LFPMeta Class Reference

Inheritance diagram for LFPMeta:

Public Member Functions
function	LFPMeta (in varargin)
	Constructor.
function	add (in me, in varargin)
	add LFPAnalysis objects to the meta list
function	process (in me, in varargin)
function	run (in me, in varargin)
	run the averaging of the data
function	load (in me, in varargin)
function	save (in me, in varargin)
function	spawn (in me, in varargin)
function	toggleSaccades (in me, in varargin)
function get	nSites (in me)
	get method for nSites
function	quit (in me, in varargin)
function	cleanPaths (in me, in varargin)
function	select (in me, in varargin)
	plot individual
function	plotSite (in me, in varargin)
	plot individual
function	plot (in me, in varargin)
	plot individual
function	setOptions (in me, in varargin)
	setOptions shows the analysis options
function	editweight (in me, in varargin)
function	remove (in me, in varargin)
function	reparse (in me, in varargin)
function	parse (in me, in varargin)
function	reset (in me, in varargin)
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 sessionPrefix, in lab, in create)
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)
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	initialiseGlobals (in me, in doReset, in doOpen)
function	initialiseSaveFile (in me)
	Initialise Save prefix.
function	checkPaths (in me)
	checks the paths are valid

Public Attributes
Property	verbose
Property	sites
	LFP sites.
Property	list
	display list
Property	raw
	raw LFP objects
Property	results
	meta result
Property	version
	version
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	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	generateSitesInfo (in me, in idx)
	generates the selection information
function	generateSitesList (in me)
	generates the list shown in the GUI
function	closeUI (in me)
function	makeUI (in me)
function	notifyUI (in me, in varargin)
function	updateUI (in me)
Protected Member Functions inherited from analysisCore
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	makeArgs (in args)
	Converts cell args to structure array.
static function	addDefaults (in args, in defs)
	add 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

LFPMeta()

function LFPMeta::LFPMeta

(

in

varargin

)

Constructor.

Parameters

varargin

Returns

Member Function Documentation

add()

function LFPMeta::add	(	in	me,
		in	varargin
	)

add LFPAnalysis objects to the meta list

Parameters

return

cleanPaths()

function LFPMeta::cleanPaths	(	in	me,
		in	varargin
	)

Parameters

return

closeUI()

function LFPMeta::closeUI ( in  me )

protectedvirtual

Parameters

return

Reimplemented from analysisCore.

editweight()

function LFPMeta::editweight	(	in	me,
		in	varargin
	)

Parameters

return

generateSitesInfo()

function LFPMeta::generateSitesInfo ( in  me, in  idx  )

protected

generates the selection information

Parameters

return

generateSitesList()

function LFPMeta::generateSitesList ( in  me )

protected

generates the list shown in the GUI

Parameters

return

load()

function LFPMeta::load	(	in	me,
		in	varargin
	)

Parameters

return

makeUI()

function LFPMeta::makeUI ( in  me )

protectedvirtual

Parameters

return

Reimplemented from analysisCore.

notifyUI()

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

protectedvirtual

Parameters

return

Reimplemented from analysisCore.

nSites()

function get LFPMeta::nSites

(

in

me

)

get method for nSites

Parameters

return

parse()

function LFPMeta::parse	(	in	me,
		in	varargin
	)

Parameters

return

plot()

function LFPMeta::plot	(	in	me,
		in	varargin
	)

plot individual

Parameters

return

plotSite()

function LFPMeta::plotSite	(	in	me,
		in	varargin
	)

plot individual

Parameters

return

process()

function LFPMeta::process	(	in	me,
		in	varargin
	)

Parameters

return

quit()

function LFPMeta::quit	(	in	me,
		in	varargin
	)

Parameters

return

remove()

function LFPMeta::remove	(	in	me,
		in	varargin
	)

Parameters

return

reparse()

function LFPMeta::reparse	(	in	me,
		in	varargin
	)

Parameters

return

reset()

function LFPMeta::reset	(	in	me,
		in	varargin
	)

Parameters

return

run()

function LFPMeta::run	(	in	me,
		in	varargin
	)

run the averaging of the data

Parameters

return

save()

function LFPMeta::save	(	in	me,
		in	varargin
	)

Parameters

return

select()

function LFPMeta::select	(	in	me,
		in	varargin
	)

plot individual

Parameters

return

setOptions()

function LFPMeta::setOptions	(	in	me,
		in	varargin
	)

setOptions shows the analysis options

Parameters

return

spawn()

function LFPMeta::spawn	(	in	me,
		in	varargin
	)

Parameters

return

toggleSaccades()

function LFPMeta::toggleSaccades	(	in	me,
		in	varargin
	)

Parameters

return

updateUI()

function LFPMeta::updateUI ( in  me )

protectedvirtual

Parameters

return

Reimplemented from analysisCore.

Member Data Documentation

list

Property LFPMeta::list

display list

raw

Property LFPMeta::raw

raw LFP objects

results

Property LFPMeta::results

meta result

sites

Property LFPMeta::sites

LFP sites.

verbose

Property LFPMeta::verbose

version

Property LFPMeta::version

version

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

• analysis/LFPMeta.m