KomaMRIIO subpackage

.github/workflows/ci.yml

@@ -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: |
@@ -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
@@ -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
@@ -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: |

.gitignore

@@ -2,7 +2,7 @@
 *.jl.cov
 *.jl.mem
 .DS_Store
-*Manifest.toml
+**/Manifest.toml
 /test/Manifest.toml
 /dev/
 .vscode/settings.json

CONTRIBUTING.md

@@ -0,0 +1,64 @@
+# Contributing Guidelines
+
+Thanks for taking the time to contribute to KomaMRI! ❤️
+
+We appreciate your interest in improving this project. Before you start contributing, please take a moment to review the following guidelines.
+
+
+## Reporting Issues
+
+First off, we assume that you have read the available [Documentation](https://cncastillo.github.io/KomaMRI.jl).
+
+Before you report an issue, it is best to search for existing [Issues](https://github.com/cncastillo/KomaMRI.jl/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue.
+
+If you then still feel the need to report an issue, we recommend the following:
+
+- Open an [Issue](https://github.com/cncastillo/KomaMRI.jl/issues/new).
+- Provide as much context as you can about what you're running into.
+- Provide project and platform versions, depending on what seems relevant.
+
+We will then take care of the issue as soon as possible.
+
+
+## How to Contribute
+
+1. **Fork KomaMRI Repository**: Fork the [KomaMRI.jl repository](https://github.com/cncastillo/KomaMRI.jl) to your GitHub account to create a personal copy.
+
+2. **Clone Fork to Local Machine**: Clone your fork of the repository to your local machine using the following Git command:
+
+   ```bash
+   git clone [email protected]:<your-username>/KomaMRI.jl.git
+   ```
+
+3. **Create Contribution Branch**: Create a new branch dedicated to your contribution within the cloned repository.
+
+   ```bash
+   git checkout -b feature/your-feature
+   ```
+
+4. **Implement Code Changes**: Introduce your modifications, ensuring adherence to the [Julia Blue Style Guidelines](https://github.com/invenia/BlueStyle). For new features, include informative comments, docstrings, and consider enriching the documentation with relevant examples.
+
+5. **Validate Changes with Tests**: Execute existing tests to verify the compatibility of your alterations with the current functionality. If applicable, incorporate additional tests to validate your new contributions.
+
+6. **Commit Code Changes**: Commit your modifications with a precise and descriptive commit message using the following Git command:
+
+   ```bash
+   git commit -m "Add a concise summary of your changes"
+   ```
+
+7. **Push Changes to Your Fork**: Push your committed changes to the corresponding branch on your forked repository:
+
+   ```bash
+   git push origin feature/your-feature
+   ```
+
+8. **Initiate Pull Request (PR)**: Propose your changes by creating a pull request against the `master` branch of the KomaMRI repository. Provide a clear title and a detailed description of your modifications. Ensure that your pull request is linked to an issue by including its #ID in the description.
+
+9. **Undergo Code Review**: Subject your code to review by maintainers, who will provide feedback and may request further adjustments before merging.
+
+
+## License
+
+By contributing to KomaMRI, you agree that your contributions will be licensed under the [MIT License](https://github.com/cncastillo/KomaMRI.jl/blob/master/LICENSE).
+
+Thank you for contributing to KomaMRI! 🌟

KomaMRICore/Project.toml

@@ -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"
@@ -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"

KomaMRICore/src/KomaMRICore.jl

@@ -12,11 +12,9 @@ using Parameters
 using Interpolations
 using CUDA
 #Reconstruction
-using MRIBase, MRIFiles
-@reexport using MRIBase: Profile, RawAcquisitionData, AcquisitionData, AcquisitionHeader
-@reexport using MRIFiles: ISMRMRDFile
-#IO
-using FileIO, HDF5, MAT, JLD2
+using MRIBase
+@reexport using MRIBase: EncodingCounters, Profile, RawAcquisitionData, AcquisitionData, AcquisitionHeader
+using MAT   # For loading example phantoms
 
 global γ = 42.5774688e6; #Hz/T gyromagnetic constant for H1, JEMRIS uses 42.5756 MHz/T
 
@@ -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")
@@ -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
 

KomaMRICore/src/datatypes/Phantom.jl

@@ -390,3 +390,79 @@
     )
 	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

KomaMRICore/src/io/ISMRMRD.jl → KomaMRICore/src/rawdata/ISMRMRD.jl

@@ -1,3 +1,12 @@
+"""
+It is the same as defined in MRIFiles without the need to import MRIFiles
+"""
+struct Limit
+    minimum::Int
+    maximum::Int
+    center::Int
+end
+
 """
     raw = signal_to_raw_data(signal, seq; phantom_name, sys, sim_params)
 
@@ -79,7 +88,7 @@ function signal_to_raw_data(
         "reconFOV"                       => [FOVx, FOVy, 1.0],    #reconSpace>fieldOfView_mm
         "encodedSize"                    => [Nx, Ny, 1],            #encodedSpace>matrixSize
         "reconSize"                      => [Nx+Nx%2, Ny+Ny%2, 1],  #reconSpace>matrixSize
-        #encodingLimits>
+        #encoding limits
         "enc_lim_kspace_encoding_step_1" => Limit(0, Nx-1, ceil(Int, Nx / 2)),   #min, max, center, e.g. phase encoding line number
         "enc_lim_kspace_encoding_step_2" => Limit(0, 0, 0),     #min, max, center, e.g. partition encoding number
         "enc_lim_average"                => Limit(0, 0, 0),     #min, max, center, e.g. signal average number
@@ -99,7 +108,7 @@ function signal_to_raw_data(
 
     #Then, we define the Profiles
     profiles = Profile[]
-    t_acq = get_adc_sampling_times(seq)
+    t_acq = KomaMRICore.get_adc_sampling_times(seq)
     Nadcs = sum(is_ADC_on.(seq))
     NadcsPerImage = floor(Int, Nadcs / Nz)
     scan_counter = 0

KomaMRICore/src/simulation/SimulatorCore.jl

@@ -262,7 +262,7 @@
     seq::Sequence;
     z=range(-2.e-2, 2.e-2, 200), sim_params=Dict{String,Any}("Δt_rf" => 1e-6)
 )
-    sim_params["return_type"] = "state"
+    sim_params["return_type"] = SpinsStateSimOutput()
     sys = Scanner()
     obj = Phantom{Float64}(x=zeros(size(z)), z=Array(z))
     mag = simulate(obj, seq, sys; sim_params)

KomaMRICore/test/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+KomaMRIIO = "fcf631a6-1c7e-4e88-9e64-b8888386d9dc"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"