Use package extensions, not Requires; to v0.5 (#66)

* Extensions for plots and units

* import

* Update import etc.

* Purge Requires

Project.toml

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

docs/lit/examples/04-fan-arc.jl

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

docs/lit/examples/05-fan-flat.jl

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

docs/lit/examples/06-fan-short.jl

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

docs/lit/examples/07-fdk.jl

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

ext/Sinograms_Plots.jl

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

ext/Sinograms_Units.jl

@@ -0,0 +1,63 @@
+# Sinograms_Units.jl
+# Support data with units iff user has loaded Unitful
+
+module Sinograms_Units
+
+# extended:
+import Sinograms: fft_filter, to_radians, _unit_precision
+import FFTW: fft, ifft
+import Unitful: uconvert
+
+using Sinograms: _fft_filter, _reale
+using Unitful: °, rad, NoDims, unit
+using Unitful: Units, Quantity, convfact, ustrip
+
+
+#=
+https://github.com/PainterQubits/Unitful.jl/issues/375
+=#
+function uconvert(a::Units, x::Quantity{T,D,U}) where {T<:AbstractFloat,D,U}
+    return Quantity(x.val * T(convfact(a, U())), a)
+end
+
+
+"""
+    to_radians(angles::AbstractArray{Unitful.Quantity})
+
+Convert `Unitful` quantity array to radians.
+"""
+function to_radians(aa::AbstractArray{<: Quantity{T}}) where {T <: AbstractFloat}
+    U = eltype(aa)
+    c = rad(oneunit(U)) / oneunit(U)
+    return aa * c
+end
+
+
+_unit_precision(x::Quantity{T}) where {T <: Number} = "Unit{$T}"
+
+
+# generic unitless linear operation applied to data with units
+function _linear_fun(fun::Function,
+    x::AbstractArray{<: Quantity},
+    args...
+)
+    x0 = ustrip(x) # unitless view into x data
+    y0 = fun(x0, args...)
+    u = unit(eltype(x))
+    Tu = typeof(one(eltype(y0)) * unit(eltype(x)))
+    return reinterpret(Tu, y0)
+end
+
+# fft for data with units
+fft(x::AbstractArray{<: Quantity}, args...) =
+    _linear_fun(fft, x, args...)
+ifft(x::AbstractArray{<: Quantity}, args...) =
+    _linear_fun(ifft, x, args...)
+
+fft_filter(data::AbstractArray{<: Quantity{<:Complex}}, args...) =
+    _fft_filter(data, args...)
+
+fft_filter(data::AbstractArray{<: Quantity{<:Real}}, args...) =
+    _reale(_fft_filter(data, args...))
+
+end # module

src/fbp3/ct-plot.jl → ext/ct-plot.jl

@@ -4,10 +4,10 @@ Show CT geometries.
 2022-10-01, Jeff Fessler
 =#
 
-export ct_geom_plot2!, ct_geom_plot3
+import Sinograms: ct_geom_plot2!, ct_geom_plot3 # extended here
 
-#using Sinograms: CtGeom, RealU, source_zs
-using .Plots: plot, plot!, default
+using Sinograms: CtGeom, CtFan, RealU, _t, _source_zs
+using Plots: plot, plot!, default
 using ImageGeoms: axes
 
 

src/fbp2/sino-plot.jl → ext/sino-plot.jl

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

src/Sinograms.jl

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

src/exts.jl

@@ -0,0 +1,11 @@
+# exts.jl
+
+# methods defined in the extension(s)
+export sino_plot_rays, sino_geom_plot!
+export ct_geom_plot2!, ct_geom_plot3
+
+sino_plot_rays(::Nothing) = throw("Run `using Plots` first")
+sino_geom_plot!(::Nothing) = throw("Run `using Plots` first")
+
+ct_geom_plot2!(::Nothing) = throw("Run `using Plots` first")
+ct_geom_plot3(::Nothing) = throw("Run `using Plots` first")

src/unit.jl

@@ -0,0 +1,12 @@
+# unit.jl
+
+export to_radians
+
+"""
+    to_radians(angles::AbstractArray{<:AbstractFloat})
+When Unitful package not loaded,
+assume `angles` are in degrees and convert to radians.
+"""
+to_radians(aa::AbstractArray{T}) where {T <: AbstractFloat} = aa * T(deg2rad(1))
+
+_unit_precision(x::T) where {T <: Number} = T

test/Project.toml

@@ -2,7 +2,6 @@
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 ImageGeoms = "9ee76f2b-840d-4475-b6d6-e485c9297852"
 ImagePhantoms = "71a99df6-f52c-4da1-bd2a-69d6f37f3252"
-InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 LazyGrids = "7031d0ef-c40d-4431-b2f8-61a8d2f650db"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

test/geom/ct-geom.jl

@@ -25,7 +25,7 @@ function values(rg::R) where {R <: CtGeom}
 end
 
 
-function _test_construct(geo ; ds=2mm, orbit=180.0°)
+function _test_construct3(geo ; ds=2mm, orbit=180.0°)
     rg = @inferred geo(; ds, orbit)
     args = values(rg)
     Td = typeof(ds)
@@ -48,7 +48,7 @@ end
     ds, orbit = 2mm, 180.0° # stress
     for geo in list
         @test (@inferred geo(; ds, orbit)) isa CtGeom
-        @test _test_construct(geo)
+        @test _test_construct3(geo)
     end
 
     rg = @inferred ge1( ; unit = oneunit(ds), orbit=:short)

test/geom/sino-geom.jl

@@ -24,7 +24,7 @@ function values(rg::R) where {R <: SinoGeom}
 end
 
 
-function _test_construct(geo ; d=2mm, orbit=180.0°)
+function _test_construct2(geo ; d=2mm, orbit=180.0°)
     rg = @inferred geo(; d, orbit)
     args = values(rg)
     Td = typeof(d)
@@ -46,7 +46,7 @@ end
     d, orbit = 2mm, 180.0° # stress
     for geo in list
         @test (@inferred geo(; d, orbit)) isa SinoGeom
-        @test _test_construct(geo)
+        @test _test_construct2(geo)
     end
 
     rg = @inferred ge1( ; unit = oneunit(d), orbit=:short)