From c14ee7fbdbb7211b551ab01a25eb247f5ef16e07 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Sat, 27 Jan 2024 18:49:01 +0000
Subject: [PATCH] Fix containers and sequences
---
src/MRIBuilder.jl | 4 ++--
src/building_blocks.jl | 6 ++---
src/containers/containers.jl | 2 +-
src/containers/fixed_blocks.jl | 2 ++
src/containers/sequences.jl | 41 ++++++++++++++++++++++++----------
5 files changed, 37 insertions(+), 18 deletions(-)
diff --git a/src/MRIBuilder.jl b/src/MRIBuilder.jl
index 5f75a24..09a90fc 100644
--- a/src/MRIBuilder.jl
+++ b/src/MRIBuilder.jl
@@ -32,8 +32,8 @@ export ConcreteBlocks, AbstractConcreteBlock
import .Wait: WaitBlock
export WaitBlock
-import .Containers: Sequence, FixedBlock
-export Sequence, FixedBlock
+import .Containers: Sequence, FixedBlock, FixedSequence
+export Sequence, FixedBlock, FixedSequence
import .Gradients: PulsedGradient, InstantGradientBlock, FixedGradient
export PulsedGradient, InstantGradientBlock, FixedGradient
diff --git a/src/building_blocks.jl b/src/building_blocks.jl
index a28ba2b..ba927b0 100644
--- a/src/building_blocks.jl
+++ b/src/building_blocks.jl
@@ -9,7 +9,7 @@ Parent type for all individual components out of which a sequence can be built.
Required methods:
- [`duration`](@ref)(block, parameters): Return block duration in ms.
-- [`fixed`](block): Return an equivalent fixed BuildingBlock (i.e., `FixedBlock`, `FixedPulse`, `FixedGradient`, `FixedInstantPulse`, `FixedInstantGradient`, or `InstantReadout`). These all have in common that they have no free variables and explicitly set any gradient and RF pulse profiles.
+- [`fixed`](block): Return the equivalent fixed BuildingBlock (i.e., `FixedBlock`, `FixedPulse`, `FixedGradient`, `FixedInstantPulse`, `FixedInstantGradient`, or `InstantReadout`). These all have in common that they have no free variables and explicitly set any gradient and RF pulse profiles.
- [`variables`](@ref): A list of all functions that are used to compute variables of the building block. Any of these can be used in constraints or objective functions.
"""
abstract type BuildingBlock end
@@ -71,9 +71,9 @@ to_block(bb::BuildingBlock) = bb
"""
fixed(block::BuildingBlock)
-Return an equivalent fixed BuildingBlock.
+Return the fixed equivalent of the `BuildingBlock`
-Possible return types are `FixedBlock`, `FixedPulse`, `FixedGradient`, `FixedInstantPulse`, `FixedInstantGradient`, or `InstantReadout`.
+Possible return types are `FixedSequence`, `FixedBlock`, `FixedPulse`, `FixedGradient`, `FixedInstantPulse`, `FixedInstantGradient`, or `InstantReadout`.
These all have in common that they have no free variables and explicitly set any gradient and RF pulse profiles.
"""
function fixed end
diff --git a/src/containers/containers.jl b/src/containers/containers.jl
index 28e1a9e..9ef11dd 100644
--- a/src/containers/containers.jl
+++ b/src/containers/containers.jl
@@ -11,5 +11,5 @@ include("sequences.jl")
import ..BuildingBlocks: ContainerBlock, get_children_blocks
import ..FixedBlocks: FixedBlock
-import .Sequences: Sequence
+import .Sequences: Sequence, FixedSequence
end
\ No newline at end of file
diff --git a/src/containers/fixed_blocks.jl b/src/containers/fixed_blocks.jl
index 086f725..6443f63 100644
--- a/src/containers/fixed_blocks.jl
+++ b/src/containers/fixed_blocks.jl
@@ -5,6 +5,7 @@ import ...BuildingBlocks: ContainerBlock
import ...Gradients: FixedGradient
import ...Pulses: FixedPulse
import ...Variables: duration, variables
+import ...WaitBlocks: WaitBlock
"""
FixedBlock(duration=nothing; pulse_delay=0., pulse=nothing, gradient_delay=0., gradient=nothing, readout_times=[])
@@ -47,6 +48,7 @@ duration(fb::FixedBlock) = fb.duration
variables(::Type{<:FixedBlock}) = []
+fixed(wb::WaitBlock) = FixedBlock(value(duration(wb)))
end
\ No newline at end of file
diff --git a/src/containers/sequences.jl b/src/containers/sequences.jl
index 0422e06..6692d51 100644
--- a/src/containers/sequences.jl
+++ b/src/containers/sequences.jl
@@ -5,7 +5,10 @@ module Sequences
import JuMP: Model, @constraint
import ...BuildSequences: @global_model_constructor
import ...Variables: variables, start_time, duration, VariableType, get_free_variable, TR
-import ...BuildingBlocks: BuildingBlock, ContainerBlock, to_block, get_children_blocks, scanner_constraints!
+import ...BuildingBlocks: BuildingBlock, ContainerBlock, to_block, get_children_blocks, scanner_constraints!, fixed
+import ..FixedBlocks: FixedBlock
+
+abstract type AbstractSequence <: ContainerBlock end
"""
Sequence(building_blocks...; TR=nothing, scanner=nothing)
@@ -21,7 +24,7 @@ or be embedded as a [`BuildingBlock`](@ref) into higher-order `Sequence` or othe
## Variables
- [`TR`](@ref): repetition time of sequence in ms.
"""
-struct Sequence <: ContainerBlock
+struct Sequence <: AbstractSequence
model :: Model
blocks :: Vector{<:BuildingBlock}
TR :: VariableType
@@ -43,9 +46,9 @@ end
Sequence(model::Model, blocks...; TR=nothing, scanner=nothing) = Sequence(model, [blocks...]; TR=TR, scanner=scanner)
-Base.length(seq::Sequence) = length(seq.blocks)
-Base.getindex(seq::Sequence, index) = seq.blocks[index]
-get_children_blocks(seq::Sequence) = enumerate(seq.blocks)
+Base.length(seq::AbstractSequence) = length(seq.blocks)
+Base.getindex(seq::AbstractSequence, index) = seq.blocks[index]
+get_children_blocks(seq::AbstractSequence) = enumerate(seq.blocks)
"""
start_time(sequence::Sequence, index::Integer, args...)
@@ -54,9 +57,9 @@ Returns the starting time of the [`BuildingBlock`](@ref) with index `index`.
Additional `args` can be used to select a sub-block of that [`BuildingBlock`](@ref).
The starting time is returned with respect to the start of this sequence.
"""
-start_time(seq::Sequence) = 0.
-start_time(seq::Sequence, index::Integer) = iszero(index) ? start_time(seq) : (start_time(seq, index-1) + duration(seq[index]))
-start_time(seq::Sequence, index::Integer, args...) = start_time(seq, index) + start_time(seq[index], args...)
+start_time(seq::AbstractSequence) = 0.
+start_time(seq::AbstractSequence, index::Integer) = iszero(index) ? start_time(seq) : (start_time(seq, index-1) + duration(seq[index]))
+start_time(seq::AbstractSequence, index::Integer, args...) = start_time(seq, index) + start_time(seq[index], args...)
"""
end_time(sequence::Sequence, index::Integer, args...)
@@ -65,15 +68,29 @@ Returns the end time of the [`BuildingBlock`](@ref) with index `index`.
Additional `args` can be used to select a sub-block of that [`BuildingBlock`](@ref).
The end time is returned with respect to the start of this sequence.
"""
-end_time(seq::Sequence, index::Integer) = start_time(seq, index) + duration(seq[index])
-end_time(seq::Sequence, index::Integer, args...) = start_time(seq, index) + end_time(seq[index], args...)
+end_time(seq::AbstractSequence, index::Integer) = start_time(seq, index) + duration(seq[index])
+end_time(seq::AbstractSequence, index::Integer, args...) = start_time(seq, index) + end_time(seq[index], args...)
-duration(seq::Sequence) = end_time(seq, length(seq))
+duration(seq::AbstractSequence) = end_time(seq, length(seq))
-TR(seq::Sequence) = seq.TR
+TR(seq::AbstractSequence) = seq.TR
variables(::Type{<:Sequence}) = [TR]
+struct FixedSequence <: AbstractSequence
+ blocks :: Vector{<:BuildingBlock}
+ TR :: Number
+end
+
+function fixed(seq::Sequence)
+ FixedSequence(
+ fixed.(seq.blocks),
+ value(TR(seq))
+ )
+end
+
+variables(::Type{<:FixedSequence}) = []
+
end
--
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