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Define variables through new @defvar macro

Merged Define variables through new @defvar macro
new_variables into main
Merged Michiel Cottaar requested to merge new_variables into main
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test/test_sequences.jl
+ 62
− 63
@@ -2,22 +2,22 @@
@testset "GradientEcho" begin
seq = GradientEcho(TE=40)
@test length(seq) == 3
@test duration(seq) == 40
@test all(isapprox.(duration.(seq), [0., 40., 0.], atol=1e-6))
@test variables.duration(seq) == 40
@test all(isapprox.(variables.duration.(seq), [0., 40., 0.], atol=1e-6))
@test length(collect(iter_instant_pulses(seq))) == 1
@test length(collect(iter_instant_gradients(seq))) == 0.
@test duration_dephase(seq) ≈ 40.
@test duration_transverse(seq) ≈ 40.
@test variables.duration_dephase(seq) ≈ 40.
@test variables.duration_transverse(seq) ≈ 40.
end
@testset "SpinEcho" begin
seq = SpinEcho(TE=40)
@test length(seq) == 5
@test duration(seq) == 40
@test all(isapprox.(duration.(seq), [0., 20., 0., 20., 0.], atol=1e-6))
@test variables.duration(seq) == 40
@test all(isapprox.(variables.duration.(seq), [0., 20., 0., 20., 0.], atol=1e-6))
@test length(collect(iter_instant_pulses(seq))) == 2
@test length(collect(iter_instant_gradients(seq))) == 0.
@test duration_dephase(seq) ≈ 0. atol=1e-4
@test duration_transverse(seq) ≈ 40.
@test variables.duration_dephase(seq) ≈ 0. atol=1e-4
@test variables.duration_transverse(seq) ≈ 40.
end
@testset "DW-SE" begin
@@ -26,111 +26,110 @@
@testset "Minimise TE" begin
seq = DiffusionSpinEcho(TE=:min, bval=1.)
@test length(seq) == 9
grad_duration = TE(seq) / 2
@test all(isapprox.(duration.(seq), [0., 0., grad_duration, 0., 0., 0., grad_duration, 0., 0.], atol=1e-6))
grad_duration = variables.TE(seq) / 2
@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 bval(seq) ≈ 1.
@test 40. < TE(seq) < 50.
@test TR(seq) ≈ TE(seq)
@test rise_time(seq[:gradient]) ≈ min_rise_time rtol=1e-4
@test variables.bval(seq) ≈ 1.
@test 40. < variables.TE(seq) < 50.
@test variables.duration(seq) ≈ variables.TE(seq)
@test variables.rise_time(seq[:gradient]) ≈ min_rise_time rtol=1e-4
end
@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 TE(seq) ≈ 80.
@test TR(seq) ≈ 80.
@test 4.8 < bval(seq) < 4.9
@test rise_time(seq[:gradient]) ≈ min_rise_time rtol=1e-4
@test variables.TE(seq) ≈ 80.
@test variables.duration(seq) ≈ 80.
@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 TE(seq) ≈ TE(seq2) atol=1e-4 rtol=1e-4
@test bval(seq) ≈ bval(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 Δ(seq) ≈ 70.
@test TE(seq) ≈ 80.
@test TR(seq) ≈ 80.
@test 0.72 < bval(seq) < 0.73
@test readout_times(seq)[1] ≈ TE(seq)
@test rise_time(seq[:gradient]) ≈ min_rise_time 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.
@test 0.72 < variables.bval(seq) < 0.73
@test variables.readout_times(seq)[1] ≈ variables.TE(seq)
@test variables.rise_time(seq[:gradient]) ≈ min_rise_time rtol=1e-4
@test all(isapprox.(edge_times(seq), [0., min_rise_time, 10. - min_rise_time, 10., 40, 70, 70 + min_rise_time, 80 - min_rise_time, 80.], atol=1e-4))
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 Δ(seq) ≈ 70. rtol=1e-4
@test TE(seq) ≈ 80.
@test TR(seq) ≈ 80.
@test 0.72 < bval(seq) < 0.73
@test readout_times(seq)[1] ≈ TE(seq)
@test rise_time(seq[:gradient]) ≈ min_rise_time 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.
@test 0.72 < variables.bval(seq) < 0.73
@test variables.readout_times(seq)[1] ≈ variables.TE(seq)
@test variables.rise_time(seq[:gradient]) ≈ min_rise_time rtol=1e-4
end
end
@testset "DW-SE with finite RF pulses" begin
@testset "slice-select DW-SE" begin
seq = DiffusionSpinEcho(TR=:min, bval=2., slice_thickness=2.)
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 bval(seq) ≈ 2.
@test length(readout_times(seq)) == 1
@test readout_times(seq)[1] > TE(seq)
@test variables.duration(seq[:gradient]) ≈ variables.duration(seq[:gradient2])
@test variables.bval(seq) ≈ 2.
@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(TR=:min, bval=2., voxel_size=2., fov=(20, 20, 20))
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 bval(seq) ≈ 2.
@test length(readout_times(seq)) > 50
@test 67 < TE(seq) < 68
@test 72 < TR(seq) < 73
@test variables.duration(seq[:gradient]) ≈ variables.duration(seq[:gradient2])
@test variables.bval(seq) ≈ 2.
@test length(variables.readout_times(seq)) > 50
@test 67 < variables.TE(seq) < 68
@test 72 < variables.duration(seq) < 73
(pulse, t_pulse) = get_pulse(seq, 1.)
@test 1. - t_pulse ≈ min_rise_time rtol=1e-4
@test flip_angle(pulse) ≈ 90.
@test iszero(phase(pulse))
@test iszero(phase(seq, 1.))
@test iszero(frequency(seq, 1.))
@test variables.flip_angle(pulse) ≈ 90.
@test iszero(variables.phase(pulse))
@test iszero(variables.phase(seq, 1.))
@test iszero(variables.frequency(seq, 1.))
@test isnothing(get_pulse(seq, 10.))
@test isnan(phase(seq, 10.))
@test isnan(frequency(seq, 10.))
@test isnan(variables.phase(seq, 10.))
@test isnan(variables.frequency(seq, 10.))
gp = GenericPulse(pulse, 0., 1.)
@test gp.amplitude[1] ≈ 0. atol=1e-8
@test gp.amplitude[end] ≈ amplitude(pulse, 1.) rtol=1e-2
@test gp.amplitude[end] ≈ variables.amplitude(pulse, 1.) rtol=1e-2
@test all(iszero.(gp.phase))
(pulse, t_pulse) = get_pulse(seq, 35.)
@test 1.1 < t_pulse < 1.2
@test flip_angle(pulse) ≈ 180.
@test iszero(phase(pulse))
@test variables.flip_angle(pulse) ≈ 180.
@test iszero(variables.phase(pulse))
end
end
end
end
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