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Merge pull request #231 from cncastillo/komaio
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KomaMRIIO subpackage
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@cncastillo
cncastillo authored Dec 1, 2023
2 parents 8e6ac21 + 435f8f8 commit 879894a
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25 changes: 25 additions & 0 deletions .github/workflows/ci.yml
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Expand Up @@ -40,12 +40,26 @@ jobs:
${{ runner.os }}-test-${{ env.cache-name }}-
${{ runner.os }}-test-
${{ runner.os }}-
- name: "KomaMRICore dev setup"
shell: bash
run: |
julia --color=yes --project="KomaMRICore" -e "using Pkg; Pkg.develop(PackageSpec(; path=\"./KomaMRIIO\"));"
- uses: julia-actions/julia-buildpkg@v1
with:
project: KomaMRICore
- uses: julia-actions/julia-runtest@v1
with:
project: KomaMRICore
- name: "KomaMRIIO dev setup"
shell: bash
run: |
julia --color=yes --project="KomaMRIIO" -e "using Pkg; Pkg.develop(PackageSpec(; path=\"./KomaMRICore\"));"
- uses: julia-actions/julia-buildpkg@v1
with:
project: KomaMRIIO
- uses: julia-actions/julia-runtest@v1
with:
project: KomaMRIIO
- name: "KomaMRIPlots dev setup"
shell: bash
run: |
Expand All @@ -61,6 +75,7 @@ jobs:
shell: julia --color=yes --project {0}
run: |
using Pkg
Pkg.develop(PackageSpec(path=pwd(), subdir="KomaMRIIO"))
Pkg.develop(PackageSpec(path=pwd(), subdir="KomaMRICore"))
Pkg.develop(PackageSpec(path=pwd(), subdir="KomaMRIPlots"))
- uses: julia-actions/julia-buildpkg@v1
Expand Down Expand Up @@ -88,6 +103,13 @@ jobs:
with:
files: lcov.info
flags: plots
- uses: julia-actions/julia-processcoverage@v1
with:
directories: KomaMRIIO/src
- uses: codecov/codecov-action@v3
with:
files: lcov.info
flags: io
docs:
name: Documentation
runs-on: ubuntu-latest
Expand All @@ -99,6 +121,9 @@ jobs:
- run: |
julia --project=docs -e '
using Pkg
Pkg.develop(PackageSpec(path=pwd(), subdir="KomaMRIIO"))
Pkg.develop(PackageSpec(path=pwd(), subdir="KomaMRICore"))
Pkg.develop(PackageSpec(path=pwd(), subdir="KomaMRIPlots"))
Pkg.develop(PackageSpec(path=pwd()))
Pkg.instantiate()'
- run: |
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -2,7 +2,7 @@
*.jl.cov
*.jl.mem
.DS_Store
*Manifest.toml
**/Manifest.toml
/test/Manifest.toml
/dev/
.vscode/settings.json
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8 changes: 0 additions & 8 deletions KomaMRICore/Project.toml
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Expand Up @@ -6,14 +6,10 @@ version = "0.7.7"
[deps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
MRIBase = "f7771a9a-6e57-4e71-863b-6e4b6a2f17df"
MRIFiles = "5a6f062f-bf45-497d-b654-ad17aae2a530"
Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
Expand All @@ -24,14 +20,10 @@ ThreadsX = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d"
[compat]
Adapt = "3"
CUDA = "3, 4, 5"
FileIO = "1"
Functors = "0.4"
HDF5 = "0.16, 0.17"
Interpolations = "0.13, 0.14"
JLD2 = "0.4"
MAT = "0.10"
MRIBase = "0.3, 0.4"
MRIFiles = "0.1, 0.2"
Parameters = "0.12"
Pkg = "1.4"
ProgressMeter = "1"
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20 changes: 7 additions & 13 deletions KomaMRICore/src/KomaMRICore.jl
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Expand Up @@ -12,11 +12,9 @@ using Parameters
using Interpolations
using CUDA
#Reconstruction
using MRIBase, MRIFiles
using MRIBase
@reexport using MRIBase: Profile, RawAcquisitionData, AcquisitionData, AcquisitionHeader
@reexport using MRIFiles: ISMRMRDFile
#IO
using FileIO, HDF5, MAT, JLD2
using MAT # For loading example phantoms

global γ = 42.5774688e6; #Hz/T gyromagnetic constant for H1, JEMRIS uses 42.5756 MHz/T

Expand All @@ -29,11 +27,10 @@ include("datatypes/sequence/ADC.jl")
include("simulation/KeyValuesCalculation.jl")
include("datatypes/Sequence.jl")
include("datatypes/sequence/Delay.jl")
include("io/Pulseq.jl")
#Phantom
include("datatypes/Phantom.jl")
include("io/JEMRIS.jl")
include("io/MRiLab.jl")
#Rawdata
include("rawdata/ISMRMRD.jl")
#Simulator
include("datatypes/simulation/DiscreteSequence.jl")
include("datatypes/simulation/Spinor.jl")
Expand All @@ -43,23 +40,20 @@ include("simulation/GPUFunctions.jl")
# include("simulation/other/OffResonanceModel.jl")
include("simulation/TrapezoidalIntegration.jl")
include("simulation/SimulatorCore.jl")
include("io/ISMRMRD.jl")

#Main
export γ #gyro-magnetic ratio [Hz/T]
export Scanner, Sequence, Phantom
export Grad, RF, ADC, Delay
export Mag, dur
#Pulseq
export read_seq
#ISMRMRD
export signal_to_raw_data
#Phantom
export brain_phantom2D, brain_phantom3D, read_phantom_jemris, read_phantom_MRiLab
export brain_phantom2D, brain_phantom3D
#Spinors
export Spinor, Rx, Ry, Rz, Q, Un
#Secondary
export get_kspace, rotx, roty, rotz
#ISMRMRD
export signal_to_raw_data
#Simulator
export simulate, simulate_slice_profile

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76 changes: 76 additions & 0 deletions KomaMRICore/src/datatypes/Phantom.jl
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Expand Up @@ -390,3 +390,79 @@ function brain_phantom3D(;ss=4,start_end=[160, 200])
)
return obj
end

"""
obj = pelvis_phantom2D(; ss=4)
Creates a two-dimensional pelvis Phantom struct.
# Keywords
- `ss`: (`::Integer`, `=4`) subsampling parameter
# Returns
- `obj`: (`::Phantom`) Phantom struct
# Examples
```julia-repl
julia> obj = pelvis_phantom2D(; ss=1)
julia> pelvis_phantom2D(obj, :ρ)
```
"""
function pelvis_phantom2D(; ss=4)

# Get data from .mat file
path = @__DIR__
data = MAT.matread(path*"/phantom/pelvis2D.mat")
class = data["pelvis3D_slice"][1:ss:end,1:ss:end]

# Define spin position vectors
Δx = .5e-3*ss
M, N = size(class)
FOVx = (M-1)*Δx # [m]
FOVy = (N-1)*Δx # [m]
x = -FOVx/2:Δx:FOVx/2 # spin coordinates
y = -FOVy/2:Δx:FOVy/2 # spin coordinates
x, y = x .+ y'*0, x*0 .+ y' # grid points

# Define spin property vectors
ρ = (class.==51)*.001 .+ # Air
(class.==102)*.86 .+ # Fat
(class.==153)*.9 .+ # SoftTissue
(class.==204)*.4 .+ # SpongyBone
(class.==255)*.2 # CorticalBone
T1 = (class.==51)*.001 .+ # Air
(class.==102)*366 .+ # Fat
(class.==153)*1200 .+ # SoftTissue
(class.==204)*381 .+ # SpongyBone
(class.==255)*100 # CorticalBone
T2 = (class.==51)*.001 .+ # Air
(class.==102)*70 .+ # Fat
(class.==153)*80 .+ # SoftTissue
(class.==204)*52 .+ # SpongyBone
(class.==255)*.3 # CorticalBone
T2s = (class.==51)*.001 .+ # Air
(class.==102)*70 .+ # Fat
(class.==153)*80 .+ # SoftTissue
(class.==204)*52 .+ # SpongyBone
(class.==255)*.3 # CorticalBone
Δw_fat = -220 * 2π
Δw = (class.==102) * Δw_fat # FAT1
T1 = T1*1e-3
T2 = T2*1e-3
T2s = T2s*1e-3

# Define and return the Phantom struct
obj = Phantom{Float64}(
name = "pelvis2D",
x = y[ρ.!=0],
y = x[ρ.!=0],
z = 0*x[ρ.!=0],
ρ = ρ[ρ.!=0],
T1 = T1[ρ.!=0],
T2 = T2[ρ.!=0],
T2s = T2s[ρ.!=0],
Δw = Δw[ρ.!=0],
)
return obj
end
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2 comments on commit 879894a

@beorostica
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@JuliaRegistrator register subdir=KomaMRIIO

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Registration pull request created: JuliaRegistries/General/96325

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a KomaMRIIO-v0.7.7 -m "<description of version>" 879894a7cfd7eb3dd4d4085361c3f33f06c17516
git push origin KomaMRIIO-v0.7.7

Also, note the warning: This looks like a new registration that registers version 0.7.7.
Ideally, you should register an initial release with 0.0.1, 0.1.0 or 1.0.0 version numbers
This can be safely ignored. However, if you want to fix this you can do so. Call register() again after making the fix. This will update the Pull request.

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