From 271d98f9fc7cd64a00568cb8e7c0dacd8f18a11d Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Sun, 22 Sep 2024 20:13:33 -0300
Subject: [PATCH 01/19] Custom values for brain_phantom
---
KomaMRIBase/src/datatypes/Phantom.jl | 374 +++++++++++++++++++--------
1 file changed, 264 insertions(+), 110 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 5f155f28e..11fb813b9 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -212,7 +212,7 @@ 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
-
+- `custom_values`: (`::Dict`, `=nothing`) phantom custom values in ms and Hz considering the available tissues
# Returns
- `obj`: (`::Phantom`) Phantom struct
@@ -223,11 +223,21 @@ julia> obj = brain_phantom2D(; axis="sagittal", ss=1)
julia> obj = brain_phantom2D(; axis="axial", us=[1, 2])
+julia> phantom_values = Dict(
+ #CSF, GM, WM, FAT1, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW
+ "T1"=> [2569, 1153, 746, 0, 0, 0, 0, 0, 0, 0, 0],
+ "T2" => [329, 83, 70, 0, 0, 0, 0, 0, 0, 0, 0],
+ "T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
+ "ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
+ "Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+julia> obj = brain_phantom2D(; custom_values=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, custom_values = 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 +257,127 @@ 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
+
+ if !isnothing(custom_values)
+ # Define spin property vectors
+ T2 =
+ (class .== 23) * custom_values["T2"][1] .+ #CSF
+ (class .== 46) * custom_values["T2"][2] .+ #GM
+ (class .== 70) * custom_values["T2"][3] .+ #WM
+ (class .== 93) * custom_values["T2"][4] .+ #FAT1
+ (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["T2"][7] .+ #SKULL
+ (class .== 185) * custom_values["T2"][8] .+ #VESSELS
+ (class .== 209) * custom_values["T2"][9] .+ #FAT2
+ (class .== 232) * custom_values["T2"][10] .+ #DURA
+ (class .== 255) * custom_values["T2"][11] #MARROW
+ T2s =
+ (class .== 23) * custom_values["T2s"][1] .+ #CSF
+ (class .== 46) * custom_values["T2s"][2] .+ #GM
+ (class .== 70) * custom_values["T2s"][3] .+ #WM
+ (class .== 93) * custom_values["T2s"][4] .+ #FAT1
+ (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["T2s"][7] .+ #SKULL
+ (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
+ (class .== 209) * custom_values["T2s"][9] .+ #FAT2
+ (class .== 232) * custom_values["T2s"][10] .+ #DURA
+ (class .== 255) * custom_values["T2s"][11] #MARROW
+ T1 =
+ (class .== 23) * custom_values["T1"][1] .+ #CSF
+ (class .== 46) * custom_values["T1"][2] .+ #GM
+ (class .== 70) * custom_values["T1"][3] .+ #WM
+ (class .== 93) * custom_values["T1"][4] .+ #FAT1
+ (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["T1"][7] .+ #SKULL
+ (class .== 185) * custom_values["T1"][8] .+ #VESSELS
+ (class .== 209) * custom_values["T1"][9] .+ #FAT2
+ (class .== 232) * custom_values["T1"][10] .+ #DURA
+ (class .== 255) * custom_values["T1"][11] #MARROW
+ ρ =
+ (class .== 23) * custom_values["ρ"][1] .+ #CSF
+ (class .== 46) * custom_values["ρ"][2] .+ #GM
+ (class .== 70) * custom_values["ρ"][3] .+ #WM
+ (class .== 93) * custom_values["ρ"][4] .+ #FAT1
+ (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["ρ"][7] .+ #SKULL
+ (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
+ (class .== 209) * custom_values["ρ"][9] .+ #FAT2
+ (class .== 232) * custom_values["ρ"][10] .+ #DURA
+ (class .== 255) * custom_values["ρ"][11] #MARROW
+
+ Δw =
+ (class .== 23) * custom_values["Δw"][1] .+ #CSF
+ (class .== 46) * custom_values["Δw"][2] .+ #GM
+ (class .== 70) * custom_values["Δw"][3] .+ #WM
+ (class .== 93) * custom_values["Δw"][4] .+ #FAT1
+ (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["Δw"][7] .+ #SKULL
+ (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
+ (class .== 209) * custom_values["Δw"][9] .+ #FAT2
+ (class .== 232) * custom_values["Δw"][10] .+ #DURA
+ (class .== 255) * custom_values["Δw"][11] #MARROW
+ Δw = -2π.*Δw
+
+ else
+ # 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
+ end
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
@@ -318,7 +396,6 @@ function brain_phantom2D(; axis="axial", ss=4, us=1)
)
return obj
end
-
"""
obj = brain_phantom3D(; ss=4, us=1, start_end=[160,200])
@@ -336,6 +413,7 @@ 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
+- `custom_values`: (`::Dict`, `=nothing`) phantom custom values in ms and Hz considering the available tissues
# Returns
- `obj`: (`::Phantom`) 3D Phantom struct
@@ -346,10 +424,19 @@ julia> obj = brain_phantom3D(; ss=5)
julia> obj = brain_phantom3D(; us=[2, 2, 1])
+julia> phantom_values = Dict(
+ #CSF, GM, WM, FAT1, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW
+ "T1"=> [2569, 1153, 746, 0, 0, 0, 0, 0, 0, 0, 0],
+ "T2" => [329, 83, 70, 0, 0, 0, 0, 0, 0, 0, 0],
+ "T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
+ "ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
+ "Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+julia> obj = brain_phantom3D(; custom_values=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], custom_values=nothing)
# check and filter input
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(3, ss, us)
@@ -378,59 +465,126 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
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
+ if !isnothing(custom_values)
+ # Define spin property vectors
+ T2 =
+ (class .== 23) * custom_values["T2"][1] .+ #CSF
+ (class .== 46) * custom_values["T2"][2] .+ #GM
+ (class .== 70) * custom_values["T2"][3] .+ #WM
+ (class .== 93) * custom_values["T2"][4] .+ #FAT1
+ (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["T2"][7] .+ #SKULL
+ (class .== 185) * custom_values["T2"][8] .+ #VESSELS
+ (class .== 209) * custom_values["T2"][9] .+ #FAT2
+ (class .== 232) * custom_values["T2"][10] .+ #DURA
+ (class .== 255) * custom_values["T2"][11] #MARROW
+ T2s =
+ (class .== 23) * custom_values["T2s"][1] .+ #CSF
+ (class .== 46) * custom_values["T2s"][2] .+ #GM
+ (class .== 70) * custom_values["T2s"][3] .+ #WM
+ (class .== 93) * custom_values["T2s"][4] .+ #FAT1
+ (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["T2s"][7] .+ #SKULL
+ (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
+ (class .== 209) * custom_values["T2s"][9] .+ #FAT2
+ (class .== 232) * custom_values["T2s"][10] .+ #DURA
+ (class .== 255) * custom_values["T2s"][11] #MARROW
+ T1 =
+ (class .== 23) * custom_values["T1"][1] .+ #CSF
+ (class .== 46) * custom_values["T1"][2] .+ #GM
+ (class .== 70) * custom_values["T1"][3] .+ #WM
+ (class .== 93) * custom_values["T1"][4] .+ #FAT1
+ (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["T1"][7] .+ #SKULL
+ (class .== 185) * custom_values["T1"][8] .+ #VESSELS
+ (class .== 209) * custom_values["T1"][9] .+ #FAT2
+ (class .== 232) * custom_values["T1"][10] .+ #DURA
+ (class .== 255) * custom_values["T1"][11] #MARROW
+ ρ =
+ (class .== 23) * custom_values["ρ"][1] .+ #CSF
+ (class .== 46) * custom_values["ρ"][2] .+ #GM
+ (class .== 70) * custom_values["ρ"][3] .+ #WM
+ (class .== 93) * custom_values["ρ"][4] .+ #FAT1
+ (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["ρ"][7] .+ #SKULL
+ (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
+ (class .== 209) * custom_values["ρ"][9] .+ #FAT2
+ (class .== 232) * custom_values["ρ"][10] .+ #DURA
+ (class .== 255) * custom_values["ρ"][11] #MARROW
+
+ Δw =
+ (class .== 23) * custom_values["Δw"][1] .+ #CSF
+ (class .== 46) * custom_values["Δw"][2] .+ #GM
+ (class .== 70) * custom_values["Δw"][3] .+ #WM
+ (class .== 93) * custom_values["Δw"][4] .+ #FAT1
+ (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
+ (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * custom_values["Δw"][7] .+ #SKULL
+ (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
+ (class .== 209) * custom_values["Δw"][9] .+ #FAT2
+ (class .== 232) * custom_values["Δw"][10] .+ #DURA
+ (class .== 255) * custom_values["Δw"][11] #MARROW
+ Δw = -2π.*Δw
+
+ else
+ # 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
+ end
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
From a67c5bdf1267e6672c8aa7e36aac578b07025440 Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Mon, 23 Sep 2024 10:44:08 -0300
Subject: [PATCH 02/19] Update Phantom.jl
Changing from `custom_values` to `tissue_properties`
---
KomaMRIBase/src/datatypes/Phantom.jl | 399 +++++++++++----------------
1 file changed, 155 insertions(+), 244 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 11fb813b9..c4fceffcb 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -195,6 +195,7 @@ function heart_phantom(;
return phantom
end
+
"""
phantom = brain_phantom2D(;axis="axial", ss=4)
@@ -212,7 +213,7 @@ 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
-- `custom_values`: (`::Dict`, `=nothing`) phantom custom values in ms and Hz considering the available tissues
+- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
# Returns
- `obj`: (`::Phantom`) Phantom struct
@@ -230,12 +231,12 @@ julia> phantom_values = Dict(
"T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
"ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
"Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
-julia> obj = brain_phantom2D(; custom_values=phantom_values)
+julia> obj = brain_phantom2D(; tissue_properties=phantom_values)
julia> plot_phantom_map(obj, :ρ)
```
"""
-function brain_phantom2D(; axis="axial", ss=4, us=1, custom_values = nothing)
+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)
@@ -258,126 +259,81 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, custom_values = nothing)
x, y = x .+ y' * 0, x * 0 .+ y' #grid points
- if !isnothing(custom_values)
- # Define spin property vectors
- T2 =
- (class .== 23) * custom_values["T2"][1] .+ #CSF
- (class .== 46) * custom_values["T2"][2] .+ #GM
- (class .== 70) * custom_values["T2"][3] .+ #WM
- (class .== 93) * custom_values["T2"][4] .+ #FAT1
- (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2"][7] .+ #SKULL
- (class .== 185) * custom_values["T2"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2"][9] .+ #FAT2
- (class .== 232) * custom_values["T2"][10] .+ #DURA
- (class .== 255) * custom_values["T2"][11] #MARROW
- T2s =
- (class .== 23) * custom_values["T2s"][1] .+ #CSF
- (class .== 46) * custom_values["T2s"][2] .+ #GM
- (class .== 70) * custom_values["T2s"][3] .+ #WM
- (class .== 93) * custom_values["T2s"][4] .+ #FAT1
- (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2s"][7] .+ #SKULL
- (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2s"][9] .+ #FAT2
- (class .== 232) * custom_values["T2s"][10] .+ #DURA
- (class .== 255) * custom_values["T2s"][11] #MARROW
- T1 =
- (class .== 23) * custom_values["T1"][1] .+ #CSF
- (class .== 46) * custom_values["T1"][2] .+ #GM
- (class .== 70) * custom_values["T1"][3] .+ #WM
- (class .== 93) * custom_values["T1"][4] .+ #FAT1
- (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T1"][7] .+ #SKULL
- (class .== 185) * custom_values["T1"][8] .+ #VESSELS
- (class .== 209) * custom_values["T1"][9] .+ #FAT2
- (class .== 232) * custom_values["T1"][10] .+ #DURA
- (class .== 255) * custom_values["T1"][11] #MARROW
- ρ =
- (class .== 23) * custom_values["ρ"][1] .+ #CSF
- (class .== 46) * custom_values["ρ"][2] .+ #GM
- (class .== 70) * custom_values["ρ"][3] .+ #WM
- (class .== 93) * custom_values["ρ"][4] .+ #FAT1
- (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
- (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["ρ"][7] .+ #SKULL
- (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
- (class .== 209) * custom_values["ρ"][9] .+ #FAT2
- (class .== 232) * custom_values["ρ"][10] .+ #DURA
- (class .== 255) * custom_values["ρ"][11] #MARROW
-
- Δw =
- (class .== 23) * custom_values["Δw"][1] .+ #CSF
- (class .== 46) * custom_values["Δw"][2] .+ #GM
- (class .== 70) * custom_values["Δw"][3] .+ #WM
- (class .== 93) * custom_values["Δw"][4] .+ #FAT1
- (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
- (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["Δw"][7] .+ #SKULL
- (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
- (class .== 209) * custom_values["Δw"][9] .+ #FAT2
- (class .== 232) * custom_values["Δw"][10] .+ #DURA
- (class .== 255) * custom_values["Δw"][11] #MARROW
- Δw = -2π.*Δw
-
- else
- # 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
+ if isnothing(tissue_properties)
+ # Load default tissue properties
+ tissue_properties = Dict(
+ #CSF, GM, WM, FAT1, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW
+ "T1"=> [2569, 833, 500, 350, 900, 569, 0, 0, 500, 2569, 500],
+ "T2" => [329, 83, 70, 70, 47, 329, 0, 0, 70, 329, 70],
+ "T2s" => [58, 69, 61, 58, 30, 58, 0, 0, 61, 58, 61],
+ "ρ" => [1, 0.86, 0.77, 1, 1, 1, 0, 0, 0.77, 1, 0.77],
+ "Δw" => [0, 0, 0, -220, 0, 0, 0, 0, -220, 0, 0]
+ )
end
+ # Define spin property vectors
+ T2 =
+ (class .== 23) * tissue_properties["T2"][1] .+ #CSF
+ (class .== 46) * tissue_properties["T2"][2] .+ #GM
+ (class .== 70) * tissue_properties["T2"][3] .+ #WM
+ (class .== 93) * tissue_properties["T2"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["T2"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["T2"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["T2"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["T2"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["T2"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["T2"][10] .+ #DURA
+ (class .== 255) * tissue_properties["T2"][11] #MARROW
+ T2s =
+ (class .== 23) * tissue_properties["T2s"][1] .+ #CSF
+ (class .== 46) * tissue_properties["T2s"][2] .+ #GM
+ (class .== 70) * tissue_properties["T2s"][3] .+ #WM
+ (class .== 93) * tissue_properties["T2s"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["T2s"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["T2s"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["T2s"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["T2s"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["T2s"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["T2s"][10] .+ #DURA
+ (class .== 255) * tissue_properties["T2s"][11] #MARROW
+ T1 =
+ (class .== 23) * tissue_properties["T1"][1] .+ #CSF
+ (class .== 46) * tissue_properties["T1"][2] .+ #GM
+ (class .== 70) * tissue_properties["T1"][3] .+ #WM
+ (class .== 93) * tissue_properties["T1"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["T1"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["T1"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["T1"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["T1"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["T1"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["T1"][10] .+ #DURA
+ (class .== 255) * tissue_properties["T1"][11] #MARROW
+ ρ =
+ (class .== 23) * tissue_properties["ρ"][1] .+ #CSF
+ (class .== 46) * tissue_properties["ρ"][2] .+ #GM
+ (class .== 70) * tissue_properties["ρ"][3] .+ #WM
+ (class .== 93) * tissue_properties["ρ"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["ρ"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["ρ"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["ρ"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["ρ"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["ρ"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["ρ"][10] .+ #DURA
+ (class .== 255) * tissue_properties["ρ"][11] #MARROW
+
+ Δw =
+ (class .== 23) * tissue_properties["Δw"][1] .+ #CSF
+ (class .== 46) * tissue_properties["Δw"][2] .+ #GM
+ (class .== 70) * tissue_properties["Δw"][3] .+ #WM
+ (class .== 93) * tissue_properties["Δw"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["Δw"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["Δw"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["Δw"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["Δw"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["Δw"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["Δw"][10] .+ #DURA
+ (class .== 255) * tissue_properties["Δw"][11] #MARROW
+ Δw = -2π.*Δw
+
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
@@ -396,6 +352,7 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, custom_values = nothing)
)
return obj
end
+
"""
obj = brain_phantom3D(; ss=4, us=1, start_end=[160,200])
@@ -413,7 +370,7 @@ 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
-- `custom_values`: (`::Dict`, `=nothing`) phantom custom values in ms and Hz considering the available tissues
+- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
# Returns
- `obj`: (`::Phantom`) 3D Phantom struct
@@ -431,12 +388,12 @@ julia> phantom_values = Dict(
"T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
"ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
"Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
-julia> obj = brain_phantom3D(; custom_values=phantom_values)
+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], custom_values=nothing)
+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)
@@ -465,126 +422,80 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], custom_values=nothi
y = 0 * xx .+ 1 * yy .+ 0 * zz
z = 0 * xx .+ 0 * yy .+ 1 * zz
- if !isnothing(custom_values)
- # Define spin property vectors
- T2 =
- (class .== 23) * custom_values["T2"][1] .+ #CSF
- (class .== 46) * custom_values["T2"][2] .+ #GM
- (class .== 70) * custom_values["T2"][3] .+ #WM
- (class .== 93) * custom_values["T2"][4] .+ #FAT1
- (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2"][7] .+ #SKULL
- (class .== 185) * custom_values["T2"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2"][9] .+ #FAT2
- (class .== 232) * custom_values["T2"][10] .+ #DURA
- (class .== 255) * custom_values["T2"][11] #MARROW
- T2s =
- (class .== 23) * custom_values["T2s"][1] .+ #CSF
- (class .== 46) * custom_values["T2s"][2] .+ #GM
- (class .== 70) * custom_values["T2s"][3] .+ #WM
- (class .== 93) * custom_values["T2s"][4] .+ #FAT1
- (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2s"][7] .+ #SKULL
- (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2s"][9] .+ #FAT2
- (class .== 232) * custom_values["T2s"][10] .+ #DURA
- (class .== 255) * custom_values["T2s"][11] #MARROW
- T1 =
- (class .== 23) * custom_values["T1"][1] .+ #CSF
- (class .== 46) * custom_values["T1"][2] .+ #GM
- (class .== 70) * custom_values["T1"][3] .+ #WM
- (class .== 93) * custom_values["T1"][4] .+ #FAT1
- (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T1"][7] .+ #SKULL
- (class .== 185) * custom_values["T1"][8] .+ #VESSELS
- (class .== 209) * custom_values["T1"][9] .+ #FAT2
- (class .== 232) * custom_values["T1"][10] .+ #DURA
- (class .== 255) * custom_values["T1"][11] #MARROW
- ρ =
- (class .== 23) * custom_values["ρ"][1] .+ #CSF
- (class .== 46) * custom_values["ρ"][2] .+ #GM
- (class .== 70) * custom_values["ρ"][3] .+ #WM
- (class .== 93) * custom_values["ρ"][4] .+ #FAT1
- (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
- (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["ρ"][7] .+ #SKULL
- (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
- (class .== 209) * custom_values["ρ"][9] .+ #FAT2
- (class .== 232) * custom_values["ρ"][10] .+ #DURA
- (class .== 255) * custom_values["ρ"][11] #MARROW
-
- Δw =
- (class .== 23) * custom_values["Δw"][1] .+ #CSF
- (class .== 46) * custom_values["Δw"][2] .+ #GM
- (class .== 70) * custom_values["Δw"][3] .+ #WM
- (class .== 93) * custom_values["Δw"][4] .+ #FAT1
- (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
- (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["Δw"][7] .+ #SKULL
- (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
- (class .== 209) * custom_values["Δw"][9] .+ #FAT2
- (class .== 232) * custom_values["Δw"][10] .+ #DURA
- (class .== 255) * custom_values["Δw"][11] #MARROW
- Δw = -2π.*Δw
-
- else
- # 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
+ if isnothing(tissue_properties)
+ # Load default tissue properties
+ tissue_properties = Dict(
+ #CSF, GM, WM, FAT1, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW
+ "T1"=> [2569, 833, 500, 350, 900, 569, 0, 0, 500, 2569, 500],
+ "T2" => [329, 83, 70, 70, 47, 329, 0, 0, 70, 329, 70],
+ "T2s" => [58, 69, 61, 58, 30, 58, 0, 0, 61, 58, 61],
+ "ρ" => [1, 0.86, 0.77, 1, 1, 1, 0, 0, 0.77, 1, 0.77],
+ "Δw" => [0, 0, 0, -220, 0, 0, 0, 0, -220, 0, 0]
+ )
end
+ # Define spin property vectors
+ T2 =
+ (class .== 23) * tissue_properties["T2"][1] .+ #CSF
+ (class .== 46) * tissue_properties["T2"][2] .+ #GM
+ (class .== 70) * tissue_properties["T2"][3] .+ #WM
+ (class .== 93) * tissue_properties["T2"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["T2"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["T2"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["T2"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["T2"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["T2"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["T2"][10] .+ #DURA
+ (class .== 255) * tissue_properties["T2"][11] #MARROW
+ T2s =
+ (class .== 23) * tissue_properties["T2s"][1] .+ #CSF
+ (class .== 46) * tissue_properties["T2s"][2] .+ #GM
+ (class .== 70) * tissue_properties["T2s"][3] .+ #WM
+ (class .== 93) * tissue_properties["T2s"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["T2s"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["T2s"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["T2s"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["T2s"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["T2s"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["T2s"][10] .+ #DURA
+ (class .== 255) * tissue_properties["T2s"][11] #MARROW
+ T1 =
+ (class .== 23) * tissue_properties["T1"][1] .+ #CSF
+ (class .== 46) * tissue_properties["T1"][2] .+ #GM
+ (class .== 70) * tissue_properties["T1"][3] .+ #WM
+ (class .== 93) * tissue_properties["T1"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["T1"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["T1"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["T1"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["T1"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["T1"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["T1"][10] .+ #DURA
+ (class .== 255) * tissue_properties["T1"][11] #MARROW
+ ρ =
+ (class .== 23) * tissue_properties["ρ"][1] .+ #CSF
+ (class .== 46) * tissue_properties["ρ"][2] .+ #GM
+ (class .== 70) * tissue_properties["ρ"][3] .+ #WM
+ (class .== 93) * tissue_properties["ρ"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["ρ"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["ρ"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["ρ"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["ρ"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["ρ"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["ρ"][10] .+ #DURA
+ (class .== 255) * tissue_properties["ρ"][11] #MARROW
+
+ Δw =
+ (class .== 23) * tissue_properties["Δw"][1] .+ #CSF
+ (class .== 46) * tissue_properties["Δw"][2] .+ #GM
+ (class .== 70) * tissue_properties["Δw"][3] .+ #WM
+ (class .== 93) * tissue_properties["Δw"][4] .+ #FAT1
+ (class .== 116) * tissue_properties["Δw"][5] .+ #MUSCLE
+ (class .== 139) * tissue_properties["Δw"][6] .+ #SKIN/MUSCLE
+ (class .== 162) * tissue_properties["Δw"][7] .+ #SKULL
+ (class .== 185) * tissue_properties["Δw"][8] .+ #VESSELS
+ (class .== 209) * tissue_properties["Δw"][9] .+ #FAT2
+ (class .== 232) * tissue_properties["Δw"][10] .+ #DURA
+ (class .== 255) * tissue_properties["Δw"][11] #MARROW
+ Δw = -2π.*Δw
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
From afbd05b3460a102965ce8a0287de8d9f98144251 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Thu, 26 Sep 2024 18:52:32 -0300
Subject: [PATCH 03/19] Introducing default brain phantom properties Including
magnetization states for storing purposes in phantom
---
KomaMRIBase/src/datatypes/Phantom.jl | 372 +++++++++------------------
1 file changed, 122 insertions(+), 250 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 11fb813b9..8c008f672 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/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))
@@ -212,7 +216,7 @@ 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
-- `custom_values`: (`::Dict`, `=nothing`) phantom custom values in ms and Hz considering the available tissues
+- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
# Returns
- `obj`: (`::Phantom`) Phantom struct
@@ -230,12 +234,12 @@ julia> phantom_values = Dict(
"T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
"ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
"Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
-julia> obj = brain_phantom2D(; custom_values=phantom_values)
+julia> obj = brain_phantom2D(; tissue_properties=phantom_values)
julia> plot_phantom_map(obj, :ρ)
```
"""
-function brain_phantom2D(; axis="axial", ss=4, us=1, custom_values = nothing)
+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)
@@ -257,127 +261,9 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, custom_values = nothing)
y = (-FOVy / 2):Δy:(FOVy / 2) #spin coordinates
x, y = x .+ y' * 0, x * 0 .+ y' #grid points
-
- if !isnothing(custom_values)
- # Define spin property vectors
- T2 =
- (class .== 23) * custom_values["T2"][1] .+ #CSF
- (class .== 46) * custom_values["T2"][2] .+ #GM
- (class .== 70) * custom_values["T2"][3] .+ #WM
- (class .== 93) * custom_values["T2"][4] .+ #FAT1
- (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2"][7] .+ #SKULL
- (class .== 185) * custom_values["T2"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2"][9] .+ #FAT2
- (class .== 232) * custom_values["T2"][10] .+ #DURA
- (class .== 255) * custom_values["T2"][11] #MARROW
- T2s =
- (class .== 23) * custom_values["T2s"][1] .+ #CSF
- (class .== 46) * custom_values["T2s"][2] .+ #GM
- (class .== 70) * custom_values["T2s"][3] .+ #WM
- (class .== 93) * custom_values["T2s"][4] .+ #FAT1
- (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2s"][7] .+ #SKULL
- (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2s"][9] .+ #FAT2
- (class .== 232) * custom_values["T2s"][10] .+ #DURA
- (class .== 255) * custom_values["T2s"][11] #MARROW
- T1 =
- (class .== 23) * custom_values["T1"][1] .+ #CSF
- (class .== 46) * custom_values["T1"][2] .+ #GM
- (class .== 70) * custom_values["T1"][3] .+ #WM
- (class .== 93) * custom_values["T1"][4] .+ #FAT1
- (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T1"][7] .+ #SKULL
- (class .== 185) * custom_values["T1"][8] .+ #VESSELS
- (class .== 209) * custom_values["T1"][9] .+ #FAT2
- (class .== 232) * custom_values["T1"][10] .+ #DURA
- (class .== 255) * custom_values["T1"][11] #MARROW
- ρ =
- (class .== 23) * custom_values["ρ"][1] .+ #CSF
- (class .== 46) * custom_values["ρ"][2] .+ #GM
- (class .== 70) * custom_values["ρ"][3] .+ #WM
- (class .== 93) * custom_values["ρ"][4] .+ #FAT1
- (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
- (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["ρ"][7] .+ #SKULL
- (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
- (class .== 209) * custom_values["ρ"][9] .+ #FAT2
- (class .== 232) * custom_values["ρ"][10] .+ #DURA
- (class .== 255) * custom_values["ρ"][11] #MARROW
-
- Δw =
- (class .== 23) * custom_values["Δw"][1] .+ #CSF
- (class .== 46) * custom_values["Δw"][2] .+ #GM
- (class .== 70) * custom_values["Δw"][3] .+ #WM
- (class .== 93) * custom_values["Δw"][4] .+ #FAT1
- (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
- (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["Δw"][7] .+ #SKULL
- (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
- (class .== 209) * custom_values["Δw"][9] .+ #FAT2
- (class .== 232) * custom_values["Δw"][10] .+ #DURA
- (class .== 255) * custom_values["Δw"][11] #MARROW
- Δw = -2π.*Δw
-
- else
- # 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
- end
+ # Get tissue properties
+ T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
+ Δw = -2π.*Δw
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
@@ -396,6 +282,7 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, custom_values = nothing)
)
return obj
end
+
"""
obj = brain_phantom3D(; ss=4, us=1, start_end=[160,200])
@@ -413,7 +300,7 @@ 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
-- `custom_values`: (`::Dict`, `=nothing`) phantom custom values in ms and Hz considering the available tissues
+- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
# Returns
- `obj`: (`::Phantom`) 3D Phantom struct
@@ -431,15 +318,15 @@ julia> phantom_values = Dict(
"T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
"ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
"Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
-julia> obj = brain_phantom3D(; custom_values=phantom_values)
+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], custom_values=nothing)
+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")
@@ -465,126 +352,9 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], custom_values=nothi
y = 0 * xx .+ 1 * yy .+ 0 * zz
z = 0 * xx .+ 0 * yy .+ 1 * zz
- if !isnothing(custom_values)
- # Define spin property vectors
- T2 =
- (class .== 23) * custom_values["T2"][1] .+ #CSF
- (class .== 46) * custom_values["T2"][2] .+ #GM
- (class .== 70) * custom_values["T2"][3] .+ #WM
- (class .== 93) * custom_values["T2"][4] .+ #FAT1
- (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2"][7] .+ #SKULL
- (class .== 185) * custom_values["T2"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2"][9] .+ #FAT2
- (class .== 232) * custom_values["T2"][10] .+ #DURA
- (class .== 255) * custom_values["T2"][11] #MARROW
- T2s =
- (class .== 23) * custom_values["T2s"][1] .+ #CSF
- (class .== 46) * custom_values["T2s"][2] .+ #GM
- (class .== 70) * custom_values["T2s"][3] .+ #WM
- (class .== 93) * custom_values["T2s"][4] .+ #FAT1
- (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2s"][7] .+ #SKULL
- (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2s"][9] .+ #FAT2
- (class .== 232) * custom_values["T2s"][10] .+ #DURA
- (class .== 255) * custom_values["T2s"][11] #MARROW
- T1 =
- (class .== 23) * custom_values["T1"][1] .+ #CSF
- (class .== 46) * custom_values["T1"][2] .+ #GM
- (class .== 70) * custom_values["T1"][3] .+ #WM
- (class .== 93) * custom_values["T1"][4] .+ #FAT1
- (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T1"][7] .+ #SKULL
- (class .== 185) * custom_values["T1"][8] .+ #VESSELS
- (class .== 209) * custom_values["T1"][9] .+ #FAT2
- (class .== 232) * custom_values["T1"][10] .+ #DURA
- (class .== 255) * custom_values["T1"][11] #MARROW
- ρ =
- (class .== 23) * custom_values["ρ"][1] .+ #CSF
- (class .== 46) * custom_values["ρ"][2] .+ #GM
- (class .== 70) * custom_values["ρ"][3] .+ #WM
- (class .== 93) * custom_values["ρ"][4] .+ #FAT1
- (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
- (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["ρ"][7] .+ #SKULL
- (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
- (class .== 209) * custom_values["ρ"][9] .+ #FAT2
- (class .== 232) * custom_values["ρ"][10] .+ #DURA
- (class .== 255) * custom_values["ρ"][11] #MARROW
-
- Δw =
- (class .== 23) * custom_values["Δw"][1] .+ #CSF
- (class .== 46) * custom_values["Δw"][2] .+ #GM
- (class .== 70) * custom_values["Δw"][3] .+ #WM
- (class .== 93) * custom_values["Δw"][4] .+ #FAT1
- (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
- (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["Δw"][7] .+ #SKULL
- (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
- (class .== 209) * custom_values["Δw"][9] .+ #FAT2
- (class .== 232) * custom_values["Δw"][10] .+ #DURA
- (class .== 255) * custom_values["Δw"][11] #MARROW
- Δw = -2π.*Δw
-
- else
- # 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
- end
+ # Get tissue properties
+ T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
+ Δw = -2π.*Δw
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
@@ -636,7 +406,7 @@ 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
@@ -766,5 +536,107 @@ 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
\ No newline at end of file
From cf83a9e985cbd5f392413a2dd0060045f8954955 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Thu, 26 Sep 2024 18:58:08 -0300
Subject: [PATCH 04/19] Details on documentation
---
KomaMRIBase/src/datatypes/Phantom.jl | 289 +++-----------------
KomaMRICore/src/simulation/SimulatorCore.jl | 2 +
KomaMRIPlots/src/ui/DisplayFunctions.jl | 246 +++++++++++++++++
3 files changed, 281 insertions(+), 256 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 25d8faf14..a4e287185 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -228,13 +228,20 @@ julia> obj = brain_phantom2D(; axis="sagittal", ss=1)
julia> obj = brain_phantom2D(; axis="axial", us=[1, 2])
-julia> phantom_values = Dict(
- #CSF, GM, WM, FAT1, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW
- "T1"=> [2569, 1153, 746, 0, 0, 0, 0, 0, 0, 0, 0],
- "T2" => [329, 83, 70, 0, 0, 0, 0, 0, 0, 0, 0],
- "T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
- "ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
- "Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+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)
@@ -262,127 +269,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = nothing
y = (-FOVy / 2):Δy:(FOVy / 2) #spin coordinates
x, y = x .+ y' * 0, x * 0 .+ y' #grid points
-
- if !isnothing(custom_values)
- # Define spin property vectors
- T2 =
- (class .== 23) * custom_values["T2"][1] .+ #CSF
- (class .== 46) * custom_values["T2"][2] .+ #GM
- (class .== 70) * custom_values["T2"][3] .+ #WM
- (class .== 93) * custom_values["T2"][4] .+ #FAT1
- (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2"][7] .+ #SKULL
- (class .== 185) * custom_values["T2"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2"][9] .+ #FAT2
- (class .== 232) * custom_values["T2"][10] .+ #DURA
- (class .== 255) * custom_values["T2"][11] #MARROW
- T2s =
- (class .== 23) * custom_values["T2s"][1] .+ #CSF
- (class .== 46) * custom_values["T2s"][2] .+ #GM
- (class .== 70) * custom_values["T2s"][3] .+ #WM
- (class .== 93) * custom_values["T2s"][4] .+ #FAT1
- (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2s"][7] .+ #SKULL
- (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2s"][9] .+ #FAT2
- (class .== 232) * custom_values["T2s"][10] .+ #DURA
- (class .== 255) * custom_values["T2s"][11] #MARROW
- T1 =
- (class .== 23) * custom_values["T1"][1] .+ #CSF
- (class .== 46) * custom_values["T1"][2] .+ #GM
- (class .== 70) * custom_values["T1"][3] .+ #WM
- (class .== 93) * custom_values["T1"][4] .+ #FAT1
- (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T1"][7] .+ #SKULL
- (class .== 185) * custom_values["T1"][8] .+ #VESSELS
- (class .== 209) * custom_values["T1"][9] .+ #FAT2
- (class .== 232) * custom_values["T1"][10] .+ #DURA
- (class .== 255) * custom_values["T1"][11] #MARROW
- ρ =
- (class .== 23) * custom_values["ρ"][1] .+ #CSF
- (class .== 46) * custom_values["ρ"][2] .+ #GM
- (class .== 70) * custom_values["ρ"][3] .+ #WM
- (class .== 93) * custom_values["ρ"][4] .+ #FAT1
- (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
- (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["ρ"][7] .+ #SKULL
- (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
- (class .== 209) * custom_values["ρ"][9] .+ #FAT2
- (class .== 232) * custom_values["ρ"][10] .+ #DURA
- (class .== 255) * custom_values["ρ"][11] #MARROW
-
- Δw =
- (class .== 23) * custom_values["Δw"][1] .+ #CSF
- (class .== 46) * custom_values["Δw"][2] .+ #GM
- (class .== 70) * custom_values["Δw"][3] .+ #WM
- (class .== 93) * custom_values["Δw"][4] .+ #FAT1
- (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
- (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["Δw"][7] .+ #SKULL
- (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
- (class .== 209) * custom_values["Δw"][9] .+ #FAT2
- (class .== 232) * custom_values["Δw"][10] .+ #DURA
- (class .== 255) * custom_values["Δw"][11] #MARROW
- Δw = -2π.*Δw
-
- else
- # 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
- end
+ # 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
@@ -430,13 +318,20 @@ julia> obj = brain_phantom3D(; ss=5)
julia> obj = brain_phantom3D(; us=[2, 2, 1])
-julia> phantom_values = Dict(
- #CSF, GM, WM, FAT1, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW
- "T1"=> [2569, 1153, 746, 0, 0, 0, 0, 0, 0, 0, 0],
- "T2" => [329, 83, 70, 0, 0, 0, 0, 0, 0, 0, 0],
- "T2s" => [58, 69, 61, 0, 0, 0, 0, 0, 0, 0, 0],
- "ρ" => [1, 0.86, 0.77, 0, 0, 0, 0, 0, 0, 0, 0],
- "Δw" => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+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)
@@ -470,127 +365,9 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=n
x = 1 * xx .+ 0 * yy .+ 0 * zz
y = 0 * xx .+ 1 * yy .+ 0 * zz
z = 0 * xx .+ 0 * yy .+ 1 * zz
-
- if !isnothing(custom_values)
- # Define spin property vectors
- T2 =
- (class .== 23) * custom_values["T2"][1] .+ #CSF
- (class .== 46) * custom_values["T2"][2] .+ #GM
- (class .== 70) * custom_values["T2"][3] .+ #WM
- (class .== 93) * custom_values["T2"][4] .+ #FAT1
- (class .== 116) * custom_values["T2"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2"][7] .+ #SKULL
- (class .== 185) * custom_values["T2"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2"][9] .+ #FAT2
- (class .== 232) * custom_values["T2"][10] .+ #DURA
- (class .== 255) * custom_values["T2"][11] #MARROW
- T2s =
- (class .== 23) * custom_values["T2s"][1] .+ #CSF
- (class .== 46) * custom_values["T2s"][2] .+ #GM
- (class .== 70) * custom_values["T2s"][3] .+ #WM
- (class .== 93) * custom_values["T2s"][4] .+ #FAT1
- (class .== 116) * custom_values["T2s"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T2s"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T2s"][7] .+ #SKULL
- (class .== 185) * custom_values["T2s"][8] .+ #VESSELS
- (class .== 209) * custom_values["T2s"][9] .+ #FAT2
- (class .== 232) * custom_values["T2s"][10] .+ #DURA
- (class .== 255) * custom_values["T2s"][11] #MARROW
- T1 =
- (class .== 23) * custom_values["T1"][1] .+ #CSF
- (class .== 46) * custom_values["T1"][2] .+ #GM
- (class .== 70) * custom_values["T1"][3] .+ #WM
- (class .== 93) * custom_values["T1"][4] .+ #FAT1
- (class .== 116) * custom_values["T1"][5] .+ #MUSCLE
- (class .== 139) * custom_values["T1"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["T1"][7] .+ #SKULL
- (class .== 185) * custom_values["T1"][8] .+ #VESSELS
- (class .== 209) * custom_values["T1"][9] .+ #FAT2
- (class .== 232) * custom_values["T1"][10] .+ #DURA
- (class .== 255) * custom_values["T1"][11] #MARROW
- ρ =
- (class .== 23) * custom_values["ρ"][1] .+ #CSF
- (class .== 46) * custom_values["ρ"][2] .+ #GM
- (class .== 70) * custom_values["ρ"][3] .+ #WM
- (class .== 93) * custom_values["ρ"][4] .+ #FAT1
- (class .== 116) * custom_values["ρ"][5] .+ #MUSCLE
- (class .== 139) * custom_values["ρ"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["ρ"][7] .+ #SKULL
- (class .== 185) * custom_values["ρ"][8] .+ #VESSELS
- (class .== 209) * custom_values["ρ"][9] .+ #FAT2
- (class .== 232) * custom_values["ρ"][10] .+ #DURA
- (class .== 255) * custom_values["ρ"][11] #MARROW
-
- Δw =
- (class .== 23) * custom_values["Δw"][1] .+ #CSF
- (class .== 46) * custom_values["Δw"][2] .+ #GM
- (class .== 70) * custom_values["Δw"][3] .+ #WM
- (class .== 93) * custom_values["Δw"][4] .+ #FAT1
- (class .== 116) * custom_values["Δw"][5] .+ #MUSCLE
- (class .== 139) * custom_values["Δw"][6] .+ #SKIN/MUSCLE
- (class .== 162) * custom_values["Δw"][7] .+ #SKULL
- (class .== 185) * custom_values["Δw"][8] .+ #VESSELS
- (class .== 209) * custom_values["Δw"][9] .+ #FAT2
- (class .== 232) * custom_values["Δw"][10] .+ #DURA
- (class .== 255) * custom_values["Δw"][11] #MARROW
- Δw = -2π.*Δw
-
- else
- # 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
- end
+
+ # 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
diff --git a/KomaMRICore/src/simulation/SimulatorCore.jl b/KomaMRICore/src/simulation/SimulatorCore.jl
index 6ba42e583..519d83734 100644
--- a/KomaMRICore/src/simulation/SimulatorCore.jl
+++ b/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)
diff --git a/KomaMRIPlots/src/ui/DisplayFunctions.jl b/KomaMRIPlots/src/ui/DisplayFunctions.jl
index 9dab997ac..a3a22482e 100644
--- a/KomaMRIPlots/src/ui/DisplayFunctions.jl
+++ b/KomaMRIPlots/src/ui/DisplayFunctions.jl
@@ -985,6 +985,252 @@ function plot_kspace(seq::Sequence; width=nothing, height=nothing, darkmode=fals
return plot_koma(p, l; config)
end
+# TODO Adapt the documentation
+
+"""
+ p = plot_state_map(obj::Phantom, key::Symbol; kwargs...)
+
+Plots a phantom map for a specific spin parameter given by `key`.
+
+# Arguments
+- `obj`: (`::Phantom`) Phantom struct
+- `key`: (`::Symbol`, opts: [`:ρ`, `:T1`, `:T2`, `:T2s`, `:x`, `:y`, `:z`]) symbol for
+ displaying different parameters of the phantom spins
+
+# Keywords
+- `height`: (`::Integer`, `=600`) plot height
+- `width`: (`::Integer`, `=nothing`) plot width
+- `darkmode`: (`::Bool`, `=false`) boolean to indicate whether to display darkmode style
+- `view_2d`: (`::Bool`, `=false`) boolean to indicate whether to use a 2D scatter plot
+- `colorbar`: (`::Bool`, `=true`) boolean to indicate whether to display a colorbar
+
+# Returns
+- `p`: (`::PlotlyJS.SyncPlot`) plot of the phantom map for a specific spin parameter
+
+# References
+Colormaps from https://github.com/markgriswold/MRFColormaps
+Towards Unified Colormaps for Quantitative MRF Data, Mark Griswold, et al. (2018).
+
+# Examples
+```julia-repl
+julia> obj2D, obj3D = brain_phantom2D(), brain_phantom3D();
+
+julia> plot_phantom_map(obj2D, :ρ)
+
+julia> plot_phantom_map(obj3D, :ρ)
+```
+"""
+function plot_state_map(
+ ph,
+ key::Symbol;
+ height=700,
+ width=nothing,
+ darkmode=false,
+ view_2d=true,
+ colorbar=true,
+ intermediate_time_samples=0,
+ max_time_samples=100,
+ max_spins=100_000,
+ frame_duration_ms=250,
+ kwargs...,
+)
+ function decimate_uniform_phantom(ph::Phantom, num_points::Int)
+ dimx, dimy, dimz = KomaMRIBase.get_dims(ph)
+ ss = Int(ceil((length(ph) / num_points)^(1 / sum(KomaMRIBase.get_dims(ph)))))
+ ssx = dimx ? ss : 1
+ ssy = dimy ? ss : 1
+ ssz = dimz ? ss : 1
+ ix = sortperm(ph.x)[1:ssx:end]
+ iy = sortperm(ph.y)[1:ssy:end]
+ iz = sortperm(ph.z)[1:ssz:end]
+ idx = intersect(ix, iy, iz)
+ return ph[idx]
+ end
+
+ if length(ph.x) > max_spins
+ ph = decimate_uniform_phantom(ph, max_spins)
+ @warn "For performance reasons, the number of displayed spins was capped to `max_spins`=$(max_spins)."
+ end
+
+
+ path = @__DIR__
+ if key == :Mxy || key == :Mz || key == :∠Mxy || key == :RealOfMxy || key ==:ImagOfMxy
+ cmin_key = 0
+ factor = 1
+ unit = " a.u."
+ colormap = "Greys"
+ if key == :Mxy
+ cmax_key = maximum(abs.(ph.Mxy))
+ cmin_key = minimum(abs.(ph.Mxy))
+ x, y, z = ph.x, ph.y, abs.(ph.Mxy)
+ elseif key == :Mz
+ cmax_key = maximum(abs.(ph.Mz))
+ cmin_key = minimum(abs.(ph.Mz))
+ x, y, z = ph.x, ph.y, abs.(ph.Mz)
+ elseif key == :∠Mxy
+ cmax_key = maximum(angle.(ph.Mxy))
+ cmin_key = minimum(angle.(ph.Mxy))
+ x, y, z = ph.x, ph.y, angle.(ph.Mxy)
+ elseif key == :RealOfMxy
+ cmax_key = maximum(real.(ph.Mxy))
+ cmin_key = minimum(real.(ph.Mxy))
+ x, y, z = ph.x, ph.y, real.(ph.Mxy)
+ elseif key == :ImagOfMxy
+ cmax_key = maximum(imag.(ph.Mxy))
+ cmin_key = minimum(imag.(ph.Mxy))
+ x, y, z = ph.x, ph.y, imag.(ph.Mxy)
+ end
+ else
+ factor = 1
+ cmin_key = minimum(getproperty(ph, key))
+ cmax_key = maximum(getproperty(ph, key))
+ unit = ""
+ colormap = "Greys"
+ x, y, z = ph.x, ph.y, ph.z
+ end
+
+ x0 = -maximum(abs.([ph.x ph.y ph.z])) * 1e2
+ xf = maximum(abs.([ph.x ph.y ph.z])) * 1e2
+
+ if view_2d
+ trace = [
+ scatter(;
+ x=(x[:, 1]) * 1e2,
+ y=(y[:, 1]) * 1e2,
+ mode="markers",
+ marker=attr(;
+ color=z,
+ showscale=colorbar,
+ colorscale=colormap,
+ colorbar=attr(; ticksuffix=unit, title=string(key)),
+ cmin=cmin_key,
+ cmax=cmax_key,
+ size=4,
+ ),
+ showlegend=false,
+ text=z,
+ #text=round.(getproperty(ph, key) * factor, digits=4),
+ hovertemplate="x: %{x:.1f} cm<br>y: %{y:.1f} cm<br><b>$(string(key))</b>: %{text}$unit<extra></extra>",
+ ),
+ ]
+ else
+ trace = [
+ scatter3d(;
+ x=(x[:, 1]) * 1e2,
+ y=(y[:, 1]) * 1e2,
+ z=(z[:, 1]) * 1e2,
+ mode="markers",
+ marker=attr(;
+ color=getproperty(ph, key) * factor,
+ showscale=colorbar,
+ colorscale=colormap,
+ colorbar=attr(; ticksuffix=unit, title=string(key)),
+ cmin=cmin_key,
+ cmax=cmax_key,
+ size=2,
+ ),
+ showlegend=false,
+ text=round.(getproperty(ph, key) * factor, digits=4),
+ hovertemplate="x: %{x:.1f} cm<br>y: %{y:.1f} cm<br>z: %{z:.1f} cm<br><b>$(string(key))</b>: %{text}$unit<extra></extra>",
+ ),
+ ]
+
+ end
+
+ buttons_attr = [
+ attr(;
+ label="▶", # play symbol
+ method="animate",
+ args=[
+ nothing,
+ attr(;
+ fromcurrent=true,
+ transition=(duration=frame_duration_ms,),
+ frame=attr(; duration=frame_duration_ms, redraw=true),
+ ),
+ ],
+ ),
+ attr(;
+ label="◼", # pause symbol
+ method="animate",
+ args=[
+ [nothing],
+ attr(;
+ mode="immediate",
+ fromcurrent=true,
+ transition=attr(; duration=frame_duration_ms),
+ frame=attr(; duration=frame_duration_ms, redraw=true),
+ ),
+ ],
+ ),
+ ]
+
+ #Layout
+ bgcolor, text_color, plot_bgcolor, grid_color, sep_color = theme_chooser(darkmode)
+ l = Layout(;
+ title=ph.name * ": " * string(key),
+ xaxis_title="x",
+ yaxis_title="y",
+ xaxis_range=[x0, xf],
+ yaxis_range=[x0, xf],
+ xaxis_ticksuffix=" cm",
+ yaxis_ticksuffix=" cm",
+ plot_bgcolor=plot_bgcolor,
+ paper_bgcolor=bgcolor,
+ xaxis_gridcolor=grid_color,
+ yaxis_gridcolor=grid_color,
+ xaxis_zerolinecolor=grid_color,
+ yaxis_zerolinecolor=grid_color,
+ font_color=text_color,
+ scene=attr(;
+ xaxis=attr(;
+ title="x",
+ range=[x0, xf],
+ ticksuffix=" cm",
+ backgroundcolor=plot_bgcolor,
+ gridcolor=grid_color,
+ zerolinecolor=grid_color,
+ ),
+ yaxis=attr(;
+ title="y",
+ range=[x0, xf],
+ ticksuffix=" cm",
+ backgroundcolor=plot_bgcolor,
+ gridcolor=grid_color,
+ zerolinecolor=grid_color,
+ ),
+ zaxis=attr(;
+ title="z",
+ range=[x0, xf],
+ ticksuffix=" cm",
+ backgroundcolor=plot_bgcolor,
+ gridcolor=grid_color,
+ zerolinecolor=grid_color,
+ ),
+ aspectmode="manual",
+ aspectratio=attr(; x=1, y=1, z=1),
+ ),
+ margin=attr(; t=50, l=0, r=0, b=0),
+ modebar=attr(;
+ orientation="h", bgcolor=bgcolor, color=text_color, activecolor=plot_bgcolor
+ ),
+ xaxis=attr(; constrain="domain"),
+ yaxis=attr(; scaleanchor="x"),
+ hovermode="closest",
+ )
+
+ if height !== nothing
+ l.height = height
+ end
+ if width !== nothing
+ l.width = width
+ end
+
+ return Plot(trace, l)
+end
+
+
+
"""
p = plot_phantom_map(obj::Phantom, key::Symbol; kwargs...)
From f858ef10c047b016daec834535fcd418a2be8aff Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Thu, 26 Sep 2024 22:44:32 +0000
Subject: [PATCH 05/19] Updating to remove unnecessary things
---
KomaMRICore/src/simulation/SimulatorCore.jl | 2 -
KomaMRIPlots/src/ui/DisplayFunctions.jl | 246 --------------------
2 files changed, 248 deletions(-)
diff --git a/KomaMRICore/src/simulation/SimulatorCore.jl b/KomaMRICore/src/simulation/SimulatorCore.jl
index 519d83734..6ba42e583 100644
--- a/KomaMRICore/src/simulation/SimulatorCore.jl
+++ b/KomaMRICore/src/simulation/SimulatorCore.jl
@@ -409,8 +409,6 @@ 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)
diff --git a/KomaMRIPlots/src/ui/DisplayFunctions.jl b/KomaMRIPlots/src/ui/DisplayFunctions.jl
index a3a22482e..9dab997ac 100644
--- a/KomaMRIPlots/src/ui/DisplayFunctions.jl
+++ b/KomaMRIPlots/src/ui/DisplayFunctions.jl
@@ -985,252 +985,6 @@ function plot_kspace(seq::Sequence; width=nothing, height=nothing, darkmode=fals
return plot_koma(p, l; config)
end
-# TODO Adapt the documentation
-
-"""
- p = plot_state_map(obj::Phantom, key::Symbol; kwargs...)
-
-Plots a phantom map for a specific spin parameter given by `key`.
-
-# Arguments
-- `obj`: (`::Phantom`) Phantom struct
-- `key`: (`::Symbol`, opts: [`:ρ`, `:T1`, `:T2`, `:T2s`, `:x`, `:y`, `:z`]) symbol for
- displaying different parameters of the phantom spins
-
-# Keywords
-- `height`: (`::Integer`, `=600`) plot height
-- `width`: (`::Integer`, `=nothing`) plot width
-- `darkmode`: (`::Bool`, `=false`) boolean to indicate whether to display darkmode style
-- `view_2d`: (`::Bool`, `=false`) boolean to indicate whether to use a 2D scatter plot
-- `colorbar`: (`::Bool`, `=true`) boolean to indicate whether to display a colorbar
-
-# Returns
-- `p`: (`::PlotlyJS.SyncPlot`) plot of the phantom map for a specific spin parameter
-
-# References
-Colormaps from https://github.com/markgriswold/MRFColormaps
-Towards Unified Colormaps for Quantitative MRF Data, Mark Griswold, et al. (2018).
-
-# Examples
-```julia-repl
-julia> obj2D, obj3D = brain_phantom2D(), brain_phantom3D();
-
-julia> plot_phantom_map(obj2D, :ρ)
-
-julia> plot_phantom_map(obj3D, :ρ)
-```
-"""
-function plot_state_map(
- ph,
- key::Symbol;
- height=700,
- width=nothing,
- darkmode=false,
- view_2d=true,
- colorbar=true,
- intermediate_time_samples=0,
- max_time_samples=100,
- max_spins=100_000,
- frame_duration_ms=250,
- kwargs...,
-)
- function decimate_uniform_phantom(ph::Phantom, num_points::Int)
- dimx, dimy, dimz = KomaMRIBase.get_dims(ph)
- ss = Int(ceil((length(ph) / num_points)^(1 / sum(KomaMRIBase.get_dims(ph)))))
- ssx = dimx ? ss : 1
- ssy = dimy ? ss : 1
- ssz = dimz ? ss : 1
- ix = sortperm(ph.x)[1:ssx:end]
- iy = sortperm(ph.y)[1:ssy:end]
- iz = sortperm(ph.z)[1:ssz:end]
- idx = intersect(ix, iy, iz)
- return ph[idx]
- end
-
- if length(ph.x) > max_spins
- ph = decimate_uniform_phantom(ph, max_spins)
- @warn "For performance reasons, the number of displayed spins was capped to `max_spins`=$(max_spins)."
- end
-
-
- path = @__DIR__
- if key == :Mxy || key == :Mz || key == :∠Mxy || key == :RealOfMxy || key ==:ImagOfMxy
- cmin_key = 0
- factor = 1
- unit = " a.u."
- colormap = "Greys"
- if key == :Mxy
- cmax_key = maximum(abs.(ph.Mxy))
- cmin_key = minimum(abs.(ph.Mxy))
- x, y, z = ph.x, ph.y, abs.(ph.Mxy)
- elseif key == :Mz
- cmax_key = maximum(abs.(ph.Mz))
- cmin_key = minimum(abs.(ph.Mz))
- x, y, z = ph.x, ph.y, abs.(ph.Mz)
- elseif key == :∠Mxy
- cmax_key = maximum(angle.(ph.Mxy))
- cmin_key = minimum(angle.(ph.Mxy))
- x, y, z = ph.x, ph.y, angle.(ph.Mxy)
- elseif key == :RealOfMxy
- cmax_key = maximum(real.(ph.Mxy))
- cmin_key = minimum(real.(ph.Mxy))
- x, y, z = ph.x, ph.y, real.(ph.Mxy)
- elseif key == :ImagOfMxy
- cmax_key = maximum(imag.(ph.Mxy))
- cmin_key = minimum(imag.(ph.Mxy))
- x, y, z = ph.x, ph.y, imag.(ph.Mxy)
- end
- else
- factor = 1
- cmin_key = minimum(getproperty(ph, key))
- cmax_key = maximum(getproperty(ph, key))
- unit = ""
- colormap = "Greys"
- x, y, z = ph.x, ph.y, ph.z
- end
-
- x0 = -maximum(abs.([ph.x ph.y ph.z])) * 1e2
- xf = maximum(abs.([ph.x ph.y ph.z])) * 1e2
-
- if view_2d
- trace = [
- scatter(;
- x=(x[:, 1]) * 1e2,
- y=(y[:, 1]) * 1e2,
- mode="markers",
- marker=attr(;
- color=z,
- showscale=colorbar,
- colorscale=colormap,
- colorbar=attr(; ticksuffix=unit, title=string(key)),
- cmin=cmin_key,
- cmax=cmax_key,
- size=4,
- ),
- showlegend=false,
- text=z,
- #text=round.(getproperty(ph, key) * factor, digits=4),
- hovertemplate="x: %{x:.1f} cm<br>y: %{y:.1f} cm<br><b>$(string(key))</b>: %{text}$unit<extra></extra>",
- ),
- ]
- else
- trace = [
- scatter3d(;
- x=(x[:, 1]) * 1e2,
- y=(y[:, 1]) * 1e2,
- z=(z[:, 1]) * 1e2,
- mode="markers",
- marker=attr(;
- color=getproperty(ph, key) * factor,
- showscale=colorbar,
- colorscale=colormap,
- colorbar=attr(; ticksuffix=unit, title=string(key)),
- cmin=cmin_key,
- cmax=cmax_key,
- size=2,
- ),
- showlegend=false,
- text=round.(getproperty(ph, key) * factor, digits=4),
- hovertemplate="x: %{x:.1f} cm<br>y: %{y:.1f} cm<br>z: %{z:.1f} cm<br><b>$(string(key))</b>: %{text}$unit<extra></extra>",
- ),
- ]
-
- end
-
- buttons_attr = [
- attr(;
- label="▶", # play symbol
- method="animate",
- args=[
- nothing,
- attr(;
- fromcurrent=true,
- transition=(duration=frame_duration_ms,),
- frame=attr(; duration=frame_duration_ms, redraw=true),
- ),
- ],
- ),
- attr(;
- label="◼", # pause symbol
- method="animate",
- args=[
- [nothing],
- attr(;
- mode="immediate",
- fromcurrent=true,
- transition=attr(; duration=frame_duration_ms),
- frame=attr(; duration=frame_duration_ms, redraw=true),
- ),
- ],
- ),
- ]
-
- #Layout
- bgcolor, text_color, plot_bgcolor, grid_color, sep_color = theme_chooser(darkmode)
- l = Layout(;
- title=ph.name * ": " * string(key),
- xaxis_title="x",
- yaxis_title="y",
- xaxis_range=[x0, xf],
- yaxis_range=[x0, xf],
- xaxis_ticksuffix=" cm",
- yaxis_ticksuffix=" cm",
- plot_bgcolor=plot_bgcolor,
- paper_bgcolor=bgcolor,
- xaxis_gridcolor=grid_color,
- yaxis_gridcolor=grid_color,
- xaxis_zerolinecolor=grid_color,
- yaxis_zerolinecolor=grid_color,
- font_color=text_color,
- scene=attr(;
- xaxis=attr(;
- title="x",
- range=[x0, xf],
- ticksuffix=" cm",
- backgroundcolor=plot_bgcolor,
- gridcolor=grid_color,
- zerolinecolor=grid_color,
- ),
- yaxis=attr(;
- title="y",
- range=[x0, xf],
- ticksuffix=" cm",
- backgroundcolor=plot_bgcolor,
- gridcolor=grid_color,
- zerolinecolor=grid_color,
- ),
- zaxis=attr(;
- title="z",
- range=[x0, xf],
- ticksuffix=" cm",
- backgroundcolor=plot_bgcolor,
- gridcolor=grid_color,
- zerolinecolor=grid_color,
- ),
- aspectmode="manual",
- aspectratio=attr(; x=1, y=1, z=1),
- ),
- margin=attr(; t=50, l=0, r=0, b=0),
- modebar=attr(;
- orientation="h", bgcolor=bgcolor, color=text_color, activecolor=plot_bgcolor
- ),
- xaxis=attr(; constrain="domain"),
- yaxis=attr(; scaleanchor="x"),
- hovermode="closest",
- )
-
- if height !== nothing
- l.height = height
- end
- if width !== nothing
- l.width = width
- end
-
- return Plot(trace, l)
-end
-
-
-
"""
p = plot_phantom_map(obj::Phantom, key::Symbol; kwargs...)
From 0294f4bacd4c9b2cf79e7009c96ff318f5bbabda Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Thu, 26 Sep 2024 22:47:43 +0000
Subject: [PATCH 06/19] Returning phantom to original code
---
KomaMRIBase/src/datatypes/Phantom.jl | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index a4e287185..b5b3bbf9f 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -18,8 +18,6 @@ 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
@@ -31,7 +29,7 @@ julia> obj = Phantom(x=[0.0])
julia> obj.ρ
```
"""
-@with_kw mutable struct Phantom{T<:Number}
+@with_kw mutable struct Phantom{T<:Real}
name::String = "spins"
x :: AbstractVector{T}
y::AbstractVector{T} = zeros(eltype(x), size(x))
@@ -50,8 +48,6 @@ 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))
From 165b7933891f937d17bd76f1b6eef53fb7652966 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Fri, 27 Sep 2024 11:54:38 -0300
Subject: [PATCH 07/19] Resolving problems in brain phantom
---
KomaMRIBase/src/datatypes/Phantom.jl | 203 ++++++++++-----------------
1 file changed, 74 insertions(+), 129 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index a4e287185..b52e8c7e3 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -18,8 +18,6 @@ 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
@@ -31,7 +29,7 @@ julia> obj = Phantom(x=[0.0])
julia> obj.ρ
```
"""
-@with_kw mutable struct Phantom{T<:Number}
+@with_kw mutable struct Phantom{T<:Real}
name::String = "spins"
x :: AbstractVector{T}
y::AbstractVector{T} = zeros(eltype(x), size(x))
@@ -50,8 +48,6 @@ 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))
@@ -217,7 +213,7 @@ 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
+- `tissue_properties`: (`::Dict`, `=Dict()`) phantom tissue properties in SI units considering the available tissues
# Returns
- `obj`: (`::Phantom`) Phantom struct
@@ -231,23 +227,23 @@ 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],
+ "CSF" => [2.569, 0.329, 0.058, 1, 0],
+ "GM" => [1.153, 0.083, 0.069, 0.86, 0],
+ "WM" => [0.746, 0.070, 0.061, 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, tissue_properties = nothing)
+function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
# check and filter input
# check more spins
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(2, ss, us)
@@ -257,12 +253,12 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = nothing
data = MAT.matread(path * "/phantom/brain2D.mat")
# subsample or upsample the phantom data
- class = repeat(data[axis][1:ssx:end, 1:ssy:end]; inner=[usx, usy])
+ labels = repeat(data[axis][1:ssx:end, 1:ssy:end]; inner=[usx, usy])
# Define spin position vectors
Δx = .5e-3 * ssx / usx
Δy = .5e-3 * ssy / usy
- M, N = size(class)
+ M, N = size(labels)
FOVx = (M - 1) * Δx #[m]
FOVy = (N - 1) * Δy #[m]
x = (-FOVx / 2):Δx:(FOVx / 2) #spin coordinates
@@ -270,10 +266,7 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = nothing
x, y = x .+ y' * 0, x * 0 .+ y' #grid points
# 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
+ T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
# Define and return the Phantom struct
obj = Phantom{Float64}(;
@@ -307,7 +300,7 @@ 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
+- `tissue_properties`: (`::Dict`, `=Dict()`) phantom tissue properties in SI units considering the available tissues
# Returns
- `obj`: (`::Phantom`) 3D Phantom struct
@@ -321,23 +314,23 @@ 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],
+ "CSF" => [2.569, 0.329, 0.058, 1, 0],
+ "GM" => [1.153, 0.083, 0.069, 0.86, 0],
+ "WM" => [0.746, 0.070, 0.061, 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> obj = brain_phantom2D(; tissue_properties=phantom_values)
julia> plot_phantom_map(obj, :ρ)
```
"""
-function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=nothing)
+function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=Dict())
# check and filter input
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(3, ss, us)
@@ -346,7 +339,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=n
data = MAT.matread(path * "/phantom/brain3D.mat")
# subsample or upsample the phantom data
- class = repeat(
+ labels = repeat(
data["data"][1:ssx:end, 1:ssy:end, start_end[1]:ssz:start_end[2]];
inner=[usx, usy, usz],
)
@@ -355,7 +348,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=n
Δx = .5e-3 * ssx / usx
Δy = .5e-3 * ssy / usy
Δz = .5e-3 * ssz / usz
- M, N, Z = size(class)
+ M, N, Z = size(labels)
FOVx = (M - 1) * Δx #[m]
FOVy = (N - 1) * Δy #[m]
FOVz = (Z - 1) * Δz #[m]
@@ -365,12 +358,9 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=n
x = 1 * xx .+ 0 * yy .+ 0 * zz
y = 0 * xx .+ 1 * yy .+ 0 * zz
z = 0 * xx .+ 0 * yy .+ 1 * zz
-
+
# 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
+ T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
# Define and return the Phantom struct
obj = Phantom{Float64}(;
@@ -554,102 +544,57 @@ function check_phantom_arguments(nd, ss, us)
end
"""
- T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties = nothing)
+ T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties = nothing)
-This function returns the default brain tissue properties using a class identifier Matrix
+This function returns the default brain tissue properties using a labels 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
+- `labels` : (`::Matrix`) the labels identifier matrix of the phantom
+- `tissue_properties` : (`::Dict`, `=Dict()`) 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
+- `T1, T2, T2s, ρ, Δw`: (`::Matrix`) matrices of the same size of labels 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(labels, tissue_properties)
-julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class)
+julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels)
```
"""
-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
+function default_brain_tissue_properties(labels, tissue_properties = Dict())
+ # Load default tissue properties
+ default_properties = Dict(
+ # T1, T2, T2*, ρ, Δw
+ "CSF" => [2.569, 0.329, 0.058, 1, 0],
+ "GM" => [0.833, 0.083, 0.069, 0.86, 0],
+ "WM" => [0.500, 0.070, 0.061, 0.77, 0],
+ "FAT1" => [0.350, 0.070, 0.058, 1, -3.84], #-220 Hz
+ "MUSCLE" => [0.900, 0.047, 0.030, 1, 0],
+ "SKIN/MUSCLE" => [0.569, 0.329, 0.058, 1, 0],
+ "SKULL" => [0, 0, 0, 0, 0],
+ "VESSELS" => [0, 0, 0, 0, 0],
+ "FAT2" => [0.500, 0.070, 0.061, 0.77, -3.84], #-220 Hz
+ "DURA" => [2.569, 0.329, 0.058, 1, 0],
+ "MARROW" => [0.500, 0.070, 0.061, 0.77, 0])
+
+ tissue_properties = merge(default_properties, tissue_properties)
+ flat_labels = reshape(labels, :)
+ properties = zeros(length(flat_labels)..., 5)
+ for i=1:5
+ properties[:, i] =
+ (flat_labels .== 23) * tissue_properties["CSF"][i] .+ #CSF
+ (flat_labels .== 46) * tissue_properties["GM"][i] .+ #GM
+ (flat_labels .== 70) * tissue_properties["WM"][i] .+ #WM
+ (flat_labels .== 93) * tissue_properties["FAT1"][i] .+ #FAT1
+ (flat_labels .== 116) * tissue_properties["MUSCLE"][i] .+ #MUSCLE
+ (flat_labels .== 139) * tissue_properties["SKIN/MUSCLE"][i] .+ #SKIN/MUSCLE
+ (flat_labels .== 162) * tissue_properties["SKULL"][i] .+ #SKULL
+ (flat_labels .== 185) * tissue_properties["VESSELS"][i] .+ #VESSELS
+ (flat_labels .== 209) * tissue_properties["FAT2"][i] .+ #FAT2
+ (flat_labels .== 232) * tissue_properties["DURA"][i] .+ #DURA
+ (flat_labels .== 255) * tissue_properties["MARROW"][i] #MARROW
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
+ properties = reshape(properties, (size(labels)..., 5))
- 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
+ return selectdim(properties, ndims(properties), 1), selectdim(properties, ndims(properties), 2), selectdim(properties, ndims(properties), 3), selectdim(properties, ndims(properties), 4), selectdim(properties, ndims(properties), 5)
end
\ No newline at end of file
From 5b6e25d2517973e9d52ce30f004337f3c54d3e21 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Fri, 4 Oct 2024 12:09:30 -0300
Subject: [PATCH 08/19] Avoiding flat arrays.
---
KomaMRIBase/src/datatypes/Phantom.jl | 33 ++++++++++++++--------------
1 file changed, 16 insertions(+), 17 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index b52e8c7e3..00e3a3d62 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -47,7 +47,7 @@ julia> obj.ρ
Dθ::AbstractVector{T} = zeros(eltype(x), size(x))
#Diff::Vector{DiffusionModel} #Diffusion map
#Motion
- motion::AbstractMotion{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))
@@ -578,23 +578,22 @@ function default_brain_tissue_properties(labels, tissue_properties = Dict())
"MARROW" => [0.500, 0.070, 0.061, 0.77, 0])
tissue_properties = merge(default_properties, tissue_properties)
- flat_labels = reshape(labels, :)
- properties = zeros(length(flat_labels)..., 5)
+ properties = []
for i=1:5
- properties[:, i] =
- (flat_labels .== 23) * tissue_properties["CSF"][i] .+ #CSF
- (flat_labels .== 46) * tissue_properties["GM"][i] .+ #GM
- (flat_labels .== 70) * tissue_properties["WM"][i] .+ #WM
- (flat_labels .== 93) * tissue_properties["FAT1"][i] .+ #FAT1
- (flat_labels .== 116) * tissue_properties["MUSCLE"][i] .+ #MUSCLE
- (flat_labels .== 139) * tissue_properties["SKIN/MUSCLE"][i] .+ #SKIN/MUSCLE
- (flat_labels .== 162) * tissue_properties["SKULL"][i] .+ #SKULL
- (flat_labels .== 185) * tissue_properties["VESSELS"][i] .+ #VESSELS
- (flat_labels .== 209) * tissue_properties["FAT2"][i] .+ #FAT2
- (flat_labels .== 232) * tissue_properties["DURA"][i] .+ #DURA
- (flat_labels .== 255) * tissue_properties["MARROW"][i] #MARROW
+ temp =
+ (labels .== 23) * tissue_properties["CSF"][i] .+ #CSF
+ (labels .== 46) * tissue_properties["GM"][i] .+ #GM
+ (labels .== 70) * tissue_properties["WM"][i] .+ #WM
+ (labels .== 93) * tissue_properties["FAT1"][i] .+ #FAT1
+ (labels .== 116) * tissue_properties["MUSCLE"][i] .+ #MUSCLE
+ (labels .== 139) * tissue_properties["SKIN/MUSCLE"][i] .+ #SKIN/MUSCLE
+ (labels .== 162) * tissue_properties["SKULL"][i] .+ #SKULL
+ (labels .== 185) * tissue_properties["VESSELS"][i] .+ #VESSELS
+ (labels .== 209) * tissue_properties["FAT2"][i] .+ #FAT2
+ (labels .== 232) * tissue_properties["DURA"][i] .+ #DURA
+ (labels .== 255) * tissue_properties["MARROW"][i] #MARROW
+ push!(properties, temp)
end
- properties = reshape(properties, (size(labels)..., 5))
- return selectdim(properties, ndims(properties), 1), selectdim(properties, ndims(properties), 2), selectdim(properties, ndims(properties), 3), selectdim(properties, ndims(properties), 4), selectdim(properties, ndims(properties), 5)
+ return properties
end
\ No newline at end of file
From 3689518cb8f864c054316dafb0b4f0a833e59621 Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Sat, 9 Nov 2024 20:39:15 -0300
Subject: [PATCH 09/19] Update Phantom.jl
---
KomaMRIBase/src/datatypes/Phantom.jl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 00e3a3d62..882a9e376 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -47,7 +47,7 @@ julia> obj.ρ
Dθ::AbstractVector{T} = zeros(eltype(x), size(x))
#Diff::Vector{DiffusionModel} #Diffusion map
#Motion
- motion::AbstractMotion{T} = NoMotion{eltype(x)}()
+ motion::Union{NoMotion, MotionList{T}} = NoMotion()
end
const NON_STRING_PHANTOM_FIELDS = Iterators.filter(x -> fieldtype(Phantom, x) != String, fieldnames(Phantom))
@@ -596,4 +596,4 @@ function default_brain_tissue_properties(labels, tissue_properties = Dict())
end
return properties
-end
\ No newline at end of file
+end
From 9cc9d2956d533df4d2b3d0b02d03b010ae68b120 Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:05:58 -0300
Subject: [PATCH 10/19] Update KomaMRIBase/src/datatypes/Phantom.jl
Co-authored-by: Carlos Castillo Passi <cncastillo@uc.cl>
---
KomaMRIBase/src/datatypes/Phantom.jl | 1 -
1 file changed, 1 deletion(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 8869ac348..3dfe620a1 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -333,7 +333,6 @@ julia> plot_phantom_map(obj, :ρ)
function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=Dict())
# 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")
From 1b9aa93d84431389fff10c7e6b06a5c1a4653d8b Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:06:42 -0300
Subject: [PATCH 11/19] Update KomaMRIBase/src/datatypes/Phantom.jl
Co-authored-by: Carlos Castillo Passi <cncastillo@uc.cl>
---
KomaMRIBase/src/datatypes/Phantom.jl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 3dfe620a1..a3a64e979 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -325,7 +325,7 @@ julia> phantom_values =
"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> obj = brain_phantom3D(; tissue_properties=phantom_values)
julia> plot_phantom_map(obj, :ρ)
```
From bd6b91ec29e29f430abff21f49bd9996ff08c5d5 Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:06:54 -0300
Subject: [PATCH 12/19] Update KomaMRIBase/src/datatypes/Phantom.jl
Co-authored-by: Carlos Castillo Passi <cncastillo@uc.cl>
---
KomaMRIBase/src/datatypes/Phantom.jl | 1 -
1 file changed, 1 deletion(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index a3a64e979..ba3c495ae 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -245,7 +245,6 @@ julia> plot_phantom_map(obj, :ρ)
"""
function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
# check and filter input
- # check more spins
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(2, ss, us)
# Get data from .mat file
From f55d3874578079d1d9599920f198a15d8b0befec Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:07:09 -0300
Subject: [PATCH 13/19] Update KomaMRIBase/src/datatypes/Phantom.jl
Co-authored-by: Carlos Castillo Passi <cncastillo@uc.cl>
---
KomaMRIBase/src/datatypes/Phantom.jl | 1 -
1 file changed, 1 deletion(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index ba3c495ae..ef9c82261 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -195,7 +195,6 @@ function heart_phantom(;
return phantom
end
-
"""
phantom = brain_phantom2D(;axis="axial", ss=4)
From ecc9bbeaa1e060a48a163bc362e493bc955a4ed5 Mon Sep 17 00:00:00 2001
From: Guillermo Sahonero Alvarez <gsahonero@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:07:18 -0300
Subject: [PATCH 14/19] Update KomaMRIBase/src/datatypes/Phantom.jl
Co-authored-by: Carlos Castillo Passi <cncastillo@uc.cl>
---
KomaMRIBase/src/datatypes/Phantom.jl | 1 -
1 file changed, 1 deletion(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index ef9c82261..7a26f2c50 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -406,7 +406,6 @@ 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
From 1079053ebfe6e9d435689e4b41f393542cc96f7a Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Tue, 10 Dec 2024 23:32:43 -0300
Subject: [PATCH 15/19] Requested changes
---
KomaMRIBase/src/datatypes/Phantom.jl | 116 +++++++++++++--------------
1 file changed, 57 insertions(+), 59 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 7a26f2c50..78975147d 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -225,18 +225,18 @@ julia> obj = brain_phantom2D(; axis="axial", us=[1, 2])
julia> phantom_values =
Dict(
- # T1, T2, T2*, ρ, Δw
- "CSF" => [2.569, 0.329, 0.058, 1, 0],
- "GM" => [1.153, 0.083, 0.069, 0.86, 0],
- "WM" => [0.746, 0.070, 0.061, 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])
+ # ρ, T1, T2, T2*, Δw
+ "CSF" => [1, 2.569, 0.329, 0.058, 0],
+ "GM" => [0.86, 0.833, 0.083, 0.069, 0],
+ "WM" => [0.77, 0.500, 0.070, 0.061, 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)
@@ -264,8 +264,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
x, y = x .+ y' * 0, x * 0 .+ y' #grid points
# Get tissue properties
- T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
-
+ ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
+ println("size of ", size(T1))
# Define and return the Phantom struct
obj = Phantom{Float64}(;
name="brain2D_" * axis,
@@ -311,18 +311,18 @@ julia> obj = brain_phantom3D(; us=[2, 2, 1])
julia> phantom_values =
Dict(
- # T1, T2, T2*, ρ, Δw
- "CSF" => [2.569, 0.329, 0.058, 1, 0],
- "GM" => [1.153, 0.083, 0.069, 0.86, 0],
- "WM" => [0.746, 0.070, 0.061, 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])
+ # ρ, T1, T2, T2*, Δw
+ "CSF" => [1, 2.569, 0.329, 0.058, 0],
+ "GM" => [0.86, 0.833, 0.083, 0.069, 0],
+ "WM" => [0.77, 0.500, 0.070, 0.061, 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)
@@ -357,7 +357,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=D
z = 0 * xx .+ 0 * yy .+ 1 * zz
# Get tissue properties
- T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
+ ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
# Define and return the Phantom struct
obj = Phantom{Float64}(;
@@ -540,7 +540,7 @@ function check_phantom_arguments(nd, ss, us)
end
"""
- T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties = nothing)
+ ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties = nothing)
This function returns the default brain tissue properties using a labels identifier Matrix
# Arguments
@@ -548,48 +548,46 @@ This function returns the default brain tissue properties using a labels identif
- `tissue_properties` : (`::Dict`, `=Dict()`) phantom tissue properties in ms and Hz considering the available tissues
# Returns
-- `T1, T2, T2s, ρ, Δw`: (`::Matrix`) matrices of the same size of labels with the tissues properties information
+- `ρ, T1, T2, T2s, Δw`: (`::Matrix`) matrices of the same size of labels with the tissues properties information
# Examples
```julia-repl
-julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
+julia> ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
-julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels)
+julia> ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels)
```
"""
function default_brain_tissue_properties(labels, tissue_properties = Dict())
# Load default tissue properties
default_properties = Dict(
- # T1, T2, T2*, ρ, Δw
- "CSF" => [2.569, 0.329, 0.058, 1, 0],
- "GM" => [0.833, 0.083, 0.069, 0.86, 0],
- "WM" => [0.500, 0.070, 0.061, 0.77, 0],
- "FAT1" => [0.350, 0.070, 0.058, 1, -3.84], #-220 Hz
- "MUSCLE" => [0.900, 0.047, 0.030, 1, 0],
- "SKIN/MUSCLE" => [0.569, 0.329, 0.058, 1, 0],
- "SKULL" => [0, 0, 0, 0, 0],
- "VESSELS" => [0, 0, 0, 0, 0],
- "FAT2" => [0.500, 0.070, 0.061, 0.77, -3.84], #-220 Hz
- "DURA" => [2.569, 0.329, 0.058, 1, 0],
- "MARROW" => [0.500, 0.070, 0.061, 0.77, 0])
+ # ρ, T1, T2, T2*, Δw
+ "CSF" => [1, 2.569, 0.329, 0.058, 0],
+ "GM" => [0.86, 0.833, 0.083, 0.069, 0],
+ "WM" => [0.77, 0.500, 0.070, 0.061, 0],
+ "FAT1" => [1, 0.350, 0.070, 0.058, -220*2π], #-220 Hz
+ "MUSCLE" => [1, 0.900, 0.047, 0.030, 0],
+ "SKIN/MUSCLE" => [1, 0.569, 0.329, 0.058, 0],
+ "SKULL" => [0, 0, 0, 0, 0],
+ "VESSELS" => [0, 0, 0, 0, 0],
+ "FAT2" => [0.77, 0.500, 0.070, 0.061, -220*2π], #-220 Hz
+ "DURA" => [1, 2.569, 0.329, 0.058, 0],
+ "MARROW" => [0.77, 0.500, 0.070, 0.061, 0])
tissue_properties = merge(default_properties, tissue_properties)
- properties = []
- for i=1:5
- temp =
- (labels .== 23) * tissue_properties["CSF"][i] .+ #CSF
- (labels .== 46) * tissue_properties["GM"][i] .+ #GM
- (labels .== 70) * tissue_properties["WM"][i] .+ #WM
- (labels .== 93) * tissue_properties["FAT1"][i] .+ #FAT1
- (labels .== 116) * tissue_properties["MUSCLE"][i] .+ #MUSCLE
- (labels .== 139) * tissue_properties["SKIN/MUSCLE"][i] .+ #SKIN/MUSCLE
- (labels .== 162) * tissue_properties["SKULL"][i] .+ #SKULL
- (labels .== 185) * tissue_properties["VESSELS"][i] .+ #VESSELS
- (labels .== 209) * tissue_properties["FAT2"][i] .+ #FAT2
- (labels .== 232) * tissue_properties["DURA"][i] .+ #DURA
- (labels .== 255) * tissue_properties["MARROW"][i] #MARROW
- push!(properties, temp)
+ props = ["ρ", "T1", "T2", "T2s", "Δw"]
+ Nproperties = length(props)
+ tissue_labels = [23, 46, 70, 93, 116, 139, 162, 185, 209, 232, 255]
+ tissue_texts = ["CSF", "GM", "WM", "FAT1", "MUSCLE", "SKIN/MUSCLE", "SKULL", "VESSELS", "FAT2", "DURA", "MARROW"]
+ data_properties = zeros(Nproperties, size(labels)...)
+ dims = size(data_properties)
+ for i=1:Nproperties
+ for (label, tissue) in zip(tissue_labels, tissue_texts)
+ data_properties[i, ntuple(j -> 1:dims[j+1], length(dims)-1)...] += (labels .== label)*tissue_properties[tissue][i]
+ end
end
-
+ # To make it a tuple of five elements
+ properties = Tuple(data_properties[i, :, :, :] for i in 1:size(data_properties, 1))
+ # To avoid singleton dimensions
+ properties = Tuple(reshape(item, filter(d -> d>1, size(item))...) for item in properties)
return properties
end
From b843b60298f209543cf202cd2cd7350a1daa6ce7 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Wed, 11 Dec 2024 13:04:05 -0300
Subject: [PATCH 16/19] Removing a println
---
KomaMRIBase/src/datatypes/Phantom.jl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 78975147d..ff4332987 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -265,7 +265,7 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
# Get tissue properties
ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
- println("size of ", size(T1))
+
# Define and return the Phantom struct
obj = Phantom{Float64}(;
name="brain2D_" * axis,
From e61cd8591722af93d111ae8cbc9b3d55d427a662 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Wed, 11 Dec 2024 22:58:32 -0300
Subject: [PATCH 17/19] Reducing lines
---
KomaMRIBase/src/datatypes/Phantom.jl | 21 +++++++++++----------
1 file changed, 11 insertions(+), 10 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index ff4332987..e7c6726b7 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -252,6 +252,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
# subsample or upsample the phantom data
labels = repeat(data[axis][1:ssx:end, 1:ssy:end]; inner=[usx, usy])
+ # to make it compatible with default_brain_tissue_properties
+ labels = reshape(labels, (size(labels, 1), size(labels, 2), 1))
# Define spin position vectors
Δx = .5e-3 * ssx / usx
@@ -262,6 +264,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
x = (-FOVx / 2):Δx:(FOVx / 2) #spin coordinates
y = (-FOVy / 2):Δy:(FOVy / 2) #spin coordinates
x, y = x .+ y' * 0, x * 0 .+ y' #grid points
+ x = reshape(x, (size(x, 1), size(x, 2), 1))
+ y = reshape(y, (size(y, 1), size(y, 2), 1))
# Get tissue properties
ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
@@ -575,19 +579,16 @@ function default_brain_tissue_properties(labels, tissue_properties = Dict())
tissue_properties = merge(default_properties, tissue_properties)
props = ["ρ", "T1", "T2", "T2s", "Δw"]
- Nproperties = length(props)
- tissue_labels = [23, 46, 70, 93, 116, 139, 162, 185, 209, 232, 255]
- tissue_texts = ["CSF", "GM", "WM", "FAT1", "MUSCLE", "SKIN/MUSCLE", "SKULL", "VESSELS", "FAT2", "DURA", "MARROW"]
+ Nproperties = length(props)
+ # Order: CSF, DURA, FAT1, FAT2, GM, MARROW, MUSCLE, SKIN/MUSCLE, SKULL, vESSELS, WM
+ tissue_labels = [23, 232, 93, 209, 46, 255, 116, 139, 162, 185, 70]
+ tissue_texts = sort(collect(keys(default_properties)))#
data_properties = zeros(Nproperties, size(labels)...)
- dims = size(data_properties)
for i=1:Nproperties
for (label, tissue) in zip(tissue_labels, tissue_texts)
- data_properties[i, ntuple(j -> 1:dims[j+1], length(dims)-1)...] += (labels .== label)*tissue_properties[tissue][i]
+ data_properties[i, :, :, :] += (labels .== label)*tissue_properties[tissue][i]
end
end
- # To make it a tuple of five elements
- properties = Tuple(data_properties[i, :, :, :] for i in 1:size(data_properties, 1))
- # To avoid singleton dimensions
- properties = Tuple(reshape(item, filter(d -> d>1, size(item))...) for item in properties)
- return properties
+
+ return (data_properties[i,:,:,:] for i in 1:Nproperties)
end
From 77c599ec2c4f8fbfd414444f3495593cebe448a7 Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Mon, 27 Jan 2025 20:00:04 -0300
Subject: [PATCH 18/19] Changing labels to Dict
---
KomaMRIBase/src/datatypes/Phantom.jl | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index e7c6726b7..86efb019f 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -568,27 +568,32 @@ function default_brain_tissue_properties(labels, tissue_properties = Dict())
"CSF" => [1, 2.569, 0.329, 0.058, 0],
"GM" => [0.86, 0.833, 0.083, 0.069, 0],
"WM" => [0.77, 0.500, 0.070, 0.061, 0],
- "FAT1" => [1, 0.350, 0.070, 0.058, -220*2π], #-220 Hz
+ "FAT1" => [1, 0.350, 0.070, 0.058, -220 * 2π], #-220 Hz
"MUSCLE" => [1, 0.900, 0.047, 0.030, 0],
"SKIN/MUSCLE" => [1, 0.569, 0.329, 0.058, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
- "FAT2" => [0.77, 0.500, 0.070, 0.061, -220*2π], #-220 Hz
+ "FAT2" => [0.77, 0.500, 0.070, 0.061, -220 * 2π], #-220 Hz
"DURA" => [1, 2.569, 0.329, 0.058, 0],
"MARROW" => [0.77, 0.500, 0.070, 0.061, 0])
tissue_properties = merge(default_properties, tissue_properties)
props = ["ρ", "T1", "T2", "T2s", "Δw"]
Nproperties = length(props)
- # Order: CSF, DURA, FAT1, FAT2, GM, MARROW, MUSCLE, SKIN/MUSCLE, SKULL, vESSELS, WM
- tissue_labels = [23, 232, 93, 209, 46, 255, 116, 139, 162, 185, 70]
- tissue_texts = sort(collect(keys(default_properties)))#
+ # Order: CSF, DURA, FAT1, FAT2, GM, MARROW, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, WM
+ tissues_labels = Dict("CSF" => 23, "DURA" => 232, "FAT1" => 93, "FAT2" => 209, "GM" => 46, "MARROW" => 255, "MUSCLE" => 116, "SKIN/MUSCLE" => 139, "SKULL" => 162, "VESSELS" => 185, "WM" => 70)
data_properties = zeros(Nproperties, size(labels)...)
for i=1:Nproperties
- for (label, tissue) in zip(tissue_labels, tissue_texts)
- data_properties[i, :, :, :] += (labels .== label)*tissue_properties[tissue][i]
+ for (label, tissue) in tissues_labels
+ data_properties[i, :, :, :] += (labels .== label) * tissue_properties[tissue][i]
end
end
+ for i=1:Nproperties
+ for (label, tissue) in zip(tissue_labels, tissue_texts)
+ data_properties[i, :, :, :] += (labels .== label) * tissue_properties[tissue][i]
+ end
+ end
+
return (data_properties[i,:,:,:] for i in 1:Nproperties)
end
From dcfb73494bcea901d5233fc9339554e329d6901f Mon Sep 17 00:00:00 2001
From: Guillermo <guillermo.sahonero@gmail.com>
Date: Thu, 6 Feb 2025 00:05:03 -0300
Subject: [PATCH 19/19] Fixing order and removing lines
---
KomaMRIBase/src/datatypes/Phantom.jl | 8 +-------
1 file changed, 1 insertion(+), 7 deletions(-)
diff --git a/KomaMRIBase/src/datatypes/Phantom.jl b/KomaMRIBase/src/datatypes/Phantom.jl
index 3e1f78c4e..2ed779ce9 100644
--- a/KomaMRIBase/src/datatypes/Phantom.jl
+++ b/KomaMRIBase/src/datatypes/Phantom.jl
@@ -584,13 +584,7 @@ function default_brain_tissue_properties(labels, tissue_properties = Dict())
tissues_labels = Dict("CSF" => 23, "DURA" => 232, "FAT1" => 93, "FAT2" => 209, "GM" => 46, "MARROW" => 255, "MUSCLE" => 116, "SKIN/MUSCLE" => 139, "SKULL" => 162, "VESSELS" => 185, "WM" => 70)
data_properties = zeros(Nproperties, size(labels)...)
for i=1:Nproperties
- for (label, tissue) in tissues_labels
- data_properties[i, :, :, :] += (labels .== label) * tissue_properties[tissue][i]
- end
- end
-
- for i=1:Nproperties
- for (label, tissue) in zip(tissue_labels, tissue_texts)
+ for (tissue, label) in tissues_labels
data_properties[i, :, :, :] += (labels .== label) * tissue_properties[tissue][i]
end
end