Nice thanks!

Btw, Julia 1 changed yesterday to the new 1.11 version. Some minor modifications may be needed.

Also, unrelated, but I have seen this error occur more than once for the motion tests on Julia 1.10 (Buildkite CI job: https://buildkite.com/julialang/komamri-dot-jl/builds/1209#01927136-fd93-423f-9b2c-f55de2bc3048):

KomaMRICore.BlochSimple: Error During Test at /var/lib/buildkite-agent/builds/sagittarius-maleadt-net/julialang/komamri-dot-jl/KomaMRICore/test/runtests.jl:454
  Got exception outside of a @test
  ArgumentError: Attempt to copy a freed reference.
  Stacktrace:
    [1] copy(ref::GPUArrays.DataRef{oneAPI.oneL0.DeviceBuffer})
      @ GPUArrays ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/GPUArrays/qt4ax/src/host/abstractarray.jl:77
    [2] _
      @ ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/oneAPI/gsDml/src/array.jl:78 [inlined]
    [3] oneArray
      @ ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/oneAPI/gsDml/src/array.jl:71 [inlined]
    [4] derive
      @ ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/oneAPI/gsDml/src/array.jl:451 [inlined]
    [5] unsafe_contiguous_view
      @ ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/GPUArrays/qt4ax/src/host/base.jl:319 [inlined]
    [6] unsafe_view
      @ ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/GPUArrays/qt4ax/src/host/base.jl:314 [inlined]
    [7] view
      @ ~/.cache/julia-buildkite-plugin/depots/018dadfb-f4d5-466e-8c3f-55b5f9a75025/packages/GPUArrays/qt4ax/src/host/base.jl:310 [inlined]
    [8] get_spin_coords(ml::KomaMRIBase.MotionList{Float32}, x::oneAPI.oneArray{Float32, 1, oneAPI.oneL0.DeviceBuffer}, y::oneAPI.oneArray{Float32, 1, oneAPI.oneL0.DeviceBuffer}, z::oneAPI.oneArray{Float32, 1, oneAPI.oneL0.DeviceBuffer}, t::oneAPI.oneArray{Float32, 1, oneAPI.oneL0.DeviceBuffer})

Not sure if it always fails with BlochSimple, but it seems related to a view inside get_spin_coords.

Also, this

julia> using KomaMRI

julia> rot = Rotate(0.0, 0.0, π/2)
Rotate{Float64}
  pitch: Float64 0.0
  roll: Float64 0.0
  yaw: Float64 1.5707963267948966

julia> motion = MotionList(rot)

crashes Julia instead of throwing an error (?)

Btw, Julia 1 changed yesterday to the new 1.11 version. Some minor modifications may be needed.

Buildkite CI for julia v1 (1.11) now fails with oneAPI. I opened this issue, since it looks like a bug.

Also, unrelated, but I have seen this error occur more than once for the motion tests on Julia 1.10 (Buildkite CI job: https://buildkite.com/julialang/komamri-dot-jl/builds/1209#01927136-fd93-423f-9b2c-f55de2bc3048):

Regarding this, I will need to investigate more

For the moment, I commit some changes in order to solve this bug (and also add some useful constructors):

Also, this

julia> using KomaMRI

julia> rot = Rotate(0.0, 0.0, π/2)
Rotate{Float64}
  pitch: Float64 0.0
  roll: Float64 0.0
  yaw: Float64 1.5707963267948966

julia> motion = MotionList(rot)

crashes Julia instead of throwing an error (?)

I'm also trying to pass the docs CI

The docs are failing in Julia 1.11 due to this:

• showvalue not defined in Logging in Julia 1.11 julia-actions/GitHubActions.jl#36

There's already a PR fixing it:

• conditionally define showvalue based on version julia-actions/GitHubActions.jl#37

Codecov Report

Attention: Patch coverage is 10.00000% with 9 lines in your changes missing coverage. Please review.

Project coverage is 86.89%. Comparing base (00a8d8a) to head (022766e).

@@            Coverage Diff             @@
##           master     #495      +/-   ##
==========================================
- Coverage   90.77%   86.89%   -3.88%     
==========================================
  Files          54       54              
  Lines        3002     3007       +5     
==========================================
- Hits         2725     2613     -112     
- Misses        277      394     +117     

I still have to:

• Complete the file format section
• Write the motion section
• Tests of the new Motion methods in order to pass CI
• Improve The how-to section. Maybe I should just add a sub-section explaining how to import/export phantom files
• Solve this (402439b):

Another minor bug I found:

obj = Phantom(x=zeros(100), z=collect(range(-5e-2, 5e-2, 100)))
plot_pantom_map(obj, :T1)

This plots incorrectly.

The docs should be built correctly now.

Another minor bug I found:

obj = Phantom(x=zeros(100), z=collect(range(-5e-2, 5e-2, 100)))
plot_pantom_map(obj, :T1)

This plots incorrectly.

The docs should be built correctly now.

Are there any fixes in this branch? Maybe we can move them to the other one to tag a new patch release without waiting for the documentation.

I added an extra tutorial for simulating cardiac arrhythmia (variable RR intervals).
This should be ready to merge, but maybe after #561.

Is there a way to show how the phantom moves after the arrhythmias are introduced?

Yes! Once the variable RR intervals are introduced, just plot the phantom again:

I can plot it again in the tutorial, although for me it looks a bit repetitive. What do you think?

I think it is fine to not include it, you cant see the arrhythmia very well, maybe with a finer temporal resolution ... but don't worry about it.