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fix for noise matrix absence and allow for double wrap correction in the future #53

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merged 5 commits into from
Sep 30, 2024
Merged

fix for noise matrix absence and allow for double wrap correction in the future #53

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2bdaae1
fix for noise matrix absence in Navigator.jl
Jun 21, 2024
f846a6f
allow for double wrap correction in the future
Sep 25, 2024
32cc1b9
fix for noise matrix absence in Navigator.jl
Jun 21, 2024
ce4e71d
allow for double wrap correction in the future
Sep 25, 2024
28437ef
rebase
Sep 25, 2024
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16 changes: 10 additions & 6 deletions src/Navigator.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -43,11 +43,16 @@ function NavCorr!(nav::Array{Complex{T}, 4}, acqData::AcquisitionData, params::D
end

remove_ref_ph!(nav, addData.numlines, 1) # remove the reference phase
noisestd = std(addData.noisemat, dims=[1]).^2
if addData.noisemat != nothing
noisestd = std(addData.noisemat, dims=[1]).^2

# Compute weights for the coils average
weights = comp_weights(abs.(nav), noisestd, addData.numlines, addData.numslices)
nav = sum(weights .* nav, dims=(1,2,)) # coils and samples average for each line
# Compute weights for the coils average
weights = comp_weights(abs.(nav), noisestd, addData.numlines, addData.numslices)
nav = sum(weights .* nav, dims=(1,2,)) # coils and samples average for each line

else
nav = sum(nav, dims=(1,2,))
end

# Compute navigator phase
cartes_index = findall(x -> isnan(x), nav)
Expand Down Expand Up @@ -253,8 +258,7 @@ function wrap_corr!(nav::Array{Float64, 4}, wrapped_points::Array{Int8, 2}, corr

invertNavSign!(nav, correlation, slices)
wrapped_points_local = reshape(wrapped_points, (1, 1, size(wrapped_points)...))
idx_pos = findall(x->x==1, wrapped_points_local)
nav[idx_pos] = nav[idx_pos] .+ (2*pi)
nav = nav .+ ((2*pi) .* wrapped_points_local)
invertNavSign!(nav, correlation, slices)

return nav
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