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Adding standard T1 and T2 colormaps from QMRIColors.jl #528

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merged 4 commits into from
Dec 24, 2024
Merged

Adding standard T1 and T2 colormaps from QMRIColors.jl #528

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603a297
first tets qMRIColors
Stockless Dec 23, 2024
df05e28
Change colormap from ".mat" file to QMRIColors.jl
Stockless Dec 23, 2024
479f317
changed version specifier / corrected indentation / changed way of us…
Stockless Dec 23, 2024
de796fb
fixed indentation
Stockless Dec 23, 2024
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2 changes: 2 additions & 0 deletions KomaMRIPlots/Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ Kaleido_jll = "f7e6163d-2fa5-5f23-b69c-1db539e41963"
KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
QMRIColors = "2bec176e-9e8c-4764-a62f-295118d1ec05"
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"

[weakdeps]
Expand All @@ -24,6 +25,7 @@ KomaMRIBase = "0.9"
MAT = "0.10"
PlotlyJS = "0.18"
PlutoPlotly = "0.4, 0.5"
QMRIColors = "1"
Reexport = "1"
julia = "1.9"

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1 change: 1 addition & 0 deletions KomaMRIPlots/src/KomaMRIPlots.jl
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Expand Up @@ -2,6 +2,7 @@ module KomaMRIPlots

using KomaMRIBase
using MAT, Interpolations, PlotlyJS
using QMRIColors

include("ui/PlotBackends.jl")
include("ui/DisplayFunctions.jl")
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46 changes: 14 additions & 32 deletions KomaMRIPlots/src/ui/DisplayFunctions.jl
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Expand Up @@ -981,10 +981,10 @@ function plot_kspace(seq::Sequence; width=nothing, height=nothing, darkmode=fals
"orbitRotation",
"resetCameraDefault3d",
],
)
return plot_koma(p, l; config)
end

)
return plot_koma(p, l; config)
end
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"""
p = plot_phantom_map(obj::Phantom, key::Symbol; kwargs...)

Expand Down Expand Up @@ -1080,38 +1080,20 @@ function plot_phantom_map(
unit = " ms"
if key == :T1
cmax_key = 2500 / factor
colors = MAT.matread(path * "/assets/T1cm.mat")["T1colormap"][1:70:end, :]
N, _ = size(colors)
idx = range(0, 1; length=N) #range(0,T,N) works in Julia 1.7
colormap = [
(
idx[n],
string("rgb(",
floor(Int, colors[n,1] * 255), ",",
floor(Int, colors[n,2] * 255), ",",
floor(Int, colors[n,3] * 255), ")"
)
)
for n in 1:N
]
colors =
replace.(string.(relaxationColorMap("T1") .* 255), "RGB{Float64}" => "rgb")
N = length(colors)
indices = range(0.0; stop=1.0, length=N)
colormap = [(idx, color) for (idx, color) in zip(indices, colors)]
elseif key == :T2 || key == :T2s
if key == :T2
cmax_key = 250 / factor
end
colors = MAT.matread(path * "/assets/T2cm.mat")["T2colormap"][1:70:end, :]
N, _ = size(colors)
idx = range(0, 1; length=N) #range(0,T,N) works in Julia 1.7
colormap = [
(
idx[n],
string("rgb(",
floor(Int, colors[n,1] * 255), ",",
floor(Int, colors[n,2] * 255), ",",
floor(Int, colors[n,3] * 255), ")"
)
)
for n in 1:N
]
colors =
replace.(string.(relaxationColorMap("T2") .* 255), "RGB{Float64}" => "rgb")
N = length(colors)
indices = range(0.0; stop=1.0, length=N)
colormap = [(idx, color) for (idx, color) in zip(indices, colors)]
end
elseif key == :x || key == :y || key == :z
factor = 1e2
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