Add basic building blocks support

src/all_building_blocks/all_building_blocks.jl

+module AllBuildingBlocks
+
+
+end
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src/all_building_blocks/base_building_blocks.jl

+module BaseBuildingBlocks
+import ...ContainerBlocks: ContainerBlock, GradientWaveform, EventComponent, NoGradientBlock, ChangingGradientBlock, ConstantGradientBlock, split_gradient
+import ...Components: BaseComponent
+import ...Variables: qvec, bmat_gradient
+
+"""
+Basic BuildingBlock, which can consist of a gradient waveforms with any number of RF pulses/readouts overlaid
+
+Main interface:
+- iteration will give the gradient waveforms interspersed by RF pulses/readouts.
+    - Indiviual indices can be accessed using `keys(building_block)`
+- [`waveform_sequence`](@ref) returns just the gradient waveform as a sequence of [`GradientWaveform`](@ref) objects.
+- [`waveform`](@ref) returns just the gradient waveform as a sequence of (time, gradient_strength) tuples.
+- [`events`](@ref) returns the RF pulses and readouts.
+- [`qvec`](@ref) returns area under curve for (part of) the gradient waveform.
+
+Sub-types need to implement:
+- `Base.keys`: returns sequence of keys to all the components
+- `Base.getindex`: returns the actual component for each key
+"""
+abstract type BaseBuildingBlock <: ContainerBlock end
+
+# Iterator interface
+Base.length(c::BaseBuildingBlock) = length(keys(c))
+Base.eltype(::Type{<:BaseBuildingBlock}) = BaseComponent
+Base.iter(c::BaseBuildingBlock) = iter(c, 1)
+Base.iter(c::BaseBuildingBlock, index::Integer) = length(c) < index ? nothing : (c[keys(c)[index]], index + 1)
+
+
+"""
+    events(building_block)
+
+Returns just the non-gradient (i.e., RF pulses/readouts) events as a sequence of [`EventComponent`](@ref) objects (with their keys).
+"""
+function waveform_sequence(bb::BaseBuildingBlock)
+    return [(key, bb[key]) for key in keys(bb) if bb[key] isa EventComponent]
+end
+
+"""
+    waveform_sequence(building_block)
+
+Returns just the gradient waveform as a sequence of [`GradientWaveform`](@ref) objects (with their keys).
+"""
+function waveform_sequence(bb::BaseBuildingBlock)
+    return [(key, bb[key]) for key in keys(bb) if bb[key] isa GradientWaveform]
+end
+
+function ndim_grad(bb::BaseBuildingBlock)
+    g = waveform_sequence(bb)
+    if izero(length(g))
+        return 0
+    end
+    for N in (1, 3)
+        if all(isa.(g, GradientWaveform{N}))
+            return N
+        end
+    end
+    error("$(typeof(bb)) contains both 1D and 3D gradient waveforms.")
+end
+
+
+"""
+    waveform(building_block)
+
+Returns the gradient waveform of any [`BaseBuildingBlock`](@ref) as a sequence of control points.
+
+Each control point is stored as a tuple with the time in ms and the gradient as a length-3 vector.
+The gradient is linearly interpolated between these points (see [`waveform_sequence`](@ref)).
+"""
+function waveform(bb::BaseBuildingBlock)
+    ndim = ndim_grad(bb)
+    if ndim == 3
+        result = Tuple{VariableType, SVector{3, VariableType}}[(0., zero(SVector{3, Float64}))]
+    elseif ndim == 1
+        result = Tuple{VariableType, SVector{3, VariableType}}[(0., 0.)]
+    else
+        return []
+    end
+    for (_, block) in waveform_sequence(bb)
+        new_time = result[end][1] + max(duration(block), 0)
+        prev_grad = result[end][2]
+        if block isa NoGradientBlock
+            @assert all(abs.(prev_grad) <= 1e-12) "$(typeof(bb)) inserts NoGradientBlock before the gradient is zero. This is probably caused by an improper implementation of this BuildingBlock."
+            push!(result, (new_time, prev_grad))
+        elseif block isa ConstantGradientBlock
+            @assert all(gradient_strength(block) .≈ prev_grad) "$(typeof(bb)) inserts ConstantGradientBlock that does not match previous gradient strength. This is probably caused by an improper implementation of this BuildingBlock."
+            push!(result, (new_time, prev_grad))
+        elseif block isa ChangingGradientBlock
+            @assert all(block.gradient_strength_start .≈ prev_grad) "$(typeof(bb)) inserts ChangingGradientBlock that does not match previous gradient strength. This is probably caused by an improper implementation of this BuildingBlock."
+            push!(result, (new_time, prev_grad .+ slew_rate(block) .* duration(block)))
+        else
+            error("Unrecognised block type in BuildingBlock: $(typeof(bb)).")
+        end
+    end
+    @assert all(abs.(result[end][2]) <= 1e-12) "$(typeof(bb)) does not end up with a gradient of zero. This is probably caused by an improper implementation of this BuildingBlock."
+    return result
+end
+
+
+# Pathway support
+"""
+    waveform_sequence(building_block, first, last)
+
+Gets the sequence of [`GradientWaveform`](@ref) from the event with key `first` till the event with key `last`.
+
+Setting `first` to nothing indicates to start from the beginning of the `building_block`.
+Similarly, setting `last` to nothing indicates to continue till the end of the `building_block`.
+"""
+function waveform_seqeuence(bb::BaseBuildingBlock, first, last)
+    started = isnothing(first)
+    current_grad = current_start = nothing
+    parts = GradientWaveform[]
+    for key in bb
+        if bb[key] isa GradientWaveform
+            if started
+                push!(parts, isnothing(current_start) ? current_grad : split_gradient(current_grad, current_start)[2])
+            end
+            current_grad = bb[key]
+            current_start = nothing
+        end
+        if key == first
+            @assert !started
+            started = true
+            current_started = effective_time(bb[key])
+        end
+        if key == last
+            @assert started
+            if isnothing(current_started)
+                push!(parts, split_gradient(current_grad, effective_time(bb[key]))[1])
+            else
+                push!(parts, split_gradient(current_grad, current_started, effective_time(bb[key]))[2])
+            end
+        end
+    end
+    return parts
+end
+
+
+"""
+    qvec(overlapping[, first_event, last_event])
+
+Computes the area under the curve for the gradient waveform in [`BaseBuildingBlock`](@ref).
+
+If `first_event` is set to something else than `nothing`, only the gradient waveform after this RF pulse/Readout will be considered.
+Similarly, if `last_event` is set to something else than `nothing`, only the gradient waveform up to this RF pulse/Readout will be considered.
+"""
+function qvec(bb::BaseBuildingBlock, index1::Union{Nothing, Integer}, index2::Union{Nothing, Integer})
+    @assert isnothing(index1) || isnothing(index2) || index2 >= index1
+    if (index1 isa Number) && (index1 == index2)
+        return zeros(3)
+    end
+    sum(qvec.(get_parts(bb, index1, index2)); init=zero(SVector{3, Float64}))
+end
+qvec(bb::BaseBuildingBlock) = qvec(bb, nothing, nothing)
+
+function bmat_gradient(bb::BaseBuildingBlock, qstart, index1::Union{Nothing, Integer}, index2::Union{Nothing, Integer})
+    @assert isnothing(index1) || isnothing(index2) || index2 >= index1
+    if (index1 isa Number) && (index1 == index2)
+        return zeros(3, 3)
+    end
+    result = Matrix{VariableType}(zeros(3, 3))
+    qcurrent = Vector{VariableType}(qstart)
+
+    for part in get_parts(bb, index1, index2)
+        result = result .+ bmat_gradient(part, qcurrent)
+        qcurrent = qcurrent .+ qvec(part, qcurrent)
+    end
+    return result
+end
+bmat_gradient(bb::BaseBuildingBlock, qstart) = bmat_gradient(bb, qstart, nothing, nothing)
+
+end
+
+end
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src/container_blocks.jl

+module ContainerBlocks
+import ..Variables: AbstractBlock, duration, effective_time
+
+"""
+Parent type for `BuildingBlock` or `AbstractSequence`, i.e., any building block that contains other MRI components/blocks.
+
+Iterate over them to get the individual components.
+"""
+abstract type ContainerBlock <: AbstractBlock end
+
+
+"""
+    start_time(container, indices...)
+
+Returns the start time of component with given `indices` with respect to the start of the [`ContainerBlock`](@ref).
+
+Also see [`duration`](@ref), [`end_time`](@ref), and [`effective_time`](@ref)
+"""
+function start_time(container::ContainerBlock, index1, index2, indices...)
+    start_time(container, index1) + start_time(container[index1], index2, indices...)
+end
+
+
+"""
+    end_time(container, indices...)
+
+Returns the start time of component with given `indices` with respect to the start of the [`ContainerBlock`](@ref).
+
+Also see [`duration`](@ref), [`start_time`](@ref), and [`effective_time`](@ref)
+"""
+end_time(container::ContainerBlock, index, indices...) = start_time(container, index) + end_time(container[index], indices...)
+end_time(block::AbstractBlock) = duration(block)
+
+"""
+    effective_time(container, indices...)
+
+Returns the start time of component with given `indices` with respect to the start of the [`ContainerBlock`](@ref).
+
+This will crash if the component does not have an [`effective_time`](@ref) (e.g., if it is (part of) a gradient waveform).
+
+Also see [`duration`](@ref), [`start_time`](@ref), and [`end_time`](@ref)
+"""
+effective_time(container::ContainerBlock, index, indices...) = start_time(container, index) + effective_time(container[index], indices...)
+
+
+
+end
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