Phantom documentation

KomaMRIBase/src/datatypes/Phantom.jl

@@ -115,7 +115,7 @@ function get_dims(obj::Phantom)
     push!(dims, any(x -> x != 0, obj.x))
     push!(dims, any(x -> x != 0, obj.y))
     push!(dims, any(x -> x != 0, obj.z))
-    return dims
+    return sum(dims) > 0 ? dims : Bool[1, 0, 0]
 end
 
 """

KomaMRIBase/src/motion/motionlist/Motion.jl

@@ -32,6 +32,20 @@ julia> motion =  Motion(
     spins ::AbstractSpinSpan      = AllSpins()
 end
 
+# Main constructors
+function Motion(action) 
+    T = first(typeof(action).parameters)
+    return Motion(action, TimeRange(zero(T)), AllSpins())
+end
+function Motion(action, time::AbstractTimeSpan)
+    T = first(typeof(action).parameters)
+    return Motion(action, time, AllSpins())
+end
+function Motion(action, spins::AbstractSpinSpan)
+    T = first(typeof(action).parameters)
+    return Motion(action, TimeRange(zero(T)), spins)
+end
+
 # Custom constructors
 """
     translate = Translate(dx, dy, dz, time, spins)

KomaMRIBase/src/motion/motionlist/MotionList.jl

@@ -32,7 +32,7 @@ struct MotionList{T<:Real} <: AbstractMotion{T}
 end
 
 """ Constructors """
-MotionList(motions...) = length([motions]) > 0 ? MotionList([motions...]) : @error "You must provide at least one motion as input argument. If you do not want to define motion, use `NoMotion{T}()`"
+MotionList(motions::Motion...) = length([motions]) > 0 ? MotionList([motions...]) : @error "You must provide at least one motion as input argument. If you do not want to define motion, use `NoMotion{T}()`"
 
 """ MotionList sub-group """
 function Base.getindex(mv::MotionList{T}, p) where {T<:Real}

KomaMRIPlots/src/ui/DisplayFunctions.jl

@@ -1135,9 +1135,21 @@ function plot_phantom_map(
     l = Layout(;title=obj.name*": "*string(key))
 
     if view_2d # 2D
+        function get_displayed_dims(v)
+            if sum(v) == 1
+                idx = argmax(v)[1] 
+                return [idx in [1, 3], idx in [1, 2], idx in [2,3]]
+            else
+                return v
+            end
+        end 
+
         # Layout config
+        dims = get_displayed_dims(KomaMRIBase.get_dims(obj))
+        axis = ["x", "y", "z"][dims]
+
         l[:xaxis] = attr(
-            title="x",
+            title=axis[1],
             range=[x0, xf],
             ticksuffix=" cm",
             backgroundcolor=plot_bgcolor,
@@ -1146,7 +1158,7 @@ function plot_phantom_map(
             scaleanchor="y"
         )
         l[:yaxis] = attr(
-            title="y",
+            title=axis[2],
             range=[x0, xf],
             ticksuffix=" cm",
             backgroundcolor=plot_bgcolor,
@@ -1158,8 +1170,8 @@ function plot_phantom_map(
         # Add traces
         for i in 1:length(t)
             push!(traces, scattergl( 
-                x=(x[:,i])*1e2,
-                y=(y[:,i])*1e2,
+                x=dims[1]           ? (x[:,i])*1e2 : (y[:,i])*1e2,
+                y=dims[1] & dims[2] ? (y[:,i])*1e2 : (z[:,i])*1e2,
                 mode="markers",
                 marker=attr(color=getproperty(obj,key)*factor,
                             showscale=colorbar,
@@ -1244,7 +1256,7 @@ function plot_phantom_map(
             )
             for (i, t0) in enumerate(t)
         ],
-        currentvalue_prefix="x = ",
+        currentvalue_prefix="t = ",
         currentvalue_suffix="ms",
     )]
     l[:margin] = attr(t=50, l=0, r=0)

README.md

@@ -60,7 +60,7 @@ KomaMRI.jl is a Julia package for highly efficient ⚡ MRI simulations. KomaMRI
 ## News
 
 - **(1 Oct 2024)** [KomaMRI v0.9](https://github.com/JuliaHealth/KomaMRI.jl/releases/tag/v0.9.0): device-agnostic simulations, improved performance (**4-5x faster and 80x less memory**), distributed simulations, GPU benchmarking, mix-and-match motion definitions, improved dynamic phantom plotting, and a new phantom file format!
-- **(29 Aug 2024)** Our first GSoC student, Ryan Kierulf, presented his fantastic work at the JuliaHealth monthly meeting 🥳! (presentation available [here](https://www.youtube.com/watch?v=R6Z20G0J4bM)) More info in the docs: [GPU Parallelization](https://juliahealth.org/KomaMRI.jl/dev/explanation/4-gpu-explanation/), [Distributed Simulations](https://juliahealth.org/KomaMRI.jl/dev/how-to/4-run-distributed-simulations/) and [Ryan's JuliaHealth blog](https://juliahealth.org/JuliaHealthBlog/posts/ryan-gsoc/Ryan_GSOC.html)
+- **(29 Aug 2024)** Our first GSoC student, Ryan Kierulf, presented his fantastic work at the JuliaHealth monthly meeting 🥳! (presentation available [here](https://www.youtube.com/watch?v=R6Z20G0J4bM)) More info in the docs: [GPU Parallelization](https://juliahealth.org/KomaMRI.jl/dev/explanation/7-gpu-explanation/), [Distributed Simulations](https://juliahealth.org/KomaMRI.jl/dev/how-to/4-run-distributed-simulations/) and [Ryan's JuliaHealth blog](https://juliahealth.org/JuliaHealthBlog/posts/ryan-gsoc/Ryan_GSOC.html)
 - **(7 Dec 2023)** Koma was present in [MRI Together](https://mritogether.esmrmb.org/) 😼. The talk is available [here](https://www.youtube.com/watch?v=9mRQH8um4-A). Also, I uploaded the promised [educational example](https://juliahealth.org/KomaMRI.jl/stable/tutorial-pluto/01-gradient-echo-spin-echo/).
 - **(17 Nov 2023)** Pretty excited of being part of [ISMRM Pulseq's virtual meeting](https://github.com/pulseq/ISMRM-Virtual-Meeting--November-15-17-2023). The slides available [here](https://github.com/pulseq/ISMRM-Virtual-Meeting--November-15-17-2023/blob/35a8da7eaa0bf42f2127e1338a440ccd4e3ef53c/slides/day3_KomaMRI_simulator_Quantitative_MRI.pdf).
 - **(27 Jul 2023)** I gave a talk at MIT 😄 for [JuliaCon 2023](https://juliacon.org/2023/)! A video of the presentation can be seen [here](https://www.youtube.com/watch?v=WVT9wJegC6Q).
@@ -117,7 +117,7 @@ KomaUI()
 Press the button that says "Simulate!" to do your first simulation :). Then, a notification will emerge telling you that the simulation was successful. In this notification, you can either select to (1) see the Raw Data or (2) to proceed with the reconstruction.
 
 > [!IMPORTANT]
-> Starting from **KomaMRI v0.9** we are using [package extensions](https://pkgdocs.julialang.org/v1/creating-packages/#Conditional-loading-of-code-in-packages-(Extensions)) to deal with GPU dependencies, meaning that to run simulations on the GPU, installing (`add CUDA/AMDGPU/Metal/oneAPI`) and loading (`using CUDA/AMDGPU/Metal/oneAPI`) the desired backend will be necessary (see [GPU Parallelization](https://JuliaHealth.github.io/KomaMRI.jl/dev/explanation/4-gpu-explanation) and [Tested compatibility](#tested-compatibility)).  
+> Starting from **KomaMRI v0.9** we are using [package extensions](https://pkgdocs.julialang.org/v1/creating-packages/#Conditional-loading-of-code-in-packages-(Extensions)) to deal with GPU dependencies, meaning that to run simulations on the GPU, installing (`add CUDA/AMDGPU/Metal/oneAPI`) and loading (`using CUDA/AMDGPU/Metal/oneAPI`) the desired backend will be necessary (see [GPU Parallelization](https://JuliaHealth.github.io/KomaMRI.jl/dev/explanation/7-gpu-explanation) and [Tested compatibility](#tested-compatibility)).  
 
 ## How to Contribute
 KomaMRI exists thanks to all our contributors: