From 6ec81d187366bf7e0b5ab95ab2027cb33d93bc58 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Mon, 25 Mar 2024 16:50:24 +0000
Subject: [PATCH] Add instant gradients to pathway
---
src/components/instant_gradients.jl | 8 ++++----
src/pathways.jl | 19 ++++++++++++++++++-
2 files changed, 22 insertions(+), 5 deletions(-)
diff --git a/src/components/instant_gradients.jl b/src/components/instant_gradients.jl
index dadd65e..8785641 100644
--- a/src/components/instant_gradients.jl
+++ b/src/components/instant_gradients.jl
@@ -4,7 +4,7 @@ import ...Variables: VariableType, duration, qval, bmat_gradient, get_free_varia
import ..AbstractTypes: EventComponent, GradientWaveform
"""
- InstantGradient1D(; orientation=nothing, group=nothing, variables...)
+ InstantGradient(; orientation=nothing, group=nothing, variables...)
If the `orientation` is set an [`InstantGradient1D`](@ref) is returned, otherwise an [`InstantGradient3D`](@ref).
@@ -16,7 +16,7 @@ If the `orientation` is set an [`InstantGradient1D`](@ref) is returned, otherwis
- [`qval`](@ref): Spatial frequency on which spins will be dephased due to this pulsed gradient in rad/um (scalar if `orientation` is set and vector otherwise).
- [`spoiler_scale`](@ref): Length-scale on which spins will be dephased by exactly 2Ï€ in mm.
"""
-abstract type InstantGradient <: EventComponent end
+abstract type InstantGradient{N} <: EventComponent end
function (::Type{InstantGradient})(; orientation=nothing, group=nothing, qval=nothing, variables...)
if isnothing(orientation)
@@ -31,7 +31,7 @@ end
"""
An [`InstantGradient`](@ref) with a fixed orientation.
"""
-struct InstantGradient1D <: InstantGradient
+struct InstantGradient1D <: InstantGradient{1}
qval :: VariableType
orientation :: SVector{3, Number}
group :: Union{Nothing, Symbol}
@@ -42,7 +42,7 @@ qval(ig::InstantGradient1D) = ig.qval
"""
An [`InstantGradient`](@ref) with a variable orientation.
"""
-struct InstantGradient3D <: InstantGradient
+struct InstantGradient3D <: InstantGradient{3}
qvec :: SVector{3, VariableType}
group :: Union{Nothing, Symbol}
end
diff --git a/src/pathways.jl b/src/pathways.jl
index ed08660..359507a 100644
--- a/src/pathways.jl
+++ b/src/pathways.jl
@@ -285,7 +285,6 @@ The function should return `true` if the `Pathway` has reached its end (i.e., th
function walk_pathway!(seq::Sequence, walker::PathwayWalker, pulse_effects::Vector{Symbol}, nreadout::Ref{Int})
current_TR = 0
nwait = length(pulse_effects) + nreadout[]
- println("processing")
while !(walk_pathway!(seq, walker, pulse_effects, nreadout, current_TR * TR(seq)))
new_nwait = length(pulse_effects) + nreadout[]
if nwait == new_nwait
@@ -341,6 +340,8 @@ function walk_pathway!(block::BaseBuildingBlock, walker::PathwayWalker, pulse_ef
# apply interrupt
if interruption isa RFPulseComponent
update_walker_pulse!(walker, pulse_effects, current_time)
+ elseif interruption isa InstantGradient
+ update_walker_instant_gradient!(interruption, walker, current_time)
end
current_index = index_inter
if length(pulse_effects) == 0 && nreadout[] == 0
@@ -491,6 +492,22 @@ function update_walker_gradient!(gradient::GradientWaveform, walker::PathwayWalk
end
end
+"""
+ update_walker_instant_gradient!(gradient, walker)
+"""
+function update_walker_instant_gradient!(gradient::InstantGradient{N}, walker::PathwayWalker, gradient_start_time::VariableType) where {N}
+ if N == 1
+ qvec3 = qval(gradient) .* gradient.orientation
+ else
+ qvec3 = qval(gradient)
+ end
+ for key in (isnothing(gradient.group) ? [nothing] : [nothing, gradient.group])
+ update_gradient_tracker_till_time!(walker, key, gradient_start_time)
+ tracker = walker.gradient_trackers[key]
+ tracker.qvec = tracker.qvec .+ qvec3
+ end
+end
+
"""
duration_state_index(transverse, positive)
--
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