coil_sens removal from Phantom structure

Author: Stockless

KomaMRIBase/src/datatypes/Phantom.jl

@@ -76,17 +76,16 @@ end
 """Separate object spins in a sub-group"""
 function Base.getindex(obj::Phantom, p)
     fields = []
-    for field in Iterators.filter(x -> !(x == :name) && !(x == :coil_sens), fieldnames(Phantom))
+    for field in NON_STRING_PHANTOM_FIELDS
         push!(fields, (field, getfield(obj, field)[p]))
     end
-    push!(fields, (:coil_sens, getfield(obj, :coil_sens)[p, :]))
+    return Phantom(; name=obj.name, fields...)
 end
 function Base.view(obj::Phantom, p)
     fields = []
-    for field in Iterators.filter(x -> !(x == :name) && !(x == :coil_sens), fieldnames(Phantom))
+    for field in NON_STRING_PHANTOM_FIELDS
         push!(fields, (field, @view(getfield(obj, field)[p])))
     end
-    push!(fields, (:coil_sens, @view(getfield(obj, :coil_sens)[p, :])))
     return Phantom(; name=obj.name, fields...)
 end
 

KomaMRICore/src/simulation/SimMethods/BlochSimple/BlochSimple.jl

@@ -6,26 +6,6 @@ struct BlochSimple <: SimulationMethod end
 
 export BlochSimple
 
-
-function sim_output_dim(
-    obj::Phantom{T}, seq::Sequence, sys::Scanner, sim_method::SimulationMethod
-) where {T<:Real}
-    # Determine the number of coils
-    n_coils = size(obj.coil_sens, 2)
-    return (sum(seq.ADC.N), n_coils) # Nt x Ncoils
-end
-
-"""Magnetization initialization for Bloch simulation method."""
-function initialize_spins_state(
-    obj::Phantom{T}, sim_method::SimulationMethod
-) where {T<:Real}
-    Nspins = length(obj)
-    Mxy = zeros(T, Nspins)
-    Mz = obj.ρ
-    Xt = Mag{T}(Mxy, Mz)
-    return Xt, obj
-end
-
 """
     run_spin_precession(obj, seq, Xt, sig)
 

KomaMRICore/src/simulation/SimMethods/SimulationMethod.jl

@@ -11,7 +11,7 @@ function sim_output_dim(
     obj::Phantom{T}, seq::Sequence, sys::Scanner, sim_method::SimulationMethod
 ) where {T<:Real}
     # Determine the number of coils
-    n_coils = size(obj.coil_sens, 2)
+    n_coils = size(sys.rf_coils.coil_sens, 2)
     return (sum(seq.ADC.N), n_coils) # Nt x Ncoils
 end
 

examples/3.tutorials/lit-08-CoilsCircle.jl

@@ -23,7 +23,8 @@ end
 coil_sens = hcat(coil_sensitivities...)
 
 # Assign to object
-sys.rf_coils = ArbitraryRFCoils(obj.x, obj.y, obj.z, complex.(coil_sens), complex.(ones(size(coil_sens))))
+sys.rf_coils = RFCoilsSensDefinedAtPhantomPositions(complex.(coil_sens))
+#sys.rf_coils = ArbitraryRFCoils(obj.x, obj.y, obj.z, complex.(coil_sens), complex.(ones(size(coil_sens))))
 
 seq_file = joinpath(
     dirname(pathof(KomaMRI)),
@@ -33,7 +34,7 @@ seq = read_seq(seq_file)
 # And simulate:
 
 sim_params = KomaMRICore.default_sim_params()
-sim_params["sim_method"] = BlochSimple()
+sim_params["sim_method"] = Bloch()
 raw = simulate(obj, seq, sys; sim_params)
 
 acq = AcquisitionData(raw) # hide