From b82fb7a34fb38d2870add76388d4caa2254835a6 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Wed, 21 Feb 2024 15:15:48 +0000
Subject: [PATCH] Add pathway variables the proper way to the variables list
---
src/MRIBuilder.jl | 2 +-
src/pathways.jl | 3 +-
src/printing.jl | 109 +++-------------------------------------------
src/variables.jl | 8 +++-
4 files changed, 14 insertions(+), 108 deletions(-)
diff --git a/src/MRIBuilder.jl b/src/MRIBuilder.jl
index 9eddcdb..f0086cb 100644
--- a/src/MRIBuilder.jl
+++ b/src/MRIBuilder.jl
@@ -10,7 +10,7 @@ include("components/components.jl")
include("containers/containers.jl")
include("pathways.jl")
include("parts/parts.jl")
-#include("printing.jl")
+include("printing.jl")
import .BuildSequences: build_sequence, global_model, global_scanner, fixed
export build_sequence, global_model, global_scanner, fixed
diff --git a/src/pathways.jl b/src/pathways.jl
index 4ef0139..6fc3a77 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, variables
+import ..Variables: qvec, qval, bmat_gradient, VariableType, effective_time, duration, TR, bmat, bval, area_under_curve, duration_dephase, duration_transverse
"""
@@ -180,7 +180,6 @@ for fn in (:qvec, :area_under_curve, :bmat, :bval, :duration_dephase, :duration_
end
error("get_pathway returned unexpected type for $seq")
end
- @eval variables[$(QuoteNode(fn))] = $fn
end
diff --git a/src/printing.jl b/src/printing.jl
index 5cdbe53..95eebcd 100644
--- a/src/printing.jl
+++ b/src/printing.jl
@@ -1,26 +1,7 @@
module Printing
import JuMP: value
import Printf: @sprintf
-import ..BuildingBlocks: BuildingBlock, get_children_indices, VariableNotAvailable
-import ..Alternatives: AlternativeBlocks
-import ..Overlapping: AbstractOverlapping, waveform, interruptions
-import ..Sequences: Sequence
-import ..Variables: VariableType, duration, start_time, variables, alternative_variables, effective_time, flip_angle
-import ..Pulses: GenericPulse
-
-struct BuildingBlockPrinter{T<:BuildingBlock}
- bb::T
- start_time::Union{Nothing, Number}
- spaces::Int
-end
-
-Base.show(io::IO, block::BuildingBlock) = print(io, BuildingBlockPrinter(block, nothing, 0))
-Base.show(io::IO, seq::Sequence) = print(io, BuildingBlockPrinter(seq, 0., 0))
-
-function Base.show(io::IO, alt_printer::BuildingBlockPrinter{<:AlternativeBlocks})
- block = alt_printer.bb
- print(io, "AlternativeBlocks(", block.name, ", ", length(block), " options)")
-end
+import ..Variables: VariableType, variables, AbstractBlock, VariableNotAvailable, alternative_variables
function _robust_value(possible_number::VariableType)
@@ -42,21 +23,8 @@ end
_robust_value(possible_tuple::Tuple) = _robust_value([possible_tuple...])
-function Base.show(io::IO, printer::BuildingBlockPrinter)
- block = printer.bb
+function Base.show(io::IO, block::AbstractBlock)
print(io, nameof(typeof(block)), "(")
- printed_duration = false
- if !isnothing(printer.start_time)
- print(io, "t=", @sprintf("%.3g", printer.start_time))
-
- dur = _robust_value(duration(block))
- @assert !(dur isa AbstractVector)
- if !isnothing(dur) && !iszero(dur)
- print(io, "-", @sprintf("%.3g", printer.start_time + dur))
- printed_duration = true
- end
- print(io, ", ")
- end
for name in propertynames(block)
ft = fieldtype(typeof(block), name)
if (
@@ -67,11 +35,9 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
continue
end
if (
- block isa AbstractOverlapping && (
- ft <: Union{Nothing, BuildingBlock} ||
- (ft <: AbstractVector && eltype(ft) <: BuildingBlock) ||
- name == :interruptions
- ))
+ ft <: Union{Nothing, AbstractBlock} ||
+ (ft <: AbstractVector && eltype(ft) <: AbstractBlock)
+ )
continue
end
@@ -79,9 +45,6 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
end
for fn in values(variables)
- if printed_duration && fn == duration
- continue
- end
if fn in [fn_alt for (fn_alt, _, _, _) in values(alternative_variables)]
continue
end
@@ -104,68 +67,6 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
end
end
print(io, ")")
- if block isa AbstractOverlapping
- print(io, ":")
- ref_start_time = isnothing(printer.start_time) ? 0. : printer.start_time
- inter = copy(interruptions(block))
- prev_time = 0.
- for (index_grad, (time, grad)) in enumerate(waveform(block))
- while length(inter) > 0 && index_grad == (inter[1].index + 1)
- to_print = popfirst!(inter)
- t_eff = ref_start_time + prev_time + to_print.time
- as_printer = BuildingBlockPrinter(to_print.object, t_eff - effective_time(to_print.object), printer.spaces + 2)
- print(io, "\n", repeat(' ', printer.spaces + 2), "- ", @sprintf("%.3g", t_eff), ": ", as_printer)
- end
- printed_grad = "[" * join(map(v -> @sprintf("%.3g", v), grad), ", ") * "]"
- print(io, "\n", repeat(' ', printer.spaces + 2), "- ", @sprintf("%.3g", ref_start_time + time), ": ", printed_grad)
- prev_time = time
- end
- end
-end
-
-function Base.show(io::IO, printer::BuildingBlockPrinter{<:Sequence})
- seq = printer.bb
- print(io, "Sequence(")
- d = _robust_value(duration(seq))
- if !isnothing(d)
- if !isnothing(printer.start_time)
- print(io, "t=", @sprintf("%.3g", printer.start_time), "-", @sprintf("%.3g", printer.start_time + d), ", ")
- else
- print(io, "duration=", @sprintf("%.3g", d), ",")
- end
- end
- TR = _robust_value(seq.TR)
- if !isnothing(TR) && isfinite(TR)
- print(io, "TR=", Int(round(TR)))
- end
- print(io, "):")
-
- for child_index in get_children_indices(seq)
- child_block = seq[child_index]
- child_printer = BuildingBlockPrinter(
- child_block,
- isnothing(printer.start_time) ? nothing : _robust_value(start_time(seq, child_index) + printer.start_time),
- printer.spaces + 2
- )
- print(io, "\n", repeat(' ', printer.spaces + 2), "- ", child_index, ": ", child_printer)
- end
-
end
-function Base.show(io::IO, printer::BuildingBlockPrinter{<:GenericPulse})
- fp = printer.bb
- pp(value::Number) = @sprintf("%.3g", value)
-
- print(io, "GenericPulse(")
- if isnothing(printer.start_time)
- print(io, "duration=", pp(duration(fp)))
- else
- print(io, "t=", pp(printer.start_time), "-", pp(printer.start_time + duration(fp)))
- end
- print(io, ", flip_angle=", pp(flip_angle(fp)), ", effective_time=", pp(effective_time(fp)), ")")
-end
-
-
-
-
end
\ No newline at end of file
diff --git a/src/variables.jl b/src/variables.jl
index 8ff7409..9a15631 100644
--- a/src/variables.jl
+++ b/src/variables.jl
@@ -36,6 +36,12 @@ all_variables_symbols = [
:sequence => [
:TR => "Time on which an MRI sequence repeats itself in ms.",
:Δ => "Diffusion time in ms (i.e., time between start of the diffusion-weighted gradients).",
+ :qvec => "Net dephasing due to gradients in rad/um.",
+ :area_under_curve => "Net dephasing due to gradients in rad/um (same as [`qvec`](@ref)).",
+ :bmat => "Full 3x3 diffusion-weighting matrix in ms/um^2.",
+ :bval => "Size of diffusion-weighting in ms/um^2 (trace of [`bmat`](@ref)).",
+ :duration_dephase => "Net T2' dephasing experienced over a sequence (in ms).",
+ :duration_transverse => "Net T2 signal loss experienced over a sequence (in ms). This is the total duration spins spent in the transverse plane.",
],
:pulse => [
:flip_angle => "The flip angle of the RF pulse in degrees",
@@ -70,7 +76,7 @@ all_variables_symbols = [
:resolution => "Number of voxels in the final readout. During the optimisation this might produce non-integer values, but this will be fixed after optimsation.",
:oversample => "How much to oversample with ([`nsamples`](@ref) / [`resolution`](@ref))",
:ramp_overlap => "Fraction of overlap between ADC event and underlying gradient pulse ramp (between 0 and 1)."
- ]
+ ],
]
"""
--
GitLab