added docs, fix bugs

Project.toml

@@ -18,6 +18,7 @@ ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TopoPlots = "2bdbdf9c-dbd8-403f-947b-1a4e0dd41a7a"
 Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"

docs/Project.toml

@@ -11,6 +11,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 MakieThemes = "e296ed71-da82-5faf-88ab-0034a9761098"
+PyMNE = "6c5003b2-cbe8-491c-a0d1-70088e6a0fd6"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 TopoPlots = "2bdbdf9c-dbd8-403f-947b-1a4e0dd41a7a"
 Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"

docs/src/literate/reference/positions.jl

@@ -0,0 +1,23 @@
+using UnfoldMakie
+using TopoPlots
+using PyMNE
+
+
+# # get MNE-positions
+# Generate a fake MNE structure
+# [taken from mne documentation](https://mne.tools/0.24/auto_examples/visualization/eeglab_head_sphere.html)
+
+biosemi_montage = PyMNE.channels.make_standard_montage("biosemi64")
+n_channels = length(biosemi_montage.ch_names)
+fake_info = PyMNE.create_info(ch_names=biosemi_montage.ch_names, sfreq=250.,
+                            ch_types="eeg")
+data = rand(n_channels,1) * 1e-6
+fake_evoked = PyMNE.EvokedArray(data, fake_info)
+fake_evoked.set_montage(biosemi_montage)
+
+pos = UnfoldMakie.toPositions(fake_evoked)
+
+# # project from 3D electrode locations to 2D
+pos3d = hcat(values(pyconvert(Dict,biosemi_montage.get_positions()["ch_pos"]))...)
+
+pos2 = to_positions(pos3d)

ext/UnfoldMakiePyMNEExt.jl

@@ -2,14 +2,14 @@ module UnfoldMakiePyMNEExt
 
 using GeometryBasics
 using PyMNE
-
+using UnfoldMakie
 """
-toPositions(raw::PyMNE.Py;kwargs...)
+to_positions(raw::PyMNE.Py;kwargs...)
 
 calls MNE-pythons make_eeg_layout (with optional kwargs)
 Returns an array of Points
     """
-function toPositions(raw::PyMNE.Py;kwargs...)
+function UnfoldMakie.to_positions(raw::PyMNE.Py;kwargs...)
 layout_from_raw = PyMNE.channels.make_eeg_layout(raw.info;kwargs...).pos
 positions = pyconvert(Array,layout_from_raw)[:,1:2]
 

src/UnfoldMakie.jl

@@ -19,6 +19,7 @@ using DataStructures
 using DataFrames
 using SparseArrays
 using CategoricalArrays # for cut for TopoPlotSeries
+using StaticArrays
 
 using CoordinateTransformations # for 3D positions to 2D
 
@@ -65,5 +66,6 @@ export plot_circulareegtopoplot!
 export plot_topoplotseries
 export plot_topoplotseries!
 
-export nonnumeric
+export to_positions
+export nonnumeric # reexport from AoG
 end

src/eeg_positions.jl

@@ -380,15 +380,17 @@ end
 
 
 """
-toPositions(x,y,z;sphere=[0,0,0.])
-toPositions(pos::AbstractMatrix;sphere=[0,0,0.])
+to_positions(x,y,z;sphere=[0,0,0.])
+to_positions(pos::AbstractMatrix;sphere=[0,0,0.])
 Projects 3D electrode positions to a 2D layout.
 
 The matrix case, assumes `size(pos) = (3,nChannels)`
 Re-implementation of the MNE algorithm.
+
+Tipp: You can directly get positions from an MNE object after loading PyMNE and thus activating the UnfoldMakie PyMNE extension
 """
-toPositions(pos::AbstractMatrix;kwargs...) = toPositions(pos[1,:],pos[2,:],pos[3,:];kwargs)
-function toPositions(x,y,z;sphere=[0,0,0.])
+to_positions(pos::AbstractMatrix;kwargs...) = to_positions(pos[1,:],pos[2,:],pos[3,:];kwargs...)
+function to_positions(x,y,z;sphere=[0,0,0.])
 	#cart3d_to_spherical(x,y,z)
 
 # translate to sphere origin