Add axes (#41)

* Add axes

* Test axes

* Use Base.axes

* Use axes

Author: JeffFessler

docs/lit/examples/01-tomography.jl

@@ -1,8 +1,6 @@
-#---------------------------------------------------------
-# # [Tomography overview](@id 01-tomography)
-#---------------------------------------------------------
-
 #=
+# [Tomography overview](@id 01-tomography)
+
 This page gives an overview of the Julia package
 [`Sinograms.jl`](https://github.com/JuliaImageRecon/Sinograms.jl).
 
@@ -30,7 +28,7 @@ using MIRTjim: jim, prompt
 using InteractiveUtils: versioninfo
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);

docs/lit/examples/02-sino-geom.jl

@@ -1,8 +1,6 @@
-#---------------------------------------------------------
-# # [2D sinogram geometry](@id 02-sino-geom)
-#---------------------------------------------------------
-
 #=
+# [2D sinogram geometry](@id 02-sino-geom)
+
 This page describes the 2D sinogram geometries
 available in the Julia package
 [`Sinograms.jl`](https://github.com/JuliaImageRecon/Sinograms.jl).
@@ -34,7 +32,7 @@ using MIRTjim: jim, prompt
 using InteractiveUtils: versioninfo
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);

docs/lit/examples/03-parallel-beam.jl

@@ -1,8 +1,6 @@
-#---------------------------------------------------------
-# # [Parallel-beam tomography](@id 03-parallel-beam)
-#---------------------------------------------------------
-
 #=
+# [Parallel-beam tomography](@id 03-parallel-beam)
+
 This page describes parallel-beam tomographic image reconstruction
 using the Julia package
 [`Sinograms.jl`](https://github.com/JuliaImageRecon/Sinograms.jl).
@@ -33,7 +31,7 @@ using Unitful: mm
 using MIRTjim: jim, prompt
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
@@ -65,7 +63,7 @@ ob = shepp_logan(SheppLogan(); fovs = fovs(ig), u = (1, 1, μ))
 
 # Radon transform of Shepp-Logan phantom:
 sino = radon(rays(sg), ob)
-jim(sg.r, sg.ad, sino; title="Shepp-Logan sinogram", xlabel="r", ylabel="ϕ")
+jim(axes(sg), sino; title="Shepp-Logan sinogram", xlabel="r", ylabel="ϕ")
 
 ## Image reconstruction via FBP
 # Here we start with a "plan",

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

@@ -1,8 +1,6 @@
-#---------------------------------------------------------
-# # [Fan-beam tomography: arc detector](@id 04-fan-arc)
-#---------------------------------------------------------
-
 #=
+# [Fan-beam tomography: arc detector](@id 04-fan-arc)
+
 This page describes fan-beam tomographic image reconstruction
 using the Julia package
 [`Sinograms.jl`](https://github.com/JuliaImageRecon/Sinograms.jl).
@@ -43,14 +41,14 @@ using ImagePhantoms: SheppLogan, shepp_logan, radon, phantom
 using MIRTjim: jim, prompt
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
 #=
-### Fan-beam sinogram of Shepp-Logan phantom
+## Fan-beam sinogram of Shepp-Logan phantom
 
 For illustration,
 we start by synthesizing
@@ -81,7 +79,7 @@ ob = shepp_logan(SheppLogan(); fovs = fovs(ig), u = (1, 1, μ))
 
 # Arc fan-beam sinogram for Shepp-Logan phantom:
 sino = radon(rays(sg), ob)
-jim(sg.r, sg.ad, sino; title="Shepp-Logan sinogram", xlabel="r", ylabel="ϕ")
+jim(axes(sg), sino; title="Shepp-Logan sinogram", xlabel="r", ylabel="ϕ")
 
 
 #=

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

@@ -1,8 +1,6 @@
-#---------------------------------------------------------
-# # [Fan-beam tomography: flat detector](@id 05-fan-flat)
-#---------------------------------------------------------
-
 #=
+# [Fan-beam tomography: flat detector](@id 05-fan-flat)
+
 This page describes fan-beam tomographic image reconstruction
 using the Julia package
 [`Sinograms.jl`](https://github.com/JuliaImageRecon/Sinograms.jl).
@@ -38,7 +36,7 @@ using ImagePhantoms: SheppLogan, shepp_logan, radon, phantom
 using MIRTjim: jim, prompt
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
@@ -77,7 +75,7 @@ ob = shepp_logan(SheppLogan(); fovs = fovs(ig), u = (1, 1, μ))
 
 # Arc fan-beam sinogram for Shepp-Logan phantom:
 sino = radon(rays(sg), ob)
-jim(sg.r, sg.ad, sino; title="Shepp-Logan sinogram", xlabel="r", ylabel="ϕ")
+jim(axes(sg), sino; title="Shepp-Logan sinogram", xlabel="r", ylabel="ϕ")
 
 
 #=

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

@@ -1,5 +1,5 @@
 #=
-# [Fan-beam tomography: arc detector](@id 06-fan-short)
+# [Fan-beam tomography: short scan](@id 06-fan-short)
 
 This page describes fan-beam tomographic image reconstruction
 using the Julia package
@@ -45,14 +45,14 @@ using ImagePhantoms: SheppLogan, shepp_logan, radon, phantom
 using MIRTjim: jim, prompt
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
 #=
-### Fan-beam sinogram of Shepp-Logan phantom
+## Fan-beam sinogram of Shepp-Logan phantom
 
 For illustration,
 we start by synthesizing
@@ -67,13 +67,19 @@ but units are optional.
 # Use `ImageGeom` to define the image geometry.
 ig = ImageGeom(MaskCircle(); dims=(128,126), deltas = (2mm,2mm) )
 
-# Use `SinoFanArc` to define the sinogram geometry,
-# with the `:short` option for `orbit` to make a short scan.
+#=
+Use `SinoFanArc` to define the sinogram geometry,
+with the `:short` option for `orbit` to make a short scan.
+Note that even though we specify `na = 100`
+we end up with `na = 67` views
+because of the `:short` option.
+=#
 sg = SinoFanArc( :short, ;
     nb = 130, d = 3.2mm, na = 100, dsd = 400mm, dod = 140mm,
 )
 
-# Examine the geometry to verify the FOV:
+# Examine the geometry to verify the FOV.
+# The `na=67` blue dots show the `:short` scan.
 jim(axes(ig), ig.mask; prompt=false)
 sino_geom_plot!(sg, ig)
 
@@ -86,7 +92,7 @@ ob = shepp_logan(SheppLogan(); fovs = fovs(ig), u = (1, 1, μ))
 
 # Short arc fan-beam sinogram for Shepp-Logan phantom:
 sino = radon(rays(sg), ob)
-jim(sg.r, sg.ad, sino; title="Shepp-Logan 'short' sinogram",
+jim(axes(sg), sino; title="Shepp-Logan 'short' sinogram",
     xlabel="r", ylabel="ϕ")
 
 
@@ -98,17 +104,21 @@ which would save work if we were reconstructing many images.
 
 plan = plan_fbp(sg, ig)
 
-# Examine Parker weights
-jim(sg.r, sg.ad, plan.parker_weight; title = "Parker weights",
+# Examine Parker weights:
+jim(axes(sg), plan.parker_weight; title = "Parker weights",
     xlabel="r", ylabel="ϕ")
 
-# Finally perform FBP
+# Finally perform FBP:
 fbp_image, sino_filt = fbp(plan, sino);
 
 # A narrow color window is needed to see the soft tissue structures:
 clim = (0.9, 1.1) .* μ
 jim(axes(ig), fbp_image, "FBP image for 'short' arc case"; clim)
 
-# For comparison, here is the ideal phantom image
+# For comparison, here is the ideal phantom image:
 true_image = phantom(axes(ig)..., ob, 2)
 jim(axes(ig)..., true_image, "True phantom image"; clim)
+
+# Here is the difference image.
+# Better sampling would reduce the errors.
+jim(axes(ig)..., fbp_image - true_image, "Error image")

docs/lit/examples/07-fdk.jl

@@ -1,8 +1,6 @@
-#---------------------------------------------------------
-# # [CBCT FDK](@id 07-fdk)
-#---------------------------------------------------------
-
 #=
+# [CBCT FDK](@id 07-fdk)
+
 This page describes image reconstruction
 for cone-beam computed tomography (CBCT)
 with both arc and flat detectors
@@ -38,7 +36,7 @@ using ImagePhantoms: radon, phantom
 using MIRTjim: jim, prompt
 
 
-# The following line is helpful when running this example.jl file as a script;
+# The following line is helpful when running this file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
 
 isinteractive() ? jim(:prompt, true) : prompt(:draw);

src/geom/ct-geom.jl

@@ -6,13 +6,16 @@ using the parallel, fan beam arc, or flat fan beam geometry.
 2022-05-11, Jason Hu, Jeff Fessler translated from ct_geom.m in MIRT
 =#
 
-export dims, downsample, oversample, rays
+export dims, downsample, oversample, rays, axes
 
 
 # Methods common to all types
 
 dims(st::CtGeom) = (st.ns, st.nt, st.na)::NTuple{3,Int}
 
+# use ° via `angles()` because mainly for plots
+Base.axes(st::CtGeom) = (ct_geom_s(st), ct_geom_t(st), angles(st))
+
 ct_geom_ws(st::CtGeom) = ((st.ns-1)//2 + st.offset_s)::Toffset
 ct_geom_wt(st::CtGeom) = ((st.nt-1)//2 + st.offset_t)::Toffset
 

src/geom/sino-geom.jl

@@ -5,13 +5,16 @@ sinogram geometry definitions for 2D tomographic image reconstruction
 2022-01-22, copied from MIRT.jl and updated to support Unitful values
 =#
 
-export dims, downsample, oversample, rays
+export dims, downsample, oversample, rays, axes
 export sino_w, sino_s
 
 # Methods common to all types
 
 dims(sg::SinoGeom) = (sg.nb, sg.na)::NTuple{2,Int}
 
+# use ° via `angles()` because mainly for plots
+Base.axes(sg::SinoGeom) = (sino_s(sg), angles(sg))
+
 sino_w(sg::SinoGeom) = Toffset((sg.nb-1)/2 + sg.offset)::Toffset
 
 #sino_s(sg::SinoGeom) = sg.d * ((0:sg.nb-1) .- sino_w(sg))

test/geom/ct-geom.jl

@@ -5,7 +5,7 @@ test/geom/ct-geom.jl
 using Sinograms: RealU, CtSourceHelix
 using Sinograms: CtGeom, CtParallel, CtFan
 using Sinograms: CtPar, CtFanArc, CtFanFlat
-using Sinograms: dims, ones, zeros, angles, rays, downsample, oversample
+using Sinograms: dims, ones, zeros, angles, rays, axes, downsample, oversample
 using Sinograms: footprint_size
 import Sinograms as SG
 using ImageGeoms: ImageGeom
@@ -78,6 +78,7 @@ function _test_prop(
     # common methods
     D = length(dims(st))
     @test (@inferred dims(st)) isa Dims{D}
+    @test (@inferred axes(st)) isa Tuple
     @test (@inferred angles(st)) isa AbstractVector
     @test (@inferred ones(st)) isa Array{Float32,D}
     @test (@inferred zeros(st)) isa Array{Float32,D}