Scanner object considering multiple coils#548

Draft

Stockless wants to merge 204 commits intomasterfrom

scanner-develop

Commits on Mar 14, 2025

Coil-sens on Scanner
cncastillo
committed
Delete unintended and unnecesary elements

Stockless
authored and
cncastillo
committed
coil_sens removal from Phantom structure

Stockless
authored and
cncastillo
committed

Commits on Mar 20, 2025

Correction of Scanner argument at run_spin_precession functions
Stockless
committed

Commits on Mar 26, 2025

adding specific dispatch for CPU
Stockless
committed

Commits on Mar 27, 2025

Commits on Mar 31, 2025

Commits on May 26, 2025

admission of ArbitraryRFCoils simulation without interpolation (only coils_coords at phantom positions)
Stockless
committed

Commits on May 28, 2025

Commits on Jun 17, 2025

Interpolation Incorporation
Stockless
committed

Commits on Jun 19, 2025

add coil_sens view
Stockless
committed

Commits on Jun 24, 2025

initialize interpolated_coil_sens with similar()
Stockless
committed

Commits on Jun 30, 2025

simulate with interpolation (reconstruction missing)
Stockless
committed

Commits on Jul 1, 2025

re-organize coils definition example
Stockless
committed

Commits on Jul 3, 2025

change coil_sens_recon
Stockless
committed
Modified `center-images.css` to avoid centering badges.

cncastillo
authored and
Stockless
committed
restrict PlutoPlotly to version 0.5
Stockless
committed
trivial change to test documentation
Stockless
committed
bump KomaMRIPlots to version 0.9.2
Stockless
committed
Notebook Update
Stockless
committed
hide reproducibility raw md text
Stockless
committed
update Bloch_RF_accuracy test to use DiffEq instead of pre-calculated reference values.
Stockless
committed
delete debugging test
Stockless
committed
Bloch_RF_accuracy NRMSE improve to be > 0.1
Stockless
committed
rm println
Stockless
committed
Bump julia-actions/julia-format from 3 to 4

dependabot[bot]
authored and
Stockless
committed
Initial commit

rkierulf
authored and
Stockless
committed
add -g2 to AMD and CUDA tests to see error

rkierulf
authored and
Stockless
committed
synchronize immediately after kernels finish

rkierulf
authored and
Stockless
committed
change synchronization back

rkierulf
authored and
Stockless
committed
remove -g2

rkierulf
authored and
Stockless
committed
fix sequence indexing issue

rkierulf
authored and
Stockless
committed
Adapt to KernelAbstractions 0.9.34 + clean up code

rkierulf
authored and
Stockless
committed
Use shuffle_down intrinsic for faster reduction

rkierulf
authored and
Stockless
committed
Fix typo

rkierulf
authored and
Stockless
committed
fix warp reduction

rkierulf
authored and
Stockless
committed
change default precession groupsize to 256

rkierulf
authored and
Stockless
committed
Is warp reduction actually faster?

rkierulf
authored and
Stockless
committed
Continue using warp reduction

rkierulf
authored and
Stockless
committed
Update docs

rkierulf
authored and
Stockless
committed
Debug AMDGPU error

rkierulf
authored and
Stockless
committed
Undo debug statements skip benchmarks skip ci

rkierulf
authored and
Stockless
committed
Temporarily add HIP_LAUNCH_BLOCKING

rkierulf
authored and
Stockless
committed
Print matrix values skip benchmarks

rkierulf
authored and
Stockless
committed
Remove suppress

rkierulf
authored and
Stockless
committed
Remove debug statements skip benchmarks skip ci

rkierulf
authored and
Stockless
committed
Update Phantom use on examples
Stockless
committed
Update Phantom use on tests
Stockless
committed
Update Phantom use on definitions (UI,Base,Core)
Stockless
committed
add tags to PR
Stockless
committed
Remove Kaleido_jll compat entry

cncastillo
authored and
Stockless
committed
Add "How to test contributions" in "How to contribute to Koma" documentation
Stockless
committed
Instructions less verbose
Stockless
committed
How to add a new test
Stockless
committed
Redaction corrections
Stockless
committed
julia code block correction
Stockless
committed
Generate preview
Stockless
committed
Corrected redaction according to review
Stockless
committed
Improve test-komamricore image resolution
Stockless
committed
Improved redaction based on review
Stockless
committed
add space after images
Stockless
committed
Remove unnecesary itemization
Stockless
committed
Remove CSS specification to generate space after image
Stockless
committed
First commit

pvillacorta
authored and
Stockless
committed
Commit of the following:

pvillacorta
authored and
Stockless
committed
Commit of the following:

pvillacorta
authored and
Stockless
committed
Solve bugs:

pvillacorta
authored and
Stockless
committed
Commit of the following:

pvillacorta
authored and
Stockless
committed
Commit with the following:

pvillacorta
authored and
Stockless
committed
Correct docstring

pvillacorta
authored and
Stockless
committed
Fix formatting of the '.phantom' file extension in documentation

pvillacorta
authored and
Stockless
committed
Merge branch `master` into `docs-phantom`

pvillacorta
authored and
Stockless
committed
Adapt current docs to the new v0.9.1 `Phantom`

pvillacorta
authored and
Stockless
committed
Update image source in Phantom format documentation

pvillacorta
authored and
Stockless
committed
Write the motion section and minor changes in other related sections

pvillacorta
authored and
Stockless
committed
Fix typos in lit-2-motion.jl

pvillacorta
authored and
Stockless
committed
Hide lines in lit-2-motion.jl and plot entire phantom

pvillacorta
authored and
Stockless
committed
Fix relative paths in lit-2-motion.jl for correct navigation

pvillacorta
authored and
Stockless
committed
Definitely fix relative paths in lit-2-motion.jl

pvillacorta
authored and
Stockless
committed
Update references and adjust plot heights in lit-2-motion.jl and 2-koma-base.md

pvillacorta
authored and
Stockless
committed
Fix erroneous semicolons in lit-2-motion.jl

pvillacorta
authored and
Stockless
committed
Fix cross-reference links to `KomaMRIBase.TimeCurve`

pvillacorta
authored and
Stockless
committed
Fix comment line

pvillacorta
authored and
Stockless
committed
Add section on Phantom File I/O and clarify .phantom format description

pvillacorta
authored and
Stockless
committed
Extend "Create your own Phantom" section

pvillacorta
authored and
Stockless
committed
Reduce plots height and improve introductive paragraph.

pvillacorta
authored and
Stockless
committed
Remove unnecessary example output

pvillacorta
authored and
Stockless
committed
Add sequence scripts folder and new `lit-07-RRVariability.jl` tutorial

pvillacorta
authored and
Stockless
committed
Remove CUDA import from `examples/3.tutorials/lit-07-RRVariability.jl`

pvillacorta
authored and
Stockless
committed
Rename bSSFP_cine.jl and fix include functions

pvillacorta
authored and
Stockless
committed
Update docs/Project.toml to include Plots and Printf

pvillacorta
authored and
Stockless
committed
Utils file redistribution and correct bugs that difficulted docs build

pvillacorta
authored and
Stockless
committed
Make struct definitions mutable for TimeCurve, AllSpins, SpinRange, FlowPath, Path, HeartBeat, Rotate, and Translate

pvillacorta
authored and
Stockless
committed
Finish lit-07 tutorial and redistribute /utils files

pvillacorta
authored and
Stockless
committed
Fix commands tagged with `#nb` and `#jl`

pvillacorta
authored and
Stockless
committed
Apply suggested changes, add phantom plot, resize figures

pvillacorta
authored and
Stockless
committed
Refactor displacement functions to center coordinates before rotation calculations

pvillacorta
authored and
Stockless
committed
Update rotation tests for KomaMRIBase

pvillacorta
authored and
Stockless
committed
Remove `mutable` from all the motion-related structs

pvillacorta
authored and
Stockless
committed
Correct lit-07-RRVariability.jl to modify non-mutable structs

pvillacorta
authored and
Stockless
committed
Commit of the following:

pvillacorta
authored and
Stockless
committed
News 16.Jun.2025
Stockless
committed
Update README.md

cncastillo
authored and
Stockless
committed
Add files via upload

cncastillo
authored and
Stockless
committed
Delete assets/OSI2Logo.svg

cncastillo
authored and
Stockless
committed
Add files via upload

cncastillo
authored and
Stockless
committed
Rename DIN SPEC 3105_ OSI² CAB_ 1.svg to DIN_SPEC_3105_OSI2_CAB_1.svg

cncastillo
authored and
Stockless
committed
Added OSI2 badge

cncastillo
authored and
Stockless
committed
Added OSI2 badge properly

cncastillo
authored and
Stockless
committed
Delete assets/DIN_SPEC_3105_OSI2_CAB_1.svg

cncastillo
authored and
Stockless
committed
fix tabulation errors
Stockless
committed
Fixed inconsistencies in header capitalization, found and fixed various typos and unclear language

KookiesNKareem
authored and
Stockless
committed
Fixed more capitalization inconsistencies and typos. Clarified the sync changes step in "How To Commit"

KookiesNKareem
authored and
Stockless
committed
Unsafe_blink macro implementation
Stockless
committed
test new function instead of macro
Stockless
committed
using blink outside linux condition
Stockless
committed
"static if" and rm innecesary export
Stockless
committed
include macos in temporary fix
Stockless
committed
add sleep after window generation
Stockless
committed
temporary change
Stockless
committed
Always return window.

cncastillo
authored and
Stockless
committed
Just import Blink.

cncastillo
authored and
Stockless
committed
Always return window.

cncastillo
authored and
Stockless
committed
test using Blink.Window directly
Stockless
committed
window without arguments
Stockless
committed
replace setup-julia@v2 with latest
Stockless
committed
Add lynx for debugging electron
Stockless
committed
test sleep on ExportUIFunctions.jl
Stockless
committed
add actions to test
Stockless
committed
sleep closer to window generation
Stockless
committed
skip macos ui tests
Stockless
committed
fix if statement
Stockless
committed
using Blink outside condition
Stockless
committed
restablish commented sections of tests
Stockless
committed
comment unnecesary "include"s
Stockless
committed
final changes to temporary fix
Stockless
committed
Update lit-01-FID.jl

cncastillo
authored and
Stockless
committed
modified duration = dur(seq)
Stockless
committed
Reformat test

cncastillo
authored and
Stockless
committed
Coil-sens on Scanner

cncastillo
authored and
Stockless
committed
Delete unintended and unnecesary elements
Stockless
committed
remove unnecesary example file, remove unnecesary packages call and add a getprperty to the Scanner.limits.symbol values.
Stockless
committed
add a get_n_coils function, re-add KomaMRI subpackages to KomaMRI [compact] and another small changes
Stockless
committed
Correction of Scanner argument at run_spin_precession functions
Stockless
committed
Moved coils_sens interpolation to SimulatorCore
Stockless
committed
Fix sys::Scanner -> sys::Scanner{T}
Stockless
committed
Interpolation Incorporation
Stockless
committed
rebase remaining fixes
Stockless
committed
Merge branch 'master' into scanner-develop
Stockless
authored
complete rebase
Stockless
committed

Commits on Jul 4, 2025

3D interpolation
Stockless
committed

Commits on Jul 14, 2025

CompatHelper: bump compat for oneAPI in [weakdeps] to 2 for package KomaMRICore, (keep existing compat)

CompatHelper Julia
authored and
Stockless
committed
Update README.md [skip CI]

cncastillo
authored and
Stockless
committed
Update README.md [skip CI]

cncastillo
authored and
Stockless
committed
CompatHelper: bump compat for AcceleratedKernels to 0.4 for package KomaMRICore, (keep existing compat)

CompatHelper Julia
authored and
Stockless
committed
Update runbenchmarks.jl
Stockless
committed
update enviroments for buildkite test
Stockless
committed
Fix environment in which tests are run

cncastillo
authored and
Stockless
committed
Test environment change

cncastillo
authored and
Stockless
committed
Update test environment setup (again)

cncastillo
authored and
Stockless
committed
Last update to test environment setup

cncastillo
authored and
Stockless
committed
Add GPU backend to test environment

cncastillo
authored and
Stockless
committed
Fix GPU tests re-resolving test environment

cncastillo
authored and
Stockless
committed
KomaMRIBase dev'ed in project environment

cncastillo
authored and
Stockless
committed
Dev packages to test environment

cncastillo
authored and
Stockless
committed
Only use tests environment for GPU tests

cncastillo
authored and
Stockless
committed
Test environment setup different for 1.10

cncastillo
authored and
Stockless
committed
Fix oneAPI bool indexing issues

cncastillo
authored and
Stockless
committed

Commits on Jul 21, 2025

CompatHelper: bump compat for PlutoPlotly in [weakdeps] to 0.6 for package KomaMRIPlots, (keep existing compat)

CompatHelper Julia
authored and
Stockless
committed
Update runbenchmarks.jl
Stockless
committed
update enviroments for buildkite test
Stockless
committed
Fix environment in which tests are run

cncastillo
authored and
Stockless
committed
Test environment change

cncastillo
authored and
Stockless
committed
Update test environment setup (again)

cncastillo
authored and
Stockless
committed
Last update to test environment setup

cncastillo
authored and
Stockless
committed
Add GPU backend to test environment

cncastillo
authored and
Stockless
committed
Fix GPU tests re-resolving test environment

cncastillo
authored and
Stockless
committed
KomaMRIBase dev'ed in project environment

cncastillo
authored and
Stockless
committed
Dev packages to test environment

cncastillo
authored and
Stockless
committed
Only use tests environment for GPU tests

cncastillo
authored and
Stockless
committed
Test environment setup different for 1.10

cncastillo
authored and
Stockless
committed
Fixes oneAPI indexing issues.

cncastillo
authored and
Stockless
committed
Add tags to Buildkite codecov process

cncastillo
authored and
Stockless
committed
CompatHelper: bump compat for Interpolations to 0.16 for package KomaMRIPlots, (keep existing compat)

CompatHelper Julia
authored and
Stockless
committed
CompatHelper: bump compat for Interpolations to 0.16 for package KomaMRIBase, (keep existing compat)

CompatHelper Julia
authored and
Stockless
committed
Update README.md [skip CI]

cncastillo
authored and
Stockless
committed
Flags added to official julia-coverage

cncastillo
authored and
Stockless
committed
Update README.md [skip CI]

cncastillo
authored and
Stockless
committed

Commits on Jul 23, 2025

interpolate 2D/3D cases
Stockless
committed

Commits on Jul 30, 2025

Replace coil_tange example definition
Stockless
committed

Commits on Aug 18, 2025

`sig[1]` fill correction
Stockless
committed

Commits on Aug 28, 2025

Commits on Sep 1, 2025

phantom with complex rho
Stockless
committed

Commits on Sep 2, 2025

Merge branch 'master' into scanner-develop
Stockless
committed