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Merge pull request #34 from MagneticParticleImaging/nh/gpuSupport
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Add GPU support
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@nHackel
nHackel authored Jul 12, 2024
2 parents f168899 + 13b977a commit e964253
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Showing 25 changed files with 506 additions and 310 deletions.
37 changes: 37 additions & 0 deletions .buildkite/pipeline.yml
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steps:
- label: "Nvidia GPUs -- MPIReco.jl"
plugins:
- JuliaCI/julia#v1:
version: "1.10"
agents:
queue: "juliagpu"
cuda: "*"
command: |
julia --color=yes --project -e '
using Pkg
Pkg.add("TestEnv")
using TestEnv
TestEnv.activate();
Pkg.add("CUDA")
Pkg.instantiate()
include("test/gpu/cuda.jl")'
timeout_in_minutes: 30

- label: "AMD GPUs -- MPIReco.jl"
plugins:
- JuliaCI/julia#v1:
version: "1.10"
agents:
queue: "juliagpu"
rocm: "*"
rocmgpu: "*"
command: |
julia --color=yes --project -e '
using Pkg
Pkg.add("TestEnv")
using TestEnv
TestEnv.activate();
Pkg.add("AMDGPU")
Pkg.instantiate()
include("test/gpu/rocm.jl")'
timeout_in_minutes: 30
12 changes: 7 additions & 5 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "MPIReco"
uuid = "e4246700-6248-511e-8146-a1d1f47669d2"
authors = ["Tobias Knopp <tobias@knoppweb.de>"]
version = "0.5.4"
version = "0.6.0"

[deps]
DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
Expand Down Expand Up @@ -31,13 +31,14 @@ DistributedArrays = "0.6"
FFTW = "1.3"
ImageUtils = "0.2"
IniFile = "0.5"
JLArrays = "0.1"
LinearAlgebra = "1"
LinearOperators = "2.3.3"
LinearOperatorCollection = "1.2"
LinearOperators = "2.3"
LinearOperatorCollection = "2"
MPIFiles = "0.13, 0.14, 0.15, 0.16"
ProgressMeter = "1.2"
Reexport = "1.0"
RegularizedLeastSquares = "0.14"
RegularizedLeastSquares = "0.16"
SparseArrays = "1"
Statistics = "1"
ThreadPools = "2.1.1"
Expand All @@ -47,6 +48,7 @@ julia = "1.9"
[extras]
FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
JLArrays = "27aeb0d3-9eb9-45fb-866b-73c2ecf80fcb"
LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
Scratch = "6c6a2e73-6563-6170-7368-637461726353"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
Expand All @@ -55,4 +57,4 @@ ImageQualityIndexes = "2996bd0c-7a13-11e9-2da2-2f5ce47296a9"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"

[targets]
test = ["Test", "HTTP", "FileIO", "LazyArtifacts", "Scratch", "ImageMagick", "ImageQualityIndexes", "Unitful"]
test = ["Test", "HTTP", "FileIO", "LazyArtifacts", "Scratch", "ImageMagick", "ImageQualityIndexes", "Unitful", "JLArrays"]
0 test/recoPlans/MultiPatch.toml → config/MultiPatch.toml
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0 test/recoPlans/Motion.toml → config/MultiPatchMotion.toml
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98 changes: 98 additions & 0 deletions config/SinglePatch.toml
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_module = "MPIReco"
_type = "RecoPlan{SinglePatchReconstructionAlgorithm}"

[parameter]
_module = "MPIReco"
_type = "RecoPlan{SinglePatchParameters}"

[parameter.reco]
_module = "MPIReco"
_type = "RecoPlan{SinglePatchReconstructionParameter}"

[parameter.reco.sfLoad]
_module = "AbstractImageReconstruction"
_type = "RecoPlan{ProcessResultCache}"

[parameter.reco.sfLoad.param]
_module = "MPIReco"
_type = "RecoPlan{DenseSystemMatixLoadingParameter}"

[parameter.reco.sfLoad.param.freqFilter]
_module = "MPIReco"
_type = "RecoPlan{SNRThresholdFrequencyFilterParameter}"

[parameter.reco.sfLoad.param.gridding]
_module = "MPIReco"
_type = "RecoPlan{SystemMatrixGriddingParameter}"


[[parameter.reco._listener.sf]]
field = "fov"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "gridding"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterCalibFov"
[[parameter.reco._listener.sf]]
field = "center"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "gridding"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterCalibCenter"
[[parameter.reco._listener.sf]]
field = "gridsize"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "gridding"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterGridSize"
[[parameter.reco._listener.sf]]
field = "minFreq"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "freqFilter"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterMinFreq"
[[parameter.reco._listener.sf]]
field = "maxFreq"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "freqFilter"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterMaxFreq"
[[parameter.reco._listener.sf]]
field = "recChannels"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "freqFilter"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterRecChannels"

[parameter.reco.solverParams]
_module = "MPIReco"
_type = "RecoPlan{ElaborateSolverParameters}"

[parameter.pre]
_module = "AbstractImageReconstruction"
_type = "RecoPlan{ProcessResultCache}"

[parameter.pre.param]
_module = "MPIReco"
_type = "RecoPlan{CommonPreProcessingParameters}"

[parameter.post]
_module = "MPIReco"
_type = "RecoPlan{NoPostProcessing}"
70 changes: 70 additions & 0 deletions config/SinglePatchSparse.toml
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_module = "MPIReco"
_type = "RecoPlan{SinglePatchReconstructionAlgorithm}"

[parameter]
_module = "MPIReco"
_type = "RecoPlan{SinglePatchParameters}"

[parameter.reco]
_module = "MPIReco"
_type = "RecoPlan{SinglePatchReconstructionParameter}"

[parameter.reco.sfLoad]
_module = "AbstractImageReconstruction"
_type = "RecoPlan{ProcessResultCache}"

[parameter.reco.sfLoad.param]
_module = "MPIReco"
_type = "RecoPlan{SparseSystemMatrixLoadingParameter}"

[parameter.reco.sfLoad.param.freqFilter]
_module = "MPIReco"
_type = "RecoPlan{SNRThresholdFrequencyFilterParameter}"

[parameter.reco.sfLoad.param.gridding]
_module = "MPIReco"
_type = "RecoPlan{SystemMatrixGriddingParameter}"

[[parameter.reco._listener.sf]]
field = "minFreq"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "freqFilter"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterMinFreq"
[[parameter.reco._listener.sf]]
field = "maxFreq"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "freqFilter"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterMaxFreq"
[[parameter.reco._listener.sf]]
field = "recChannels"
_module = "AbstractImageReconstruction"
_type = "LinkedFieldListener"
plan = ["parameter", "reco", "sfLoad", "param", "freqFilter"]

[parameter.reco._listener.sf.fn]
_module = "MPIReco"
_type = "defaultParameterRecChannels"

[parameter.reco.solverParams]
_module = "MPIReco"
_type = "RecoPlan{ElaborateSolverParameters}"

[parameter.pre]
_module = "AbstractImageReconstruction"
_type = "RecoPlan{ProcessResultCache}"

[parameter.pre.param]
_module = "MPIReco"
_type = "RecoPlan{CommonPreProcessingParameters}"

[parameter.post]
_module = "MPIReco"
_type = "RecoPlan{NoPostProcessing}"
19 changes: 18 additions & 1 deletion src/AlgorithmInterface.jl
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Expand Up @@ -42,9 +42,26 @@ struct MixedAlgorithm <: ReconstructionAlgorithmType end
# TODO recoAlgorithmType
# TODO undefined for certain "Algorithm" components
#recoAlgorithmTypes(::Type{ConcreteRecoAlgorithm}) = SystemMatrixBasedAlgorithm()
export plandir
export planpath, plandir
plandir() = abspath(homedir(), ".mpi", "RecoPlans")

function planpath(name::AbstractString)
for dir in [joinpath(@__DIR__, "..", "config"),plandir()]
filename = joinpath(dir, string(name, ".toml"))
if isfile(filename)
return filename
end
end
throw(ArgumentError("Could not find a suitable MPI reconstruction plan with name $name.\nCustom plans can be stored in $(plandir())."))
end

export reconstruct
function reconstruct(name::AbstractString, data::MPIFile; kwargs...)
plan = loadPlan(MPIReco, name, [AbstractImageReconstruction, MPIFiles, MPIReco, RegularizedLeastSquares])
setAll!(plan; kwargs...)
return reconstruct(build(plan), data)
end

# Check if contains
isSystemMatrixBased(::T) where T <: AbstractImageReconstructionAlgorithm = recoAlgorithmTypes(T) isa SystemMatrixBasedAlgorithm
isXSpaceBased(::T) where T <: AbstractImageReconstructionAlgorithm = recoAlgorithmTypes(T) isa XSpaceBasedAlgorithm
Expand Down
3 changes: 2 additions & 1 deletion src/Algorithms/SinglePatchAlgorithms/SinglePatchAlgorithm.jl
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Expand Up @@ -44,6 +44,7 @@ function process(algo::SinglePatchReconstructionAlgorithm, params::Union{A, Proc
@warn "System matrix and measurement have different element data type. Mapping measurment data to system matrix element type."
result = map(eltype(algo.S),result)
end
result = copyto!(similar(algo.S, size(result)...), result)
return result
end

Expand All @@ -67,5 +68,5 @@ function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::Sin
end

function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchReconstructionParameter{<:SparseSystemMatrixLoadingParameter, S}) where {S}
return createLinearOperator(params.sfLoad.sparseTrafo, eltype(algo.S); shape=tuple(shape(algo.grid)...))
return process(algo, params.sfLoad, eltype(algo.S), tuple(shape(algo.grid)...))
end
16 changes: 9 additions & 7 deletions src/LeastSquares.jl
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Expand Up @@ -28,15 +28,17 @@ end
export ElaborateSolverParameters
Base.@kwdef mutable struct ElaborateSolverParameters{SL} <: AbstractSolverParameters{SL}
solver::Type{SL}
iterations::Int64=10
enforceReal::Bool=true
enforcePositive::Bool=true
iterations::Int64 = 10
enforceReal::Bool = true
enforcePositive::Bool = true
kwargWarning::Bool = true
# Union of all kwargs
normalizeReg::AbstractRegularizationNormalization = SystemMatrixBasedNormalization()
randomized::Union{Nothing, Bool} = false
randomized::Union{Nothing, Bool, Symbol} = nothing
seed::Union{Nothing, Int64} = nothing
shuffleRows::Union{Nothing, Bool} = false
rho::Union{Nothing, Float64} = nothing
normalize_rho::Union{Nothing, Bool} = nothing
vary_rho::Union{Nothing, Symbol} = nothing
theta::Union{Nothing, Float64} = nothing
restart::Union{Nothing, Symbol} = nothing
regTrafo::Union{Nothing, Vector{Union{AbstractArray, AbstractLinearOperator}}} = nothing
Expand All @@ -51,7 +53,7 @@ Base.propertynames(params::RecoPlan{ElaborateSolverParameters}) = union([:solver

getSolverKwargs(::Type{SL}) where SL <: AbstractLinearSolver = intersect(union(Base.kwarg_decl.(methods(SL))...), fieldnames(ElaborateSolverParameters))

function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::LeastSquaresParameters{SL}, u::Array) where SL
function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::LeastSquaresParameters{SL}, u::AbstractArray) where SL

N = size(params.S, 2)
M = div(length(params.S), N)
Expand Down Expand Up @@ -79,7 +81,7 @@ function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::LeastSquaresParame
if !isnothing(params.op)
d[:] = params.op*d
end
c[:, l] = real(d)
c[:, l] = Array(real(d))
end

return c
Expand Down
4 changes: 2 additions & 2 deletions src/MPIReco.jl
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Expand Up @@ -16,10 +16,10 @@ module MPIReco
using DistributedArrays
# using TensorDecompositions
using IniFile
import LinearAlgebra: ldiv!, \
import LinearAlgebra: ldiv!, \, mul!
# TODO sort out import for Base and AbstractImageReconstruction to avoid boiler plate
import Base: put!, take!
import AbstractImageReconstruction: process, parameter
import AbstractImageReconstruction: process, parameter, reconstruct
using FFTW
using LinearOperatorCollection

Expand Down
9 changes: 8 additions & 1 deletion src/SystemMatrix/SystemMatrix.jl
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Expand Up @@ -52,11 +52,12 @@ export AbstractSystemMatrixLoadingParameter
abstract type AbstractSystemMatrixLoadingParameter <: AbstractSystemMatrixParameter end

export DenseSystemMatixLoadingParameter
Base.@kwdef struct DenseSystemMatixLoadingParameter{F<:AbstractFrequencyFilterParameter, G<:AbstractSystemMatrixGriddingParameter} <: AbstractSystemMatrixLoadingParameter
Base.@kwdef struct DenseSystemMatixLoadingParameter{F<:AbstractFrequencyFilterParameter, matT <: AbstractArray, G<:AbstractSystemMatrixGriddingParameter} <: AbstractSystemMatrixLoadingParameter
freqFilter::F
gridding::G
bgCorrection::Bool = false
loadasreal::Bool = false
arrayType::Type{matT} = Array
end
function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::DenseSystemMatixLoadingParameter, sf::MPIFile)
# Construct freqFilter
Expand All @@ -66,6 +67,9 @@ end
function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::DenseSystemMatixLoadingParameter, sf::MPIFile, frequencies::Vector{CartesianIndex{2}})
S, grid = getSF(sf, frequencies, nothing; toKwargs(params)...)
@info "Loading SM"
if !isa(S, params.arrayType)
S = params.arrayType(S)
end
return S, grid
end

Expand All @@ -88,6 +92,9 @@ function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::SparseSystemMatrix
S, grid = getSF(sf, frequencies, params.sparseTrafo; toKwargs(params)...)
return S, grid
end
function process(t::Type{<:AbstractMPIRecoAlgorithm}, params::SparseSystemMatrixLoadingParameter, elType::Type{<:Number}, shape::NTuple{N, Int64}) where N
return createLinearOperator(params.sparseTrafo, elType; shape)
end

function converttoreal(S::AbstractArray{Complex{T}},f) where T
N = prod(calibSize(f))
Expand Down
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Registration pull request created: JuliaRegistries/General/110932

Tip: Release Notes

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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 v0.6.0 -m "<description of version>" e96425384f36c936002878adacfd53ac0bc5f724
git push origin v0.6.0

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