From 99a8cd883f259bb4d740f3be067a520fc19e8df2 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Mon, 12 Feb 2024 17:30:46 +0000
Subject: [PATCH] Add spoilt select gradients
---
.../all_building_blocks.jl | 2 +
.../spoilt_slice_selects.jl | 64 +++++++++----------
src/all_building_blocks/trapezoids.jl | 2 +-
3 files changed, 34 insertions(+), 34 deletions(-)
rename src/{overlapping/gradient_pulses => all_building_blocks}/spoilt_slice_selects.jl (57%)
diff --git a/src/all_building_blocks/all_building_blocks.jl b/src/all_building_blocks/all_building_blocks.jl
index 9581851..8a4d260 100644
--- a/src/all_building_blocks/all_building_blocks.jl
+++ b/src/all_building_blocks/all_building_blocks.jl
@@ -2,9 +2,11 @@ module AllBuildingBlocks
include("base_building_blocks.jl")
include("building_blocks.jl")
include("trapezoids.jl")
+include("spoilt_slice_selects.jl")
import .BaseBuildingBlocks: waveform, waveform_sequence, events, BaseBuildingBlock
import .BuildingBlocks: BuildingBlock
import .Trapezoids: Trapezoid, SliceSelect, LineReadout
+import .SpoiltSliceSelects: SpoiltSliceSelect
end
\ No newline at end of file
diff --git a/src/overlapping/gradient_pulses/spoilt_slice_selects.jl b/src/all_building_blocks/spoilt_slice_selects.jl
similarity index 57%
rename from src/overlapping/gradient_pulses/spoilt_slice_selects.jl
rename to src/all_building_blocks/spoilt_slice_selects.jl
index bd675fd..1a2f438 100644
--- a/src/overlapping/gradient_pulses/spoilt_slice_selects.jl
+++ b/src/all_building_blocks/spoilt_slice_selects.jl
@@ -2,12 +2,11 @@ module SpoiltSliceSelects
import LinearAlgebra: norm
import StaticArrays: SVector
-import JuMP: @variable, @constraint, @objective, objective_function
-import ....BuildingBlocks: RFPulseBlock, set_simple_constraints!
-import ....BuildSequences: global_model, global_scanner
-import ....Variables: VariableType, variables, duration, rise_time, flat_time, effective_time, qvec, gradient_strength, slew_rate, inverse_slice_thickness
-import ....Gradients: ChangingGradientBlock, ConstantGradientBlock
-import ...Abstract: interruptions, waveform_sequence, AbstractOverlapping
+import JuMP: @constraint, @objective, objective_function
+import ...BuildSequences: global_model, global_scanner
+import ...Variables: VariableType, duration, rise_time, flat_time, effective_time, qvec, gradient_strength, slew_rate, inverse_slice_thickness, get_free_variable
+import ...Components: ChangingGradient, ConstantGradient, RFPulseComponent
+import ..BaseBuildingBlocks: BaseBuildingBlock
"""
@@ -17,7 +16,7 @@ Adds slice selection to the `pulse` and surrounds it with spoiler gradients.
## Parameters
- `orientation`: vector with orientation of the slice selection and the spoilers (default: [0, 0, 1])
-- `rotate`: with which user-set parameter will this gradient be rotated (e.g., :FOV). Default: no rotation.
+- `group`: name of the group of the gradient. This will be used to scale and rotate the gradients after optimisation. Scaling is not recommended as this might ruin the spoiling.
## Variables
- `duration`: total duration of the block in ms.
@@ -29,24 +28,24 @@ struct SpoiltSliceSelect <: AbstractOverlapping
rise_time1 :: VariableType
flat_time1 :: VariableType
diff_time :: VariableType
- pulse :: RFPulseBlock
+ pulse :: RFPulseComponent
flat_time2 :: VariableType
fall_time2 :: VariableType
- rotate :: Union{Nothing, Symbol}
+ group :: Union{Nothing, Symbol}
slew_rate :: Number
end
-function SpoiltSliceSelect(pulse; orientation=[0, 0, 1], rotate=nothing, spoiler_scale=nothing, kwargs...)
+function SpoiltSliceSelect(pulse::RFPulseComponent; orientation=[0, 0, 1], group=nothing, spoiler_scale=nothing, kwargs...)
model = global_model()
res = SpoiltSliceSelect(
orientation ./ norm(orientation),
- @variable(model, start=0.1),
- @variable(model, start=0.1),
- @variable(model, start=0.05),
+ get_free_variable(nothing; start=0.1)
+ get_free_variable(nothing; start=0.1)
+ get_free_variable(nothing; start=0.05)
pulse,
- @variable(model, start=0.1),
- @variable(model, start=0.1),
- rotate,
+ get_free_variable(nothing; start=0.1)
+ get_free_variable(nothing; start=0.1)
+ group,
slew_rate(global_scanner())
)
for time_var in (res.rise_time1, res.flat_time1, res.diff_time, res.flat_time2, res.fall_time2)
@@ -55,15 +54,14 @@ function SpoiltSliceSelect(pulse; orientation=[0, 0, 1], rotate=nothing, spoiler
@constraint model res.diff_time <= res.rise_time1
@constraint model res.diff_time <= res.fall_time2
- dim = findfirst(v -> !iszero(v), res.orientation)
- @constraint model qvec(res, nothing, 1)[dim] == qvec(res, 1, nothing)[dim]
+ @constraint model qvec(res, nothing, 1) == qvec(res, 1, nothing)
if !isnothing(spoiler_scale)
if spoiler_scale == :min # note that spoiler_scale is inverse of qvec
- @objective model Min objective_function(model) - qvec(res, nothing, 1)[dim]
+ @objective model Min objective_function(model) - qvec(res, nothing, 1)
elseif spoiler_scale == :max
- @objective model Min objective_function(model) + qvec(res, nothing, 1)[dim]
+ @objective model Min objective_function(model) + qvec(res, nothing, 1)
else
- @constraint model (qvec(res, nothing, 1)[dim] ./ res.orientation[dim]) >= 2Ï€ * 1e-3 / spoiler_scale
+ @constraint model qvec(res, nothing, 1) >= 2Ï€ * 1e-3 / spoiler_scale
end
end
set_simple_constraints!(res, kwargs)
@@ -79,15 +77,15 @@ duration_trap2(spoilt::SpoiltSliceSelect) = 2 * spoilt.fall_time2 + spoilt.flat_
function waveform_sequence(spoilt::SpoiltSliceSelect)
slew = slew_rate(spoilt)
- (grad1, grad2, grad3) = [g .* spoilt.orientation for g in all_gradient_strengths(spoilt)]
+ (grad1, grad2, grad3) = [g for g in all_gradient_strengths(spoilt)]
return [
- ChangingGradientBlock(zeros(3), slew, rise_time(spoilt)[1], spoilt.rotate, nothing),
- ConstantGradientBlock(grad1, flat_time(spoilt)[1], spoilt.rotate, nothing),
- ChangingGradientBlock(grad1, -slew, fall_time(spoilt)[1], spoilt.rotate, nothing),
- ConstantGradientBlock(grad2, duration(spoilt.pulse), spoilt.rotate, nothing),
- ChangingGradientBlock(grad2, slew, rise_time(spoilt)[2], spoilt.rotate, nothing),
- ConstantGradientBlock(grad3, flat_time(spoilt)[2], spoilt.rotate, nothing),
- ChangingGradientBlock(grad3, -slew, fall_time(spoilt)[2], spoilt.rotate, nothing),
+ ChangingGradient(0., slew, rise_time(spoilt)[1], spoilt.rotate, nothing),
+ ConstantGradient(grad1, flat_time(spoilt)[1], spoilt.rotate, nothing),
+ ChangingGradient(grad1, -slew, fall_time(spoilt)[1], spoilt.rotate, nothing),
+ ConstantGradient(grad2, duration(spoilt.pulse), spoilt.rotate, nothing),
+ ChangingGradient(grad2, slew, rise_time(spoilt)[2], spoilt.rotate, nothing),
+ ConstantGradient(grad3, flat_time(spoilt)[2], spoilt.rotate, nothing),
+ ChangingGradient(grad3, -slew, fall_time(spoilt)[2], spoilt.rotate, nothing),
]
end
interruptions(spoilt::SpoiltSliceSelect) = [(index=4, time=effective_time(spoilt.pulse), object=spoilt.pulse)]
@@ -96,12 +94,12 @@ rise_time(spoilt::SpoiltSliceSelect) = (spoilt.rise_time1, spoilt.fall_time2 - s
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.orientation .* spoilt.slew_rate
+slew_rate(spoilt::SpoiltSliceSelect) = spoilt.slew_rate
inverse_slice_thickness(spoilt::SpoiltSliceSelect) = spoilt.slew_rate * spoilt.diff_time * duration(spoilt.pulse) * 1e3
function all_gradient_strengths(spoilt::SpoiltSliceSelect)
- grad1 = spoilt.slew_rate .* rise_time(spoilt)[1]
- grad2 = grad1 .- spoilt.slew_rate .* flat_time(spoilt)[1]
- grad3 = spoilt.slew_rate .* fall_time(spoilt)[2]
+ grad1 = spoilt.slew_rate * rise_time(spoilt)[1]
+ grad2 = grad1 - spoilt.slew_rate * flat_time(spoilt)[1]
+ grad3 = spoilt.slew_rate * fall_time(spoilt)[2]
return [grad1, grad2, grad3]
end
diff --git a/src/all_building_blocks/trapezoids.jl b/src/all_building_blocks/trapezoids.jl
index e3678e8..21a1dff 100644
--- a/src/all_building_blocks/trapezoids.jl
+++ b/src/all_building_blocks/trapezoids.jl
@@ -9,7 +9,7 @@ import LinearAlgebra: norm
import ...Variables: qvec, rise_time, flat_time, slew_rate, gradient_strength, variables, duration, δ, get_free_variable, VariableType, inverse_bandwidth, effective_time, qval_square, duration, set_simple_constraints!, scanner_constraints!, inverse_slice_thickness
import ...Variables: Variables, all_variables_symbols, dwell_time, inverse_fov, inverse_voxel_size, fov, voxel_size
import ...BuildSequences: global_model
-import ...Components: ChangingGradient, ConstantGradient, NoGradient, RFPulseComponent, ADC
+import ...Components: ChangingGradient, ConstantGradient, RFPulseComponent, ADC
import ..BaseBuildingBlocks: BaseBuildingBlock
--
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