Electric Field Measurement Relacs Plugins  0.9.8
Classes | Public Member Functions | List of all members
JAR Class Reference

#include <jar.h>

Inheritance diagram for JAR:
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Collaboration diagram for JAR:
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Public Member Functions

 JAR (void)
 
virtual int main (void)
 
virtual void sessionStarted (void)
 
virtual void sessionStopped (bool saved)
 
void save (void)
 
void saveJAR (const Options &header)
 
void saveMeanJAR (const Options &header)
 
void saveEOD (const Options &header)
 
void saveTrace (void)
 
void saveEODFreq (const Options &header)
 
void saveChirps (const Options &header)
 
void saveChirpTraces (const Options &header)
 
void saveChirpEOD (const Options &header)
 
void reset (bool saved)
 
void plot (void)
 
void analyze (void)
 
- 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)
 

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)
 
- Protected Attributes inherited from ConfigDialog
Options DialogOptions
 
- 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] Measure the fishes jamming avoidance response and chirp characteristics at different delta f's and beat contrasts.

Author
Jan Benda
Version
2.2 (Sep 21, 2011)
Bug:
EOD waveform stimulus broken (samplerate!).
Options
  • Stimulation
  • duration=10seconds: Signal duration (number)
  • pause=20seconds: Pause between signals (number)
  • ramp=0.5seconds: Duration of linear ramp (number)
  • deltafstep=2Hz: Delta f steps (number)
  • deltafmax=12Hz: Maximum delta f (number)
  • deltafmin=-12Hz: Minimum delta f (number)
  • deltafrange=: Range of delta f's (string)
  • amplsel=contrast: Stimulus amplitude (string)
  • contrastmax=20%: Maximum contrast (number)
  • contrastmin=10%: Minimum contrast (number)
  • contraststep=10%: Contrast steps (number)
  • amplmin=1mV/cm: Minimum amplitude (number)
  • amplmax=2mV/cm: Maximum amplitude (number)
  • amplstep=1mV/cm: Amplitude steps (number)
  • repeats=200: Repeats (integer)
  • Stimulus
  • genstim=true: Generate stimulus (boolean)
  • sinewave=false: Use sine wave (boolean)
  • file=: Stimulus file (string)
  • sigstdev=1: Standard deviation of signal (number)
  • warpfile=false: Warp stimulus file to the requested Delta fs (boolean)
  • Analysis
  • before=1seconds: Time before stimulation to be analyzed (number)
  • after=5seconds: Time after stimulation to be analyzed (number)
  • savetraces=true: Save traces during pause (boolean)
  • jaraverage=500ms: Time for measuring EOD rate (number)
  • chirpaverage=20ms: Time for measuring chirp data (number)
  • eodsavetime=1000ms: Duration of EOD to be saved (number)
Files
  • jar.dat : summary for each jamming stimulus.
  • jarmeans.dat : summary averaged over stimuli with same delta f and contrast.
  • jareod.dat : the fishes EOD (actually the stimulus!)
  • jareodtraces.dat : frequency, amplitude, and phase of the transdermal EOD during each stimulus.
  • jarchirps.dat : data about each chirp.
  • jarchirptraces.dat : frequency, amplitude, phase, beat, and beatphase for each chirp.
  • jarchirpeod.dat : EOD for each chirp.
Plots
  • EOD frequency (upper plot): time course of the fishes EOD frequency (green). Chirps are marked by yellow dots.
  • JAR (lower left plot): Frequency change (yellow, last stimulus red) versus stimulus delta f.
  • Chirps (lower middle plot): Number of chirps (yellow) and chirp phase shift (times ten, blue) versus stimulus delta f.
  • Chirps (lower right plot): EOD frequency (yellow) and chirp phase shift (time 40, red) for each chirp evoked by the last stimulus.
Requirements
  • EOD recording (EODTrace1) and events (EODEvents1).
  • Transdermal EOD recording (EODTrace2) and events (EODEvents2).
  • Recording of the stimulus events (SignalEvents1).

Constructor & Destructor Documentation

JAR ( void  )

References Array< T >::clear(), RangeLoop::clear(), EventData::clear(), Map< T >::clear(), MultiPlot::lock(), MultiPlot::resize(), and MultiPlot::unlock().

Member Function Documentation

int main ( void  )
virtual

Implements RePro.

References JAR::analyze(), Array< T >::assign(), RangeLoop::blockRepeat(), DaqError::busy(), OutData::clear(), RangeLoop::clear(), Map< T >::clear(), EventData::clear(), MultiPlot::clearPlots(), MultiPlot::draw(), OutData::duration(), OutData::empty(), EODTools::eodAmplitude(), Traces::EODEvents, Traces::EODTrace, DaqError::error(), DaqError::errorText(), Str::expandPath(), DaqError::failed(), OutData::fixSample(), floor(), Traces::GlobalEField, OutData::indices(), OutData::intensity(), OutData::length(), OutData::load(), Traces::LocalBeatPeakEvents, Traces::LocalEODEvents, Traces::LocalEODTrace, MultiPlot::lock(), OutData::maximize(), RangeLoop::maxValue(), RangeLoop::minValue(), Str::name(), DaqError::OverflowUnderrun, JAR::plot(), OutData::ramp(), RangeLoop::remainingBlockCount(), OutData::repeat(), RangeLoop::reset(), OutData::resize(), JAR::save(), JAR::saveTrace(), RangeLoop::set(), OutData::setCarrierFreq(), OutData::setDelay(), OutData::setIdent(), OutData::setIntensity(), OutData::setPriority(), OutData::setSampleRate(), RangeLoop::setSequence(), OutData::setStartSource(), OutData::setTrace(), OutData::sineWave(), RangeLoop::singleRepeat(), RangeLoop::size(), Array< T >::size(), OutData::size(), and MultiPlot::unlock().

void sessionStarted ( void  )
virtual
void sessionStopped ( bool  saved)
virtual
void save ( void  )

Save results data.

References JAR::saveEOD(), JAR::saveJAR(), and JAR::saveMeanJAR().

Referenced by JAR::main().

void saveJAR ( const Options &  header)

Save JAR for each stimulus.

References TableKey::addNumber(), TableKey::newSection(), TableKey::save(), TableKey::saveKey(), sqrt(), and RangeLoop::value().

Referenced by JAR::save().

void saveMeanJAR ( const Options &  header)

Save mean JAR for each delta f.

References TableKey::addNumber(), TableKey::newSection(), TableKey::save(), TableKey::saveKey(), sqrt(), and RangeLoop::value().

Referenced by JAR::save().

void saveEOD ( const Options &  header)

Save EOD stimulus.

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

Referenced by JAR::save().

void saveTrace ( void  )

Save trace data.

References JAR::saveChirpEOD(), JAR::saveChirps(), JAR::saveChirpTraces(), and JAR::saveEODFreq().

Referenced by JAR::main().

void saveEODFreq ( const Options &  header)

Save EOD frequency and amplitude.

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

Referenced by JAR::saveTrace().

void saveChirps ( const Options &  header)

Save chirp parameter.

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

Referenced by JAR::saveTrace().

void saveChirpTraces ( const Options &  header)

Save chirp frequency, amplitude and phase traces.

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

Referenced by JAR::saveTrace().

void saveChirpEOD ( const Options &  header)

Save the EOD around each chirp.

References TableKey::addNumber(), Traces::EODEvents, Traces::EODTrace, TableKey::save(), and TableKey::saveKey().

Referenced by JAR::saveTrace().

void reset ( bool  saved)
void plot ( void  )

Plot data.

References MultiPlot::clear(), Map< T >::clear(), MultiPlot::draw(), MultiPlot::lock(), Str::name(), RangeLoop::pos(), Map< T >::push(), Map< T >::reserve(), Map< T >::resize(), Map< T >::size(), RangeLoop::size(), MultiPlot::unlock(), RangeLoop::value(), Map< T >::x(), and Map< T >::y().

Referenced by JAR::main().

void analyze ( void  )

Analyze data.

References EventData::assign(), EventData::back(), EODTools::beatContrast(), EventData::begin(), ceil(), Traces::ChirpEvents, EventData::clear(), Map< T >::clear(), EventData::end(), EODTools::eodAmplitude(), Traces::EODEvents, Traces::EODTrace, EventData::eventSize(), EventData::eventWidth(), floor(), EventData::frequency(), Traces::GlobalEFieldEvents, EventIterator::index(), Traces::LocalEODEvents, Traces::LocalEODTrace, EventData::meanSize(), EventData::next(), RangeLoop::pos(), EventData::previous(), EventData::previousTime(), Map< T >::push(), Map< T >::reserve(), Map< T >::size(), EventData::size(), EventIterator::time(), Map< T >::x(), and Map< T >::y().

Referenced by JAR::main().

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