Add jump times to discrete sequence in discretize

JuliaHealth · Dec 10, 2024 · a3f66ce · a3f66ce
1 parent 85fd5da
commit a3f66ce
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Showing 6 changed files with 18 additions and 5 deletions.
diff --git a/KomaMRIBase/src/datatypes/simulation/DiscreteSequence.jl b/KomaMRIBase/src/datatypes/simulation/DiscreteSequence.jl
@@ -85,8 +85,9 @@ based on simulation parameters.
 # Returns
 - `seqd`: (`::DiscreteSequence`) DiscreteSequence struct
 """
-function discretize(seq::Sequence; sampling_params=default_sampling_params())
+function discretize(seq::Sequence; sampling_params=default_sampling_params(), add_times=[])
     t, Δt      = get_variable_times(seq; Δt=sampling_params["Δt"], Δt_rf=sampling_params["Δt_rf"])
+    sort!(unique!(append!(t, add_times)))
     B1, Δf     = get_rfs(seq, t)
     Gx, Gy, Gz = get_grads(seq, t)
     tadc       = get_adc_sampling_times(seq)

diff --git a/KomaMRIBase/src/motion/Motion.jl b/KomaMRIBase/src/motion/Motion.jl
@@ -202,4 +202,6 @@ end
 
 # Auxiliary functions
 times(m::Motion) = times(m.time)
-is_composable(m::Motion) = is_composable(m.action)
+is_composable(m::Motion) = is_composable(m.action)
+get_jump_times(m::Motion) = get_jump_times(m.action, m.time)
+get_jump_times(::AbstractAction, ::AbstractTimeSpan) = []
diff --git a/KomaMRIBase/src/motion/MotionList.jl b/KomaMRIBase/src/motion/MotionList.jl
@@ -1,6 +1,6 @@
-include("Action.jl")
 include("SpinSpan.jl")
 include("TimeSpan.jl")
+include("Action.jl")
 include("Motion.jl")
 
 """
@@ -202,3 +202,11 @@ function sort_motions!(m::MotionList)
     sort!(m.motions; by=m -> times(m)[1])
     return nothing
 end
+
+function get_jump_times(ml::MotionList{T}) where {T<:Real}
+    jump_times = T[]
+    for m in ml.motions
+        append!(jump_times, get_jump_times(m))
+    end
+    return jump_times
+end
diff --git a/KomaMRIBase/src/motion/NoMotion.jl b/KomaMRIBase/src/motion/NoMotion.jl
@@ -49,3 +49,4 @@ function get_spin_coords(
 ) where {T<:Real}
     return x, y, z
 end
+get_jump_times(::NoMotion) = []
diff --git a/KomaMRIBase/src/motion/actions/arbitraryactions/FlowPath.jl b/KomaMRIBase/src/motion/actions/arbitraryactions/FlowPath.jl
@@ -34,4 +34,5 @@ julia> flowpath = FlowPath(
     dy::AbstractArray{T}
     dz::AbstractArray{T}
     spin_reset::AbstractArray{Bool}
-end
+end
+get_jump_times(a::FlowPath, t::AbstractTimeSpan) = (times(t)[end] - times(t)[1])/(size(a.spin_reset)[2]-1) * (getindex.(findall(a.spin_reset .== 1), 2) .- 1) .- 1e-6
diff --git a/KomaMRICore/src/simulation/SimulatorCore.jl b/KomaMRICore/src/simulation/SimulatorCore.jl
@@ -336,7 +336,7 @@ function simulate(
         """ maxlog=1
     end
     # Simulation init
-    seqd = discretize(seq; sampling_params=sim_params) # Sampling of Sequence waveforms
+    seqd = discretize(seq; sampling_params=sim_params, add_times=KomaMRIBase.get_jump_times(obj.motion)) # Sampling of Sequence waveforms
     parts, excitation_bool = get_sim_ranges(seqd; Nblocks=sim_params["Nblocks"]) # Generating simulation blocks
     t_sim_parts = [seqd.t[p[1]] for p in parts]
     append!(t_sim_parts, seqd.t[end])