makieorg / topoplots.jl Goto Github PK

As you can see in documentation example it is impossible to show label text for electrodes.
Seems like a bug.

I converted some MNE code to convert form x/y/z to eeg_topoplot coordinates.

Now the big question is, can/should this be included here in TopoPlots.jl, or somehwere else?

using CoordinateTransformations

	"""
		convert x/y/z electrode montage positions to spherical coordinate representation. output is a matrix
	"""
	function cart3d_to_spherical(x,y,z)
		sph = SphericalFromCartesian().(SVector.(x,y,z))
		sph = [vcat(s.r,s.θ,π/2 - s.ϕ) for s in sph] 
		sph = hcat(sph...)'
		return sph
	end

		
"""
Projects 3D electrode positions to a 2D layout.

Re-implementation of the MNE algorithm.

If you put sphere to 
"""
function pos3D_to_layout(x,y,z;sphere=[0,0,0.])
	#cart3d_to_spherical(x,y,z)
	
# translate to sphere origin
	x .-= sphere[1]
	y .-= sphere[2]
	z .-= sphere[3]
	
	# convert to spherical coordinates
	sph = cart3d_to_spherical(x,y,z)

	# get rid of of the radius for now
	pol_a = sph[:,3]
	pol_b = sph[:,2]
	
	# use only theta & phi, convert back to cartesian coordinates
	p_x = pol_a .* cos.(pol_b)
	p_y = pol_a .* sin.(pol_b)

	# scale by the radius
	p_x .*= sph[:,1] ./(π/2)
	p_y .*= sph[:,1] ./(π/2)

	# move back by the sphere coordinates
	p_x .+= sphere[1]
	p_y .+= sphere[2]

  return Point2f.(p_x,p_y)
end
		  		



	  

(for full reproducibility)

begin
using CSV
	using LinearAlgebra
	using HTTP
	using CoordinateTransformations
	using WGLMakie
using StaticArrays
using DataFrames
end
begin
pos3d = CSV.read(download("https://raw.githubusercontent.com/lrkrol/SEREEGA/b5dec01e8b98260904906cc19c38853bfbb2ff19/leadfield/hartmut/chanlocs-hartmut-NYhead_small.xyz"),DataFrame,header=false)
rename!(pos3d,:Column1=>:ix,:Column2=>:x,:Column3=>:y,:Column4=>:z,:Column5=>:label)

	# remove some whitespace in the labels
transform!(pos3d,:label=>(x->strip.(x))=>:label)

	# remove some weird channels
	subset!(pos3d,:label=>ByRow(l -> l ∉ ["Nk1","Nk2","Nk3","Nk4"]));

out =   pos3D_to_layout(pos3d.x,pos3d.y,pos3d.z)

eeg_topoplot(1:size(out,1),pos3d.label;positions=out, interpolation=NullInterpolator(),label_text=true,enlarge=0.5)
end;

Hi,
I am plotting some EEG topographies together with @behinger. We observed strange interpolation at the top boundary. This is with the default interpolator ClaughTochter

DelaunyMesh has same issue

Any ideas? Has it to do with the fill-value?
Cheers,
Vladimir & Bene

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Reading https://discourse.julialang.org/t/ann-pythoncall-and-juliacall/76778/24 and seeing the much better python package installation integration, it seems worth quite a bit to switch to PythonCall directly to call our one python dependency...

Currently, if I do data, positions = TopoPlots.example_data() I have only opportunity to get 64 channel position.
But if I want 32, or 128 channels layout? Would be nice to have such arrangements too.

Has anyone used this recently? I'm pretty sure it used to work at some point, but now it seems quite broken:

using TopoPlots
labels = ["cz", "fp1", "fp2", "fz"]
TopoPlots.eeg_topoplot(ones(length(labels)), labels; label_text=true, label_scatter=(markersize=10, strokewidth=2, strokecolor=:white))

... does neither prodcue correct sensor locations (look at Cz) nor does it plot any text for me:

I believe this is related to: #18, so it seems to be an unfortunate consequence of some design decisions. Nevertheless, I think this warrants fixing as the current behavior is extremely surprising.

Would it make sense to add a plottype kwarg to TopoPlot, which would allow any HeatmapLike plot to be used in place of contourf? I would love to use surface or even contour, for example.

Hi, I noticed a small problem when setting the 'colorrange' attribute for the eeg_topoplot() function. The colors inside the circles that indicate channel locations are unaffected by the new colorrange if the data is passed as Vector{Any} instead of Vector{Float32}.

Nowhere in the documentation is there a description of the data dimensions for this code:
data, positions = TopoPlots.example_data().
It has three dimensions: 64×400×3. But what do they represent?
Specifying this will greatly improve the usability of the package, especially for new users.

Hello,
we noticed a weird behavior with the head position in a eeg_topoplot when the data points are asymmetrical or only in one corner.

In the image we are drawing two eeg topoplots with points in the top right and bottom left and our expected behavior was to see both heads overlap and contain all points instead of two smaller local heads.
This is the code used to draw them:

f = Figure()
axis = Axis(f[1, 1], aspect = 1)
xlims!(low = -2, high = 2)
ylims!(low = -2, high = 2)

data = [0, 0, 0]
pos1 = [Point2f(-1, -1), Point2f(-1.0, 0.0), Point2f(0, -1)]
pos2 = [Point2f(1, 1), Point2f(1.0, 0.0), Point2f(0, 1)]

eeg_topoplot!(axis, data, positions=pos1)
eeg_topoplot!(axis, data, positions=pos2)

Is there some workaround to keep the head location and size independent from the point locations ?
Or would it be possible to either add a way to set a position and size for the head or expose the draw_ear_nose! function ?

Thank you very much and kind regards,
Daniel, Sören, Niklas

I got this message when trying to update makie to 0.19.0
It would be nice to change it somehow because in new Makie version they changed some functions.

checkout if we can now use
Interpolators.jl

maybe optimize the use of
ScatteredInterpolators.jl

I didnt fully understand this line of code - do we need it?

It seems to be a stub to use the default values. params is not used though?

Context:

labels = ["cz", "fp1", "fp2", "fz"]
TopoPlots.eeg_topoplot(1:length(labels),labels;                        label_text = true) # doesnt work
TopoPlots.eeg_topoplot(1:length(labels),labels; labels=labels, label_text = true) # works

is necessary. The reason most likely is that in the recipe label is used as this "named"-input

later it is referenced in the plot! function via

not sure why the first case, labels seem to not be picked up correctly. Maybe a hint: Attributes(plot) is used, and in there, labels = nothing. Even though plot.labels is correctly showing the Array. - I dont know enough to understand this

maybe @SimonDanisch any insights?

(This was not the case in topoplots 1.3, with pre 0.20 makie (didnt test all iterations))

pinging @marcpabst for pushing me to this issue

I think we should allow
interpolation = False

This would allow to plot things like:

and

Should be straight forward to add another if interpolation == False catch where we select for Delauny/Splines Interpolations, right?