From 6ae11cdfd52785c68ddd27d416da4e6b1dbdd6f5 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Tue, 20 Feb 2024 13:35:58 +0000
Subject: [PATCH] Refactor abstract containers away from concrete containers
---
src/MRIBuilder.jl | 24 +---
.../all_building_blocks.jl | 14 ---
src/all_building_blocks/building_blocks.jl | 94 ---------------
src/all_building_blocks/wait_blocks.jl | 23 ----
src/all_sequences/all_sequences.jl | 13 --
src/all_sequences/sequences.jl | 57 ---------
.../abstract.jl} | 4 +-
src/{ => containers}/alternatives.jl | 6 +-
.../building_blocks.jl} | 114 +++++++++++++++++-
src/containers/containers.jl | 12 ++
.../sequences.jl} | 60 ++++++++-
src/{all_sequences => parts}/epi_readouts.jl | 4 +-
src/{ => parts}/helper_functions.jl | 14 ++-
src/parts/parts.jl | 15 +++
.../slice_select_rephases.jl | 4 +-
.../spoilt_slice_selects.jl | 2 +-
.../trapezoids.jl | 2 +-
src/pathways.jl | 5 +-
18 files changed, 220 insertions(+), 247 deletions(-)
delete mode 100644 src/all_building_blocks/all_building_blocks.jl
delete mode 100644 src/all_building_blocks/building_blocks.jl
delete mode 100644 src/all_building_blocks/wait_blocks.jl
delete mode 100644 src/all_sequences/all_sequences.jl
delete mode 100644 src/all_sequences/sequences.jl
rename src/{container_blocks.jl => containers/abstract.jl} (94%)
rename src/{ => containers}/alternatives.jl (93%)
rename src/{all_building_blocks/base_building_blocks.jl => containers/building_blocks.jl} (61%)
create mode 100644 src/containers/containers.jl
rename src/{all_sequences/base_sequences.jl => containers/sequences.jl} (56%)
rename src/{all_sequences => parts}/epi_readouts.jl (96%)
rename src/{ => parts}/helper_functions.jl (96%)
create mode 100644 src/parts/parts.jl
rename src/{all_sequences => parts}/slice_select_rephases.jl (92%)
rename src/{all_building_blocks => parts}/spoilt_slice_selects.jl (99%)
rename src/{all_building_blocks => parts}/trapezoids.jl (99%)
diff --git a/src/MRIBuilder.jl b/src/MRIBuilder.jl
index f26f66f..9352a7e 100644
--- a/src/MRIBuilder.jl
+++ b/src/MRIBuilder.jl
@@ -7,12 +7,9 @@ include("scanners.jl")
include("build_sequences.jl")
include("variables.jl")
include("components/components.jl")
-include("container_blocks.jl")
-include("all_building_blocks/all_building_blocks.jl")
-include("all_sequences/all_sequences.jl")
-include("alternatives.jl")
+include("containers/containers.jl")
include("pathways.jl")
-include("helper_functions.jl")
+include("parts/parts.jl")
#include("printing.jl")
import .BuildSequences: build_sequence, global_model, global_scanner
@@ -24,26 +21,17 @@ export Scanner, B0, Siemens_Connectom, Siemens_Prisma, Siemens_Terra
import .Variables: variables, duration, effective_time, flip_angle, amplitude, phase, frequency, bandwidth, N_left, N_right, qval, δ, rise_time, flat_time, slew_rate, gradient_strength, qvec, qval_square, slice_thickness, inverse_slice_thickness, fov, inverse_fov, voxel_size, inverse_voxel_size, resolution, nsamples, oversample, dwell_time, ramp_overlap, spoiler_scale
export variables, duration, effective_time, flip_angle, amplitude, phase, frequency, bandwidth, N_left, N_right, qval, δ, rise_time, flat_time, slew_rate, gradient_strength, qvec, qval_square, slice_thickness, inversne_slice_thickness, fov, inverse_fov, voxel_size, inverse_voxel_size, resolution, nsamples, oversample, dwell_time, ramp_overlap, spoiler_scale
-import .ContainerBlocks: ContainerBlock, start_time, end_time
-export start_time, end_time
-
import .Components: InstantPulse, ConstantPulse, SincPulse, GenericPulse, InstantGradient, SingleReadout, ADC
export InstantPulse, ConstantPulse, SincPulse, GenericPulse, InstantGradient, SingleReadout, ADC
-import .AllBuildingBlocks: waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Trapezoid, SliceSelect, LineReadout, SpoiltSliceSelect, Wait
-export waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Trapezoid, SliceSelect, LineReadout, SpoiltSliceSelect, Wait
-
-import .AllSequences: BaseSequence, nrepeat, Sequence, EPIReadout
-export BaseSequence, nrepeat, Sequence, EPIReadout
-
-import .Alternatives: AlternativeBlocks, match_blocks!
-export AlternativeBlocks, match_blocks!
+import .Containers: ContainerBlock, start_time, end_time, waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Wait, BaseSequence, nrepeat, Sequence, AlternativeBlocks, match_blocks!, get_index_single_TR
+export ContainerBlock, start_time, end_time, waveform, waveform_sequence, events, BaseBuildingBlock, BuildingBlock, Wait, BaseSequence, nrepeat, Sequence, AlternativeBlocks, match_blocks!, get_index_single_TR
import .Pathways: Pathway, duration_transverse, duration_dephase, bval, bmat
export Pathway, duration_transverse, duration_dephase, bval, bmat
-import .HelperFunctions: excitation_pulse, refocus_pulse, epi_readout, single_line_readout
-export excitation_pulse, refocus_pulse, epi_readout, single_line_readout
+import .Parts: excitation_pulse, refocus_pulse, epi_readout, single_line_readout, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout
+export excitation_pulse, refocus_pulse, epi_readout, single_line_readout, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout
import JuMP: @constraint, @objective, objective_function, value, Model
export @constraint, @objective, objective_function, value, Model
diff --git a/src/all_building_blocks/all_building_blocks.jl b/src/all_building_blocks/all_building_blocks.jl
deleted file mode 100644
index e841e50..0000000
--- a/src/all_building_blocks/all_building_blocks.jl
+++ /dev/null
@@ -1,14 +0,0 @@
-module AllBuildingBlocks
-include("base_building_blocks.jl")
-include("building_blocks.jl")
-include("trapezoids.jl")
-include("spoilt_slice_selects.jl")
-include("wait_blocks.jl")
-
-import .BaseBuildingBlocks: waveform, waveform_sequence, events, BaseBuildingBlock
-import .BuildingBlocks: BuildingBlock
-import .Trapezoids: Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines
-import .SpoiltSliceSelects: SpoiltSliceSelect
-import .WaitBlocks: Wait
-
-end
\ No newline at end of file
diff --git a/src/all_building_blocks/building_blocks.jl b/src/all_building_blocks/building_blocks.jl
deleted file mode 100644
index 92ae8e2..0000000
--- a/src/all_building_blocks/building_blocks.jl
+++ /dev/null
@@ -1,94 +0,0 @@
-module BuildingBlocks
-import LinearAlgebra: norm
-import ..BaseBuildingBlocks: BaseBuildingBlock, events, waveform_sequence
-import ...Variables: VariableType, duration, make_generic, get_pulse, get_readout, scanner_constraints!
-import ...Components: BaseComponent, DelayedEvent, RFPulseComponent, ReadoutComponent
-
-"""
- BuildingBlock(waveform, events; duration=nothing, orientation=nothing, group)
-
-Generic [`BaseBuildingBlock`](@ref) that can capture any overlapping gradients, RF pulses, and/or readouts.
-The gradients cannot contain any free variables.
-
-## Arguments
-- `waveform`: Sequence of 2-element tuples with (time, (Gx, Gy, Gz)). If `orientation` is set then the tuple is expected to look like (time, G). This cannot contain any free variables.
-- `events`: Sequence of 2-element tuples with (index, pulse/readout). The start time of the pulse/readout at the start of the gradient waveform element with index `index` (use [`DelayedEvent`](@ref) to make this earlier or later).
-- `duration`: duration of this `BuildingBlock`. If not set then it will be assumed to be the time of the last element in `waveform`.
-- `orientation`: orientation of the gradients in the waveform. If not set, then the full gradient vector should be given explicitly.
-- `group`: group of the gradient waveform
-"""
-struct BuildingBlock <: BaseBuildingBlock
- parts :: Vector{<:BaseComponent}
- function BuildingBlock(parts::AbstractVector{<:BaseComponent})
- res = new(duration, parts)
- for (_, part) in waveform_sequence(parts)
- scanner_constraints!(part)
- end
- return res
- end
-end
-
-function BuildingBlock(waveform::AbstractVector, events::AbstractVector; duration=nothing, orientation=nothing, group=nothing)
- events = Any[events...]
- waveform = Any[waveform...]
- ndim = isnothing(orientation) ? 1 : 3
- zero_grad = isnothing(orientation) ? zeros(3) : 0.
- if length(waveform) == 0 || waveform[1][1] > 0.
- pushfirst!(waveform, (0., zero_grad))
- events = [(i+1, e) for (i, e) in events]
- end
-
- if isnothing(duration)
- duration = waveform[end][1]
- end
- if !(duration ≈ waveform[end][1])
- @assert duration > waveform[end][1]
- push!(waveform, (duration, zero_grad))
- end
- components = BaseComponent[]
- for (index_grad, ((prev_time, prev_grad), (time, grad))) in enumerate(zip(waveform[1:end-1], waveform[2:end]))
- duration = time - prev_time
- if norm(prev_grad) <= 1e-12 && norm(grad) <= 1e-12
- push!(components, NoGradient{ndim}(duration))
- elseif norm(prev_grad) ≈ norm(grad)
- push!(components, ConstantGradient(prev_grad, orientation, duration, group))
- else
- push!(components, ChangingGradient(prev_grad, (grad .- prev_grad) ./ duration, orientation, duration, group))
- end
- while length(events) > 0 && index_grad == events[1][1]
- (_, event) = popfirst!(events)
- push!(components, event)
- end
- end
- return components
-end
-
-make_generic(other_block::BaseBuildingBlock) = BuildingBlock(duration(other_block), [other_block...])
-Base.keys(bb::BuildingBlock) = 1:length(bb.parts)
-Base.getindex(bb::BuildingBlock, i::Integer) = bb.parts[i]
-
-duration(bb::BuildingBlock) = sum(duration, waveform_sequence(bb); init=0.)
-
-function get_pulse(bb::BuildingBlock)
- pulses = [p for p in events(bb) if p isa RFPulseComponent]
- if length(pulses) == 0
- error("BuildingBlock does not contain any pulses.")
- end
- if length(pulses) == 1
- return pulses[1]
- end
- error("BuildingBlock contains more than one pulse. Not sure which one to return.")
-end
-
-function get_readout(bb::BuildingBlock)
- readouts = [r for r in events(bb) if r isa ReadoutComponent]
- if length(readouts) == 0
- error("BuildingBlock does not contain any readouts.")
- end
- if length(readouts) == 1
- return readouts[1]
- end
- error("BuildingBlock contains more than one readout. Not sure which one to return.")
-end
-
-end
\ No newline at end of file
diff --git a/src/all_building_blocks/wait_blocks.jl b/src/all_building_blocks/wait_blocks.jl
deleted file mode 100644
index f55383f..0000000
--- a/src/all_building_blocks/wait_blocks.jl
+++ /dev/null
@@ -1,23 +0,0 @@
-module WaitBlocks
-import JuMP: @constraint
-import ...BuildSequences: global_model
-import ...Variables: get_free_variable, VariableType, duration
-import ...Components: NoGradient
-import ..BaseBuildingBlocks: BaseBuildingBlock
-
-struct Wait <: BaseBuildingBlock
- duration :: VariableType
- function Wait(var)
- res = new(get_free_variable(var))
- if !(res.duration isa Number)
- @constraint global_model() res.duration >= 0
- end
- return res
- end
-end
-
-duration(wb::Wait) = wb.duration
-Base.keys(::Wait) = (Val(:empty),)
-Base.getindex(wb::Wait, ::Val{:empty}) = NoGradient{1}(wb.duration)
-
-end
\ No newline at end of file
diff --git a/src/all_sequences/all_sequences.jl b/src/all_sequences/all_sequences.jl
deleted file mode 100644
index 0e56ea7..0000000
--- a/src/all_sequences/all_sequences.jl
+++ /dev/null
@@ -1,13 +0,0 @@
-module AllSequences
-include("base_sequences.jl")
-include("sequences.jl")
-include("slice_select_rephases.jl")
-include("epi_readouts.jl")
-
-import .BaseSequences: BaseSequence, nrepeat
-import .Sequences: Sequence
-import .SliceSelectRephases: SliceSelectRephase
-import .EPIReadouts: EPIReadout
-
-
-end
\ No newline at end of file
diff --git a/src/all_sequences/sequences.jl b/src/all_sequences/sequences.jl
deleted file mode 100644
index 81de052..0000000
--- a/src/all_sequences/sequences.jl
+++ /dev/null
@@ -1,57 +0,0 @@
-module Sequences
-import StaticArrays: SVector
-import JuMP: @constraint
-import ...Variables: get_free_variable, TR, VariableType, duration
-import ...AllBuildingBlocks: Wait, BuildingBlock
-import ...BuildSequences: global_model
-import ...Components: EventComponent
-import ..BaseSequences: ContainerBlock, BaseSequence, nrepeat, get_index_single_TR
-
-"""
- Sequence(blocks; TR=:min, nrepeat=0)
- Sequence(blocks...; TR=:min, nrepeat=0)
-
-Defines an MRI sequence from a vector of building blocks.
-
-## Arguments
-- [`nrepeat`](@ref): how often the sequence will repeat itself (keep at default of 0 to repeat indefinetely).
-- [`TR`](@ref): how long between repeats in ms (defaults to the duration of the sequence). Can be set to `nothing` to be a free variable.
-"""
-struct Sequence{N} <: BaseSequence{N}
- blocks :: SVector{N, <:ContainerBlock}
- TR :: VariableType
-end
-
-function Sequence(blocks::AbstractVector; TR=:min)
- blocks = to_block.(blocks)
- actual_duration = sum(duration, blocks; init=0.)
- if TR == :min
- TR = actual_duration
- end
- res = Sequence{length(blocks)}(SVector{length(blocks)}(blocks), get_free_variable(TR))
- if !(res.TR isa Number) || !(duration(res) isa Number)
- @constraint global_model() res.TR >= actual_duration
- end
- return res
-end
-
-Sequence(blocks...; kwargs...) = Sequence([blocks...]; kwargs...)
-
-get_index_single_TR(s::Sequence, i::Integer) = s.blocks[i]
-nrepeat(::Sequence) = 0
-
-"""
- to_block(block_like)
-
-Converst object into something that can be included in the sequence:
-- :min/:max/number/variable/nothing => [`Wait`](@ref).
-- `building_block` or `sequence` => no change.
-- RF pulse/readout => will be embedded within a [`BuildingBlock`](@ref).
-"""
-to_block(cb::ContainerBlock) = cb
-to_block(s::Symbol) = to_block(Val(s))
-to_block(s::Union{VariableType, Nothing, Val{:min}, Val{:max}}) = Wait(s)
-to_block(ec::EventComponent) = BuildingBlock([], [(0, ec)]; duration=duration(ec))
-
-
-end
\ No newline at end of file
diff --git a/src/container_blocks.jl b/src/containers/abstract.jl
similarity index 94%
rename from src/container_blocks.jl
rename to src/containers/abstract.jl
index e20828f..669ff1b 100644
--- a/src/container_blocks.jl
+++ b/src/containers/abstract.jl
@@ -1,5 +1,5 @@
-module ContainerBlocks
-import ..Variables: AbstractBlock, duration, effective_time
+module Abstract
+import ...Variables: AbstractBlock, duration, effective_time
"""
Parent type for `BuildingBlock` or `BaseSequence`, i.e., any building block that contains other MRI components/blocks.
diff --git a/src/alternatives.jl b/src/containers/alternatives.jl
similarity index 93%
rename from src/alternatives.jl
rename to src/containers/alternatives.jl
index f92a86e..2b00577 100644
--- a/src/alternatives.jl
+++ b/src/containers/alternatives.jl
@@ -1,8 +1,8 @@
module Alternatives
import JuMP: @constraint
-import ..ContainerBlocks: ContainerBlock
-import ..BuildSequences: global_model, fixed
-import ..Variables: duration, make_generic
+import ..Abstract: ContainerBlock
+import ...BuildSequences: global_model, fixed
+import ...Variables: duration, make_generic
"""
AlternativeBlocks(name, blocks)
diff --git a/src/all_building_blocks/base_building_blocks.jl b/src/containers/building_blocks.jl
similarity index 61%
rename from src/all_building_blocks/base_building_blocks.jl
rename to src/containers/building_blocks.jl
index cb8c762..f3aa83d 100644
--- a/src/all_building_blocks/base_building_blocks.jl
+++ b/src/containers/building_blocks.jl
@@ -1,7 +1,13 @@
-module BaseBuildingBlocks
-import ...ContainerBlocks: ContainerBlock
-import ...Components: BaseComponent, GradientWaveform, EventComponent, NoGradient, ChangingGradient, ConstantGradient, split_gradient
+"""
+Defines [`BaseBuildingBlock`](@ref), [`BuildingBlock`](@ref) and [`Wait`](@ref).
+"""
+module BuildingBlocks
+import LinearAlgebra: norm
+import JuMP: @constraint
+import ..Abstract: ContainerBlock
+import ...Components: BaseComponent, GradientWaveform, EventComponent, NoGradient, ChangingGradient, ConstantGradient, split_gradient, DelayedEvent, RFPulseComponent, ReadoutComponent
import ...Variables: qval, bmat_gradient, effective_time
+import ...Variables: VariableType, duration, make_generic, get_pulse, get_readout, scanner_constraints!
"""
Basic BuildingBlock, which can consist of a gradient waveforms with any number of RF pulses/readouts overlaid
@@ -175,4 +181,106 @@ function bmat_gradient(bb::BaseBuildingBlock, qstart, index1, index2)
end
bmat_gradient(bb::BaseBuildingBlock, qstart) = bmat_gradient(bb, qstart, nothing, nothing)
+"""
+ BuildingBlock(waveform, events; duration=nothing, orientation=nothing, group)
+
+Generic [`BaseBuildingBlock`](@ref) that can capture any overlapping gradients, RF pulses, and/or readouts.
+The gradients cannot contain any free variables.
+
+## Arguments
+- `waveform`: Sequence of 2-element tuples with (time, (Gx, Gy, Gz)). If `orientation` is set then the tuple is expected to look like (time, G). This cannot contain any free variables.
+- `events`: Sequence of 2-element tuples with (index, pulse/readout). The start time of the pulse/readout at the start of the gradient waveform element with index `index` (use [`DelayedEvent`](@ref) to make this earlier or later).
+- `duration`: duration of this `BuildingBlock`. If not set then it will be assumed to be the time of the last element in `waveform`.
+- `orientation`: orientation of the gradients in the waveform. If not set, then the full gradient vector should be given explicitly.
+- `group`: group of the gradient waveform
+"""
+struct BuildingBlock <: BaseBuildingBlock
+ parts :: Vector{<:BaseComponent}
+ function BuildingBlock(parts::AbstractVector{<:BaseComponent})
+ res = new(duration, parts)
+ for (_, part) in waveform_sequence(parts)
+ scanner_constraints!(part)
+ end
+ return res
+ end
+end
+
+function BuildingBlock(waveform::AbstractVector, events::AbstractVector; duration=nothing, orientation=nothing, group=nothing)
+ events = Any[events...]
+ waveform = Any[waveform...]
+ ndim = isnothing(orientation) ? 1 : 3
+ zero_grad = isnothing(orientation) ? zeros(3) : 0.
+ if length(waveform) == 0 || waveform[1][1] > 0.
+ pushfirst!(waveform, (0., zero_grad))
+ events = [(i+1, e) for (i, e) in events]
+ end
+
+ if isnothing(duration)
+ duration = waveform[end][1]
+ end
+ if !(duration ≈ waveform[end][1])
+ @assert duration > waveform[end][1]
+ push!(waveform, (duration, zero_grad))
+ end
+ components = BaseComponent[]
+ for (index_grad, ((prev_time, prev_grad), (time, grad))) in enumerate(zip(waveform[1:end-1], waveform[2:end]))
+ duration = time - prev_time
+ if norm(prev_grad) <= 1e-12 && norm(grad) <= 1e-12
+ push!(components, NoGradient{ndim}(duration))
+ elseif norm(prev_grad) ≈ norm(grad)
+ push!(components, ConstantGradient(prev_grad, orientation, duration, group))
+ else
+ push!(components, ChangingGradient(prev_grad, (grad .- prev_grad) ./ duration, orientation, duration, group))
+ end
+ while length(events) > 0 && index_grad == events[1][1]
+ (_, event) = popfirst!(events)
+ push!(components, event)
+ end
+ end
+ return components
+end
+
+make_generic(other_block::BaseBuildingBlock) = BuildingBlock(duration(other_block), [other_block...])
+Base.keys(bb::BuildingBlock) = 1:length(bb.parts)
+Base.getindex(bb::BuildingBlock, i::Integer) = bb.parts[i]
+
+duration(bb::BuildingBlock) = sum(duration, waveform_sequence(bb); init=0.)
+
+function get_pulse(bb::BuildingBlock)
+ pulses = [p for p in events(bb) if p isa RFPulseComponent]
+ if length(pulses) == 0
+ error("BuildingBlock does not contain any pulses.")
+ end
+ if length(pulses) == 1
+ return pulses[1]
+ end
+ error("BuildingBlock contains more than one pulse. Not sure which one to return.")
+end
+
+function get_readout(bb::BuildingBlock)
+ readouts = [r for r in events(bb) if r isa ReadoutComponent]
+ if length(readouts) == 0
+ error("BuildingBlock does not contain any readouts.")
+ end
+ if length(readouts) == 1
+ return readouts[1]
+ end
+ error("BuildingBlock contains more than one readout. Not sure which one to return.")
+end
+
+struct Wait <: BaseBuildingBlock
+ duration :: VariableType
+ function Wait(var)
+ res = new(get_free_variable(var))
+ if !(res.duration isa Number)
+ @constraint global_model() res.duration >= 0
+ end
+ return res
+ end
+end
+
+duration(wb::Wait) = wb.duration
+Base.keys(::Wait) = (Val(:empty),)
+Base.getindex(wb::Wait, ::Val{:empty}) = NoGradient{1}(wb.duration)
+
end
\ No newline at end of file
diff --git a/src/containers/containers.jl b/src/containers/containers.jl
new file mode 100644
index 0000000..c62f548
--- /dev/null
+++ b/src/containers/containers.jl
@@ -0,0 +1,12 @@
+module Containers
+include("abstract.jl")
+include("building_blocks.jl")
+include("sequences.jl")
+include("alternatives.jl")
+
+import .Abstract: ContainerBlock, start_time, end_time, effective_time
+import .BuildingBlocks: BaseBuildingBlock, BuildingBlock, Wait, waveform, waveform_sequence, events
+import .Sequences: BaseSequence, Sequence, nrepeat, get_index_single_TR
+import .Alternatives: AlternativeBlocks, match_blocks!
+
+end
\ No newline at end of file
diff --git a/src/all_sequences/base_sequences.jl b/src/containers/sequences.jl
similarity index 56%
rename from src/all_sequences/base_sequences.jl
rename to src/containers/sequences.jl
index 4c6df22..41df737 100644
--- a/src/all_sequences/base_sequences.jl
+++ b/src/containers/sequences.jl
@@ -1,7 +1,14 @@
-module BaseSequences
-import ...ContainerBlocks: ContainerBlock, start_time
-import ...AllBuildingBlocks: BaseBuildingBlock
-import ...Variables: TR, duration
+"""
+Defines [`BaseSequence`](@ref) and [`Sequence`](@ref)
+"""
+module Sequences
+import StaticArrays: SVector
+import JuMP: @constraint
+import ...Variables: get_free_variable, TR, VariableType, duration
+import ...BuildSequences: global_model
+import ...Components: EventComponent
+import ..Abstract: ContainerBlock, start_time
+import ..BuildingBlocks: Wait, BuildingBlock, BaseBuildingBlock
"""
Super-type of any sequence of non-overlapping building blocks that should be played after each other.
@@ -77,5 +84,50 @@ TR(bs::BaseSequence) = duration(bs)
duration(bs::BaseSequence{0}) = 0.
duration(bs::BaseSequence) = sum(duration.(bs); init=0.)
+"""
+ Sequence(blocks; TR=:min, nrepeat=0)
+ Sequence(blocks...; TR=:min, nrepeat=0)
+
+Defines an MRI sequence from a vector of building blocks.
+
+## Arguments
+- [`nrepeat`](@ref): how often the sequence will repeat itself (keep at default of 0 to repeat indefinetely).
+- [`TR`](@ref): how long between repeats in ms (defaults to the duration of the sequence). Can be set to `nothing` to be a free variable.
+"""
+struct Sequence{N} <: BaseSequence{N}
+ blocks :: SVector{N, <:ContainerBlock}
+ TR :: VariableType
+end
+
+function Sequence(blocks::AbstractVector; TR=:min)
+ blocks = to_block.(blocks)
+ actual_duration = sum(duration, blocks; init=0.)
+ if TR == :min
+ TR = actual_duration
+ end
+ res = Sequence{length(blocks)}(SVector{length(blocks)}(blocks), get_free_variable(TR))
+ if !(res.TR isa Number) || !(duration(res) isa Number)
+ @constraint global_model() res.TR >= actual_duration
+ end
+ return res
+end
+
+Sequence(blocks...; kwargs...) = Sequence([blocks...]; kwargs...)
+
+get_index_single_TR(s::Sequence, i::Integer) = s.blocks[i]
+nrepeat(::Sequence) = 0
+
+"""
+ to_block(block_like)
+
+Converst object into something that can be included in the sequence:
+- :min/:max/number/variable/nothing => [`Wait`](@ref).
+- `building_block` or `sequence` => no change.
+- RF pulse/readout => will be embedded within a [`BuildingBlock`](@ref).
+"""
+to_block(cb::ContainerBlock) = cb
+to_block(s::Symbol) = to_block(Val(s))
+to_block(s::Union{VariableType, Nothing, Val{:min}, Val{:max}}) = Wait(s)
+to_block(ec::EventComponent) = BuildingBlock([], [(0, ec)]; duration=duration(ec))
end
diff --git a/src/all_sequences/epi_readouts.jl b/src/parts/epi_readouts.jl
similarity index 96%
rename from src/all_sequences/epi_readouts.jl
rename to src/parts/epi_readouts.jl
index 3ea831b..7f1e6b6 100644
--- a/src/all_sequences/epi_readouts.jl
+++ b/src/parts/epi_readouts.jl
@@ -1,8 +1,8 @@
module EPIReadouts
-import ...AllBuildingBlocks: LineReadout, Trapezoid, opposite_kspace_lines
+import ...Containers: BaseSequence, get_index_single_TR
+import ..Trapezoids: Trapezoid, opposite_kspace_lines, LineReadout
import ...Components: ADC
import ...Variables: get_free_variable, VariableType, qval, qvec, set_simple_constraints!, resolution, inverse_voxel_size, inverse_fov, resolution, get_readout, apply_simple_constraint!
-import ..BaseSequences: BaseSequence, get_index_single_TR
"""
EPIReadout(resolution; ky_lines=-resolution[2]:resolution[2], recenter=false, group=:FOV, variables...)
diff --git a/src/helper_functions.jl b/src/parts/helper_functions.jl
similarity index 96%
rename from src/helper_functions.jl
rename to src/parts/helper_functions.jl
index b27221b..105b112 100644
--- a/src/helper_functions.jl
+++ b/src/parts/helper_functions.jl
@@ -1,11 +1,13 @@
module HelperFunctions
import JuMP: @constraint
-import ..AllBuildingBlocks: BuildingBlock, Trapezoid, SpoiltSliceSelect, opposite_kspace_lines, SliceSelect
-import ..BuildSequences: global_model, build_sequence
-import ..AllSequences: Sequence, SliceSelectRephase
-import ..Components: SincPulse, ConstantPulse, InstantPulse
-import ..Variables: qvec, flat_time, rise_time
-import ..Alternatives: AlternativeBlocks, match_blocks!
+import ...Containers: AlternativeBlocks, match_blocks!, BuildingBlock
+import ..Trapezoids: Trapezoid, opposite_kspace_lines, SliceSelect
+import ..SpoiltSliceSelects: SpoiltSliceSelect
+import ..SliceSelectRephases: SliceSelectRephase
+import ...BuildSequences: global_model, build_sequence
+import ...Containers: Sequence
+import ...Components: SincPulse, ConstantPulse, InstantPulse
+import ...Variables: qvec, flat_time, rise_time
function _get_pulse(shape, flip_angle, phase, frequency, Nzeros, group, bandwidth, duration)
diff --git a/src/parts/parts.jl b/src/parts/parts.jl
new file mode 100644
index 0000000..d4914e4
--- /dev/null
+++ b/src/parts/parts.jl
@@ -0,0 +1,15 @@
+module Parts
+include("trapezoids.jl")
+include("slice_select_rephases.jl")
+include("spoilt_slice_selects.jl")
+include("epi_readouts.jl")
+include("helper_functions.jl")
+
+import .Trapezoids: Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines
+import .SpoiltSliceSelects: SpoiltSliceSelect
+import .SliceSelectRephases: SliceSelectRephase
+import .EPIReadouts: EPIReadout
+import .HelperFunctions: excitation_pulse, refocus_pulse, epi_readout, single_line_readout
+
+
+end
\ No newline at end of file
diff --git a/src/all_sequences/slice_select_rephases.jl b/src/parts/slice_select_rephases.jl
similarity index 92%
rename from src/all_sequences/slice_select_rephases.jl
rename to src/parts/slice_select_rephases.jl
index 9486a64..e458073 100644
--- a/src/all_sequences/slice_select_rephases.jl
+++ b/src/parts/slice_select_rephases.jl
@@ -1,6 +1,6 @@
module SliceSelectRephases
-import ..BaseSequences: BaseSequence, get_index_single_TR
-import ...AllBuildingBlocks: SliceSelect, Trapezoid
+import ...Containers: BaseSequence, get_index_single_TR
+import ..Trapezoids: SliceSelect, Trapezoid
import ...Variables: get_pulse, qval, apply_simple_constraint!
import ...Components: RFPulseComponent
diff --git a/src/all_building_blocks/spoilt_slice_selects.jl b/src/parts/spoilt_slice_selects.jl
similarity index 99%
rename from src/all_building_blocks/spoilt_slice_selects.jl
rename to src/parts/spoilt_slice_selects.jl
index c07d073..34aefd3 100644
--- a/src/all_building_blocks/spoilt_slice_selects.jl
+++ b/src/parts/spoilt_slice_selects.jl
@@ -6,7 +6,7 @@ import JuMP: @constraint, @objective, objective_function
import ...BuildSequences: global_model, global_scanner
import ...Variables: VariableType, duration, rise_time, flat_time, effective_time, qval, gradient_strength, slew_rate, inverse_slice_thickness, get_free_variable, get_pulse, set_simple_constraints!, gradient_orientation
import ...Components: ChangingGradient, ConstantGradient, RFPulseComponent
-import ..BaseBuildingBlocks: BaseBuildingBlock
+import ...Containers: BaseBuildingBlock
"""
diff --git a/src/all_building_blocks/trapezoids.jl b/src/parts/trapezoids.jl
similarity index 99%
rename from src/all_building_blocks/trapezoids.jl
rename to src/parts/trapezoids.jl
index d504533..4a0a64d 100644
--- a/src/all_building_blocks/trapezoids.jl
+++ b/src/parts/trapezoids.jl
@@ -10,7 +10,7 @@ import ...Variables: qval, rise_time, flat_time, slew_rate, gradient_strength, v
import ...Variables: Variables, all_variables_symbols, dwell_time, inverse_fov, inverse_voxel_size, fov, voxel_size, get_gradient, get_pulse, get_readout, gradient_orientation, ramp_overlap
import ...BuildSequences: global_model
import ...Components: ChangingGradient, ConstantGradient, RFPulseComponent, ADC
-import ..BaseBuildingBlocks: BaseBuildingBlock
+import ...Containers: BaseBuildingBlock
"""
diff --git a/src/pathways.jl b/src/pathways.jl
index 9f081bd..1724950 100644
--- a/src/pathways.jl
+++ b/src/pathways.jl
@@ -2,11 +2,8 @@ module Pathways
import LinearAlgebra: norm, tr
import StaticArrays: SVector, SMatrix
import ..Components: NoGradient, RFPulseComponent, ReadoutComponent, InstantGradient, GradientWaveform, DelayedEvent
-import ..AllSequences: BaseSequence, Sequence
-import ..AllBuildingBlocks: BaseBuildingBlock, waveform, events, waveform_sequence
+import ..Containers: BaseSequence, Sequence, BaseBuildingBlock, waveform, events, waveform_sequence, start_time, AlternativeBlocks
import ..Variables: qvec, qval, bmat_gradient, VariableType, effective_time, duration, TR
-import ..ContainerBlocks: start_time
-import ..Alternatives: AlternativeBlocks
"""
--
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