Merge branch 'master' into fix-599-colab-plots

Author: Mxyank24

KomaMRIBase/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRIBase"
 uuid = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
 
-version = "0.11.1"
+version = "0.11.2"
 authors = ["Carlos Castillo Passi <cncastillo@uc.cl>"]
 
 [workspace]

KomaMRIBase/src/motion/actions/simpleactions/Rotate.jl

@@ -79,39 +79,43 @@ get_center(center::CenterOfMass, x, y, z) = (sum(x) / length(x), sum(y) / length
 get_center(center::NTuple, x, y, z)       = center
 
 function displacement_x!(ux, action::Rotate, x, y, z, t)
-    # Not using sind and cosd functions until bug with oneAPI is solved: 
-    # https://github.com/JuliaGPU/oneAPI.jl/issues/65
-    α = t .* (action.yaw*π/180)
-    β = t .* (action.roll*π/180)
-    γ = t .* (action.pitch*π/180)
     cx, cy, cz = get_center(action.center, x, y, z)
-    x0, y0, z0 = x .- cx, y .- cy, z .- cz
-    ux .= cos.(α) .* cos.(β) .* x0 +
-         (cos.(α) .* sin.(β) .* sin.(γ) .- sin.(α) .* cos.(γ)) .* y0 +
-         (cos.(α) .* sin.(β) .* cos.(γ) .+ sin.(α) .* sin.(γ)) .* z0 .+ cx .- x
+    α = deg2rad(action.yaw)
+    β = deg2rad(action.roll)
+    γ = deg2rad(action.pitch)
+    
+    @. ux =  cos(α * t) * cos(β * t) * (x - cx) +
+            (cos(α * t) * sin(β * t) * sin(γ * t) - sin(α * t) * cos(γ * t)) * (y - cy) +
+            (cos(α * t) * sin(β * t) * cos(γ * t) + sin(α * t) * sin(γ * t)) * (z - cz) + 
+            cx - x
+            
     return nothing
 end
 
 function displacement_y!(uy, action::Rotate, x, y, z, t)
-    α = t .* (action.yaw*π/180)
-    β = t .* (action.roll*π/180)
-    γ = t .* (action.pitch*π/180)
     cx, cy, cz = get_center(action.center, x, y, z)
-    x0, y0, z0 = x .- cx, y .- cy, z .- cz
-    uy .= sin.(α) .* cos.(β) .* x0 +
-         (sin.(α) .* sin.(β) .* sin.(γ) .+ cos.(α) .* cos.(γ)) .* y0 +
-         (sin.(α) .* sin.(β) .* cos.(γ) .- cos.(α) .* sin.(γ)) .* z0 .+ cy .- y
+    α = deg2rad(action.yaw)
+    β = deg2rad(action.roll)
+    γ = deg2rad(action.pitch)
+    
+    @. uy =  sin(α * t) * cos(β * t) * (x - cx) +
+            (sin(α * t) * sin(β * t) * sin(γ * t) + cos(α * t) * cos(γ * t)) * (y - cy) +
+            (sin(α * t) * sin(β * t) * cos(γ * t) - cos(α * t) * sin(γ * t)) * (z - cz) + 
+            cy - y
+            
     return nothing
 end
 
 function displacement_z!(uz, action::Rotate, x, y, z, t)
-    α = t .* (action.yaw*π/180)
-    β = t .* (action.roll*π/180)
-    γ = t .* (action.pitch*π/180)
     cx, cy, cz = get_center(action.center, x, y, z)
-    x0, y0, z0 = x .- cx, y .- cy, z .- cz
-    uz .=  -sin.(β) .* x0 + 
-            cos.(β) .* sin.(γ) .* y0 +
-            cos.(β) .* cos.(γ) .* z0 .+ cz .- z
+    α = deg2rad(action.yaw)
+    β = deg2rad(action.roll)
+    γ = deg2rad(action.pitch)
+    
+    @. uz = -sin(β * t) * (x - cx) + 
+             cos(β * t) * sin(γ * t) * (y - cy) +
+             cos(β * t) * cos(γ * t) * (z - cz) + 
+             cz - z
+            
     return nothing
 end

KomaMRICore/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRICore"
 uuid = "4baa4f4d-2ae9-40db-8331-a7d1080e3f4e"
 authors = ["Carlos Castillo Passi <cncastillo@uc.cl>"]
-version = "0.11.1"
+version = "0.11.2"
 
 [deps]
 AcceleratedKernels = "6a4ca0a5-0e36-4168-a932-d9be78d558f1"

KomaMRICore/src/rawdata/ISMRMRD.jl

@@ -144,7 +144,7 @@ function signal_to_raw_data(
         "enc_lim_repetition"             => Limit(0, 0, max_enc.REP),                     #min, max, center, e.g. dynamic number for dynamic scanning
         "enc_lim_set"                    => Limit(0, 0, max_enc.SET),                     #min, max, center, e.g. flow encoding set
         "enc_lim_segment"                => Limit(0, 0, max_enc.SEG),                     #min, max, center, e.g. segment number for segmented acquisition
-        "trajectory"                     => "other",
+        "trajectory"                     => "custom",
         #sequenceParameters
         # "TR"                             => 0,
         # "TE"                             => 0,
@@ -264,4 +264,4 @@ Base.isapprox(sig1::RawAcquisitionData, sig2::RawAcquisitionData; kwargs...) = b
     end
 
     return true
-end
+end

KomaMRICore/src/simulation/SimulatorCore.jl

@@ -271,6 +271,16 @@ macro maybe_time(verbose, expr)
     end
 end
 
+function _assert_nonnegative_adc_labels(seq::Sequence)
+    for (block, labels) in enumerate(get_labels(seq))
+        for name in fieldnames(AdcLabels)
+            value = getfield(labels, name)
+            value < 0 && error("Negative ADC label found at block $block: `$name` with value `$value`.")
+        end
+    end
+    return nothing
+end
+
 """
     out = simulate(obj::Phantom, seq::Sequence, sys::Scanner; sim_params, w)
 
@@ -308,6 +318,7 @@ julia> plot_signal(raw)
 function simulate(
     obj::Phantom, seq::Sequence, sys::Scanner; sim_params=Dict{String,Any}(), verbose=true, callbacks=()
 )
+    _assert_nonnegative_adc_labels(seq)
     #Simulation parameter unpacking, and setting defaults if key is not defined
     sim_params = default_sim_params(sim_params)
     #Warn if user is trying to run on CPU without enabling multi-threading

KomaMRICore/test/runtests.jl

@@ -218,6 +218,15 @@ end
     @test true
 end
 
+@testitem "simulate rejects negative labels" tags=[:core, :nomotion] begin
+    obj = Phantom(x=[0.0])
+    seq = Sequence([Grad(0, 1e-3)])
+    for label in (LabelSet(-1, "LIN"), LabelInc(-1, "LIN"))
+        seq.EXT[1] = [label]
+        @test_throws Exception simulate(obj, seq, Scanner(); verbose=false)
+    end
+end
+
 @testitem "Bloch" tags=[:important, :core, :nomotion, :bloch] begin
     include("initialize_backend.jl")
     include(joinpath(@__DIR__, "test_files", "utils.jl"))

docs/EmbeddPlotlyJSSyncPlotLiterate.jl

@@ -21,13 +21,17 @@ function Base.show(io::IO, ::MIME"text/html", fig::PlotlyJS.SyncPlot)
     # Copy is required because we pop layout width/height for Plotly's inner JSON.
     # Mutating fig.plot directly would change size(fig) and user-visible behavior.
     plot = copy(fig.plot)
+    plot.frames = fig.plot.frames
+    plot.config = deepcopy(fig.plot.config)
+    plot.config.displayModeBar = false
     default_width = layout_to_html_default_size!(plot.layout.fields, :width, get(plot.layout.fields, :width, nothing))
     default_height = layout_to_html_default_size!(plot.layout.fields, :height, get(plot.layout.fields, :height, nothing))
 
     html_buffer = IOBuffer()
     PlotlyJS.PlotlyBase.to_html(
         html_buffer,
         plot;
+        autoplay=false,
         full_html=true,
         include_plotlyjs="cdn",
         default_width=default_width,