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Verified Commit a8d36ddd authored by Michiel Cottaar's avatar Michiel Cottaar
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Remove bad capitalisation from Pathway

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...@@ -4,7 +4,7 @@ import StaticArrays: SVector, SMatrix ...@@ -4,7 +4,7 @@ import StaticArrays: SVector, SMatrix
import ..Variables: qval, bval import ..Variables: qval, bval
""" """
PathWay(sequence::Sequence, pulse_effects::Vector{:Symbol/Number}, readout_index=1) Pathway(sequence::Sequence, pulse_effects::Vector{:Symbol/Number}, readout_index=1)
Describes how a specific spin/isochromat might experience the sequence. Describes how a specific spin/isochromat might experience the sequence.
...@@ -37,10 +37,10 @@ Over the pathway the following values are computed. Each can be accessed by call ...@@ -37,10 +37,10 @@ Over the pathway the following values are computed. Each can be accessed by call
### Effect of gradients ### Effect of gradients
- [`qvec`](@ref): Net displacement vector in k-space/q-space. - [`qvec`](@ref): Net displacement vector in k-space/q-space.
- [`qval`](@ref)/[`area_under_curve`](@ref): size of the displacement in k-space/q-space. For a spoiled pathway, this should be large compared with 1/voxel size; for unspoiled pathways it should be (close to) zero. - [`qval`](@ref)/[`area_under_curve`](@ref): size of the displacement in k-space/q-space. For a spoiled pathway, this should be large compared with 1/voxel size; for unspoiled pathways it should be (close to) zero.
- [`bmat`](@ref): Net diffusion weighting due to gradients along the [`PathWay`](@ref) in matrix form. - [`bmat`](@ref): Net diffusion weighting due to gradients along the [`Pathway`](@ref) in matrix form.
- [`bval`](@ref): Net diffusion weighting due to gradients along the [`PathWay`](@ref) as a single number. - [`bval`](@ref): Net diffusion weighting due to gradients along the [`Pathway`](@ref) as a single number.
""" """
struct PathWay struct Pathway
# user provided # user provided
sequence :: Sequence sequence :: Sequence
pulse_effects :: Vector{Union{:Symbol, :Number}} pulse_effects :: Vector{Union{:Symbol, :Number}}
...@@ -53,9 +53,9 @@ struct PathWay ...@@ -53,9 +53,9 @@ struct PathWay
end end
""" """
duration_state(pathway::PathWay, transverse::Bool, positive::Bool) duration_state(pathway::Pathway, transverse::Bool, positive::Bool)
Returns how long the [`PathWay`](@ref) spent in a specific state. Returns how long the [`Pathway`](@ref) spent in a specific state.
The requested state can be set using `transverse` and `positive` as follows: The requested state can be set using `transverse` and `positive` as follows:
- `transverse=false`, `positive=true`: +longitudinal - `transverse=false`, `positive=true`: +longitudinal
...@@ -63,7 +63,7 @@ The requested state can be set using `transverse` and `positive` as follows: ...@@ -63,7 +63,7 @@ The requested state can be set using `transverse` and `positive` as follows:
- `transverse=false`, `positive=false`: -longitudinal - `transverse=false`, `positive=false`: -longitudinal
- `transverse=true`, `positive=false`: -transverse - `transverse=true`, `positive=false`: -transverse
""" """
function duration_state(pathway::PathWay, transverse, positive) function duration_state(pathway::Pathway, transverse, positive)
index = Dict([ index = Dict([
(false, true) => 1, (false, true) => 1,
(true, true) => 2, (true, true) => 2,
...@@ -74,9 +74,9 @@ function duration_state(pathway::PathWay, transverse, positive) ...@@ -74,9 +74,9 @@ function duration_state(pathway::PathWay, transverse, positive)
end end
""" """
duration_transverse(pathway::PathWay) duration_transverse(pathway::Pathway)
Returns the total amount of time that spins following the given [`PathWay`](@ref) spent in the transverse plane. Returns the total amount of time that spins following the given [`Pathway`](@ref) spent in the transverse plane.
This determines the amount of T2-weighting as ``e^{t/T_2}``, where ``t`` is the `duration_transverse`. This determines the amount of T2-weighting as ``e^{t/T_2}``, where ``t`` is the `duration_transverse`.
Also see [`duration_dephase`](@ref) for T2'-weighting. Also see [`duration_dephase`](@ref) for T2'-weighting.
...@@ -86,9 +86,9 @@ function duration_transverse(pathway::Pathway) ...@@ -86,9 +86,9 @@ function duration_transverse(pathway::Pathway)
end end
""" """
duration_dephase(pathway::PathWay) duration_dephase(pathway::Pathway)
Returns the net time that spins following the given [`PathWay`](@ref) spent in the +transverse versus the -transverse state. Returns the net time that spins following the given [`Pathway`](@ref) spent in the +transverse versus the -transverse state.
This determines the amount of T2'-weighting as ``e^{t/T_2'}``, where ``t`` is the `duration_dephase`. This determines the amount of T2'-weighting as ``e^{t/T_2'}``, where ``t`` is the `duration_dephase`.
Also see [`duration_transverse`](@ref) for T2-weighting. Also see [`duration_transverse`](@ref) for T2-weighting.
...@@ -99,39 +99,39 @@ end ...@@ -99,39 +99,39 @@ end
""" """
qvec(pathway::PathWay) qvec(pathway::Pathway)
Return net displacement vector in k-space/q-space experienced by the spins following a specific [`PathWay`](@ref). Return net displacement vector in k-space/q-space experienced by the spins following a specific [`Pathway`](@ref).
Only gradients active while the spins are in the transverse plane are considered. Only gradients active while the spins are in the transverse plane are considered.
""" """
qvec(pathway::PathWay) = pathway.qvec qvec(pathway::Pathway) = pathway.qvec
""" """
qval(pathway::PathWay) qval(pathway::Pathway)
Return net displacement in k-space/q-space experienced by the spins following a specific [`PathWay`](@ref). Return net displacement in k-space/q-space experienced by the spins following a specific [`Pathway`](@ref).
Only gradients active while the spins are in the transverse plane are considered. Only gradients active while the spins are in the transverse plane are considered.
""" """
qval(pathway::PathWay) = norm(qvec(pathway)) qval(pathway::Pathway) = norm(qvec(pathway))
""" """
bmat(pathway::PathWay) bmat(pathway::Pathway)
Return 3x3 diffusion-weighted matrix experienced by the spins following a specific [`PathWay`](@ref). Return 3x3 diffusion-weighted matrix experienced by the spins following a specific [`Pathway`](@ref).
Only gradients active while the spins are in the transverse plane are considered. Only gradients active while the spins are in the transverse plane are considered.
""" """
bmat(pathway::PathWay) = pathway.bmat bmat(pathway::Pathway) = pathway.bmat
""" """
bval(pathway::PathWay) bval(pathway::Pathway)
Return size of diffusion-weighting experienced by the spins following a specific [`PathWay`](@ref). Return size of diffusion-weighting experienced by the spins following a specific [`Pathway`](@ref).
Only gradients active while the spins are in the transverse plane are considered. Only gradients active while the spins are in the transverse plane are considered.
""" """
bval(pathway::PathWay) = norm(bmat(pathway)) bval(pathway::Pathway) = norm(bmat(pathway))
end end
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