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Clean up toolbox #20

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e01cfce
beginning of clean up
ReneSkukies Oct 16, 2025
fb615e9
add functionality to provide own formula for UnfoldRIDE
ReneSkukies Oct 21, 2025
b1d4063
fix typos, add formula to docs and readme
ReneSkukies Oct 23, 2025
b2a3b9e
add compats
ReneSkukies Oct 23, 2025
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14 changes: 13 additions & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ authors = ["Till Prölß", " René Skukies", " Benedikt Ehinger"]
version = "0.1.0"

[deps]
CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964"
Expand All @@ -16,3 +15,16 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"

[compat]
DSP = "0.8"
DataFrames = "1"
DataFramesMeta = "0.15"
Distributions = "0.25"
FFTW = "1"
Parameters = "0.12"
Peaks = "0.5, 0.6"
StableRNGs = "1"
Statistics = "1"
Unfold = "0.8"
julia = "1.11"
1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -53,6 +53,7 @@ cfg = RideConfig(
r_range = [0, 0.4],
c_range = [-0.4, 0.4],
#the range in which the initial peak estimation for the C component is performed
formulas = [@formula(0 ~ 1), @formula(0 ~ 1), @formula(0 ~ 1)] # formulas used for S, R, and C component (in this order!); if not specified these will default to `@formula(0~1)`
c_estimation_range = [0, 0.9],
#the range for one epoch
epoch_range = [-0.1, 1]
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1 change: 1 addition & 0 deletions dev/Project.toml
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Expand Up @@ -18,6 +18,7 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"
UnfoldBIDS = "b54e767b-1ebd-4480-ac2a-f5f4d8853074"
UnfoldSim = "ed8ae6d2-84d3-44c6-ab46-0baf21700804"
UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"

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8 changes: 4 additions & 4 deletions dev/runner.jl
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Expand Up @@ -12,7 +12,7 @@ using BenchmarkTools
#simulate data
begin
sim_inputs = simulation_inputs()
sim_inputs.noise = PinkNoise(; noiselevel = 1)
sim_inputs.noise = PinkNoise(; noiselevel = 0)
#sim_inputs.c_width = 30
#sim_inputs.c_offset = 10
#sim_inputs.r_width = 60
Expand Down Expand Up @@ -47,15 +47,15 @@ begin
save_interim_results = true,
)

save_to_hdf5_ride_format(
#=save_to_hdf5_ride_format(
"./dev/data/simulated_data.h5",
data,
evts,
cfg.epoch_range,
'S',
'R',
cfg.sfreq,
)
)=#

#remove the C events from the evts table, these will be estimated by the ride algorithm
evts_without_c = @subset(evts, :event .!= 'C')
Expand Down Expand Up @@ -120,7 +120,7 @@ begin
Legend(f[1, 2], [s, r, c], ["S", "R", "C"])
Label(f[0, :], text = "Expected Results")
display(f)
save("actual_erps.png", f)
#save("actual_erps.png", f)
end

if true == false
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1 change: 1 addition & 0 deletions docs/src/11-running_ride.md
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Expand Up @@ -27,6 +27,7 @@ begin
r_range = [0, 0.4],
c_range = [-0.4, 0.4],
#the range in which the initial peak estimation for the C component is performed
formulas = [@formula(0 ~ 1), @formula(0 ~ 1), @formula(0 ~ 1)] # formulas used for S, R, and C component; if not specified these will default to `@formula(0~1)`
c_estimation_range = [0, 0.9],
#the range for one epoch
epoch_range = [-0.1, 1]
Expand Down
4 changes: 2 additions & 2 deletions src/ride/ride_classic_algorithm.jl
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Expand Up @@ -28,7 +28,7 @@ function ride_algorithm(

## data_preparation
data_reshaped = reshape(data, (1, :))
evts_s = @subset(evts, :event .== 'S')
evts_s = @subset(evts, :event .== 'S') # TODO: Let user define event names
evts_r = @subset(evts, :event .== 'R')
interim_results = Vector{RideResults}()

Expand Down Expand Up @@ -134,7 +134,7 @@ function ride_algorithm(
[(evts_s, s_erp, cfg.s_range), (evts_r, r_erp, cfg.r_range)],
cfg.sfreq,
)
if cfg.filtering
if cfg.filtering # TODO: Check if this is correct; also check for filter artefacts
data_subtracted_s_and_r = dspfilter(data_subtracted_s_and_r[1, :], 5, 20)
end
data_epoched_subtracted_s_and_r, n = Unfold.epoch(
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4 changes: 4 additions & 0 deletions src/ride/ride_structs.jl
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Expand Up @@ -13,6 +13,8 @@ through manual inspection of the data.
through manual inspection of the data.
- `c_estimation_range::Vector{Float64}`: The range used for the intial C
component latency estimation through peak picking.
- formulas = [@formula(0 ~ 1), @formula(0 ~ 1), @formula(0 ~ 1)]: Vector containing formulas for the S, R, and C component (in this order!!!).
Only used during the UnfoldRIDE algorithm.
- `epoch_range::Vector{Float64}`: The range of one epoch centered around the stimulus onset.
- `iteration_limit::Int = 4`: The maximum number of iterations of the RIDE algorithm. This
is for the outer decomposition-latency estimation loop.
Expand All @@ -39,6 +41,7 @@ cfg = RideConfig(
r_range = [0, 0.8],
c_range = [-0.4, 0.4],
c_estimation_range = [-0.1, 0.9],
formulas = [@formula(0 ~ 1), @formula(0 ~ 1), @formula(0 ~ 1 + reaction_time)] # formulas used for S, R, and C component
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@behinger behinger Nov 5, 2025

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would it make sense to do:
formulas = ['S'=>@formula(0~1),'C'=>@formula(0~1),'R'=>@formula(0~1)], e.g. as a list of pairs? that would generalize to more events more readily and doesnt have the issue of order. You the only have to splice in the firbasis in the fit command down below

epoch_range = [-0.3, 1.6],
iteration_limit = 5,
heuristic1 = true,
Expand All @@ -54,6 +57,7 @@ cfg = RideConfig(
r_range::Vector{Float64}
c_range::Vector{Float64}
c_estimation_range::Vector{Float64}
formulas = [@formula(0 ~ 1), @formula(0 ~ 1), @formula(0 ~ 1)] # formulas used for S, R, and C component
epoch_range::Vector{Float64}
iteration_limit::Int = 4
heuristic1::Bool = true
Expand Down
4 changes: 2 additions & 2 deletions src/ride/ride_unfold_algorithm.jl
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Expand Up @@ -44,8 +44,8 @@ function ride_algorithm(
m = fit(
UnfoldModel,
[
'S' => (@formula(0 ~ 1), firbasis(cfg.s_range, cfg.sfreq, "")),
'R' => (@formula(0 ~ 1), firbasis(cfg.r_range, cfg.sfreq, "")),
'S' => (cfg.formulas[1], firbasis(cfg.s_range, cfg.sfreq, "")), # TODO: Let user supply bfdict
'R' => (cfg.formulas[2], firbasis(cfg.r_range, cfg.sfreq, "")),
],
evts,
data,
Expand Down
6 changes: 3 additions & 3 deletions src/ride/ride_unfold_methods.jl
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Expand Up @@ -26,10 +26,10 @@ function unfold_decomposition(data, evts_with_c, cfg)
m = fit(
UnfoldModel,
[
'S' => (@formula(0 ~ 1), firbasis(cfg.s_range, cfg.sfreq, "")),
'R' => (@formula(0 ~ 1), firbasis(cfg.r_range, cfg.sfreq, "")),
'S' => (cfg.formulas[1], firbasis(cfg.s_range, cfg.sfreq, "")), # TODO: Let user supply bfdict
'R' => (cfg.formulas[2], firbasis(cfg.r_range, cfg.sfreq, "")),
'C' => (
@formula(0 ~ 1),
cfg.formulas[3],
firbasis(c_range_adjusted(cfg.c_range), cfg.sfreq, ""),
),
],
Expand Down
4 changes: 3 additions & 1 deletion test/simulate_test_data.jl
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Expand Up @@ -30,6 +30,7 @@ end
components_onset::Vector{AbstractOnset}
end


function UnfoldSim.simulate_onsets(rng, onset::SequenceOnset, simulation::Simulation)
#calculate stimulus onsets
stimulus_onsets =
Expand All @@ -54,7 +55,8 @@ function UnfoldSim.simulate_onsets(rng, onset::SequenceOnset, simulation::Simula
end

#cut result to the design size
result = result[1:size(simulation.design)]
@debug "Type of simulation desing: " typeof(simulation.design)
result = result[1:size(rng, simulation.design)]
return result
end

Expand Down
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