diff --git a/src/sequence_io/pulseq_io/components.jl b/src/sequence_io/pulseq_io/components.jl
index cd5b38b750af18bffb5b1dc82b926ea80e5c197a..fd189e2d95ee60e73fb621d3a4bdd2655c3a32e5 100644
--- a/src/sequence_io/pulseq_io/components.jl
+++ b/src/sequence_io/pulseq_io/components.jl
@@ -15,13 +15,13 @@ struct PulseqComponents
pulses:: Dict{Int, PulseqRFPulse}
grads:: Dict{Int, AnyPulseqGradient}
adc:: Dict{Int, PulseqADC}
- extensions:: Dict{Int, PulseqExtension}
+ extensions:: Dict{Int, Any}
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),
+ _convert_to_dict(extensions, Any),
)
end
diff --git a/src/sequence_io/pulseq_io/extensions.jl b/src/sequence_io/pulseq_io/extensions.jl
new file mode 100644
index 0000000000000000000000000000000000000000..2984c877da57c2f48f6c287826f36f109087b48a
--- /dev/null
+++ b/src/sequence_io/pulseq_io/extensions.jl
@@ -0,0 +1,55 @@
+"""
+Defines the Pulseq IO extension interface with default implementations
+"""
+module Extensions
+import ..Types: PulseqExtension, PulseqExtensionDefinition
+
+struct UnknownExtensionMapper
+ ext::PulseqExtensionDefinition
+end
+
+Base.getindex(mapper::UnknownExtensionMapper, i::Int) = PulseqExtension(mapper.ext, i)
+
+"""
+ parse_extension(ext::PulseqExtensionDefinition{name})
+
+Parse a Pulseq extension definition into a dictionary-like object
+that maps integer reference IDs to any object describing the extension.
+
+This can be overriden to support the reading of a specific extension type.
+For example, to define a parser for an extension with the name "LABELSET":
+```
+function PulseqIO.parse_extension(ext::PulseqExtensionDefinition{:LABELSET})
+ ...
+end
+```
+"""
+function parse_extension(ext::PulseqExtensionDefinition{N}) where {N}
+ @warn "Parsing unknown extension: {N}"
+ return UnknownExtensionMapper(ext)
+end
+
+
+"""
+ get_extension_name(obj)
+
+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
+
+"""
+ add_extension_definition!(content::Vector{String}, obj)
+
+Add the object to the extension definition and returns the reference index.
+
+The extension definition is passed on as a vector of strings.
+This vector can be appended to, when adding a new object.
+
+If the object is already in the `definition` the reference index of the already existing object should be returned instead.
+"""
+add_extension_definition!(content::Vector{String}, ext::PulseqExtension) = ext.index
+
+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
index e75298c096e09f624f27efa03b59e417f2d8d9b1..fac6d32595def5f32e8b0e38b8f3f14624666b40 100644
--- a/src/sequence_io/pulseq_io/parsers/extensions.jl
+++ b/src/sequence_io/pulseq_io/parsers/extensions.jl
@@ -1,14 +1,16 @@
+import ..Extensions: parse_extension, get_extension_name, add_extension_definition!
+
function parse_section(section::PulseqSection{:extensions}; kwargs...)
current_extension = -1
pre_amble = true
linked_list = Dict{Int, NTuple{3, Int}}()
- extensions = Dict{Int, PulseqExtension}()
+ extensions = Dict{Int, PulseqExtensionDefinition}()
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[])
+ extensions[current_extension] = PulseqExtensionDefinition{name}(String[])
elseif pre_ample
(id, type, ref, next) = int.(split(line))
linked_list[id] = (type=type, ref=ref, next=next)
@@ -17,15 +19,69 @@ function parse_section(section::PulseqSection{:extensions}; kwargs...)
end
end
+ extension_mappers = Dict(key => parse_extension(ext) for (key, ext) in extensions)
+
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))
+ pushfirst!(base, extension_mappers[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 gen_section(comp:: PulseqComponents, ::Val{:extensions})
+ definitions = Dict{Symbol, PulseqExtensionDefinition}()
+ extensions_ref_id = Dict{Any, Int}()
+ for ext_vec in comp.extensions
+ for ext in ext_vec
+ name = get_extension_name(ext)
+ if !(name in keys(definitions))
+ definitions[name] = PulseqExtensionDefinition{name}(String[])
+ end
+ extensions_ref_id[ext] = add_extension_definition!(definitions[name].content, ext)
+ end
+ end
+
+ definitions_order = [keys(definitions)...]
+
+ extension_vec_id = Dict{Vector, Int}()
+
+ labels = Tuple{Int, Int, Int}[]
+ function add_extension_vec!(ext_vec::Vector)
+ if length(ext_vec) == 0
+ return 0
+ end
+ next_id = add_extension_vec!(ext_vec[2:end])
+ ext = ext_vec[1]
+ type_id = findfirst(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)
+ else
+ push!(labels, all_ids)
+ extension_vec_id[ext_vec] = length(lables)
+ end
+ end
+ add_extension_definition!.(values(comp.extensions))
+
+ content = String[]
+ for (id0, (id1, id2, id3)) in enumerate(labels)
+ push!(content, "$id0 $id1 $id2 $id3")
+ end
+ push!(content, "")
+
+ for (index, name) in enumerate(definitions_order)
+ def = definitions[name]
+ push!(content, "extension $(string(name)) $(string(index))")
+ append!(content, def.content)
+ push!(content, "")
+ end
+
+ return PulseqSection{:extensions}(content)
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 278e20775d3f9439eb7fe5ac9e4ad1d7ab2e2224..e2170991e9b5d1627aa7733dcfc1ccb8f0a12e9f 100644
--- a/src/sequence_io/pulseq_io/pulseq_io.jl
+++ b/src/sequence_io/pulseq_io/pulseq_io.jl
@@ -6,6 +6,7 @@ The translation of these types into MRIBuilder types is defined in "../pulseq.jl
"""
module PulseqIO
include("types.jl")
+include("extensions.jl")
include("basic_parsers.jl")
include("sections_io.jl")
include("components.jl")
@@ -13,6 +14,7 @@ include("parsers/parsers.jl")
include("parse_sections.jl")
import .Types: PulseqSequence
+import .Extensions: parse_extension, get_extension_name, add_extension_definition!
"""
diff --git a/src/sequence_io/pulseq_io/types.jl b/src/sequence_io/pulseq_io/types.jl
index 3aa40897171687fde9ed213eed36e51a161d7fca..d093917b74f544fd98ed3317c4ce9bc568b1bc83 100644
--- a/src/sequence_io/pulseq_io/types.jl
+++ b/src/sequence_io/pulseq_io/types.jl
@@ -94,18 +94,17 @@ end
Abstract definition of an unknown Pulseq extension.
"""
-struct PulseqExtensionDefinition
- name :: String
+struct PulseqExtensionDefinition{N}
content :: Vector{String}
end
"""
PulseqExtension(definition::PulseqExtensionDefinition, id::Int)
-Reference to a specific implementation of the [`PulseqExtensionDefinition`](@ref).
+Reference to a specific implementation of a [`PulseqExtensionDefinition`](@ref).
"""
-struct PulseqExtension <: AnyPulseqComponent
- definition::PulseqExtensionDefinition
+struct PulseqExtension{N} <: AnyPulseqComponent
+ definition::PulseqExtensionDefinition{N}
id :: Int
end