From 6909c0269c1126756983360d136b722423eb3302 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Sat, 25 May 2024 15:51:36 +0100
Subject: [PATCH] Use variables. to get variables
---
src/pathways.jl | 26 +++++++++++++-------------
1 file changed, 13 insertions(+), 13 deletions(-)
diff --git a/src/pathways.jl b/src/pathways.jl
index ca8402c..7fd46b5 100644
--- a/src/pathways.jl
+++ b/src/pathways.jl
@@ -71,7 +71,7 @@ function Pathway(sequence::Sequence, pulse_effects::AbstractVector, readout_inde
)
end
-@defvar function duration_state(pathway::Pathway, transverse, positive)
+@defvar pathway function duration_state(pathway::Pathway, transverse, positive)
return pathway.duration_states[duration_state_index(transverse, positive)]
end
@@ -88,7 +88,7 @@ The requested state can be set using `transverse` and `positive` as follows:
"""
duration_state
-@defvar function duration_transverse(pathway::Pathway)
+@defvar pathway function duration_transverse(pathway::Pathway)
return duration_state(pathway, true, true) + duration_state(pathway, true, false)
end
"""
@@ -101,7 +101,7 @@ Also see [`duration_dephase`](@ref) for T2'-weighting.
"""
duration_transverse
-@defvar function duration_dephase(pathway::Pathway)
+@defvar pathway function duration_dephase(pathway::Pathway)
return duration_state(pathway, true, true) - duration_state(pathway, true, false)
end
"""
@@ -115,7 +115,7 @@ Also see [`duration_transverse`](@ref) for T2-weighting.
duration_dephase
-@defvar net_dephasing(pathway::Pathway) = pathway.qvec
+@defvar pathway net_dephasing(pathway::Pathway) = pathway.qvec
"""
net_dephasing(pathway::Pathway)
@@ -128,7 +128,7 @@ Returns a NamedTuple with the `qvec` for all gradient groups.
net_dephasing
-@defvar area_under_curve(pathway::Pathway) = norm(qvec(pathway))
+@defvar pathway area_under_curve(pathway::Pathway) = norm(qvec(pathway))
"""
area_under_curve(pathway::Pathway)
@@ -141,7 +141,7 @@ Returns a NamedTuple with the `area_under_curve` for all gradient groups.
area_under_curve
-@defvar bmat(pathway::Pathway) = pathway.bmat
+@defvar pathway bmat(pathway::Pathway) = pathway.bmat
"""
bmat(pathway::Pathway)
@@ -153,7 +153,7 @@ Returns a NamedTuple with the `bmat` for all gradient groups.
"""
bmat
-@defvar bval(pathway::Pathway) = tr(bmat(pathway))
+@defvar pathway bval(pathway::Pathway) = tr(bmat(pathway))
"""
bval(pathway::Pathway)
@@ -271,7 +271,7 @@ 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[]
- while !(walk_pathway!(seq, walker, pulse_effects, nreadout, current_TR * TR(seq)))
+ while !(walk_pathway!(seq, walker, pulse_effects, nreadout, current_TR * variables.duration(seq)))
new_nwait = length(pulse_effects) + nreadout[]
if nwait == new_nwait
not_seen = iszero(length(pulse_effects)) ? "readout" : "pulse"
@@ -320,7 +320,7 @@ function walk_pathway!(block::BaseBuildingBlock, walker::PathwayWalker, pulse_ef
# apply gradients up till interrupt
for (_, part) in waveform_sequence(block, current_index, index_inter)
update_walker_gradient!(part, walker, current_time)
- current_time = current_time + duration(part)
+ current_time = current_time + variables.duration(part)
end
# apply interrupt
@@ -339,7 +339,7 @@ function walk_pathway!(block::BaseBuildingBlock, walker::PathwayWalker, pulse_ef
# apply remaining gradients
for (_, part) in waveform_sequence(block, current_index, nothing)
update_walker_gradient!(part, walker, current_time)
- current_time = current_time + duration(part)
+ current_time = current_time + variables.duration(part)
end
return false
end
@@ -472,9 +472,9 @@ function update_walker_gradient!(gradient::GradientWaveform, walker::PathwayWalk
# update qvec/bmat during gradient
tracker = walker.gradient_trackers[key]
- tracker.bmat = tracker.bmat .+ bmat_gradient(gradient, tracker.qvec)
- tracker.qvec = tracker.qvec .+ qval3(gradient)
- tracker.last_gradient_time = gradient_start_time + duration(gradient)
+ tracker.bmat = tracker.bmat .+ variables.bmat_gradient(gradient, tracker.qvec)
+ tracker.qvec = tracker.qvec .+ variables.qval3(gradient)
+ tracker.last_gradient_time = gradient_start_time + variables.duration(gradient)
end
end
--
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