analysisCore base class inherited by other analysis classes. analysisCore is itself derived from optickaCore. Provides a set of shared methods and some core properties and stats GUI for various analysis classes.
Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
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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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| 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 | 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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| 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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| virtual function | notifyUI (in me, in varargin) |
| | modify text of 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 analysisCore::pupilConversion |
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value, |
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cal, |
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calSize |
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[mm, cf] = pupilConversion(value, calibration, calSize) eyelink uses arbitrary area units, convert to mm using this function e.g. [mm, rs] = pupilConversion(2000, 8890, 8)
| static function analysisCore::stderr |
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data, |
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type, |
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onlyerror, |
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alpha, |
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dim, |
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avgfn |
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static |
Plots mean and error choosable by switches
[mean,error] = stderr(data,type,onlyerror,alpha)
Switches: SE 2SE SD 2SD 3SD V FF CV AF
Public Member Functions inherited from optickaCore
1.9.8