Class containing SAMPIC data loader and Event Builder. More...

#include <ReadSampic.h>

Inheritance diagram for ReadSampic:

Collaboration diagram for ReadSampic:

Classes
struct	HitInfoReduced
	Stores additional information with the waveforms. More...

Public Member Functions
void	EventBuilder (double, vector< float >={}, vector< int > channels={}, unsigned int=1, bool=false)
	Construct events based on coincident amplitude thresholds within a time window for different channels. It currently constructs the events from the first waveform above the set amplitude threshold. ToDo: .

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

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

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

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

void	PlotWF (int, float=0, float=0)
	Plot any Waveform (can be called before EventBuilder to check data)

void	ReadFile (string, bool=true, int=0, string="out.root", bool=false, long long=0) override
	Routine to read files created by SAMPIC DAQ.

	ReadSampic (int last_bin_file=0, int first_bin_file=0)
	Initializer will call initializer of ReadRun class.

bool	SkipEvent (int, int=-1) override
	Check if event has skipped flag. Will return true if event flag is false but channel does not exist in data.

Public Member Functions inherited from ReadRun
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.

int	CheckBoundsX (int)
	Check if index exists in time of waveforms.

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

void	CorrectBaseline_function (vector< float > &, 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, int, int)
	Wrapper for backwards compatibility.

void	CorrectBaselineMin (vector< float >, double=0, 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, int, int)
	Wrapper for backwards compatibility.

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

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

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

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

array< int, 3 >	GetIntWindow (const vector< float > &, float, float, float, float, int=0)
	Determine indices for integration window for peaks.

array< int, 3 >	GetIntWindow (const vector< float > &, int, int, int, int, int=0)
	Determine indices for integration window for peaks with bin indices.

array< int, 3 >	GetIntWindow (TH1F *, float, float, float, float, int=0)
	Determine indices for integration window for peaks.

float	GetPeakIntegral (const vector< float > &, float, float, float, float, int=0)
	Calculate the integral around a peak with several options explained in GetIntWindow().

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, 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.

template<typename T >
T *	getx (double shift=0.)
	Get array of x axis (time of the bin centers) 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.

float	IndexToTime (int)
	Convert the bin number of the waveform to the time of the left bin edge

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 on z axis.

virtual int	Nevents_good (int=0)
	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=kRainBow)
	Plot stacks of all non-skipped waveforms for all active channels.

vector< bool >	PolarityMap (bool, int)
	Channel map of polarity changes during reading. For parameters see ReadFile().

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 on z axis.

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.

	ReadRun (int last_bin_file=0, int first_bin_file=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.

int	TimeToIndex (float)
	Convert time to the bin number of the waveform.

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.

Public Attributes
vector< vector< int > >	ch_nr_event_storage
	Stores all channel numbers assigned to events.

vector< double >	event_time_stamps
	Stores all event times.

vector< HitInfoReduced >	hitInfo
	Stores additional info about wf.

vector< vector< int > >	wf_nr_event_storage
	Stores all waveform numbers assigned to events.

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

vector< vector< 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
	Number of bins (usually 1024 samples per waveform).

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.

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

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

int	LastBinFileToRead
	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.

vector< 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	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 = 0
	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.

vector< vector< float > >	rundata
	Stores waveforms.

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.

float	SP_inv = 1 / .3125
	1/SP

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()

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 (bool isBaselineCorrection=false) const override
	Primitive check to see if data has been loaded.

Protected Attributes
bool	eventsBuilt = false
	Check if the data is grouped in events (SAMPIC needs manual event building)

Protected Attributes inherited from ReadRun
int	PlotChannelAverages_cnt
	Index for multiple executions of the same plotting function.

int	PlotWFHeatmaps_cnt
	Index for multiple executions of the same plotting function.

int	PrintChargeSpectrum_cnt
	Index for multiple executions of the same plotting function.

int	PrintWFProjection_cnt
	Index for multiple executions of the same plotting function.

Additional Inherited Members
Static Public Member Functions inherited from ReadRun
static pair< float, bool >	LinearInterpolation (float, float, float, float, float, bool=false)
	Simple linear interpolation for x.

Detailed Description

Class containing SAMPIC data loader and Event Builder.

Definition at line 8 of file ReadSampic.h.

Constructor & Destructor Documentation

◆ ReadSampic()

ReadSampic::ReadSampic	(	int	last_bin_file = `0`,
		int	first_bin_file = `0`
	)

inline

Initializer will call initializer of ReadRun class.

Parameters

last_bin_file	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.
first_bin_file	Number first of .bin file to be read in. Can be used to batch read large datasets in chunks of files.

Definition at line 65 of file ReadSampic.h.

Member Function Documentation

◆ checkData()

void ReadSampic::checkData ( bool isBaselineCorrection = false ) const

inlineoverrideprotectedvirtual

Primitive check to see if data has been loaded.

Reimplemented from ReadRun.

Definition at line 43 of file ReadSampic.h.

◆ EventBuilder()

void ReadSampic::EventBuilder	(	double	coincidence_time_window,
		vector< float >	thresholds = `{}`,
		vector< int >	channels = `{}`,
		unsigned int	min_coincidences = `1`,
		bool	shift_relative = `false`
	)

Construct events based on coincident amplitude thresholds within a time window for different channels.
It currently constructs the events from the first waveform above the set amplitude threshold.
ToDo:
.

Add option to create event from most coincidences, not from first

Add option for integral threshold? (Would require parameters for integration window -> separate function?)

Parameters

coincidence_time_window	Event time window in ns. All hits within time window will be added to event. Starts at the beginning of the first channel above threshold and will include all channels which start recording before the end of the coincidence time window. This means the peak might be after the end of the coincidence time window. If you want to include only waveforms with the signal inside the time window you would need to subtract the length of a waveform (depends on SAMPIC settings) from the time window. Must be shorter than the dead time of SAMPIC (<1000 ns).
thresholds	Vector of thresholds for all channels in ascending order (lowest channel number in data is the first entry). If you specify only a single value {val}, it will be used for all channels. The amplitude must be larger than the specified threshold.
channels	Vector of channels to be used. If left empty {} all channels will be used. Provide the actual channel numbers from SAMPIC (e. g. {10, 28}).
min_coincidences	Minimum number of channels above threshold. Events will be constructed if at least min_coincidences channels are above their threshold.
shift_relative	Shift waveforms relative to first timestamp in event NOT WORKING YET

Definition at line 228 of file ReadSampic.cc.

◆ GetCurrentChannel()

int ReadSampic::GetCurrentChannel ( int waveform_index )

overridevirtual

Get the current channel index for a certain waveform index.

Parameters

waveform_index

Returns: Current channel index

Reimplemented from ReadRun.

Definition at line 399 of file ReadSampic.cc.

◆ GetCurrentEvent()

int ReadSampic::GetCurrentEvent ( int waveform_index )

overridevirtual

Get the current event index for a certain waveform index.

Parameters

waveform_index

Returns: Current event index. If the waveform is not assigned to an event it will return -1.

Reimplemented from ReadRun.

Definition at line 406 of file ReadSampic.cc.

◆ GetWaveformIndex()

int ReadSampic::GetWaveformIndex	(	int	eventnr,
		int	channel_index
	)

overridevirtual

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

Parameters

eventnr	Event number as stored in the data.
channel_index	Channel index as stored in the data.

Returns: Corresponding waveform number in the internal data structure.

Reimplemented from ReadRun.

Definition at line 384 of file ReadSampic.cc.

◆ Getwf()

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

overridevirtual

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

Reimplemented from ReadRun.

Definition at line 348 of file ReadSampic.cc.

◆ PlotWF()

void ReadSampic::PlotWF	(	int	wfNumber,
		float	ymin = `0`,
		float	ymax = `0`
	)

Plot any Waveform (can be called before EventBuilder to check data)

Parameters

wfNumber	Number of the waveform (hit number)
ymin	scale of y axis
ymax	scale of y axis

Definition at line 194 of file ReadSampic.cc.

◆ ReadFile()

void ReadSampic::ReadFile	(	string	path,
		bool	change_polarity = `true`,
		int	change_sign_from_to_ch_num = `0`,
		string	out_file_name = `"out.root"`,
		bool	debug = `false`,
		long long	max_nfs_to_read = `0`
	)

overridevirtual

Routine to read files created by SAMPIC DAQ.

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.
SAMPIC reference: https://doi.org/10.1109/NSSMIC.2014.7431231
Please note that the absolute time is not yet implemented (for CFD timing, plotting waveforms etc.).

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.
max_nfs_to_read	Maximum number of events to be read per file. For quick testing of analysis on subset of the data.

Reimplemented from ReadRun.

Definition at line 23 of file ReadSampic.cc.

◆ SkipEvent()

bool ReadSampic::SkipEvent	(	int	event_index,
		int	channel_index = `-1`
	)

overridevirtual

Check if event has skipped flag. Will return true if event flag is false but channel does not exist in data.

Parameters

event_index	Index of the event
channel_index	Index of the channel

Reimplemented from ReadRun.

Definition at line 413 of file ReadSampic.cc.

Member Data Documentation

◆ ch_nr_event_storage

vector<vector<int> > ReadSampic::ch_nr_event_storage

Stores all channel numbers assigned to events.

Definition at line 100 of file ReadSampic.h.

◆ event_time_stamps

vector<double> ReadSampic::event_time_stamps

Stores all event times.

Definition at line 102 of file ReadSampic.h.

◆ eventsBuilt

bool ReadSampic::eventsBuilt = false

protected

Check if the data is grouped in events (SAMPIC needs manual event building)

Definition at line 41 of file ReadSampic.h.

◆ hitInfo

vector<HitInfoReduced> ReadSampic::hitInfo

Stores additional info about wf.

Definition at line 96 of file ReadSampic.h.

◆ wf_nr_event_storage

vector<vector<int> > ReadSampic::wf_nr_event_storage

Stores all waveform numbers assigned to events.

Definition at line 98 of file ReadSampic.h.

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

src/ReadSampic.h
src/ReadSampic.cc

Classes

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ReadSampic()

Member Function Documentation

◆ checkData()

◆ EventBuilder()

◆ GetCurrentChannel()

◆ GetCurrentEvent()

◆ GetWaveformIndex()

◆ Getwf()

◆ PlotWF()

◆ ReadFile()

◆ SkipEvent()

Member Data Documentation

◆ ch_nr_event_storage

◆ event_time_stamps

◆ eventsBuilt

◆ hitInfo

◆ wf_nr_event_storage