iRecAnalysis offers a set of methods to load, parse & plot raw CSV files. It understands opticka trials (where CSV messages INT start a trial and 255 ends a trial by default) so can parse eye data and plot it for trial groups. You can also manually find microsaccades, and perform ROI/TOI filtering on the eye movements. More...

Detailed Description

iRecAnalysis offers a set of methods to load, parse & plot raw CSV files. It understands opticka trials (where CSV messages INT start a trial and 255 ends a trial by default) so can parse eye data and plot it for trial groups. You can also manually find microsaccades, and perform ROI/TOI filtering on the eye movements.

Inheritance diagram for iRecAnalysis:

Public Member Functions
function	iRecAnalysis (in varargin)

function	load (in me, in force)

function	parseSimple (in me)

function	parse (in me)

function	parseSaccades (in me)
	parse saccade related data

function	pruneNonRTTrials (in me)
	remove trials from correct list that did not use a rt start or end message

function	updateCorrectIndex (in me, in idx)
	update correct index list

function	pruneTrials (in me, in num)
	prunetrials – very rarely (n=1) we lose a trial strobe in the plexon data and thus when we try to align the plexon trial index and CSV trial index they are off-by-one, this function is used once the index of the trial is know to prune it out of the CSV data set and recalculate the indexes.

function	plot (in me, in select, in type, in seperateVars, in name, in handle)
	give a list of trials and it will plot both the raw eye position and the events

function	clickMe (in src, in ignoredArg)

function	spawnMe (in src, in ignoredArg)

function	parseROI (in me)

function	parseTOI (in me)

function	plotROI (in me)

function	clickMeROI (in src, in ignoredArg)

function	plotTOI (in me)

function	clickMeTOI (in src, in ignoredArg)

function get	ppd (in me)

function	fixVarNames (in me)

function	removeRawData (in me)

function	reparseVars (in me)

function	plotNH (in me, in trial, in handle)

function	explore (in me, in close)

function	exploreNext (in src, in ignoredArg)

function	explorePrevious (in src, in ignoredArg)

function	exploreClose (in src, in ignoredArg)

Public Member Functions inherited from analysisCore
function	analysisCore (in varargin)
	Class constructor.

function	checkPaths (in me, in varargin)
	checkPaths: if we've saved an object then load it on a new machine paths to source files may be wrong. If so then allows us to find a new directory for the source files.

function	showEyePlots (in me, in varargin)
	showEyePlots if we have a linked eyelink file show the raw data plots

function	showInfo (in me, in varargin)
	showInfo shows the info box for the plexon parsed data

function	setStats (in me, in varargin)
	setStats set up the stats structure used in many Fieldtrip analyses

function set	baselineWindow (in me, in in)

function	optimiseSize (in me)
	optimiseSize remove the raw matrices etc. to reduce memory

function	GUI (in me, in varargin)
	show a GUI if available for analysis object

function	initialise (in me, in varargin)

function	setTimeFreqOptions (in me, in varargin)
	setTimeFreqOptions for Fieldtrip time freq analysis of LFP data

Public Member Functions inherited from optickaCore
function	optickaCore (in varargin)
	Class constructor.

function get	fullName (in me)

function	getALF (in me, in subject, in lab, in create)
	get the ALF path

function	makeReport (in me, in rpt)
	Generate a detailed report for the opticka object.

function	findAttributes (in me, in attrName, in attrValue)

function	findAttributesandType (in me, in attrName, in attrValue, in type)
	find properties of object with specific attributes, for example all properties whose GetAcccess attribute is public and type is logical.

function	findPropertyDefault (in me, in propName)
	Return the declared default value for a class property.

function	clone (in me)
	Use this syntax to make a deep copy of the object, i.e. OBJ_OUT has the same field values, but will not behave as a handle-copy of me anymore.

function	checkSuperclasses (in List)

function	editProperties (in me, in properties)
	method to modify a set of properties

function	setProp (in me, in property, in value)
	method to fast change a particular value. This is useful for use in anonymous functions, like in the state machine.

function	initialiseSaveFile (in me, in varargin)
	just get date fragment for backwards compatibility

function	checkPaths (in me)
	checks the paths are valid

Public Attributes
Property	fileName
	file name

Property	trialStartMessageName
	which message contains the trial start tag

Property	variableMessageName
	which message contains the variable name or value

Property	trialEndMessage
	message name to signal end of the trial

Property	rtStartMessage

Property	rtEndMessage
	CSV message name to end the stimulus presentation or subject repsonse.

Property	rtOverrideMessage
	override the rtStart time with a custom message?

Property	minSaccadeDistance
	minimum saccade distance in degrees

Property	VFAC
	relative velocity threshold

Property	MINDUR
	minimum saccade duration

Property	tS
	the temporary experiement structure which contains the eyePos recorded from opticka

Property	excludeIncorrect
	exclude incorrect trials when indexing (trials contain an idx and correctedIdx value and you can use either)

Property	ROI
	region of interest?

Property	TOI
	time of interest?

Property	verbose
	verbose output?

Property	pixelsPerCm
	screen resolution

Property	distance
	screen distance

Property	resolution
	screen resolution

Property	ETparams
	For Dee's analysis edit these settings.

Property	relativeMarkers

Property	SYNCTIME

Property	END_FIX

Property	END_RT

Property	END_EXP

Property	correctValue

Property	incorrectValue

Property	breakFixValue

Property	trialsToPrune

Property	rtLimits
	these are used for spikes spike saccade time correlations

Property	rtDivision

Property	trialOverride
	trial list from the saved behavioural data, used to fix trial name bug in old files

Property	xCenter
	screen X center in pixels

Property	yCenter
	screen Y center in pixels

Property	override573
	57.3 bug override

Property	downSample
	downsample the data for plotting

Property	excludeTrials

Public Attributes inherited from analysisCore
Property	doPlots
	generate plots?

Property	baselineWindow
	+- time window (s) for baseline estimation/removal [-0.2 0]

Property	measureRange
	default range (s) to measure values from

Property	plotRange
	default range to plot data

Property	rootDirectory
	root directory to check for data if files can't be found

Property	gd
	getDensity stats object, used for group comparisons

Property	options
	various stats values in a structure for different analyses

Property	openUI
	is the UI opened?

Public Attributes inherited from optickaCore
Property	name
	object name

Property	comment
	comment

Property	verbose
	verbose logging, subclasses must assign this. This is normally logical true/false

Property	optickaVersion
	version number

Property	dateStamp
	clock() dateStamp set on construction

Property	uuid
	universal ID

Property	paths
	storage of various paths

Property	fullName
	The fullName is the object name combined with its uuid and class name.

Protected Member Functions
function	closeUI (in me, in varargin)

function	makeUI (in me, in varargin)

function	updateUI (in me, in varargin)

function	notifyUI (in me, in varargin)

function	parseEvents (in me)
	main parse loop for CSV events, has to be one big serial loop

function	parseAsVars (in me)

function	parseSecondaryEyePos (in me)

function	parseFixationPositions (in me)

function	toDegrees (in me, in in)

function	toPixels (in me, in in)

function	computeFullSaccades (in me)

function	computeMicrosaccades (in me)

function	vecvel (in xx, in SAMPLING, in TYPE)

function	microsacc (in x, in vel, in VFAC, in MINDUR)

function	binsacc (in sacl, in sacr)

function	saccpar (in bsac)

function	getTrialDef (in me)

Protected Member Functions inherited from analysisCore
virtual function	makeUI (in me)
	make the UI for the analysis object

virtual function	closeUI (in me)
	close the UI for the analysis object

virtual function	updateUI (in me)
	update the UI for the analysis object

function	initialiseOptions (in me)
	initialise settings for fieldtrip time frequency analysis

function	inheritPlxReader (in me, in p)
	Allows two analysis objects to share a single plxReader object. This is important in cases where for e.g. an LFPAnalysis object uses the same plexon file as its spikeAnalysis child used for spike-LFP anaysis.

function	setSelection (in me, in in)
	set trials / var parsing from outside, override dialog, used when yoked to another analysis object, for example when spikeAnalysis is a child of LFPAnalysis

function	initialiseStats (in me)
	initialise the statistics options, see setStats()

function	formatByClass (in me, in dp, in dn)
	format data for ROC

function	roc (in me, in data)
	ROC see http://www.subcortex.net/research/code/area_under_roc_curve.

function	auc (in me, in data, in alpha, in flag, in nboot, in varargin)
	Area under ROC.

function	aucBootstrap (in me, in data, in nboot, in flag, in H0)
	AUC bootstrap.

Protected Member Functions inherited from optickaCore
function	parseArgs (in me, in args, in allowedProperties)
	Sets properties from a structure or normal arguments pairs, ignores invalid or non-allowed properties.

function	addArgs (in me, in args)

function	setPaths (in me)
	Sets properties from a structure or normal arguments pairs, ignores invalid or non-allowed properties.

function	getFonts (in me)
	set paths for object

function	toStructure (in me)
	Converts properties to a structure.

function	getType (in me, in in)

function	logOutput (in me, in in, in message, in override)
	Give a metaproperty return the likely property class.

function	salutation (in me, in varargin)
	Prints messages dependent on verbosity.

Additional Inherited Members
Static Public Member Functions inherited from analysisCore
static function	doFFT (in p, in fs, in ff, in normalise, in useHanning)
	phaseDifference basic phase diff measurement

static function	phaseDifference (in x, in y)
	phaseDifference basic phase diff measurement

static function	phase (in x)
	phase basic phase measurement

static function	subselectFieldTripTrials (in ft, in idx)
	subselectFieldTripTrials sub-select trials where the ft function fails to use cfg.trials

static function	findNearest (in in, in value)
	find nearest value in a vector, if more than 1 index return the first

static function	linearFit (in x, in y)

static function	var2SE (in var, in dof)
	convert variance to standard error

static function	rad2ang (in alphain, in rect, in rot)

static function	ang2rad (in alpha)

static function	stderr (in data, in type, in onlyerror, in alpha, in dim, in avgfn)

static function	areabar (in xv, in yv, in ev, in c1, in alpha, in varargin)

static function	pupilConversion (in value, in cal, in calSize)

static function	cellArray2Num (in data)

static function	optimalLayout (in len)
	calculates preferred row col layout for multiple plots

static function	optimalColours (in n_colors, in bg, in func)
	make optimally different colours for plots Copyright 2010-2011 by Timothy E. Holy

static function	parsecolor (in s)

static function	colorstr2rgb (in c)

Static Public Member Functions inherited from optickaCore
static function	initialiseGlobals (in doReset, in doOpen)

static function	makeArgs (in args)
	Converts cell args to structure array.

static function	addDefaults (in args, in defs)
	regularises and adds default options to arg input

static function	hasKey (in in, in key)
	check if a struct / object has a propery / field

static function	getKeys (in device)
	PTB Get key presses, stops key bouncing.

Protected Attributes inherited from analysisCore
Property	panels
	UI panels.

Property	yokedSelection
	do we yoke the selection to the parent object (e.g. LFPAnalysis > spikeAnalysis)

Property	handles
	handles for the GUI

Protected Attributes inherited from optickaCore
Property	cloning
	are we cloning this from another object

Property	mversion
	Matlab version number, this is transient so it is not saved.

Property	sansFont
	sans font

Property	monoFont
	monoFont

Property	className
	class name

Property	savePrefix
	save prefix generated from clock time

Property	fullName_
	cached full name

Constructor & Destructor Documentation

◆ iRecAnalysis()

function iRecAnalysis::iRecAnalysis ( in varargin )

Member Function Documentation

◆ binsacc()

function iRecAnalysis::binsacc	(	in	sacl,
		in	sacr
	)

protected

◆ clickMe()

function iRecAnalysis::clickMe	(	in	src,
		in	ignoredArg
	)

◆ clickMeROI()

function iRecAnalysis::clickMeROI	(	in	src,
		in	ignoredArg
	)

◆ clickMeTOI()

function iRecAnalysis::clickMeTOI	(	in	src,
		in	ignoredArg
	)

◆ closeUI()

function iRecAnalysis::closeUI	(	in	me,
		in	varargin
	)

protected

Parameters

return

◆ computeFullSaccades()

function iRecAnalysis::computeFullSaccades ( in me )

protected

◆ computeMicrosaccades()

function iRecAnalysis::computeMicrosaccades ( in me )

protected

◆ explore()

function iRecAnalysis::explore	(	in	me,
		in	close
	)

Parameters

return

◆ exploreClose()

function iRecAnalysis::exploreClose	(	in	src,
		in	ignoredArg
	)

◆ exploreNext()

function iRecAnalysis::exploreNext	(	in	src,
		in	ignoredArg
	)

◆ explorePrevious()

function iRecAnalysis::explorePrevious	(	in	src,
		in	ignoredArg
	)

◆ fixVarNames()

function iRecAnalysis::fixVarNames ( in me )

Parameters

return

◆ getTrialDef()

function iRecAnalysis::getTrialDef ( in me )

protected

◆ load()

function iRecAnalysis::load	(	in	me,
		in	force
	)

Parameters

return

◆ makeUI()

function iRecAnalysis::makeUI	(	in	me,
		in	varargin
	)

protected

Parameters

return

◆ microsacc()

function iRecAnalysis::microsacc	(	in	x,
		in	vel,
		in	VFAC,
		in	MINDUR
	)

protected

◆ notifyUI()

function iRecAnalysis::notifyUI	(	in	me,
		in	varargin
	)

protectedvirtual

Parameters

return

Reimplemented from analysisCore.

◆ parse()

function iRecAnalysis::parse ( in me )

Parameters

return

◆ parseAsVars()

function iRecAnalysis::parseAsVars ( in me )

protected

Parameters

return

◆ parseEvents()

function iRecAnalysis::parseEvents ( in me )

protected

main parse loop for CSV events, has to be one big serial loop

Parameters

return

◆ parseFixationPositions()

function iRecAnalysis::parseFixationPositions ( in me )

protected

Parameters

return

◆ parseROI()

function iRecAnalysis::parseROI ( in me )

Parameters

return

◆ parseSaccades()

function iRecAnalysis::parseSaccades ( in me )

parse saccade related data

Parameters

return

◆ parseSecondaryEyePos()

function iRecAnalysis::parseSecondaryEyePos ( in me )

protected

Parameters

return

◆ parseSimple()

function iRecAnalysis::parseSimple ( in me )

Parameters

return

◆ parseTOI()

function iRecAnalysis::parseTOI ( in me )

Parameters

return

◆ plot()

function iRecAnalysis::plot	(	in	me,
		in	select,
		in	type,
		in	seperateVars,
		in	name,
		in	handle
	)

give a list of trials and it will plot both the raw eye position and the events

Parameters

return

◆ plotNH()

function iRecAnalysis::plotNH	(	in	me,
		in	trial,
		in	handle
	)

Parameters

return

◆ plotROI()

function iRecAnalysis::plotROI ( in me )

Parameters

return

◆ plotTOI()

function iRecAnalysis::plotTOI ( in me )

Parameters

return

◆ ppd()

function get iRecAnalysis::ppd ( in me )

Parameters

return

◆ pruneNonRTTrials()

function iRecAnalysis::pruneNonRTTrials ( in me )

remove trials from correct list that did not use a rt start or end message

Parameters

return

◆ pruneTrials()

function iRecAnalysis::pruneTrials	(	in	me,
		in	num
	)

prunetrials – very rarely (n=1) we lose a trial strobe in the plexon data and thus when we try to align the plexon trial index and CSV trial index they are off-by-one, this function is used once the index of the trial is know to prune it out of the CSV data set and recalculate the indexes.

Parameters

return

◆ removeRawData()

function iRecAnalysis::removeRawData ( in me )

Parameters

return

◆ reparseVars()

function iRecAnalysis::reparseVars ( in me )

Parameters

return

◆ saccpar()

function iRecAnalysis::saccpar ( in bsac )

protected

◆ spawnMe()

function iRecAnalysis::spawnMe	(	in	src,
		in	ignoredArg
	)

◆ toDegrees()

function iRecAnalysis::toDegrees	(	in	me,
		in	in
	)

protected

◆ toPixels()

function iRecAnalysis::toPixels	(	in	me,
		in	in
	)

protected

◆ updateCorrectIndex()

function iRecAnalysis::updateCorrectIndex	(	in	me,
		in	idx
	)

update correct index list

Parameters

return

◆ updateUI()

function iRecAnalysis::updateUI	(	in	me,
		in	varargin
	)

protected

Parameters

return

◆ vecvel()

function iRecAnalysis::vecvel	(	in	xx,
		in	SAMPLING,
		in	TYPE
	)

protected

Member Data Documentation

◆ breakFixValue

Property iRecAnalysis::breakFixValue

◆ correctValue

Property iRecAnalysis::correctValue

◆ distance

Property iRecAnalysis::distance

screen distance

◆ downSample

Property iRecAnalysis::downSample

downsample the data for plotting

◆ END_EXP

Property iRecAnalysis::END_EXP

◆ END_FIX

Property iRecAnalysis::END_FIX

◆ END_RT

Property iRecAnalysis::END_RT

◆ ETparams

Property iRecAnalysis::ETparams

For Dee's analysis edit these settings.

◆ excludeIncorrect

Property iRecAnalysis::excludeIncorrect

exclude incorrect trials when indexing (trials contain an idx and correctedIdx value and you can use either)

◆ excludeTrials

Property iRecAnalysis::excludeTrials

◆ fileName

Property iRecAnalysis::fileName

file name

◆ incorrectValue

Property iRecAnalysis::incorrectValue

◆ MINDUR

Property iRecAnalysis::MINDUR

minimum saccade duration

◆ minSaccadeDistance

Property iRecAnalysis::minSaccadeDistance

minimum saccade distance in degrees

◆ override573

Property iRecAnalysis::override573

57.3 bug override

◆ pixelsPerCm

Property iRecAnalysis::pixelsPerCm

screen resolution

◆ relativeMarkers

Property iRecAnalysis::relativeMarkers

Is measure range relative to start and end markers or absolute to start marker?

◆ resolution

Property iRecAnalysis::resolution

screen resolution

◆ ROI

Property iRecAnalysis::ROI

region of interest?

◆ rtDivision

Property iRecAnalysis::rtDivision

◆ rtEndMessage

Property iRecAnalysis::rtEndMessage

CSV message name to end the stimulus presentation or subject repsonse.

◆ rtLimits

Property iRecAnalysis::rtLimits

these are used for spikes spike saccade time correlations

◆ rtOverrideMessage

Property iRecAnalysis::rtOverrideMessage

override the rtStart time with a custom message?

◆ rtStartMessage

Property iRecAnalysis::rtStartMessage

the CSV message name to start measuring stimulus presentation, and this is the 0 time in the analysis by default, can be overridden by send SYNCTIME or rtOverrideMessage

◆ SYNCTIME

Property iRecAnalysis::SYNCTIME

◆ TOI

Property iRecAnalysis::TOI

time of interest?

◆ trialEndMessage

Property iRecAnalysis::trialEndMessage

message name to signal end of the trial

◆ trialOverride

Property iRecAnalysis::trialOverride

trial list from the saved behavioural data, used to fix trial name bug in old files

◆ trialStartMessageName

Property iRecAnalysis::trialStartMessageName

which message contains the trial start tag

◆ trialsToPrune

Property iRecAnalysis::trialsToPrune

◆ tS

Property iRecAnalysis::tS

the temporary experiement structure which contains the eyePos recorded from opticka

◆ variableMessageName

Property iRecAnalysis::variableMessageName

which message contains the variable name or value

◆ verbose

Property iRecAnalysis::verbose

verbose output?

◆ VFAC

Property iRecAnalysis::VFAC

relative velocity threshold

◆ xCenter

Property iRecAnalysis::xCenter

screen X center in pixels

◆ yCenter

Property iRecAnalysis::yCenter

screen Y center in pixels

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

analysis/iRecAnalysis.m

Detailed Description

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ iRecAnalysis()

Member Function Documentation

◆ binsacc()

◆ clickMe()

◆ clickMeROI()

◆ clickMeTOI()

◆ closeUI()

◆ computeFullSaccades()

◆ computeMicrosaccades()

◆ explore()

◆ exploreClose()

◆ exploreNext()

◆ explorePrevious()

◆ fixVarNames()

◆ getTrialDef()

◆ load()

◆ makeUI()

◆ microsacc()

◆ notifyUI()

◆ parse()

◆ parseAsVars()

◆ parseEvents()

◆ parseFixationPositions()

◆ parseROI()

◆ parseSaccades()

◆ parseSecondaryEyePos()

◆ parseSimple()

◆ parseTOI()

◆ plot()

◆ plotNH()

◆ plotROI()

◆ plotTOI()

◆ ppd()

◆ pruneNonRTTrials()

◆ pruneTrials()

◆ removeRawData()

◆ reparseVars()

◆ saccpar()

◆ spawnMe()

◆ toDegrees()

◆ toPixels()

◆ updateCorrectIndex()

◆ updateUI()

◆ vecvel()

Member Data Documentation

◆ breakFixValue

◆ correctValue

◆ distance

◆ downSample

◆ END_EXP

◆ END_FIX

◆ END_RT

◆ ETparams

◆ excludeIncorrect

◆ excludeTrials

◆ fileName

◆ incorrectValue

◆ MINDUR

◆ minSaccadeDistance

◆ override573

◆ pixelsPerCm

◆ relativeMarkers

◆ resolution

◆ ROI

◆ rtDivision

◆ rtEndMessage

◆ rtLimits

◆ rtOverrideMessage

◆ rtStartMessage

◆ SYNCTIME

◆ TOI

◆ trialEndMessage

◆ trialOverride

◆ trialStartMessageName