GitHub

Speed measurement

Here we will compare the speed of plotting UnfoldMakie with MNE (Python) and EEGLAB (MATLAB).

Three cases are measured:

  • Single topoplot
  • Topoplot series with 50 topoplots
  • Topoplott animation with 50 timestamps

Note that the results of benchmarking on your computer and on Github may differ.

using UnfoldMakie
using TopoPlots
using BenchmarkTools
using Observables
using CairoMakie
using PythonPlot;
using PyMNE;
    CondaPkg Found dependencies: /home/runner/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Found dependencies: /home/runner/.julia/packages/PyMNE/cNGDN/CondaPkg.toml
    CondaPkg Found dependencies: /home/runner/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
    CondaPkg Found dependencies: /home/runner/.julia/packages/PythonPlot/oS8x4/CondaPkg.toml
    CondaPkg Resolving changes
             + libstdcxx
             + libstdcxx-ng
             + matplotlib
             + mne (pip)
             + openssl
             + python
             + uv
    CondaPkg Initialising pixi
             │ /home/runner/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /home/runner/work/UnfoldMakie.jl/UnfoldMakie.jl/docs/.CondaPkg
✔ Created /home/runner/work/UnfoldMakie.jl/UnfoldMakie.jl/docs/.CondaPkg/pixi.toml
    CondaPkg Wrote /home/runner/work/UnfoldMakie.jl/UnfoldMakie.jl/docs/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ uv = ">=0.4"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ matplotlib = ">=1"
             │
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = ">=3.9,<4, >=3.4,<4"
             │
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge", "anaconda"]
             │ channel-priority = "strict"
             │ description = "automatically generated by CondaPkg.jl"
             │
             │ [pypi-dependencies]
             └ mne = ">=1.4"
    CondaPkg Installing packages
             │ /home/runner/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /home/runner/work/UnfoldMakie.jl/UnfoldMakie.jl/docs/.CondaPkg/pixi.toml
✔ The default environment has been installed.

Data input

dat, positions = TopoPlots.example_data()
df = UnfoldMakie.eeg_array_to_dataframe(dat[:, :, 1], string.(1:length(positions)));

Topoplots

UnfoldMakie.jl

@benchmark plot_topoplot(dat[:, 320, 1]; positions = positions)
BenchmarkTools.Trial: 153 samples with 1 evaluation per sample.
 Range (min … max):  28.451 ms … 186.806 ms  ┊ GC (min … max): 0.00% … 64.63%
 Time  (median):     29.461 ms               ┊ GC (median):    0.00%
 Time  (mean ± σ):   32.649 ms ±  20.578 ms  ┊ GC (mean ± σ):  6.71% ±  8.77%

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  28.5 ms       Histogram: log(frequency) by time       165 ms <

 Memory estimate: 7.69 MiB, allocs estimate: 114690.

UnfoldMakie.jl with DelaunayMesh

@benchmark plot_topoplot(
    dat[:, 320, 1];
    positions = positions,
    topo_interpolation = (; interpolation = DelaunayMesh()),
)
BenchmarkTools.Trial: 151 samples with 1 evaluation per sample.
 Range (min … max):  28.265 ms … 207.620 ms  ┊ GC (min … max): 0.00% … 62.48%
 Time  (median):     29.896 ms               ┊ GC (median):    0.00%
 Time  (mean ± σ):   33.368 ms ±  22.507 ms  ┊ GC (mean ± σ):  7.08% ±  8.76%

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  28.3 ms       Histogram: log(frequency) by time       173 ms <

 Memory estimate: 7.69 MiB, allocs estimate: 114697.

MNE

posmat = collect(reduce(hcat, [[p[1], p[2]] for p in positions])')
pypos = Py(posmat).to_numpy()
pydat = Py(dat[:, 320, 1])

@benchmark begin
    f = PythonPlot.figure()
    PyMNE.viz.plot_topomap(
        pydat,
        pypos,
        sphere = 1.1,
        extrapolate = "box",
        cmap = "RdBu_r",
        sensors = false,
        contours = 6,
    )
    f.show()
end
BenchmarkTools.Trial: 341 samples with 1 evaluation per sample.
 Range (min … max):  12.051 ms … 255.957 ms  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):     12.744 ms               ┊ GC (median):    0.00%
 Time  (mean ± σ):   14.674 ms ±  19.068 ms  ┊ GC (mean ± σ):  0.00% ± 0.00%

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  12.1 ms         Histogram: frequency by time         23.1 ms <

 Memory estimate: 3.30 KiB, allocs estimate: 98.

Topoplot series

Note that UnfoldMakie and MNE have different defaults for displaying topoplot series. UnfoldMakie in plot_topoplot averages over time samples. MNE in plot_topopmap displays single samples without averaging.

UnfoldMakie.jl

@benchmark begin
    plot_topoplotseries(
        df;
        bin_num = 50,
        positions = positions,
        axis = (; xlabel = "Time windows [s]"),
    )
end
BenchmarkTools.Trial: 3 samples with 1 evaluation per sample.
 Range (min … max):  1.655 s …   1.823 s  ┊ GC (min … max): 0.00% … 6.48%
 Time  (median):     1.670 s              ┊ GC (median):    0.00%
 Time  (mean ± σ):   1.716 s ± 92.850 ms  ┊ GC (mean ± σ):  2.30% ± 3.74%

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  1.65 s         Histogram: frequency by time        1.82 s <

 Memory estimate: 310.04 MiB, allocs estimate: 3799886.

MNE

easycap_montage = PyMNE.channels.make_standard_montage("standard_1020")
ch_names = pyconvert(Vector{String}, easycap_montage.ch_names)[1:64]
info = PyMNE.create_info(PyList(ch_names), ch_types = "eeg", sfreq = 1)
info.set_montage(easycap_montage)
simulated_epochs = PyMNE.EvokedArray(Py(dat[:, :, 1]), info)

@benchmark simulated_epochs.plot_topomap(1:50)
BenchmarkTools.Trial: 6 samples with 1 evaluation per sample.
 Range (min … max):  711.361 ms …    1.195 s  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):     718.626 ms               ┊ GC (median):    0.00%
 Time  (mean ± σ):   866.339 ms ± 234.226 ms  ┊ GC (mean ± σ):  0.00% ± 0.00%

  █                                                              
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  711 ms           Histogram: frequency by time          1.19 s <

 Memory estimate: 2.39 KiB, allocs estimate: 69.

MATLAB

Running MATLAB on a GitHub Action is not easy. So we benchmarked three consecutive executions (on a screenshot) on a server with an AMD EPYC 7452 32-core processor. Note that Github and the server we used for MATLAB benchmarking are two different computers, which can give different timing results.

Animation

The main advantage of Julia is the speed with which the figures are updated.

timestamps = range(1, 50, step = 1)
framerate = 50
50

UnfoldMakie with .gif

@benchmark begin
    f = Makie.Figure()
    dat_obs = Observable(dat[:, 1, 1])
    plot_topoplot!(f[1, 1], dat_obs, positions = positions)
    record(f, "topoplot_animation_UM.gif", timestamps; framerate = framerate) do t
        dat_obs[] = @view(dat[:, t, 1])
    end
end
BenchmarkTools.Trial: 2 samples with 1 evaluation per sample.
 Range (min … max):  3.983 s …   4.059 s  ┊ GC (min … max): 1.02% … 0.45%
 Time  (median):     4.021 s              ┊ GC (median):    0.73%
 Time  (mean ± σ):   4.021 s ± 54.206 ms  ┊ GC (mean ± σ):  0.73% ± 0.40%

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  3.98 s         Histogram: frequency by time        4.06 s <

 Memory estimate: 682.09 MiB, allocs estimate: 874999.

MNE with .gif

@benchmark begin
    fig, anim = simulated_epochs.animate_topomap(
        times = Py(timestamps),
        frame_rate = framerate,
        blit = false,
        image_interp = "cubic", # same as CloughTocher
    )
    anim.save("topomap_animation_mne.gif", writer = "ffmpeg", fps = framerate)
end
BenchmarkTools.Trial: 1 sample with 1 evaluation per sample.
 Single result which took 9.653 s (0.00% GC) to evaluate,
 with a memory estimate of 3.03 KiB, over 96 allocations.

Note, that due to some bugs in (probably) PythonCall topoplot is black and white.

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