From c86d3118b783021d5af848890fcdc1a26943ebde Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Thu, 30 May 2024 14:54:40 +0100
Subject: [PATCH] Fix tests
---
.../constant_gradient_blocks.jl | 2 +-
src/components/instant_gradients.jl | 4 +--
src/components/pulses/generic_pulses.jl | 10 +++---
src/components/pulses/sinc_pulses.jl | 2 +-
src/containers/abstract.jl | 7 ++--
src/containers/building_blocks.jl | 2 +-
src/parts/trapezoids.jl | 8 ++---
src/pathways.jl | 4 +--
src/variables.jl | 5 +--
test/test_IO.jl | 8 ++---
test/test_components.jl | 2 +-
test/test_sequences.jl | 32 +++++++++----------
12 files changed, 42 insertions(+), 44 deletions(-)
diff --git a/src/components/gradient_waveforms/constant_gradient_blocks.jl b/src/components/gradient_waveforms/constant_gradient_blocks.jl
index 7e6252f..0fb86ba 100644
--- a/src/components/gradient_waveforms/constant_gradient_blocks.jl
+++ b/src/components/gradient_waveforms/constant_gradient_blocks.jl
@@ -66,7 +66,7 @@ _mult(g1::AbstractVector, g2::AbstractVector) = g1 .* permutedims(g2)
end
function split_gradient(cgb::ConstantGradient, times::VariableType...)
- durations = [times[1], [t[2] - t[1] for t in zip(times[1:end-1], times[2:end])]..., duration(cgb) - times[end]]
+ durations = [times[1], [t[2] - t[1] for t in zip(times[1:end-1], times[2:end])]..., variables.duration(cgb) - times[end]]
if cgb isa ConstantGradient1D
return [ConstantGradient1D(cgb.gradient_strength, cgb.orientation, d, cgb.group) for d in durations]
else
diff --git a/src/components/instant_gradients.jl b/src/components/instant_gradients.jl
index ce1127b..ca2def1 100644
--- a/src/components/instant_gradients.jl
+++ b/src/components/instant_gradients.jl
@@ -57,8 +57,8 @@ end
@defvar gradient qvec(ig::InstantGradient3D) = ig.qvec
-variables.duration.f(::InstantGradient) = 0.
-variables.effective_time.f(::InstantGradient) = 0.
+@defvar duration(::InstantGradient) = 0.
+@defvar effective_time(::InstantGradient) = 0.
@defvar gradient bmat_gradient(::InstantGradient, qstart=nothing) = zero(SMatrix{3, 3, Float64, 3})
make_generic(ig::InstantGradient) = ig
diff --git a/src/components/pulses/generic_pulses.jl b/src/components/pulses/generic_pulses.jl
index 9696194..af88e4f 100644
--- a/src/components/pulses/generic_pulses.jl
+++ b/src/components/pulses/generic_pulses.jl
@@ -31,7 +31,7 @@ struct GenericPulse <: RFPulseComponent
@assert all(time .>= 0)
if isnothing(effective_time)
test_res = new(Float64.(time), Float64.(amplitude), Float64.(phase), 0.)
- effective_time = time_halfway_flip(test_res)
+ effective_time = variables.time_halfway_flip(test_res)
end
return new(Float64.(time), Float64.(amplitude), Float64.(phase), Float64(effective_time))
end
@@ -56,12 +56,12 @@ function GenericPulse(pulse::GenericPulse, t1::Number, t2::Number)
pnew = pulse.phase[use]
if !(t1 ≈ tnew[1])
pushfirst!(tnew, t1)
- pushfirst!(anew, amplitude(pulse, t1))
- pushfirst!(pnew, phase(pulse, t1))
+ pushfirst!(anew, variables.amplitude(pulse, t1))
+ pushfirst!(pnew, variables.phase(pulse, t1))
elseif !(t2 ≈ tnew[end])
push!(tnew, t2)
- push!(anew, amplitude(pulse, t2))
- push!(pnew, phase(pulse, t2))
+ push!(anew, variables.amplitude(pulse, t2))
+ push!(pnew, variables.phase(pulse, t2))
end
return GenericPulse(tnew .- t1, anew, pnew, pulse.effective_time - t1)
end
diff --git a/src/components/pulses/sinc_pulses.jl b/src/components/pulses/sinc_pulses.jl
index 74efad5..5d92a74 100644
--- a/src/components/pulses/sinc_pulses.jl
+++ b/src/components/pulses/sinc_pulses.jl
@@ -99,7 +99,7 @@ end
end
@defvar begin
- amplitude(pulse::SincPulse, time::Number) = variables.amplitude(pulse) * normalised_function(abs((time - variables.effective_time(pulse))) / variables.lobe_duration(pulse), N_left(pulse), N_right(pulse); apodise=pulse.apodise)
+ amplitude(pulse::SincPulse, time::Number) = variables.amplitude(pulse) * normalised_function(abs((time - variables.effective_time(pulse))) / variables.lobe_duration(pulse), variables.N_left(pulse), variables.N_right(pulse); apodise=pulse.apodise)
phase(pulse::SincPulse, time::Number) = variables.phase(pulse) + variables.frequency(pulse) * (time - variables.effective_time(pulse)) * 360.
frequency(pulse::SincPulse, time::Number) = variables.frequency(pulse)
end
diff --git a/src/containers/abstract.jl b/src/containers/abstract.jl
index 16f66ff..195af76 100644
--- a/src/containers/abstract.jl
+++ b/src/containers/abstract.jl
@@ -37,6 +37,7 @@ end_time(block::Tuple{<:VariableType, <:AbstractBlock}) = variables.duration(blo
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...)
@@ -46,7 +47,7 @@ This will crash if the component does not have an [`effective_time`](@ref) (e.g.
Also see [`variables.duration`](@ref), [`start_time`](@ref), and [`end_time`](@ref)
"""
-effective_time
+variables.effective_time
"""
@@ -147,8 +148,8 @@ function get_gradient end
Returns all the times that the sequence will readout.
"""
-readout_times
+variables.readout_times
-iter(component::Tuple{<:Number, <:ReadoutComponent}, ::Val{:readout}) = [(time, nothing) for time in readout_times(component[2])]
+iter(component::Tuple{<:Number, <:ReadoutComponent}, ::Val{:readout}) = [(time, nothing) for time in variables.readout_times(component[2])]
end
\ No newline at end of file
diff --git a/src/containers/building_blocks.jl b/src/containers/building_blocks.jl
index 7d2db3d..b399f2e 100644
--- a/src/containers/building_blocks.jl
+++ b/src/containers/building_blocks.jl
@@ -232,7 +232,7 @@ Computes the area under the curve for the gradient waveform in [`BaseBuildingBlo
If `first_event` is set to something else than `nothing`, only the gradient waveform after this RF pulse/Readout will be considered.
Similarly, if `last_event` is set to something else than `nothing`, only the gradient waveform up to this RF pulse/Readout will be considered.
"""
-qvec
+variables.qvec
function edge_times(bb::BaseBuildingBlock)
res = Float64[]
diff --git a/src/parts/trapezoids.jl b/src/parts/trapezoids.jl
index 9dd2b5d..2deab41 100644
--- a/src/parts/trapezoids.jl
+++ b/src/parts/trapezoids.jl
@@ -170,12 +170,12 @@ struct SliceSelect{N} <: BaseTrapezoid{N}
pulse :: RFPulseComponent
end
-function SliceSelect(pulse::RFPulseComponent; orientation=nothing, rise_time=nothing, group=nothing, slew_rate=nothing, variables...)
+function SliceSelect(pulse::RFPulseComponent; orientation=nothing, rise_time=nothing, group=nothing, slew_rate=nothing, vars...)
res = SliceSelect(
- Trapezoid(; orientation=orientation, rise_time=rise_time, flat_time=duration(pulse), group=group, slew_rate=slew_rate),
+ Trapezoid(; orientation=orientation, rise_time=rise_time, flat_time=variables.duration(pulse), group=group, slew_rate=slew_rate),
pulse
)
- set_simple_constraints!(res, variables)
+ set_simple_constraints!(res, vars)
return res
end
@@ -225,7 +225,7 @@ function LineReadout(adc::ADC; ramp_overlap=nothing, orientation=nothing, group=
end
Base.keys(::LineReadout) = (Val(:rise), Val(:adc), Val(:flat), Val(:fall))
-Base.getindex(lr::LineReadout, ::Val{:adc}) = ((1 - ramp_overlap(lr)) * rise_time(lr), lr.adc)
+Base.getindex(lr::LineReadout, ::Val{:adc}) = ((1 - variables.ramp_overlap(lr)) * variables.rise_time(lr), lr.adc)
@defvar begin
ramp_overlap(lr::LineReadout) = lr.ramp_overlap
diff --git a/src/pathways.jl b/src/pathways.jl
index 3283817..54ba18c 100644
--- a/src/pathways.jl
+++ b/src/pathways.jl
@@ -27,7 +27,7 @@ The RF pulses cause mappings between these different states as described below.
- `:refocus`/`:invert`/180: Flips the sign of the spin state (i.e., +longitudinal <-> -longitudinal, +transverse <-> -transverse)
- `:excite`/90: Takes spin state one step along the following sequence +longitudinal -> +transverse -> -longitudinal -> -transverse -> +longitudinal
- `:neg_excite`/270/-90: Inverse step compared with `:excite`.
-- `readout_index`: After encountering the number of pulses as defined in `pulse_effects`, continue the `PathWay` until the readout given by `index` is reached. If set to 0 the `PathWay` is terminated immediately after the last RF pulse.
+- `readout_index`: After encountering the number of pulses as defined in `pulse_effects`, continue the `Pathway` until the readout given by `index` is reached. If set to 0 the `Pathway` is terminated immediately after the last RF pulse.
- `group`: which gradient grouping to consider for the `qvec` and `bmat`. If not set, all gradients will be considered (using their current alignment).
## Attributes
@@ -169,7 +169,7 @@ variables.bval
"""
get_pathway(sequence)
-Gets the main [`PathWay`](@ref) that spins are expected to experience in the 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.
"""
diff --git a/src/variables.jl b/src/variables.jl
index 29779ee..903497b 100644
--- a/src/variables.jl
+++ b/src/variables.jl
@@ -92,7 +92,7 @@ Main module containing all the MRIBuilder sequence variables.
All variables are available as members of this module, e.g.
`variables.echo_time` returns the echo time variable.
-New variables can be defined using [`@defvar`](@ref).
+New variables can be defined using `@defvar`.
Set constraints on variables by passing them on as keywords during the sequence generation,
e.g., `seq=SpinEcho(echo_time=70)`.
@@ -360,9 +360,6 @@ Returns the gradient orientation.
function gradient_orientation end
-@defvar function effective_time end
-
-
function (var::Variable)(block::AbstractBlock, args...; kwargs...)
if !applicable(var.f, block, args...) && !isnothing(var.getter)
apply_to = var.getter(block)
diff --git a/test/test_IO.jl b/test/test_IO.jl
index ce838f9..493161b 100644
--- a/test/test_IO.jl
+++ b/test/test_IO.jl
@@ -24,7 +24,7 @@
end
# Single ADC event
- @test length(readout_times(seq)) == 1024
+ @test length(variables.readout_times(seq)) == 1024
@test variables.readout_times(seq)[1] ≈ 0.22 + 5 + 0.02 + 0.5 * 0.3125
@test variables.readout_times(seq)[end] ≈ 0.22 + 5 + 0.02 + 1023.5 * 0.3125
@@ -56,7 +56,7 @@
0.02 + # RF ringdown time (added by block duration)
29.730 # Delay until ADC start (to get start at ADC at TE=30)
)
- @test length(readout_times(seq)) == 8192
+ @test length(variables.readout_times(seq)) == 8192
@test variables.readout_times(seq)[1] ≈ start_adc + 0.5 * 0.03125
@test variables.readout_times(seq)[end] ≈ start_adc + 8191.5 * 0.03125
end
@@ -101,7 +101,7 @@
seq_json = read_sequence(io, format=:serialize)
@test variables.duration(seq_orig) == variables.duration(seq_json)
@test length(seq_orig) == length(seq_json)
- @test all(duration.(seq_orig) .== duration.(seq_json))
+ @test all(variables.duration.(seq_orig) .== variables.duration.(seq_json))
@test iszero(length(iter_instant_gradients(seq_json)))
@test iszero(length(iter_instant_pulses(seq_json)))
@test all(variables.readout_times(seq_json) .== variables.readout_times(seq_orig))
@@ -120,7 +120,7 @@
seq_json = read_sequence(io; format=:serialize)
@test variables.duration(seq_orig) == variables.duration(seq_json)
@test length(seq_orig) == length(seq_json)
- @test all(duration.(seq_orig) .== duration.(seq_json))
+ @test all(variables.duration.(seq_orig) .== variables.duration.(seq_json))
@test length(iter_instant_gradients(seq_json)) == length(iter_instant_gradients(seq_json))
@test length(iter_instant_pulses(seq_json)) == length(iter_instant_pulses(seq_json))
@test all(variables.readout_times(seq_json) .== variables.readout_times(seq_orig))
diff --git a/test/test_components.jl b/test/test_components.jl
index f92736e..e8f6109 100644
--- a/test/test_components.jl
+++ b/test/test_components.jl
@@ -26,7 +26,7 @@
@testset "SincPulse" begin
sp = SincPulse(amplitude=1., frequency=2., phase=0., lobe_duration=10., Nzeros=(2, 1))
- @test duration(sp) ≈ 30.
+ @test variables.duration(sp) ≈ 30.
@test variables.amplitude(sp, 20) ≈ 1.
@test variables.amplitude(sp, 0) ≈ 0. atol=1e-8
diff --git a/test/test_sequences.jl b/test/test_sequences.jl
index 057b679..caa4834 100644
--- a/test/test_sequences.jl
+++ b/test/test_sequences.jl
@@ -27,7 +27,7 @@
seq = DiffusionSpinEcho(TE=:min, bval=1.)
@test length(seq) == 9
grad_duration = variables.TE(seq) / 2
- @test all(isapprox.(duration.(seq), [0., 0., grad_duration, 0., 0., 0., grad_duration, 0., 0.], atol=1e-6))
+ @test all(isapprox.(variables.duration.(seq), [0., 0., grad_duration, 0., 0., 0., grad_duration, 0., 0.], atol=1e-6))
@test length([iter_instant_pulses(seq)...]) == 2
@test length([iter_instant_gradients(seq)...]) == 0.
@test variables.bval(seq) ≈ 1.
@@ -38,24 +38,24 @@
@testset "Maximise b-value" begin
seq = DiffusionSpinEcho(TE=80., bval=:max)
@test length(seq) == 9
- @test all(isapprox.(duration.(seq), [0., 0., 40., 0., 0., 0., 40., 0., 0.], atol=1e-4, rtol=1e-4))
+ @test all(isapprox.(variables.duration.(seq), [0., 0., 40., 0., 0., 0., 40., 0., 0.], atol=1e-4, rtol=1e-4))
@test length([iter_instant_pulses(seq)...]) == 2
@test length([iter_instant_gradients(seq)...]) == 0.
@test variables.TE(seq) ≈ 80.
@test variables.duration(seq) ≈ 80.
- @test 4.8 < bval(seq) < 4.9
+ @test 4.8 < variables.bval(seq) < 4.9
@test variables.rise_time(seq[:gradient]) ≈ min_rise_time rtol=1e-4
@test all(isapprox.(edge_times(seq, tol=1e-3), [0., min_rise_time, 40. - min_rise_time, 40, 40 + min_rise_time, 80 - min_rise_time, 80.], atol=1e-4))
# can also maximise q-value
seq2 = DiffusionSpinEcho(TE=80., qval=:max)
- @test all(isapprox.(duration.(seq), duration.(seq2), atol=1e-4, rtol=1e-4))
+ @test all(isapprox.(variables.duration.(seq), variables.duration.(seq2), atol=1e-4, rtol=1e-4))
@test variables.TE(seq) ≈ variables.TE(seq2) atol=1e-4 rtol=1e-4
@test variables.bval(seq) ≈ variables.bval(seq2) atol=1e-4 rtol=1e-4
end
@testset "Set diffusion time Δ" begin
seq = DiffusionSpinEcho(TE=80., Δ=70., qval=:max)
- @test all(isapprox.(duration.(seq), [0., 0., 10., 30., 0., 30., 10., 0., 0.], atol=1e-4, rtol=1e-4))
+ @test all(isapprox.(variables.duration.(seq), [0., 0., 10., 30., 0., 30., 10., 0., 0.], atol=1e-4, rtol=1e-4))
@test variables.Δ(seq) ≈ 70.
@test variables.TE(seq) ≈ 80.
@test variables.duration(seq) ≈ 80.
@@ -66,7 +66,7 @@
end
@testset "Set gradient duration" begin
seq = DiffusionSpinEcho(TE=80., gradient=(duration=10., ), bval=:max)
- @test all(isapprox.(duration.(seq), [0., 0., 10., 30., 0., 30., 10., 0., 0.], atol=1e-4, rtol=1e-4))
+ @test all(isapprox.(variables.duration.(seq), [0., 0., 10., 30., 0., 30., 10., 0., 0.], atol=1e-4, rtol=1e-4))
@test variables.Δ(seq) ≈ 70. rtol=1e-4
@test variables.TE(seq) ≈ 80.
@test variables.duration(seq) ≈ 80.
@@ -79,33 +79,33 @@
@testset "slice-select DW-SE" begin
seq = DiffusionSpinEcho(duration=:min, bval=2., slice_thickness=2.)
@test length(seq) == 9
- @test duration(seq[1]) > 1.
+ @test variables.duration(seq[1]) > 1.
for index in 1:9
if index in [2, 4, 8, 9]
- @test abs(duration(seq[index])) < 1e-6
+ @test abs(variables.duration(seq[index])) < 1e-6
else
- @test abs(duration(seq[index])) > 1
+ @test abs(variables.duration(seq[index])) > 1
end
end
- @test duration(seq[:gradient]) ≈ duration(seq[:gradient2])
+ @test variables.duration(seq[:gradient]) ≈ variables.duration(seq[:gradient2])
@test variables.bval(seq) ≈ 2.
- @test length(readout_times(seq)) == 1
+ @test length(variables.readout_times(seq)) == 1
@test variables.readout_times(seq)[1] > variables.TE(seq)
end
@testset "voxel-wise DW-SE" begin
seq = DiffusionSpinEcho(duration=:min, bval=2., voxel_size=2., fov=(20, 20, 20))
@test length(seq) == 9
- @test duration(seq[1]) > 1.
+ @test variables.duration(seq[1]) > 1.
for index in 1:9
if index in [2, 6, 8]
- @test abs(duration(seq[index])) < 1e-6
+ @test abs(variables.duration(seq[index])) < 1e-6
else
- @test abs(duration(seq[index])) > 1
+ @test abs(variables.duration(seq[index])) > 1
end
end
- @test duration(seq[:gradient]) ≈ duration(seq[:gradient2])
+ @test variables.duration(seq[:gradient]) ≈ variables.duration(seq[:gradient2])
@test variables.bval(seq) ≈ 2.
- @test length(readout_times(seq)) > 50
+ @test length(variables.readout_times(seq)) > 50
@test 67 < variables.TE(seq) < 68
@test 72 < variables.duration(seq) < 73
--
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