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JeffFesslerJeffFessler
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Use package extensions, not Requires; to v0.5 (#66)
* Extensions for plots and units * import * Update import etc. * Purge Requires
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17 files changed

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‎Project.toml‎

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@@ -1,19 +1,26 @@
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name = "Sinograms"
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uuid = "02a14def-c6e6-4ab0-b2df-0ab64bc8cdd7"
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authors = ["fessler <[email protected]>"]
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version = "0.4.1"
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version = "0.5"
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[deps]
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FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
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ImageGeoms = "9ee76f2b-840d-4475-b6d6-e485c9297852"
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Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
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LazyGrids = "7031d0ef-c40d-4431-b2f8-61a8d2f650db"
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Requires = "ae029012-a4dd-5104-9daa-d747884805df"
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[compat]
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FFTW = "1.4.5, 1.5"
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ImageGeoms = "0.9, 0.10"
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FFTW = "1.5"
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ImageGeoms = "0.11"
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Interpolations = "0.14, 0.15"
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LazyGrids = "0.4, 0.5, 1"
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Requires = "1.3"
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LazyGrids = "1"
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Unitful = "1.19"
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julia = "1.10"
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[weakdeps]
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
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[extensions]
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Sinograms_Plots = "Plots"
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Sinograms_Units = "Unitful"

‎docs/lit/examples/04-fan-arc.jl‎

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@@ -22,7 +22,7 @@ anti-scatter grids.
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# Packages needed here.
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using Plots: plot, gui # these 2 must precede Sinograms for Requires to work!
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using Plots: plot, gui
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using Unitful: mm
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using Sinograms: SinoFanArc, rays, plan_fbp, fbp, sino_geom_plot!
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using ImageGeoms: ImageGeom, fovs, MaskCircle

‎docs/lit/examples/05-fan-flat.jl‎

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@@ -17,7 +17,7 @@ as used in many cone-beam CT (CBCT) systems.
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# Packages needed here.
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using Plots: plot, gui # these 2 must precede Sinograms for Requires to work!
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using Plots: plot, gui
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using Unitful: cm
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using Sinograms: SinoFanFlat, rays, plan_fbp, Window, Hamming, fbp, sino_geom_plot!
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using ImageGeoms: ImageGeom, fovs, MaskCircle

‎docs/lit/examples/06-fan-short.jl‎

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@@ -26,7 +26,7 @@ anti-scatter grids.
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# Packages needed here.
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using Plots: plot, gui # these 2 must precede Sinograms for Requires to work!
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using Plots: plot, gui
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using Unitful: mm
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using Sinograms: SinoFanArc, rays, plan_fbp, fbp, sino_geom_plot!
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using ImageGeoms: ImageGeom, fovs, MaskCircle

‎docs/lit/examples/07-fdk.jl‎

Lines changed: 1 addition & 1 deletion
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@@ -14,7 +14,7 @@ using the Julia package
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# Packages needed here.
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17-
using Plots: plot, gui # these 2 must precede Sinograms for Requires to work!
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using Plots: plot, gui
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using Unitful: cm
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using Sinograms: CtFanArc, CtFanFlat # CtPar
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using Sinograms: rays, plan_fbp, Window, Hamming, fdk, ct_geom_plot3

‎ext/Sinograms_Plots.jl‎

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@@ -0,0 +1,9 @@
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# Sinograms_Plots.jl
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# support plots (possibly with units) iff user has loaded Plots
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module Sinograms_Plots
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include("sino-plot.jl") # fbp2
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include("ct-plot.jl") # fbp3
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end # module

‎ext/Sinograms_Units.jl‎

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# Sinograms_Units.jl
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# Support data with units iff user has loaded Unitful
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module Sinograms_Units
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# extended:
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import Sinograms: fft_filter, to_radians, _unit_precision
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import FFTW: fft, ifft
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import Unitful: uconvert
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using Sinograms: _fft_filter, _reale
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using Unitful: °, rad, NoDims, unit
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using Unitful: Units, Quantity, convfact, ustrip
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#=
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https://github.com/PainterQubits/Unitful.jl/issues/375
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=#
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function uconvert(a::Units, x::Quantity{T,D,U}) where {T<:AbstractFloat,D,U}
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return Quantity(x.val * T(convfact(a, U())), a)
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end
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"""
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to_radians(angles::AbstractArray{Unitful.Quantity})
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Convert `Unitful` quantity array to radians.
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"""
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function to_radians(aa::AbstractArray{<: Quantity{T}}) where {T <: AbstractFloat}
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U = eltype(aa)
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c = rad(oneunit(U)) / oneunit(U)
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return aa * c
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end
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_unit_precision(x::Quantity{T}) where {T <: Number} = "Unit{$T}"
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# generic unitless linear operation applied to data with units
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function _linear_fun(fun::Function,
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x::AbstractArray{<: Quantity},
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args...
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)
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x0 = ustrip(x) # unitless view into x data
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y0 = fun(x0, args...)
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u = unit(eltype(x))
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Tu = typeof(one(eltype(y0)) * unit(eltype(x)))
48+
return reinterpret(Tu, y0)
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end
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# fft for data with units
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fft(x::AbstractArray{<: Quantity}, args...) =
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_linear_fun(fft, x, args...)
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ifft(x::AbstractArray{<: Quantity}, args...) =
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_linear_fun(ifft, x, args...)
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fft_filter(data::AbstractArray{<: Quantity{<:Complex}}, args...) =
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_fft_filter(data, args...)
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fft_filter(data::AbstractArray{<: Quantity{<:Real}}, args...) =
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_reale(_fft_filter(data, args...))
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end # module

src/fbp3/ct-plot.jl renamed to ext/ct-plot.jl

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,10 +4,10 @@ Show CT geometries.
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2022-10-01, Jeff Fessler
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=#
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7-
export ct_geom_plot2!, ct_geom_plot3
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import Sinograms: ct_geom_plot2!, ct_geom_plot3 # extended here
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#using Sinograms: CtGeom, RealU, source_zs
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using .Plots: plot, plot!, default
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using Sinograms: CtGeom, CtFan, RealU, _t, _source_zs
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using Plots: plot, plot!, default
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using ImageGeoms: axes
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src/fbp2/sino-plot.jl renamed to ext/sino-plot.jl

Lines changed: 10 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -4,17 +4,19 @@ Show 2D sinogram geometries.
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2022-01-23, Jeff Fessler
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=#
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7-
export sino_plot_rays, sino_geom_plot!
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import Sinograms: sino_plot_rays, sino_geom_plot! # extended here
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9-
#using Sinograms: SinoGeom, RealU
10-
using .Plots: scatter, plot, plot!, default, xlims!
9+
using Sinograms: SinoGeom, RealU, rays, SinoPar, SinoFan, SinoMoj
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using Sinograms: _ar, _rfov, _dso, _xds, _yds, _d_moj
11+
using Plots: scatter, plot, plot!, default, xlims!
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using ImageGeoms: ImageGeom
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"""
1416
sino_plot_rays(rg::SinoGeom ; kwargs...)
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Make a scatter plot of the `(r, ϕ)` sample locations for all rays.
17-
Requires `Plots`.
19+
Needs `Plots`.
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"""
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function sino_plot_rays(rg::SinoGeom; kwargs...)
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# r, phi = rays(rg)
@@ -101,12 +103,12 @@ function sino_geom_plot_fan!(
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ylims = (-1,1) .* dso
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tmp = ar .+ π/2 # trick: angle beta defined ccw from y axis
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scat!([p0[1]], [p0[2]], color=:blue, marker=:square, # source
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; xlims, ylims)
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plot!(dso * cos.(t), dso * sin.(t), color=:cyan) # source circle
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; xlims, ylims, label="")
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plot!(dso * cos.(t), dso * sin.(t), color=:cyan, label="") # source circle
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scat!(dso * cos.(tmp), dso * sin.(tmp),
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color=:blue, marker=:circle, markersize=2) # source points
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color=:blue, marker=:circle, markersize=2, label="") # source points
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scat!(vec(pd[1,:]), vec(pd[2,:]), marker=:circle,
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color=:orange, markersize=1) # detectors
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color=:orange, markersize=1, label="") # detectors
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plot!([pd[1,1], p0[1], pd[1,end]], [pd[2,1], p0[2], pd[2,end]],
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color=:red, label="")

‎src/Sinograms.jl‎

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@@ -3,10 +3,11 @@
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"""
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module Sinograms
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6-
using Requires: @require
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const RealU = Number # Real or Unitful
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8+
include("unit.jl")
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include("exts.jl")
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include("geom/util.jl")
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include("geom/ct-source.jl")
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include("geom/type2.jl")
@@ -43,28 +44,4 @@ include("sys2/footprint.jl")
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include("sys2/zwart_powell.jl")
4445
include("sys2/bdd_2d.jl")
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46-
47-
"""
48-
to_radians(angles::AbstractArray{<:AbstractFloat})
49-
When Unitful package not loaded,
50-
assume `angles` are in degrees and convert to radians.
51-
"""
52-
to_radians(aa::AbstractArray{T}) where {T <: AbstractFloat} = aa * T(deg2rad(1))
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_unit_precision(x::T) where {T <: Number} = T
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# support Plots (with units) iff user has loaded the relevant packages
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function __init__()
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@require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
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include("fbp2/sino-plot.jl")
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include("fbp3/ct-plot.jl")
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end
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64-
@require Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" begin
65-
include("units.jl")
66-
end
67-
end
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end # module

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