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| { | ||
| "projectName": "UnfoldSim.jl", | ||
| "projectOwner": "unfoldtoolbox", | ||
| "files": [ | ||
| "README.md" | ||
| ], | ||
| "commitType": "docs", | ||
| "commitConvention": "angular", | ||
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| "name": "Maanik Marathe", | ||
| "avatar_url": "https://avatars.githubusercontent.com/u/66105649?v=4", | ||
| "profile": "https://github.com/maanikmarathe", | ||
| "contributions": [ | ||
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| "name": "Benedikt Ehinger", | ||
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| "profile": "http://www.benediktehinger.de", | ||
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| "code", | ||
| "doc", | ||
| "ideas", | ||
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| "name": "Judith Schepers", | ||
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| "name": "René Skukies", | ||
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| } |
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| name: DARUS dataverse sync | ||
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| types: [labeled, opened, synchronize, reopened] | ||
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| jobs: | ||
| dv-sync: | ||
| runs-on: ubuntu-latest | ||
| if: contains(github.event.pull_request.labels.*.name, 'sync darus') | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Synchronize to DV | ||
| uses: SimTech-Research-Data-Management/dataverse-sync@main | ||
| with: | ||
| dataverse_url: "https://darus.uni-stuttgart.de/" | ||
| api_token: ${{ secrets.DV_API_TOKEN }} | ||
| persistent_id: "doi:10.18419/darus-3804" |
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| name: Format suggestions | ||
| on: | ||
| pull_request: | ||
| jobs: | ||
| code-style: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: julia-actions/[email protected] |
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| - name: Open Journals PDF Generator | ||
| uses: openjournals/[email protected] |
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| /docs/Manifest.toml | ||
| /docs/build/ | ||
| /docs/src/literate/*/*.md | ||
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| [hartmut] | ||
| git-tree-sha1 = "07d7f285b4fed914b2ab5dc25dae3e108b8ce35e" | ||
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| [[hartmut.download]] | ||
| sha256 = "8fa88ed124e2307ad757956fcdf4f670193a6c58974f3adb8473b56afeb995a7" | ||
| url = "https://gist.github.com/behinger/96973aae77e56a73ddeea83792bc52ad/raw/07d7f285b4fed914b2ab5dc25dae3e108b8ce35e.tar.gz" |
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| using UnfoldSim | ||||||||||||||||||||||||||||||||||||||||||||||||||
| using UnfoldMakie | ||||||||||||||||||||||||||||||||||||||||||||||||||
| using CairoMakie | ||||||||||||||||||||||||||||||||||||||||||||||||||
| using DataFrames | ||||||||||||||||||||||||||||||||||||||||||||||||||
| using Random | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # ## Specifying a design | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # We are using a one-level design for testing here. | ||||||||||||||||||||||||||||||||||||||||||||||||||
| design = SingleSubjectDesign(conditions=Dict(:condA=>["levelA"])) | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # Next we generate two simple components at two different times without any formula attached (we have a single condition anyway) | ||||||||||||||||||||||||||||||||||||||||||||||||||
| c = LinearModelComponent(;basis=p100(),formula = @formula(0~1),β = [1]); | ||||||||||||||||||||||||||||||||||||||||||||||||||
| c2 = LinearModelComponent(;basis=p300(),formula = @formula(0~1),β = [1]); | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # ## The multichannel component | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # next similar to the nested design above, we can nest the component in a `MultichannelComponent`. We could either provide the projection marix manually, e.g.: | ||||||||||||||||||||||||||||||||||||||||||||||||||
| mc = UnfoldSim.MultichannelComponent(c, [1,2,-1,3,5,2.3,1]) | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # or maybe more convenient: use the pair-syntax: Headmodel=>Label which makes use of a headmodel (HaRTmuT is currently easily available in UnfoldSim) | ||||||||||||||||||||||||||||||||||||||||||||||||||
| hart = headmodel(type="hartmut") | ||||||||||||||||||||||||||||||||||||||||||||||||||
| mc = UnfoldSim.MultichannelComponent(c, hart=>"Left Postcentral Gyrus") | ||||||||||||||||||||||||||||||||||||||||||||||||||
| mc2 = UnfoldSim.MultichannelComponent(c2, hart=>"Right Occipital Pole") | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # !!! hint | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # You could also specify a noise-specific component which is applied prior to projection & summing with other components | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # finally we need to define the onsets of the signal | ||||||||||||||||||||||||||||||||||||||||||||||||||
| onset = UniformOnset(;width=20,offset=4); | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # ## Simulation | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # Now as usual we simulate data. Inspecting data shows our result is now indeed ~230 Electrodes large! Nice! | ||||||||||||||||||||||||||||||||||||||||||||||||||
| data,events = simulate(MersenneTwister(1),design, [mc,mc2], onset, PinkNoise(noiselevel=0.05)) | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| size(data) | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # !!! hint | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # The noise declared in the `simulate` function is added after mixing to channels, each channel receives independent noise. It is also possible to add noise to each individual component+source prior to projection. This would introduce correlated noise. | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # ## Plotting | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # Let's plot using Butterfly & Topoplot | ||||||||||||||||||||||||||||||||||||||||||||||||||
| # first we convert the electrodes to positions usable in TopoPlots.jl | ||||||||||||||||||||||||||||||||||||||||||||||||||
| pos3d = hart.electrodes["pos"]; | ||||||||||||||||||||||||||||||||||||||||||||||||||
| pos2d = to_positions(pos3d') | ||||||||||||||||||||||||||||||||||||||||||||||||||
| pos2d = [Point2f(p[1]+0.5,p[2]+0.5) for p in pos2d]; | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| # now plot! | ||||||||||||||||||||||||||||||||||||||||||||||||||
| f = Figure() | ||||||||||||||||||||||||||||||||||||||||||||||||||
| df = DataFrame(:estimate => data[:],:channel => repeat(1:size(data,1),outer=size(data,2)),:time => repeat(1:size(data,2),inner=size(data,1))) | ||||||||||||||||||||||||||||||||||||||||||||||||||
| plot_butterfly!(f[1,1:2],df;positions=pos2d) | ||||||||||||||||||||||||||||||||||||||||||||||||||
| plot_topoplot!(f[2,1],df[df.time .== 28,:];positions=pos2d,visual=(;enlarge=0.5,label_scatter=false),axis=(;limits=((0,1),(0,0.9)))) | ||||||||||||||||||||||||||||||||||||||||||||||||||
| plot_topoplot!(f[2,2],df[df.time .== 48,:];positions=pos2d,visual=(;enlarge=0.5,label_scatter=false),axis=(;limits=((0,1),(0,0.9)))) | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| f | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| @@ -1,18 +1,16 @@ | ||||||||||||||||||||
| # # New component: Duration + Shift | ||||||||||||||||||||
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| # We want a new component that changes its duration and shift depending on a column in the event-design. This is somewhat already implemented in the HRF + Pupil bases | ||||||||||||||||||||
| using UnfoldSim | ||||||||||||||||||||
| using Unfold | ||||||||||||||||||||
| using Random | ||||||||||||||||||||
| using DSP | ||||||||||||||||||||
| using CairoMakie, UnfoldMakie | ||||||||||||||||||||
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| sfreq = 100; | ||||||||||||||||||||
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| # ## Design | ||||||||||||||||||||
| # Let's generate a design with two columns, shift + duration | ||||||||||||||||||||
| design = UnfoldSim.SingleSubjectDesign(;conditions= Dict( | ||||||||||||||||||||
| :shift => rand(100).*sfreq/5, | ||||||||||||||||||||
| :duration=>20 .+rand(100).*sfreq/5)) | ||||||||||||||||||||
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@@ -24,7 +22,7 @@ struct TimeVaryingComponent <: AbstractComponent | |||||||||||||||||||
| maxlength | ||||||||||||||||||||
| end | ||||||||||||||||||||
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| # We have to define the length of a component | ||||||||||||||||||||
| Base.length(c::TimeVaryingComponent) = length(c.maxlength) | ||||||||||||||||||||
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| # While we could have put the TimeVaryingComponent.basisfunction directly into the simulate function, I thought this is a bit more modular | ||||||||||||||||||||
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| erp = UnfoldSim.simulate(MersenneTwister(1),TimeVaryingComponent(basis_shiftduration,50),design) | ||||||||||||||||||||
| plot_erpimage(hcat(erp...),sortvalues=generate(design).shift) | ||||||||||||||||||||
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[JuliaFormatter] reported by reviewdog 🐶