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)

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)

KomaMRI v0.8.0

Diff since v0.7.5

Merged pull requests:

• Improve UI Observables management (#210) (@beorostica)
• Fix StackOverflow error plots of big sequences (#220) (@gabuzi)
• KomaMRIIO subpackage (#231) (@beorostica)
• Add contibuting guidelines (#234) (@beorostica)
• KomaMRIBase (#239) (@cncastillo)
• KomaMRIBase/KomaMRIFiles: Avoid Circular Deps (#240) (@beorostica)
• Add contributors in README and GUI (#247) (@beorostica)
• Add educational example to docs (#248) (@beorostica)
• Create Template for Issues (#249) (@beorostica)
• Add Template for Issues (#250) (@beorostica)
• Add educational Pluto example (#253) (@beorostica)
• Templates for Issues (#254) (@beorostica)
• Update Issue Templates (#257) (@beorostica)
• Fix multiple docs warnings (#258) (@beorostica)
• Include Koma subpackages in CompatHelper (#259) (@beorostica)
• CompatHelper: bump compat for Adapt to 4 for package KomaMRICore, (keep existing compat) (#261) (@github-actions[bot])
• CompatHelper: bump compat for Interpolations to 0.15 for package KomaMRICore, (keep existing compat) (#262) (@github-actions[bot])
• CompatHelper: bump compat for Interpolations to 0.15 for package KomaMRIPlots, (keep existing compat) (#263) (@github-actions[bot])
• Fix URL for educational Pluto example (#266) (@beorostica)
• Pluto Educational Example (#267) (@beorostica)
• Update README.md (#269) (@pabloirarrazaval)
• Fixing precompilation problems in Julia 1.10.0 (#277) (@cncastillo)
• Add test for simulate_slice_profile function (#280) (@beorostica)
• Run nightly CI on push trigger (#283) (@beorostica)
• Transform text to path in .svg image (#285) (@beorostica)
• Update koma subdir image (#289) (@beorostica)
• Patch CI for compat (#290) (@beorostica)
• CompatHelper: bump compat for Interpolations to 0.15 for package KomaMRIBase, (keep existing compat) (#292) (@github-actions[bot])
• Improve the visualization of the contributors in the UI (#294) (@beorostica)
• Display Koma package versions in issue template (#296) (@beorostica)

Closed issues:

• Annoying random update of plots in GUI (#66)
• Separate KomaMRI into simpler subpackages (#92)
• Add contributors to UI (#191)
• Be more clear about the package versions in the UI (#192)
• Koma logo in the docs is incorrect (#193)
• Update pipeline figure to show the current organization of the Koma submodules (#194)
• GUI gets stuck when simulating twice (#198)
• Unattractive group of legends and colors in subplots (#199)
• Add Contributing Guidelines (#209)
• Add the ability to modify the seq, obj, sys, raw and image used in the UI from the REPL (#211)
• MRD Data opened in Python appears corrupted (#214)
• StackOverflowError on plots of large sequences (#221)
• Precompiling KomaMRIPlots hangs on Windows (#225)
• Add a template for reporting issues (#228)
• KomaMRIFiles (#232)
• Additional <userParameters> tag within XML header of exported MRD (#236)
• Upload educational Pluto notebook (#242)
• Update Subpackages in README (#244)
• Update CompatHelper to also check subpacakge's compat (#245)
• Add MRI together's talk to News section in README (#246)
• Generete a test for slice simulation (#252)
• Avoid Warnings During Document Generation (#255)
• KomaMRIBase (#265)
• Basic trapezoidal Grad usage, parameter definition with a plot. (#270)
• KomaMRIPlots doesn't precompile in Julia 1.10.0 (#274)
• Move Julia compat to 1.9 (#275)
• Use nightly tests in CI (#281)
• Increment code coverage (#282)
• Improve the visualization of contributors and colors in the UI (#293)

KomaMRI v0.7.5

Diff since v0.7.4

Merged pull requests:

• Use reshape() instead of ;; (#177) (@beorostica)
• Fix long names displayed in the sidebar (#180) (@beorostica)
• UI update. (#181) (@cncastillo)
• Update README.md [skip ci] (#182) (@cncastillo)
• Update README.md [skip ci] (#185) (@cncastillo)
• CompatHelper: bump compat for MRIReco to 0.8, (keep existing compat) (#186) (@github-actions[bot])
• KomaMRIPlots Pluto compatibility (#195) (@cncastillo)

Closed issues:

• Edge cases arise during simple 1-spin simulation (#85)
• Plots fail when used in Pluto notebooks (#166)
• Default KomaUI sequence is different in julia versions 1.6 and 1.9 (#175)
• Long file names overflow from UI's navbar (#176)
• Adding code style, compatible Julia version, and license to README.md (#188)
• Add KomaMRI.jl to MRHub (#196)
• Bug with Δf in RF_sinc function (#197)
• Replicate pulseq functions to create sequences (#206)

KomaMRI v0.7.4

Diff since v0.7.3

Closed issues:

• Exporting results to .mat from the GUI (#70)
• Solve edge-case for avoiding additional delay in the acquisition (#88)
• Separate simulation base to KomaMRIBase subpackage (#92)
• Problem with ADC next to RF object (#161)
• Discretization of gradient waveform fails for square gradients / very high slew rates (#162)
• KomaUI not working in Julia 1.9 (#168)

Merged pull requests:

• Modules KomaMRICore and KomaMRIPlots (#148) (@beorostica)
• Fix for no-gpu devices (#153) (@beorostica)
• CompatHelper: add new compat entry for KomaMRICore at version 0.7, (keep existing compat) (#154) (@github-actions[bot])
• Change UUID of KomaMRIPlots subpackage (#156) (@beorostica)
• Add compat version 0.7 for KomaMRICore (#157) (@beorostica)
• Apidocs (#158) (@beorostica)
• CompatHelper: add new compat entry for KomaMRIPlots at version 0.7, (keep existing compat) (#159) (@github-actions[bot])
• Update ci.yml for codecov subpackages (#160) (@beorostica)
• KomaMRI v0.7.4: Bug fixes and minor features (#163) (@cncastillo)
• Avoid dialog (#171) (@beorostica)
• CompatHelper: add new compat entry for MAT at version 0.10, (keep existing compat) (#172) (@github-actions[bot])
• Update Project.toml for KomaMRIPlots to v0.7.6 (#173) (@beorostica)

KomaMRI v0.7.3

Diff since v0.7.2

Closed issues:

• Two definitions for DiscreteSequence #146 (@cncastillo)
• Hwloc still being used in KomaUI #144 (@cncastillo)
• Blink v0.12.6 removed functions AtomShell.isinstalled() and AtomShell.install() used in KomaMRI.jl #143 (@cncastillo)

KomaMRI v0.7.2

Diff since v0.7.1

Closed issues:

• Default number of threads for CPU parallelization (#141) (@cncastillo )

Merged pull requests:

• Literate (#140) (@beorostica)

KomaMRI v0.7.1

Diff since v0.7.0

Closed issues:

• DisplayFunctions: RF phase is incorrectly calculated (#130) @cncastillo
• DisplayFunctions: Timings of RF waveform are slightly incorrect when rf_max_samples is less than the actual number of samples (#131) @cncastillo
• Signal was being conjugated (affected "return_type" => "raw") (#129) @cncastillo
• Pulseq read_seq prints unnecessary spaces (#133) @cncastillo
• KomaUI prints some unnecessary spaces (#135) @cncastillo
• Clean /examples/ folder (#137) @cncastillo

KomaMRI v0.7.0

Diff since v0.6.7

Closed issues:

• RF implementation with GPU acceleration (#2) @cncastillo
• Documentation versions (stable & dev) (#115) @beorostica
• Move gpu function calls to simulate (#116) @cncastillo
• Solve edge-case for one acquisition sample (#117) @cncastillo
• T2 decay was incorrectly calculated for the first sample after a delay. (#118) @cncastillo
• Move get_grad and get_rfs function calls to simulate, to used them only once. (Low priority) (#119) @cncastillo
• Type stability in core simulation types and functions (Phantom, DiscreteSequence, Magnetization). (#120) @cncastillo

Merged pull requests:

• Update make.jl (#114) (@beorostica)
• CompatHelper: add new compat entry for Adapt at version 3, (keep existing compat) (#122) (@github-actions[bot])
• CompatHelper: add new compat entry for Functors at version 0.4, (keep existing compat) (#123) (@github-actions[bot])
• CompatHelper: add new compat entry for Parameters at version 0.12, (keep existing compat) (#124) (@github-actions[bot])

KomaMRI v0.6.7

Diff since v0.6.6

Closed issues:

• Margins of plot_signal are not consistent with plot_seq (#84)
• Plot functions throw error in Julia REPL (#86)
• Reconstructing without simulating first gives an error (#91)
• [Important] Simulation inconsistency in GUI due to thread racing condition (#94)
• Progress bar in GUI is not working (#95)

Merged pull requests:

• CompatHelper: bump compat for MRIReco to 0.6, (keep existing compat) (#93) (@github-actions[bot])
• Removed simulation inconsistency and other fixes (#96) (@cncastillo)
• CompatHelper: add new compat entry for Scanf at version 0.5, (keep existing compat) (#98) (@github-actions[bot])
• CompatHelper: add new compat entry for ThreadsX at version 0.1, (keep existing compat) (#99) (@github-actions[bot])
• Fix #86 (#101) (@beorostica)
• Add MRIReco v0.7 compatibility (#103) (@beorostica)
• Fix bug for Reconstruct button (#104) (@beorostica)
• Add codecov.yml configuration file (#106) (@beorostica)
• Remove target in codecov configuration (#107) (@beorostica)
• Add patch threshold to codecov settings (#108) (@beorostica)
• Set patch as informational in codecov configuration (#109) (@beorostica)
• Update API docstrings (#110) (@beorostica)
• Add 3D simulation example (#111) (@beorostica)
• Clean Packages (#112) (@beorostica)