From 1427f18a14ca7978a0cf8d0d6064a4c54ba928e5 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Mon, 20 May 2024 15:53:13 +0100
Subject: [PATCH] Write MRIBuilder.Sequence to pulseq file
---
src/sequence_io/pulseq.jl | 88 +++++++++++++++++--
.../pulseq_io/parsers/definitions.jl | 1 +
src/sequence_io/pulseq_io/pulseq_io.jl | 1 +
src/sequence_io/sequence_io.jl | 12 +--
4 files changed, 92 insertions(+), 10 deletions(-)
diff --git a/src/sequence_io/pulseq.jl b/src/sequence_io/pulseq.jl
index 4477b6e..fd25519 100644
--- a/src/sequence_io/pulseq.jl
+++ b/src/sequence_io/pulseq.jl
@@ -3,14 +3,16 @@ Module converting MRIBuilder sequences to and from sequences recognised by [`Pul
"""
module Pulseq
import Interpolations: linear_interpolation
-import ..PulseqIO.Types: PulseqSequence, PulseqBlock, PulseqTrapezoid, PulseqGradient
-import ...Containers: Sequence, BuildingBlock
-import ...Components: GenericPulse, ADC
+import ..PulseqIO.Types: PulseqSequence, PulseqBlock, PulseqTrapezoid, PulseqGradient, PulseqRFPulse, PulseqShape, PulseqADC, PulseqExtension
+import ...Containers: Sequence, BuildingBlock, BaseBuildingBlock, events, waveform, iter_blocks
+import ...Components: GenericPulse, ADC, RFPulseComponent
import ...Scanners: Scanner
+import ...Variables: duration, nsamples, dwell_time, make_generic
-function Sequence(pulseq::PulseqSequence; scanner=nothing, B0=3)
+function Sequence(pulseq::PulseqSequence; scanner=nothing, B0=nothing)
if isnothing(scanner)
- scanner = Scanner(B0=B0)
+ use_B0 = isnothing(B0) ? get(pulseq.definitions, :B0, 3.) : B0
+ scanner = Scanner(B0=use_B0)
end
blocks = BuildingBlock.(pulseq.blocks; pulseq.definitions...)
return Sequence(blocks; name=Symbol(get(pulseq.definitions, :name, "from_pulseq")), scanner=scanner)
@@ -88,4 +90,80 @@ function _get_amplitude(grad::PulseqGradient, time::Number, raster::Number)
end
+function PulseqSequence(seq::Sequence{S}) where {S}
+ definitions = (
+ name=S,
+ AdcRasterTime=1e-9,
+ BlockDurationRaster=1e-9,
+ RadiofrequencyRasterTime=1e-9,
+ GradientRasterTime=1e-9,
+ TotalDuration=duration(seq) * 1e-3,
+ B0=seq.scanner.B0,
+ )
+ blocks = [PulseqBlock(block; definitions...) for (_, block) in iter_blocks(seq)]
+ return PulseqSequence(
+ v"1.4.0",
+ definitions,
+ blocks
+ )
+end
+
+function PulseqBlock(block::BaseBuildingBlock; BlockDurationRaster, AdcRasterTime, kwargs...)
+ rf = nothing
+ adc = nothing
+ for (delay, event) in events(block)
+ if event isa RFPulseComponent
+ if !isnothing(rf)
+ error("Pulseq does not support a single building block containing multiple RF pulses.")
+ end
+ gen = make_generic(event)
+ rf = PulseqRFPulse(
+ maximum(gen.amplitude) * 1e3,
+ PulseqShape(gen.amplitude ./ maximum(gen.amplitude)),
+ PulseqShape(deg2rad.(gen.phase)),
+ PulseqShape(gen.time .* 1e-3),
+ Int(div(delay, 1e-3)),
+ 0.,
+ 0.
+ )
+ elseif event isa ADC
+ if !isnothing(rf)
+ error("Pulseq does not support a single building block containing multiple ADC events.")
+ end
+ adc = PulseqADC(
+ nsamples(event),
+ div(dwell_time(event), AdcRasterTime),
+ Int(div(delay, 1e-3)),
+ 0., 0.
+ )
+ else
+ error("Cannot write $(typeof(event)) to Pulseq.")
+ end
+ end
+
+ grads = []
+ 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.))
+ push!(grads, nothing)
+ else
+ push!(grads, PulseqGradient(
+ maximum(amplitudes) * 1e3,
+ PulseqShape(amplitudes ./ maximum(amplitudes)),
+ PulseqShape(times .* 1e-3),
+ 0.,
+ ))
+ end
+ end
+
+ return PulseqBlock(
+ Int(div(1e-3 * duration(block), BlockDurationRaster)),
+ rf,
+ grads...,
+ adc,
+ Tuple{PulseqExtension, Int}[]
+ )
+end
+
end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/definitions.jl b/src/sequence_io/pulseq_io/parsers/definitions.jl
index 2da9962..5ba67c7 100644
--- a/src/sequence_io/pulseq_io/parsers/definitions.jl
+++ b/src/sequence_io/pulseq_io/parsers/definitions.jl
@@ -4,6 +4,7 @@ function parse_section(section:: PulseqSection{:definitions}; kwargs...)
end
_to_string_value(value::AbstractString) = value
+_to_string_value(value::Symbol) = string(value)
_to_string_value(value::Number) = string(value)
_to_string_value(value::Vector) = join(_to_string_value.(value), " ")
diff --git a/src/sequence_io/pulseq_io/pulseq_io.jl b/src/sequence_io/pulseq_io/pulseq_io.jl
index d60141e..278e207 100644
--- a/src/sequence_io/pulseq_io/pulseq_io.jl
+++ b/src/sequence_io/pulseq_io/pulseq_io.jl
@@ -12,6 +12,7 @@ include("components.jl")
include("parsers/parsers.jl")
include("parse_sections.jl")
+import .Types: PulseqSequence
"""
diff --git a/src/sequence_io/sequence_io.jl b/src/sequence_io/sequence_io.jl
index 062a156..e0ebd01 100644
--- a/src/sequence_io/sequence_io.jl
+++ b/src/sequence_io/sequence_io.jl
@@ -4,7 +4,7 @@ include("pulseq_io/pulseq_io.jl")
include("pulseq.jl")
import Serialization: serialize, deserialize
-import .PulseqIO: read_pulseq
+import .PulseqIO: read_pulseq, write_pulseq, PulseqSequence
import ..Containers: Sequence
@@ -14,7 +14,7 @@ function read_sequence(filename::AbstractString, args...; kwargs...)
end
end
-function read_sequence(io::IO; format=nothing, kwargs...)
+function read_sequence(io::IO; format=nothing, B0=nothing, scanner=nothing,kwargs...)
if isnothing(format)
pos = position(io)
for format in (:pulseq, :serialize)
@@ -27,7 +27,7 @@ function read_sequence(io::IO; format=nothing, kwargs...)
error("Could not read the input filename. Tried all formats (:pulseq/:serialize).")
end
if format == :pulseq
- return Sequence(read_pulseq(io, kwargs...))
+ return Sequence(read_pulseq(io, kwargs...), B0=B0, scanner=scanner)
elseif format == :serialize
return deserialize(io, kwargs...)
else
@@ -42,8 +42,10 @@ function write_sequence(filename::AbstractString, args...; kwargs...)
end
end
-function write_sequence(io::IO, sequence; format::Symbol=:serialize)
- if format == :serialize
+function write_sequence(io::IO, sequence; format::Symbol=:pulseq)
+ if format == :pulseq
+ write_pulseq(io, PulseqSequence(sequence))
+ elseif format == :serialize
serialize(io, sequence)
else
error("Unrecognised selected format for output ($format). Only :serialize is supported..")
--
GitLab