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.
Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
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function | iRecAnalysis (in varargin) |
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function | load (in me, in force) |
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function | parseSimple (in me) |
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function | parse (in me) |
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function | parseSaccades (in me) |
| parse saccade related data
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function | pruneNonRTTrials (in me) |
| remove trials from correct list that did not use a rt start or end message
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function | updateCorrectIndex (in me, in idx) |
| update correct index list
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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.
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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
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function | clickMe (in src, in ignoredArg) |
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function | spawnMe (in src, in ignoredArg) |
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function | parseROI (in me) |
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function | parseTOI (in me) |
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function | plotROI (in me) |
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function | clickMeROI (in src, in ignoredArg) |
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function | plotTOI (in me) |
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function | clickMeTOI (in src, in ignoredArg) |
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function get | ppd (in me) |
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function | fixVarNames (in me) |
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function | removeRawData (in me) |
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function | reparseVars (in me) |
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function | plotNH (in me, in trial, in handle) |
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function | explore (in me, in close) |
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function | exploreNext (in src, in ignoredArg) |
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function | explorePrevious (in src, in ignoredArg) |
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function | exploreClose (in src, in ignoredArg) |
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function | analysisCore (in varargin) |
| Class constructor.
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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.
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function | showEyePlots (in me, in varargin) |
| showEyePlots if we have a linked eyelink file show the raw data plots
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function | showInfo (in me, in varargin) |
| showInfo shows the info box for the plexon parsed data
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function | setStats (in me, in varargin) |
| setStats set up the stats structure used in many Fieldtrip analyses
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function set | baselineWindow (in me, in in) |
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function | optimiseSize (in me) |
| optimiseSize remove the raw matrices etc. to reduce memory
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function | GUI (in me, in varargin) |
| show a GUI if available for analysis object
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function | initialise (in me, in varargin) |
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function | setTimeFreqOptions (in me, in varargin) |
| setTimeFreqOptions for Fieldtrip time freq analysis of LFP data
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function | optickaCore (in varargin) |
| Class constructor.
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function get | fullName (in me) |
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function | getALF (in me, in subject, in sessionPrefix, in lab, in create) |
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function | findAttributes (in me, in attrName, in attrValue) |
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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.
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function | findPropertyDefault (in me, in propName) |
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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.
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function | checkSuperclasses (in List) |
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function | editProperties (in me, in properties) |
| method to modify a set of properties
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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.
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function | initialiseGlobals (in me, in doReset, in doOpen) |
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function | initialiseSaveFile (in me) |
| Initialise Save prefix.
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function | checkPaths (in me) |
| checks the paths are valid
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Property | fileName |
| file name
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Property | trialStartMessageName |
| which message contains the trial start tag
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Property | variableMessageName |
| which message contains the variable name or value
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Property | trialEndMessage |
| message name to signal end of the trial
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Property | rtStartMessage |
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Property | rtEndMessage |
| CSV message name to end the stimulus presentation or subject repsonse.
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Property | rtOverrideMessage |
| override the rtStart time with a custom message?
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Property | minSaccadeDistance |
| minimum saccade distance in degrees
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Property | VFAC |
| relative velocity threshold
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Property | MINDUR |
| minimum saccade duration
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Property | tS |
| the temporary experiement structure which contains the eyePos recorded from opticka
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Property | excludeIncorrect |
| exclude incorrect trials when indexing (trials contain an idx and correctedIdx value and you can use either)
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Property | ROI |
| region of interest?
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Property | TOI |
| time of interest?
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Property | verbose |
| verbose output?
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Property | pixelsPerCm |
| screen resolution
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Property | distance |
| screen distance
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Property | resolution |
| screen resolution
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Property | ETparams |
| For Dee's analysis edit these settings.
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Property | relativeMarkers |
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Property | SYNCTIME |
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Property | END_FIX |
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Property | END_RT |
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Property | END_EXP |
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Property | correctValue |
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Property | incorrectValue |
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Property | breakFixValue |
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Property | trialsToPrune |
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Property | rtLimits |
| these are used for spikes spike saccade time correlations
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Property | rtDivision |
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Property | trialOverride |
| trial list from the saved behavioural data, used to fix trial name bug in old files
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Property | xCenter |
| screen X center in pixels
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Property | yCenter |
| screen Y center in pixels
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Property | override573 |
| 57.3 bug override
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Property | downSample |
| downsample the data for plotting
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Property | excludeTrials |
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Property | doPlots |
| generate plots?
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Property | baselineWindow |
| +- time window (s) for baseline estimation/removal [-0.2 0]
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Property | measureRange |
| default range (s) to measure values from
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Property | plotRange |
| default range to plot data
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Property | rootDirectory |
| root directory to check for data if files can't be found
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Property | gd |
| getDensity stats object, used for group comparisons
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Property | options |
| various stats values in a structure for different analyses
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Property | openUI |
| is the UI opened?
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Property | name |
| object name
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Property | comment |
| comment
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Property | verbose |
| verbose logging, subclasses must assign this. This is normally logical true/false
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Property | dateStamp |
| clock() dateStamp set on construction
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Property | uuid |
| universal ID
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Property | paths |
| storage of various paths
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Property | fullName |
| The fullName is the object name combined with its uuid and class name.
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function | closeUI (in me, in varargin) |
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function | makeUI (in me, in varargin) |
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function | updateUI (in me, in varargin) |
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function | notifyUI (in me, in varargin) |
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function | parseEvents (in me) |
| main parse loop for CSV events, has to be one big serial loop
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function | parseAsVars (in me) |
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function | parseSecondaryEyePos (in me) |
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function | parseFixationPositions (in me) |
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function | toDegrees (in me, in in) |
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function | toPixels (in me, in in) |
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function | computeFullSaccades (in me) |
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function | computeMicrosaccades (in me) |
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function | vecvel (in xx, in SAMPLING, in TYPE) |
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function | microsacc (in x, in vel, in VFAC, in MINDUR) |
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function | binsacc (in sacl, in sacr) |
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function | saccpar (in bsac) |
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function | getTrialDef (in me) |
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virtual function | makeUI (in me) |
| make the UI for the analysis object
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virtual function | closeUI (in me) |
| close the UI for the analysis object
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virtual function | updateUI (in me) |
| update the UI for the analysis object
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function | initialiseOptions (in me) |
| initialise settings for fieldtrip time frequency analysis
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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.
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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
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function | initialiseStats (in me) |
| initialise the statistics options, see setStats()
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function | formatByClass (in me, in dp, in dn) |
| format data for ROC
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function | roc (in me, in data) |
| ROC see http://www.subcortex.net/research/code/area_under_roc_curve.
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function | auc (in me, in data, in alpha, in flag, in nboot, in varargin) |
| Area under ROC.
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function | aucBootstrap (in me, in data, in nboot, in flag, in H0) |
| AUC bootstrap.
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function | parseArgs (in me, in args, in allowedProperties) |
| Sets properties from a structure or normal arguments pairs, ignores invalid or non-allowed properties.
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function | addArgs (in me, in args) |
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function | setPaths (in me) |
| Sets properties from a structure or normal arguments pairs, ignores invalid or non-allowed properties.
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function | getFonts (in me) |
| set paths for object
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function | toStructure (in me) |
| Converts properties to a structure.
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function | getType (in me, in in) |
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function | logOutput (in me, in in, in message, in override) |
| Give a metaproperty return the likely property class.
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function | salutation (in me, in varargin) |
| Prints messages dependent on verbosity.
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static function | doFFT (in p, in fs, in ff, in normalise, in useHanning) |
| phaseDifference basic phase diff measurement
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static function | phaseDifference (in x, in y) |
| phaseDifference basic phase diff measurement
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static function | phase (in x) |
| phase basic phase measurement
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static function | subselectFieldTripTrials (in ft, in idx) |
| subselectFieldTripTrials sub-select trials where the ft function fails to use cfg.trials
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static function | findNearest (in in, in value) |
| find nearest value in a vector, if more than 1 index return the first
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static function | linearFit (in x, in y) |
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static function | var2SE (in var, in dof) |
| convert variance to standard error
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static function | rad2ang (in alphain, in rect, in rot) |
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static function | ang2rad (in alpha) |
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static function | stderr (in data, in type, in onlyerror, in alpha, in dim, in avgfn) |
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static function | areabar (in xv, in yv, in ev, in c1, in alpha, in varargin) |
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static function | pupilConversion (in value, in cal, in calSize) |
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static function | cellArray2Num (in data) |
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static function | optimalLayout (in len) |
| calculates preferred row col layout for multiple plots
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static function | optimalColours (in n_colors, in bg, in func) |
| make optimally different colours for plots Copyright 2010-2011 by Timothy E. Holy
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static function | parsecolor (in s) |
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static function | colorstr2rgb (in c) |
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static function | makeArgs (in args) |
| Converts cell args to structure array.
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static function | addDefaults (in args, in defs) |
| add default options to arg input
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static function | hasKey (in in, in key) |
| check if a struct / object has a propery / field
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static function | getKeys (in device) |
| PTB Get key presses, stops key bouncing.
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Property | panels |
| UI panels.
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Property | yokedSelection |
| do we yoke the selection to the parent object (e.g. LFPAnalysis > spikeAnalysis)
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Property | handles |
| handles for the GUI
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Property | cloning |
| are we cloning this from another object
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Property | mversion |
| Matlab version number, this is transient so it is not saved.
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Property | sansFont |
| sans font
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Property | monoFont |
| monoFont
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Property | className |
| class name
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Property | savePrefix |
| save prefix generated from clock time
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Property | fullName_ |
| cached full name
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