bugfixes

Author: JakobAsslaender

.github/workflows/CI.yml

@@ -40,7 +40,8 @@ jobs:
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: MagneticResonanceImaging/MRIRealign.jl
   docs:
     name: Documentation
     runs-on: ubuntu-latest

docs/src/index.md

@@ -17,12 +17,7 @@ MRIRealign.realign!
 
 ## Helper functions
 
-```@autodocs
-Modules = [MRIRealign]
-Filter = """
-b -> begin
-    obj = Documenter.DocSystem.getobject(b)
-    !(obj === realign!)
-end
-"""
+```@docs
+MRIRealign.create_rotation_matrix
+MRIRealign.create_affine_matrix
 ```

src/MRIRealign.jl

@@ -76,7 +76,7 @@ function realign!(img::AbstractArray{Tin,4};
     end
 
     # random shifts seem to help with the speed of convertion (cf. SPM)
-    mask_inds = [Tuple(idx) .+ rand(NTuple{3,T}) .- T(0.5) for idx ∈ findall(mask)]
+    mask_inds = [Tuple(idx) .+ ntuple(_ -> rand(T), 3) .- T(0.5) for idx ∈ findall(mask)]
 
     _motion_params = Array{T}(undef, 6, length(img_itp), length(t_refs))
     for (i_ref, t_ref) ∈ enumerate(t_refs)

test/runtests.jl

@@ -33,7 +33,7 @@ img_itp = extrapolate(interpolate(image, BSpline(Cubic())), Interpolations.Flat(
 
 
 ## test gradients
-inds = [Tuple(idx) .+ rand(NTuple{3,Float64}) .- 0.5 for idx ∈ CartesianIndices(image)]
+inds = [Tuple(idx) .+ ntuple(_ -> rand(Float64), 3) .- 0.5 for idx ∈ CartesianIndices(image)]
 # inds = CartesianIndices(image)
 reference = [img_itp(idx[1], idx[2], idx[3]) for idx in inds]
 grad_field = [Interpolations.gradient(img_itp, idx[1], idx[2], idx[3]) for idx ∈ inds]