Merge branch 'master' into 3D_recon

Conflicts: (fixed)
KomaMRICore/src/rawdata/ISMRMRD.jl

Changes to be committed:
modified:   KomaMRIBase/Project.toml
modified:   KomaMRIBase/src/KomaMRIBase.jl
modified:   KomaMRICore/Project.toml
modified:   KomaMRICore/src/KomaMRICore.jl
modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   KomaMRICore/src/simulation/SimulatorCore.jl
modified:   KomaMRICore/test/Project.toml
deleted:    KomaMRICore/test/initialize.jl
new file:   KomaMRICore/test/initialize_backend.jl
modified:   KomaMRICore/test/runtests.jl
modified:   KomaMRIFiles/Project.toml
modified:   KomaMRIFiles/src/KomaMRIFiles.jl
modified:   KomaMRIFiles/src/Phantom/Phantom.jl
modified:   KomaMRIPlots/Project.toml
modified:   KomaMRIPlots/src/KomaMRIPlots.jl
modified:   Project.toml
modified:   src/KomaMRI.jl
modified:   src/KomaUI.jl

KomaMRIBase/Project.toml

@@ -8,17 +8,15 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
 MRIBase = "f7771a9a-6e57-4e71-863b-6e4b6a2f17df"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 
 [compat]
 Interpolations = "0.13, 0.14, 0.15"
 MAT = "0.10"
 MRIBase = "0.4"
 Parameters = "0.12"
-Pkg = "1.4"
 Reexport = "1"
 julia = "1.9"
 
 [workspace]
-projects = ["test"]
+projects = ["test"]

KomaMRIBase/src/KomaMRIBase.jl

@@ -64,10 +64,4 @@ export get_Mk, get_kspace, get_M0, get_M1, get_M2
 include("sequences/PulseDesigner.jl")
 export PulseDesigner
 
-#Package version, KomaMRIBase.__VERSION__
-using Pkg
-__VERSION__ = VersionNumber(
-    Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))["version"]
-)
-
 end # module KomaMRIBase

KomaMRICore/Project.toml

@@ -8,7 +8,6 @@ Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 ThreadsX = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d"
@@ -26,19 +25,18 @@ KomaMetalExt = "Metal"
 KomaoneAPIExt = "oneAPI"
 
 [compat]
-Adapt = "3, 4"
 AMDGPU = "0.9"
+Adapt = "3, 4"
 CUDA = "3, 4, 5"
 Functors = "0.4"
 KernelAbstractions = "0.9"
 KomaMRIBase = "0.9"
 Metal = "1"
-oneAPI = "1"
-Pkg = "1.4"
 ProgressMeter = "1"
 Reexport = "1"
 ThreadsX = "0.1"
 julia = "1.9"
+oneAPI = "1"
 
 [workspace]
 projects = ["test"]

KomaMRICore/src/KomaMRICore.jl

@@ -30,8 +30,4 @@ export simulate, simulate_slice_profile, default_sim_params
 # Spinors
 export Spinor, Rx, Ry, Rz, Q, Un
 
-#Package version, KomaMRICore.__VERSION__
-using Pkg
-__VERSION__ = VersionNumber(Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))["version"])
-
 end

KomaMRICore/src/rawdata/ISMRMRD.jl

@@ -82,8 +82,7 @@ function signal_to_raw_data(
     phantom_name="Phantom", sys=Scanner(), sim_params=Dict{String,Any}(), ndims=2, use_ndseq=true
 )
     version = string(VersionNumber(Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "..", "Project.toml"))["version"]))
-
-    #Estimate sequence reconstruction dimension, using seq.DEF and potentially other information
+    #Number of samples and FOV
     Nd_seq, Nx, Ny, Nz, Ns, FOVx, FOVy, FOVz, Δx, ktraj = estimate_seq_recon_dimension(seq; sim_params)
     if use_ndseq
         if ndims != Nd_seq; @warn("Using estimated dimension of $Nd_seq for .mrd file."); ndims = Nd_seq; end
@@ -204,7 +203,7 @@ function signal_to_raw_data(
                 Float32.((0, 0, 0)), #patient_table_position float32x3: Patient table off-center
                 EncodingCounters( #idx uint16x17: Encoding loop counters
                     UInt16(ny), #kspace_encode_step_1 uint16: e.g. phase encoding line number
-                    UInt16(nz), #kspace_encode_step_2 uint16: e.g. partition encoding number
+                    UInt16(nz), #slice uint16: e.g. imaging slice number
                     UInt16(0),  #average uint16: e.g. signal average number
                     UInt16(ns), #slice uint16: e.g. imaging slice number
                     UInt16(0),  #contrast uint16: e.g. echo number in multi-echo
@@ -231,7 +230,7 @@ function signal_to_raw_data(
             end
             ny = ny % Ny
             if scan_counter % NroPerPE2 == 0
-                nz += 1 #another kspace_encode_step_2
+                nz += 1 #another image
             end
             nz = nz % Nz
             if  scan_counter % NroPerSlice == 0

KomaMRICore/src/simulation/SimulatorCore.jl

@@ -368,7 +368,7 @@ function simulate(
 
     # Simulation
     @info "Running simulation in the $(backend isa KA.GPU ? "GPU ($gpu_name)" : "CPU with $(sim_params["Nthreads"]) thread(s)")" koma_version =
-        __VERSION__ sim_method = sim_params["sim_method"] spins = length(obj) time_points = length(
+        pkgversion(@__MODULE__) sim_method = sim_params["sim_method"] spins = length(obj) time_points = length(
         seqd.t
     ) adc_points = Ndims[1]
     @time timed_tuple = @timed run_sim_time_iter!(

KomaMRICore/test/Project.toml

@@ -3,8 +3,11 @@ HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
 KomaMRICore = "4baa4f4d-2ae9-40db-8331-a7d1080e3f4e"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
+
+[preferences.KomaMRICore]
+test_backend = "CPU"

KomaMRICore/test/initialize_backend.jl

@@ -0,0 +1,27 @@
+# Filtering ARGS (useful for VSCode testing)
+AVAILABLE_GPU_BACKENDS = ["CUDA", "AMDGPU", "Metal", "oneAPI"]
+TEST_BACKENDS = filter(x->x in [AVAILABLE_GPU_BACKENDS; "CPU"], ARGS)
+# Use package preferences if test_args are not specified
+if isempty(TEST_BACKENDS)
+    using Preferences
+    TEST_BACKENDS = [load_preference(KomaMRICore, "test_backend", "CPU")]
+    @info "Using [preferences.KomaMRICore]." backend=first(TEST_BACKENDS)
+else
+    @info "Using test_args" backend=first(TEST_BACKENDS)
+end
+# For testing with CUDA:   ] add CUDA   to KomaMRICore/test/Project.toml
+# For testing with AMDGPU: ] add AMDGPU to KomaMRICore/test/Project.toml
+# For testing with Metal:  ] add Metal  to KomaMRICore/test/Project.toml
+# For testing with oneAPI: ] add oneAPI to KomaMRICore/test/Project.toml
+USE_GPU = any(AVAILABLE_GPU_BACKENDS .∈ Ref(TEST_BACKENDS))
+if "CUDA" in TEST_BACKENDS
+    using CUDA
+elseif "AMDGPU" in TEST_BACKENDS
+    using AMDGPU
+elseif "Metal" in TEST_BACKENDS
+    using Metal
+elseif "oneAPI" in TEST_BACKENDS
+    using oneAPI
+else
+    @info "CPU using $(Threads.nthreads()) thread(s)" maxlog=1
+end

KomaMRICore/test/runtests.jl

@@ -1,22 +1,36 @@
 using TestItems, TestItemRunner
 
-### NOTE: by default, tests are run on the CPU with the number of threads set to 
-#   Threads.nthreads(). To run on a specific GPU backend, add the name of the 
+### NOTE: by default, tests are run on the CPU with the number of threads set to
+#   Threads.nthreads(). To run on a specific GPU backend, add the name of the
 #   backend package ("AMDGPU", "CUDA", "Metal", or "oneAPI") to the test/Project.toml
 #   file in KomaMRICore and pass the name as a test argument.
-#   
+#
 #   Example:
 #
 #   import Pkg
 #   Pkg.test("KomaMRICore"; test_args=["CUDA"])
 #
-#   To run on the cpu with a specific number of threads, pass the number of threads 
+#   To run on the cpu with a specific number of threads, pass the number of threads
 #   as a julia argument.
 #
 #   Example:
-#   
+#
 #   import Pkg
 #   Pkg.test("KomaMRICore"; julia_args=`--threads=4`)
+#
+#   For changing the default backend used for testing,
+#   modify the [preferences.KomaMRICore] section in the test/Project.toml:
+#
+#     [preferences.KomaMRICore]
+#     test_backend = "CPU"
+#
+#   For the backend preference to take effect, you need to:
+#   - REPL testing: No action needed. `] test` should pick up the preference right away.
+#   - VSCode testing: You need to restart VSCode.
+#
+#   Sadly, LocalPreferences.toml are not picked up by VScode (that could be .gitignore'd),
+#   so we had put them into the test/Project.toml.
+#
 ###
 
 #Environment variable set by CI
@@ -158,7 +172,7 @@ end
 # Test ISMRMRD
 @testitem "signal_to_raw_data" tags=[:core] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
 
     seq = PulseDesigner.EPI_example()
     sys = Scanner()
@@ -188,7 +202,7 @@ end
 
 @testitem "Bloch" tags=[:important, :core] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
     include(joinpath(@__DIR__, "test_files", "utils.jl"))
 
     sig_jemris = signal_sphere_jemris()
@@ -211,7 +225,7 @@ end
 
 @testitem "Bloch_RF_accuracy" tags=[:important, :core] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
 
     Tadc = 1e-3
     Trf = Tadc
@@ -258,7 +272,7 @@ end
 
 @testitem "Bloch_phase_compensation" tags=[:important, :core] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
 
     Tadc = 1e-3
     Trf = Tadc
@@ -289,10 +303,10 @@ end
 
 @testitem "Bloch SimpleMotion" tags=[:important, :core, :skipci] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
     include(joinpath(@__DIR__, "test_files", "utils.jl"))
 
-    sig_jemris = signal_brain_motion_jemris()  
+    sig_jemris = signal_brain_motion_jemris()
     seq = seq_epi_100x100_TE100_FOV230()
     sys = Scanner()
     obj = phantom_brain_simple_motion()
@@ -309,10 +323,10 @@ end
 
 @testitem "Bloch ArbitraryMotion"  tags=[:important, :core, :skipci] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
     include(joinpath(@__DIR__, "test_files", "utils.jl"))
 
-    sig_jemris = signal_brain_motion_jemris()  
+    sig_jemris = signal_brain_motion_jemris()
     seq = seq_epi_100x100_TE100_FOV230()
     sys = Scanner()
     obj = phantom_brain_arbitrary_motion()
@@ -329,15 +343,15 @@ end
 
 @testitem "BlochDict" tags=[:important, :core] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
     include(joinpath(@__DIR__, "test_files", "utils.jl"))
 
     seq = seq_epi_100x100_TE100_FOV230()
     obj = Phantom{Float64}(x=[0.], T1=[1000e-3], T2=[100e-3])
     sys = Scanner()
     sim_params = Dict(
-        "gpu"=>USE_GPU, 
-        "sim_method"=>KomaMRICore.Bloch(), 
+        "gpu"=>USE_GPU,
+        "sim_method"=>KomaMRICore.Bloch(),
         "return_type"=>"mat")
     sig = @suppress simulate(obj, seq, sys; sim_params)
     sig = sig / prod(size(obj))
@@ -353,7 +367,7 @@ end
 
 @testitem "simulate_slice_profile" tags=[:core] begin
     using Suppressor
-    include("initialize.jl")
+    include("initialize_backend.jl")
 
     # This is a sequence with a sinc RF 30° excitation pulse
     sys = Scanner()
@@ -380,24 +394,25 @@ end
 @testitem "GPU Functions" tags=[:core] begin
     using Suppressor
     import KernelAbstractions as KA
-    include("initialize.jl")
+    include("initialize_backend.jl")
 
     x = ones(Float32, 1000)
+
     @suppress begin
-        y = x |> gpu
         if USE_GPU
+            y = x |> gpu
             @test KA.get_backend(y) isa KA.GPU
             y = y |> cpu
             @test KA.get_backend(y) isa KA.CPU
         else
             # Test that gpu and cpu are no-ops
+            y = x |> gpu
             @test y == x
             y = y |> cpu
             @test y == x
         end
     end
 
-
     @suppress print_devices()
     @test true
-end
+end

KomaMRIFiles/Project.toml

@@ -10,7 +10,6 @@ InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
 MRIFiles = "5a6f062f-bf45-497d-b654-ad17aae2a530"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Scanf = "6ef1bc8b-493b-44e1-8d40-549aa65c4b41"
 
@@ -21,10 +20,9 @@ InteractiveUtils = "1"
 KomaMRIBase = "0.9"
 MAT = "0.10"
 MRIFiles = "0.1, 0.2, 0.3"
-Pkg = "1.4"
 Reexport = "1"
 Scanf = "0.5"
 julia = "1.9"
 
 [workspace]
-projects = ["test"]
+projects = ["test"]

KomaMRIFiles/src/KomaMRIFiles.jl

@@ -17,8 +17,4 @@ include("Phantom/Phantom.jl")
 export read_seq                                                                     # Pulseq
 export read_phantom_jemris, read_phantom_MRiLab, read_phantom, write_phantom        # Phantom
 
-# Package version: KomaMRIFiles.__VERSION__
-using Pkg
-__VERSION__ = VersionNumber(Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))["version"])
-
 end # module KomaMRIFiles

KomaMRIFiles/src/Phantom/Phantom.jl

@@ -70,7 +70,7 @@ function import_motion!(
     for key in keys(types_group)
         type_group = types_group[key]
         type_str = split(key, "_")[2]
-        @assert type_str in last.(split.(string.(subtypes(SimpleMotionType)), ".")) "Simple Motion Type: $(type_str) has not been implemented in KomaMRIBase $(KomaMRIBase.__VERSION__)"
+        @assert type_str in last.(split.(string.(subtypes(SimpleMotionType)), ".")) "Simple Motion Type: $(type_str) has not been implemented in KomaMRIBase $(pkgversion(KomaMRIBase))"
         for SMT in subtypes(SimpleMotionType)
             args = []
             if type_str == last(split(string(SMT), "."))
@@ -111,7 +111,7 @@ function write_phantom(
     # Create HDF5 phantom file
     fid = h5open(filename, "w")
     # Root attributes
-    HDF5.attributes(fid)["Version"] = string(KomaMRIFiles.__VERSION__)
+    HDF5.attributes(fid)["Version"] = string(pkgversion(KomaMRIFiles))
     HDF5.attributes(fid)["Name"] = obj.name
     HDF5.attributes(fid)["Ns"] = length(obj.x)
     dims = KomaMRIBase.get_dims(obj)