Add pathway variables the proper way to the variables list

src/MRIBuilder.jl

@@ -10,7 +10,7 @@ include("components/components.jl")
 include("containers/containers.jl")
 include("pathways.jl")
 include("parts/parts.jl")
-#include("printing.jl")
+include("printing.jl")
 
 import .BuildSequences: build_sequence, global_model, global_scanner, fixed
 export build_sequence, global_model, global_scanner, fixed

src/pathways.jl

@@ -3,7 +3,7 @@ import LinearAlgebra: norm, tr
 import StaticArrays: SVector, SMatrix
 import ..Components: NoGradient, RFPulseComponent, ReadoutComponent, InstantGradient, GradientWaveform, DelayedEvent
 import ..Containers: BaseSequence, Sequence, BaseBuildingBlock, waveform, events, waveform_sequence, start_time, AlternativeBlocks
-import ..Variables: qvec, qval, bmat_gradient, VariableType, effective_time, duration, TR, variables
+import ..Variables: qvec, qval, bmat_gradient, VariableType, effective_time, duration, TR, bmat, bval, area_under_curve, duration_dephase, duration_transverse
 
 
 """
@@ -180,7 +180,6 @@ for fn in (:qvec, :area_under_curve, :bmat, :bval, :duration_dephase, :duration_
         end
         error("get_pathway returned unexpected type for $seq")
     end
-    @eval variables[$(QuoteNode(fn))] = $fn
 end
 
 

src/printing.jl

 module Printing
 import JuMP: value
 import Printf: @sprintf
-import ..BuildingBlocks: BuildingBlock, get_children_indices, VariableNotAvailable
-import ..Alternatives: AlternativeBlocks
-import ..Overlapping: AbstractOverlapping, waveform, interruptions
-import ..Sequences: Sequence
-import ..Variables: VariableType, duration, start_time, variables, alternative_variables, effective_time, flip_angle
-import ..Pulses: GenericPulse
-
-struct BuildingBlockPrinter{T<:BuildingBlock}
-    bb::T
-    start_time::Union{Nothing, Number}
-    spaces::Int
-end
-
-Base.show(io::IO, block::BuildingBlock) = print(io, BuildingBlockPrinter(block, nothing, 0))
-Base.show(io::IO, seq::Sequence) = print(io, BuildingBlockPrinter(seq, 0., 0))
-
-function Base.show(io::IO, alt_printer::BuildingBlockPrinter{<:AlternativeBlocks})
-    block = alt_printer.bb
-    print(io, "AlternativeBlocks(", block.name, ", ", length(block), " options)")
-end
+import ..Variables: VariableType, variables, AbstractBlock, VariableNotAvailable, alternative_variables
 
 
 function _robust_value(possible_number::VariableType)
@@ -42,21 +23,8 @@ end
 _robust_value(possible_tuple::Tuple) = _robust_value([possible_tuple...])
 
 
-function Base.show(io::IO, printer::BuildingBlockPrinter)
-    block = printer.bb
+function Base.show(io::IO, block::AbstractBlock)
     print(io, nameof(typeof(block)), "(")
-    printed_duration = false
-    if !isnothing(printer.start_time)
-        print(io, "t=", @sprintf("%.3g", printer.start_time))
-
-        dur = _robust_value(duration(block))
-        @assert !(dur isa AbstractVector)
-        if !isnothing(dur) && !iszero(dur)
-            print(io, "-", @sprintf("%.3g", printer.start_time + dur))
-            printed_duration = true
-        end
-        print(io, ", ")
-    end
     for name in propertynames(block)
         ft = fieldtype(typeof(block), name)
         if (
@@ -67,11 +35,9 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
             continue
         end
         if (
-            block isa AbstractOverlapping && (
-            ft <: Union{Nothing, BuildingBlock} ||
-            (ft <: AbstractVector && eltype(ft) <: BuildingBlock) ||
-            name == :interruptions
-        ))
+            ft <: Union{Nothing, AbstractBlock} ||
+            (ft <: AbstractVector && eltype(ft) <: AbstractBlock)
+        )
             continue
         end
 
@@ -79,9 +45,6 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
     end
 
     for fn in values(variables)
-        if printed_duration && fn == duration
-            continue
-        end
         if fn in [fn_alt for (fn_alt, _, _, _) in values(alternative_variables)]
             continue
         end
@@ -104,68 +67,6 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
         end
     end
     print(io, ")")
-    if block isa AbstractOverlapping
-        print(io, ":")
-        ref_start_time = isnothing(printer.start_time) ? 0. : printer.start_time
-        inter = copy(interruptions(block))
-        prev_time = 0.
-        for (index_grad, (time, grad)) in enumerate(waveform(block))
-            while length(inter) > 0 && index_grad == (inter[1].index + 1)
-                to_print = popfirst!(inter)
-                t_eff = ref_start_time + prev_time + to_print.time
-                as_printer = BuildingBlockPrinter(to_print.object, t_eff - effective_time(to_print.object), printer.spaces + 2)
-                print(io, "\n", repeat(' ', printer.spaces + 2), "- ", @sprintf("%.3g", t_eff), ": ", as_printer)
-            end
-            printed_grad = "[" * join(map(v -> @sprintf("%.3g", v), grad), ", ") * "]"
-            print(io, "\n", repeat(' ', printer.spaces + 2), "- ", @sprintf("%.3g", ref_start_time + time), ": ", printed_grad)
-            prev_time = time
-        end
-    end
-end
-
-function Base.show(io::IO, printer::BuildingBlockPrinter{<:Sequence})
-    seq = printer.bb
-    print(io, "Sequence(")
-    d = _robust_value(duration(seq))
-    if !isnothing(d)
-        if !isnothing(printer.start_time)
-            print(io, "t=", @sprintf("%.3g", printer.start_time), "-", @sprintf("%.3g", printer.start_time + d), ", ")
-        else
-            print(io, "duration=", @sprintf("%.3g", d), ",")
-        end
-    end
-    TR = _robust_value(seq.TR)
-    if !isnothing(TR) && isfinite(TR)
-        print(io, "TR=", Int(round(TR)))
-    end
-    print(io, "):")
-
-    for child_index in get_children_indices(seq)
-        child_block = seq[child_index]
-        child_printer = BuildingBlockPrinter(
-            child_block,
-            isnothing(printer.start_time) ? nothing : _robust_value(start_time(seq, child_index) + printer.start_time),
-            printer.spaces + 2
-        )
-        print(io, "\n", repeat(' ', printer.spaces + 2), "- ", child_index, ": ", child_printer)
-    end
-
 end
 
-function Base.show(io::IO, printer::BuildingBlockPrinter{<:GenericPulse})
-    fp = printer.bb
-    pp(value::Number) = @sprintf("%.3g", value)
-
-    print(io, "GenericPulse(")
-    if isnothing(printer.start_time)
-        print(io, "duration=", pp(duration(fp)))
-    else
-        print(io, "t=", pp(printer.start_time), "-", pp(printer.start_time + duration(fp)))
-    end
-    print(io, ", flip_angle=", pp(flip_angle(fp)), ", effective_time=", pp(effective_time(fp)), ")")
-end
-
-
-
-
 end
\ No newline at end of file

src/variables.jl

@@ -36,6 +36,12 @@ all_variables_symbols = [
     :sequence => [
         :TR => "Time on which an MRI sequence repeats itself in ms.",
         :Δ => "Diffusion time in ms (i.e., time between start of the diffusion-weighted gradients).",
+        :qvec => "Net dephasing due to gradients in rad/um.",
+        :area_under_curve => "Net dephasing due to gradients in rad/um (same as [`qvec`](@ref)).",
+        :bmat => "Full 3x3 diffusion-weighting matrix in ms/um^2.",
+        :bval => "Size of diffusion-weighting in ms/um^2 (trace of [`bmat`](@ref)).",
+        :duration_dephase => "Net T2' dephasing experienced over a sequence (in ms).",
+        :duration_transverse => "Net T2 signal loss experienced over a sequence (in ms). This is the total duration spins spent in the transverse plane.",
     ],
     :pulse => [
         :flip_angle => "The flip angle of the RF pulse in degrees",
@@ -70,7 +76,7 @@ all_variables_symbols = [
         :resolution => "Number of voxels in the final readout. During the optimisation this might produce non-integer values, but this will be fixed after optimsation.",
         :oversample => "How much to oversample with ([`nsamples`](@ref) / [`resolution`](@ref))",
         :ramp_overlap => "Fraction of overlap between ADC event and underlying gradient pulse ramp (between 0 and 1)."
-    ]
+    ],
 ]
 
 """