Merge remote-tracking branch 'origin/master' into JA/sm-whitening-weights

jusack · jusack · commit b1ce1564b245 · 2026-06-28T13:04:24.000+02:00
diff --git a/.github/workflows/Semgrep.yml b/.github/workflows/Semgrep.yml
@@ -24,18 +24,18 @@ jobs:
     steps:
         # Checkout the repository.
       - name: Clone source code
-        uses: actions/checkout@v6
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
         # Checkout custom rules
       - name: Checkout custom rules
-        uses: actions/checkout@v6
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           repository: JuliaComputing/semgrep-rules-julia
           ref: main
           path: ./JuliaRules
 
         # Prepare Python
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: '3.10'
 
@@ -54,13 +54,13 @@ jobs:
                 --exclude=JuliaRules
     
       - name: Save Semgrep report
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
         with:
           name: report.sarif
           path: report.sarif
       
       - name: Upload Semgrep report
-        uses: github/codeql-action/upload-sarif@v4
+        uses: github/codeql-action/upload-sarif@4e94bd11f71e507f7f87df81788dff88d1dacbfb # v4.34.1
         with:
           sarif_file: report.sarif
           category: semgrep
diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -9,7 +9,7 @@ jobs:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
-      - uses: JuliaRegistries/TagBot@v1
+      - uses: JuliaRegistries/TagBot@bdfeaa1ff40e0ea449f9539aa21b2e587431ed49 # v1.24.6
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -26,12 +26,12 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v6
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: julia-actions/setup-julia@4c0cb0fce8556fdb04a90347310e5db8b1f98fb9 # v2.7.0
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v5
+      - uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         env:
           cache-name: cache-artifacts
         with:
@@ -41,10 +41,10 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-      - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v5
+      - uses: julia-actions/julia-buildpkg@e3eb439fad4f9aba7da2667e7510e4a46ebc46e1 # v1.7.0
+      - uses: julia-actions/julia-runtest@d60b785c6f2bdf4ebfb18b2b6f7d93b7dfb0efe3 # v1.11.4
+      - uses: julia-actions/julia-processcoverage@03114f09f119417c3242a9fb6e0b722676aedf38 # v1.2.2
+      - uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
@@ -53,8 +53,8 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: julia-actions/setup-julia@4c0cb0fce8556fdb04a90347310e5db8b1f98fb9 # v2.7.0
         with:
           version: '1'
       - run: |
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "MPIReco"
 uuid = "e4246700-6248-511e-8146-a1d1f47669d2"
 authors = ["Tobias Knopp <tobias@knoppweb.de>"]
-version = "0.9.5"
+version = "0.9.7"
 
 [deps]
 AbstractImageReconstruction = "a4b4fdbf-6459-4ec9-990d-77e1fa24a91b"
@@ -56,7 +56,7 @@ LRUCache = "1.6"
 LinearAlgebra = "1"
 LinearOperatorCollection = "2.1"
 LinearOperators = "2.3"
-MPIFiles = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18"
+MPIFiles = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19"
 ProgressMeter = "1.2"
 Reexport = "1.0"
 RegularizedLeastSquares = "0.16"
diff --git a/docs/src/literate/explanations/recoplans.jl b/docs/src/literate/explanations/recoplans.jl
@@ -27,7 +27,7 @@ plan = toPlan(parameter)
 plan.frames = missing
 
 # Or use the `clear!` method, which preserves the structure of a blueprint by default:
-clear!(plan)
+AbstractImageReconstruction.clear!(plan)
 
 # `RecoPlans` can be written to and read from files:
 plan.frames = 1:42
diff --git a/src/Algorithms/HandsFreeAlgorithms/HandsFreeSinglePatch.jl b/src/Algorithms/HandsFreeAlgorithms/HandsFreeSinglePatch.jl
@@ -34,10 +34,10 @@ function process(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchHa
   return gridresult(result, algo.grid, algo.sf)
 end
 
-function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchHandsFreeReconstructionParameter{<:DenseSystemMatixLoadingParameter, S}) where {S}
+function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchHandsFreeReconstructionParameter)
   return nothing
 end
 
-function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchHandsFreeReconstructionParameter{<:SparseSystemMatrixLoadingParameter, S}) where {S}
+function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchHandsFreeReconstructionParameter{<:SparseSystemMatrixLoadingParameter})
   return process(algo, params.sfLoad, eltype(algo.S), algo.arrayType, tuple(shape(algo.grid)...))
 end
diff --git a/src/Algorithms/SinglePatchAlgorithms/SinglePatchAlgorithm.jl b/src/Algorithms/SinglePatchAlgorithms/SinglePatchAlgorithm.jl
@@ -80,10 +80,10 @@ function process(algo::SinglePatchReconstructionAlgorithm, params::Union{W, Proc
   return algo.weights
 end
 
-function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchReconstructionParameter{<:DenseSystemMatixLoadingParameter, S}) where {S}
+function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchReconstructionParameter)
   return nothing
 end
 
-function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchReconstructionParameter{<:SparseSystemMatrixLoadingParameter, S}) where {S}
+function getLinearOperator(algo::SinglePatchReconstructionAlgorithm, params::SinglePatchReconstructionParameter{<:SparseSystemMatrixLoadingParameter})
   return process(algo, params.sfLoad, algo.sf, eltype(algo.S), algo.arrayType, tuple(shape(algo.grid)...))
 end
diff --git a/src/SystemMatrix/SMExtrapolation.jl b/src/SystemMatrix/SMExtrapolation.jl
@@ -216,7 +216,7 @@ function extrapolateSM(SM::AbstractMatrix, grid::RegularGridPositions, ex_size::
             next!(p)
         end
 		extrfov = (2 .* [ex_size[1], ex_size[2], ex_size[3]] .* (grid.fov ./ grid.shape)) .+ grid.fov
-		extrgrid = RegularGridPositions{Float64}([M1,M2,M3], extrfov, grid.center, grid.sign)
+		extrgrid = RegularGridPositions([M1,M2,M3], extrfov, grid.center, grid.sign)
         extrSM = transposed ? transpose(reshape(S_extr[1+Int(P1/2):end-Int(P1/2),1+Int(P2/2):end-Int(P2/2),1+Int(P3/2):end-Int(P3/2),:],(M1*M2*M3,K))) : reshape(S_extr[1+Int(P1/2):end-Int(P1/2),1+Int(P2/2):end-Int(P2/2),1+Int(P3/2):end-Int(P3/2),:],(M1*M2*M3,K))
 		return extrSM,extrgrid
     else
@@ -235,7 +235,7 @@ function extrapolateSM(SM::AbstractMatrix, grid::RegularGridPositions, ex_size::
             next!(p)
         end
 		extrfov = (2 .* [ex_size[1], ex_size[2], 0] .* (grid.fov ./ grid.shape)) .+ grid.fov
-		extrgrid = RegularGridPositions{Float64}([M1,M2,1], extrfov, grid.center, grid.sign)
+		extrgrid = RegularGridPositions([M1,M2,1], extrfov, grid.center, grid.sign)
 		extrSM = transposed ? transpose(reshape(S_extr[1+Int(P1/2):end-Int(P1/2),1+Int(P2/2):end-Int(P2/2),1,:],(M1*M2,K))) : reshape(S_extr[1+Int(P1/2):end-Int(P1/2),1+Int(P2/2):end-Int(P2/2),1,:],(M1*M2,K))
         return extrSM,extrgrid
     end
diff --git a/src/SystemMatrix/SystemMatrix.jl b/src/SystemMatrix/SystemMatrix.jl
@@ -226,9 +226,10 @@ function getSF(bSF::MPIFile,saveto::String;recChannels=1:numReceivers(bSF),kargs
     bG = params[:measData][acqNumFGFrames(bSF)+1:end,:,:,:]
     params[:measData]=vcat(reshape(S,size(S,1),Int(size(S,2)/3),3,1),bG)
     params[:acqNumFrames]=size(vcat(reshape(S,size(S,1),Int(size(S,2)/3),3,1),bG),1)
-    params[:calibFov]=grid.fov
-    params[:calibSize]=grid.shape
-    params[:calibFovCenter]=grid.center
+    # Turn SVectors to Vectors for HDF5 write
+    params[:calibFov]=Vector(grid.fov)
+    params[:calibSize]=Vector(grid.shape)
+    params[:calibFovCenter]=Vector(grid.center)
     # Wann ist diese Zuordnung nicht einfach fortlaufend..dieser Fall ist so nicht abgedeckt
     params[:measIsBGFrame]=(i-> i in collect(size(S,1)+1:size(S,1)+size(bG,1))).(collect(1:size(S,1)+size(bG,1)))
     saveasMDF(saveto, params)
diff --git a/src/Utils.jl b/src/Utils.jl
@@ -11,7 +11,7 @@ squeeze(A) = dropdims(A, dims=tuple(findall(([size(A)...].==1))...))
 gridresult(result::Array, grid, ::MPIFile) = gridresult(result, grid, 1)
 gridresult(result::Array, grid, sf::AbstractVector{MPIFile}) = gridresult(result, grid, length(sf))
 gridresult(result::Array, grid::RegularGridPositions, numcolors::Int64) = gridresult(result, shape(grid), numcolors)
-function gridresult(result::Array, shp::Vector{Int64}, numcolors::Int64)
+function gridresult(result::Array, shp::AbstractVector{Int64}, numcolors::Int64)
   cArray = Array{Float32}(undef, numcolors, shp..., size(result)[end])
   result = reshape(result, reduce(*, shp), numcolors, :)
   result = permutedims(result, [2, 1, 3])
