plxReader Class Reference

Inheritance diagram for plxReader:

Public Member Functions
function	plxReader (in varargin)
	Constructor.
function	parse (in me)
	parse all data denovo and sync plx / behaviour / eyelink info
function	reparse (in me)
	reparse only reparse eye data and spikes from the raw loaded structures
function	parseEvents (in me)
	only parse the behavioural events and EDF, used by LFPAnalysis
function	lazyParse (in me)
	only parse what needs parsing
function	readLFPs (in me)
	read continuous LFP from PLX/PL2 file into a structure
function get	isEDF (in me)
	get method to check if EDF file is present
function get	isPL2 (in me)
	get method to check if this is a newer pl2 plexon file
function get	trodality (in me)
	get method to check if the spike data was recorded using a tetrode
function	getFieldTripSpikes (in me)
	generate a FieldTrip formatted spike structure
function	integrateEyeData (in me)
	integrate the saccade information into the trial event data, somewhat complicated as not all EDF parsed trials are exactly matched to the plexon event markers.
function	infoBox (in me, in info)
	make a GUI box with all the data information available, including a plot of all event markers, which is defered from being drawn until the axis is clicked on.
function	deferDraw (in src, in ignoredArg)
function	editComment (in src, in ignoredArg)
function	generateInfo (in me)
	generate text info about loaded data
function	exportToRawSpikes (in me, in var, in firstunit, in StartTrial, in EndTrial, in trialtime, in modtime, in cuttime)
	exportToRawSpikes for legacy spikes support
function	syncData (in me, in inplx, in exclude)
	allows data from another plxReader object to be used, useful for example when you load LFP data in 1 plxReader and spikes in another but they are using the same behaviour files etc.
function	drawEvents (in me, in h)
	drawEvents plot a timeline of all event data
function	forwardPlot (in ignoredArg, in ignoredArg)
function	backPlot (in ignoredArg, in ignoredArg)
function	getFiles (in me, in force)
	get file names and directories for plexon, opticka and EDF files.
function	optimiseSize (in me)
	remove the raw wave matrices etc to reduce memory
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

Static Public Member Functions
static function	loadMat (in fn, in pn)
	load the opticka object mat file This needs to be static as it may load data called "me" which will conflict with the me object in the class.
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.

Public Attributes
Property	file
	plx/pl2 file name
Property	dir
	file directory
Property	matfile
	the opticka experimental object mat filename
Property	matdir
	the opticka file directory
Property	edffile
	Eyelink edf file name (should be same directory as opticka file).
Property	eventWindow
	use the event on/off markers if empty, or a timerange around the event otherwise
Property	eventSearchWindow
	the window to check before/after trial end for a behavioural marker
Property	startOffset
	used by legacy spikes to allow negative time offsets
Property	saccadeRealign
	Use first saccade to realign time 0 for data?
Property	channelReduction
	reduce the duplicate tetrode channels?
Property	verbose
	verbose?
Property	cellmap
	used for legacy cell channel mapping (SMRs only have 6 channels)
Property	info
	general info formatted as cellstrings for display
Property	eventList
	parsed event list from plexon strobed words/TTLs
Property	tsList
	parsed timestamped spikes
Property	meta
	general metadata (useful for legacy spikes analysis routines)
Property	rE
	the experimental runExperiment object (loaded from the matfile)
Property	eA
	the eyelink data parsed as an eyelinkAnalysis object (loaded from edffile)
Property	pl2
	the raw pl2 structure if this is a plexon pl2 file
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 Attributes
Property	isPL2
	is this a PL2 file?
Property	isEDF
	is an EDF eyelink file present?
Property	trodality
	is trodal?
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

Additional Inherited Members
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.

Constructor & Destructor Documentation

plxReader()

function plxReader::plxReader

(

in

varargin

)

Constructor.

Parameters

varargin

Returns

Member Function Documentation

backPlot()

function plxReader::backPlot	(	in	ignoredArg,
		in	ignoredArg
	)

deferDraw()

function plxReader::deferDraw	(	in	src,
		in	ignoredArg
	)

drawEvents()

function plxReader::drawEvents	(	in	me,
		in	h
	)

drawEvents plot a timeline of all event data

Parameters

h	an existing axis handle, otherwise make new figure

Returns

editComment()

function plxReader::editComment	(	in	src,
		in	ignoredArg
	)

exportToRawSpikes()

function plxReader::exportToRawSpikes	(	in	me,
		in	var,
		in	firstunit,
		in	StartTrial,
		in	EndTrial,
		in	trialtime,
		in	modtime,
		in	cuttime
	)

exportToRawSpikes for legacy spikes support

Parameters

return x spike data structure for spikes.m to read.

forwardPlot()

function plxReader::forwardPlot	(	in	ignoredArg,
		in	ignoredArg
	)

generateInfo()

function plxReader::generateInfo

(

in

me

)

generate text info about loaded data

Parameters

return

getFieldTripSpikes()

function plxReader::getFieldTripSpikes

(

in

me

)

generate a FieldTrip formatted spike structure

Parameters

return

getFiles()

function plxReader::getFiles	(	in	me,
		in	force
	)

get file names and directories for plexon, opticka and EDF files.

Parameters

force

force new files to be selected even if there are existing ones

Returns

infoBox()

function plxReader::infoBox	(	in	me,
		in	info
	)

make a GUI box with all the data information available, including a plot of all event markers, which is defered from being drawn until the axis is clicked on.

Parameters

info	a cellstring info structure, optional

Returns

integrateEyeData()

function plxReader::integrateEyeData

(

in

me

)

integrate the saccade information into the trial event data, somewhat complicated as not all EDF parsed trials are exactly matched to the plexon event markers.

Parameters

return

isEDF()

function get plxReader::isEDF

(

in

me

)

get method to check if EDF file is present

Parameters

return

isPL2()

function get plxReader::isPL2

(

in

me

)

get method to check if this is a newer pl2 plexon file

Parameters

return

lazyParse()

function plxReader::lazyParse

(

in

me

)

only parse what needs parsing

Parameters

return

loadMat()

static function plxReader::loadMat ( in  fn, in  pn  )

static

load the opticka object mat file This needs to be static as it may load data called "me" which will conflict with the me object in the class.

Parameters

return

optimiseSize()

function plxReader::optimiseSize

(

in

me

)

remove the raw wave matrices etc to reduce memory

Parameters

return

parse()

function plxReader::parse

(

in

me

)

parse all data denovo and sync plx / behaviour / eyelink info

Parameters

return

parseEvents()

function plxReader::parseEvents

(

in

me

)

only parse the behavioural events and EDF, used by LFPAnalysis

Parameters

return

readLFPs()

function plxReader::readLFPs

(

in

me

)

read continuous LFP from PLX/PL2 file into a structure

Parameters

return

reparse()

function plxReader::reparse

(

in

me

)

reparse only reparse eye data and spikes from the raw loaded structures

Parameters

return

syncData()

function plxReader::syncData	(	in	me,
		in	inplx,
		in	exclude
	)

allows data from another plxReader object to be used, useful for example when you load LFP data in 1 plxReader and spikes in another but they are using the same behaviour files etc.

Parameters

inplx	another plxReader instance for syncing to
exclude	a regex of properties to exclude from syncing

Returns

trodality()

function get plxReader::trodality

(

in

me

)

get method to check if the spike data was recorded using a tetrode

Parameters

return

Member Data Documentation

cellmap

Property plxReader::cellmap

used for legacy cell channel mapping (SMRs only have 6 channels)

channelReduction

Property plxReader::channelReduction

reduce the duplicate tetrode channels?

dir

Property plxReader::dir

file directory

eA

Property plxReader::eA

the eyelink data parsed as an eyelinkAnalysis object (loaded from edffile)

edffile

Property plxReader::edffile

Eyelink edf file name (should be same directory as opticka file).

eventList

Property plxReader::eventList

parsed event list from plexon strobed words/TTLs

eventSearchWindow

Property plxReader::eventSearchWindow

the window to check before/after trial end for a behavioural marker

eventWindow

Property plxReader::eventWindow

use the event on/off markers if empty, or a timerange around the event otherwise

file

Property plxReader::file

plx/pl2 file name

PLXREADER Reads in Plexon .plx and .pl2 files along with metadata and eyelink EDF files. Parses the trial event / behaviour structure. Integrates EDF events and raw X/Y data into trial LFP/spike structures. Converts into Fieldtrip and custom structures. The plexon files contain the neural data and the strobed words and TTLs. Each strobed word represents a 15bit trial number, and there are 8 additional TTL lines. The opticka mat file includes the experimental structure (stimulusSequence), the stimuli (metaStimulus) and all other parameters. The strobed word trial order can be linked to the opticka trial order to determine what stimuli were shown. The EDF file contains the eyelink data timestamped for each trial along with trial numbers and other trial information.

info

Property plxReader::info

general info formatted as cellstrings for display

isEDF

Property plxReader::isEDF

protected

is an EDF eyelink file present?

isPL2

Property plxReader::isPL2

protected

is this a PL2 file?

matdir

Property plxReader::matdir

the opticka file directory

matfile

Property plxReader::matfile

the opticka experimental object mat filename

meta

Property plxReader::meta

general metadata (useful for legacy spikes analysis routines)

pl2

Property plxReader::pl2

the raw pl2 structure if this is a plexon pl2 file

rE

Property plxReader::rE

the experimental runExperiment object (loaded from the matfile)

saccadeRealign

Property plxReader::saccadeRealign

Use first saccade to realign time 0 for data?

startOffset

Property plxReader::startOffset

used by legacy spikes to allow negative time offsets

trodality

Property plxReader::trodality

protected

is trodal?

tsList

Property plxReader::tsList

parsed timestamped spikes

verbose

Property plxReader::verbose

verbose?

---

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

• omniplex/plxReader.m