@testset "test_IO.jl" begin
directory = joinpath(pwd(), "example_pulseseq")
@testset "read v1.3.1 fiddisp.seq file" begin
seq = read_sequence(joinpath(directory, "fiddisp_v131.seq"))
@test length(seq) == 3
# starting with RF pulse
@test length(events(seq[1])) == 1
(index, pulse) = events(seq[1])[1]
@test start_time(seq, 1, index) == 0.1
@test end_time(seq, 1, index) == 0.22
for (time, ampl, phase_check) in [
(0.09, 0., isnan),
(0.11, 2.5, iszero),
(0.19, 2.5, iszero),
(0.21, 0., iszero),
(0.23, 0., isnan),
]
@test phase_check(phase(seq, time))
@test amplitude(seq, time) ≈ ampl
end
# Single ADC event
@test length(readout_times(seq)) == 1024
@test readout_times(seq)[1] ≈ 0.22 + 5 + 0.02 + 0.5 * 0.3125
@test readout_times(seq)[end] ≈ 0.22 + 5 + 0.02 + 1023.5 * 0.3125
@test TR(seq) ≈ 0.22 + 5 + 0.02 + 1024 * 0.3125
end
@testset "read all v1.4.0 files in 01_from_FID_to_PRESS" begin
path = joinpath(directory, "01_from_FID_to_PRESS_v140")
for fn in readdir(path)
if !endswith(fn, ".seq")
continue
end
full_filename = joinpath(path, fn)
seq = read_sequence(full_filename)
end
end
@testset "check 01_from_FID_to_PRESS/01_FID.seq" begin
fn = joinpath(directory, "01_from_FID_to_PRESS_v140", "01_FID.seq")
seq = read_sequence(fn)
@test length(seq) == 2
(index, pulse) = events(seq[1])[1]
@test flip_angle(pulse) ≈ 90
@test start_time(seq, 1, index) ≈ 0.1 # determined by RF dead time
@test end_time(seq, 1, index) ≈ 0.6 # RF dead time + RF duration
@test phase(seq, 0.3) == 0
@test amplitude(seq, 0.3) ≈ 0.5
start_adc = (
0.6 + # end of RF pulse
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 readout_times(seq)[1] ≈ start_adc + 0.5 * 0.03125
@test readout_times(seq)[end] ≈ start_adc + 8191.5 * 0.03125
end
@testset "check 01_from_FID_to_PRESS/06_PRESS_center.seq" begin
fn = joinpath(directory, "01_from_FID_to_PRESS_v140", "06_PRESS_center.seq")
seq = read_sequence(fn)
@test length(seq) == 7
(index, excitation) = events(seq[1])[1]
#@test flip_angle(excitation) ≈ 90
@test start_time(seq, 1, index) ≈ 0.1 # determined by RF dead time
@test end_time(seq, 1, index) ≈ 3.1 # RF dead time + RF duration
@test phase(seq, 0.3) ≈ 0 + rad2deg(0.5)
@test phase(seq, 1.6) ≈ 0
@test length(readout_times(seq)) == 4096
refocus_pulses = (
events(seq[3])[1][2],
events(seq[5])[1][2],
)
for p in refocus_pulses
@test duration(p) ≈ 3 # should have been 4 for refocus pulses, but there is an error in the matlab generation
@test phase(p, 0.) ≈ 90 rtol=1e-5
@test phase(p, 0.38) ≈ 90 + rad2deg(0.5) rtol=1e-5
@test phase(p, 1.5) ≈ 90 rtol=1e-5
end
end
if false
# JSON encoding has not been implemented yet
@testset "check that JSON encoding works for all v1.4.0 files in 01_from_FID_to_PRESS" begin
path = joinpath(directory, "01_from_FID_to_PRESS_v140")
for fn in readdir(path)
@testset "checking $fn" begin
if !endswith(fn, ".seq")
continue
end
full_filename = joinpath(path, fn)
seq_orig = read_sequence(full_filename)
io = IOBuffer()
write_sequence(io, seq_orig)
s = String(io.data)
seq_json = read_sequence(s)
@test seq_orig.TR == seq_json.TR
@test length(seq_orig.gradients) == length(seq_json.gradients)
for (g1, g2) in zip(seq_orig.gradients, seq_json.gradients)
@test all(g1.origin .== g2.origin)
@test all(g1.shape.times .== g2.shape.times)
@test all(g1.shape.amplitudes .== g2.shape.amplitudes)
end
@test length(seq_orig.pulses) == length(seq_json.pulses)
for (p1, p2) in zip(seq_orig.pulses, seq_json.pulses)
@test p1.max_amplitude == p2.max_amplitude
@test all(p1.amplitude.times .== p2.amplitude.times)
@test all(p1.amplitude.amplitudes .== p2.amplitude.amplitudes)
@test all(p1.phase.times .== p2.phase.times)
@test all(p1.phase.amplitudes .== p2.phase.amplitudes)
end
@test iszero(length(seq_json.instants))
@test length(seq_json.readout_times) > 0
@test all(seq_json.readout_times .== seq_orig.readout_times)
end
end
end
@testset "check that JSON encoding works for some sequences with instant pulses/gradients" begin
for seq_orig in [
DWI(TE=80., bval=2., TR=100., scanner=Siemens_Connectom),
DWI(TE=80., bval=2., gradient_duration=0., TR=100, scanner=Siemens_Terra),
SpinEcho(TE=30., TR=100., scanner=Scanner(B0=1.5)),
]
io = IOBuffer()
write_sequence(io, seq_orig)
s = String(io.data)
seq_json = read_sequence(s)
@test seq_json.TR == 100.
@test seq_json.scanner.B0 == seq_orig.scanner.B0
@test seq_json.scanner.gradient == seq_orig.scanner.gradient
@test seq_json.scanner.slew_rate == seq_orig.scanner.slew_rate
@test length(seq_orig.gradients) == length(seq_json.gradients)
for (g1, g2) in zip(seq_orig.gradients, seq_json.gradients)
@test all(g1.origin .== g2.origin)
@test all(g1.shape.times .== g2.shape.times)
@test all(g1.shape.amplitudes .== g2.shape.amplitudes)
end
@test iszero(length(seq_json.pulses))
@test length(seq_json.instants) == length(seq_orig.instants)
for (i1, i2) in zip(seq_orig.instants, seq_json.instants)
@test i1.time == i2.time
if i1 isa mr.InstantRFPulse
@test i2 isa mr.InstantRFPulse
@test i1.flip_angle == i2.flip_angle
@test i1.phase == i2.phase
else
@test i1 isa mr.InstantGradient
@test i2 isa mr.InstantGradient
@test all(i1.origin .== i2.origin)
@test all(i1.qvec .== i2.qvec)
end
end
@test length(seq_json.readout_times) > 0
@test all(seq_json.readout_times .== seq_orig.readout_times)
end
end
end
end