IntraSpikeDetector Class Reference

#include <intraspikedetector.h>

Inheritance diagram for IntraSpikeDetector:

Collaboration diagram for IntraSpikeDetector:

Public Member Functions
	IntraSpikeDetector (const string &ident="", int mode=0)
	~IntraSpikeDetector (void)
virtual int	init (const InData &data, EventData &outevents, const EventList &other, const EventData &stimuli)
virtual void	notify (void)
virtual void	save (const string &param)
void	save (void)
virtual int	detect (const InData &data, EventData &outevents, const EventList &other, const EventData &stimuli)
int	checkEvent (InData::const_iterator first, InData::const_iterator last, InData::const_iterator event, InData::const_range_iterator eventtime, InData::const_iterator index, InData::const_range_iterator indextime, InData::const_iterator prevevent, InData::const_range_iterator prevtime, EventData &outevents, double &threshold, double &minthresh, double &maxthresh, double &time, double &size, double &width)
Public Member Functions inherited from Filter
	Filter (const string &ident, int mode, FilterType type, int outtraces=0, const string &name="", const string &pluginset="", const string &author="unknown", const string &version="unknown", const string &date=__DATE__)
virtual	~Filter (void)
virtual int	init (const InData &indata, InData &outdata)
virtual int	init (const InList &indata, InList &outdata)
virtual int	init (const EventData &inevents, InData &outdata)
virtual int	init (const EventList &inevents, InList &outdata)
virtual int	init (const InList &indata, EventList &outevents, const EventList &other, const EventData &stimuli)
virtual int	init (const EventData &inevents, EventData &outevents, const EventList &other, const EventData &stimuli)
virtual int	init (const EventList &inevents, EventList &outevents, const EventList &other, const EventData &stimuli)
virtual int	adjust (const InData &indata, InData &outdata)
virtual int	adjust (const InList &indata, InList &outdata)
virtual int	adjust (const EventData &inevents, InData &outdata)
virtual int	adjust (const EventList &inevents, InList &outdata)
virtual int	adjust (const InData &indata)
virtual int	adjust (const InList &indata)
virtual int	adjust (const EventData &inevents)
virtual int	adjust (const EventList &inevents)
virtual int	autoConfigure (const InData &indata, double tbegin, double tend)
virtual int	autoConfigure (const InList &indata, double tbegin, double tend)
virtual int	autoConfigure (const EventData &inevents, double tbegin, double tend)
virtual int	autoConfigure (const EventList &inevents, double tbegin, double tend)
virtual int	filter (const InData &indata, InData &outdata)
virtual int	filter (const InList &indata, InList &outdata)
virtual int	filter (const EventData &inevents, InData &outdata)
virtual int	filter (const EventList &inevents, InList &outdata)
virtual int	detect (const InList &data, EventList &outevents, const EventList &other, const EventData &stimuli)
virtual int	detect (const EventData &inevents, EventData &outevents, const EventList &other, const EventData &stimuli)
virtual int	detect (const EventList &inevents, EventList &outevents, const EventList &other, const EventData &stimuli)
void	save (void)
const string &	ident (void) const
virtual void	setIdent (const string &ident)
virtual void	setName (const string &name)
FilterType	type (void) const
int	outTraces (void) const
int	mode (void) const
void	setMode (int mode)
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
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)

Protected Attributes
Detector < InData::const_iterator, InData::const_range_iterator >	D
double	Threshold
double	AbsPeak
bool	TestWidth
double	MaxWidth
bool	FitPeak
double	FitWidth
int	FitIndices
bool	LogHistogram
double	UpdateTime
double	HistoryTime
double	SizeResolution
OptWidget	SDW
QTime	Update
Plot *	P
SampleDataD	GoodSpikesHist
SampleDataD	BadSpikesHist
SampleDataD	AllSpikesHist
Protected Attributes inherited from ConfigDialog
Options	DialogOptions

Additional Inherited Members
Public Types inherited from Filter
enum	FilterType
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)

Detailed Description

[Detector] A detector for spikes in intracellular recordings.

Author

Jan Benda

Version

1.2 (Oct 24, 2016)

Options

• Detector
• threshold=10mV: Detection threshold (number)
• abspeak=0mV: Absolute threshold (number)
• testwidth=true: Test spike width (boolean)
• maxwidth=1.5ms: Maximum spike width (number)
• fitpeak=false: Fit parabula to peak of spike (boolean)
• fitwidth=0.5ms: Width of parabula fit (number)
• Indicators
• resolution=1mV: Resolution of spike size (number)
• log=false: Logarithmic histograms (boolean)
• update=1sec: Update time interval (number)
• history=10sec: Maximum history time (number)
• rate=1e-12Hz: Rate (number)
• size=0mV: Spike size (number)
• width=0ms: Spike width (number)

Constructor & Destructor Documentation

IntraSpikeDetector	(	const string &	ident = "",
		int	mode = 0
	)

The constructor.

References IntraSpikeDetector::AbsPeak, OptWidget::assign(), ConfigDialog::dialog(), IntraSpikeDetector::FitIndices, IntraSpikeDetector::FitPeak, IntraSpikeDetector::FitWidth, ConfigDialog::help(), IntraSpikeDetector::HistoryTime, Plot::lock(), IntraSpikeDetector::LogHistogram, IntraSpikeDetector::MaxWidth, ConfigDialog::mutex(), Plot::noGrid(), IntraSpikeDetector::P, IntraSpikeDetector::SDW, ConfigClass::setConfigSelectMask(), ConfigDialog::setDialogSelectMask(), Plot::setLMarg(), OptWidget::setMargins(), Plot::setRMarg(), Plot::setTMarg(), OptWidget::setVerticalSpacing(), Plot::setXLabel(), Plot::setXLabelPos(), Plot::setXTics(), Plot::setYLabel(), Plot::setYRange(), IntraSpikeDetector::SizeResolution, IntraSpikeDetector::TestWidth, IntraSpikeDetector::Threshold, Plot::unlock(), IntraSpikeDetector::Update, and IntraSpikeDetector::UpdateTime.

~IntraSpikeDetector

(

void

)

The destructor.

Member Function Documentation

int init ( const InData &  data, EventData &  outevents, const EventList &  other, const EventData &  stimuli  )

virtual

Reimplemented from Filter.

References InData::begin(), IntraSpikeDetector::D, InData::end(), IntraSpikeDetector::HistoryTime, Detector< DataIter, TimeIter >::init(), IntraSpikeDetector::SDW, Detector< DataIter, TimeIter >::setHistorySize(), EventData::setSizeFormat(), EventData::setSizeScale(), EventData::setSizeUnit(), EventData::setWidthFormat(), EventData::setWidthScale(), EventData::setWidthUnit(), InData::timeBegin(), InData::unit(), and OptWidget::updateValues().

void notify ( void  )

virtual

References IntraSpikeDetector::AbsPeak, IntraSpikeDetector::AllSpikesHist, IntraSpikeDetector::BadSpikesHist, IntraSpikeDetector::D, IntraSpikeDetector::FitPeak, IntraSpikeDetector::FitWidth, Parameter::flags(), floor(), IntraSpikeDetector::GoodSpikesHist, IntraSpikeDetector::HistoryTime, IntraSpikeDetector::LogHistogram, IntraSpikeDetector::MaxWidth, Parameter::number(), IntraSpikeDetector::SDW, Detector< DataIter, TimeIter >::setHistorySize(), IntraSpikeDetector::SizeResolution, IntraSpikeDetector::TestWidth, IntraSpikeDetector::Threshold, OptWidget::updateSettings(), IntraSpikeDetector::UpdateTime, and OptWidget::updateValues().

void save ( const string &  param )

virtual

Reimplemented from Filter.

References IntraSpikeDetector::save().

void save

(

void

)

References TableKey::addNumber(), IntraSpikeDetector::AllSpikesHist, IntraSpikeDetector::BadSpikesHist, IntraSpikeDetector::GoodSpikesHist, Filter::ident(), ConfigDialog::lock(), max(), ConfigDialog::name(), SampleData< T >::pos(), TableKey::save(), TableKey::saveKey(), SampleData< T >::size(), and ConfigDialog::unlock().

Referenced by IntraSpikeDetector::save().

int detect ( const InData &  data, EventData &  outevents, const EventList &  other, const EventData &  stimuli  )

virtual

Detect spikes in a single trace of the analog data ID.

Reimplemented from Filter.

References IntraSpikeDetector::AllSpikesHist, Detector< DataIter, TimeIter >::badEvents(), IntraSpikeDetector::BadSpikesHist, Plot::clear(), IntraSpikeDetector::D, Plot::draw(), InData::end(), IntraSpikeDetector::FitIndices, IntraSpikeDetector::FitWidth, Detector< DataIter, TimeIter >::goodEvents(), IntraSpikeDetector::GoodSpikesHist, IntraSpikeDetector::HistoryTime, InData::indices(), Plot::lock(), log(), IntraSpikeDetector::LogHistogram, EventData::meanRate(), EventData::meanSize(), EventData::meanWidth(), InData::minBegin(), Plot::noYTics(), IntraSpikeDetector::P, Detector< DataIter, TimeIter >::peakHist(), Plot::plot(), Plot::plotVLine(), SampleData< T >::pos(), IntraSpikeDetector::SDW, Plot::setXRange(), Plot::setYTics(), SampleData< T >::size(), EventData::sizeHist(), IntraSpikeDetector::Threshold, Plot::unlock(), IntraSpikeDetector::Update, IntraSpikeDetector::UpdateTime, OptWidget::updateValues(), and Plot::zoomedXRange().

int checkEvent	(	InData::const_iterator	first,
		InData::const_iterator	last,
		InData::const_iterator	event,
		InData::const_range_iterator	eventtime,
		InData::const_iterator	index,
		InData::const_range_iterator	indextime,
		InData::const_iterator	prevevent,
		InData::const_range_iterator	prevtime,
		EventData &	outevents,
		double &	threshold,
		double &	minthresh,
		double &	maxthresh,
		double &	time,
		double &	size,
		double &	width
	)

Returns 1: this is an event, 0: this is not an event, -1: resume next time at lastindex. Update the threshold threshold. After each call of checkEvent() the threshold is bounded to minthresh and maxthresh.

References IntraSpikeDetector::AbsPeak, chisq(), IntraSpikeDetector::FitIndices, IntraSpikeDetector::FitPeak, linearFit(), IntraSpikeDetector::MaxWidth, Map< T >::push(), Map< T >::reserve(), Map< T >::size(), IntraSpikeDetector::TestWidth, Map< T >::x(), and Map< T >::y().

Member Data Documentation

Detector< InData::const_iterator, InData::const_range_iterator > D

protected

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::init(), and IntraSpikeDetector::notify().

double Threshold

protected

The threshold for detecting spikes.

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

double AbsPeak

protected

Absolute height of a spike peak.

Referenced by IntraSpikeDetector::checkEvent(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

bool TestWidth

protected

Test spike width?

Referenced by IntraSpikeDetector::checkEvent(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

double MaxWidth

protected

Maximum width of a spike in seconds.

Referenced by IntraSpikeDetector::checkEvent(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

bool FitPeak

protected

Fit a parabula to the spike peak?

Referenced by IntraSpikeDetector::checkEvent(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

double FitWidth

protected

Width of the parabula fit in seconds.

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

int FitIndices

protected

Width of the parabula fit in indices of the input trace.

Referenced by IntraSpikeDetector::checkEvent(), IntraSpikeDetector::detect(), and IntraSpikeDetector::IntraSpikeDetector().

bool LogHistogram

protected

Plot histogram logarithmically.

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

double UpdateTime

protected

Update time for histograms and indicators.

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

double HistoryTime

protected

Maximum time for history spike events.

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::init(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

double SizeResolution

protected

Resolution of spike sizes and thresholds.

Referenced by IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

OptWidget SDW

protected

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::init(), IntraSpikeDetector::IntraSpikeDetector(), and IntraSpikeDetector::notify().

QTime Update

protected

Referenced by IntraSpikeDetector::detect(), and IntraSpikeDetector::IntraSpikeDetector().

Plot* P

protected

Referenced by IntraSpikeDetector::detect(), and IntraSpikeDetector::IntraSpikeDetector().

SampleDataD GoodSpikesHist

protected

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::notify(), and IntraSpikeDetector::save().

SampleDataD BadSpikesHist

protected

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::notify(), and IntraSpikeDetector::save().

SampleDataD AllSpikesHist

protected

Referenced by IntraSpikeDetector::detect(), IntraSpikeDetector::notify(), and IntraSpikeDetector::save().

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

• intraspikedetector.h
• intraspikedetector.cc