diff --git a/src/sequence_io/pulseq.jl b/src/sequence_io/pulseq.jl
index 5f84e23d561ebb6776ce5496f36c395a5cf5633c..2aeb46cf9c907b344e2f732ffdcb30f627b72302 100644
--- a/src/sequence_io/pulseq.jl
+++ b/src/sequence_io/pulseq.jl
@@ -66,7 +66,7 @@ function BuildingBlock(pulseq::PulseqBlock; version, BlockDurationRaster, Radiof
)
if min_duration > stated_duration
- if version == v"1.3.1"
+ if version == v"1.3.1" || isapprox(min_duration, stated_duration, rtol=1e-3)
stated_duration = min_duration
else
error("Minimum duration to play all RF/gradient/ADC events exceeds stated duration.")
@@ -177,12 +177,13 @@ function PulseqBlock(block::BaseBuildingBlock; BlockDurationRaster, AdcRasterTim
times = [t for (t, _) in waveform(block)]
for dim in 1:3
amplitudes = [g[dim] for (_, g) in waveform(block)]
- if iszero(maximum(abs.(amplitudes); init=0.))
+ max_ampl = maximum(abs.(amplitudes); init=0.)
+ if iszero(max_ampl)
push!(grads, nothing)
else
push!(grads, PulseqGradient(
- maximum(amplitudes) * 1e3,
- PulseqShape(amplitudes ./ maximum(amplitudes)),
+ max_ampl * 1e3,
+ PulseqShape(amplitudes ./ max_ampl),
PulseqShape(times .* 1e-3),
0.,
))
diff --git a/src/sequence_io/pulseq_io/parsers/shapes.jl b/src/sequence_io/pulseq_io/parsers/shapes.jl
index ef0a30f79365855f2f143906a85909e1016a3fda..3a062f7f6251e7b979d3fc84c68ad35afcbcc731 100644
--- a/src/sequence_io/pulseq_io/parsers/shapes.jl
+++ b/src/sequence_io/pulseq_io/parsers/shapes.jl
@@ -1,6 +1,6 @@
struct CompressedPulseqShape
num :: Int
- samples :: Vector{Float64}
+ samples :: Vector{Number}
end
@@ -57,14 +57,48 @@ function uncompress(compressed::CompressedPulseqShape)
return PulseqShape(amplitudes)
end
+function compress(shape::PulseqShape)
+ amplitudes = shape.samples
+ derivative = amplitudes[2:end] - amplitudes[1:end-1]
+
+ current_value = amplitudes[1]
+ compressed = Number[amplitudes[1]]
+
+ nrepeats = -1
+ for sample in derivative
+ if sample ≈ current_value
+ nrepeats += 1
+ if iszero(nrepeats)
+ push!(compressed, current_value)
+ end
+ else
+ if nrepeats != -1
+ push!(compressed, nrepeats)
+ nrepeats = -1
+ end
+ current_value = sample
+ push!(compressed, current_value)
+ end
+ end
+ if nrepeats >= 0
+ push!(compressed, nrepeats)
+ end
+ if length(compressed) >= length(amplitudes)
+ return CompressedPulseqShape(length(amplitudes), amplitudes)
+ else
+ return CompressedPulseqShape(length(amplitudes), compressed)
+ end
+end
+
function gen_section(comp:: PulseqComponents, ::Val{:shapes})
res = PulseqSection{:shapes}(String[])
for index in sort([keys(comp.shapes)...])
- shape = comp.shapes[index]
+ shape = compress(comp.shapes[index])
+ @assert all(isfinite.(shape.samples))
append!(res.content, [
"",
"shape_id $index",
- "num_samples $(length(shape.samples))"
+ "num_samples $(shape.num)"
])
for sample in shape.samples
push!(res.content, string(sample))
diff --git a/test/test_IO.jl b/test/test_IO.jl
index 12c10efb74ca70c5869fd50059097fc728ec3628..32bcfa8fc1c7b5eb55b6b2ce43a3e3adf0a84ab1 100644
--- a/test/test_IO.jl
+++ b/test/test_IO.jl
@@ -111,6 +111,7 @@
@testset "check that format $(format) works for some sequences with instant pulses/gradients/readouts" begin
for seq_orig in [
DWI(TE=80., bval=2., scanner=Siemens_Connectom),
+ DWI(TE=80., bval=2., scanner=Siemens_Connectom, fov=(10, 10, 10), voxel_size=2.),
DWI(TE=80., bval=2., scanner=Siemens_Terra, gradient=(type=:instant, )),
SpinEcho(TE=30.),
]
@@ -118,14 +119,30 @@
write_sequence(io, seq_orig; format=format)
seek(io, 0)
seq_json = read_sequence(io; format=format)
- @test isapprox(variables.duration(seq_orig), variables.duration(seq_json), atol=1e-5)
- @test length(seq_orig) == length(seq_json)
- @test all(isapprox.(variables.duration.(seq_orig), variables.duration.(seq_json), atol=1e-5))
+ @test isapprox(variables.duration(seq_orig), variables.duration(seq_json), atol=1e-3)
+ @test length(iter_blocks(seq_orig)) == length(iter_blocks(seq_json))
+ @test all(isapprox.(variables.duration.(last.(iter_blocks(seq_orig))), variables.duration.(last.(iter_blocks(seq_json))), atol=1e-3))
@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 length(variables.readout_times(seq_orig)) == length(variables.readout_times(seq_json))
- @test all(isapprox.(variables.readout_times(seq_orig), variables.readout_times(seq_json), atol=1e-5))
+ @test all(isapprox.(variables.readout_times(seq_orig), variables.readout_times(seq_json), atol=1e-3))
end
end
end
+ @testset "Test Pulseq shape compression" begin
+ import MRIBuilder.SequenceIO.PulseqIO.Parsers: compress, uncompress
+ import MRIBuilder.SequenceIO.PulseqIO.Types: PulseqShape
+
+ for (amplitudes, result) in [
+ ([0., 0.1, 0.25, 0.5, ones(7)..., 0.75, 0.5, 0.25, 0.], [0., 0.1, 0.15, 0.25, 0.5, 0., 0., 4, -0.25, -0.25, 2]),
+ (zeros(100), [0., 0., 98]),
+ (ones(100), [1., 0., 0., 97]),
+ ]
+ shape = PulseqShape(amplitudes)
+ res = compress(shape)
+ @test res.num == length(amplitudes)
+ @test all(res.samples == result)
+ @test all(uncompress(res).samples == amplitudes)
+ end
+ end
end
\ No newline at end of file