Fix urls (#78)

JuliaImageRecon · Feb 15, 2023 · 63d0258 · 63d0258
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diff --git a/docs/inc/reproduce.jl b/docs/inc/reproduce.jl
@@ -0,0 +1,9 @@
+
+# ### Reproducibility
+
+# This page was generated with the following version of Julia:
+using InteractiveUtils: versioninfo
+io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
+
+# And with the following package versions
+import Pkg; Pkg.status()
diff --git a/docs/inc/urls.jl b/docs/inc/urls.jl
@@ -0,0 +1,14 @@
+
+#=
+This page comes from a single Julia file:
+[`@__NAME__.jl`](xxxrepo/@__NAME__.jl).
+
+You can access the source code
+for such Julia documentation
+using the 'Edit on GitHub' link in the top right.
+You can view the corresponding notebook in
+[nbviewer](https://nbviewer.org/) here:
+[`@__NAME__.ipynb`](xxxnb/@__NAME__.ipynb),
+or open it in [binder](https://mybinder.org/) here:
+[`@__NAME__.ipynb`](xxxbinder/@__NAME__.ipynb).
+=#
diff --git a/docs/lit/examples/01-overview.jl b/docs/lit/examples/01-overview.jl
@@ -1,24 +1,11 @@
-#---------------------------------------------------------
-# # [ImagePhantoms overview](@id 01-overview)
-#---------------------------------------------------------
-
 #=
+# [ImagePhantoms overview](@id 01-overview)
+
 This page explains the Julia package
 [`ImagePhantoms`](https://github.com/JuliaImageRecon/ImagePhantoms.jl).
-
-This page was generated from a single Julia file:
-[01-overview.jl](@__REPO_ROOT_URL__/01-overview.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`01-overview.ipynb`](@__NBVIEWER_ROOT_URL__/01-overview.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`01-overview.ipynb`](@__BINDER_ROOT_URL__/01-overview.ipynb).
+#srcURL
 
 
 # ### Setup
@@ -41,9 +28,9 @@ using InteractiveUtils: versioninfo
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
-# ### Overview
-
 #=
+## Overview
+
 When developing image reconstruction methods,
 it can be helpful to simulate data (e.g., sinograms)
 using software-defined images called phantoms.
@@ -56,9 +43,9 @@ image = shepp_logan(256) # CT version by default
 jim(image, "SheppLogan"; clim=(0.9, 1.1))
 
 
-# ## Sinograms
-
 #=
+## Sinograms
+
 Often for image reconstruction algorithm development,
 we need not only the phantom image, but also its
 [sinogram, i.e., Radon transform](https://en.wikipedia.org/wiki/Radon_transform)
@@ -462,7 +449,7 @@ jim(p0a, p1a)
 
 
 #=
-### Spectra rotation
+## Spectra rotation
 
 The `spectrum` method
 accounts for the translation, rotation, and scaling
@@ -495,13 +482,4 @@ kspace0r = spectrum(kr, [ellipsoid0]) # evaluate spectrum at rotated tuples
 @assert kspace0r ≈ kspace1
 
 
-# ## Reproducibility
-
-# This page was generated with the following version of Julia:
-
-io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
-
-
-# And with the following package versions
-
-import Pkg; Pkg.status()
+include("../../../inc/reproduce.jl")
diff --git a/docs/lit/examples/02-ellipse.jl b/docs/lit/examples/02-ellipse.jl
@@ -1,24 +1,11 @@
-#---------------------------------------------------------
-# # [Ellipse](@id 02-ellipse)
-#---------------------------------------------------------
-
 #=
+# [Ellipse](@id 02-ellipse)
+
 This page illustrates the `Ellipse` shape in the Julia package
 [`ImagePhantoms`](https://github.com/JuliaImageRecon/ImagePhantoms.jl).
-
-This page was generated from a single Julia file:
-[02-ellipse.jl](@__REPO_ROOT_URL__/02-ellipse.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`02-ellipse.ipynb`](@__NBVIEWER_ROOT_URL__/02-ellipse.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`02-ellipse.ipynb`](@__BINDER_ROOT_URL__/02-ellipse.ipynb).
+#srcURL
 
 
 # ### Setup
@@ -41,9 +28,9 @@ default(markerstrokecolor=:auto)
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
-# ### Overview
-
 #=
+## Overview
+
 A useful shape
 for constructing 2D digital image phantoms
 is the ellipse,
@@ -88,7 +75,7 @@ area = IP.area(ob)
 
 
 #=
-### Spectrum using `spectrum`
+## Spectrum using `spectrum`
 
 There are two ways to examine the spectrum of this image:
 * using the analytical Fourier transform of the object via `spectrum`
@@ -122,10 +109,12 @@ p4 = jim(axesf(ig), 1e3*abs.(spectrum_fft - spectrum_exact),
 jim(p1, p4, p2, p3)
 
 
-# ### Radon transform using `radon`
+#=
+## Radon transform using `radon`
 
-# Examine the Radon transform of the object using `radon`,
-# and validate it using the projection-slice theorem aka Fourier-slice theorem.
+Examine the Radon transform of the object using `radon`,
+and validate it using the projection-slice theorem aka Fourier-slice theorem.
+=#
 
 dr = 0.2mm # radial sample spacing
 nr = 2^10 # radial sinogram bins
@@ -149,7 +138,7 @@ but one could make a fan-beam sinogram by sampling `(r, ϕ)` appropriately.
 =#
 
 
-# ### Fourier-slice theorem illustration
+# ## Fourier-slice theorem illustration
 
 # Pick one particular view angle (55°) and look at its slice and spectra.
 ia = argmin(abs.(ϕ .- 55°))

diff --git a/docs/lit/examples/03-rect.jl b/docs/lit/examples/03-rect.jl
@@ -1,24 +1,11 @@
-#---------------------------------------------------------
-# # [Rectangle](@id 03-rect)
-#---------------------------------------------------------
-
 #=
+# [Rectangle](@id 03-rect)
+
 This page illustrates the `Rect` shape in the Julia package
 [`ImagePhantoms`](https://github.com/JuliaImageRecon/ImagePhantoms.jl).
-
-This page was generated from a single Julia file:
-[03-rect.jl](@__REPO_ROOT_URL__/03-rect.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`03-rect.ipynb`](@__NBVIEWER_ROOT_URL__/03-rect.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`03-rect.ipynb`](@__BINDER_ROOT_URL__/03-rect.ipynb).
+#srcURL
 
 
 # ### Setup
@@ -41,9 +28,9 @@ default(markerstrokecolor=:auto)
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
-# ### Overview
-
 #=
+## Overview
+
 A useful shape
 for constructing 2D digital image phantoms
 is the rectangle,
@@ -88,7 +75,7 @@ area = IP.area(ob)
 
 
 #=
-### Spectrum using `spectrum`
+## Spectrum using `spectrum`
 
 There are two ways to examine the spectrum of this image:
 * using the analytical Fourier transform of the object via `spectrum`
@@ -122,10 +109,12 @@ p4 = jim(axesf(ig), 1e3*abs.(spectrum_fft - spectrum_exact),
 jim(p1, p4, p2, p3)
 
 
-# ### Radon transform using `radon`
+#=
+## Radon transform using `radon`
 
-# Examine the Radon transform of the object using `radon`,
-# and validate it using the projection-slice theorem aka Fourier-slice theorem.
+Examine the Radon transform of the object using `radon`,
+and validate it using the projection-slice theorem aka Fourier-slice theorem.
+=#
 
 dr = 0.2mm # radial sample spacing
 nr = 2^10 # radial sinogram bins
@@ -149,7 +138,7 @@ but one could make a fan-beam sinogram by sampling `(r, ϕ)` appropriately.
 =#
 
 
-# ### Fourier-slice theorem illustration
+# ## Fourier-slice theorem illustration
 
 # Pick one particular view angle (55°) and look at its slice and spectra.
 ia = argmin(abs.(ϕ .- 55°))

diff --git a/docs/lit/examples/04-gauss.jl b/docs/lit/examples/04-gauss.jl
@@ -1,25 +1,11 @@
-#---------------------------------------------------------
-# # [2D Gaussian](@id 04-gauss)
-#---------------------------------------------------------
-
 #=
+# [2D Gaussian](@id 04-gauss)
+
 This page illustrates the `Gauss2` shape in the Julia package
 [`ImagePhantoms`](https://github.com/JuliaImageRecon/ImagePhantoms.jl).
-
-This page was generated from a single Julia file:
-[04-gauss.jl](@__REPO_ROOT_URL__/04-gauss.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`04-gauss.ipynb`](@__NBVIEWER_ROOT_URL__/04-gauss.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`04-gauss.ipynb`](@__BINDER_ROOT_URL__/04-gauss.ipynb).
-
+#srcURL
 
 # ### Setup
 
@@ -41,9 +27,9 @@ default(markerstrokecolor=:auto)
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
-# ### Overview
-
 #=
+## Overview
+
 A useful shape
 for constructing 2D digital image phantoms
 is the 2D Gaussian,
@@ -88,7 +74,7 @@ area = IP.area(ob)
 
 
 #=
-### Spectrum using `spectrum`
+## Spectrum using `spectrum`
 
 There are two ways to examine the spectrum of this image:
 * using the analytical Fourier transform of the object via `spectrum`
@@ -126,10 +112,12 @@ p4 = jim(axesf(ig), 1e3*abs.(spectrum_fft - spectrum_exact),
 jim(p1, p4, p2, p3)
 
 
-# ### Radon transform using `radon`
+#=
+## Radon transform using `radon`
 
-# Examine the Radon transform of the object using `radon`,
-# and validate it using the projection-slice theorem aka Fourier-slice theorem.
+Examine the Radon transform of the object using `radon`,
+and validate it using the projection-slice theorem aka Fourier-slice theorem.
+=#
 
 dr = 0.2mm # radial sample spacing
 nr = 2^10 # radial sinogram bins
@@ -153,7 +141,7 @@ but one could make a fan-beam sinogram by sampling `(r, ϕ)` appropriately.
 =#
 
 
-# ### Fourier-slice theorem illustration
+# ## Fourier-slice theorem illustration
 
 # Pick one particular view angle (55°) and look at its slice and spectra.
 ia = argmin(abs.(ϕ .- 55°))