From 65d76dcc3c8c76aa8b872af92735ecc3a783befe Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Tue, 20 Feb 2024 18:53:57 +0000
Subject: [PATCH] Treat pathway values as variables
---
src/MRIBuilder.jl | 4 ++--
src/pathways.jl | 61 ++++++++++++++++++++++++++++++++++-------------
2 files changed, 46 insertions(+), 19 deletions(-)
diff --git a/src/MRIBuilder.jl b/src/MRIBuilder.jl
index cf2f428..ec1160c 100644
--- a/src/MRIBuilder.jl
+++ b/src/MRIBuilder.jl
@@ -27,8 +27,8 @@ 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
export ContainerBlock, start_time, end_time, waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Wait, BaseSequence, nrepeat, Sequence, AlternativeBlocks, match_blocks!, get_index_single_TR
-import .Pathways: Pathway, duration_transverse, duration_dephase, bval, bmat
-export Pathway, duration_transverse, duration_dephase, bval, bmat
+import .Pathways: Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
+export Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
import .Parts: excitation_pulse, refocus_pulse, epi_readout, single_line_readout, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout
export excitation_pulse, refocus_pulse, epi_readout, single_line_readout, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout
diff --git a/src/pathways.jl b/src/pathways.jl
index 1724950..3e020fe 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, DelayedEvent
import ..Containers: BaseSequence, Sequence, BaseBuildingBlock, waveform, events, waveform_sequence, start_time, AlternativeBlocks
-import ..Variables: qvec, qval, bmat_gradient, VariableType, effective_time, duration, TR
+import ..Variables: qvec, qval, bmat_gradient, VariableType, effective_time, duration, TR, variables
"""
@@ -112,54 +112,81 @@ end
"""
- qvec(pathway::Pathway; group=nothing)
+ qvec(pathway::Pathway)
Return net displacement vector in k-space/q-space experienced by the spins following a specific [`Pathway`](@ref).
Only gradients active while the spins are in the transverse plane are considered.
-By default gradients that have been added to a specific `group` are ignored.
-You can set `group=<name>` to consider a specific `group.
+Returns a NamedTuple with the `qvec` for all gradient groups.
"""
-qvec(pathway::Pathway; group=nothing) = get(pathway.qvec, group, zero(SVector{3, Float64}))
+qvec(pathway::Pathway, group) = pathway.qvec[group]
"""
- area_under_curve(pathway::Pathway; group=nothing)
+ area_under_curve(pathway::Pathway)
Return net displacement in k-space (i.e., spoiling) experienced by the spins following a specific [`Pathway`](@ref).
Only gradients active while the spins are in the transverse plane are considered.
-By default gradients that have been added to a specific `group` are ignored.
-You can set `group=<name>` to consider a specific `group.
+Returns a NamedTuple with the `area_under_curve` for all gradient groups.
"""
-area_under_curve(pathway::Pathway; group=nothing) = qval(pathway; group=group)
+area_under_curve(pathway::Pathway, group) = norm(qvec(pathway, group))
"""
- bmat(pathway::Pathway; group=nothing)
+ bmat(pathway::Pathway)
Return 3x3 diffusion-weighted matrix experienced by the spins following a specific [`Pathway`](@ref) in rad^2 ms/um^2.
Only gradients active while the spins are in the transverse plane are considered.
-By default gradients that have been added to a specific `group` are ignored.
-You can set `group=<name>` to consider a specific `group.
+Returns a NamedTuple with the `bmat` for all gradient groups.
"""
-bmat(pathway::Pathway; group=nothing) = get(pathway.bmat, group, zero(SMatrix{3, 3, Float64, 9}))
+bmat(pathway::Pathway, group) = pathway.bmat[group]
"""
- bval(pathway::Pathway; group=nothing)
+ bval(pathway::Pathway)
Return size of diffusion-weighting experienced by the spins following a specific [`Pathway`](@ref) in rad^2 ms/um^2.
Only gradients active while the spins are in the transverse plane will contribute to the diffusion weighting.
-By default gradients that have been added to a specific `group` are ignored.
-You can set `group=<name>` to consider a specific `group.
+Returns a NamedTuple with the `bval` for all gradient groups.
"""
-bval(pathway::Pathway; group=nothing) = tr(bmat(pathway; group=group))
+bval(pathway::Pathway, group) = tr(bmat(pathway, group))
+
+
+"""
+ get_pathway(sequence)
+
+Gets the main [`PathWay`](@ref) that spins are expected to experience in the sequence.
+
+Multiple pathways might be returned as an array or (named)tuple.
+"""
+function get_pathway end
+
+for fn in (:qvec, :area_under_curve, :bmat, :bval)
+ @eval function $fn(pathway::Pathway)
+ return NamedTuple(group => $fn(pathway, group) for group in keys(pathway.qvec))
+ end
+end
+
+for fn in (:qvec, :area_under_curve, :bmat, :bval, :duration_dephase, :duration_transverse)
+ @eval function $fn(seq::Sequence)
+ pathway = get_pathway(seq)
+ 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 $seq")
+ end
+ @eval variables[$(QuoteNode(fn))] = $fn
+end
"""
--
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