add SRCPMG

Author: arismav

docs/src/types_structs.md

@@ -20,6 +20,7 @@ SR
 CPMG
 PFG
 IRCPMG
+SRCPMG
 CPMGCPMG
 ```
 

ext/gui_2D.jl

@@ -83,24 +83,24 @@ function Makie.plot!(fig::Union{Makie.Figure,Makie.GridPosition}, res::NMRInvers
     x = res.X_indirect
     y = res.X_direct
 
-    xlbl = if seq == IRCPMG
+    xlbl = if seq in (IRCPMG, SRCPMG)
         L"T_1 \, \textrm{(s)}"
     elseif seq == PFGCPMG
         L"D \, \textrm{(m^2/s)}"
     elseif seq == CPMGCPMG
         L"T_{2A} \,\textrm{(s)}"
     end
 
-    ylbl = if seq in [IRCPMG, PFGCPMG]
+    ylbl = if seq in (IRCPMG, SRCPMG, PFGCPMG)
         L"T_2 \,\textrm{(s)}"
     elseif seq == CPMGCPMG
         L"T_{2B} \,\textrm{(s)}"
     end
 
-    x_low = seq in (IRCPMG, CPMGCPMG) ? exp10(floor(log10(min(x[1],y[1])))) : exp10(floor(log10(x[1])))
-    x_high = seq in (IRCPMG, CPMGCPMG) ? exp10(ceil(log10(max(x[end],y[end])))) : exp10(ceil(log10(x[end])))
-    y_low = seq in (IRCPMG, CPMGCPMG) ? exp10(floor(log10(min(x[1],y[1])))) : exp10(floor(log10(y[1])))
-    y_high = seq in (IRCPMG, CPMGCPMG) ? exp10(ceil(log10(max(x[end],y[end])))) : exp10(ceil(log10(y[end])))
+    x_low = seq in (IRCPMG, SRCPMG, CPMGCPMG) ? exp10(floor(log10(min(x[1],y[1])))) : exp10(floor(log10(x[1])))
+    x_high = seq in (IRCPMG, SRCPMG, CPMGCPMG) ? exp10(ceil(log10(max(x[end],y[end])))) : exp10(ceil(log10(x[end])))
+    y_low = seq in (IRCPMG, SRCPMG, CPMGCPMG) ? exp10(floor(log10(min(x[1],y[1])))) : exp10(floor(log10(y[1])))
+    y_high = seq in (IRCPMG, SRCPMG, CPMGCPMG) ? exp10(ceil(log10(max(x[end],y[end])))) : exp10(ceil(log10(y[end])))
 
     gr = fig[1:10, 1:10] = GridLayout()
 
@@ -207,7 +207,7 @@ function draw_on_axes(
     markers = collect('a':'z')
     colors = cgrad(:tab10)
 
-    if res.seq in (IRCPMG, CPMGCPMG)
+    if res.seq in (IRCPMG, SRCPMG, CPMGCPMG)
         plot_diagonal(axmain,x,y)
     end
 
@@ -224,7 +224,7 @@ function draw_on_axes(
         xc = xdist ⋅ x / sum(spo)
         yc = ydist ⋅ y / sum(spo)
 
-        lbl = if res.seq == IRCPMG
+        lbl = if res.seq in (IRCPMG, SRCPMG)
             "T₁/T₂ = $(round(wa_indir[i]/wa_dir[i] , digits=1)) \nVolume = $(round(volumes[i] *100 ,digits = 1))%"
         elseif res.seq == PFGCPMG
             "D = $(round(wa_indir[i], sigdigits=3)), T₂ = $(round(wa_dir[i], sigdigits=3))\nVolume = $(round(volumes[i] *100 ,digits = 1))%"
@@ -349,15 +349,15 @@ function Makie.plot(res::NMRInversions.inv_out_2D)
     coord_label = Observable("")
     coord_label[] = "Hover mouse over plot to view coordinates."
 
-    xlbl = if res.seq == IRCPMG
+    xlbl = if res.seq in (IRCPMG, SRCPMG)
         "T₁"
     elseif res.seq == PFGCPMG
         "D"
     elseif res.seq == CPMGCPMG
         "T₂ₐ"
     end
 
-    ylbl = if res.seq in [IRCPMG, PFGCPMG]
+    ylbl = if res.seq in (IRCPMG, SRCPMG, PFGCPMG)
         "T₂"
     elseif res.seq == CPMGCPMG
         "T₂ᵦ"

ext/gui_data.jl

@@ -91,7 +91,7 @@ function Makie.plot(data::NMRInversions.input2D)
     ax_dir.xlabel = "time (s)"
     ax_full.xlabel = "time (s)"
 
-    if data.seq in (IRCPMG, CPMGCPMG)
+    if data.seq in (IRCPMG, SRCPMG, CPMGCPMG)
         ax_indir.xlabel = "time (s)"
         ax_full.ylabel = "time (s)"
     elseif data.seq == PFGCPMG

src/import_data.jl

@@ -203,7 +203,7 @@ function import_tnt(seq::Type{<:Union{pulse_sequence1D, pulse_sequence2D}},
         x = read_tnt_echo_times(filename, length(y), echotime)
         return autophase(input1D(seq, x, y))
 
-    elseif seq in (IRCPMG, CPMGCPMG)
+    elseif seq in (IRCPMG, CPMGCPMG, SRCPMG)
 
         data_mat = reshape(y , :, header["actual_points_2d"]) 
         x_dir = read_tnt_echo_times(filename, size(data_mat,1), echotime)

src/inversion_functions.jl

@@ -150,10 +150,10 @@ function invert(
     end
 
     if isa(lims2, Type{<:pulse_sequence2D})
-        if lims2 in (IRCPMG, CPMGCPMG)
-            X_indirect = collect(NMRInversions.logrange(minimum(x_indirect)/7, maximum(x_indirect)*7, 64)) 
-        elseif lims2 == PFGCPMG
+        if lims2 == PFGCPMG
             X_indirect = collect(NMRInversions.logrange(minimum(x_indirect)*7, maximum(x_indirect)*10, 64)) 
+        else
+            X_indirect = collect(NMRInversions.logrange(minimum(x_indirect)/7, maximum(x_indirect)*7, 64)) 
         end
     elseif isa(lims2, Tuple)
         X_indirect = exp10.(range(lims2...))

src/kernels.jl

@@ -139,6 +139,9 @@ function create_kernel(seq::Type{<:pulse_sequence2D},
     elseif seq == PFGCPMG
         K_dir = create_kernel(CPMG, x_direct, X_direct, y = vec(Data[:,1]))
         K_indir = create_kernel(PFG, x_indirect, X_indirect, y = vec(Data[1,:]))
+    elseif seq == SRCPMG
+        K_dir = create_kernel(CPMG, x_direct, X_direct, y = vec(Data[:,end]))
+        K_indir = create_kernel(SR, x_indirect, X_indirect, y = vec(Data[1,:]))
     elseif seq == CPMGCPMG
         K_dir = create_kernel(CPMG, x_direct, X_direct, y = vec(Data[:,1]))
         K_indir = create_kernel(CPMG, x_indirect, X_indirect, y = vec(Data[1,:]))

src/misc.jl

@@ -104,7 +104,7 @@ function autophase(data::input2D; rotation::Real=0)
 
         if data.seq in (PFGCPMG, CPMGCPMG) && d < 0
             return autophase(data, rotation = pi)
-        elseif data.seq in (IRCPMG,) && d > 0
+        elseif data.seq in (IRCPMG, SRCPMG) && d > 0
             return autophase(data, rotation = pi)
         end
     end
@@ -225,7 +225,7 @@ function weighted_averages(r::inv_out_2D; silent::Bool = false)
         volumes[i] = sum(spo)/sum(z)
 
         dir_lbl = ["<T₂>","s"]
-        ind_lbl = if r.seq == IRCPMG
+        ind_lbl = if r.seq in (IRCPMG, SRCPMG)
             ["<T₁>","s"]
         elseif r.seq == PFGCPMG
             ["<D>", "m²/s"]
@@ -235,7 +235,7 @@ function weighted_averages(r::inv_out_2D; silent::Bool = false)
             display("Selection $(collect('a':'z')[i]) :")
             display(ind_lbl[1] * " = $(round(wa_indir[i], sigdigits=4)) "*ind_lbl[2])
             display(dir_lbl[1] * " = $(round(wa_dir[i], sigdigits=4)) "*dir_lbl[2])
-            if r.seq == IRCPMG
+            if r.seq in (IRCPMG, SRCPMG)
                 display("T₁/T₂ = $(round(wa_indir[i]/wa_dir[i], sigdigits=2)) ")
             end
             display("Volume = $(round(volumes[i], sigdigits=4) * 100) %")

src/types.jl

@@ -1,7 +1,7 @@
 ## The following are custom types, defined mainly for multiple dispatch purposes
 
 export pulse_sequence1D, pulse_sequence2D
-export IR, SR, CPMG, PFG, IRCPMG, PFGCPMG, CPMGCPMG
+export IR, SR, CPMG, PFG, IRCPMG, SRCPMG, PFGCPMG, CPMGCPMG
 export alpha_optimizer, regularization_solver
 
 abstract type pulse_sequence1D end
@@ -44,6 +44,13 @@ It can be used wherever the `seq` argument is required.
 """
 struct IRCPMG <: pulse_sequence2D end
 
+"""
+Saturation recovery - CPMG pulse sequence for 2D relaxation experiments (T1-T2).
+The direct dimension is the T2, and the indirect dimension is the T1 acquisition times.
+It can be used wherever the `seq` argument is required.
+"""
+struct SRCPMG <: pulse_sequence2D end
+
 """
 PFG - CPMG pulse sequence for 2D D-T2 experiments.
 It can be used wherever the `seq` argument is required.