From 1b66a519d88f5afd2c2fcb614c2cb1a6b441d49c Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Mon, 5 Feb 2024 17:00:04 +0000
Subject: [PATCH] Support new variables interface
---
src/building_blocks.jl | 28 ++++-----
src/overlapping/abstract.jl | 6 +-
.../gradient_readouts/single_lines.jl | 6 +-
src/readouts/ADCs.jl | 9 +--
src/variables.jl | 57 +++----------------
5 files changed, 34 insertions(+), 72 deletions(-)
diff --git a/src/building_blocks.jl b/src/building_blocks.jl
index 252b4b7..653502c 100644
--- a/src/building_blocks.jl
+++ b/src/building_blocks.jl
@@ -129,7 +129,7 @@ for variable_func in keys(variables)
value = alt_var(bb)
catch e
if e isa VariableNotAvailable
- throw(VariableNotAvailable(typeof(bb), variable_func))
+ throw(VariableNotAvailable(typeof(bb), Variables.$variable_func))
end
rethrow()
end
@@ -138,9 +138,9 @@ for variable_func in keys(variables)
elseif value isa AbstractArray{<:Number}
return backward.(value)
end
- throw(VariableNotAvailable(typeof(bb), variable_func, alt_var))
+ throw(VariableNotAvailable(typeof(bb), Variables.$variable_func, alt_var))
end
- throw(VariableNotAvailable(typeof(bb), variable_func))
+ throw(VariableNotAvailable(typeof(bb), Variables.$variable_func))
end
end
@@ -208,21 +208,21 @@ function Base.show(io::IO, printer::BuildingBlockPrinter)
end
try
numeric_value = _robust_value(fn(block))
+ if isnothing(numeric_value)
+ continue
+ end
+ if numeric_value isa AbstractVector
+ printed_value = "[" * join(map(v -> @sprintf("%.3g", v), numeric_value), ", ") * "]"
+ else
+ printed_value = @sprintf("%.3g", numeric_value)
+ end
+ print(io, "$(nameof(fn))=$(printed_value), ")
catch e
if e isa VariableNotAvailable
continue
end
rethrow()
end
- if isnothing(numeric_value)
- continue
- end
- if numeric_value isa AbstractVector
- printed_value = "[" * join(map(v -> @sprintf("%.3g", v), numeric_value), ", ") * "]"
- else
- printed_value = @sprintf("%.3g", numeric_value)
- end
- print(io, "$(nameof(fn))=$(printed_value), ")
end
print(io, ")")
end
@@ -239,8 +239,8 @@ If set to `:min` or `:max`, minimising or maximising this function will be added
"""
function set_simple_constraints!(block::BuildingBlock, kwargs)
for (key, value) in kwargs
- if key in keys(alternative_variables)
- alt_var, forward, backward, to_invert = alternative_variables[Variables.$variable_func]
+ if variables[key] in keys(alternative_variables)
+ alt_var, forward, backward, to_invert = alternative_variables[variables[key]]
invert_value(value::VariableType) = forward(value)
invert_value(value::Symbol) = invert_value(Val(value))
invert_value(::Val{:min}) = to_invert ? Val(:max) : Val(:min)
diff --git a/src/overlapping/abstract.jl b/src/overlapping/abstract.jl
index f2c9d76..4936fe1 100644
--- a/src/overlapping/abstract.jl
+++ b/src/overlapping/abstract.jl
@@ -1,6 +1,6 @@
module Abstract
-import ...BuildingBlocks: BuildingBlock, ContainerBlock, RFPulseBlock, get_children_indices
+import ...BuildingBlocks: BuildingBlock, ContainerBlock, RFPulseBlock, get_children_indices, VariableNotAvailable
import ...Wait: WaitBlock
import ...Readouts: InstantReadout
import ...Gradients: GradientBlock, split_gradient
@@ -59,9 +59,9 @@ for (func_symbol, _) in [Dict(all_variables_symbols)[:pulse]..., :effective_time
@eval function $func_symbol(ao::AbstractOverlapping, args...; kwargs...)
single_pulse = pulses(ao)
if iszero(length(single_pulse))
- error("Building block does not contain any RF pulse, so cannot compute $func_symbol.")
+ throw(VariableNotAvailable(typeof(ao), $func_symbol))
elseif length(single_pulse) > 1
- error("Building block has multipl pulses, so cannot compute $func_symbol.")
+ error("Building block has multipl pulses, so cannot compute ", $func_symbol, ".")
end
$func_symbol(single_pulse[1], args...; kwargs...)
end
diff --git a/src/overlapping/gradient_readouts/single_lines.jl b/src/overlapping/gradient_readouts/single_lines.jl
index 4a174d1..6228e2a 100644
--- a/src/overlapping/gradient_readouts/single_lines.jl
+++ b/src/overlapping/gradient_readouts/single_lines.jl
@@ -1,7 +1,7 @@
module SingleLines
import ....BuildingBlocks: set_simple_constraints!
import ....Readouts: ADC
-import ....Variables: dwell_time, fov, resolution, nsamples, effective_time, gradient_strength, slew_rate, voxel_size, rise_time, duration, variables
+import ....Variables: dwell_time, inverse_fov, resolution, nsamples, effective_time, gradient_strength, slew_rate, inverse_voxel_size, rise_time, duration, variables
import ...Abstract: AbstractOverlapping, waveform, interruptions
import ...GradientPulses: TrapezoidGradient
@@ -27,8 +27,8 @@ effective_time(sl::SingleLine) = rise_time(sl.grad) + effective_time(sl.adc)
dwell_time(sl::SingleLine) = dwell_time(sl.adc)
slew_rate(sl::SingleLine) = slew_rate(sl.grad)[1]
gradient_strenth(sl::SingleLine) = slew_rate(sl) * rise_time(sl.grad)
-fov_inverse(sl::SingleLine) = 1e3 * dwell_time(sl) * gradient_strenth(sl)
-voxel_size_inverse(sl::SingleLine) = 1e3 * duration(sl.adc) * gradient_strenth(sl)
+inverse_fov(sl::SingleLine) = 1e3 * dwell_time(sl) * gradient_strenth(sl)
+inverse_voxel_size(sl::SingleLine) = 1e3 * duration(sl.adc) * gradient_strenth(sl)
nsamples(sl::SingleLine) = nsamples(sl.adc)
resolution(sl::SingleLine) = resolution(sl.adc)
duration(sl::SingleLine) = duration(sl.grad)
diff --git a/src/readouts/ADCs.jl b/src/readouts/ADCs.jl
index d40e38b..1f3b30c 100644
--- a/src/readouts/ADCs.jl
+++ b/src/readouts/ADCs.jl
@@ -1,5 +1,5 @@
module ADCs
-import JuMP: @constraint
+import JuMP: @constraint, value
import ...Variables: variables, dwell_time, duration, effective_time, get_free_variable, VariableType, nsamples, resolution, oversample
import ...BuildingBlocks: BuildingBlock, apply_simple_constraint!, set_simple_constraints!, fixed
import ...BuildSequences: global_model
@@ -53,9 +53,10 @@ resolution(adc::ADC) = adc.resolution
function fixed(adc::ADC)
# round nsamples during fixing
- nsamples = Int(round(adc.nsamples))
- dwell_time = duration(adc) / nsamples
- return ADC(nsamples, dwell_time, time_to_center(adc))
+ r = Int(round(value(resolution(adc))))
+ n = Int(round(value(nsamples(adc))))
+ oversample = n // r
+ return ADC(r, value(adc.dwell_time), value(adc.time_to_center), oversample)
end
end
\ No newline at end of file
diff --git a/src/variables.jl b/src/variables.jl
index 3e43d15..9d65d52 100644
--- a/src/variables.jl
+++ b/src/variables.jl
@@ -16,16 +16,19 @@ all_variables_symbols = [
:amplitude => "The maximum amplitude of an RF pulse in kHz",
:phase => "The angle of the phase of an RF pulse in KHz",
:frequency => "The off-resonance frequency of an RF pulse (relative to the Larmor frequency of water) in KHz",
- :bandwidth => "Bandwidth of the RF pulse in kHz. To set constraints it is often better to use [`inverse_bandwidth`](@ref)",
+ :bandwidth => "Bandwidth of the RF pulse in kHz. To set constraints it is often better to use [`inverse_bandwidth`](@ref).",
+ :inverse_bandwidth => "Inverse of bandwidth of the RF pulse in 1/kHz. Also see [`bandwidth`](@ref).",
:N_left => "The number of zero crossings of the RF pulse before the main peak",
:N_right => "The number of zero crossings of the RF pulse after the main peak",
:slice_thickness => "Slice thickness of an RF pulse that is active during a gradient in mm. To set constraints it is often better to use [`inverse_slice_thickness`](@ref).",
+ :inverse_slice_thickness => "Inverse of slice thickness of an RF pulse that is active during a gradient in 1/mm. Also, see [`slice_thickness`](@ref).",
],
# gradients
:gradient => [
:qvec => "The spatial range and orientation on which the displacements can be detected due to this gradient in rad/um.",
- :qval => "The spatial range on which the displacements can be detected due to this gradient in rad/um (i.e., norm of [`qvec`](@ref)).",
+ :qval => "The spatial range on which the displacements can be detected due to this gradient in rad/um (i.e., norm of [`qvec`](@ref)). To set constraints it is often better to use [`qvec`](@ref) or [`qval_square`](@ref).",
+ :qval_square => "Square of [`qval`](@ref) in rad^2/um^2.",
:δ => "Effective duration of a gradient pulse ([`rise_time`](@ref) + [`flat_time`](@ref)) in ms.",
:rise_time => "Time for gradient pulse to reach its maximum value in ms.",
:flat_time => "Time of gradient pulse at maximum value in ms.",
@@ -35,8 +38,10 @@ all_variables_symbols = [
:readout => [
:dwell_time => "Time between two samples in an `ADC` in ms.",
:nsamples => "Number of samples during a readout. During the optimisation this might produce non-integer values.",
- :fov => "Size of the field of view in mm.",
- :voxel_size => "Size of each voxel in mm.",
+ :fov => "Size of the field of view in mm. To set constraints it is often better to use [`inverse_fov`](@ref).",
+ :inverse_fov => "Inverse of size of the field of view in 1/mm. Also see [`fov`](@ref).",
+ :voxel_size => "Size of each voxel in mm. To set constraints it is often better to use [`inverse_voxel_size`](@ref).",
+ :inverse_voxel_size => "Inverse of voxel size in 1/mm. Also see [`voxel_size`](@ref).",
: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))",
]
@@ -60,54 +65,10 @@ end
# helper functions
-"""
- inverse_slice_thickness(pulse)
-
-Inverse of [`slice_thickness`](@ref) in ms.
-
-It is defined separately from `slice_thickness` to avoid unnecessary divisions in any constraint.
-"""
-function inverse_slice_thickness end
-
-"""
- inverse_bandwidth(pulse)
-
-Inverse of [`bandwidth`](@ref) in 1/mm.
-
-It is defined separately from `bandwidth` to avoid unnecessary divisions in any constraint.
-"""
-function inverse_bandwidth end
-
-"""
- inverse_fov(readout)
-
-Inverse of [`fov`](@ref) in 1/mm.
-
-It is defined separately from `fov` to avoid unnecessary divisions in any constraint.
-"""
-function inverse_fov end
-
-"""
- inverse_voxel_size(readout)
-
-Inverse of [`voxel_size`](@ref) in 1/mm.
-
-It is defined separately from `voxel_size` to avoid unnecessary divisions in any constraint.
-"""
-function inverse_voxel_size end
-
-"""
- qval_square(gradient)
-
-Square of [`qval`](@ref) in rad/um.
-
-It is defined separately from `qval` to avoid unnecessary square root in any constraint.
-"""
function qval_square(bb, args...; kwargs...)
vec = qvec(bb, args...; kwargs...)
return vec[1]^2 + vec[2]^2 + vec[3]^2
end
-qval(bb; kwargs...) = sqrt(qval_square(bb))
alternative_variables = Dict(
qval => (qval_square, n->n^2, sqrt, false),
--
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