diff --git a/src/sequence_io/pulseq_io/components.jl b/src/sequence_io/pulseq_io/components.jl
index fd189e2d95ee60e73fb621d3a4bdd2655c3a32e5..252a443517fd96f53c246a2a40515792dc417cb4 100644
--- a/src/sequence_io/pulseq_io/components.jl
+++ b/src/sequence_io/pulseq_io/components.jl
@@ -15,13 +15,11 @@ struct PulseqComponents
pulses:: Dict{Int, PulseqRFPulse}
grads:: Dict{Int, AnyPulseqGradient}
adc:: Dict{Int, PulseqADC}
- extensions:: Dict{Int, Any}
- PulseqComponents(shapes, pulses, grads, adc, extensions) = new(
+ PulseqComponents(shapes, pulses, grads, adc) = 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, Any),
)
end
@@ -30,21 +28,11 @@ _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[],
)
"""
diff --git a/src/sequence_io/pulseq_io/extensions.jl b/src/sequence_io/pulseq_io/extensions.jl
index 2984c877da57c2f48f6c287826f36f109087b48a..d8c50ce3aadce61578a8878ef60e98e5a52bb6a8 100644
--- a/src/sequence_io/pulseq_io/extensions.jl
+++ b/src/sequence_io/pulseq_io/extensions.jl
@@ -38,7 +38,7 @@ Get the name under which the given `obj` should be stored in a Pulseq extension.
To write an object to a Pulseq file extension,
one needs to define both this function and [`add_extension_definition`](@ref).
"""
-get_extension_name(ext::PulseqExtension{N}) where {N} = N
+get_extension_name(::PulseqExtension{N}) where {N} = N
"""
add_extension_definition!(content::Vector{String}, obj)
diff --git a/src/sequence_io/pulseq_io/parse_sections.jl b/src/sequence_io/pulseq_io/parse_sections.jl
index 1c3f86b56d12d4ec2f9f51b0efda94dd6ea63915..2130db831dcb17b2afc2b2fe83637d7b01740566 100644
--- a/src/sequence_io/pulseq_io/parse_sections.jl
+++ b/src/sequence_io/pulseq_io/parse_sections.jl
@@ -33,9 +33,11 @@ function gen_all_sections(seq:: PulseqSequence)
sections = Dict{Symbol, PulseqSection}()
sections[:version] = gen_section(seq, Val(:version))
sections[:definitions] = gen_section(seq, Val(:definitions))
+ (section, extension_mapping) = gen_section(seq, Val(:extensions))
+ sections[:extensions] = section
comp = PulseqComponents()
- sections[:blocks] = gen_section(seq, comp, Val(:blocks))
+ sections[:blocks] = gen_section(seq, comp, Val(:blocks), extension_mapping)
for symbol in [:rf, :gradients, :trap, :adc, :shapes]
sections[symbol] = gen_section(comp, Val(symbol))
end
diff --git a/src/sequence_io/pulseq_io/parsers/blocks.jl b/src/sequence_io/pulseq_io/parsers/blocks.jl
index f22f893a633c0e293a823adefa5a60b60505e3dc..172847ba0aa06f591d997070cd5d729f2e7d07c4 100644
--- a/src/sequence_io/pulseq_io/parsers/blocks.jl
+++ b/src/sequence_io/pulseq_io/parsers/blocks.jl
@@ -25,7 +25,7 @@ function parse_section(section::PulseqSection{:blocks}; version, rf=Dict(), grad
return res
end
-function gen_section(seq::PulseqSequence, comp:: PulseqComponents, ::Val{:blocks})
+function gen_section(seq::PulseqSequence, comp:: PulseqComponents, ::Val{:blocks}, extension_mapping::Dict{Vector, Int})
res = PulseqSection{:blocks}(String[])
for (i, block) in enumerate(seq.blocks)
@@ -39,9 +39,10 @@ function gen_section(seq::PulseqSequence, comp:: PulseqComponents, ::Val{:blocks
]
push!(values, add_components!(comp, search_vec, part))
end
- push!(values, 0)
if length(block.ext) > 0
- error("Cannot write extensions yet.")
+ push!(values, extension_mapping[block.ext])
+ else
+ push!(values, 0)
end
push!(res.content, join(string.(values), " "))
end
diff --git a/src/sequence_io/pulseq_io/parsers/extensions.jl b/src/sequence_io/pulseq_io/parsers/extensions.jl
index fac6d32595def5f32e8b0e38b8f3f14624666b40..9d39c8ce142a9bcd668f7fa6c8a0edf82d3593fa 100644
--- a/src/sequence_io/pulseq_io/parsers/extensions.jl
+++ b/src/sequence_io/pulseq_io/parsers/extensions.jl
@@ -34,10 +34,12 @@ function parse_section(section::PulseqSection{:extensions}; kwargs...)
return Dict(key => get_extension_list(key) for key in keys(linked_list))
end
-function gen_section(comp:: PulseqComponents, ::Val{:extensions})
+function gen_section(seq:: PulseqSequence, ::Val{:extensions})
definitions = Dict{Symbol, PulseqExtensionDefinition}()
extensions_ref_id = Dict{Any, Int}()
- for ext_vec in comp.extensions
+
+ all_ext_vec = [block.ext for block in seq.blocks if length(block.ext) > 0]
+ for ext_vec in all_ext_vec
for ext in ext_vec
name = get_extension_name(ext)
if !(name in keys(definitions))
@@ -58,17 +60,17 @@ function gen_section(comp:: PulseqComponents, ::Val{:extensions})
end
next_id = add_extension_vec!(ext_vec[2:end])
ext = ext_vec[1]
- type_id = findfirst(get_extension_name(ext), definitions_order)
+ type_id = findfirst(isequal(get_extension_name(ext)), definitions_order)
ref_id = extensions_ref_id[ext]
all_ids = (type_id, ref_id, next_id)
if all_ids in labels
- extension_vec_id[ext_vec] = findfirst(lables, all_ids)
+ extension_vec_id[ext_vec] = findfirst(isequal(all_ids), labels)
else
push!(labels, all_ids)
- extension_vec_id[ext_vec] = length(lables)
+ extension_vec_id[ext_vec] = length(labels)
end
end
- add_extension_definition!.(values(comp.extensions))
+ add_extension_vec!.(all_ext_vec)
content = String[]
for (id0, (id1, id2, id3)) in enumerate(labels)
@@ -83,5 +85,5 @@ function gen_section(comp:: PulseqComponents, ::Val{:extensions})
push!(content, "")
end
- return PulseqSection{:extensions}(content)
+ return PulseqSection{:extensions}(content), extension_vec_id
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
index e2170991e9b5d1627aa7733dcfc1ccb8f0a12e9f..6eb637fa2b6654338af64ab0ea1e0aa91ea18281 100644
--- a/src/sequence_io/pulseq_io/pulseq_io.jl
+++ b/src/sequence_io/pulseq_io/pulseq_io.jl
@@ -38,7 +38,7 @@ function write_pulseq(io::IO, sequence::Types.PulseqSequence)
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]
+ for key in [:version, :definitions, :blocks, :rf, :gradients, :trap, :adc, :extensions, :shapes]
if length(sections[key].content) == 0
continue
end
diff --git a/src/sequence_io/pulseq_io/types.jl b/src/sequence_io/pulseq_io/types.jl
index d093917b74f544fd98ed3317c4ce9bc568b1bc83..d94aca9553eaeb2450eb28803b92f7e720aa06d6 100644
--- a/src/sequence_io/pulseq_io/types.jl
+++ b/src/sequence_io/pulseq_io/types.jl
@@ -125,7 +125,7 @@ struct PulseqBlock
gy :: Union{Nothing, AnyPulseqGradient}
gz :: Union{Nothing, AnyPulseqGradient}
adc :: Union{Nothing, PulseqADC}
- ext :: Vector{<:Tuple{PulseqExtension, Int}}
+ ext :: Vector
end
"""