BaselineActivity Class Reference

#include <baselineactivity.h>

Inheritance diagram for BaselineActivity:

Collaboration diagram for BaselineActivity:

Public Member Functions
	BaselineActivity (void)
	~BaselineActivity (void)
virtual int	main (void)
void	saveSpikes (int trace, const Options &header, const EventList &spikes)
void	saveISIH (int trace, const Options &header, const vector< SampleDataD > &isih)
void	saveRate (int trace, const Options &header, const vector< SampleDataD > &spikerate, const SampleDataD &eodcycle)
void	saveNerve (const Options &header, const MapD &nerveamplp, const MapD &nerveamplt, const MapD &nerveamplm, const SampleDataD &nerveampls)
void	saveEODTrace (const Options &header, double eodduration)
void	saveEODTimes (const Options &header, const EventData &eodtimes)
void	save (bool saveeodtrace, double eodduration, bool saveeodtimes, const EventData &eodtimes, const SampleDataD &eodcycle, const EventList &spikes, const vector< SampleDataD > &isih, const vector< SampleDataD > &spikerate, const MapD &nerveamplp, const MapD &nerveamplt, const MapD &nerveamplm, const SampleDataD &nerveampls)
void	plot (const SampleDataD &eodcycle, const vector< vector< ArrayD > > &eodspikes, const vector< SampleDataD > &isih, const vector< SampleDataD > &spikerate, const MapD &nerveamplm)
void	analyzeSpikes (const EventData &se, EventData &eodtimes, int k, vector< vector< ArrayD > > &eodspikes, EventList &spikes, vector< SampleDataD > &isih, vector< SampleDataD > &spikerate, vector< int > &trials)
void	analyze (int autodetect, SampleDataD &eodcycle, EventData &eodtimes, vector< vector< ArrayD > > &eodspikes, EventList &spikes, vector< SampleDataD > &isih, vector< SampleDataD > &spikerate, vector< int > &trials, MapD &nerveamplp, MapD &nerveamplt, MapD &nerveamplm, SampleDataD &nerveampls)
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)

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)
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)
Protected Attributes inherited from ConfigDialog
Options	DialogOptions

Detailed Description

[RePro] ISI statistics and EOD locking of baseline activity.

Author

Jan Benda

Version

2.2 (Oct 23, 2014)

Todo:

Put beat detector auto settings into beat detector.

Options

• duration (number, ms): Duration of single sweep.
• repeats (integer): Maximum number of sweeps (repeats=0: infinite).
• isimax (number, ms): Maximum ISI length displayed in the ISIH plot.
• isistep (number, ms): Resolution of the ISI histogram.
• ratedt (number, ms): Resolution of the firing rate.
• ratemax (number, ms): Maximum time for measuring firing frequency for each EOD cycle.
• eodduration (number, ms): Duration of EOD stored into file.
• saveeodtimes (boolean): Save EOD times in a file.
• auto (integer): 1) Adjust detector parameter automatically, 2) + reset beat and chirp detector.
• adjust (boolean): Adjust input gains.

Files

PUnitSearch writes some information about baseline activity if repeats>0.

• basespikes#.dat : the spiketrain of trace #.
• baseisih#.dat : the interspike-interval histogram of trace #.
• baserate#.dat : the cyclic firing rate for a single EOD period of trace #.
• basenerveampl.dat : the nerve potential.
• basenervesmoothampl.dat : the smoothed nerve potential.
• baseeodtrace.dat : eodduration ms of the EOD.
• baseeodtimes.dat : times of the eod peaks, saved only if saveeodtimes is true.

Plots

• ISI Histogram: The interspike-interval histogram. The vertical lines are multiple of the EOD period.
• EOD Firing Rate: Spikes (red) and cyclic firing rate (yellow) in comparision with one EOD period (green).

Requirements

• Transdermal EOD recording (EODTrace2) and events (EODEvents2).
• One or more spike events (SpikeEvents[*]) or nerve recordings (NerveTrace1).

Constructor & Destructor Documentation

BaselineActivity

(

void

)

~BaselineActivity

(

void

)

Member Function Documentation

int main ( void  )

virtual

Implements RePro.

References BaselineActivity::analyze(), EventData::capacity(), EventList::clear(), Map< T >::clear(), OutData::constWave(), MultiPlot::lock(), OutData::mute(), BaselineActivity::plot(), OutList::push(), Map< T >::reserve(), EventList::reserve(), EventData::reserve(), MultiPlot::resize(), BaselineActivity::save(), OutData::setIdent(), OutData::setTrace(), and MultiPlot::unlock().

void saveSpikes	(	int	trace,
		const Options &	header,
		const EventList &	spikes
	)

Save all spikes of the whole run of PUnitSearch.

References TableKey::addNumber(), TableKey::save(), TableKey::saveKey(), and EventList::size().

Referenced by BaselineActivity::save().

void saveISIH	(	int	trace,
		const Options &	header,
		const vector< SampleDataD > &	isih
	)

Save the interspike interval histogram.

References TableKey::addNumber(), TableKey::save(), and TableKey::saveKey().

Referenced by BaselineActivity::save().

void saveRate	(	int	trace,
		const Options &	header,
		const vector< SampleDataD > &	spikerate,
		const SampleDataD &	eodcycle
	)

Save the cyclic spike rate.

References TableKey::addNumber(), TableKey::save(), and TableKey::saveKey().

Referenced by BaselineActivity::save().

void saveNerve	(	const Options &	header,
		const MapD &	nerveamplp,
		const MapD &	nerveamplt,
		const MapD &	nerveamplm,
		const SampleDataD &	nerveampls
	)

Save potential of the nerve recording for the whole run of PUnitSearch.

References TableKey::addNumber(), Map< T >::empty(), SampleData< T >::empty(), TableKey::newSection(), SampleData< T >::pos(), TableKey::save(), TableKey::saveKey(), SampleData< T >::size(), Map< T >::size(), Map< T >::x(), and Map< T >::y().

Referenced by BaselineActivity::save().

void saveEODTrace	(	const Options &	header,
		double	eodduration
	)

Save the fishes EOD waveform.

References TableKey::addNumber(), InData::indices(), InData::interval(), InData::minIndex(), TableKey::save(), TableKey::saveKey(), and InData::size().

Referenced by BaselineActivity::save().

void saveEODTimes	(	const Options &	header,
		const EventData &	eodtimes
	)

Save the fishes EOD times.

References TableKey::addNumber(), TableKey::save(), TableKey::saveKey(), and EventData::size().

Referenced by BaselineActivity::save().

void save	(	bool	saveeodtrace,
		double	eodduration,
		bool	saveeodtimes,
		const EventData &	eodtimes,
		const SampleDataD &	eodcycle,
		const EventList &	spikes,
		const vector< SampleDataD > &	isih,
		const vector< SampleDataD > &	spikerate,
		const MapD &	nerveamplp,
		const MapD &	nerveamplt,
		const MapD &	nerveamplm,
		const SampleDataD &	nerveampls
	)

Save results data.

References BaselineActivity::saveEODTimes(), BaselineActivity::saveEODTrace(), BaselineActivity::saveISIH(), BaselineActivity::saveNerve(), BaselineActivity::saveRate(), and BaselineActivity::saveSpikes().

Referenced by BaselineActivity::main().

void plot	(	const SampleDataD &	eodcycle,
		const vector< vector< ArrayD > > &	eodspikes,
		const vector< SampleDataD > &	isih,
		const vector< SampleDataD > &	spikerate,
		const MapD &	nerveamplm
	)

References MultiPlot::back(), Array< T >::back(), ceil(), MultiPlot::clear(), MultiPlot::draw(), MultiPlot::lock(), MultiPlot::size(), MultiPlot::unlock(), and Map< T >::x().

Referenced by BaselineActivity::main().

void analyzeSpikes	(	const EventData &	se,
		EventData &	eodtimes,
		int	k,
		vector< vector< ArrayD > > &	eodspikes,
		EventList &	spikes,
		vector< SampleDataD > &	isih,
		vector< SampleDataD > &	spikerate,
		vector< int > &	trials
	)

References EventData::addIntervalHistogram(), EventData::addRate(), EventList::clear(), EventData::interval(), EventData::latency(), EventData::rate(), and EventData::size().

Referenced by BaselineActivity::analyze().

void analyze	(	int	autodetect,
		SampleDataD &	eodcycle,
		EventData &	eodtimes,
		vector< vector< ArrayD > > &	eodspikes,
		EventList &	spikes,
		vector< SampleDataD > &	isih,
		vector< SampleDataD > &	spikerate,
		vector< int > &	trials,
		MapD &	nerveamplp,
		MapD &	nerveamplt,
		MapD &	nerveamplm,
		SampleDataD &	nerveampls
	)

References BaselineActivity::analyzeSpikes(), EventData::append(), EventList::back(), InData::begin(), EventData::clear(), Map< T >::clear(), SampleData< T >::clear(), InData::copy(), EventData::empty(), InData::end(), EventData::frequency(), EventList::front(), Detector< DataIter, TimeIter >::init(), InData::maxValue(), InData::mean(), Detector< DataIter, TimeIter >::peakTrough(), SampleData< T >::pos(), EventData::previousTime(), Map< T >::push(), SampleData< T >::rangeBack(), Map< T >::reserve(), EventList::size(), EventData::size(), SampleData< T >::size(), Map< T >::size(), InData::stdev(), InData::timeBegin(), and InData::unit().

Referenced by BaselineActivity::main().

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

• baselineactivity.h
• baselineactivity.cc