#include <beats.h>

Inheritance diagram for Beats:

Collaboration diagram for Beats:

Public Member Functions
	Beats (void)

virtual int	main (void)

virtual void	sessionStarted (void)

void	analyze (double signaltime, double before, double fishrate, bool initeoditer[], EventIterator eoditer[], MapD eodfrequencies[], MapD eodamplitudes[], int eodinx[], MapD &eodfrequency, bool &initstimiter, EventFrequencyIterator &stimiter, MapD &stimfrequency)

void	initPlot (double deltaf, double amplitude, double duration, double eodf, const MapD &eodfrequency, const EventData &fishchirps, bool showstimulus, const MapD &stimfrequency, const EventData &chirptimes)

void	save (double deltaf, double amplitude, double duration, double pause, int amtype, const vector< double > &amampls, const vector< double > &amfreqs, double fishrate, double stimulusrate, int nfft, double eodfreqprec, const MapD eodfrequencies[], const MapD eodamplitudes[], const MapD &eodfrequency, const EventData &fishchirps, const EventData &playedchirpevents, const MapD &stimfrequency, const Options &chirpheader, bool split, int count)

void	saveEODFreq (int trace, const string &es, const Options &header, const MapD &eodfrequency, const MapD &eodamplitude, bool split, int count)

void	saveMergedEODFreq (const Options &header, const MapD &eodfrequency, bool split, int count)

void	saveChirps (const Options &header, const EventData &chirps, bool split, int count)

void	savePlayedChirps (const Options &header, const EventData &chirps, bool split, int count)

Public Member Functions inherited from ConfigDialog
	ConfigDialog (const string &configident="", int configgroup=0, const string &name="", const string &author="", const string &version="", const string &date=__DATE__)

virtual	~ConfigDialog (void)

string	name (void) const

virtual void	setName (const string &name)

string	author (void) const

virtual void	setAuthor (const string &author)

string	version (void) const

virtual void	setVersion (const string &version)

string	date (void) const

virtual void	setDate (const string &date)

virtual OptWidget *	dialogOptions (OptDialog od, string tabhotkeys=0)

virtual void	dialogButtons (OptDialog *od)

virtual void	dialogEmptyMessage (OptDialog *od)

int	dialogSelectMask (void) const

void	setDialogSelectMask (int mask)

void	addDialogSelectMask (int mask)

int	dialogReadOnlyMask (void) const

void	setDialogReadOnlyMask (int mask)

void	addDialogReadOnlyMask (int mask)

int	dialogStyle (void) const

void	setDialogStyle (int style)

void	addDialogStyle (int style)

string	dialogCaption (void) const

void	setDialogCaption (const string &caption)

bool	dialogHeader (void) const

void	setDialogHeader (bool d)

string	headerBackgroundColor (void) const

void	setHeaderBackgroundColor (const string &color)

string	headerForegroundColor (void) const

void	setHeaderForegroundColor (const string &color)

string	headerImageFile (void) const

void	setHeaderImageFile (const string &file)

virtual void	dialogHeaderWidget (OptDialog *od)

bool	dialogHelp (void) const

void	setDialogHelp (bool d)

string	helpCaption (void) const

void	setHelpCaption (const string &caption)

string	helpPath (int inx=0) const

int	helpPathes (void) const

void	clearHelpPathes (void)

void	setHelpPath (const string &path)

void	addHelpPath (const string &path)

virtual string	helpFileName (void) const

bool	dialogOpen (void) const

bool	helpOpen (void) const

QWidget *	mainWidget (void)

virtual void	setMainWidget (QWidget *widget)

void	lock () const

void	unlock () const

bool	tryLock (int timeout=1)

QMutex *	mutex (void)

Public Member Functions inherited from ConfigClass
	ConfigClass (const string &ident, int group=0, int mode=0xffff, int selectmask=0)

	ConfigClass (const ConfigClass &C)

virtual	~ConfigClass (void)

const string &	configIdent (void) const

void	setConfigIdent (const string &ident)

int	configGroup (void) const

void	setConfigGroup (int group)

int	configMode (void) const

void	setConfigMode (int mode)

void	addConfigMode (int mode)

void	delConfigMode (int mode)

int	configSelectMask (void) const

void	setConfigSelectMask (int mask)

void	addConfig (void)

void	readConfig (void)

virtual void	readConfig (StrQueue &sq)

virtual void	saveConfig (ofstream &str)

virtual int	configSize (void) const

virtual void	config (void)

virtual void	preConfig (void)

Public Member Functions inherited from Traces
	Traces (void)

Public Member Functions inherited from StandardTraces
	StandardTraces (void)

Public Member Functions inherited from EODTools
	EODTools (void)

double	eodThreshold (const InData &data, double tbegin, double tend, double contrast=0.2)

void	eodPeaks (const InData &data, double tbegin, double tend, double threshold, EventData &peaks)

void	eodTroughs (const InData &data, double tbegin, double tend, double threshold, EventData &troughs)

void	eodPeaksTroughs (const InData &data, double tbegin, double tend, double threshold, EventData &peaks, EventData &troughs)

double	meanPeaks (const InData &data, double tbegin, double tend, double threshold)

double	meanTroughs (const InData &data, double tbegin, double tend, double threshold)

double	eodAmplitude (const InData &data, double tbegin, double tend)

void	beatAmplitudes (const InData &eodd, double tbegin, double tend, double period, double contrast, double &uppermean, double &upperampl, double &lowermean, double &lowerampl)

double	beatAmplitude (const InData &eodd, double tbegin, double tend, double period, double contrast=0.2)

double	beatContrast (const InData &eodd, double tbegin, double tend, double period, double contrast=0.2)

Protected Attributes
Plot	P

bool	Start

int	FileCount

Protected Attributes inherited from ConfigDialog
Options	DialogOptions

Additional Inherited Members
Public Types inherited from ConfigClass
enum	Action

Public Slots inherited from ConfigDialog
virtual void	dialog (void)

virtual void	help (void)

virtual void	notifyDialog (const Options &opt)

Signals inherited from ConfigDialog
void	dialogAccepted (void)

void	dialogAction (int r)

void	dialogClosed (int r)

Static Public Member Functions inherited from ConfigClass
static void	setConfigureClasses (ConfigureClasses *cfg)

Static Public Member Functions inherited from Traces
static void	initialize (const RELACSPlugin *rp, const InList &data, const EventList &events)

Protected Slots inherited from ConfigDialog
void	notificationFromDialog (const Parameter &p)

virtual void	dClosed (int r)

virtual void	hClosed (int r)

Protected Member Functions inherited from ConfigDialog
void	setDialogOpen (bool open=true)

void	setHelpOpen (bool open=true)

Static Protected Member Functions inherited from StandardTraces
static void	clearIndices (int *traceindices, int n=-1)

static void	initStandardTraces (const InList &data, int ntraces, int traceindices, const string *names, string &namelist, bool alpha=false)

static void	initStandardEventTraces (const InList &data, const EventList &events, int ntraces, int traceindices, int eventindices, const string tracenames, const string *eventnames, string &tracenamelist, string &eventnamelist, bool alpha=false)

static void	initStandardOutputs (const RELACSPlugin rp, int ntraces, int traceindices, const string names, string &namelist, bool alpha=false)

Static Protected Attributes inherited from Traces
static int	EODTrace = -1

static int	EODEvents = -1

static int	ChirpEvents = -1

static int	LocalEODTraces = 0

static int	LocalEODTrace [MaxTraces] = { -1, -1, -1, -1 }

static int	LocalEODEvents [MaxTraces] = { -1, -1, -1, -1 }

static int	LocalChirpEvents [MaxTraces] = { -1, -1, -1, -1 }

static int	LocalBeatPeakEvents [MaxTraces] = { -1, -1, -1, -1 }

static int	LocalBeatTroughEvents [MaxTraces] = { -1, -1, -1, -1 }

static int	FishEODTanks = 0

static int	FishEODTraces [MaxTraces] = { 0, 0, 0, 0 }

static int	FishEODTrace [MaxTraces][MaxTraces] = { { -1, -1, -1, -1 }, { -1, -1, -1, -1 } }

static int	FishEODEvents [MaxTraces][MaxTraces] = { { -1, -1, -1, -1 }, { -1, -1, -1, -1 } }

static int	FishChirpEvents [MaxTraces][MaxTraces] = { { -1, -1, -1, -1 }, { -1, -1, -1, -1 } }

static int	GlobalEField = -1

static int	GlobalAMEField = -1

static int	LocalEFields = 0

static int	LocalEField [MaxTraces] = { -1, -1, -1, -1 }

static int	LocalAMEFields = 0

static int	LocalAMEField [MaxTraces] = { -1, -1, -1, -1 }

static int	FishEFields = 0

static int	FishEField [MaxTraces] = { -1, -1, -1, -1 }

static int	EFields = 0

static int	EField [2 *MaxTraces] = { -1, -1, -1, -1 }

static int	GlobalEFieldTrace = -1

static int	GlobalEFieldEvents = -1

static int	LocalEFieldTraces = 0

static int	LocalEFieldTrace [MaxTraces] = { -1, -1, -1, -1 }

static int	LocalEFieldEvents [MaxTraces] = { -1, -1, -1, -1 }

static int	FishEFieldTraces = 0

static int	FishEFieldTrace [MaxTraces] = { -1, -1, -1, -1 }

static int	FishEFieldEvents [MaxTraces] = { -1, -1, -1, -1 }

Static Protected Attributes inherited from StandardTraces
static const int	MaxTraces

Detailed Description

[RePro] Play EOD mimicks with optional chirps from a range of automatically set difference frequencies and amplitudes.

Author: Jan Benda

Version: 2.6 (Nov 4, 2016)

Options

Stimulation
- duration=10seconds: Signal duration (number)
- pause=20seconds: Pause between signals (number)
- ramp=0.5seconds: Duration of linear ramp (number)
- deltafrange=10: Range of delta f's (string)
- deltafshuffle=Up: Order of delta f's (string)
- fixeddf=false: Keep delta f fixed (boolean)
- amplitude=1mV/cm: Amplitude (number)
- amtype=none: Amplitude modulation of signal (string)
- amfreq=1: Frequencies of amplitude modulation (list of numbers)
- amamplitude=100: Corresponding amplitudes (list of numbers)
- repeats=10: Repeats (integer)
- fakefish=0Hz: Assume a fish with frequency (number)
Chirps
- generatechirps=false: Generate chirps (boolean)
- chirpsize=100Hz: Size of chirp (number)
- chirpwidth=100ms: Width of chirp (number)
- chirpampl=0%: Amplitude reduction during chirp (number)
- chirpkurtosis=1: Kurtosis of Gaussian chirp (number)
- chirpfrequencies=: Chirp frequencies for each delta f (string)
- chirptimesfile=: File with chirp times (string)
- chirptimeshuffle=Up: Order of chirp-time sequences (string)
Analysis
- before=1seconds: Time before stimulation to be analyzed (number)
- after=1seconds: Time after stimulation to be analyzed (number)
- averagetime=1seconds: Time for computing EOD frequency (number)
- usepsd=true: Use power spectrum to measure EOD frequency (boolean)
- mineodfreq=100Hz: Minimum expected EOD frequency (number)
- maxeodfreq=2000Hz: Maximum expected EOD frequency (number)
- eodfreqprec=1Hz: Precision of EOD frequency measurement (number)
- neod=2: Number of attempts for measuring EOD frequency (integer)
- showstimulus=false: Plot frequency of stimulus (boolean)
- split=false: Save each run into a separate file (boolean)
- savetraces=false: Save traces during pause (boolean)

Chirps

Chirps are generated whenever at least one frequency of chirps (chirpfrequency) or a file containing the timepoints of chirps is specified. If only a chirp frequency is specified, then series of evenly spaced chirps with that frequency are produced. If only a file containing times is specified (no chirpfrequency) then the chirps are positioned as specified in the file. If in addition a chirp frequency is specified, the timepoints in the file are scaled with the inverse frequency. By specifying as many chirp frequencies as there are delta f's the chirp frequency can be made dependent on delta f.

The chirptimesfile may contain several blocks of chirp time sequences. These are then used one after the other as specified by chirptimeshuffle.

LED Output

In case an "LED-1" output channel is defined, a 5 V signal is put out during stimulation. During generated chirps this signal is set to -5 V.

Constructor & Destructor Documentation

Beats ( void )

References Beats::FileCount, Plot::lock(), Beats::P, Plot::setBMarg(), Plot::setLMarg(), Plot::setRMarg(), Plot::setTMarg(), Plot::setXLabel(), Plot::setYLabel(), Plot::setYRange(), and Plot::unlock().

Member Function Documentation

int main ( void )

virtual

Implements RePro.

References Beats::analyze(), EventData::assign(), EventList::back(), OutData::back(), OutData::bestSampleInterval(), ceil(), Plot::clear(), Map< T >::clear(), EventData::clear(), OutData::clear(), DataFile::col(), OutData::constWave(), DataFile::data(), OutData::description(), Plot::draw(), EventList::empty(), Traces::EODEvents, DaqError::errorText(), OutList::errorText(), EventData::eventSize(), exp(), DaqError::failed(), OutList::failed(), Beats::FileCount, OutData::fill(), Traces::FishChirpEvents, Traces::FishEField, Traces::FishEODEvents, Traces::FishEODTanks, Traces::FishEODTrace, Traces::FishEODTraces, OutData::fixedSampleRate(), floor(), Traces::GlobalEField, OutData::index(), OutData::indices(), Beats::initPlot(), OutData::length(), Plot::lock(), log(), SampleData< T >::max(), max(), RangeLoop::maxCount(), EventData::meanSize(), OutData::minSampleInterval(), nextPowerOfTwo(), Beats::P, peaks(), Plot::plotVLine(), RangeLoop::pos(), OutData::pos(), pow(), power(), OutData::pulseWave(), OutList::push(), EventData::push(), EventList::push(), OutData::ramp(), OutData::rampWave(), Str::range(), DataFile::read(), OutData::rectangleWave(), RangeLoop::remainingCount(), Map< T >::reserve(), EventData::reserve(), RangeLoop::reset(), EventData::resize(), OutData::resize(), TableData::rows(), rPSD(), Beats::save(), OutData::setDelay(), OutList::setDelay(), OutData::setIdent(), OutData::setIntensity(), OutData::setSampleInterval(), RangeLoop::setSequence(), OutData::setTrace(), OutData::setTraceName(), OutData::setUnit(), Plot::setXRange(), OutData::sineWave(), RangeLoop::size(), EventData::size(), OutData::size(), EventList::size(), OutData::stepsize(), and Plot::unlock().

void sessionStarted ( void )

virtual

References Beats::FileCount.

void analyze	(	double	signaltime,
		double	before,
		double	fishrate,
		bool	initeoditer[],
		EventIterator	eoditer[],
		MapD	eodfrequencies[],
		MapD	eodamplitudes[],
		int	eodinx[],
		MapD &	eodfrequency,
		bool &	initstimiter,
		EventFrequencyIterator &	stimiter,
		MapD &	stimfrequency
	)

References EventData::begin(), EventData::end(), Traces::FishEFieldEvents, Traces::FishEODEvents, Traces::FishEODTraces, Map< T >::push(), EventIterator::time(), Map< T >::x(), and Map< T >::y().

Referenced by Beats::main().

void initPlot	(	double	deltaf,
		double	amplitude,
		double	duration,
		double	eodf,
		const MapD &	eodfrequency,
		const EventData &	fishchirps,
		bool	showstimulus,
		const MapD &	stimfrequency,
		const EventData &	chirptimes
	)

References Plot::clear(), Plot::draw(), Plot::keepPointer(), Plot::lock(), ConfigDialog::mutex(), Beats::P, Plot::plot(), Plot::plotVLine(), Plot::setDataMutex(), Plot::setTitle(), Plot::setYFallBackRange(), Plot::setYRange(), and Plot::unlock().

Referenced by Beats::main().

void save	(	double	deltaf,
		double	amplitude,
		double	duration,
		double	pause,
		int	amtype,
		const vector< double > &	amampls,
		const vector< double > &	amfreqs,
		double	fishrate,
		double	stimulusrate,
		int	nfft,
		double	eodfreqprec,
		const MapD	eodfrequencies[],
		const MapD	eodamplitudes[],
		const MapD &	eodfrequency,
		const EventData &	fishchirps,
		const EventData &	playedchirpevents,
		const MapD &	stimfrequency,
		const Options &	chirpheader,
		bool	split,
		int	count
	)