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Renamed potentially confusing variables #137

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Feb 5, 2025
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Renamed potentially confusing variables #137

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46 changes: 26 additions & 20 deletions src/simulation.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,24 +7,30 @@ Simulation(
) = Simulation(design, [component], onset, noisetype)


function simulate(design::AbstractDesign, signal, onset::AbstractOnset, args...; kwargs...)
function simulate(
design::AbstractDesign,
components,
onset::AbstractOnset,
args...;
kwargs...,
)
@warn "No random generator defined, used the default (`Random.MersenneTwister(1)`) with a fixed seed. This will always return the same results and the user is strongly encouraged to provide their own random generator!"
simulate(MersenneTwister(1), design, signal, onset, args...; kwargs...)
simulate(MersenneTwister(1), design, components, onset, args...; kwargs...)
end

"""
simulate(
rng::AbstractRNG,
design::AbstractDesign,
signal,
components,
onset::AbstractOnset,
noise::AbstractNoise = NoNoise();
return_epoched = false,
)

simulate(
design::AbstractDesign,
signal,
components,
onset::AbstractOnset,
noise::AbstractNoise = NoNoise();
return_epoched = false,
Expand All @@ -36,7 +42,7 @@ optional `noise` and `rng`. Main simulation function.
# Arguments
- `rng::AbstractRNG` (optional): Random number generator, important to ensure reproducibility.
- `design::AbstractDesign`: Desired experimental design.
- `signal`: `Component`(s) for the desired signal.
- `components`: `Component`(s) for the desired signal.
- `onset::AbstractOnset`: Desired inter-onset distance distribution.
- `noise::AbstractNoise = NoNoise()` (optional): Desired noise.

Expand All @@ -59,7 +65,7 @@ julia> design =
SingleSubjectDesign(; conditions = Dict(:cond_A => ["level_A", "level_B"])) |>
x -> RepeatDesign(x, 10);

julia> signal = LinearModelComponent(;
julia> component = LinearModelComponent(;
basis = [0, 0, 0, 0.5, 1, 1, 0.5, 0, 0],
formula = @formula(0 ~ 1 + cond_A),
β = [1, 0.5],
Expand All @@ -70,7 +76,7 @@ julia> onset = UniformOnset(; width = 20, offset = 4);
julia> noise = PinkNoise(; noiselevel = 0.2);

# Variant 1: Use a custom RNG.
julia> data, events = simulate(MersenneTwister(2), design, signal, onset, noise);
julia> data, events = simulate(MersenneTwister(2), design, component, onset, noise);

julia> data
293-element Vector{Float64}:
Expand All @@ -96,7 +102,7 @@ julia> events
13 rows omitted

# Variant 2: Without specifying an RNG, MersenneTwister(1) will be used for the simulation.
julia> data1, events1 = simulate(design, signal, onset, noise);
julia> data1, events1 = simulate(design, component, onset, noise);
┌ Warning: No random generator defined, used the default (`Random.MersenneTwister(1)`) with a fixed seed. This will always return the same results and the user is strongly encouraged to provide their own random generator!
```

Expand All @@ -115,11 +121,11 @@ Additional remarks on the overlap of adjacent signals when `return_epoched = tru
simulate(
rng::AbstractRNG,
design::AbstractDesign,
signal,
components,
onset::AbstractOnset,
noise::AbstractNoise = NoNoise();
kwargs...,
) = simulate(rng, Simulation(design, signal, onset, noise); kwargs...)
) = simulate(rng, Simulation(design, components, onset, noise); kwargs...)


function simulate(rng::AbstractRNG, simulation::Simulation; return_epoched::Bool = false)
Expand Down Expand Up @@ -284,9 +290,9 @@ end


"""
add_responses!(signal, responses::Vector, e, s, tvec, erpvec)
add_responses!(signal, responses::Matrix, e, s, tvec, erpvec)
add_responses!(signal, responses::AbstractArray, e, s, tvec, erpvec)
add_responses!(signal, responses::Vector, e, s, tvec, trial_idx)
add_responses!(signal, responses::Matrix, e, s, tvec, trial_idx)
add_responses!(signal, responses::AbstractArray, e, s, tvec, trial_idx)

Add (in-place) the given `responses` to the `signal`, for both 2D (1 channel) and 3D (X channel case). Helper function.

Expand All @@ -296,7 +302,7 @@ Add (in-place) the given `responses` to the `signal`, for both 2D (1 channel) an
- `e`: Index of the channel (in `signal`) for which to add the response.
- `s`: Index of the subject (in `signal`) for which to add the response.
- `tvec`: Time points (indices in `signal`) at which to add the response.
- `erpvec`: Index of the particular trial (in `responses`) from where the response is to be added.
- `trial_idx`: Index of the particular trial (in `responses`) from where the response is to be added.

# Returns
- `Nothing`: `signal` is modified in-place.
Expand Down Expand Up @@ -324,12 +330,12 @@ julia> signal
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
```
"""
function add_responses!(signal, responses::Vector, e, s, tvec, erpvec)
@views signal[e, tvec, s] .+= responses[:, erpvec]
function add_responses!(signal, responses::Vector, e, s, tvec, trial_idx)
@views signal[e, tvec, s] .+= responses[:, trial_idx]
end
function add_responses!(signal, responses::Matrix, e, s, tvec, erpvec)
@views signal[e, tvec, s] .+= responses[:, erpvec]
function add_responses!(signal, responses::Matrix, e, s, tvec, trial_idx)
@views signal[e, tvec, s] .+= responses[:, trial_idx]
end
function add_responses!(signal, responses::AbstractArray, e, s, tvec, erpvec)
@views signal[e, tvec, s] .+= responses[e, :, erpvec]
function add_responses!(signal, responses::AbstractArray, e, s, tvec, trial_idx)
@views signal[e, tvec, s] .+= responses[e, :, trial_idx]
end
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