Suggested changes

KomaMRIBase/src/KomaMRIBase.jl

@@ -26,7 +26,7 @@ include("timing/KeyValuesCalculation.jl")
 include("datatypes/Sequence.jl")
 include("datatypes/sequence/Delay.jl")
 # Motion
-include("motion/MotionSet.jl")
+include("motion/AbstractMotion.jl")
 # Phantom
 include("datatypes/Phantom.jl")
 # Simulator

KomaMRIBase/src/datatypes/Phantom.jl

@@ -17,7 +17,7 @@ a property value representing a spin. This struct serves as an input for the sim
 - `Dλ1`: (`::AbstractVector{T<:Real}`) spin Dλ1 (diffusion) parameter vector
 - `Dλ2`: (`::AbstractVector{T<:Real}`) spin Dλ2 (diffusion) parameter vector
 - `Dθ`: (`::AbstractVector{T<:Real}`) spin Dθ (diffusion) parameter vector
-- `motion`: (`::AbstractMotionSet{T<:Real}`) motion set
+- `motion`: (`::AbstractMotion{T<:Real}`) motion
 
 # Returns
 - `obj`: (`::Phantom`) Phantom struct
@@ -47,7 +47,7 @@ julia> obj.ρ
  Dθ::AbstractVector{T} = zeros(eltype(x), size(x))
  #Diff::Vector{DiffusionModel} #Diffusion map
  #Motion
- motion::AbstractMotionSet{T} = NoMotion{eltype(x)}() 
+ motion::AbstractMotion{T} = NoMotion{eltype(x)}() 
 end
 
 const NON_STRING_PHANTOM_FIELDS = Iterators.filter(x -> fieldtype(Phantom, x) != String, fieldnames(Phantom))

KomaMRIBase/src/motion/MotionSet.jl → KomaMRIBase/src/motion/AbstractMotion.jl

@@ -1,4 +1,4 @@
-abstract type AbstractMotionSet{T<:Real} end
+abstract type AbstractMotion{T<:Real} end
 
 # NoMotion
 include("nomotion/NoMotion.jl")

KomaMRIBase/src/motion/motionlist/MotionList.jl

@@ -27,7 +27,7 @@ julia> motionlist = MotionList(
  )
 ```
 """
-struct MotionList{T<:Real} <: AbstractMotionSet{T}
+struct MotionList{T<:Real} <: AbstractMotion{T}
  motions::Vector{<:Motion{T}}
 end
 
@@ -91,7 +91,7 @@ Calculates the position of each spin at a set of arbitrary time instants, i.e. t
 For each dimension (x, y, z), the output matrix has ``N_{\t{spins}}`` rows and `length(t)` columns.
 
 # Arguments
-- `motionset`: (`::AbstractMotionSet{T<:Real}`) phantom motion
+- `motionset`: (`::AbstractMotion{T<:Real}`) phantom motion
 - `x`: (`::AbstractVector{T<:Real}`, `[m]`) spin x-position vector
 - `y`: (`::AbstractVector{T<:Real}`, `[m]`) spin y-position vector
 - `z`: (`::AbstractVector{T<:Real}`, `[m]`) spin z-position vector
@@ -148,7 +148,7 @@ If `motionset::NoMotion`, this function does nothing.
 If `motionset::MotionList`, this function sorts its motions.
 
 # Arguments
-- `motionset`: (`::AbstractMotionSet{T<:Real}`) phantom motion
+- `motionset`: (`::AbstractMotion{T<:Real}`) phantom motion
 
 # Returns
 - `nothing`

KomaMRIBase/src/motion/nomotion/NoMotion.jl

@@ -11,7 +11,7 @@ NoMotion struct. It is used to create static phantoms.
 julia> nomotion = NoMotion{Float64}()
 ```
 """
-struct NoMotion{T<:Real} <: AbstractMotionSet{T} end
+struct NoMotion{T<:Real} <: AbstractMotion{T} end
 
 Base.getindex(mv::NoMotion, p) = mv 
 Base.view(mv::NoMotion, p) = mv

KomaMRICore/src/simulation/Functors.jl

@@ -99,9 +99,8 @@ f64(m) = paramtype(Float64, m)
 
 # Koma motion-related adapts
 adapt_storage(backend::KA.GPU, xs::MotionList) = MotionList(gpu.(xs.motions, Ref(backend)))
-adapt_storage(T::Type{<:Real}, xs::NoMotion) = NoMotion{T}()
 adapt_storage(T::Type{<:Real}, xs::MotionList) = MotionList(paramtype.(T, xs.motions))
-adapt_storage(T::Type{<:Real}, xs::Motion) = Motion(paramtype(T, xs.action), paramtype(T, xs.time), xs.spins)
+adapt_storage(T::Type{<:Real}, xs::NoMotion) = NoMotion{T}()
 
 #The functor macro makes it easier to call a function in all the parameters
 # Phantom

docs/src/reference/2-koma-base.md

@@ -22,7 +22,7 @@ heart_phantom
 
 ## `Motion`-related functions
 
-### `AbstractMotionSet` types and related functions
+### `AbstractMotion` types and related functions
 ```@docs
 NoMotion
 MotionList

examples/3.tutorials/lit-05-SimpleMotion.jl

@@ -4,7 +4,7 @@ using KomaMRI # hide
 sys = Scanner() # hide
 
 # It can also be interesting to see the effect of the patient's motion during an MRI scan.
-# For this, Koma provides the ability to add `motion <: AbstractMotionSet` to the phantom.
+# For this, Koma provides the ability to add `motion <: AbstractMotion` to the phantom.
 # In this tutorial, we will show how to add a [`Translate`](@ref) motion to a 2D brain phantom.
 
 # First, let's load the 2D brain phantom used in the previous tutorials:
@@ -67,7 +67,7 @@ p2 = plot_image(abs.(image1[:, :, 1]); height=400) # hide
 # S_{\mathrm{MC}}\left(t\right)=S\left(t\right)\cdot\mathrm{e}^{\mathrm{i}\Delta\phi_{\mathrm{corr}}}=S\left(t\right)\cdot\mathrm{e}^{\mathrm{i}2\pi\boldsymbol{k}\left(t\right)\cdot\boldsymbol{u}\left(t\right)}
 # ```
 
-# In practice, we would need to estimate or measure the motion before performing a motion-corrected reconstruction, but for this example, we will directly use the displacement functions ``\boldsymbol{u}(\boldsymbol{x}, t)`` defined by `obj.motion::SimpleAction`. 
+# In practice, we would need to estimate or measure the motion before performing a motion-corrected reconstruction, but for this example, we will directly use the displacement functions ``\boldsymbol{u}(\boldsymbol{x}, t)`` defined by `obj.motion::MotionList`. 
 # Since translations are rigid motions (``\boldsymbol{u}(\boldsymbol{x}, t)=\boldsymbol{u}(t)`` no position dependence), we can obtain the required displacements by calculating ``\boldsymbol{u}(\boldsymbol{x}=\boldsymbol{0},\ t=t_{\mathrm{adc}})``.
 sample_times = get_adc_sampling_times(seq1)
 displacements = hcat(get_spin_coords(obj.motion, [0.0], [0.0], [0.0], sample_times)...)