From 44a2dffeae06477bd4a9c10c05cef5f4b9b21460 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Fri, 24 May 2024 15:44:12 +0100
Subject: [PATCH] Update pathways to use @defvar
---
src/MRIBuilder.jl | 6 ++---
src/pathways.jl | 60 ++++++++++++++++++-----------------------------
2 files changed, 26 insertions(+), 40 deletions(-)
diff --git a/src/MRIBuilder.jl b/src/MRIBuilder.jl
index ed57857..ae8cbbb 100644
--- a/src/MRIBuilder.jl
+++ b/src/MRIBuilder.jl
@@ -8,7 +8,7 @@ include("build_sequences.jl")
include("variables.jl")
include("components/components.jl")
include("containers/containers.jl")
-#include("pathways.jl")
+include("pathways.jl")
#include("parts/parts.jl")
#include("post_hoc.jl")
#include("sequences/sequences.jl")
@@ -31,8 +31,8 @@ export InstantPulse, ConstantPulse, SincPulse, GenericPulse, InstantGradient, Si
import .Containers: ContainerBlock, start_time, end_time, waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Wait, BaseSequence, nrepeat, Sequence, AlternativeBlocks, match_blocks!, get_index_single_TR, readout_times, iter_blocks, iter_instant_gradients, iter_instant_pulses
export ContainerBlock, start_time, end_time, waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Wait, BaseSequence, nrepeat, Sequence, AlternativeBlocks, match_blocks!, get_index_single_TR, readout_times, iter_blocks, iter_instant_gradients, iter_instant_pulses
-#import .Pathways: Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
-#export Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
+import .Pathways: Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
+export Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
#import .Parts: dwi_gradients, readout_event, excitation_pulse, refocus_pulse, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout, interpret_image_size
#export dwi_gradients, readout_event, excitation_pulse, refocus_pulse, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout, interpret_image_size
diff --git a/src/pathways.jl b/src/pathways.jl
index 3586145..ca8402c 100644
--- a/src/pathways.jl
+++ b/src/pathways.jl
@@ -3,7 +3,7 @@ import LinearAlgebra: norm, tr
import StaticArrays: SVector, SMatrix
import ..Components: NoGradient, RFPulseComponent, ReadoutComponent, InstantGradient, GradientWaveform
import ..Containers: BaseSequence, Sequence, BaseBuildingBlock, waveform, events, waveform_sequence, start_time, AlternativeBlocks
-import ..Variables: qvec, qval, qval3, bmat_gradient, VariableType, effective_time, duration, TR, bmat, bval, area_under_curve, duration_dephase, duration_transverse, VariableNotAvailable
+import ..Variables: VariableType, get_pathway, variables, @defvar
"""
@@ -71,6 +71,9 @@ function Pathway(sequence::Sequence, pulse_effects::AbstractVector, readout_inde
)
end
+@defvar function duration_state(pathway::Pathway, transverse, positive)
+ return pathway.duration_states[duration_state_index(transverse, positive)]
+end
"""
duration_state(pathway::Pathway, transverse::Bool, positive::Bool)
@@ -83,10 +86,11 @@ The requested state can be set using `transverse` and `positive` as follows:
- `transverse=false`, `positive=false`: -longitudinal
- `transverse=true`, `positive=false`: -transverse
"""
-function duration_state(pathway::Pathway, transverse, positive)
- return pathway.duration_states[duration_state_index(transverse, positive)]
-end
+duration_state
+@defvar function duration_transverse(pathway::Pathway)
+ return duration_state(pathway, true, true) + duration_state(pathway, true, false)
+end
"""
duration_transverse(pathway::Pathway)
@@ -95,10 +99,11 @@ This determines the amount of T2-weighting as ``e^{t/T_2}``, where ``t`` is the
Also see [`duration_dephase`](@ref) for T2'-weighting.
"""
-function duration_transverse(pathway::Pathway)
- return duration_state(pathway, true, true) + duration_state(pathway, true, false)
-end
+duration_transverse
+@defvar function duration_dephase(pathway::Pathway)
+ return duration_state(pathway, true, true) - duration_state(pathway, true, false)
+end
"""
duration_dephase(pathway::Pathway)
@@ -107,23 +112,23 @@ This determines the amount of T2'-weighting as ``e^{t/T_2'}``, where ``t`` is th
Also see [`duration_transverse`](@ref) for T2-weighting.
"""
-function duration_dephase(pathway::Pathway)
- return duration_state(pathway, true, true) - duration_state(pathway, true, false)
-end
+duration_dephase
+@defvar net_dephasing(pathway::Pathway) = pathway.qvec
"""
- qvec(pathway::Pathway)
+ net_dephasing(pathway::Pathway)
-Return net displacement vector in k-space/q-space experienced by the spins following a specific [`Pathway`](@ref).
+Return net displacement vector in k-space/q-space experienced by the spins following a specific [`Pathway`](@ref) in kHz/um.
Only gradients active while the spins are in the transverse plane are considered.
Returns a NamedTuple with the `qvec` for all gradient groups.
"""
-qvec(pathway::Pathway) = pathway.qvec
+net_dephasing
+@defvar area_under_curve(pathway::Pathway) = norm(qvec(pathway))
"""
area_under_curve(pathway::Pathway)
@@ -133,9 +138,10 @@ Only gradients active while the spins are in the transverse plane are considered
Returns a NamedTuple with the `area_under_curve` for all gradient groups.
"""
-area_under_curve(pathway::Pathway) = norm(qvec(pathway))
+area_under_curve
+@defvar bmat(pathway::Pathway) = pathway.bmat
"""
bmat(pathway::Pathway)
@@ -145,8 +151,9 @@ Only gradients active while the spins are in the transverse plane are considered
Returns a NamedTuple with the `bmat` for all gradient groups.
"""
-bmat(pathway::Pathway) = pathway.bmat
+bmat
+@defvar bval(pathway::Pathway) = tr(bmat(pathway))
"""
bval(pathway::Pathway)
@@ -156,7 +163,7 @@ Only gradients active while the spins are in the transverse plane will contribut
Returns a NamedTuple with the `bval` for all gradient groups.
"""
-bval(pathway::Pathway) = tr(bmat(pathway))
+bval
"""
@@ -168,27 +175,6 @@ Multiple pathways might be returned as an array or (named)tuple.
"""
function get_pathway end
-for fn in (:qvec, :area_under_curve, :bmat, :bval, :duration_dephase, :duration_transverse)
- @eval function $fn(seq::Sequence)
- pathway = try
- get_pathway(seq)
- catch e
- if e isa MethodError
- throw(VariableNotAvailable(typeof(seq), $fn))
- end
- rethrow()
- end
- if pathway isa Pathway
- return $fn(pathway)
- elseif pathway isa AbstractVector || pathway isa Tuple
- return $fn.(pathway)
- elseif pathway isa NumedTuple
- return NamedTuple(k => $fn(v) for (k, v) in pairs(pathway))
- end
- error("get_pathway returned unexpected type for $seq")
- end
-end
-
"""
interpret_pulse_effects(number_or_symbol)
--
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