From 83da9a5ddaff9830abc2e62623012be9835c7ec1 Mon Sep 17 00:00:00 2001
From: beorostica-asusFX505GT-win <beorostica@uc.cl>
Date: Wed, 27 Mar 2024 11:24:38 -0300
Subject: [PATCH] Add temporal time_shape_id property to Grad struct for
 debuging

---
 KomaMRIBase/src/datatypes/sequence/Grad.jl | 1 +
 KomaMRIFiles/src/Sequence/Pulseq.jl        | 9 ++++++++-
 KomaMRIFiles/test/runtests.jl              | 2 +-
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/KomaMRIBase/src/datatypes/sequence/Grad.jl b/KomaMRIBase/src/datatypes/sequence/Grad.jl
index 0bf6554ce..f4f22f13e 100644
--- a/KomaMRIBase/src/datatypes/sequence/Grad.jl
+++ b/KomaMRIBase/src/datatypes/sequence/Grad.jl
@@ -76,6 +76,7 @@ mutable struct Grad
 	delay::Real
     first
     last
+    time_shape_id
     function Grad(A, T, rise, fall, delay)
 		all(T .< 0) || rise < 0 || fall < 0 || delay < 0 ? error("Gradient timings must be positive.") : new(A, T, rise, fall, delay)
     end
diff --git a/KomaMRIFiles/src/Sequence/Pulseq.jl b/KomaMRIFiles/src/Sequence/Pulseq.jl
index f4417004d..cbec969b7 100644
--- a/KomaMRIFiles/src/Sequence/Pulseq.jl
+++ b/KomaMRIFiles/src/Sequence/Pulseq.jl
@@ -450,7 +450,7 @@ function read_seq(filename)
                         grad_prev_last = 0
                     end
                     seq.GR[gi, bi].first = grad_prev_last
-                    if length(gr.T) > 1    # this is for time-shaped case (I assume it is the extended trapezoid case)
+                    if length(gr.T) > 1 || (isdefined(gr, :time_shape_id) && gr.time_shape_id != 0)    # this is for time-shaped case (I assume it is the extended trapezoid case)
                         seq.GR[gi, bi].last = gr.A[end]   #I need to check this or [end-1]
                     else
                         odd_step1 = [seq.GR[gi, bi].first; 2 * gr.A]
@@ -524,6 +524,9 @@ function read_Grad(gradLibrary, shapeLibrary, Δt_gr, i)
         delay =         g[4]
         #Amplitude
         gA = amplitude * decompress_shape(shapeLibrary[amp_shape_id]...)
+        if length(gA) == 1
+            gA = gA[1]
+        end
         Nrf = length(gA) - 1
         #Creating timings
         if time_shape_id == 0 #no time waveform
@@ -533,8 +536,12 @@ function read_Grad(gradLibrary, shapeLibrary, Δt_gr, i)
         else
             gt = decompress_shape(shapeLibrary[time_shape_id]...)
             gT = (gt[2:end] .- gt[1:end-1]) * Δt_gr
+            if length(gT) == 1
+                gT = gT[1]
+            end
             G = Grad(gA,gT,0,0,delay)
         end
+        G.time_shape_id = time_shape_id
     end
     G
 end
diff --git a/KomaMRIFiles/test/runtests.jl b/KomaMRIFiles/test/runtests.jl
index dba7504f7..4ad1247d9 100644
--- a/KomaMRIFiles/test/runtests.jl
+++ b/KomaMRIFiles/test/runtests.jl
@@ -91,7 +91,7 @@ end
         if Namp == 1 && Ntim == 1
             return 1e-3*γ*KomaMRIBase.get_theo_A(gr; off_val=0)
         elseif  Namp > 1 && Ntim == 1
-            return 1e-3*γ*[KomaMRIBase.get_theo_A(gr; off_val=0)[2:end-1]; gr.last]
+            return 1e-3*γ*[gr.first; KomaMRIBase.get_theo_A(gr; off_val=0)[3:end-1]; gr.last]
         elseif Namp > 1 && Ntim > 1
             return 1e-3*γ*KomaMRIBase.get_theo_A(gr; off_val=0)[2:end]
         end