Merge pull request #43 from NordicMRspine/smallfixes

Smallfixes

src/NavData.jl

@@ -80,8 +80,13 @@ end
 mutable struct navOutput
 
     navigator::Array{Float64, 4}
+    nav_time::Union{Array{Float64, 2}, Nothing}
+    trace_aligned::Union{Array{Float64, 1}, Nothing}
+    trace_time::Union{Array{Float64, 1}, Nothing}
+    trace_interpolated::Union{Array{Float64, 2}, Nothing}
     centerline::Union{Array{Float64, 1}, Nothing}
     correlation::Union{Array{Float64, 1}, Matrix{Float64}, Nothing}
     wrapped_points::Union{Array{Int8, 2}, Nothing}
 
+
 end

src/Navigator.jl

@@ -63,7 +63,8 @@ function NavCorr!(nav::Array{Complex{T}, 4}, acqData::AcquisitionData, params::D
     corr_type = split(params[:corr_type], "_")
     if size(corr_type, 1) == 2
         if corr_type[2] == "unwrap"
-            (wrapped_points, correlation) = find_wrapped(nav, addData.nav_time, addData.trace, addData.numslices)
+            (wrapped_points, correlation, trace_data, trace_time, trace_data_int) =
+                find_wrapped(nav, addData.nav_time, addData.trace, addData.numslices)
             nav = wrap_corr!(nav, wrapped_points, correlation, addData.numslices)
         end
     end
@@ -77,7 +78,7 @@ function NavCorr!(nav::Array{Complex{T}, 4}, acqData::AcquisitionData, params::D
     # Apply the correction to the data
     apply_corr!(nav, acqData, addData.numechoes,addData.numlines, addData.numsamples, addData.numslices)
 
-    return navOutput(nav_return, centerline, correlation, wrapped_points)
+    return navOutput(nav_return, addData.nav_time, trace_data, trace_time, trace_data_int, centerline, correlation, wrapped_points)
 
 end
 
@@ -97,20 +98,21 @@ function comp_weights(navabs::Array{T, 4}, noisestd::Matrix{T}, lines::Int64, sl
 
     # weights[points, coils, lines, slices]
     coils = size(navabs, 2)
-    weights = zeros(size(navabs))
-    for ii=1:coils
-        weights[:,ii,:,:] = navabs[:,ii,:,:] ./ noisestd[1,ii]
-    end
+    weights = ones(size(navabs))
+    if !any(noisestd .== 0)
+        for ii=1:coils
+            weights[:,ii,:,:] = navabs[:,ii,:,:] ./ noisestd[1,ii]
+        end
 
-    weightsnorm = sum(weights, dims=(1,2))
+        weightsnorm = sum(weights, dims=(1,2))
 
-    for ii=1:lines
-        for ll=1:slices
-            weights[:,:,ii,ll] = weights[:,:,ii,ll] ./ weightsnorm[1,1,ii,ll]
+        for ii=1:lines
+            for ll=1:slices
+                weights[:,:,ii,ll] = weights[:,:,ii,ll] ./ weightsnorm[1,1,ii,ll]
+            end
         end
     end
     return weights
-
 end
 
 """
@@ -126,7 +128,7 @@ function comp_centerline_pos(addData::additionalNavInput)
     # Compute resolution and disc
     freq_enc_ref_res = addData.freq_enc_FoV[1] / addData.freq_enc_samples[1]
     freq_enc_img_res = addData.freq_enc_FoV[2] / addData.freq_enc_samples[2]
-    freq_enc_FoV_disc = Int64((addData.freq_enc_FoV[1] - addData.freq_enc_FoV[2]) / freq_enc_ref_res / 2)
+    freq_enc_FoV_disc = round(Int64,(addData.freq_enc_FoV[1] - addData.freq_enc_FoV[2]) / freq_enc_ref_res / 2)
 
     start_voxel = div(addData.freq_enc_samples[1] - addData.phase_enc_samples[1], 2)
 

src/Unwrap.jl

@@ -4,7 +4,7 @@ export find_wrapped
     find_wrapped(nav::Array{Float64, 4}, nav_time::Array{Float64, 2}, trace::Array{Float64, 2}, slices::Int64)
 
 Identify the position of the wrapped points in the navigator phase estimates. The respiratory belt recording is necessary.
-Return the position of the wrapped points and the correlation between each navigator slice and the trace data.
+Return the position of the wrapped points, the correlation between each navigator slice and the trace data, the aligned and interpolated trace data.
 
 # Arguments
 * `nav::Array{Float64, 4}`      - navigator phase estimates
@@ -87,25 +87,26 @@ function find_wrapped(nav::Array{Float64, 4}, nav_time::Array{Float64, 2}, trace
 
     nowrap_slices = findall(possible_wrap_slices .== false)
     nav_norm[:, nowrap_slices] .= 1
-    trace_data_int[:, nowrap_slices] .= 1
+    trace_data_int_lim = deepcopy(trace_data_int)
+    trace_data_int_lim[:, nowrap_slices] .= 1
 
     # renormalize nav data
     for ii = 1:slices
         nav_norm[:,ii] = nav_norm[:,ii] ./ findmax(nav_norm[:,ii], dims =1)[1]
     end
 
     # compute navigator baseline
-    nav_baseline = find_baseline(nav_norm, trace_data_int, slices)
+    nav_baseline = find_baseline(nav_norm, trace_data_int_lim, slices)
 
     # reposition data to align the baseline
     for ii = 1:slices
         nav_norm[:,ii] = nav_norm[:,ii] .- nav_baseline[ii]
     end
 
-    wrapped_points = find_wrapped_points(nav_norm, trace_data_int, slices)
+    wrapped_points = find_wrapped_points(nav_norm, trace_data_int_lim, slices)
 
     # return position wrapped points and field shift direction
-    return wrapped_points, correlation
+    return wrapped_points, correlation, trace_data, trace_time, trace_data_int
 
 end