From 98c4258cdc2173d32db1548f0191188cd62a3352 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Mon, 20 May 2024 13:11:39 +0100
Subject: [PATCH] Refactor pulseq.jl into multiple files
---
src/sequence_io/pulseq.jl | 670 ------------------
src/sequence_io/pulseq_io/basic_parsers.jl | 62 ++
src/sequence_io/pulseq_io/components.jl | 115 +++
src/sequence_io/pulseq_io/parse_sections.jl | 45 ++
src/sequence_io/pulseq_io/parsers/adc.jl | 34 +
src/sequence_io/pulseq_io/parsers/blocks.jl | 49 ++
.../pulseq_io/parsers/definitions.jl | 13 +
src/sequence_io/pulseq_io/parsers/delays.jl | 11 +
.../pulseq_io/parsers/extensions.jl | 31 +
.../pulseq_io/parsers/gradients.jl | 44 ++
src/sequence_io/pulseq_io/parsers/parsers.jl | 37 +
src/sequence_io/pulseq_io/parsers/rf.jl | 47 ++
src/sequence_io/pulseq_io/parsers/shapes.jl | 68 ++
.../pulseq_io/parsers/trapezoids.jl | 37 +
src/sequence_io/pulseq_io/parsers/version.jl | 13 +
src/sequence_io/pulseq_io/pulseq_io.jl | 46 ++
src/sequence_io/pulseq_io/sections_io.jl | 49 ++
src/sequence_io/pulseq_io/types.jl | 143 ++++
src/sequence_io/sequence_io.jl | 4 +-
19 files changed, 846 insertions(+), 672 deletions(-)
delete mode 100644 src/sequence_io/pulseq.jl
create mode 100644 src/sequence_io/pulseq_io/basic_parsers.jl
create mode 100644 src/sequence_io/pulseq_io/components.jl
create mode 100644 src/sequence_io/pulseq_io/parse_sections.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/adc.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/blocks.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/definitions.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/delays.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/extensions.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/gradients.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/parsers.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/rf.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/shapes.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/trapezoids.jl
create mode 100644 src/sequence_io/pulseq_io/parsers/version.jl
create mode 100644 src/sequence_io/pulseq_io/pulseq_io.jl
create mode 100644 src/sequence_io/pulseq_io/sections_io.jl
create mode 100644 src/sequence_io/pulseq_io/types.jl
diff --git a/src/sequence_io/pulseq.jl b/src/sequence_io/pulseq.jl
deleted file mode 100644
index 346b67d..0000000
--- a/src/sequence_io/pulseq.jl
+++ /dev/null
@@ -1,670 +0,0 @@
-module Pulseq
-
-
-"""
- parse_pulseq_dict(line, names, dtypes)
-
-Parse a line of integers/floats with known names and dtypes.
-
-This is useful to parse most of the columnar data in Pulseq, such as in BLOCKS, RF, GRADIENTS, etc.
-"""
-function parse_pulseq_dict(line, names, dtypes)
- parts = split(line)
- @assert length(parts) == length(names)
- values = parse.(dtypes, split(line))
- @assert names[1] == :id
- return Dict(Symbol(name) => value for (name, value) in zip(names, values))
-end
-
-"""
- parse_pulseq_properties(lines)
-
-Parse any `pulseq` section formatted as:
-```
-<name> <value>
-<name2> <value2>
-...
-```
-
-This includes the VERSION, DEFINITIONS, and part of the SHAPES
-"""
-function parse_pulseq_properties(strings::Vector{<:AbstractString})
- result = Dict{String, Any}()
- for s in strings
- (name, value) = split(s, limit=2)
- result[name] = _parse_value(value)
- end
- return result
-end
-
-function _parse_value(value::AbstractString)
- for t in (Int, Float64)
- try
- return parse(t, value)
- catch
- end
- end
- for t in (Int, Float64)
- try
- return parse.(t, split(value))
- catch
- end
- end
- return value
-end
-
-
-
-"""
- PulseqSection(:<title>)(lines)
-
-Represents a section in the pulseq file format.
-"""
-struct PulseqSection{T}
- content :: Vector{String}
-end
-
-"""
- parse_pulseq_sections(io)
-
-Reads a Pulseq file into a dictionary of [`PulseqSection`](@ref) objects.
-"""
-function parse_pulseq_sections(io::IO)
- sections = Dict{String, PulseqSection}()
- current_title = ""
- for line in readlines(io)
- line = strip(line)
- if length(line) == 0 || line[1] == '#'
- continue # ignore comments
- end
- if line[1] == '[' && line[end] == ']'
- # new section starts
- current_title = lowercase(line[2:end-1])
- sections[current_title] = PulseqSection{Symbol(current_title)}(String[])
- elseif length(current_title) > 0
- push!(sections[current_title].content, line)
- else
- error("Content found in pulseq file before first section")
- end
- end
- return sections
-end
-
-function write_pulseq_section(io::IO, section::PulseqSection{T}) where {T}
- title = uppercase(string(T))
- write(io, "[$title]\n")
- for line in section.content
- if iszero(length(line)) || line[end] != '\n'
- line = line * '\n'
- end
- write(io, line)
- end
- write(io, "\n")
- write(io, "\n")
-end
-
-struct PulseqShape
- samples :: Vector{Float64}
-end
-
-struct PulseqRFPulse
- amplitude :: Float64
- magnitude :: PulseqShape
- phase :: PulseqShape
- time :: Union{Nothing, PulseqShape}
- delay :: Int
- frequency :: Float64
- phase_offset :: Float64
-end
-
-abstract type AnyPulseqGradient end
-struct PulseqGradient <: AnyPulseqGradient
- amplitude :: Float64
- shape :: PulseqShape
- time :: Union{Nothing, PulseqShape}
- delay :: Int
-end
-
-struct PulseqTrapezoid <:AnyPulseqGradient
- amplitude :: Float64
- rise :: Int
- flat :: Int
- fall :: Int
- delay :: Int
-end
-
-struct PulseqADC
- num :: Int
- dwell :: Float64
- delay :: Int
- frequency :: Float64
- phase :: Float64
-end
-
-struct PulseqExtension
- name :: String
- content :: Vector{String}
-end
-
-struct PulseqBlock
- duration :: Int
- rf :: Union{Nothing, PulseqRFPulse}
- gx :: Union{Nothing, AnyPulseqGradient}
- gy :: Union{Nothing, AnyPulseqGradient}
- gz :: Union{Nothing, AnyPulseqGradient}
- adc :: Union{Nothing, PulseqADC}
- ext :: Vector{<:Tuple{PulseqExtension, Int}}
-end
-
-struct PulseqSequence
- version:: VersionNumber
- definitions:: NamedTuple
- blocks:: Vector{PulseqBlock}
-end
-
-"""
- PulseqComponents(sequence::PulseqSequence)
-
-Indentifies and lists all the unique components in the sequence.
-"""
-struct PulseqComponents
- shapes:: Vector{PulseqShape}
- pulses:: Vector{PulseqRFPulse}
- grads:: Vector{AnyPulseqGradient}
- adc:: Vector{PulseqADC}
- extensions:: Vector{PulseqExtension}
-end
-
-PulseqComponents() = PulseqComponents(
- PulseqShape[],
- PulseqRFPulse[],
- AnyPulseqGradient[],
- PulseqADC[],
- PulseqExtension[],
-)
-
-add_components!(::PulseqComponents, search_vec::Vector, ::Nothing) = 0
-function add_components!(comp::PulseqComponents, search_vec::Vector{<:T}, component::T) where {T}
- for (i, c) in enumerate(search_vec)
- if same_component(comp, c, component)
- return i
- end
- end
- push!(search_vec, component)
- return length(search_vec)
-end
-
-same_component(::PulseqComponents, ::Any, ::Any) = false
-function same_component(comp::PulseqComponents, a::T, b::T) where {T}
- for name in fieldnames(T)
- v1 = getfield(a, name)
- v2 = getfield(b, name)
-
- if v1 isa PulseqShape
- v1 = add_components!(comp, v1)
- end
- if v2 isa PulseqShape
- v2 = add_components!(comp, v2)
- end
- if v1 != v2
- return false
- end
- end
- return true
-end
-
-
-add_components!(comp::PulseqComponents, ::Nothing) = 0
-function add_components!(comp::PulseqComponents, shape::PulseqShape)
- for (i, s) in enumerate(comp.shapes)
- if same_shape(s, shape)
- return i
- end
- end
- push!(comp.shapes, shape)
- return length(comp.shapes)
-end
-same_shape(shape1::PulseqShape, shape2::PulseqShape) = length(shape1.samples) == length(shape2.samples) && all(shape1.samples .≈ shape2.samples)
-
-
-# I/O all sections
-function parse_all_sections(sections:: Dict{String, PulseqSection})
- sections = copy(sections)
- all_parts = Dict{Symbol, Any}()
- for name in ["version", "definitions", "delays", "shapes", "rf", "gradients", "trap", "adc", "extensions", "blocks"]
- if name in keys(sections)
- section = pop!(sections, name)
- all_parts[Symbol(name)] = parse_section(section; all_parts...)
- end
- end
- if length(sections) > 0
- @warn "Following sections in pulseq input file are not being used: $(keys(sections))"
- end
- return PulseqSequence(all_parts[:version], all_parts[:definitions], all_parts[:blocks])
-end
-
-function gen_all_sections(seq:: PulseqSequence)
- sections = Dict{Symbol, PulseqSection}()
- sections[:version] = gen_section(seq, Val(:version))
- sections[:definitions] = gen_section(seq, Val(:definitions))
-
- comp = PulseqComponents()
- sections[:blocks] = gen_section(seq, comp, Val(:blocks))
- for symbol in [:rf, :gradients, :trap, :adc, :shapes]
- sections[symbol] = gen_section(comp, Val(symbol))
- end
- return sections
-end
-
-# Version I/O
-
-"""
- parse_section(section)
-
-Parses any [`PulseqSection`](@ref) and return the appropriate type.
-
-The opposite is [`gen_section`](@ref).
-"""
-function parse_section(section:: PulseqSection{:version}; kwargs...)
- props = parse_pulseq_properties(section.content)
- return VersionNumber(props["major"], props["minor"], props["revision"])
-end
-
-"""
- gen_section(sequence, Val(:<title>))
-
-Creates a specific [`PulseqSection`](@ref){<title>} from a part of the PulseqSequence.
-
-This is the opposite of [`parse_section`](@ref)
-"""
-function gen_section(seq::PulseqSequence, ::Val{:version})
- version = seq.version
- return PulseqSection{:version}([
- "major $(version.major)",
- "minor $(version.minor)",
- "revision $(version.patch)",
- ])
-end
-
-# Definitions I/O
-
-function parse_section(section:: PulseqSection{:definitions}; kwargs...)
- props = parse_pulseq_properties(section.content)
- return NamedTuple(Symbol(key) => value for (key, value) in props)
-end
-
-_to_string_value(value::AbstractString) = value
-_to_string_value(value::Number) = string(value)
-_to_string_value(value::Vector) = join(_to_string_value.(value), " ")
-
-function gen_section(seq:: PulseqSequence, ::Val{:definitions})
- definitions = seq.definitions
- return PulseqSection{:definitions}(["$(key) $(_to_string_value(value))" for (key, value) in pairs(definitions)])
-end
-
-
-# Shapes I/O
-struct CompressedPulseqShape
- num :: Int
- samples :: Vector{Float64}
-end
-
-
-function parse_section(section:: PulseqSection{:shapes}; kwargs...)
- current_id = -1
- shapes = Dict{Int, CompressedPulseqShape}()
- for line in section.content
- if startswith(lowercase(line), "shape_id")
- current_id = parse(Int, line[9:end])
- continue
- end
- for text in ("num_uncompressed", "num_samples")
- if startswith(lowercase(line), text)
- @assert current_id != -1
- if current_id in keys(shapes)
- error("Multiple shapes with the same ID detected.")
- end
- shapes[current_id] = CompressedPulseqShape(parse(Int, line[length(text)+1:end]), Float64[])
- end
- end
- if !startswith(lowercase(line), "num")
- push!(shapes[current_id].samples, parse(Float64, line))
- end
- end
- return Dict(key => uncompress(shape) for (key, shape) in shapes)
-end
-
-function uncompress(compressed::CompressedPulseqShape)
- if compressed.num == length(compressed.samples)
- # not actually compressed
- return PulseqShape(compressed.samples)
- end
- amplitudes = [compressed.samples[1]]
- repeating = false
- prev_sample = compressed.samples[1]
- for sample in compressed.samples[2:end]
- if repeating
- for _ in 1:Int(sample)
- push!(amplitudes, prev_sample)
- end
- repeating = false
- else
- push!(amplitudes, sample)
- if sample == prev_sample
- repeating = true
- end
- end
- end
- return PulseqShape(amplitudes)
-end
-
-function gen_section(comp:: PulseqComponents, ::Val{:shapes})
- res = PulseqSection{:shapes}(String[])
- for (index, shape) in enumerate(comp.shapes)
- append!(res.content, [
- "",
- "shape_id $index",
- "num_samples $(length(shape.samples))"
- ])
- for sample in shape.samples
- push!(res.content, string(sample))
- end
- end
- return res
-end
-
-function parse_section(section::PulseqSection{:delays}; version, kwargs...)
- if version > v"1.3.1"
- error("Did not expect a [DELAYS] section in pulseq file with version $(version)")
- end
- delays = Dict{Int, Int}()
- for line in section.content
- (id, delay) = parse.(Int, split(line))
- delays[id] = delay
- end
- return delays
-end
-
-# Components I/O
-_get_component(id::Int, shapes::Dict) = iszero(id) ? nothing : shapes[id]
-
-function parse_section(section::PulseqSection{:rf}; shapes::Dict{Int, PulseqShape}, version, kwargs...)
- result = Dict{Int, PulseqRFPulse}()
- for line in section.content
- if version == v"1.3.1"
- props = parse_pulseq_dict(
- line,
- [:id, :amp, :mag_id, :phase_id, :delay, :freq, :phase],
- [Int, Float64, Int, Int, Int, Float64, Float64],
- )
- props[:time_id] = 0
- else
- props = parse_pulseq_dict(
- line,
- [:id, :amp, :mag_id, :phase_id, :time_id, :delay, :freq, :phase],
- [Int, Float64, Int, Int, Int, Int, Float64, Float64],
- )
- end
- result[props[:id]] = PulseqRFPulse(
- props[:amp],
- _get_component(props[:mag_id], shapes),
- _get_component(props[:phase_id], shapes),
- _get_component(props[:time_id], shapes),
- props[:delay],
- props[:freq],
- props[:phase],
- )
- end
- return result
-end
-
-function gen_section(comp:: PulseqComponents, ::Val{:rf})
- res = PulseqSection{:rf}(String[])
- for (i, pulse) in enumerate(comp.pulses)
- values = string.(Any[
- i,
- pulse.amplitude,
- add_components!(comp, pulse.magnitude),
- add_components!(comp, pulse.phase),
- add_components!(comp, pulse.time),
- pulse.delay,
- pulse.frequency,
- pulse.phase_offset
- ])
- push!(res.content, join(values, " "))
- end
- return res
-end
-
-function parse_section(section::PulseqSection{:gradients}; shapes::Dict{Int, PulseqShape}, version::VersionNumber, kwargs...)
- result = Dict{Int, PulseqGradient}()
- for line in section.content
- if version == v"1.3.1"
- props = parse_pulseq_dict(
- line,
- [:id, :amp, :shape_id, :delay],
- [Int, Float64, Int, Int]
- )
- props[:time_id] = 0
- else
- props = parse_pulseq_dict(
- line,
- [:id, :amp, :shape_id, :time_id, :delay],
- [Int, Float64, Int, Int, Int]
- )
- end
- result[props[:id]] = PulseqGradient(
- props[:amp],
- _get_component(props[:shape_id], shapes),
- _get_component(props[:time_id], shapes),
- props[:delay]
- )
- end
- return result
-end
-
-function gen_section(comp:: PulseqComponents, ::Val{:gradients})
- res = PulseqSection{:gradients}(String[])
- for (i, grad) in enumerate(comp.grads)
- if !(grad isa PulseqGradient)
- continue
- end
- values = string.(Any[
- i,
- grad.amplitude,
- add_components!(comp, grad.shape),
- add_components!(comp, grad.time),
- grad.delay,
- ])
- push!(res.content, join(values, " "))
- end
- return res
-end
-
-function parse_section(section::PulseqSection{:trap}; kwargs...)
- result = Dict{Int, PulseqTrapezoid}()
- for line in section.content
- props = parse_pulseq_dict(
- line,
- [:id, :amp, :rise, :flat, :fall, :delay],
- [Int, Float64, Int, Int, Int, Int],
- )
- result[props[:id]] = PulseqTrapezoid(
- props[:amp],
- props[:rise],
- props[:flat],
- props[:fall],
- props[:delay],
- )
- end
- return result
-end
-
-function gen_section(comp:: PulseqComponents, ::Val{:trap})
- res = PulseqSection{:trap}(String[])
- for (i, grad) in enumerate(comp.grads)
- if !(grad isa PulseqTrapezoid)
- continue
- end
- values = string.(Any[
- i,
- grad.amplitude,
- grad.rise,
- grad.flat,
- grad.fall,
- grad.delay,
- ])
- push!(res.content, join(values, " "))
- end
- return res
-end
-
-function parse_section(section::PulseqSection{:adc}; kwargs...)
- result = Dict{Int, PulseqADC}()
- for line in section.content
- props = parse_pulseq_dict(
- line,
- [:id, :num, :dwell, :delay, :freq, :phase],
- [Int, Int, Float64, Int, Float64, Float64],
- )
- result[props[:id]] = PulseqADC(
- props[:num],
- props[:dwell],
- props[:delay],
- props[:freq],
- props[:phase],
- )
- end
- return result
-end
-
-function gen_section(comp:: PulseqComponents, ::Val{:adc})
- res = PulseqSection{:adc}(String[])
- for (i, adc) in enumerate(comp.adc)
- values = string.(Any[
- i,
- adc.num,
- adc.dwell,
- adc.delay,
- adc.frequency,
- adc.phase,
- ])
- push!(res.content, join(values, " "))
- end
- return res
-end
-
-function parse_section(section::PulseqSection{:extensions}; kwargs...)
- current_extension = -1
- pre_amble = true
- linked_list = Dict{Int, NTuple{3, Int}}()
- extensions = Dict{Int, PulseqExtension}()
- for line in section.content
- if startswith(line, "extension ")
- pre_amble = false
- (_, name, str_id) = split(line)
- current_extension = int(str_id)
- extensions[current_extension] = PulseqExtension(name, String[])
- elseif pre_ample
- (id, type, ref, next) = int.(split(line))
- linked_list[id] = (type=type, ref=ref, next=next)
- else
- push!(extensions[current_extension], line)
- end
- end
-
- function get_extension_list(key::Int)
- if iszero(key)
- return Tuple{PulseqExtension, Int}[]
- else
- base = get_extension_list(linked_list[key].next)
- pushfirst!(base, (extensions[linked_list[key].type], linked_list[key].ref))
- return base
- end
- end
-
- return Dict(key => get_extension_list(key) for key in keys(linked_list))
-end
-
-function parse_section(section::PulseqSection{:blocks}; version, rf=Dict(), gradients=Dict(), trap=Dict(), adc=Dict(), extensions=Dict(), delays=nothing, kwargs...)
- all_grad = merge(gradients, trap)
-
- res = Vector{PulseqBlock}()
- for line in section.content
- props = parse_pulseq_dict(
- line,
- [:id, :duration, :rf, :gx, :gy, :gz, :adc, :ext],
- fill(Int, 8),
- )
- if version == v"1.3.1"
- props[:duration] = iszero(props[:duration]) ? 0 : delays[props[:duration]]
- end
- @assert length(res) + 1 == props[:id]
- push!(res, PulseqBlock(
- props[:duration],
- _get_component(props[:rf], rf),
- _get_component(props[:gx], all_grad),
- _get_component(props[:gy], all_grad),
- _get_component(props[:gz], all_grad),
- _get_component(props[:adc], adc),
- iszero(props[:ext]) ? Tuple{PulseqExtension, Int}[] : _get_component(props[:ext], extensions),
- ))
- end
- return res
-end
-
-function gen_section(seq::PulseqSequence, comp:: PulseqComponents, ::Val{:blocks})
- res = PulseqSection{:blocks}(String[])
-
- for (i, block) in enumerate(seq.blocks)
- values = Any[i, block.duration]
- for (search_vec, part) in [
- (comp.pulses, block.rf)
- (comp.grads, block.gx)
- (comp.grads, block.gy)
- (comp.grads, block.gz)
- (comp.adc, block.adc)
- ]
- push!(values, add_components!(comp, search_vec, part))
- end
- push!(values, 0)
- if length(block.ext) > 0
- error("Cannot write extensions yet.")
- end
- push!(res.content, join(string.(values), " "))
- end
- return res
-end
-
-"""
- read_pulseq(IO)
-
-Reads a sequence from a pulseq file (http://pulseq.github.io/).
-Pulseq files can be produced using matlab (http://pulseq.github.io/) or python (https://pypulseq.readthedocs.io/en/master/).
-"""
-function read_pulseq(io::IO)
- sections = parse_pulseq_sections(io)
- return parse_all_sections(sections)
-end
-
-"""
- write_pulseq(IO, sequence)
-
-Writes a sequence to an output IO file.
-"""
-function write_pulseq(io::IO, sequence::PulseqSequence)
- if sequence.version < v"1.4"
- error("Can only write to pulseq version 1.4 or later.")
- end
- sections = gen_all_sections(sequence)
- for key in [:version, :definitions, :blocks, :rf, :gradients, :trap, :adc, :shapes]
- if length(sections[key].content) == 0
- continue
- end
- write_pulseq_section(io, sections[key])
- end
-end
-
-
-
-end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/basic_parsers.jl b/src/sequence_io/pulseq_io/basic_parsers.jl
new file mode 100644
index 0000000..42c3761
--- /dev/null
+++ b/src/sequence_io/pulseq_io/basic_parsers.jl
@@ -0,0 +1,62 @@
+module BasicParsers
+
+"""
+ parse_pulseq_dict(line, names, dtypes)
+
+Parse a line of integers/floats with known names and dtypes.
+
+This is useful to parse most of the columnar data in Pulseq, such as in BLOCKS, RF, GRADIENTS, etc.
+"""
+function parse_pulseq_dict(line, names, dtypes)
+ parts = split(line)
+ @assert length(parts) == length(names)
+ values = parse.(dtypes, split(line))
+ @assert names[1] == :id
+ return Dict(Symbol(name) => value for (name, value) in zip(names, values))
+end
+
+"""
+ parse_pulseq_properties(lines)
+
+Parse any `pulseq` section formatted as:
+```
+<name> <value>
+<name2> <value2>
+...
+```
+
+This includes the VERSION, DEFINITIONS, and part of the SHAPES
+"""
+function parse_pulseq_properties(strings::Vector{<:AbstractString})
+ result = Dict{String, Any}()
+ for s in strings
+ (name, value) = split(s, limit=2)
+ result[name] = parse_value(value)
+ end
+ return result
+end
+
+"""
+ parse_value(string)
+
+Tries to value the `string` as a number of sequence of numbers.
+If that does not work, the `string` is returned.
+"""
+function parse_value(value::AbstractString)
+ for t in (Int, Float64)
+ try
+ return parse(t, value)
+ catch
+ end
+ end
+ for t in (Int, Float64)
+ try
+ return parse.(t, split(value))
+ catch
+ end
+ end
+ return value
+end
+
+
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/components.jl b/src/sequence_io/pulseq_io/components.jl
new file mode 100644
index 0000000..cd5b38b
--- /dev/null
+++ b/src/sequence_io/pulseq_io/components.jl
@@ -0,0 +1,115 @@
+"""Define a list of all the [`PulseqShape`](@ref) and [`PulseqComponent`](@ref) that are used in a [`PulseqSequence`](@ref)."""
+module Components
+
+import ..Types: AnyPulseqComponent, PulseqShape, PulseqRFPulse, AnyPulseqGradient, PulseqADC, PulseqExtension, PulseqSequence
+
+"""
+ PulseqComponents(shapes, pulses, grads, adcs, extensions)
+
+All the shapes, pulses, grads, adcs, and extensions used in a [`PulseqSequence`](@ref).
+
+They can be provided as a dictionary from the integer ID to the object or as a vector.
+"""
+struct PulseqComponents
+ shapes:: Dict{Int, PulseqShape}
+ pulses:: Dict{Int, PulseqRFPulse}
+ grads:: Dict{Int, AnyPulseqGradient}
+ adc:: Dict{Int, PulseqADC}
+ extensions:: Dict{Int, PulseqExtension}
+ PulseqComponents(shapes, pulses, grads, adc, extensions) = new(
+ _convert_to_dict(shapes, PulseqShape),
+ _convert_to_dict(pulses, PulseqRFPulse),
+ _convert_to_dict(grads, AnyPulseqGradient),
+ _convert_to_dict(adc, PulseqADC),
+ _convert_to_dict(extensions, PulseqExtension),
+ )
+end
+
+_convert_to_dict(d::Dict{Int, Any}, ::Type{T}) where {T} = Dict(Int, T)(d)
+_convert_to_dict(d::Dict{Int, T}, ::Type{T}) where {T} = d
+_convert_to_dict(vec::Vector, ::Type{T}) where {T} = Dict{Int, T}(i => v for (i, v) in enumerate(vec))
+
+
+"""
+ PulseqComponents(sequence::PulseqSequence)
+
+Indentifies and lists all the unique components in the sequence.
+"""
+function PulseqComponents(sequence::PulseqSequence)
+
+end
+
+PulseqComponents() = PulseqComponents(
+ PulseqShape[],
+ PulseqRFPulse[],
+ AnyPulseqGradient[],
+ PulseqADC[],
+ PulseqExtension[],
+)
+
+"""
+ add_components(comp::PulseqComponents, search_vec::Vector, component)
+ add_components(comp::PulseqComponents, shape::PulseqShape)
+
+Adds a component to the [`search_vec`](@ref), which is assumed to be the appropriate vector within the `comp`.
+
+It will check whether the `component` is already part of the `search_vec` before adding it.
+The integer ID of the position of the `component` in `search_vec` is returned.
+
+0 is returned if `component` is `nothing`.
+"""
+add_components!(::PulseqComponents, search_vec::Dict{Int, <:Any}, ::Nothing) = 0
+function add_components!(comp::PulseqComponents, search_vec::Dict{Int, <:T}, component::T) where {T <: AnyPulseqComponent}
+ for (i, c) in search_vec
+ if same_component(comp, c, component)
+ return i
+ end
+ end
+ search_vec[length(search_vec) + 1] = component
+ return length(search_vec)
+end
+
+"""
+ same_component(comp::PulseqComponents, a, b)
+
+Check whether components `a` and `b` are the same when using the shapes represented in `comp`.
+"""
+same_component(::PulseqComponents, ::Any, ::Any) = false
+function same_component(comp::PulseqComponents, a::T, b::T) where {T}
+ for name in fieldnames(T)
+ v1 = getfield(a, name)
+ v2 = getfield(b, name)
+
+ if v1 isa PulseqShape
+ v1 = add_components!(comp, v1)
+ end
+ if v2 isa PulseqShape
+ v2 = add_components!(comp, v2)
+ end
+ if v1 != v2
+ return false
+ end
+ end
+ return true
+end
+
+
+add_components!(comp::PulseqComponents, ::Nothing) = 0
+function add_components!(comp::PulseqComponents, shape::PulseqShape)
+ for (i, s) in comp.shapes
+ if same_shape(s, shape)
+ return i
+ end
+ end
+ comp.shapes[length(comp.shapes) + 1] = shape
+ return length(comp.shapes)
+end
+
+"""
+ same_component(a, b)
+
+Check whether shapes `a` and `b` are the same.
+"""
+same_shape(shape1::PulseqShape, shape2::PulseqShape) = length(shape1.samples) == length(shape2.samples) && all(shape1.samples .≈ shape2.samples)
+
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parse_sections.jl b/src/sequence_io/pulseq_io/parse_sections.jl
new file mode 100644
index 0000000..1c3f86b
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parse_sections.jl
@@ -0,0 +1,45 @@
+"""
+Translate between sets of [`PulseqSection`](@ref) objects and [`PulseqSequence`](@ref).
+"""
+module ParseSections
+
+import ..Types: PulseqSequence, PulseqSection
+import ..Components: PulseqComponents
+import ..Parsers: parse_section, gen_section
+
+"""
+ parse_all_sections(sections)
+
+Parses the sections read from a Pulseq file.
+
+Returns a [`PulseqSequence`](@ref)
+"""
+function parse_all_sections(sections:: Dict{String, PulseqSection})
+ sections = copy(sections)
+ all_parts = Dict{Symbol, Any}()
+ for name in ["version", "definitions", "delays", "shapes", "rf", "gradients", "trap", "adc", "extensions", "blocks"]
+ if name in keys(sections)
+ section = pop!(sections, name)
+ all_parts[Symbol(name)] = parse_section(section; all_parts...)
+ end
+ end
+ if length(sections) > 0
+ @warn "Following sections in pulseq input file are not being used: $(keys(sections))"
+ end
+ return PulseqSequence(all_parts[:version], all_parts[:definitions], all_parts[:blocks])
+end
+
+function gen_all_sections(seq:: PulseqSequence)
+ sections = Dict{Symbol, PulseqSection}()
+ sections[:version] = gen_section(seq, Val(:version))
+ sections[:definitions] = gen_section(seq, Val(:definitions))
+
+ comp = PulseqComponents()
+ sections[:blocks] = gen_section(seq, comp, Val(:blocks))
+ for symbol in [:rf, :gradients, :trap, :adc, :shapes]
+ sections[symbol] = gen_section(comp, Val(symbol))
+ end
+ return sections
+end
+
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/adc.jl b/src/sequence_io/pulseq_io/parsers/adc.jl
new file mode 100644
index 0000000..eebeab8
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/adc.jl
@@ -0,0 +1,34 @@
+function parse_section(section::PulseqSection{:adc}; kwargs...)
+ result = Dict{Int, PulseqADC}()
+ for line in section.content
+ props = parse_pulseq_dict(
+ line,
+ [:id, :num, :dwell, :delay, :freq, :phase],
+ [Int, Int, Float64, Int, Float64, Float64],
+ )
+ result[props[:id]] = PulseqADC(
+ props[:num],
+ props[:dwell],
+ props[:delay],
+ props[:freq],
+ props[:phase],
+ )
+ end
+ return result
+end
+
+function gen_section(comp:: PulseqComponents, ::Val{:adc})
+ res = PulseqSection{:adc}(String[])
+ for (i, adc) in comp.adc
+ values = string.(Any[
+ i,
+ adc.num,
+ adc.dwell,
+ adc.delay,
+ adc.frequency,
+ adc.phase,
+ ])
+ push!(res.content, join(values, " "))
+ end
+ return res
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/blocks.jl b/src/sequence_io/pulseq_io/parsers/blocks.jl
new file mode 100644
index 0000000..f22f893
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/blocks.jl
@@ -0,0 +1,49 @@
+function parse_section(section::PulseqSection{:blocks}; version, rf=Dict(), gradients=Dict(), trap=Dict(), adc=Dict(), extensions=Dict(), delays=nothing, kwargs...)
+ all_grad = merge(gradients, trap)
+
+ res = Vector{PulseqBlock}()
+ for line in section.content
+ props = parse_pulseq_dict(
+ line,
+ [:id, :duration, :rf, :gx, :gy, :gz, :adc, :ext],
+ fill(Int, 8),
+ )
+ if version == v"1.3.1"
+ props[:duration] = iszero(props[:duration]) ? 0 : delays[props[:duration]]
+ end
+ @assert length(res) + 1 == props[:id]
+ push!(res, PulseqBlock(
+ props[:duration],
+ _get_component(props[:rf], rf),
+ _get_component(props[:gx], all_grad),
+ _get_component(props[:gy], all_grad),
+ _get_component(props[:gz], all_grad),
+ _get_component(props[:adc], adc),
+ iszero(props[:ext]) ? Tuple{PulseqExtension, Int}[] : _get_component(props[:ext], extensions),
+ ))
+ end
+ return res
+end
+
+function gen_section(seq::PulseqSequence, comp:: PulseqComponents, ::Val{:blocks})
+ res = PulseqSection{:blocks}(String[])
+
+ for (i, block) in enumerate(seq.blocks)
+ values = Any[i, block.duration]
+ for (search_vec, part) in [
+ (comp.pulses, block.rf)
+ (comp.grads, block.gx)
+ (comp.grads, block.gy)
+ (comp.grads, block.gz)
+ (comp.adc, block.adc)
+ ]
+ push!(values, add_components!(comp, search_vec, part))
+ end
+ push!(values, 0)
+ if length(block.ext) > 0
+ error("Cannot write extensions yet.")
+ end
+ push!(res.content, join(string.(values), " "))
+ end
+ return res
+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
new file mode 100644
index 0000000..2da9962
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/definitions.jl
@@ -0,0 +1,13 @@
+function parse_section(section:: PulseqSection{:definitions}; kwargs...)
+ props = parse_pulseq_properties(section.content)
+ return NamedTuple(Symbol(key) => value for (key, value) in props)
+end
+
+_to_string_value(value::AbstractString) = value
+_to_string_value(value::Number) = string(value)
+_to_string_value(value::Vector) = join(_to_string_value.(value), " ")
+
+function gen_section(seq:: PulseqSequence, ::Val{:definitions})
+ definitions = seq.definitions
+ return PulseqSection{:definitions}(["$(key) $(_to_string_value(value))" for (key, value) in pairs(definitions)])
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/delays.jl b/src/sequence_io/pulseq_io/parsers/delays.jl
new file mode 100644
index 0000000..53992db
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/delays.jl
@@ -0,0 +1,11 @@
+function parse_section(section::PulseqSection{:delays}; version, kwargs...)
+ if version > v"1.3.1"
+ error("Did not expect a [DELAYS] section in pulseq file with version $(version)")
+ end
+ delays = Dict{Int, Int}()
+ for line in section.content
+ (id, delay) = parse.(Int, split(line))
+ delays[id] = delay
+ end
+ return delays
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/extensions.jl b/src/sequence_io/pulseq_io/parsers/extensions.jl
new file mode 100644
index 0000000..e75298c
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/extensions.jl
@@ -0,0 +1,31 @@
+function parse_section(section::PulseqSection{:extensions}; kwargs...)
+ current_extension = -1
+ pre_amble = true
+ linked_list = Dict{Int, NTuple{3, Int}}()
+ extensions = Dict{Int, PulseqExtension}()
+ for line in section.content
+ if startswith(line, "extension ")
+ pre_amble = false
+ (_, name, str_id) = split(line)
+ current_extension = int(str_id)
+ extensions[current_extension] = PulseqExtension(name, String[])
+ elseif pre_ample
+ (id, type, ref, next) = int.(split(line))
+ linked_list[id] = (type=type, ref=ref, next=next)
+ else
+ push!(extensions[current_extension], line)
+ end
+ end
+
+ function get_extension_list(key::Int)
+ if iszero(key)
+ return Tuple{PulseqExtension, Int}[]
+ else
+ base = get_extension_list(linked_list[key].next)
+ pushfirst!(base, (extensions[linked_list[key].type], linked_list[key].ref))
+ return base
+ end
+ end
+
+ return Dict(key => get_extension_list(key) for key in keys(linked_list))
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/gradients.jl b/src/sequence_io/pulseq_io/parsers/gradients.jl
new file mode 100644
index 0000000..67a1cc9
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/gradients.jl
@@ -0,0 +1,44 @@
+function parse_section(section::PulseqSection{:gradients}; shapes::Dict{Int, PulseqShape}, version::VersionNumber, kwargs...)
+ result = Dict{Int, PulseqGradient}()
+ for line in section.content
+ if version == v"1.3.1"
+ props = parse_pulseq_dict(
+ line,
+ [:id, :amp, :shape_id, :delay],
+ [Int, Float64, Int, Int]
+ )
+ props[:time_id] = 0
+ else
+ props = parse_pulseq_dict(
+ line,
+ [:id, :amp, :shape_id, :time_id, :delay],
+ [Int, Float64, Int, Int, Int]
+ )
+ end
+ result[props[:id]] = PulseqGradient(
+ props[:amp],
+ _get_component(props[:shape_id], shapes),
+ _get_component(props[:time_id], shapes),
+ props[:delay]
+ )
+ end
+ return result
+end
+
+function gen_section(comp:: PulseqComponents, ::Val{:gradients})
+ res = PulseqSection{:gradients}(String[])
+ for (i, grad) in comp.grads
+ if !(grad isa PulseqGradient)
+ continue
+ end
+ values = string.(Any[
+ i,
+ grad.amplitude,
+ add_components!(comp, grad.shape),
+ add_components!(comp, grad.time),
+ grad.delay,
+ ])
+ push!(res.content, join(values, " "))
+ end
+ return res
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/parsers.jl b/src/sequence_io/pulseq_io/parsers/parsers.jl
new file mode 100644
index 0000000..a047f49
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/parsers.jl
@@ -0,0 +1,37 @@
+module Parsers
+import ..Types: PulseqSection, PulseqSequence, PulseqRFPulse, PulseqGradient, PulseqTrapezoid, PulseqExtensionDefinition, PulseqExtension, PulseqADC, PulseqBlock, PulseqShape
+import ..Components: PulseqComponents, add_components!
+import ..BasicParsers: parse_pulseq_dict, parse_pulseq_properties
+
+"""
+ parse_section(section)
+
+Parses any [`PulseqSection`](@ref) and return the appropriate type.
+
+The opposite is [`gen_section`](@ref).
+"""
+function parse_section end
+
+
+"""
+ gen_section(sequence, Val(:<title>))
+
+Creates a specific [`PulseqSection`](@ref){<title>} from a part of the PulseqSequence.
+
+This is the opposite of [`parse_section`](@ref)
+"""
+function gen_section end
+
+_get_component(id::Int, shapes::Dict) = iszero(id) ? nothing : shapes[id]
+
+include("version.jl")
+include("definitions.jl")
+include("delays.jl")
+include("shapes.jl")
+include("rf.jl")
+include("gradients.jl")
+include("trapezoids.jl")
+include("adc.jl")
+include("extensions.jl")
+include("blocks.jl")
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/rf.jl b/src/sequence_io/pulseq_io/parsers/rf.jl
new file mode 100644
index 0000000..c864259
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/rf.jl
@@ -0,0 +1,47 @@
+function parse_section(section::PulseqSection{:rf}; shapes::Dict{Int, PulseqShape}, version, kwargs...)
+ result = Dict{Int, PulseqRFPulse}()
+ for line in section.content
+ if version == v"1.3.1"
+ props = parse_pulseq_dict(
+ line,
+ [:id, :amp, :mag_id, :phase_id, :delay, :freq, :phase],
+ [Int, Float64, Int, Int, Int, Float64, Float64],
+ )
+ props[:time_id] = 0
+ else
+ props = parse_pulseq_dict(
+ line,
+ [:id, :amp, :mag_id, :phase_id, :time_id, :delay, :freq, :phase],
+ [Int, Float64, Int, Int, Int, Int, Float64, Float64],
+ )
+ end
+ result[props[:id]] = PulseqRFPulse(
+ props[:amp],
+ _get_component(props[:mag_id], shapes),
+ _get_component(props[:phase_id], shapes),
+ _get_component(props[:time_id], shapes),
+ props[:delay],
+ props[:freq],
+ props[:phase],
+ )
+ end
+ return result
+end
+
+function gen_section(comp:: PulseqComponents, ::Val{:rf})
+ res = PulseqSection{:rf}(String[])
+ for (i, pulse) in comp.pulses
+ values = string.(Any[
+ i,
+ pulse.amplitude,
+ add_components!(comp, pulse.magnitude),
+ add_components!(comp, pulse.phase),
+ add_components!(comp, pulse.time),
+ pulse.delay,
+ pulse.frequency,
+ pulse.phase_offset
+ ])
+ push!(res.content, join(values, " "))
+ end
+ return res
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/shapes.jl b/src/sequence_io/pulseq_io/parsers/shapes.jl
new file mode 100644
index 0000000..6d523df
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/shapes.jl
@@ -0,0 +1,68 @@
+struct CompressedPulseqShape
+ num :: Int
+ samples :: Vector{Float64}
+end
+
+
+function parse_section(section:: PulseqSection{:shapes}; kwargs...)
+ current_id = -1
+ shapes = Dict{Int, CompressedPulseqShape}()
+ for line in section.content
+ if startswith(lowercase(line), "shape_id")
+ current_id = parse(Int, line[9:end])
+ continue
+ end
+ for text in ("num_uncompressed", "num_samples")
+ if startswith(lowercase(line), text)
+ @assert current_id != -1
+ if current_id in keys(shapes)
+ error("Multiple shapes with the same ID detected.")
+ end
+ shapes[current_id] = CompressedPulseqShape(parse(Int, line[length(text)+1:end]), Float64[])
+ end
+ end
+ if !startswith(lowercase(line), "num")
+ push!(shapes[current_id].samples, parse(Float64, line))
+ end
+ end
+ return Dict(key => uncompress(shape) for (key, shape) in shapes)
+end
+
+function uncompress(compressed::CompressedPulseqShape)
+ if compressed.num == length(compressed.samples)
+ # not actually compressed
+ return PulseqShape(compressed.samples)
+ end
+ amplitudes = [compressed.samples[1]]
+ repeating = false
+ prev_sample = compressed.samples[1]
+ for sample in compressed.samples[2:end]
+ if repeating
+ for _ in 1:Int(sample)
+ push!(amplitudes, prev_sample)
+ end
+ repeating = false
+ else
+ push!(amplitudes, sample)
+ if sample == prev_sample
+ repeating = true
+ end
+ end
+ end
+ return PulseqShape(amplitudes)
+end
+
+function gen_section(comp:: PulseqComponents, ::Val{:shapes})
+ res = PulseqSection{:shapes}(String[])
+ for (index, shape) in comp.shapes
+ append!(res.content, [
+ "",
+ "shape_id $index",
+ "num_samples $(length(shape.samples))"
+ ])
+ for sample in shape.samples
+ push!(res.content, string(sample))
+ end
+ end
+ return res
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/parsers/trapezoids.jl b/src/sequence_io/pulseq_io/parsers/trapezoids.jl
new file mode 100644
index 0000000..990d1b7
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/trapezoids.jl
@@ -0,0 +1,37 @@
+function parse_section(section::PulseqSection{:trap}; kwargs...)
+ result = Dict{Int, PulseqTrapezoid}()
+ for line in section.content
+ props = parse_pulseq_dict(
+ line,
+ [:id, :amp, :rise, :flat, :fall, :delay],
+ [Int, Float64, Int, Int, Int, Int],
+ )
+ result[props[:id]] = PulseqTrapezoid(
+ props[:amp],
+ props[:rise],
+ props[:flat],
+ props[:fall],
+ props[:delay],
+ )
+ end
+ return result
+end
+
+function gen_section(comp:: PulseqComponents, ::Val{:trap})
+ res = PulseqSection{:trap}(String[])
+ for (i, grad) in comp.grads
+ if !(grad isa PulseqTrapezoid)
+ continue
+ end
+ values = string.(Any[
+ i,
+ grad.amplitude,
+ grad.rise,
+ grad.flat,
+ grad.fall,
+ grad.delay,
+ ])
+ push!(res.content, join(values, " "))
+ end
+ return res
+end
diff --git a/src/sequence_io/pulseq_io/parsers/version.jl b/src/sequence_io/pulseq_io/parsers/version.jl
new file mode 100644
index 0000000..d70ec1a
--- /dev/null
+++ b/src/sequence_io/pulseq_io/parsers/version.jl
@@ -0,0 +1,13 @@
+function parse_section(section:: PulseqSection{:version}; kwargs...)
+ props = parse_pulseq_properties(section.content)
+ return VersionNumber(props["major"], props["minor"], props["revision"])
+end
+
+function gen_section(seq::PulseqSequence, ::Val{:version})
+ version = seq.version
+ return PulseqSection{:version}([
+ "major $(version.major)",
+ "minor $(version.minor)",
+ "revision $(version.patch)",
+ ])
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/pulseq_io.jl b/src/sequence_io/pulseq_io/pulseq_io.jl
new file mode 100644
index 0000000..d60141e
--- /dev/null
+++ b/src/sequence_io/pulseq_io/pulseq_io.jl
@@ -0,0 +1,46 @@
+"""
+Stand-alone module that reads/writes Pulseq files.
+
+The pulseq files are read into or written from a set of types that closely match the Pulseq file format.
+The translation of these types into MRIBuilder types is defined in "../pulseq.jl" (i.e., `MRIBuilder.SequenceIO.Pulseq`)
+"""
+module PulseqIO
+include("types.jl")
+include("basic_parsers.jl")
+include("sections_io.jl")
+include("components.jl")
+include("parsers/parsers.jl")
+include("parse_sections.jl")
+
+
+
+"""
+ read_pulseq(IO)
+
+Reads a sequence from a pulseq file (http://pulseq.github.io/).
+Pulseq files can be produced using matlab (http://pulseq.github.io/) or python (https://pypulseq.readthedocs.io/en/master/).
+"""
+function read_pulseq(io::IO)
+ sections = SectionsIO.parse_pulseq_sections(io)
+ return ParseSections.parse_all_sections(sections)
+end
+
+"""
+ write_pulseq(IO, sequence)
+
+Writes a sequence to an output IO file.
+"""
+function write_pulseq(io::IO, sequence::Types.PulseqSequence)
+ if sequence.version < v"1.4"
+ error("Can only write to pulseq version 1.4 or later.")
+ end
+ sections = ParseSections.gen_all_sections(sequence)
+ for key in [:version, :definitions, :blocks, :rf, :gradients, :trap, :adc, :shapes]
+ if length(sections[key].content) == 0
+ continue
+ end
+ SectionsIO.write_pulseq_section(io, sections[key])
+ end
+end
+
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/sections_io.jl b/src/sequence_io/pulseq_io/sections_io.jl
new file mode 100644
index 0000000..96616c1
--- /dev/null
+++ b/src/sequence_io/pulseq_io/sections_io.jl
@@ -0,0 +1,49 @@
+"""Define IO for [`PulseqSection`](@ref)."""
+module SectionsIO
+import ..Types: PulseqSection
+
+"""
+ parse_pulseq_sections(io)
+
+Reads a Pulseq file into a dictionary of [`PulseqSection`](@ref) objects.
+"""
+function parse_pulseq_sections(io::IO)
+ sections = Dict{String, PulseqSection}()
+ current_title = ""
+ for line in readlines(io)
+ line = strip(line)
+ if length(line) == 0 || line[1] == '#'
+ continue # ignore comments
+ end
+ if line[1] == '[' && line[end] == ']'
+ # new section starts
+ current_title = lowercase(line[2:end-1])
+ sections[current_title] = PulseqSection{Symbol(current_title)}(String[])
+ elseif length(current_title) > 0
+ push!(sections[current_title].content, line)
+ else
+ error("Content found in pulseq file before first section")
+ end
+ end
+ return sections
+end
+
+"""
+ write_pulseq_section(io, section::PulseqSection)
+
+Writes a Pulseq `section` to the `IO`.
+"""
+function write_pulseq_section(io::IO, section::PulseqSection{T}) where {T}
+ title = uppercase(string(T))
+ write(io, "[$title]\n")
+ for line in section.content
+ if iszero(length(line)) || line[end] != '\n'
+ line = line * '\n'
+ end
+ write(io, line)
+ end
+ write(io, "\n")
+ write(io, "\n")
+end
+
+end
\ No newline at end of file
diff --git a/src/sequence_io/pulseq_io/types.jl b/src/sequence_io/pulseq_io/types.jl
new file mode 100644
index 0000000..3aa4089
--- /dev/null
+++ b/src/sequence_io/pulseq_io/types.jl
@@ -0,0 +1,143 @@
+"""
+Define the main types forming a [`PulseqSequence`](@ref).
+
+Extensions and sections types are defined in their own modules.
+"""
+module Types
+
+"""
+ PulseqSection(:<title>)(lines)
+
+Represents a section in the pulseq file format.
+"""
+struct PulseqSection{T}
+ content :: Vector{String}
+end
+
+"""
+ PulseqShape(samples)
+
+Define the shape of a [`PulseqRFPulse`](@ref) or [`PulseqGradient`](@ref).
+"""
+struct PulseqShape
+ samples :: Vector{Float64}
+end
+
+"""
+Super-type for any RF pulses/gradients/ADC/extensions that can play out during a [`PulseqBlock`](@ref).
+"""
+abstract type AnyPulseqComponent end
+
+
+"""
+ PulseqRFPulse(amplitude::Number, magnitude::PulseqShape, phase::PulseqShape, time::PulseqShape, delay::Int, frequency::Number, phase_offset::Number)
+
+An RF pulse defined in Pulseq (see [specification](https://raw.githubusercontent.com/pulseq/pulseq/master/doc/specification.pdf)).
+"""
+struct PulseqRFPulse <: AnyPulseqComponent
+ amplitude :: Float64
+ magnitude :: PulseqShape
+ phase :: PulseqShape
+ time :: Union{Nothing, PulseqShape}
+ delay :: Int
+ frequency :: Float64
+ phase_offset :: Float64
+end
+
+"""
+Super-type of Pulseq gradients:
+- [`PulseqGradient`](@ref)
+- [`PulseqTrapezoid`](@ref)
+"""
+abstract type AnyPulseqGradient <: AnyPulseqComponent end
+
+"""
+ PulseqGradient(amplitude::Number, shape::PulseqShape, time::PulseqShape, delay::int)
+
+A generic gradient waveform defined in Pulseq (see [specification](https://raw.githubusercontent.com/pulseq/pulseq/master/doc/specification.pdf)).
+"""
+struct PulseqGradient <: AnyPulseqGradient
+ amplitude :: Float64
+ shape :: PulseqShape
+ time :: Union{Nothing, PulseqShape}
+ delay :: Int
+end
+
+"""
+ PulseqTrapezoid(amplitude::Number, rise::Int, flat::Int, fall::Int, delay::Int)
+
+A trapezoidal gradient pulse defined in Pulseq (see [specification](https://raw.githubusercontent.com/pulseq/pulseq/master/doc/specification.pdf)).
+"""
+struct PulseqTrapezoid <:AnyPulseqGradient
+ amplitude :: Float64
+ rise :: Int
+ flat :: Int
+ fall :: Int
+ delay :: Int
+end
+
+"""
+ PulseqADC(num::Int, dwell::Float64, delay::Int, frequency::Number, phase::Number)
+
+A trapezoidal gradient pulse defined in Pulseq (see [specification](https://raw.githubusercontent.com/pulseq/pulseq/master/doc/specification.pdf)).
+"""
+struct PulseqADC <: AnyPulseqComponent
+ num :: Int
+ dwell :: Float64
+ delay :: Int
+ frequency :: Float64
+ phase :: Float64
+end
+
+"""
+ PulseqExtensionDefinition(name, content)
+
+Abstract definition of an unknown Pulseq extension.
+"""
+struct PulseqExtensionDefinition
+ name :: String
+ content :: Vector{String}
+end
+
+"""
+ PulseqExtension(definition::PulseqExtensionDefinition, id::Int)
+
+Reference to a specific implementation of the [`PulseqExtensionDefinition`](@ref).
+"""
+struct PulseqExtension <: AnyPulseqComponent
+ definition::PulseqExtensionDefinition
+ id :: Int
+end
+
+"""
+ PulseqBlock(duration::Int, rf::PulseqRFPulse, gx::AnyPulseqGradient, gy::AnyPulseqGradient, gz::AnyPulseqGradient, adc::PulseqADC, ext)
+
+Defines a Building Block with the Pulseq sequence (see [specification](https://raw.githubusercontent.com/pulseq/pulseq/master/doc/specification.pdf)).
+
+The RF pulse, gradients, and ADC can be set to `nothing`.
+
+The `ext` is a sequence of extension blocks that will be played out.
+Set this to a sequence of zero length to not have any extensions.
+"""
+struct PulseqBlock
+ duration :: Int
+ rf :: Union{Nothing, PulseqRFPulse}
+ gx :: Union{Nothing, AnyPulseqGradient}
+ gy :: Union{Nothing, AnyPulseqGradient}
+ gz :: Union{Nothing, AnyPulseqGradient}
+ adc :: Union{Nothing, PulseqADC}
+ ext :: Vector{<:Tuple{PulseqExtension, Int}}
+end
+
+"""
+ PulseqSequence(version::VersionNumber, definitions::NamedTuple, blocks::Vector{PulseqBlock})
+
+A full sequence defined according to the Pulseq [specification](https://raw.githubusercontent.com/pulseq/pulseq/master/doc/specification.pdf).
+"""
+struct PulseqSequence
+ version:: VersionNumber
+ definitions:: NamedTuple
+ blocks:: Vector{PulseqBlock}
+end
+
+end
\ No newline at end of file
diff --git a/src/sequence_io/sequence_io.jl b/src/sequence_io/sequence_io.jl
index 7bd11d6..a451ff6 100644
--- a/src/sequence_io/sequence_io.jl
+++ b/src/sequence_io/sequence_io.jl
@@ -1,8 +1,8 @@
module SequenceIO
-include("pulseq.jl")
+include("pulseq_io/pulseq_io.jl")
-import .Pulseq: read_pulseq
+import .PulseqIO: read_pulseq
import Serialization: serialize, deserialize
--
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