From 201ce04e6d1a067e7b22dc96d31e96d92f7c9551 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Fri, 24 May 2024 16:45:12 +0100
Subject: [PATCH] Also apply esc to variable definition body
---
.../changing_gradient_blocks.jl | 11 +++++------
.../constant_gradient_blocks.jl | 8 ++++----
.../gradient_waveforms/no_gradient_blocks.jl | 2 ++
src/components/pulses/composite_pulses.jl | 8 ++++----
src/components/pulses/constant_pulses.jl | 9 ++++++---
src/components/pulses/sinc_pulses.jl | 18 +++++++++++++-----
src/components/readouts/ADCs.jl | 12 ++++++++----
src/containers/abstract.jl | 4 ++--
src/containers/alternatives.jl | 2 +-
src/containers/base_sequences.jl | 2 +-
src/containers/building_blocks.jl | 16 ++++++++--------
src/parts/spoilt_slice_selects.jl | 7 +++++--
src/parts/trapezoids.jl | 11 +++++++----
src/variables.jl | 11 ++---------
14 files changed, 68 insertions(+), 53 deletions(-)
diff --git a/src/components/gradient_waveforms/changing_gradient_blocks.jl b/src/components/gradient_waveforms/changing_gradient_blocks.jl
index 7748a06..b831687 100644
--- a/src/components/gradient_waveforms/changing_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/changing_gradient_blocks.jl
@@ -34,17 +34,16 @@ struct ChangingGradient3D <: ChangingGradient{3}
group :: Union{Nothing, Symbol}
end
-
@defvar begin
duration(cgb::ChangingGradient) = cgb.duration
grad_start(cgb::ChangingGradient) = cgb.gradient_strength_start
slew_rate(cgb::ChangingGradient) = cgb.slew_rate
- grad_end(cgb::ChangingGradient) = grad_start(cgb) .+ slew_rate(cgb) .* duration(cgb)
- gradient_strength(cgb::ChangingGradient) = max.(grad_start(cgb), grad_end(cgb))
- qval(cgb::ChangingGradient) = (grad_start(cgb) .+ grad_end(cgb)) .* (duration(cgb) * π)
+ grad_end(cgb::ChangingGradient) = variables.grad_start(cgb) .+ variables.slew_rate(cgb) .* variables.duration(cgb)
+ gradient_strength(cgb::ChangingGradient) = max.(variables.grad_start(cgb), variables.grad_end(cgb))
+ qval(cgb::ChangingGradient) = (variables.grad_start(cgb) .+ variables.grad_end(cgb)) .* (variables.duration(cgb) * π)
- gradient_strength(cgb::ChangingGradient, time::Number) = slew_rate(cgb) .* time .+ grad_start(cgb)
+ gradient_strength(cgb::ChangingGradient, time::Number) = variables.slew_rate(cgb) .* time .+ variables.grad_start(cgb)
end
_mult(g1::VariableType, g2::VariableType) = g1 * g2
@@ -69,7 +68,7 @@ to_vec(::ChangingGradient3D, g::AbstractVector) = g
return (
_mult(qstart, qstart) .* duration(cgb) .+
duration(cgb)^2 .* _mult(qstart, grad_aver) .* 2Ï€ ./ 3 .+
- bmat_gradient(cgb)
+ variables.bmat_gradient(cgb)
)
end
diff --git a/src/components/gradient_waveforms/constant_gradient_blocks.jl b/src/components/gradient_waveforms/constant_gradient_blocks.jl
index 72559b0..0bc243a 100644
--- a/src/components/gradient_waveforms/constant_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/constant_gradient_blocks.jl
@@ -35,10 +35,10 @@ end
gradient_strength(cgb::ConstantGradient) = cgb.gradient_strength
slew_rate(::ConstantGradient1D) = 0.
slew_rate(::ConstantGradient3D) = zero(SVector{3, Float64})
- qval(cgb::ConstantGradient1D) = duration(cgb) * gradient_strength(cgb) * 2Ï€
- qval(cgb::ConstantGradient3D) = duration(cgb) .* gradient_strength(cgb) .* 2Ï€
+ qval(cgb::ConstantGradient1D) = variables.duration(cgb) * variables.gradient_strength(cgb) * 2Ï€
+ qval(cgb::ConstantGradient3D) = variables.duration(cgb) .* variables.gradient_strength(cgb) .* 2Ï€
- gradient_strength(cgb::ConstantGradient, time::Number) = gradient_strength(cgb)
+ gradient_strength(cgb::ConstantGradient, time::Number) = variables.gradient_strength(cgb)
end
_mult(g1::VariableType, g2::VariableType) = g1 * g2
@@ -62,7 +62,7 @@ to_vec(::ConstantGradient3D, g::AbstractVector) = g
return (
_mult(qstart, qstart) .* duration(cgb) .+
_mult(qstart, grad) .* duration(cgb)^2 .+
- bmat_gradient(cgb)
+ variables.bmat_gradient(cgb)
)
end
end
diff --git a/src/components/gradient_waveforms/no_gradient_blocks.jl b/src/components/gradient_waveforms/no_gradient_blocks.jl
index 93abce4..659e672 100644
--- a/src/components/gradient_waveforms/no_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/no_gradient_blocks.jl
@@ -22,7 +22,9 @@ end
@defvar begin
duration(ngb::NoGradient) = ngb.duration
gradient_strength(nb::NoGradient, time::Number) = 0.
+end
+@defvar begin
bmat_gradient(::NoGradient) = 0.
bmat_gradient(ngb::NoGradient, qstart::VariableType) = qstart^2 * duration(ngb)
bmat_gradient(ngb::NoGradient, qstart::AbstractVector{<:VariableType}) = @. qstart * permutedims(qstart) * duration(ngb)
diff --git a/src/components/pulses/composite_pulses.jl b/src/components/pulses/composite_pulses.jl
index 53d9778..91f860c 100644
--- a/src/components/pulses/composite_pulses.jl
+++ b/src/components/pulses/composite_pulses.jl
@@ -65,12 +65,12 @@ end
@defvar begin
duration(pulse::CompositePulse) = (
- 0.5 * duration(pulse.pulses[1]) +
- 0.5 * duration(pulse.pulses[end]) +
+ 0.5 * variables.duration(pulse.pulses[1]) +
+ 0.5 * variables.duration(pulse.pulses[end]) +
pulse.pulse_time * (length(pulse) - 1)
)
- flip_angle(pulse::CompositePulse) = sum(flip_angle.(pulse.pulses))
- effective_time(pulse::CompositePulse) = duration(pulse) / 2
+ flip_angle(pulse::CompositePulse) = sum(variables.flip_angle.(pulse.pulses))
+ effective_time(pulse::CompositePulse) = variables.duration(pulse) / 2
end
diff --git a/src/components/pulses/constant_pulses.jl b/src/components/pulses/constant_pulses.jl
index dfe427e..a88a4f0 100644
--- a/src/components/pulses/constant_pulses.jl
+++ b/src/components/pulses/constant_pulses.jl
@@ -43,13 +43,16 @@ end
duration(pulse::ConstantPulse) = pulse.duration
phase(pulse::ConstantPulse) = pulse.phase
frequency(pulse::ConstantPulse) = pulse.frequency
+ amplitude(pulse::ConstantPulse, time::Number) = variables.amplitude(pulse)
+end
+
+@defvar begin
flip_angle(pulse::ConstantPulse) = amplitude(pulse) * duration(pulse) * 360
inverse_bandwidth(pulse::ConstantPulse) = duration(pulse) * 4
effective_time(pulse::ConstantPulse) = duration(pulse) / 2
- amplitude(pulse::ConstantPulse, time::Number) = amplitude(pulse)
- phase(pulse::ConstantPulse, time::Number) = phase(pulse) + frequency(pulse) * (time - effective_time(pulse)) * 360.
- frequency(pulse::ConstantPulse, time::Number) = frequency(pulse)
+ phase(pulse::ConstantPulse, time::Number) = variables.phase(pulse) + variables.frequency(pulse) * (time - variables.effective_time(pulse)) * 360.
+ frequency(pulse::ConstantPulse, time::Number) = variables.frequency(pulse)
end
function make_generic(block::ConstantPulse)
diff --git a/src/components/pulses/sinc_pulses.jl b/src/components/pulses/sinc_pulses.jl
index a07d5a8..a2b630c 100644
--- a/src/components/pulses/sinc_pulses.jl
+++ b/src/components/pulses/sinc_pulses.jl
@@ -83,17 +83,25 @@ end
amplitude(pulse::SincPulse) = pulse.amplitude
N_left(pulse::SincPulse) = pulse.Nzeros[1]
N_right(pulse::SincPulse) = pulse.Nzeros[2]
- duration(pulse::SincPulse) = (N_left(pulse) + N_right(pulse)) * lobe_duration(pulse)
+end
+
+@defvar begin
phase(pulse::SincPulse) = pulse.phase
frequency(pulse::SincPulse) = pulse.frequency
- flip_angle(pulse::SincPulse) = (pulse.norm_flip_angle[1] + pulse.norm_flip_angle[2]) * amplitude(pulse) * lobe_duration(pulse) * 360
lobe_duration(pulse::SincPulse) = pulse.lobe_duration
+end
+
+@defvar begin
+ duration(pulse::SincPulse) = (N_left(pulse) + N_right(pulse)) * lobe_duration(pulse)
+ flip_angle(pulse::SincPulse) = (pulse.norm_flip_angle[1] + pulse.norm_flip_angle[2]) * amplitude(pulse) * lobe_duration(pulse) * 360
inverse_bandwidth(pulse::SincPulse) = lobe_duration(pulse)
effective_time(pulse::SincPulse) = N_left(pulse) * lobe_duration(pulse)
+end
- amplitude(pulse::SincPulse, time::Number) = amplitude(pulse) * normalised_function(abs((time - effective_time(pulse))) / lobe_duration(pulse), N_left(pulse), N_right(pulse); apodise=pulse.apodise)
- phase(pulse::SincPulse, time::Number) = phase(pulse) + frequency(pulse) * (time - effective_time(pulse)) * 360.
- frequency(pulse::SincPulse, time::Number) = frequency(pulse)
+@defvar begin
+ amplitude(pulse::SincPulse, time::Number) = variables.amplitude(pulse) * normalised_function(abs((time - effective_time(pulse))) / lobe_duration(pulse), N_left(pulse), N_right(pulse); apodise=pulse.apodise)
+ phase(pulse::SincPulse, time::Number) = variables.phase(pulse) + variables.frequency(pulse) * (time - effective_time(pulse)) * 360.
+ frequency(pulse::SincPulse, time::Number) = variables.frequency(pulse)
end
function make_generic(block::SincPulse)
diff --git a/src/components/readouts/ADCs.jl b/src/components/readouts/ADCs.jl
index 1ed5e5b..2f1a234 100644
--- a/src/components/readouts/ADCs.jl
+++ b/src/components/readouts/ADCs.jl
@@ -49,16 +49,20 @@ function ADC(; resolution=nothing, dwell_time=nothing, time_to_center=nothing, c
end
@defvar begin
- readout_times(adc::ADC) = ((1:Int(nsamples(adc))) .- 0.5) .* dwell_time(adc)
oversample(adc::ADC) = adc.oversample
- nsamples(adc::ADC) = resolution(adc) * oversample(adc)
dwell_time(adc::ADC) = adc.dwell_time
- duration(adc::ADC) = nsamples(adc) * dwell_time(adc)
time_to_center(adc::ADC) = adc.time_to_center
- effective_time(adc::ADC) = time_to_center(adc)
resolution(adc::ADC) = adc.resolution
end
+@defvar nsamples(adc::ADC) = resolution(adc) * oversample(adc)
+
+@defvar begin
+ readout_times(adc::ADC) = ((1:Int(nsamples(adc))) .- 0.5) .* dwell_time(adc)
+ duration(adc::ADC) = nsamples(adc) * dwell_time(adc)
+ effective_time(adc::ADC) = time_to_center(adc)
+end
+
function fixed(adc::ADC)
# round nsamples during fixing
r = Int(round(value(resolution(adc)), RoundNearest))
diff --git a/src/containers/abstract.jl b/src/containers/abstract.jl
index d4ed89e..ea301a8 100644
--- a/src/containers/abstract.jl
+++ b/src/containers/abstract.jl
@@ -34,8 +34,8 @@ end_time(block::AbstractBlock) = duration(block)
end_time(block::Tuple{<:VariableType, <:AbstractBlock}) = duration(block[2])
@defvar begin
- effective_time(container::ContainerBlock, index, indices...) = start_time(container, index) + effective_time(container[index], indices...)
- effective_time(block::Tuple{<:VariableType, <:AbstractBlock}) = block[1] + effective_time(block[2])
+ effective_time(container::ContainerBlock, index, indices...) = start_time(container, index) + variables.effective_time(container[index], indices...)
+ effective_time(block::Tuple{<:VariableType, <:AbstractBlock}) = block[1] + variables.effective_time(block[2])
end
"""
effective_time(container, indices...)
diff --git a/src/containers/alternatives.jl b/src/containers/alternatives.jl
index 0c75bbe..731042b 100644
--- a/src/containers/alternatives.jl
+++ b/src/containers/alternatives.jl
@@ -23,7 +23,7 @@ AlternativeBlocks(name::Symbol, options_vector::AbstractVector) = AlternativeBlo
Base.getindex(alt::AlternativeBlocks, index) = alt.options[index]
Base.length(alt::AlternativeBlocks) = length(alt.options)
-@defvar duration(alt::AlternativeBlocks) = maximum(duration.(values(alt.options)))
+@defvar duration(alt::AlternativeBlocks) = maximum(variables.duration.(values(alt.options)))
"""
match_blocks!(alternatives, function)
diff --git a/src/containers/base_sequences.jl b/src/containers/base_sequences.jl
index 5f6d45a..7f80bef 100644
--- a/src/containers/base_sequences.jl
+++ b/src/containers/base_sequences.jl
@@ -104,7 +104,7 @@ repetition_time(bs::BaseSequence) = duration(bs)
@defvar begin
duration(bs::BaseSequence{0}) = 0.
- duration(bs::BaseSequence) = sum(duration.(bs); init=0.)
+ duration(bs::BaseSequence) = sum(variables.duration.(bs); init=0.)
end
function edge_times(seq::BaseSequence; tol=1e-6)
diff --git a/src/containers/building_blocks.jl b/src/containers/building_blocks.jl
index 8849341..e46d3ea 100644
--- a/src/containers/building_blocks.jl
+++ b/src/containers/building_blocks.jl
@@ -142,7 +142,7 @@ function start_time(building_block::BaseBuildingBlock, index)
error("Building block with index '$index' not found")
end
-@defvar duration(bb::BaseBuildingBlock) = sum([duration(wv) for (_, wv) in waveform_sequence(bb)])
+@defvar duration(bb::BaseBuildingBlock) = sum([variables.duration(wv) for (_, wv) in waveform_sequence(bb)])
# Pathway support
"""
@@ -195,18 +195,18 @@ end
if (!isnothing(index1)) && (index1 == index2)
return 0.
end
- res = sum([qval(wv) for (_, wv) in waveform_sequence(bb, index1, index2)])
+ res = sum([variables.qval(wv) for (_, wv) in waveform_sequence(bb, index1, index2)])
t1 = isnothing(index1) ? 0. : start_time(bb, index1)
t2 = isnothing(index2) ? duration(bb) : start_time(bb, index2)
for (key, event) in events(bb)
if event isa InstantGradient && (t1 <= start_time(bb, key) <= t2)
- res = res .+ qval(event)
+ res = res .+ variables.qval(event)
end
end
return res
end
- qval(bb::BaseBuildingBlock) = qval(bb, nothing, nothing)
+ qval(bb::BaseBuildingBlock) = variables.qval(bb, nothing, nothing)
function bmat_gradient(bb::BaseBuildingBlock, qstart, index1, index2)
if (!isnothing(index1)) && (index1 == index2)
@@ -216,12 +216,12 @@ end
qcurrent = Vector{VariableType}(qstart)
for (_, part) in waveform_sequence(bb, index1, index2)
- result = result .+ bmat_gradient(part, qcurrent)
+ result = result .+ variables.bmat_gradient(part, qcurrent)
qcurrent = qcurrent .+ qval3(part, qcurrent)
end
return result
end
- bmat_gradient(bb::BaseBuildingBlock, qstart) = bmat_gradient(bb, qstart, nothing, nothing)
+ bmat_gradient(bb::BaseBuildingBlock, qstart) = variables.bmat_gradient(bb, qstart, nothing, nothing)
end
"""
@@ -277,7 +277,7 @@ end
@defvar function gradient_strength(bb::BaseBuildingBlock, time::Number)
(grad, time) = get_gradient(bb, time)
- return gradient_strength(grad, time)
+ return variables.gradient_strength(grad, time)
end
"""
@@ -363,7 +363,7 @@ end
error("BuildingBlock contains multiple RF pulse or readout events, so `effective_time` is not defined.")
end
index = index[1]
- return effective_time(bb, index)
+ return variables.effective_time(bb, index)
end
"""
diff --git a/src/parts/spoilt_slice_selects.jl b/src/parts/spoilt_slice_selects.jl
index ebaa4e3..fd70b36 100644
--- a/src/parts/spoilt_slice_selects.jl
+++ b/src/parts/spoilt_slice_selects.jl
@@ -112,9 +112,12 @@ Base.getindex(spoilt::SpoiltSliceSelect, ::Val{:fall2}) = ChangingGradient(slew_
rise_time(spoilt::SpoiltSliceSelect) = (spoilt.rise_time1, spoilt.fall_time2 - spoilt.diff_time)
flat_time(spoilt::SpoiltSliceSelect) = (spoilt.flat_time1, spoilt.flat_time2)
fall_time(spoilt::SpoiltSliceSelect) = (spoilt.rise_time1 - spoilt.diff_time, spoilt.fall_time2)
- duration(spoilt::SpoiltSliceSelect) = sum(rise_time(spoilt)) + sum(flat_time(spoilt)) + sum(flat_time(spoilt)) + duration(spoilt.pulse)
slew_rate(spoilt::SpoiltSliceSelect) = spoilt.slew_rate
- inverse_slice_thickness(spoilt::SpoiltSliceSelect) = spoilt.slew_rate * spoilt.diff_time * duration(spoilt.pulse) * 1e3
+end
+
+@defvar begin
+ duration(spoilt::SpoiltSliceSelect) = sum(rise_time(spoilt)) + sum(flat_time(spoilt)) + sum(flat_time(spoilt)) + variables.duration(spoilt.pulse)
+ inverse_slice_thickness(spoilt::SpoiltSliceSelect) = slew_rate(spoilt) * spoilt.diff_time * variables.duration(spoilt.pulse) * 1e3
gradient_strength(spoilt::SpoiltSliceSelect) = slew_rate(spoilt) * max(spoilt.rise_time1, spoilt.fall_time2)
end
diff --git a/src/parts/trapezoids.jl b/src/parts/trapezoids.jl
index 0059b18..7fc7aa6 100644
--- a/src/parts/trapezoids.jl
+++ b/src/parts/trapezoids.jl
@@ -109,14 +109,17 @@ get_group(pg::BaseTrapezoid) = get_group(get_gradient(pg))
@defvar begin
rise_time(pg::Trapezoid) = pg.rise_time
flat_time(pg::Trapezoid) = pg.flat_time
- gradient_strength(g::Trapezoid) = slew_rate(g) .* rise_time(g)
slew_rate(g::Trapezoid) = g.slew_rate
- diffusion_time(g::Trapezoid) = rise_time(g) + flat_time(g)
- duration(g::BaseTrapezoid) = 2 * rise_time(g) + flat_time(g)
+end
- qval(g::BaseTrapezoid, ::Nothing, ::Nothing) = δ(g) .* gradient_strength(g) .* 2π
+@defvar begin
+ gradient_strength(g::Trapezoid) = slew_rate(g) .* rise_time(g)
+ δ(g::Trapezoid) = rise_time(g) + flat_time(g)
+ duration(g::BaseTrapezoid) = 2 * rise_time(g) + flat_time(g)
end
+@defvar qval(g::BaseTrapezoid, ::Nothing, ::Nothing) = variables.δ(g) .* gradient_strength(g) .* 2π
+
adjustable(::BaseTrapezoid) = :gradient
function adjust_internal(trap::Trapezoid1D; orientation=nothing, scale=1., rotation=nothing)
diff --git a/src/variables.jl b/src/variables.jl
index 7220259..20a6541 100644
--- a/src/variables.jl
+++ b/src/variables.jl
@@ -95,6 +95,7 @@ variables = _Variables(Dict{Symbol, AnyVariable}())
Base.getindex(v::_Variables, i::Symbol) = getfield(v, :variables)[i]
Base.keys(v::_Variables) = keys(getfield(v, :variables))
+Base.values(v::_Variables) = values(getfield(v, :variables))
Base.propertynames(v::_Variables) = Tuple(keys(getfield(v, :variables)))
@@ -441,16 +442,8 @@ function scanner_constraints!(bb::AbstractBlock)
value = nothing
try
value = f(bb)
- catch e
- continue
- continue
- else
- rethrow()
- end
+ catch
continue
- else
- rethrow()
- end
end
if value isa AbstractVector
for v in value
--
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