remove LowRankApprox dependencies (#222)

* remove LowRankApprox dependencies * add tsvd * fix typo * fix docstring * fix conflict in project.toml
MagneticResonanceImaging · Jan 31, 2025 · 9c97e76 · 9c97e76
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commit 9c97e76
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Showing 4 changed files with 14 additions and 16 deletions.
diff --git a/MRIOperators/Project.toml b/MRIOperators/Project.toml
@@ -5,16 +5,16 @@ version = "0.3.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-MRIBase = "f7771a9a-6e57-4e71-863b-6e4b6a2f17df"
+FLoops = "cc61a311-1640-44b5-9fba-1b764f453329"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+LinearOperatorCollection = "a4a2c56f-fead-462a-a3ab-85921a5f2575"
+LinearOperators = "5c8ed15e-5a4c-59e4-a42b-c7e8811fb125"
+MRIBase = "f7771a9a-6e57-4e71-863b-6e4b6a2f17df"
 NFFT = "efe261a4-0d2b-5849-be55-fc731d526b0d"
-FLoops = "cc61a311-1640-44b5-9fba-1b764f453329"
-LowRankApprox = "898213cb-b102-5a47-900c-97e73b919f73"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-LinearOperators = "5c8ed15e-5a4c-59e4-a42b-c7e8811fb125"
-LinearOperatorCollection = "a4a2c56f-fead-462a-a3ab-85921a5f2575"
+TSVD = "9449cd9e-2762-5aa3-a617-5413e99d722e"
 Wavelets = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
 
 [weakdeps]
@@ -27,20 +27,18 @@ StatsBase = "0.33, 0.34"
 GPUArrays = "11"
 JLArrays = "0.2"
 KernelAbstractions = "0.9"
-julia = "1.6"
 MRIBase = "0.4"
 Reexport = "1"
 LinearOperators = "2.3"
 LinearOperatorCollection = "2"
 NFFT = "0.13"
-FLoops = "0.2"
-LowRankApprox = "0.5"
 Wavelets = "0.9, 0.10"
+julia = "1.6"
 
 [extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-MRISimulation = "8988da37-ea20-4fa6-9af7-8a6f6f9a8970"
 JLArrays = "27aeb0d3-9eb9-45fb-866b-73c2ecf80fcb"
+MRISimulation = "8988da37-ea20-4fa6-9af7-8a6f6f9a8970"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["Test", "MRISimulation", "JLArrays"]

diff --git a/MRIOperators/src/ExpApproximation.jl b/MRIOperators/src/ExpApproximation.jl
@@ -308,7 +308,7 @@ function get_A_coefficients_svd(K::Int64, times::Vector, z_p::Vector{Complex{T}}
   end
 
   # compute SVD
-  U,S,V = psvd(A, rank=2*K)
+  U,S,V = tsvd(A,K)
   # estimate accuracy of the approximation and determine rank threshold
   acc = sqrt.(cumsum(S.^2)./sum(S.^2))
   K0 = findfirst(x->x>=(1-K_tol-1e-14), acc)

diff --git a/MRIOperators/src/MRIOperators.jl b/MRIOperators/src/MRIOperators.jl
@@ -12,7 +12,7 @@ using NFFT.FFTW
 using Wavelets
 using FLoops
 
-using LowRankApprox: psvd
+using TSVD: tsvd
 using StatsBase
 
 include("Shutter.jl")

diff --git a/src/Tools/ImageData.jl b/src/Tools/ImageData.jl
@@ -1,10 +1,10 @@
 """
-    makeAxisArray(I::AbstractArray{T,5}, acqData::AcquisitionData) where T
+    makeAxisArray(I::AbstractArray{T,6}, acqData::AcquisitionData) where T
 
 creates an axes array with properly characterized axis from the image `I`.
 For this, it uses the information in `acqData`.
 The axies respectively describe the following coordinates:
-x, y, z, acqData.numEchoes, acqData.numCoils
+x, y, z, acqData.numEchoes, acqData.numCoils, acqData.numRepetitions
 """
 function makeAxisArray(I::AbstractArray{Complex{T},6}, acqData::AcquisitionData{T,D}) where {T,D}