From 75155658bff35a8f298cf5f927d4ac861496db23 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Thu, 8 Feb 2024 14:40:10 +0000
Subject: [PATCH] Add support in walk_pathway for overlapping sequences
---
src/overlapping/overlapping.jl | 2 +-
src/pathways.jl | 54 +++++++++++++++++++++++++++++++---
2 files changed, 51 insertions(+), 5 deletions(-)
diff --git a/src/overlapping/overlapping.jl b/src/overlapping/overlapping.jl
index fac3a89..774aeea 100644
--- a/src/overlapping/overlapping.jl
+++ b/src/overlapping/overlapping.jl
@@ -4,7 +4,7 @@ include("generic.jl")
include("gradient_pulses/gradient_pulses.jl")
include("gradient_readouts/gradient_readouts.jl")
-import .Abstract: AbstractOverlapping, interruptions, waveform
+import .Abstract: AbstractOverlapping, interruptions, waveform, get_parts
import .Generic: GenericOverlapping
import .GradientPulses: TrapezoidGradient, SpoiltSliceSelect
import .GradientReadouts: SingleLine, opposite_kspace_lines
diff --git a/src/pathways.jl b/src/pathways.jl
index fd2d4f2..609472b 100644
--- a/src/pathways.jl
+++ b/src/pathways.jl
@@ -3,9 +3,10 @@ import LinearAlgebra: norm, tr
import StaticArrays: SVector, SMatrix
import ..BuildingBlocks: BuildingBlock, GradientBlock, RFPulseBlock, ContainerBlock, get_children_blocks
import ..Sequences: Sequence
-import ..Variables: qvec, qval, bmat_gradient, VariableType, start_time, effective_time, duration
+import ..Variables: qvec, qval, bmat_gradient, VariableType, start_time, effective_time, duration, qval_square
import ..Wait: WaitBlock
-import ..Readouts: InstantReadout
+import ..Readouts: InstantReadout, ADC
+import ..Overlapping: AbstractOverlapping, interruptions, waveform, get_parts
"""
@@ -126,6 +127,12 @@ You can set `scale` and/or `rotate` to specific symbols to only consider gradien
"""
qvec(pathway::Pathway; scale=nothing, rotate=nothing) = get(pathway.qvec, (scale, rotate), zero(SVector{3, Float64}))
+function qval_square(pathway::Pathway; kwargs...)
+ vec = qvec(pathway; kwargs...)
+ return vec[1]^2 + vec[2]^2 + vec[3]^2
+end
+qval(pathway::Pathway; kwargs...) = sqrt(qval_square(pathway; kwargs...))
+
"""
area_under_curve(pathway::Pathway; scale=nothing, rotate=nothing)
@@ -278,7 +285,46 @@ end
walk_pathway!(wait::WaitBlock, walker::PathwayWalker, pulse_effects::Vector{Symbol}, nreadout::Ref{Int}, block_start_time=0.::VariableType) = false
-function walk_pathway!(::InstantReadout, walker::PathwayWalker, pulse_effects::Vector{Symbol}, nreadout::Ref{Int}, block_start_time=0.::VariableType)
+function walk_pathway!(ao::AbstractOverlapping, walker::PathwayWalker, pulse_effects::Vector{Symbol}, nreadout::Ref{Int}, block_start_time=0.::VariableType)
+ current_index = nothing
+ current_time = block_start_time
+ for (index_inter, interruption) in enumerate(interruptions(ao))
+ if interruption.object isa RFPulseBlock
+ if iszero(length(pulse_effects))
+ error("Pathway definition is invalid! Another RF pulse was encountered before the number of readouts expected from `nreadout` where detected.")
+ end
+ if pulse_effects[1] == :ignore
+ popfirst!(pulse_effects)
+ continue
+ end
+ elseif (interruption.object isa InstantReadout || interruption.object isa ADC)
+ if length(pulse_effects) > 0
+ continue
+ elseif nreadout[] > 0
+ nreadout[] -= 1
+ continue
+ end
+ end
+ for part in get_parts(ao, current_index, index_inter)
+ update_walker_gradient!(part, walker, current_time)
+ current_time = current_time + duration(part)
+ end
+ if interruption.object isa RFPulseBlock
+ update_walker_pulse!(walker, pulse_effects, current_time)
+ end
+ current_index = index_inter
+ if length(pulse_effects) == 0 && nreadout[] == 0
+ return true
+ end
+ end
+ for part in get_parts(ao, current_index, nothing)
+ update_walker_gradient!(part, walker, current_time)
+ current_time = current_time + duration(part)
+ end
+ return false
+end
+
+function walk_pathway!(::Union{InstantReadout, ADC}, walker::PathwayWalker, pulse_effects::Vector{Symbol}, nreadout::Ref{Int}, block_start_time=0.::VariableType)
if length(pulse_effects) > 0
return false
end
@@ -405,7 +451,7 @@ The following steps will be taken:
- update the appropriate `walker.qvec` and `walker.bmat` based on the gradient waveform. This will require appropriate `qvec`/`bmat` functions to be defined for the gradient building block.
- update `walker.last_gradient_time` to the time at the end of the gradient.
-This requires [`bmat`](@ref) and [`qvec`](@ref) to be implemented for the [`GradientBlock`](@ref).
+This requires [`bmat_gradient`](@ref) and [`qvec`](@ref) to be implemented for the [`GradientBlock`](@ref).
"""
function update_walker_gradient!(gradient::GradientBlock, walker::PathwayWalker, gradient_start_time::VariableType)
if !walker.is_transverse
--
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