Merge pull request #47 from unfoldtoolbox/preprocFunc

Allow to specify preprocessing function

src/utils.jl

@@ -5,8 +5,10 @@
 """
 
 - removeTimeexpandedXs (true): Removes the timeexpanded designmatrix which significantly reduces the memory-consumption. This Xs is rarely needed, but can be recovered (look into the Unfold.load function)
+
+extractData (function) - specify the function that translate the MNE Raw object to an data array. Default is `rawToData` which uses get_data and allows to pick `channels` - see @Ref(`rawToData`). The optional kw- arguments (e.g. channels) need to be specified directly in the `runUnfold` function as kw-args
 """
-function runUnfold(dataDF, eventsDF, bfDict; channels::AbstractVector{<:Union{String, Integer}}=[], eventcolumn="event",removeTimeexpandedXs=true)
+function runUnfold(dataDF, eventsDF, bfDict; eventcolumn="event",removeTimeexpandedXs=true, extractData = rawToData,kwargs...)
 	subjects = unique(dataDF.subject)
 
 	resultsDF = DataFrame()
@@ -16,10 +18,11 @@ function runUnfold(dataDF, eventsDF, bfDict; channels::AbstractVector{<:Union{St
 		# Get current subject
 		raw = @subset(dataDF, :subject .== sub).data
 
-		tmpData = pyconvert(Array,raw[1].get_data(picks=pylist(channels),units="uV"))
-
 		tmpEvents = @subset(eventsDF, :subject .== sub)
 
+		tmpData = extractData(raw[1],tmpEvents;kwargs...)
+
+
 		# Fit Model
 		m = fit(UnfoldModel,bfDict,tmpEvents,tmpData; eventcolumn=eventcolumn);
 
@@ -35,6 +38,14 @@ function runUnfold(dataDF, eventsDF, bfDict; channels::AbstractVector{<:Union{St
 	return resultsDF
 end
 
+# Function to run Preprocessing functions on data
+function rawToData(raw,tmpEvents;channels::AbstractVector{<:Union{String, Integer}}=[])
+	return pyconvert(Array,raw.get_data(picks=pylist(channels),units="uV"))
+end
+
+# Calculate Grand average; this is likely a TODO
+# Commented this out for now as this might go into UnfoldStats; R.S. 18/01/24
+#=
 function calculateGA(resultsDF; channels=:false)
 	GA = @chain resultsDF begin
 		# TODO: check if this works
@@ -44,7 +55,11 @@ function calculateGA(resultsDF; channels=:false)
 		# need to check which variables to use
 		@by([:basisname,:coefname,:time, :channel], :estimate = mean(estimate))
 	end
+
+    
 end
+=#
+
 #=
 # Function to run unfold on epoched data
 function runUnfold(DataDF, EventsDF, formula, sfreq, τ = (-0.3,1.); channels::Union{Nothing, String, Integer}=nothing)
@@ -83,4 +98,4 @@ function runUnfold(DataDF, EventsDF, formula, sfreq, τ = (-0.3,1.); channels::U
 	end
 	return resultsDF
 end
-=#
+=#