|
| function | spikeAnalysis (in varargin) |
| | Constructor.
|
| |
| function | getFiles (in me, in force) |
| | Constructor.
|
| |
| function | parse (in me, in varargin) |
| |
| function | reparse (in me, in varargin) |
| |
| function | lazyParse (in me) |
| |
| function | toggleSaccadeRealign (in me, in varargin) |
| | reparse data to saccade onset after an initial parse
|
| |
| function | select (in me, in varargin) |
| | selects trials/options based on many filters
|
| |
| function | PSTH (in me) |
| | doPSTH plots spike density for the selected trial groups
|
| |
| function | density (in me) |
| | doDensity plots spike density for the selected trial groups
|
| |
| function | ISI (in me) |
| | doPSTH plots spike density for the selected trial groups
|
| |
| function | getRates (in me) |
| | doPSTH plots spike density for the selected trial groups
|
| |
| function | ROC (in me) |
| | ROC plots ROC and AUC comparing group 2 and group 1 data.
|
| |
| function get | nUnits (in me) |
| |
| function get | nSelection (in me) |
| |
| function | save (in me) |
| | save saves the object with a pregenerated name
|
| |
| function | setFiles (in me, in in) |
| | Set the plxReader files from a structure, used when this is yoked to an LFPAnalysis.
|
| |
| function | chSpectrum (in me) |
| | findRepeats looks for repetition priming effects
|
| |
| function | findRepeats (in me) |
| | findRepeats looks for repetition priming effects
|
| |
| function | saccadeTimeVsResponse (in me) |
| |
| function | compareBaseline (in me) |
| |
| function | plot (in me, in varargin) |
| |
| function | getChronuxSpikes (in me) |
| | Get spike structure in chronux format to use with its functions, the results are stored in the chronux property, which is a cell array containing structures for each data selection.
|
| |
| 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
|
| |
| 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
|
| |
|
| Property | file |
| | plexon file containing the spike data
|
| |
| Property | dir |
| | data directory
|
| |
| Property | spikeWindow |
| | � time window around the trigger, if empty use event off
|
| |
| Property | startOffset |
| | used by legacy spikes to allow negative time offsets
|
| |
| Property | binSize |
| | bin size
|
| |
| Property | densityWindow |
| | gaussian/smooth window for density plots
|
| |
| Property | densityFunction |
| | density plots smooth function
|
| |
| Property | selectedUnit |
| | default Spike channel
|
| |
| Property | filterFirstSaccades |
| | saccadeFilter, if empty ignore
|
| |
| Property | selectedBehaviour |
| | default behavioural type
|
| |
| Property | ROI |
| | region of interest for eye location [x y radius include], if empty ignore
|
| |
| Property | TOI |
| | time of interest for fixation, if empty ignore
|
| |
| Property | insetRasterPlot |
| | inset raster plot?
|
| |
| Property | verbose |
| | plot verbosity
|
| |
| Property | p |
| | spike plxReader object; can be the same or different due to spike resorting
|
| |
| Property | spike |
| | spike trial structure
|
| |
| Property | names |
| | names of spike channels
|
| |
| Property | ft |
| | fieldtrip reparse
|
| |
| Property | results |
| | fieldtrip parsed results
|
| |
| Property | chronux |
| | chronux reparse, cell is condition, struct is trials
|
| |
| Property | chresults |
| | chronux parsed results
|
| |
| Property | cutTrials |
| | trials to remove in reparsing
|
| |
| Property | selectedTrials |
| | selectedTrials: each cell is a trial list grouping
|
| |
| Property | map |
| | variable selection map for 3 analysis groups
|
| |
| 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?
|
| |
| 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.
|
| |
|
| function | selectTrials (in me) |
| | selectTrials selects trials based on many filters
|
| |
| function | plotDensity (in me) |
| |
| function | plotDensitySummary (in me) |
| |
| function | plotPSTH (in me) |
| |
| function | plotISI (in me) |
| |
| function | plotWaveforms (in me, in timeWindow) |
| |
| function | appendTrialNames (in me, in hdl, in idx) |
| |
| function | makeUI (in me, in varargin) |
| |
| function | runAnal (in src, in ignoredArg) |
| |
| function | closeUI (in me, in varargin) |
| |
| function | updateUI (in me, in varargin) |
| |
| function | notifyUI (in me, in varargin) |
| |
| 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.
|
| |
| 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.
|
| |
|
| 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 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 Member Functions inherited from analysisCore
1.9.8