KomaMRIFiles-v0.9.11

What's Changed

• Load pulseq sequences faster by @artoews in #747
• Closed #224

New Contributors

• @artoews made their first contribution in #747

Full Changelog: KomaMRIFiles-v0.9.10...KomaMRIFiles-v0.9.11

KomaMRIBase-v0.9.9

Changes:

• Fixed some abstract field definitions on Grad and RF structs
• Removed type stability issues in is_*_on functions

KomaMRIFiles-v0.9.10

What's Changed

• Fix error handling when unsupported (and required) extensions are read by @pvillacorta in #729

Full Changelog: KomaMRIFiles-v0.9.9...KomaMRIFiles-v0.9.10

KomaMRIPlots-v0.9.6

What's Changed

• plot_seq: RF center is displayed including use, amplitude, and phase information.
• plot_kspace: Now considers RF use and center to compute k-space coordinates.

Full Changelog: v0.9.1...KomaMRIPlots-v0.9.6

KomaMRIFiles-v0.9.9

What's Changed

• Pulseq 1.5.1 reader support
• More tests for Pulseq versions 1.2, 1.3, 1.4 and 1.5.
• Read Pulseq 1.5.1 by @Stockless in #614

Full Changelog: v0.9.2...KomaMRIFiles-v0.9.9

KomaMRIBase-v0.9.8

What's Changed

• Inclusion of RF center, first, last and use.
• RF use is now considered in k-space calculations.
• Extensions should be more flexible now
• Read Pulseq 1.5.1 by @Stockless in #614

New Contributors

• @thePlasm made their first contribution in #645
• @nHackel made their first contribution in #661

Full Changelog: v0.9.2...KomaMRIBase-v0.9.8

v0.9.1

KomaMRI v0.9.1

Diff since v0.9.0

Motion-Related Features and Bug fixes
These updates primarily affect KomaMRIBase. Key changes include:

• Bug fixes related to phantom definition, motion lists, and flow experiments (PR #499, #511, #516, #520, #536).
• Improved motion definition, allowing for easier specification of single motion instances and flexible time spans (PR #517, #531).
• Introduction of the TimeCurve structure, enabling arbitrary temporal motion patterns that were previously challenging to replicate (PR #531).
• Added tests for motion-related functions to improve code coverage (PR #523).

Other Minor Changes

• Updated and expanded documentation for contributors to Koma, providing clearer guidelines and resources (PR #509, #510, #514, #518, #543).
• KomaMRIPlots: Standardized colormaps using QMRIColors.jl for T1 and T2 maps (PR #528).
• KomaMRICore: Removed "hack" of using cos + i sin as oneAPI.jl didn't defined cis(x) . Now we use sincos for GPU kernel code (PR #496).

Merged pull requests:

• Update README.md with v0.9 news (#493) (@calberolalopez)
• Update to use cis instead of cos + i sin (#496) (@cncastillo)
• CompatHelper: bump compat for PlutoPlotly in [weakdeps] to 0.6 for package KomaMRIPlots, (keep existing compat) (#497) (@github-actions[bot])
• Fix Phantom-related bugs (#498 and more) (#499) (@pvillacorta)
• Avoid GPU runners for CPU jobs, and fix hanging CPU tests (#502) (@cncastillo)
• CompatHelper: bump compat for Functors to 0.5 for package KomaMRICore, (keep existing compat) (#507) (@github-actions[bot])
• How to contribute to Koma docs (#509) (@Stockless)
• Fixing text some details in dev documentation (#510) (@Stockless)
• Adjust reset flag interpolation to trigger at jump (#511) (@pvillacorta)
• Bump codecov/codecov-action from 4 to 5 (#513) (@dependabot[bot])
• Fix asset paths for "5-contribute-to-koma.md" (#514) (@Stockless)
• Fixed incorrect assets path (#515) (@Stockless)
• Fix flow-related functions (#516) (@pvillacorta)
• Ease motion definition when only one motion is needed (#517) (@pvillacorta)
• Limited size of large assets in light mode (#518) (@Stockless)
• Solve bug in SpinRanges when indexing a phantom with a BitVector (#520) (@pvillacorta)
• Test motion-related functions (#523) (@pvillacorta)
• Limit 'NadcsPerImage' to be at least 1 (#527) (@Stockless)
• Adding standard T1 and T2 colormaps from QMRIColors.jl (#528) (@Stockless)
• Flexibilize the definition of motion time spans (#531) (@pvillacorta)
• Fix motion bugs and add colorscale keyword in plot_image (#536) (@pvillacorta)
• Resize contributors (#541) (@Stockless)
• Contributing guidelines update (#543) (@Stockless)
• replace all "cmin" and "cmax" with "zmin" and "zmax" respectibly (#546) (@Stockless)
• bump v0.9.0 to v0.9.1 (#547) (@Stockless)

Closed issues:

• Add Contributing Guidelines (#209)
• Include steps for contributing using VSCode (#233)
• An error of 'DivideError: integer division' occurs in the internal functions of simulate when using a sequence with spiral acquisition (#409)
• Test setting fields from a Phantom @view (#412)
• Future: use sincos once available in oneAPI.jl (#463)
• Use color-map recommendations for MR relaxometry maps by Quantitative MR Study Group (#473)
• Easily define Phantom motion field composed by only one Motion instance (#481)
• Troubles defining Float32 or empty phantoms with KomaMRI 0.9 (#498)
• Don't run CPU benchmarks on GPU workers (#501)
• Test Motion constructors (#512)
• Test motion-related functions (#522)
• Resize collaborators (#525)

v0.9.0

KomaMRI v0.9.0

Diff since v0.8.2

This new breaking release of Koma v0.9 has multiple new features. Thanks to @rkierulf, our GSoC student, for the GPU enhancements and @pvillacorta for the new motion definitions that enable flow and shareable phantoms.

(1) Device-agnostic kernel-based simulations (more info here)
We can now use various GPU backends with the help of KernelAbstractions.jl. This means that GPU-related packages like CUDA are not installed by default. Installation and loading of the desired GPU package is needed (for example ] add CUDA, using CUDA).

(2) New simulation method, faster and better
Now Bloch has specialized implementations for CPU and GPU and the previous implementation is in BlochSimple. This new simulation method is 4-5 times faster and uses around 80 times less memory. We have seen a 100-200x improvement in some sequences, especially if they have a lot of soft RF pulses.

(3) Distributed simulations (more info here)
We also tested distributed simulations with multiple GPUs and nodes :)

(4) GPU benchmarks (here)
We have a fancy new benchmarking page to ensure that there are no performance regressions.

(5)Phantom's including flexible motions and flow (more experimental)
You can now plot phantoms with motion and define them using mix-and-match motion definitions! More complex phantoms are possible including simple motions or arbitrary motions. Many more examples of using them are coming soon! 😄 including a realistic CFD-simulated aorta! All of this is done using our new reproducible phantom definition (HDF5-based), which enables the sharing of these phantoms with complex motion.

Hope these changes make your simulations faster! 😄 As always, if you have any problems, feel free to talk to me (@cncastillo ) in Slack or post an issue or discussion on GitHub.

Merged pull requests:

• Motion Phantom (#184) (@pvillacorta)
• Bump codecov/codecov-action from 4.1.1 to 4.3.0 (#384) (@dependabot[bot])
• Bump julia-actions/setup-julia from 1 to 2 (#385) (@dependabot[bot])
• Tutorial for SimpleMotion creation and simulation (#387) (@pvillacorta)
• Update nightly.yml (#388) (@cncastillo)
• Adding "How to Cite Koma" section to docs (#389) (@cncastillo)
• Bump julia-actions/julia-format from 2 to 3 (#398) (@dependabot[bot])
• Update DisplayFunctions.jl (#402) (@curtcorum)
• Add Binder badge to Literate tutorials (#403) (@cncastillo)
• Extend GPU support to Metal, ROCm, and oneAPI backends (#405) (@rkierulf)
• Fix some test failures (#406) (@rkierulf)
• Optimize ArbitraryMotion (continuation) (#408) (@pvillacorta)
• Add Buildkite GPU pipeline (#411) (@rkierulf)
• Fix plot phantom function (#413) (@pvillacorta)
• Fixing testing environments for GPU backends (#415) (@cncastillo)
• Add kernel-based matrix cumsum (#416) (@rkierulf)
• Initial benchmarking implementation: steps to run benchmarks and comb… (#418) (@rkierulf)
• Fix typos in docstrings (#419) (@pvillacorta)
• [DOCS] Add JuliaHealth Star Counter Badge to README (#420) (@TheCedarPrince)
• Updates to github-action-benchmark index.html (#421) (@rkierulf)
• Fixing issues in Julia 1.11 and Julia 1.12 (#422) (@cncastillo)
• Fix monorepo script not working for pushes to main (#423) (@rkierulf)
• Change 'main' to 'master' so benchmarking action actually runs (#424) (@rkierulf)
• Including details about prints of simulate (#431) (@gsahonero)
• Bump to 0.9.0-DEV (#434) (@cncastillo)
• New Motion (#442) (@pvillacorta)
• Optimize run_spin_precession! and run_spin_excitation! for CPU (#443) (@rkierulf)
• Change reduce(vcat, itr) to reduce(vcat, [itr]) (#444) (@cncastillo)
• Pkg version handling and choosable test backend for VSCode (#453) (@cncastillo)
• Pkg version handling and choosable test backend for VSCode (again) (#455) (@cncastillo)
• CompatHelper: bump compat for PlutoPlotly in [weakdeps] to 0.5 for package KomaMRIPlots, (keep existing compat) (#456) (@github-actions[bot])
• Fixing benchmark comments on PRs (#457) (@cncastillo)
• Optimize run_spin_precession! for GPU (#459) (@rkierulf)
• CompatHelper: bump compat for AMDGPU in [weakdeps] to 1 for package KomaMRICore, (keep existing compat) (#460) (@github-actions[bot])
• CompatHelper: bump compat for MRIReco to 0.9, (keep existing compat) (#461) (@github-actions[bot])
• Optimize run_spin_excitation! for GPU (#462) (@rkierulf)
• Fixing brain phantom values (#465) (@gsahonero)
• Add Distributed Examples to Documentation (#468) (@rkierulf)
• Include more specific SLURM instructions (#469) (@cncastillo)
• GSOC: Add GPU Explanation Section to Documentation (#470) (@rkierulf)
• Fix extra allocations when benchmarking with no motion (#483) (@pvillacorta)
• Fix bug in plot_phantom_map when length(obj) > max_spins (#485) (@pvillacorta)
• Fix sum of Grads (#486) (@pvillacorta)
• Fix bugs related with SpinRange and flow (#488) (@pvillacorta)
• Diffusion tutorial for isotropic diffusion (#489) (@tinorodriguez)
• Fix plot_phantom_map for dynamic phantoms (#490) (@pvillacorta)
• Changing size of plot for diffusion example (#491) (@cncastillo)
• KomaMRI v0.9 (#492) (@cncastillo)

Closed issues:

• CUDA memory problems? (#125)
• Using BuildKite for GPU related CI? (#147)
• Use the same functions to sample RFs in the simulation than for plotting sequence (#167)
• Separate CI for more comprehensive results (#276)
• Add simulate function for debugging purposes (#288)
• Create Pluto example for fat_sat_low_field (#291)
• Reporting of phantom spatial sampling in obj.info structure. (#322)
• GSOC Proposal Issue Tracking: Part 1 (#349)
• GSOC Proposal Issue Tracking: Part 2 (#350)
• Extend GPU support to include Apple (Metal.jl), AMD (AMDGPU.jl), and Intel (OneAPI.jl) (#351)
• Profile Bloch Simulation Method (#352)
• Create new Kernel-based Simulation Method (#353)
• Use @LocalMem inside future kernel-based simulation functions to speed up memory access (#354)
• Add example of Multi-GPU simulation (#355)
• Add example and / or support for multi-node simulation (#356)
• Simplify ArbitraryMotion struct (#371)
• Re-use weights in interpolation for ArbitraryMotion (#372)
• Define Nspins for SimpleMotion (#376)
• Applying @time to simulate reveals discrepancies on resources and timing reports (#392)
• plot_signal docstring (correction) (#401)
• [KomaUI Plotting] obj_ui[] does not draw on first time updated. Need to press :rho or other option. (#407)
• New motion approach to combine SimpleMotion and ArbitraryMotion into the same phantom (#410)
• Future: use @testsetup to reduce time to run tests on GPU (#414)
• Problems initializing KomaUI (#432)
• Brain phantom values inconsistencies (#464)
• spin_reset has eltype T and should be an AbstractMatrix{Bool} (#479)

v0.8.2

KomaMRI v0.8.2

Diff since v0.8.1

Merged pull requests:

• Documentation restructure (#377) (@beorostica)
• Update Koma package versions (#379) (@beorostica)

Closed issues:

• Modify Literate Examples Generation (#251)
• plot_seq not plotting Gx if Gy is not on and vice-versa (#374)
• KomaMRI errors when using Julia nightly (#375)
• Simulation crashes when trying to simulate soft-RF (get_rf_center) (#378)

v0.8.1

KomaMRI v0.8.1

Diff since v0.8.0

Merged pull requests:

• Add GPU tested compatibility in documentation (#300) (@beorostica)
• Update codecov to consider all subdirectories (#303) (@beorostica)
• read and store signature in seq.DEF["signature"] (#313) (@aTrotier)
• Fixes for no gradients in seq file. (#314) (@curtcorum)
• KomaMRIFiles: RF phase read with the opposite sign from Pulseq (#315) (@beorostica)
• Hot fix empty grad (#316) (@beorostica)
• Hot version updates (#317) (@beorostica)
• Upsample phantoms (#319) (@curtcorum)
• Incorrect gradient interpretation when waveforms do not end in zero (#321) (@beorostica)
• Remove deprecation warning for sort function (#327) (@beorostica)
• Fix colormap bug when ploting phantom maps (#330) (@beorostica)
• Remove air tissue from pelvis phantom example (#331) (@beorostica)
• Refactor moment functions (#332) (@beorostica)
• CI: Set up Dependabot to auto-update pinned GitHub Actions (#336) (@DilumAluthge)
• CI: Update codecov-action to v4.1.1, and pass the organization-wide CODECOV_TOKEN secret (#337) (@DilumAluthge)
• CI: Add a manual (workflow_dispatch) trigger for CompatHelper; also don't run CompatHelper on PRs (#338) (@DilumAluthge)
• Bump actions/checkout from 3 to 4 (#340) (@dependabot[bot])
• Bump actions/cache from 3 to 4 (#341) (@dependabot[bot])
• Anisotropic Phantoms (#342) (@curtcorum)
• Add an example Buildkite pipeline file (#344) (@DilumAluthge)
• Julia formatter (#369) (@cncastillo)
• Update Docs (#370) (@beorostica)

Closed issues:

• Incorrect interpretation of time shaped RFs (#200)
• Empty sequence adds an undesired block (#203)
• Unnecessary samples are considered when concatenating sequences (#205)
• Resolve Circular Dependencies in Tests Environments (#237)
• Google Summer of Code (GSoC) (#243)
• Refactor functions for computing moments (#268)
• Compatible, tested or recommended julia versions for CPU and GPU? (#295)
• Default simulate fails after clean install of KomaMRI version 0.7.5 (#298)
• MRIReco.jl v0.8.0 incorrect initialization with multiple threads (#299)
• Update codecov to consider new subpackages (#302)
• Reduce spins for pelvis Phantom (#306)
• Interpretation of '.seq' files is not matching with sequence designed on PyPulseq (#320)
• Warning: sort(d::Dict; args...) is deprecated, use sort!(OrderedDict(d); args...) instead. (#326)
• Can't define colormap ranges when plotting phantom object (#328)
• [BUG] CodeCov Not Working (#335)
• Refactor get_Mk to compute 't' and 'tadc' more efficiently (#345)
• Performance improvements for plot_seq (function and UI) (#365)