From 79cefb01846d0e366e7ae789f08e3d7c7c49eb40 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Sat, 25 May 2024 15:51:45 +0100
Subject: [PATCH] Assign type to variables
---
.../gradient_waveforms/changing_gradient_blocks.jl | 4 +++-
.../gradient_waveforms/constant_gradient_blocks.jl | 6 ++++--
src/components/gradient_waveforms/no_gradient_blocks.jl | 2 +-
src/components/instant_gradients.jl | 6 +++---
src/components/pulses/composite_pulses.jl | 5 +++--
src/components/pulses/constant_pulses.jl | 9 +++++----
src/components/pulses/generic_pulses.jl | 9 +++++----
src/components/pulses/sinc_pulses.jl | 4 ++--
src/components/readouts/ADCs.jl | 6 +++---
src/containers/building_blocks.jl | 2 +-
src/parts/epi_readouts.jl | 8 ++++----
11 files changed, 34 insertions(+), 27 deletions(-)
diff --git a/src/components/gradient_waveforms/changing_gradient_blocks.jl b/src/components/gradient_waveforms/changing_gradient_blocks.jl
index b831687..db27616 100644
--- a/src/components/gradient_waveforms/changing_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/changing_gradient_blocks.jl
@@ -36,7 +36,9 @@ end
@defvar begin
duration(cgb::ChangingGradient) = cgb.duration
+end
+@defvar gradient begin
grad_start(cgb::ChangingGradient) = cgb.gradient_strength_start
slew_rate(cgb::ChangingGradient) = cgb.slew_rate
grad_end(cgb::ChangingGradient) = variables.grad_start(cgb) .+ variables.slew_rate(cgb) .* variables.duration(cgb)
@@ -52,7 +54,7 @@ _mult(g1::AbstractVector, g2::AbstractVector) = g1 .* permutedims(g2)
to_vec(cgb::ChangingGradient1D, g::VariableType) = cgb.orientation .* g
to_vec(::ChangingGradient3D, g::AbstractVector) = g
-@defvar begin
+@defvar gradient begin
function bmat_gradient(cgb::ChangingGradient, qstart::AbstractVector)
# grad = (g1 * (duration - t) + g2 * t) / duration
# = g1 + (g2 - g1) * t / duration
diff --git a/src/components/gradient_waveforms/constant_gradient_blocks.jl b/src/components/gradient_waveforms/constant_gradient_blocks.jl
index 0bc243a..397b703 100644
--- a/src/components/gradient_waveforms/constant_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/constant_gradient_blocks.jl
@@ -30,8 +30,10 @@ struct ConstantGradient3D <: ConstantGradient{3}
group :: Union{Symbol, Nothing}
end
-@defvar begin
- duration(cgb::ConstantGradient) = cgb.duration
+
+@defvar duration(cgb::ConstantGradient) = cgb.duration
+
+@defvar gradient begin
gradient_strength(cgb::ConstantGradient) = cgb.gradient_strength
slew_rate(::ConstantGradient1D) = 0.
slew_rate(::ConstantGradient3D) = zero(SVector{3, Float64})
diff --git a/src/components/gradient_waveforms/no_gradient_blocks.jl b/src/components/gradient_waveforms/no_gradient_blocks.jl
index 659e672..cd0dbcc 100644
--- a/src/components/gradient_waveforms/no_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/no_gradient_blocks.jl
@@ -24,7 +24,7 @@ end
gradient_strength(nb::NoGradient, time::Number) = 0.
end
-@defvar begin
+@defvar gradient 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/instant_gradients.jl b/src/components/instant_gradients.jl
index 99d81a2..441a6cb 100644
--- a/src/components/instant_gradients.jl
+++ b/src/components/instant_gradients.jl
@@ -42,7 +42,7 @@ struct InstantGradient1D <: InstantGradient{1}
group :: Union{Nothing, Symbol}
end
-@defvar qval(ig::InstantGradient1D) = ig.qval
+@defvar gradient qval(ig::InstantGradient1D) = ig.qval
"""
An [`InstantGradient`](@ref) with a variable orientation.
@@ -61,12 +61,12 @@ function InstantGradient3D(; qval=[nothing, nothing, nothing], group=nothing, va
return res
end
-@defvar qval(ig::InstantGradient3D) = ig.qvec
+@defvar gradient qval(ig::InstantGradient3D) = ig.qvec
variables.duration.f(::InstantGradient) = 0.
variables.effective_time.f(::InstantGradient) = 0.
-@defvar bmat_gradient(::InstantGradient, qstart=nothing) = zero(SMatrix{3, 3, Float64, 3})
+@defvar gradient bmat_gradient(::InstantGradient, qstart=nothing) = zero(SMatrix{3, 3, Float64, 3})
make_generic(ig::InstantGradient) = ig
diff --git a/src/components/pulses/composite_pulses.jl b/src/components/pulses/composite_pulses.jl
index 91f860c..459c77f 100644
--- a/src/components/pulses/composite_pulses.jl
+++ b/src/components/pulses/composite_pulses.jl
@@ -63,12 +63,13 @@ function wait_times(comp::CompositePulse)
comp.pulse_time - (d[1:end-1] + d[2:end]) / 2
end
-@defvar begin
- duration(pulse::CompositePulse) = (
+@defvar duration(pulse::CompositePulse) = (
0.5 * variables.duration(pulse.pulses[1]) +
0.5 * variables.duration(pulse.pulses[end]) +
pulse.pulse_time * (length(pulse) - 1)
)
+
+@defvar begin
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 a88a4f0..ae9b7a0 100644
--- a/src/components/pulses/constant_pulses.jl
+++ b/src/components/pulses/constant_pulses.jl
@@ -38,18 +38,19 @@ function ConstantPulse(; amplitude=nothing, duration=nothing, phase=nothing, fre
return res
end
-@defvar begin
+@defvar duration(pulse::ConstantPulse) = pulse.duration
+@defvar effective_time(pulse::ConstantPulse) = duration(pulse) / 2
+
+@defvar pulse begin
amplitude(pulse::ConstantPulse) = pulse.amplitude
- 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
+@defvar pulse begin
flip_angle(pulse::ConstantPulse) = amplitude(pulse) * duration(pulse) * 360
inverse_bandwidth(pulse::ConstantPulse) = duration(pulse) * 4
- effective_time(pulse::ConstantPulse) = duration(pulse) / 2
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)
diff --git a/src/components/pulses/generic_pulses.jl b/src/components/pulses/generic_pulses.jl
index 90f18cc..9696194 100644
--- a/src/components/pulses/generic_pulses.jl
+++ b/src/components/pulses/generic_pulses.jl
@@ -68,10 +68,11 @@ end
GenericPulse(pulse::RFPulseComponent, t1::Number, t2::Number) = GenericPulse(make_generic(pulse), t1, t2)
-@defvar begin
- duration(fp::GenericPulse) = maximum(fp.time)
+@defvar duration(fp::GenericPulse) = maximum(fp.time)
+@defvar effective_time(pulse::GenericPulse) = pulse.time[findmax(abs.(pulse.amplitude))]
+
+@defvar pulse begin
amplitude(fp::GenericPulse) = maximum(abs.(fp.amplitude))
- effective_time(pulse::GenericPulse) = pulse.time[findmax(abs.(pulse.amplitude))]
phase(pulse::GenericPulse) = pulse.phase[findmax(abs.(pulse.amplitude))[2]]
flip_angle(pulse::GenericPulse) = sum(get_weights(pulse) .* pulse.amplitude) * 360
function time_halfway_flip(pulse::GenericPulse)
@@ -99,7 +100,7 @@ for fn in (:amplitude, :phase)
end
-@defvar function frequency(gp::GenericPulse, time::Number)
+@defvar pulse function frequency(gp::GenericPulse, time::Number)
i2 = findfirst(t -> t > time, gp.time)
if isnothing(i2)
@assert time ≈ gp.time[end]
diff --git a/src/components/pulses/sinc_pulses.jl b/src/components/pulses/sinc_pulses.jl
index a2b630c..41e9514 100644
--- a/src/components/pulses/sinc_pulses.jl
+++ b/src/components/pulses/sinc_pulses.jl
@@ -79,13 +79,13 @@ function integral_nzero(Nzeros, apodise)
return quadgk(f, 0, Nzeros)[1]
end
-@defvar begin
+@defvar pulse begin
amplitude(pulse::SincPulse) = pulse.amplitude
N_left(pulse::SincPulse) = pulse.Nzeros[1]
N_right(pulse::SincPulse) = pulse.Nzeros[2]
end
-@defvar begin
+@defvar pulse begin
phase(pulse::SincPulse) = pulse.phase
frequency(pulse::SincPulse) = pulse.frequency
lobe_duration(pulse::SincPulse) = pulse.lobe_duration
diff --git a/src/components/readouts/ADCs.jl b/src/components/readouts/ADCs.jl
index 2f1a234..430fc49 100644
--- a/src/components/readouts/ADCs.jl
+++ b/src/components/readouts/ADCs.jl
@@ -48,17 +48,17 @@ function ADC(; resolution=nothing, dwell_time=nothing, time_to_center=nothing, c
return res
end
-@defvar begin
+@defvar readout begin
oversample(adc::ADC) = adc.oversample
dwell_time(adc::ADC) = adc.dwell_time
time_to_center(adc::ADC) = adc.time_to_center
resolution(adc::ADC) = adc.resolution
end
-@defvar nsamples(adc::ADC) = resolution(adc) * oversample(adc)
+@defvar readout nsamples(adc::ADC) = resolution(adc) * oversample(adc)
+@defvar readout_times(adc::ADC) = ((1:Int(nsamples(adc))) .- 0.5) .* dwell_time(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
diff --git a/src/containers/building_blocks.jl b/src/containers/building_blocks.jl
index e46d3ea..3b67ff9 100644
--- a/src/containers/building_blocks.jl
+++ b/src/containers/building_blocks.jl
@@ -8,7 +8,7 @@ import StaticArrays: SVector
import ..Abstract: ContainerBlock, start_time, readout_times, end_time, iter
import ...BuildSequences: global_model
import ...Components: BaseComponent, GradientWaveform, EventComponent, NoGradient, ChangingGradient, ConstantGradient, split_gradient, RFPulseComponent, ReadoutComponent, InstantGradient, edge_times
-import ...Variables: VariableType, make_generic, get_pulse, get_readout, scanner_constraints!, get_gradient, gradient_orientation, variables, @defvar
+import ...Variables: VariableType, make_generic, get_pulse, get_readout, scanner_constraints!, get_gradient, gradient_orientation, variables, @defvar, get_free_variable
"""
Basic BuildingBlock, which can consist of a gradient waveforms with any number of RF pulses/readouts overlaid
diff --git a/src/parts/epi_readouts.jl b/src/parts/epi_readouts.jl
index 92fb34c..de8d2e7 100644
--- a/src/parts/epi_readouts.jl
+++ b/src/parts/epi_readouts.jl
@@ -32,7 +32,7 @@ struct EPIReadout{N} <: BaseSequence{N}
ky_lines :: AbstractVector{<:Integer}
end
-function EPIReadout(; resolution::AbstractVector{<:Integer}, recenter=false, group=:FOV, ky_lines=nothing, variables...)
+function EPIReadout(; resolution::AbstractVector{<:Integer}, recenter=false, group=:FOV, ky_lines=nothing, vars...)
if length(resolution) != 2
error("EPIReadout expects the image resolution in the x- and y-direction.")
end
@@ -49,15 +49,15 @@ function EPIReadout(; resolution::AbstractVector{<:Integer}, recenter=false, gro
get_free_variable(nothing),
ky_lines
)
- apply_simple_constraint!(variables.qval3(res.start_gradient), VariableType[-variables.qval(pos)/2, ky_lines[1] * res.ky_step, 0.])
+ apply_simple_constraint!(variables.qval(res.start_gradient), VariableType[-variables.qval(pos)/2, ky_lines[1] * res.ky_step, 0.])
if recenter
sign = isodd(length(ky_lines)) ? -1 : 1
- apply_simple_constraint!(variables.qval3(res.recenter_gradient), VariableType[sign * variables.qval(pos)/2, -ky_lines[end] * res.ky_step, 0.])
+ apply_simple_constraint!(variables.qval(res.recenter_gradient), VariableType[sign * variables.qval(pos)/2, -ky_lines[end] * res.ky_step, 0.])
end
for shift in unique(ky_lines[2:end] - ky_lines[1:end-1])
res.blips[shift] = Trapezoid(orientation=[0, shift > 0 ? 1 : -1, 0], group=group, qval=abs(shift) * res.ky_step)
end
- set_simple_constraints!(res, variables)
+ set_simple_constraints!(res, vars)
return res
end
--
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