Custom values for brain_phantom

KomaMRIBase/src/datatypes/Phantom.jl

@@ -18,6 +18,8 @@ a property value representing a spin. This struct serves as an input for the sim
 - `Dλ2`: (`::AbstractVector{T<:Real}`) spin Dλ2 (diffusion) parameter vector
 - `Dθ`: (`::AbstractVector{T<:Real}`) spin Dθ (diffusion) parameter vector
 - `motion`: (`::AbstractMotion{T<:Real}`) motion
+- `Mz`: (`::AbstractVector{ComplexF32}`) transverse magnetization parameter vector, only for storage purposes
+- `Mxy`: (`::AbstractVector{ComplexF32}`) longitudinal magnetization parameter vector, only for storage purposes
 
 # Returns
 - `obj`: (`::Phantom`) Phantom struct
@@ -29,7 +31,7 @@ julia> obj = Phantom(x=[0.0])
 julia> obj.ρ
 ```
 """
-@with_kw mutable struct Phantom{T<:Real}
+@with_kw mutable struct Phantom{T<:Number}
     name::String           = "spins"
     x                      :: AbstractVector{T}
     y::AbstractVector{T}   = zeros(eltype(x), size(x))
@@ -48,6 +50,8 @@ julia> obj.ρ
     #Diff::Vector{DiffusionModel}  #Diffusion map
     #Motion
     motion::AbstractMotion{T} = NoMotion{eltype(x)}() 
+    Mxy::AbstractVector{ComplexF32} = zeros(eltype(x), size(x)) .+ 0im
+    Mz::AbstractVector{ComplexF32} = zeros(eltype(x), size(x)) .+ 0im
 end
 
 const NON_STRING_PHANTOM_FIELDS = Iterators.filter(x -> fieldtype(Phantom, x) != String,         fieldnames(Phantom))
@@ -195,6 +199,7 @@ function heart_phantom(;
     return phantom
 end
 
+
 """
     phantom = brain_phantom2D(;axis="axial", ss=4)
 
@@ -212,7 +217,7 @@ Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 m
 - `axis`: (`::String`, `="axial"`, opts=[`"axial"`, `"coronal"`, `"sagittal"`]) orientation of the phantom
 - `ss`: (`::Integer or ::Vector{Integer}`, `=4`) subsampling parameter for all axes if scaler, per axis if 2 element vector [ssx, ssy]
 - `us`: (`::Integer or ::Vector{Integer}`, `=1`)  upsampling parameter for all axes if scaler, per axis if 2 element vector [usx, usy], if used ss is set to ss=1
-
+- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
 
 # Returns
 - `obj`: (`::Phantom`) Phantom struct
@@ -223,11 +228,28 @@ julia> obj = brain_phantom2D(; axis="sagittal", ss=1)
 
 julia> obj = brain_phantom2D(; axis="axial", us=[1, 2])
 
+julia> phantom_values = 
+    Dict(
+        # T1, T2, T2*, ρ, Δw
+        "CSF" => [2569, 329, 58, 1, 0],
+        "GM" => [1153, 83, 69, 0.86, 0],
+        "WM" => [746, 70, 61, 0.77, 0],
+        "FAT1" => [0, 0, 0, 0, 0],
+        "MUSCLE" => [0, 0, 0, 0, 0],
+        "SKIN/MUSCLE" => [0, 0, 0, 0, 0],
+        "SKULL" => [0, 0, 0, 0, 0],
+        "VESSELS" => [0, 0, 0, 0, 0],
+        "FAT2" => [0, 0, 0, 0, 0],
+        "DURA" => [0, 0, 0, 0, 0],
+        "MARROW" => [0, 0, 0, 0, 0])
+julia> obj = brain_phantom2D(; tissue_properties=phantom_values)
+
 julia> plot_phantom_map(obj, :ρ)
 ```
 """
-function brain_phantom2D(; axis="axial", ss=4, us=1)
+function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = nothing)
     # check and filter input    
+    # check more spins 
     ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(2, ss, us)
 
     # Get data from .mat file
@@ -247,59 +269,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1)
     y = (-FOVy / 2):Δy:(FOVy / 2) #spin coordinates
     x, y = x .+ y' * 0, x * 0 .+ y' #grid points
 
-    # Define spin property vectors
-    T2 =
-        (class .== 23) * 329 .+ #CSF
-        (class .== 46) * 83 .+ #GM
-        (class .== 70) * 70 .+ #WM
-        (class .== 93) * 70 .+ #FAT1
-        (class .== 116) * 47 .+ #MUSCLE
-        (class .== 139) * 329 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 70 .+ #FAT2
-        (class .== 232) * 329 .+ #DURA
-        (class .== 255) * 70 #MARROW
-    T2s =
-        (class .== 23) * 58 .+ #CSF
-        (class .== 46) * 69 .+ #GM
-        (class .== 70) * 61 .+ #WM
-        (class .== 93) * 58 .+ #FAT1
-        (class .== 116) * 30 .+ #MUSCLE
-        (class .== 139) * 58 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 61 .+ #FAT2
-        (class .== 232) * 58 .+ #DURA
-        (class .== 255) * 61 #MARROW
-    T1 =
-        (class .== 23) * 2569 .+ #CSF
-        (class .== 46) * 833 .+ #GM
-        (class .== 70) * 500 .+ #WM
-        (class .== 93) * 350 .+ #FAT1
-        (class .== 116) * 900 .+ #MUSCLE
-        (class .== 139) * 569 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 500 .+ #FAT2
-        (class .== 232) * 2569 .+ #DURA
-        (class .== 255) * 500 #MARROW
-    ρ =
-        (class .== 23) * 1 .+ #CSF
-        (class .== 46) * 0.86 .+ #GM
-        (class .== 70) * 0.77 .+ #WM
-        (class .== 93) * 1 .+ #FAT1
-        (class .== 116) * 1 .+ #MUSCLE
-        (class .== 139) * 1 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 0.77 .+ #FAT2
-        (class .== 232) * 1 .+ #DURA
-        (class .== 255) * 0.77 #MARROW
-    Δw_fat = -220 * 2π
-    Δw =
-        (class .== 93) * Δw_fat .+ #FAT1
-        (class .== 209) * Δw_fat    #FAT2
+    # Get tissue properties
+    T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
     T1 = T1 * 1e-3
     T2 = T2 * 1e-3
     T2s = T2s * 1e-3
@@ -336,6 +307,7 @@ Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 m
 - `ss`: (`::Integer or ::Vector{Integer}`, `=4`) subsampling parameter for all axes if scaler, per axis if 3 element vector [ssx, ssy, ssz]
 - `us`: (`::Integer or ::Vector{Integer}`, `=1`)  upsampling parameter for all axes if scaler, per axis if 3 element vector [usx, usy, usz]
 - `start_end`: (`::Vector{Integer}`, `=[160,200]`) z index range of presampled phantom, 180 is center
+- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
 
 # Returns
 - `obj`: (`::Phantom`) 3D Phantom struct
@@ -346,13 +318,29 @@ julia> obj = brain_phantom3D(; ss=5)
 
 julia> obj = brain_phantom3D(; us=[2, 2, 1])
 
+julia> phantom_values = 
+    Dict(
+        # T1, T2, T2*, ρ, Δw
+        "CSF" => [2569, 329, 58, 1, 0],
+        "GM" => [1153, 83, 69, 0.86, 0],
+        "WM" => [746, 70, 61, 0.77, 0],
+        "FAT1" => [0, 0, 0, 0, 0],
+        "MUSCLE" => [0, 0, 0, 0, 0],
+        "SKIN/MUSCLE" => [0, 0, 0, 0, 0],
+        "SKULL" => [0, 0, 0, 0, 0],
+        "VESSELS" => [0, 0, 0, 0, 0],
+        "FAT2" => [0, 0, 0, 0, 0],
+        "DURA" => [0, 0, 0, 0, 0],
+        "MARROW" => [0, 0, 0, 0, 0])
+julia> obj = brain_phantom3D(; tissue_properties=phantom_values)
+
 julia> plot_phantom_map(obj, :ρ)
 ```
 """
-function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
+function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=nothing)
     # check and filter input    
     ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(3, ss, us)
-
+    
     # Get data from .mat file
     path = @__DIR__
     data = MAT.matread(path * "/phantom/brain3D.mat")
@@ -377,60 +365,9 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
     x = 1 * xx .+ 0 * yy .+ 0 * zz
     y = 0 * xx .+ 1 * yy .+ 0 * zz
     z = 0 * xx .+ 0 * yy .+ 1 * zz
-
-    # Define spin property vectors
-    T2 =
-        (class .== 23) * 329 .+ #CSF
-        (class .== 46) * 83 .+ #GM
-        (class .== 70) * 70 .+ #WM
-        (class .== 93) * 70 .+ #FAT1
-        (class .== 116) * 47 .+ #MUSCLE
-        (class .== 139) * 329 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 70 .+ #FAT2
-        (class .== 232) * 329 .+ #DURA
-        (class .== 255) * 70 #MARROW
-    T2s =
-        (class .== 23) * 58 .+ #CSF
-        (class .== 46) * 69 .+ #GM
-        (class .== 70) * 61 .+ #WM
-        (class .== 93) * 58 .+ #FAT1
-        (class .== 116) * 30 .+ #MUSCLE
-        (class .== 139) * 58 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 61 .+ #FAT2
-        (class .== 232) * 58 .+ #DURA
-        (class .== 255) * 61 #MARROW
-    T1 =
-        (class .== 23) * 2569 .+ #CSF
-        (class .== 46) * 833 .+ #GM
-        (class .== 70) * 500 .+ #WM
-        (class .== 93) * 350 .+ #FAT1
-        (class .== 116) * 900 .+ #MUSCLE
-        (class .== 139) * 569 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 500 .+ #FAT2
-        (class .== 232) * 2569 .+ #DURA
-        (class .== 255) * 500 #MARROW
-    ρ =
-        (class .== 23) * 1 .+ #CSF
-        (class .== 46) * 0.86 .+ #GM
-        (class .== 70) * 0.77 .+ #WM
-        (class .== 93) * 1 .+ #FAT1
-        (class .== 116) * 1 .+ #MUSCLE
-        (class .== 139) * 1 .+ #SKIN/MUSCLE
-        (class .== 162) * 0 .+ #SKULL
-        (class .== 185) * 0 .+ #VESSELS
-        (class .== 209) * 0.77 .+ #FAT2
-        (class .== 232) * 1 .+ #DURA
-        (class .== 255) * 0.77 #MARROW
-    Δw_fat = -220 * 2π
-    Δw =
-        (class .== 93) * Δw_fat .+ #FAT1
-        (class .== 209) * Δw_fat    #FAT2
+
+    # Get tissue properties
+    T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
     T1 = T1 * 1e-3
     T2 = T2 * 1e-3
     T2s = T2s * 1e-3
@@ -482,7 +419,7 @@ function pelvis_phantom2D(; ss=4, us=1)
 
     # subsample or upsample the phantom data
     class = repeat(data["pelvis3D_slice"][1:ssx:end, 1:ssy:end]; inner=[usx, usy])
-
+    
     # Define spin position vectors
     Δx = .5e-3 * ssx / usx
     Δy = .5e-3 * ssy / usy
@@ -612,5 +549,107 @@ function check_phantom_arguments(nd, ss, us)
             ssy = ss[2]
         end
     end
+
     return ssx, ssy, ssz, usx, usy, usz
 end
+
+"""
+    T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties = nothing)
+
+This function returns the default brain tissue properties using a class identifier Matrix
+# Arguments
+- `class` : (`::Matrix`) the class identifier matrix of the phantom
+- `tissue_properties` : (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
+
+# Returns
+- `T1, T2, T2s, ρ, Δw`: (`::Matrix`) matrices of the same size of class with the tissues properties information
+
+# Examples
+```julia-repl
+julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
+
+julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class)
+```
+"""
+function default_brain_tissue_properties(class, tissue_properties = nothing)
+    if isnothing(tissue_properties)
+        # Load default tissue properties
+        tissue_properties = Dict(
+            # T1, T2, T2*, ρ, Δw
+            "CSF" => [2569, 329, 58, 1, 0],
+            "GM" => [833, 83, 69, 0.86, 0],
+            "WM" => [500, 70, 61, 0.77, 0],
+            "FAT1" => [350, 70, 58, 1, -220],
+            "MUSCLE" => [900, 47, 30, 1, 0],
+            "SKIN/MUSCLE" => [569, 329, 58, 1, 0],
+            "SKULL" => [0, 0, 0, 0, 0],
+            "VESSELS" => [0, 0, 0, 0, 0],
+            "FAT2" => [500, 70, 61, 0.77, -220],
+            "DURA" => [2569, 329, 58, 1, 0],
+            "MARROW" => [500, 70, 61, 0.77, 0])
+        # Define spin property vectors
+    end
+    T1 =
+        (class .== 23) * tissue_properties["CSF"][1] .+ #CSF
+        (class .== 46) * tissue_properties["GM"][1] .+ #GM
+        (class .== 70) * tissue_properties["WM"][1] .+ #WM
+        (class .== 93) * tissue_properties["FAT1"][1] .+ #FAT1
+        (class .== 116) * tissue_properties["MUSCLE"][1] .+ #MUSCLE
+        (class .== 139) * tissue_properties["SKIN/MUSCLE"][1] .+ #SKIN/MUSCLE
+        (class .== 162) * tissue_properties["SKULL"][1] .+ #SKULL
+        (class .== 185) * tissue_properties["VESSELS"][1] .+ #VESSELS
+        (class .== 209) * tissue_properties["FAT2"][1] .+ #FAT2
+        (class .== 232) * tissue_properties["DURA"][1] .+ #DURA
+        (class .== 255) * tissue_properties["MARROW"][1] #MARROW
+    T2 =
+        (class .== 23) * tissue_properties["CSF"][2] .+ #CSF
+        (class .== 46) * tissue_properties["GM"][2] .+ #GM
+        (class .== 70) * tissue_properties["WM"][2] .+ #WM
+        (class .== 93) * tissue_properties["FAT1"][2] .+ #FAT1
+        (class .== 116) * tissue_properties["MUSCLE"][2] .+ #MUSCLE
+        (class .== 139) * tissue_properties["SKIN/MUSCLE"][2] .+ #SKIN/MUSCLE
+        (class .== 162) * tissue_properties["SKULL"][2] .+ #SKULL
+        (class .== 185) * tissue_properties["VESSELS"][2] .+ #VESSELS
+        (class .== 209) * tissue_properties["FAT2"][2] .+ #FAT2
+        (class .== 232) * tissue_properties["DURA"][2] .+ #DURA
+        (class .== 255) * tissue_properties["MARROW"][2] #MARROW
+    T2s =
+        (class .== 23) * tissue_properties["CSF"][3] .+ #CSF
+        (class .== 46) * tissue_properties["GM"][3] .+ #GM
+        (class .== 70) * tissue_properties["WM"][3] .+ #WM
+        (class .== 93) * tissue_properties["FAT1"][3] .+ #FAT1
+        (class .== 116) * tissue_properties["MUSCLE"][3] .+ #MUSCLE
+        (class .== 139) * tissue_properties["SKIN/MUSCLE"][3] .+ #SKIN/MUSCLE
+        (class .== 162) * tissue_properties["SKULL"][3] .+ #SKULL
+        (class .== 185) * tissue_properties["VESSELS"][3] .+ #VESSELS
+        (class .== 209) * tissue_properties["FAT2"][3] .+ #FAT2
+        (class .== 232) * tissue_properties["DURA"][3] .+ #DURA
+        (class .== 255) * tissue_properties["MARROW"][3] #MARROW
+
+    ρ =
+        (class .== 23) * tissue_properties["CSF"][4] .+ #CSF
+        (class .== 46) * tissue_properties["GM"][4] .+ #GM
+        (class .== 70) * tissue_properties["WM"][4] .+ #WM
+        (class .== 93) * tissue_properties["FAT1"][4] .+ #FAT1
+        (class .== 116) * tissue_properties["MUSCLE"][4] .+ #MUSCLE
+        (class .== 139) * tissue_properties["SKIN/MUSCLE"][4] .+ #SKIN/MUSCLE
+        (class .== 162) * tissue_properties["SKULL"][4] .+ #SKULL
+        (class .== 185) * tissue_properties["VESSELS"][4] .+ #VESSELS
+        (class .== 209) * tissue_properties["FAT2"][4] .+ #FAT2
+        (class .== 232) * tissue_properties["DURA"][4] .+ #DURA
+        (class .== 255) * tissue_properties["MARROW"][4] #MARROW
+
+    Δw =
+        (class .== 23) * tissue_properties["CSF"][5] .+ #CSF
+        (class .== 46) * tissue_properties["GM"][5] .+ #GM
+        (class .== 70) * tissue_properties["WM"][5] .+ #WM
+        (class .== 93) * tissue_properties["FAT1"][5] .+ #FAT1
+        (class .== 116) * tissue_properties["MUSCLE"][5] .+ #MUSCLE
+        (class .== 139) * tissue_properties["SKIN/MUSCLE"][5] .+ #SKIN/MUSCLE
+        (class .== 162) * tissue_properties["SKULL"][5] .+ #SKULL
+        (class .== 185) * tissue_properties["VESSELS"][5] .+ #VESSELS
+        (class .== 209) * tissue_properties["FAT2"][5] .+ #FAT2
+        (class .== 232) * tissue_properties["DURA"][5] .+ #DURA
+        (class .== 255) * tissue_properties["MARROW"][5] #MARROW
+    return T1, T2, T2s, ρ, Δw
+end

KomaMRICore/src/simulation/SimulatorCore.jl

@@ -409,6 +409,8 @@ function simulate(
         out = Xt
     elseif sim_params["return_type"] == "mat"
         out = sig
+    elseif sim_params["return_type"] == "full"
+        out = Dict("state" => Xt, "mat" => sig)
     elseif sim_params["return_type"] == "raw"
         # To visually check the simulation blocks
         sim_params_raw = copy(sim_params)