Phantom documentation #495

pvillacorta · 2024-10-09T12:17:06Z

This PR aims to solve #395 and probably #394.

I am using Literate.jl to make all the new documents

https://juliahealth.org/KomaMRI.jl/previews/PR495/

cncastillo · 2024-10-09T12:41:39Z

Nice thanks!

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

cncastillo · 2024-10-09T12:45:56Z

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.

cncastillo · 2024-10-09T15:57:34Z

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 (?)

pvillacorta · 2024-10-09T21:41:05Z

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

- Solve MotionList(rot) bug - Pass Docs CI - Add useful constructors to `Motion`

cncastillo · 2024-10-09T22:11:33Z

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

- Finish lit-1-phantom.jl - New lit-3-phantom-format.jl - Upload svg files for phantom file tree - Update cross references

- Typo in lit-1-phantom.jl - Typo in ph-timespan-type svg filenames - Fix light mode for ph-timespan-type

- Change phantom-format file to pure markdown - Try `execute=true` option for Literate.markdown function - Change `plot_phantom_map` example to display T1 - Remove buildkite test to avoid overloading

codecov · 2024-10-11T10:57:57Z

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).

Files with missing lines	Patch %	Lines
KomaMRIBase/src/motion/motionlist/Motion.jl	0.00%	9 Missing ⚠️

Additional details and impacted files

@@            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

Flag	Coverage Δ
base	`86.81% <10.00%> (-0.26%)`	⬇️
core	`72.95% <ø> (-20.25%)`	⬇️
files	`93.28% <ø> (+1.58%)`	⬆️
komamri	`93.98% <ø> (ø)`
plots	`92.95% <ø> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
KomaMRIBase/src/motion/motionlist/MotionList.jl	`67.64% <100.00%> (ø)`
KomaMRIPlots/src/ui/DisplayFunctions.jl	`94.17% <ø> (ø)`
KomaMRIBase/src/motion/motionlist/Motion.jl	`58.62% <0.00%> (-26.38%)`	⬇️

... and 14 files with indirect coverage changes

- Remove `execute=true` - Update svg files for file format section - Display outputs in phantom section

pvillacorta · 2024-10-11T15:18:37Z

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.

cncastillo · 2024-10-15T13:43:45Z

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.

First commit

f1aa8a4

This was linked to issues Oct 9, 2024

Improve "How to Create your Own Phantom" section #394

Open

Add Phantom Explanation section #395

Open

pvillacorta added the documentation Improvements to docs., it also triggers doc preview label Oct 9, 2024

Commit of the following:

64c02fa

- Solve MotionList(rot) bug - Pass Docs CI - Add useful constructors to `Motion`

pvillacorta added 3 commits October 11, 2024 11:04

Commit of the following:

38b96de

- Finish lit-1-phantom.jl - New lit-3-phantom-format.jl - Upload svg files for phantom file tree - Update cross references

Solve bugs:

0548186

- Typo in lit-1-phantom.jl - Typo in ph-timespan-type svg filenames - Fix light mode for ph-timespan-type

Commit of the following:

022766e

- Change phantom-format file to pure markdown - Try `execute=true` option for Literate.markdown function - Change `plot_phantom_map` example to display T1 - Remove buildkite test to avoid overloading

pvillacorta added 2 commits October 11, 2024 17:06

Commit with the following:

d631815

- Remove `execute=true` - Update svg files for file format section - Display outputs in phantom section

Recover buildkite pipeline

5f0f8fe

pvillacorta mentioned this pull request Oct 16, 2024

Troubles defining Float32 or empty phantoms with KomaMRI 0.9 #498

Open

Solve plot_phantom_map bug for 2D and 1D phantoms

402439b

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Phantom documentation #495

Phantom documentation #495

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Phantom documentation #495

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