTimeDist (float=0, float=300, float=0, float=300, int=100, int=0, float=.3)
	Time distribution of maximum, CFD, or 10% - 90% rise time in a certain time window.

void	PrintWFProjection (float=0, float=320, float=-50, float=50, int=200)
	Plots waveform projection histograms of all channels.

void	ReadFile (string, bool=false, int=9, string="out.root", bool=false)
	Routine to read files created by the wavecatcher.

	ReadRun (int max_no_of_bin_files_to_read=0, int min_no_of_bin_files_to_read=0)
	Constructor of the class.

void	SaveChargeLists (float=20, float=80, float=0, float=300, bool=1)
	Saves TGraphs to root file with the individual "charge"/amplitude for all events and all channels.

void	ShiftAllToAverageCF ()
	This function shifts all waveforms to the average signal starting times for each channel.

void	SkipEventsPerChannel (vector< float >, float=0, float=0, bool=false)
	Skip events above/below individual thresholds per channel.

void	SkipEventsTimeDiffCut (int, int, double, double, bool=false)
	Skip events where the time difference between two channels is outside of specified range.

void	SmoothAll (double, int)
	Smoothing all waveforms which are not skipped (for testing, careful when using for analysis!)

void	SmoothAll (double, string="Gaus")
	Smoothing all waveforms which are not skipped (for testing, careful when using for analysis!)

TH1F *	TimeDist (int, float=0, float=300, float=0, float=300, int=100, int=0, float=.3)
	Time distribution of maximum, CFD, or 10% - 90% rise time in a certain time window.

void	UnskipAll ()
	Sets skip_event flag to false for all events, removing any previous cuts.

TH2F *	WFHeatmapChannel (int, float=-20, float=200, int=880)
	2D histogram of all non-skipped waveforms for one channel

TH1F *	WFProjectionChannel (int, int=0, int=1024, float=-50, float=50, int=200)
	Waveform projections for one channel.

virtual	~ReadRun ()
	Destructor.

Static Public Member Functions
static pair< float, bool >	LinearInterpolation (float, float, float, float, float)
	Simple linear interpolation for x.

Public Attributes
vector< int >	active_channels
	Stores the numbers of the active channels.

float **	amplValuessum
	Collects sums of all waveforms for each channel.

vector< vector< float > >	baseline_correction_result
	Stores baseline correction results for CorrectBaseline() and related functions.

int	binNumber = 1024
	Number of bins (always 1024 samples per waveform). Do not change!

float	DAQ_factor = 250. / 4096.
	DAQ conversion factor for wavecatcher output to mV.

string	data_path
	Path to data.

bool	discard_original_eventnr = false
	Can be used to discard the original event numbering of the data.

int	end_read_at_channel = -1
	See ReadRun::start_read_at_channel.

vector< unsigned int >	eventnr_storage
	Events will be stored here in the order they have been read.

vector< TFitResultPtr >	fit_results
	Stores the fit results of PrintChargeSpectrum() for all channels and all function calls in ascending order.

int	MaxNoOfBinFilesToRead
	Number of last .bin file to be read in.

int	maxNWF = 1e7
	Maximum possible number of waveforms in data: number of active channels x number of events.

int *	maxSumBin
	Stores bin numbers where the sum of waveforms have their maximum.

vector< float >	mean_integral
	Stores the mean integral/lightyield from PrintChargeSpectrum() for all channels.

int	MinNoOfBinFilesToRead
	Number first of .bin file to be read in.

int	nchannels
	Number of active channels in data.

int	nChannelsWC = 64
	Wavecatcher hardware max. number of channels (reduce/increase if not using the 64 channel crate)

int	nevents
	Number of triggered events in data.

int	nwf
	Total number of waveforms read from data: number of active channels x number of events.

vector< int >	plot_active_channels
	Stores the numbers of the active channels which should be plotted.

vector< vector< float > >	PrintChargeSpectrum_cal = vector(nChannelsWC, vector<float>(2, 1))
	Calibration values to normalize charge spectrum to number of photoelectrons Chennels must be ordered as in plot_active_channels. The first entry must be the gain and the second the position of the pedestal.

vector< float >	PrintChargeSpectrum_pars
	Starting values of the fit parameters for PrintChargeSpectrum()

TFile *	root_out
	Stores results of analysis.

TClonesArray *	rundata
	Stores data.

bool	Shift_WFs_in_file_loop = false
	Shift waveforms with CFD so that all events start at the same time Call after initializing class and before calling ReadFile(). Set the constant fraction, the bin to shift the signal to, and the search window with tWF_CF, tWF_CF_bin, and tWF_CF_lo and tWF_CF_hi, respectively.

vector< bool >	skip_event
	Stores the event numbers which should be skipped in the analysis.

float	SP = .3125
	Sampling: ns per bin of data, sampling rate 3.2 GS/s -> 0.3125 ns.

int	start_read_at_channel = -1
	Do analysis only for limited range of channels to reduce memory usage.

vector< int >	switch_polarity_for_channels
	Stores the channel number where the polarity should be inverted. Example use to switch polarity for channel 0 and channel 14: `mymeas.switch_polarity_for_channels = {0, 14};`. Needs to be called before ReadFile().

float	tCutEndg
	End of time window for baseline correction when using ReadRun::Using_BaselineCorrection_in_file_loop.

float	tCutg
	Start of time window for baseline correction when using ReadRun::Using_BaselineCorrection_in_file_loop.

vector< TFitResultPtr >	timing_fit_results
	Stores the fit results of Print_GetTimingCFD() for all channels.

vector< vector< float > >	timing_results
	Matrix to store timing of peaks from GetTimingCFD()

float	tWF_CF = 0.3
	Constant fraction of maximum (between ~0.1 and 1) for ReadRun::Shift_WFs_in_file_loop.

int	tWF_CF_bin = 375
	Time bin all events will be shifted to for ReadRun::Shift_WFs_in_file_loop Needs to be 300<"tWF_CF_bin"<500 ("tWF_CF_bin"=375 means all peaks will be shifted to 375*.3125 ns=117.1875 ns)

int	tWF_CF_hi = 500
	End of range of bins where the signal is expected for ReadRun::Shift_WFs_in_file_loop.

int	tWF_CF_lo = 320
	Start of range of bins where the signal is expected for ReadRun::Shift_WFs_in_file_loop.

bool	Using_BaselineCorrection_in_file_loop = false
	Set true for baseline correction during data reading. Needs to be called before ReadFile().

Protected Member Functions
void	checkData () const
	Primitive check to see if data has been loaded.

Detailed Description

Examples: read_exampledata.cc, and timing_example.cc.

Definition at line 57 of file ReadRun.h.

Constructor & Destructor Documentation

◆ ReadRun()

ReadRun::ReadRun	(	int	max_no_of_bin_files_to_read = `0`,
		int	min_no_of_bin_files_to_read = `0`
	)

Constructor of the class.

Parameters

max_no_of_bin_files_to_read	Number of last .bin file to be read in. Set it to =>1 in order to constrain the number of .bin files to be read from the target folder. Intended for quick tests on a fraction of the full dataset or for batch reading if combined with min_no_of_bin_files_to_read.
min_no_of_bin_files_to_read	Number first of .bin file to be read in. Can be used to batch read large datasets in chunks of files.

Definition at line 24 of file ReadRun.cc.

◆ ~ReadRun()

ReadRun::~ReadRun ( )

virtual

Destructor.

Definition at line 376 of file ReadRun.cc.

Member Function Documentation

◆ BaselineCorrectionResults()

TH1F * ReadRun::BaselineCorrectionResults	(	int	channel_index,
		int	which,
		float	rangestart = `-5`,
		float	rangeend = `5`,
		int	nbins = `200`
	)

Histograms of the contents of baseline_correction_result.

See PrintBaselineCorrectionResults() for parameters.

Returns: Histogram for one channel.

Definition at line 1118 of file ReadRun.cc.

◆ ChargeCorrelation()

void ReadRun::ChargeCorrelation	(	float	windowlow,
		float	windowhi,
		float	start,
		float	end,
		float	rangestart,
		float	rangeend,
		int	nbins,
		int	channel1,
		int	channel2,
		bool	ignore_skipped_events = `false`
	)

Plot correlation of integrals/amplitudes between two channels.

See GetIntWindow() and PrintChargeSpectrum() for parameters.

Integrals of the signals of two channels for each event plottet against each other. A clear correlation is visible: On average, if channel 2 records a large signal also channel 3 records a large signal. Around (0,0) the correlation of the pedestals can be seen (no signal in both channels). Code in example.

Parameters

windowlow	Integrate from "windowlow" ns from max...
windowhi	...to "windowhi" ns from max.
start	Find max from "start" in ns...
end	...to "end" in ns.
rangestart	Plot x & y range start
rangeend	Plot x & y range end
nbins	Number of x & y bins of the histogram
channel1	First channel number to compare
channel2	second channel number to compare
ignore_skipped_events	Set true to plot only events which passed filtering, else all events will be plotted

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 1765 of file ReadRun.cc.

◆ ChargeList()

float * ReadRun::ChargeList	(	int	channel_index,
		float	windowlow = `20`,
		float	windowhi = `80`,
		float	start = `0`,
		float	end = `300`,
		bool	negative_vals = `1`
	)

Returns array with the individual "charge"/amplitude for all events of one channel.

See SaveChargeLists() and GetIntWindow().

Parameters

channel_index	Index of the channel.
windowlow	Integrate from "windowlow" ns from max...
windowhi	...to "windowhi" ns from max.
start	Find max from "start" in ns...
end	...to "end" in ns.
negative_vals	If true will save negative values. If false will set negative values to 0.

Definition at line 1697 of file ReadRun.cc.

◆ ChargeSpectrum()

TH1F * ReadRun::ChargeSpectrum	(	int	channel_index,
		float	windowlow,
		float	windowhi,
		float	start = `0`,
		float	end = `300`,
		float	rangestart = `-50`,
		float	rangeend = `600`,
		int	nbins = `750`
	)

Histogram of the "charge" spectrum for one channel.

See PrintChargeSpectrum() for parameters.

Returns: Histogram for one channel.

Definition at line 1807 of file ReadRun.cc.

◆ checkData()

void ReadRun::checkData ( ) const

inlineprotected

Primitive check to see if data has been loaded.

Definition at line 113 of file ReadRun.h.

◆ CorrectBaseline()

void ReadRun::CorrectBaseline	(	float	tCut,
		float	tCutEnd = `-999`
	)

Baseline correction constant window.

Corrects the baseline (DC offset) of all waveforms.
Uses the mean between t=0 and t="tCut" or between t="tCut" and t="tCutEnd" as offset.
Call method before ReadFile() if you want it to happen while reading.

Most simple and fast method.
Useful for measurements with very few background events/dark counts.
Using a constant window for the baseline means there might be a background pulse which would lead to wrong correction.

Stores results for all channels and all events in ReadRun::baseline_correction_result.
Results will be visualized for each event in PrintChargeSpectrumWF().

Parameters

tCut	Time denoting the end or the beginning (if "tCutEnd" is set) of the integration window.
tCutEnd	Time denoting the end of the integration window.

Definition at line 707 of file ReadRun.cc.

◆ CorrectBaseline_function()

void ReadRun::CorrectBaseline_function	(	TH1F *	his,
		float	tCut,
		float	tCutEnd,
		int	nwaveform
	)

Helper function called by CorrectBaseline()

See CorrectBaseline()

Definition at line 730 of file ReadRun.cc.

◆ CorrectBaselineMin() [1/2]

void ReadRun::CorrectBaselineMin	(	int	nIntegrationWindow = `100`,
		double	sigma = `0.5`,
		int	max_bin_for_baseline = `0`,
		int	start_at = `0`,
		int	smooth_method = `2`
	)

Baseline correction using minimum sum ( \(\propto\) mean) in range for correction.

This is a deprecated version of CorrectBaselineMin. It will be removed in future releases.
Corrects the baseline (DC offset) of all waveforms.
Searches for

\(\mathbf{min}\left( \sum y_i \right) \)

in range {"start_at", "max_bin_for_baseline"}, summing over "nIntegrationWindow" bins.
Make sure the search range is shortly before the triggered signal is expected to arrive.

Helpful for (groups of/irradiated) SiPMs with very high dark count rate (DCR) where the voltage rarely relaxes back to the constant baseline before the next dark count/signal arrives:
\( \Rightarrow DCR \sim 1/t_{signal} \)

Stores results for all channels and all events in ReadRun::baseline_correction_result.
Results will be visualized for each event in PrintChargeSpectrumWF().

Parameters

nIntegrationWindow	Number of bins used for baseline correction. The correction factor will be the signal averaged over this number bins.
sigma	Number of bins before and after central bin for running average OR gauss sigma in ns for gauss kernel and convolution. Set to 0 for no smoothing. Use with care!
max_bin_for_baseline	Maximum bin for search window.
start_at	Minimum bin for search window.
smooth_method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.

Definition at line 1035 of file ReadRun.cc.

◆ CorrectBaselineMin() [2/2]

void ReadRun::CorrectBaselineMin	(	vector< float >	window,
		double	sigma = `0`,
		int	smooth_method = `2`,
		int	increment = `2`
	)

Baseline correction using minimum sum ( \(\propto\) mean) in range for correction.

Corrects the baseline (DC offset) of all waveforms.
Searches for

\(\mathbf{min}\left( \sum y_i \right) \)

in range {window[1], window[2]}, summing over window[0] ns.
Make sure the search range is shortly before the triggered signal is expected to arrive.

Helpful for (groups of/irradiated) SiPMs with very high dark count rate (DCR) where the voltage rarely relaxes back to the constant baseline before the next dark count/signal arrives:
\( \Rightarrow DCR \sim 1/t_{signal} \)

Stores results for all channels and all events in ReadRun::baseline_correction_result.
Results will be visualized for each event in PrintChargeSpectrumWF().

Parameters

window	Vector containing {length for averaging, search start, search end} in ns. Example: {20, 10, 90} would search for the best baseline candidate from 10 ns to 90 ns, averaging over 20 ns.
sigma	Number of bins before and after central bin for running average OR gauss sigma in ns for gauss kernel and convolution. Set to 0 for no smoothing. Use with care!
smooth_method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.
increment	Increment for search in bins per step. Default value is 3 (=0.9375 ns).

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 938 of file ReadRun.cc.

◆ CorrectBaselineMinSlopeRMS() [1/2]

void ReadRun::CorrectBaselineMinSlopeRMS	(	int	nIntegrationWindow = `100`,
		bool	smooth = `false`,
		double	sigma = `0.5`,
		int	max_bin_for_baseline = `0`,
		int	start_at = `0`,
		int	smooth_method = `2`
	)

Baseline correction method searching for non-monotonic, rather constant regions.

This is a deprecated version of CorrectBaselineMinSlopeRMS. It will be removed in future releases.

Corrects the baseline (DC offset) of all waveforms.
Determines the region of "nIntegrationWindow" bins where the squared sum plus the square of the sum of the slope of the (smoothed) waveform reaches its minimum:

\(\mathbf{min}\left( \sum \left(\Delta y_i \right)^2 + \left(\sum \Delta y_i \right)^2 \right) \)

Here, \(\sum \left(\Delta y_i \right)^2 \to 0\) if the region is constant and \(\left( \sum \Delta y_i \right)^2 \to 0\) if the region is constant or oscillating around a constant value. The second term penalizes monotonic regions with a small, but rather constant slope (e. g. tails).

Slow, but versatile since it searches for the optimal baseline candidate region in a defined range.
Will prefer constant sections of the waveform for the estimation of the baseline.
Not well suited if there is not constant baseline in the signal, which can happen if the dark count rate is so high that dark counts overlap (e. g. an array of SiPMs) or if the baseline level fluctuates. In such a case use CorrectBaselineMin()

Stores results for all channels and all events in ReadRun::baseline_correction_result.
Results will be visualized for each event in PrintChargeSpectrumWF().

Parameters

nIntegrationWindow	Number of bins used for baseline correction. The correction factor will be the signal averaged over this number bins.
smooth	Deprecated! If true will apply smoothing to all waveforms. This will change all waveforms, which should rather be done with SmoothAll().
sigma	Number of bins before and after central bin for running average OR gauss sigma in ns for gauss kernel and convolution. Set to 0 for no smoothing. Use with care!
max_bin_for_baseline	Maximum bin for search window.
start_at	Minimum bin for search window.
smooth_method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.

Definition at line 902 of file ReadRun.cc.

◆ CorrectBaselineMinSlopeRMS() [2/2]

void ReadRun::CorrectBaselineMinSlopeRMS	(	vector< float >	window,
		double	sigma = `0`,
		int	smooth_method = `2`,
		int	increment = `3`
	)

Baseline correction method searching for non-monotonic, rather constant regions.

Corrects the baseline (DC offset) of all waveforms.
Determines the region of window[0] ns between window[1] ns and window[2] ns where the squared sum plus the square of the sum of the slope of the (smoothed) waveform reaches its minimum:

\(\mathbf{min}\left( \sum \left(\Delta y_i \right)^2 + \left(\sum \Delta y_i \right)^2 \right) \)

Here, \(\sum \left(\Delta y_i \right)^2 \to 0\) if the region is constant and \(\left( \sum \Delta y_i \right)^2 \to 0\) if the region is constant or oscillating around a constant value. The second term penalizes monotonic regions with a small, but rather constant slope (e. g. tails).

Slow, but versatile since it searches for the optimal baseline candidate region in a defined range.
Will prefer constant sections of the waveform for the estimation of the baseline.
Not well suited if there is not constant baseline in the signal, which can happen if the dark count rate is so high that dark counts overlap (e. g. an array of SiPMs) or if the baseline level fluctuates. In such a case use CorrectBaselineMin()

Stores results for all channels and all events in ReadRun::baseline_correction_result.
Results will be visualized for each event in PrintChargeSpectrumWF().

Parameters

window	Vector containing {length for averaging, search start, search end} in ns. Example: {20, 10, 90} would search for the best baseline candidate from 10 ns to 90 ns, averaging over 20 ns.
sigma	Number of bins before and after central bin for running average OR gauss sigma in ns for gauss
smooth_method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.
increment	Increment for search in bins per step. Default value is 3 (=0.9375 ns).

Examples: read_exampledata.cc.

Definition at line 784 of file ReadRun.cc.

◆ FilterAll()

void ReadRun::FilterAll	(	double	sigma1 = `.3`,
		double	sigma2 = `.9`,
		double	factor = `.2`
	)

Filter all waveforms.

Experimental. See Filters::ResponseFilter() or Filters::SecondOrderUnderdampedFilter().

Parameters

sigma1	First.
sigma2	Second.
factor	Factor for negative part (0 < factor < 1).

Definition at line 641 of file ReadRun.cc.

◆ FractionEventsAboveThreshold()

void ReadRun::FractionEventsAboveThreshold	(	float	threshold = `4`,
		bool	max = `true`,
		bool	greater = `true`,
		double	from = `0.`,
		double	to = `0.`,
		bool	verbose = `false`
	)

Find events with max/min above/below a certain threshold.

Needs to be called before the charge spectrum etc functions.
Baseline correction should be called before this function.

Parameters

threshold	Threshold in mV.
max	If true uses max, else uses min.
greater	If true looks for events with max/min>threshold, else looks for events with max/min<threshold.
from	Start search at "from" in ns.
to	End search at "to" in ns.
verbose	Set true for extra verbosity.

Definition at line 1328 of file ReadRun.cc.

◆ GetChannelIndex()

int ReadRun::GetChannelIndex ( int channel_number )

Match channel number (wavecatcher input channel) to channel index.

Parameters

channel_number Number of the channel as defined in the wavecatcher software

Returns: Corresponding index for this channel

Definition at line 2615 of file ReadRun.cc.

◆ GetCurrentChannel()

int ReadRun::GetCurrentChannel ( int waveform_index )

Get the current channel index for a certain waveform index.

Parameters

waveform_index

Returns: Current channel index

Definition at line 2630 of file ReadRun.cc.

◆ GetCurrentEvent()

int ReadRun::GetCurrentEvent ( int waveform_index )

Get the current event index for a certain waveform index.

Parameters

waveform_index

Returns: Current event index

Definition at line 2637 of file ReadRun.cc.

◆ GetEventIndex()

int ReadRun::GetEventIndex ( unsigned int eventnr )

Returns index of a certain event number (if data files are read in parallel threads)

Parameters

eventnr Event number as stored in the data.

Returns: Corresponding event number in the internal data structure.

Definition at line 2597 of file ReadRun.cc.

◆ GetIntWindow()

int * ReadRun::GetIntWindow	(	TH1F *	his,
		float	windowlow,
		float	windowhi,
		float	start,
		float	end,
		int	channel = `0`
	)

Determine indices for integration window for peaks.

Default usage: Find maximum in range ("start", "end") and return bin numbers for [0] the max, [1] t_max - "windowlow", and [2] t_max + "windowhi".
If ("start" < 0 || "end" < 0) doesn't return max and integration window is fixed relative to the maximum of the sum of all waveforms:
t(max(sum_spectrum[channel])) +/- "windowhi"/"windowlow"
If ("windowlow" == "start" && "windowhi" == "end") doesn't return max and sets fixed integration window from "start" until "end" for all channels.

Parameters

his	Histogram to integrate.
windowlow	Integration time left to the maximum of the peak.
windowhi	Integration time right to the maximum of the peak.
start	Range for finding maximum.
end	Range for finding maximum.
channel	Channel index in case the integration should be around the maximum of the sum of all waveforms

Returns: Array { max, \( n_{t,start} \) , \( n_{t,end} \) }

Definition at line 1534 of file ReadRun.cc.

◆ GetPeakIntegral()

float ReadRun::GetPeakIntegral	(	TH1F *	his,
		float	windowlow,
		float	windowhi,
		float	start,
		float	end,
		int	channel_index = `0`
	)

Calculate the integral around a peak with several options explained in GetIntWindow().

Calculated over an integer number of bins.
If start = end = 0 will return the amplitude of the peak.
If start < 0 || end < 0 will return the integral over the fixed integration window around the maximum of the sum spectrum for each channel.
If windowlow == start && windowhi == end will return the integral over the fixed integration window for all channels.

Parameters

his	Histogram with peak.
windowlow	Integration time left to the maximum of the peak.
windowhi	Integration time right to the maximum of the peak.
start	Range for finding maximum.
end	Range for finding maximum.
channel_index	Channel index in case the integration should be around the maximum of the sum of all waveforms.

Returns: Integral/amplitude.

Definition at line 1588 of file ReadRun.cc.

◆ GetTimingCFD()

void ReadRun::GetTimingCFD	(	float	cf_r = `.3`,
		float	start_at_t = `100`,
		float	end_at_t = `140`,
		double	sigma = `0.`,
		bool	find_CF_from_start = `true`,
		int	smooth_method = `2`,
		bool	use_spline = `false`
	)

Determine the timing of the maximum peak with constant fraction discrimination.

Determines timing in the time interval ["start_at_t", "end_at_t"] with CFD for fraction of maximum "cf_r".
Stores timing information for all channels and all events in ReadRun::timing_results.
Per event results will be visualized in PrintChargeSpectrumWF().
Cumulative per channel results can be visualized with Print_GetTimingCFD().
Results can be used for time difference cuts with SkipEventsTimeDiffCut().

Parameters

cf_r	Fraction of maximum for CFD. If set > 1 it will be used as a fixed threshold in mV, so it will no longer use CFD.
start_at_t	Time in ns to start searching.
end_at_t	Time in ns to end searching.
sigma	Number of bins before and after central bin for running average OR gauss sigma in ns for gauss kernel and convolution. This will bias the results! Do not use (or use very carefully, only for noisy data)! Set to 0 if you do not want to use smoothing.
find_CF_from_start	If true will start search from "start_at_t" to find the first arriving photon (default setting). If false search backwards from the time of the maximum.
smooth_method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.
use_spline	If false will use linear interpolation between the two bins closest to cf_r. If true will use a 5th order spline and bisection method for interpolation. Performs a bit better in most cases compared to only linear interpolation.

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 1188 of file ReadRun.cc.

◆ Getwf() [1/2]

TH1F * ReadRun::Getwf ( int wf_nr )

Helper that returns the waveform histogram for a certain waveform number number.

Parameters

wf_nr Waveform number

Returns: Waveform histogram

Definition at line 2547 of file ReadRun.cc.

◆ Getwf() [2/2]

TH1F * ReadRun::Getwf	(	int	channelnr,
		int	eventnr,
		int	color = `1`
	)

Helper that returns the waveform histogram for a certain channel number and a certain event number.

Parameters

channelnr	Channel number index (not the actual channel number)
eventnr	Event number
color	Choose color of histogram

Returns: Waveform histogram

Definition at line 2557 of file ReadRun.cc.

◆ getx()

double * ReadRun::getx ( double shift = 0. )

Get array of x axis (time) for standard wavecatcher settings.

Parameters

shift Offset

Returns: Time array

Definition at line 2569 of file ReadRun.cc.

◆ gety() [1/2]

double * ReadRun::gety ( int waveform_index )

Get array of y values for a certain waveform.

Parameters

waveform_index Waveform index

Returns: Y values of waveform

Definition at line 2580 of file ReadRun.cc.

◆ gety() [2/2]

double * ReadRun::gety	(	int	channelnr,
		int	eventnr
	)

Get array of y values for a certain waveform.

Parameters

channelnr	Channel number index (not the actual channel number)
eventnr	Event number

Returns: Y values of waveform

Definition at line 2589 of file ReadRun.cc.

◆ His_GetTimingCFD()

TH1F * ReadRun::His_GetTimingCFD	(	int	channel_index,
		float	rangestart,
		float	rangeend,
		int	nbins = `-999`
	)

Plot results of GetTimingCFD()

See Print_GetTimingCFD() for parameters.

Returns: Timing histogram for one channel

Definition at line 2277 of file ReadRun.cc.

◆ His_GetTimingCFD_diff()

TH1F * ReadRun::His_GetTimingCFD_diff	(	vector< int >	channels1,
		vector< int >	channels2,
		float	rangestart,
		float	rangeend,
		int	nbins = `-999`
	)

Plot timing difference between the mean timings of two channel ranges.

See Print_GetTimingCFD_diff() for parameters.

Returns: Histogram with event-wise timing differences between two channel ranges

Definition at line 2350 of file ReadRun.cc.

◆ IntegralFilter()

void ReadRun::IntegralFilter	(	vector< float >	thresholds,
		vector< bool >	highlow,
		float	windowlow,
		float	windowhi,
		float	start = `50`,
		float	end = `250`,
		bool	use_AND_condition = `false`,
		bool	verbose = `false`
	)

Skip events with threshold on integral.

Compare with SkipEventsPerChannel()
Needs to be called before the charge spectrum etc functions in order to have an effect on them.
Baseline correction should be called before this function.

Parameters

thresholds	Vector should contain a threshold for each active channel saved in the data, in ascending order (ch0, ch1 ...). Negative thresholds mean events below threshold will be cut. A threshold of 0 means the channel will not be evaluated. If only one value is given this value will be used for all active channels.
highlow	Vector should contain a bool for each active channel. True means events with integrals above threshold will be cut, false means below threshold. If only one value is given this value will be used for all active channels.
windowlow	Integration time left to the maximum of the peak.
windowhi	Integration time right to the maximum of the peak.
start	Range for finding maximum.
end	Range for finding maximum.
use_AND_condition	If set true it will overrule previously applied cuts and un-skip events that pass integral criterium.
verbose	Set true for extra verbosity.

Examples: read_exampledata.cc, timing_example.cc, and timing_example_rebin.cc.

Definition at line 1443 of file ReadRun.cc.

◆ LinearInterpolation()

pair< float, bool > ReadRun::LinearInterpolation	(	float	ym,
		float	x1,
		float	x2,
		float	y1,
		float	y2
	)

static

Simple linear interpolation for x.

Will return the mean of x1 and x2 if y1=y2.

Parameters

ym	Y value for evaluation
x1	X1
x2	X2
y1	Y1
y2	Y2

Returns: x value at "ym"

Definition at line 2658 of file ReadRun.cc.

◆ MaxDist()

TGraph2D * ReadRun::MaxDist	(	int	channel_index,
		float	from = `0`,
		float	to = `300`
	)

Finds maximum amplitude for a given channel in time window ["from", "to"] and creates 3d map of waveforms ordered by maxima.

Use PrintMaxDist() to plot all channels. Use only for small datasets as it will contain all of the data

Returns: TGraph2D of all histograms ordered by maximum amplitude

Definition at line 2227 of file ReadRun.cc.

◆ Nevents_good()

int ReadRun::Nevents_good ( )

Number of good events that are not skipped.

Definition at line 1510 of file ReadRun.cc.

◆ PlotChannel()

bool ReadRun::PlotChannel ( int i )

Check if a channel index should be plotted according to ReadRun::plot_active_channels.

Parameters

i	Channel index.

Definition at line 2643 of file ReadRun.cc.

◆ PlotChannelAverages()

void ReadRun::PlotChannelAverages ( bool normalize = false )

Plot averages only of the good, corrected waveforms for each channel.

Similar to PlotChannelSums(), but will average all non-skipped waveforms.
Can be used to inspect average waveforms after baseline correction etc. has been applied. To do so, call function after calling correction and event filter functions.

This function plots the sum of all non-skipped waveforms for each channel, with corrections. Compare with the result for PlotChannelSums(). Code in example.

Parameters

normalize If true will normalize the maximum to 1.

Examples: read_exampledata.cc, timing_example.cc, and timing_example_rebin.cc.

Definition at line 454 of file ReadRun.cc.

◆ PlotChannelSums()

void ReadRun::PlotChannelSums	(	bool	smooth = `false`,
		bool	normalize = `false`,
		double	shift = `0.`,
		double	sigma = `0.`,
		int	smooth_method = `2`
	)

Plot sums of all raw waveforms for each channel.

To plot the average waveforms after baseline correction etc. use PlotChannelAverages().

This function plots the sum of all waveforms for each channel, without any corrections. Channel 9 was measured with an offset as visible here. Code in example.

Parameters

smooth	If true it will apply smoothing to plots. Do not use without very good reason as it biases the results.
normalize	If true will normalize the maximum to 1.
shift	Shift histogram by "shift" ns
sigma	Number of bins before and after central bin for running average OR gauss sigma in ns for gauss kernel and convolution.
smooth_method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.

Examples: read_exampledata.cc.

Definition at line 396 of file ReadRun.cc.

◆ PlotWFHeatmaps()

void ReadRun::PlotWFHeatmaps	(	float	ymin = `-20`,
		float	ymax = `200`,
		int	n_bins_y = `880`,
		string	z_opt = `""`,
		float	z_max = `0`,
		EColorPalette	palette = `kGistEarth`
	)

Plot stacks of all non-skipped waveforms for all active channels.

Classical SiPM dark count/calibration plot in the style of a phosphor oscilloscope screen.
Helpful to see the prevalence of certain signal/baseline shapes etc.
Take care not to plot too many channels at once to maintain visibility and performance (-> ReadRun::plot_active_channels).

Waveforms of all events filled into a single histogram. Code in example.

Parameters

ymin	Min. y range
ymax	Max. y range
n_bins_y	Number of bins along y
z_opt	"log": Set z logarithmic. "COLZ0": Do not plot bins with zero entries.
z_max	Max. z range. Set to zero to use auto range (default).
palette	Root color palette (see https://root.cern.ch/doc/master/classTColor.html).

Examples: read_exampledata.cc.

Definition at line 556 of file ReadRun.cc.

◆ Print_GetTimingCFD()

void ReadRun::Print_GetTimingCFD	(	float	rangestart = `100`,
		float	rangeend = `140`,
		int	do_fit = `0`,
		int	nbins = `-999`,
		string	fitoption = `"S"`,
		bool	set_errors = `true`
	)

Plot results of GetTimingCFD()

Beginning of the signals for all good events determined with constant fraction discrimination. The red lines are gauss functions fitted to the distrutions. Code in example.

Parameters

rangestart	Start of x range for plot in ns.
rangeend	End of x range for plot in ns.
do_fit	If 1: fits a gaussian. Else do not fit. Fit results per channel are stored in ReadRun::timing_fit_results.
nbins	Number of bins for histogram. Will use 320 MHz sampling rate for binning if nbins = -999.
fitoption	ROOT fit option, default is "S". See Fit(): https://root.cern/doc/master/classTH1.html
set_errors	Assign errors to the bins. Will assign errors of 1 to empty bins and \( \sqrt(N) \) if they are not empty. Can improve the chi^2 fit.

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 2300 of file ReadRun.cc.

◆ Print_GetTimingCFD_diff()

void ReadRun::Print_GetTimingCFD_diff	(	vector< int >	channels1,
		vector< int >	channels2,
		float	rangestart = `100`,
		float	rangeend = `140`,
		int	do_fit = `0`,
		int	nbins = `-999`,
		float	fitrangestart = `-999`,
		float	fitrangeend = `-999`,
		string	fitoption = `"RS"`,
		bool	set_errors = `true`
	)

Plot timing difference between the mean timings of two channel ranges.

Plots the difference between the peak times between the mean times of two ranges of channels for each event.
It calculates \( \Delta t = <t_{second,i}> - <t_{first,i}> \) .

The vectors of channels to compare are added with curly brackets:

‍mymeas.Print_GetTimingCFD_diff({ 26, 14 }, { 19 }, 0, 20, 2, 200);

would plot \( \Delta t = t_{ch19} - (t_{ch26} + t_{ch14})/2 \) from 0 ns to 20 ns with 200 bins (100 ps bin width). Another example is given in the plot below.

Event-wise time differences of the start of the signals of two channels. Code in example.

Parameters

channels1	Vector of first channel numbers (wavecatcher channel numbers).
channels2	Vector of second channel numbers to compare.
rangestart	Start of x range for plot in ns.
rangeend	End of x range for plot in ns.
do_fit	If 1: Fit a gaussian. If 2: Fit a gaussian-exponential convolution (Fitf_exp_gauss) to account for different arrival times of photons due to different possible light paths in the scintillator/light guide and/or delay due to self-absorption and reemission of photons in the scintillator. To be used for long light paths in the scintillator. See https://doi.org/10.1016/S0029-554X(79)90170-8 . This option only works for sufficient asymmetry \(\tau > \sigma/2\). Otherwise, the exponential decay time becomes too small to be fitted. If the asymmetry is too small (skewness<0.15) option 1 will be used by default. If 3: Fits the sum of two gaussians where the second gauss serves as a rough background estimate. Background means events that should have been filtered out. Else: Do not fit.
nbins	Number of bins for histogram.
fitrangestart	Start of fitting range.
fitrangeend	End of fitting range.
fitoption	ROOT fitting option. Default is "RS" (chi^2). You can try to use the likelihood method with "LRS" if the data is very clean. Outliers will influence the results for the likelihood method so it is advisable to limit the fit range to exclude outliers for "LRS".
set_errors	Assign errors to the bins. Will assign errors of 1 to empty bins and \( \sqrt(N) \) if they are not empty. Can improve the chi^2 fit.

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 2438 of file ReadRun.cc.

◆ PrintBaselineCorrectionResults()

void ReadRun::PrintBaselineCorrectionResults	(	float	rangestart = `-5`,
		float	rangeend = `5`,
		int	nbins = `200`
	)

Print histogram of the baseline correction values for all channels.

Currently only optimized for the correction values themselves.

Parameters

rangestart	Plot x range start.
rangeend	Plot x range end.
nbins	Number of bins in range.

Examples: timing_example.cc.

Definition at line 1138 of file ReadRun.cc.

◆ PrintChargeSpectrum()

void ReadRun::PrintChargeSpectrum	(	float	windowlow,
		float	windowhi,
		float	start = `0`,
		float	end = `300`,
		float	rangestart = `-50`,
		float	rangeend = `600`,
		int	nbins = `750`,
		float	fitrangestart = `0.`,
		float	fitrangeend = `0.`,
		int	max_channel_nr_to_fit = `99`,
		int	which_fitf = `0`,
		bool	use_log_y = `false`
	)

Plots the "charge" spectrums of all channels.

Integrate all pulses in range ("start", "end") from t_max - "windowlow" to t_max + "windowhi" for a given channel and return the charge histogram with x range ("rangestart", "rangeend") and the number of bins "nbins".
It is not really charge, but either amplitude (mV) or integral (mV x ns). See ChargeSpectrum() and GetIntWindow().
Can be normalised to the number of photoelectrons by defining the calibration values in PrintChargeSpectrum_cal.

Simple example of the integrated signals for a single channel. The resulting integrated signals are fitted with a Landau-Gauss convolution (-> energy deposition of a minimum ionizing particle in a thin absorber). Code in example.

Integrated signals for a SiPM in blue and a fit with the fit function Fitf for SiPMs missing after-pulses and dark counts in red. The spectrum is not well fit by the simplified model. You can try different fit models in the example cosmics-fit.ipynb.

Parameters

windowlow	Integrate from "windowlow" ns from max...
windowhi	...to "windowhi" ns from max.
start	Find max from "start" in ns...
end	...to "end" in ns.
rangestart	Plot x range start
rangeend	Plot x range end
nbins	Number of bins of histogram
fitrangestart	Fit range start
fitrangeend	Fit range end
max_channel_nr_to_fit	Fit only channels with index < "max_channel_nr_to_fit". Set to -1 to skip fitting.
which_fitf	Choose fit function: 0 - do not fit 1 - Fitf_langaus: landau gauss convolution for large number of photons 2 - Fitf_biased: if pedestal is biased because of peak finder algorithm 3 - Fitf_full: SiPM fit function with exponential delayed after pulsing 4 - Fitf_PMT_ideal: ideal PMT fit function 5 - Fitf_PMT: PMT fit function 6 - Fitf_PMT_pedestal: PMT fit function with biased pedestal 7 - Fitf_plus_DC: default SiPM fit function + dark count spectrum (for lots of false triggers) else - Fitf: default SiPM fit function
use_log_y	Set all y axes to log scale (for dark count spectra)

Examples: read_exampledata.cc, timing_example.cc, and timing_example_rebin.cc.

Definition at line 1861 of file ReadRun.cc.

◆ PrintChargeSpectrumWF()

void ReadRun::PrintChargeSpectrumWF	(	float	windowlow,
		float	windowhi,
		float	start = `0`,
		float	end = `300`,
		int	eventnr = `1`,
		float	ymin = `0.`,
		float	ymax = `0.`,
		float	xmin = `0.`,
		float	xmax = `0.`
	)

Plot waveforms of all channels for a given event number and add the determined integration windows to the plot.

See GetIntWindow() for explanation of parameters.
Will also add CFD timing if GetTimingCFD() was called before.

image html PrintChargeSpectrumWF.png "Waveforms in all channels for a single event. Code in example."

Parameters

windowlow	Integrate from "windowlow" ns from max...
windowhi	...to "windowhi" ns from max.
start	Find max from "start" in ns...
end	...to "end" in ns.
eventnr	Event number
ymin	Y axis minimum
ymax	Y axis maximum
xmin	X axis maximum
xmax	X axis maximum

Examples: read_exampledata.cc, timing_example.cc, and timing_example_rebin.cc.

Definition at line 1613 of file ReadRun.cc.

◆ PrintDCR()

void ReadRun::PrintDCR	(	float	windowlow = `15`,
		float	windowhi = `85`,
		float	rangestart = `0`,
		float	rangeend = `300`,
		double	threshold = `3`
	)

Calculate (SiPM) dark count rate.

See PrintChargeSpectrum() for parameters.

Parameters

threshold 1.5 photoelectron threshold

Definition at line 2103 of file ReadRun.cc.

◆ PrintMaxDist()

void ReadRun::PrintMaxDist	(	float	from = `0`,
		float	to = `300`
	)

Finds maximum amplitude for a given channel in time window ["from", "to"] and creates 3d map of waveforms ordered by maxima.

Prints MaxDist() for all channels. Use only for small datasets as it will contain all of the data

Parameters

from	From
to	To

Definition at line 2254 of file ReadRun.cc.

◆ PrintSkippedEvents()

void ReadRun::PrintSkippedEvents ( )

Prints a list of all skipped events into the terminal for diagnostics.

Definition at line 1491 of file ReadRun.cc.

◆ PrintTimeDist()

void ReadRun::PrintTimeDist	(	float	from = `0`,
		float	to = `300`,
		float	rangestart = `0`,
		float	rangeend = `300`,
		int	nbins = `100`,
		int	which = `0`,
		float	cf_r = `.3`
	)

Time distribution of maximum, CFD, or 10% - 90% rise time in a certain time window.

Find peak time for a given channel in time window ["from", "to"] and return the peak time histogram with x range ["rangestart", "rangeend"] and the number of bins "nbins".
Plots TimeDist() for all channels.

For CFD it is advised to use GetTimingCFD() with Print_GetTimingCFD() instead of this function.

Parameters

from	Start of time interval in ns
to	End of time interval in ns
rangestart	Start of x range of histogram
rangeend	End of x range of histogram
nbins	Number of bins of histogram
which	Options: 0 - Gives time of maximum. 1 - Gives constant fraction discrimination with fraction "cf_r" of maximum, searching backwards from the maximum until "from". else - gives the 10% - 90% rise time.
cf_r	Fraction of max for CFD.

Examples: read_exampledata.cc.

Definition at line 2191 of file ReadRun.cc.

◆ PrintWFProjection()

void ReadRun::PrintWFProjection	(	float	from = `0`,
		float	to = `320`,
		float	rangestart = `-50`,
		float	rangeend = `50`,
		int	nbins = `200`
	)

Plots waveform projection histograms of all channels.

Useful to check baseline correction. Will show if the baseline correction works as intended (gaussian shape) or if the standard deviation of the baseline is too large.

An asymmetry in the distribution might point to many dark counts in the window or a bad choice of parameters for the baseline correction. In that case the baseline correction should be revisited.

Parameters

from	Do projection in time window (from...
to	...to) in ns. This window should reflect the search window used for baseline correction.
rangestart	Plot x range start in mV.
rangeend	Plot x range end in mV.
nbins	Number of bins in range.

Examples: read_exampledata.cc, and timing_example.cc.

Definition at line 1079 of file ReadRun.cc.

◆ ReadFile()

void ReadRun::ReadFile	(	string	path,
		bool	change_polarity = `false`,
		int	change_sign_from_to_ch_num = `9`,
		string	out_file_name = `"out.root"`,
		bool	debug = `false`
	)

Routine to read files created by the wavecatcher.

Reads the data and can already do simple data manipulation during reading:

Change polarity of range of channels with parameters (explained below).
Shift all waveforms to a constant fraction such they all start at the same time (-> see ReadRun::Shift_WFs_in_file_loop )
Simple baseline correction by calling CorrectBaseline() before calling ReadFile().
Stores the data as ROOT histograms in TClonesArray rundata.

Reader modified from WaveCatcher binary -> root converter by manu chauv.nosp@m.eau@.nosp@m.cenbg.nosp@m..in2.nosp@m.p3.fr

Parameters

path	Path to the data. All files in this folder containing `.bin` in the file name will be read in.
change_polarity	Set `true` to change polarity (sign) of certain channels (see `change_sign_from_to_ch_num` below). You can also define a list of channels where the polarity should be switched with switch_polarity_for_channels.
change_sign_from_to_ch_num	All channels \( \geq \) `change_sign_from_to_ch_num` will be inverted if `change_polarity` is `true`. If negative number all channels \( \leq \) `abs(change_sign_from_to_ch_num)` will be inverted if `change_polarity` is `true`.
out_file_name	Name of the `.root` file which stores the results, e. g. `results.root`.
debug	Set `true` to increase the verbosity.

Examples: read_exampledata.cc, timing_example.cc, and timing_example_rebin.cc.

Definition at line 66 of file ReadRun.cc.

◆ SaveChargeLists()

void ReadRun::SaveChargeLists	(	float	windowlow = `20`,
		float	windowhi = `80`,
		float	start = `0`,
		float	end = `300`,
		bool	negative_vals = `1`
	)

Saves TGraphs to root file with the individual "charge"/amplitude for all events and all channels.

Event with a skip_event flag will be removed. Call before filtering or call UnskipAll() before to get all events.
See GetIntWindow().

Parameters

windowlow	Integrate from "windowlow" ns from max...
windowhi	...to "windowhi" ns from max.
start	Find max from "start" in ns...
end	...to "end" in ns.
negative_vals	If true will save negative values. If false will set negative values to 0.

Definition at line 1717 of file ReadRun.cc.

◆ ShiftAllToAverageCF()

void ReadRun::ShiftAllToAverageCF ( )

This function shifts all waveforms to the average signal starting times for each channel.

The signal starting times are determined with constant fraction discrimination. Before calling this function, please call GetTimingCFD() with suitable parameters for your data.
Additionally, PrintChargeSpectrumWF() should be called before calling this function since the timing reference (blue line) won't be shifted.

Definition at line 661 of file ReadRun.cc.

◆ SkipEventsPerChannel()

void ReadRun::SkipEventsPerChannel	(	vector< float >	thresholds,
		float	rangestart = `0`,
		float	rangeend = `0`,
		bool	verbose = `false`
	)

Skip events above/below individual thresholds per channel.

Needs to be called before the charge spectrum etc functions.
Baseline correction should be called before this function.

Parameters

thresholds	Vector should contain a threshold for each active channel saved in the data, in ascending order (ch0, ch1 ...). Negative thresholds mean events below threshold will be cut. If only one value is given this value will be used for all active channels.
rangestart	Range start in ns
rangeend	Range end in ns
verbose	Set true for extra verbosity.

Definition at line 1393 of file ReadRun.cc.

◆ SkipEventsTimeDiffCut()

void ReadRun::SkipEventsTimeDiffCut	(	int	first_channel_abs,
		int	second_channel_abs,
		double	time_diff_min,
		double	time_diff_max,
		bool	verbose = `false`
	)

Skip events where the time difference between two channels is outside of specified range.

Skip events where the time difference between channel "first_channel" and channel "second_channel" is less than "time_diff_min" or more than "time_diff_max"
Needs to be called before the charge spectrum etc functions.
Baseline correction should be called before this function.

Parameters

first_channel_abs	First channel.
second_channel_abs	Second channel.
time_diff_min	Skip events for \( \Delta t<t_{diff,min} \)
time_diff_max	Skip events for \( \Delta t>t_{diff,max} \)
verbose	Set true for extra verbosity.

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 1285 of file ReadRun.cc.

◆ SmoothAll() [1/2]

void ReadRun::SmoothAll	(	double	sigma,
		int	method
	)

Smoothing all waveforms which are not skipped (for testing, careful when using for analysis!)

See Filters::SmoothArray().

Parameters

sigma	Number of bins before and after central bin for running average OR gauss sigma in ns.
method	0: Use running average (box kernel smoothing). Simple, very fast. 2: Use 3 sigma gaussian kernel smoothing. Preferred method, fast.

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 599 of file ReadRun.cc.

◆ SmoothAll() [2/2]

void ReadRun::SmoothAll	(	double	sigma,
		string	method = `"Gaus"`
	)

Smoothing all waveforms which are not skipped (for testing, careful when using for analysis!)

See Filters::SmoothArray().

Parameters

sigma	Number of bins before and after central bin for running average OR gauss sigma in ns.
method	"Box": Use running average (box kernel smoothing). Simple, very fast. "Gaus": Use 3 sigma gaussian kernel smoothing. Preferred method, fast.

Definition at line 620 of file ReadRun.cc.

◆ TimeDist()

TH1F * ReadRun::TimeDist	(	int	channel_index,
		float	from = `0`,
		float	to = `300`,
		float	rangestart = `0`,
		float	rangeend = `300`,
		int	nbins = `100`,
		int	which = `0`,
		float	cf_r = `.3`
	)

Time distribution of maximum, CFD, or 10% - 90% rise time in a certain time window.

See PrintTimeDist() for parameters.

Definition at line 2127 of file ReadRun.cc.

◆ UnskipAll()

void ReadRun::UnskipAll ( )

Sets skip_event flag to false for all events, removing any previous cuts.

Definition at line 1504 of file ReadRun.cc.

◆ WFHeatmapChannel()

TH2F * ReadRun::WFHeatmapChannel	(	int	channel_index,
		float	ymin = `-20`,
		float	ymax = `200`,
		int	n_bins_y = `880`
	)

2D histogram of all non-skipped waveforms for one channel

See PlotWFHeatmaps()

Parameters

channel_index	Index of the channel
ymin	Min. y range
ymax	Max. y range
n_bins_y	Number of bins along y

Returns: TH2F

Definition at line 524 of file ReadRun.cc.

◆ WFProjectionChannel()

TH1F * ReadRun::WFProjectionChannel	(	int	channel_index,
		int	from_n = `0`,
		int	to_n = `1024`,
		float	rangestart = `-50`,
		float	rangeend = `50`,
		int	nbins = `200`
	)

Waveform projections for one channel.

See PrintWFProjection() for parameters.

Returns: Histogram of the projections of non-skipped waveforms for one channel.

Definition at line 1052 of file ReadRun.cc.

Member Data Documentation

◆ active_channels

vector<int> ReadRun::active_channels

Stores the numbers of the active channels.

Definition at line 290 of file ReadRun.h.

◆ amplValuessum

float** ReadRun::amplValuessum

Collects sums of all waveforms for each channel.

Definition at line 127 of file ReadRun.h.

◆ baseline_correction_result

vector<vector<float> > ReadRun::baseline_correction_result

Stores baseline correction results for CorrectBaseline() and related functions.

Definition at line 320 of file ReadRun.h.

◆ binNumber

int ReadRun::binNumber = 1024

Number of bins (always 1024 samples per waveform). Do not change!

Definition at line 280 of file ReadRun.h.

◆ DAQ_factor

float ReadRun::DAQ_factor = 250. / 4096.

DAQ conversion factor for wavecatcher output to mV.

From https://owncloud.lal.in2p3.fr/public.php?service=files&t=56e4a2c53a991cb08f73d03f1ce58ba2

Definition at line 278 of file ReadRun.h.

◆ data_path

string ReadRun::data_path

Path to data.

Can be used to save analysis results in the data folder

Definition at line 230 of file ReadRun.h.

◆ discard_original_eventnr

bool ReadRun::discard_original_eventnr = false

Can be used to discard the original event numbering of the data.

Set to true if you want to read several runs at once. The events will be numbered in the order they are read in. The original event numbers of the different runs will be lost. CAUTION: All .bin files of the different runs need to contain the same number of channels.

Definition at line 247 of file ReadRun.h.

◆ end_read_at_channel

int ReadRun::end_read_at_channel = -1

See ReadRun::start_read_at_channel.

Definition at line 260 of file ReadRun.h.

◆ eventnr_storage

vector<unsigned int> ReadRun::eventnr_storage

Events will be stored here in the order they have been read.

Definition at line 130 of file ReadRun.h.

◆ fit_results

vector<TFitResultPtr> ReadRun::fit_results

Stores the fit results of PrintChargeSpectrum() for all channels and all function calls in ascending order.

Definition at line 303 of file ReadRun.h.

◆ MaxNoOfBinFilesToRead

int ReadRun::MaxNoOfBinFilesToRead

Number of last .bin file to be read in.

Can be used to test analysis on a small sample of the data or for batch reading if combined with MinNoOfBinFilesToRead.

Definition at line 235 of file ReadRun.h.

◆ maxNWF

int ReadRun::maxNWF = 1e7

Maximum possible number of waveforms in data: number of active channels x number of events.

Default is 10 million waveforms. Increase this number for very large runs.

Definition at line 271 of file ReadRun.h.

◆ maxSumBin

int* ReadRun::maxSumBin

Stores bin numbers where the sum of waveforms have their maximum.

Can be used for fixed integration window relative to maximum of the sum of all waveforms per channel (ReadRun::amplValuessum)

Definition at line 287 of file ReadRun.h.

◆ mean_integral

vector<float> ReadRun::mean_integral

Stores the mean integral/lightyield from PrintChargeSpectrum() for all channels.

Definition at line 306 of file ReadRun.h.

◆ MinNoOfBinFilesToRead

int ReadRun::MinNoOfBinFilesToRead

Number first of .bin file to be read in.

Can be used to batch read large datasets in chunks of files.

Definition at line 239 of file ReadRun.h.

◆ nchannels

int ReadRun::nchannels

Number of active channels in data.

Definition at line 265 of file ReadRun.h.

◆ nChannelsWC

int ReadRun::nChannelsWC = 64

Wavecatcher hardware max. number of channels (reduce/increase if not using the 64 channel crate)

Definition at line 282 of file ReadRun.h.

◆ nevents

int ReadRun::nevents

Number of triggered events in data.

Examples: read_exampledata.cc, timing_example.cc, and timing_example_rebin.cc.

Definition at line 263 of file ReadRun.h.

◆ nwf

int ReadRun::nwf

Total number of waveforms read from data: number of active channels x number of events.

Definition at line 267 of file ReadRun.h.

◆ plot_active_channels

vector<int> ReadRun::plot_active_channels

Stores the numbers of the active channels which should be plotted.

You can select the channels you want with plot_active_channels.push_back(channel_to_plot); to add them to the list.
If undefined all channels will be plotted.

Examples: read_exampledata.cc.

Definition at line 295 of file ReadRun.h.

◆ PrintChargeSpectrum_cal

vector<vector<float> > ReadRun::PrintChargeSpectrum_cal = vector(nChannelsWC, vector<float>(2, 1))

Calibration values to normalize charge spectrum to number of photoelectrons Chennels must be ordered as in plot_active_channels.
The first entry must be the gain and the second the position of the pedestal.

Examples: read_exampledata.cc.

Definition at line 367 of file ReadRun.h.

◆ PrintChargeSpectrum_pars

vector<float> ReadRun::PrintChargeSpectrum_pars

Starting values of the fit parameters for PrintChargeSpectrum()

Examples: read_exampledata.cc.

Definition at line 176 of file ReadRun.h.

◆ root_out

TFile* ReadRun::root_out

Stores results of analysis.

Definition at line 338 of file ReadRun.h.

◆ rundata

TClonesArray* ReadRun::rundata

Stores data.

Definition at line 124 of file ReadRun.h.

◆ Shift_WFs_in_file_loop

bool ReadRun::Shift_WFs_in_file_loop = false

Shift waveforms with CFD so that all events start at the same time Call after initializing class and before calling ReadFile().
Set the constant fraction, the bin to shift the signal to, and the search window with tWF_CF, tWF_CF_bin, and tWF_CF_lo and tWF_CF_hi, respectively.

Definition at line 353 of file ReadRun.h.

◆ skip_event

vector<bool> ReadRun::skip_event

Stores the event numbers which should be skipped in the analysis.

To identify events to be filtered use functions IntegralFilter(), SkipEventsPerChannel(), and SkipEventsTimeDiffCut().

Examples: timing_example.cc, and timing_example_rebin.cc.

Definition at line 311 of file ReadRun.h.

◆ SP

float ReadRun::SP = .3125

Sampling: ns per bin of data, sampling rate 3.2 GS/s -> 0.3125 ns.

Definition at line 274 of file ReadRun.h.

◆ start_read_at_channel

int ReadRun::start_read_at_channel = -1

Do analysis only for limited range of channels to reduce memory usage.

For large datasets with many channels and many events
Only read and analyze channels from ReadRun::start_read_at_channel to ReadRun::end_read_at_channel.
The recorded channel with the lowest wavecatcher channel number is 0 (e.g. recorded channels 3 and 4, so start would be 0 and end 1).
If set to -1 (default) all channels will be read in one go.
Else channels from "start_read_at_channel" to "end_read_at_channel" will be read.
If "end_read_at_channel" is not defined will only read channel specified in "start_read_at_channel".

Definition at line 258 of file ReadRun.h.

◆ switch_polarity_for_channels

vector<int> ReadRun::switch_polarity_for_channels

Stores the channel number where the polarity should be inverted. Example use to switch polarity for channel 0 and channel 14: mymeas.switch_polarity_for_channels = {0, 14};. Needs to be called before ReadFile().

Examples: read_exampledata.cc.

Definition at line 300 of file ReadRun.h.

◆ tCutEndg

float ReadRun::tCutEndg

End of time window for baseline correction when using ReadRun::Using_BaselineCorrection_in_file_loop.

Definition at line 348 of file ReadRun.h.

◆ tCutg

float ReadRun::tCutg

Start of time window for baseline correction when using ReadRun::Using_BaselineCorrection_in_file_loop.

Definition at line 346 of file ReadRun.h.

◆ timing_fit_results

vector<TFitResultPtr> ReadRun::timing_fit_results

Stores the fit results of Print_GetTimingCFD() for all channels.

Definition at line 335 of file ReadRun.h.

◆ timing_results

vector<vector<float> > ReadRun::timing_results

Matrix to store timing of peaks from GetTimingCFD()

First index is the index of the waveform.
Second index is:
0: CFD bin number 1: CFD time 2: Y-value of the maximum 3: Bin number of the maximum 4: Constant fraction (maximum * cf_r) 5: Start of search window 6: End of search window

Definition at line 333 of file ReadRun.h.

◆ tWF_CF

float ReadRun::tWF_CF = 0.3

Constant fraction of maximum (between ~0.1 and 1) for ReadRun::Shift_WFs_in_file_loop.

Definition at line 355 of file ReadRun.h.

◆ tWF_CF_bin

int ReadRun::tWF_CF_bin = 375

Time bin all events will be shifted to for ReadRun::Shift_WFs_in_file_loop Needs to be 300<"tWF_CF_bin"<500 ("tWF_CF_bin"=375 means all peaks will be shifted to 375*.3125 ns=117.1875 ns)

Definition at line 358 of file ReadRun.h.

◆ tWF_CF_hi

int ReadRun::tWF_CF_hi = 500

End of range of bins where the signal is expected for ReadRun::Shift_WFs_in_file_loop.

Definition at line 362 of file ReadRun.h.

◆ tWF_CF_lo

int ReadRun::tWF_CF_lo = 320

Start of range of bins where the signal is expected for ReadRun::Shift_WFs_in_file_loop.

Definition at line 360 of file ReadRun.h.

◆ Using_BaselineCorrection_in_file_loop

bool ReadRun::Using_BaselineCorrection_in_file_loop = false

Set true for baseline correction during data reading. Needs to be called before ReadFile().

Definition at line 344 of file ReadRun.h.

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

src/ReadRun.h
src/ReadRun.cc

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ReadRun()

◆ ~ReadRun()

Member Function Documentation

◆ BaselineCorrectionResults()

◆ ChargeCorrelation()

◆ ChargeList()

◆ ChargeSpectrum()

◆ checkData()

◆ CorrectBaseline()

◆ CorrectBaseline_function()

◆ CorrectBaselineMin() [1/2]

◆ CorrectBaselineMin() [2/2]

◆ CorrectBaselineMinSlopeRMS() [1/2]

◆ CorrectBaselineMinSlopeRMS() [2/2]

◆ FilterAll()

◆ FractionEventsAboveThreshold()

◆ GetChannelIndex()

◆ GetCurrentChannel()

◆ GetCurrentEvent()

◆ GetEventIndex()

◆ GetIntWindow()

◆ GetPeakIntegral()

◆ GetTimingCFD()

◆ Getwf() [1/2]

◆ Getwf() [2/2]

◆ getx()

◆ gety() [1/2]

◆ gety() [2/2]

◆ His_GetTimingCFD()

◆ His_GetTimingCFD_diff()

◆ IntegralFilter()

◆ LinearInterpolation()

◆ MaxDist()

◆ Nevents_good()

◆ PlotChannel()

◆ PlotChannelAverages()

◆ PlotChannelSums()

◆ PlotWFHeatmaps()

◆ Print_GetTimingCFD()

◆ Print_GetTimingCFD_diff()

◆ PrintBaselineCorrectionResults()

◆ PrintChargeSpectrum()

◆ PrintChargeSpectrumWF()

◆ PrintDCR()

◆ PrintMaxDist()

◆ PrintSkippedEvents()

◆ PrintTimeDist()

◆ PrintWFProjection()

◆ ReadFile()

◆ SaveChargeLists()

◆ ShiftAllToAverageCF()

◆ SkipEventsPerChannel()

◆ SkipEventsTimeDiffCut()

◆ SmoothAll() [1/2]

◆ SmoothAll() [2/2]

◆ TimeDist()

◆ UnskipAll()

◆ WFHeatmapChannel()

◆ WFProjectionChannel()

Member Data Documentation

◆ active_channels

◆ amplValuessum

◆ baseline_correction_result

◆ binNumber

◆ DAQ_factor

◆ data_path

◆ discard_original_eventnr

◆ end_read_at_channel

◆ eventnr_storage

◆ fit_results

◆ MaxNoOfBinFilesToRead

◆ maxNWF

◆ maxSumBin

◆ mean_integral