Major overhaul to improve types

docs/lit/examples/02-ellipse.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Ellipse, phantom, radon, spectrum
+using ImagePhantoms: ellipse, phantom, radon, spectrum
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt
 using FFTW: fft, fftshift
@@ -54,7 +54,7 @@ using physical units.
 =#
 
 radii = (20mm, 80mm)
-ob = Ellipse((40mm, 30mm), radii, π/6, 1.0f0)
+ob = ellipse((40mm, 30mm), radii, π/6, 1.0f0)
 
 
 # ### Phantom image using `phantom`
@@ -176,5 +176,5 @@ The good agreement between the analytical spectra (solid lines)
 and the DFT samples (disks)
 validates that `phantom`, `radon`, and `spectrum`
 are all self consistent
-for this `Ellipse` object.
+for this `Ellipse` shape.
 =#

docs/lit/examples/03-rect.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Rect, phantom, radon, spectrum
+using ImagePhantoms: rect, phantom, radon, spectrum
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt
 using FFTW: fft, fftshift
@@ -54,7 +54,7 @@ using physical units.
 =#
 
 width = (20mm, 80mm)
-ob = Rect((40mm, 30mm), width, π/6, 1.0f0)
+ob = rect((40mm, 30mm), width, π/6, 1.0f0)
 
 
 # ### Phantom image using `phantom`
@@ -174,5 +174,5 @@ The good agreement between the analytical spectra (solid lines)
 and the DFT samples (disks)
 validates that `phantom`, `radon`, and `spectrum`
 are all self consistent
-for this `Rect` object.
+for this `Rect` shape.
 =#

docs/lit/examples/04-gauss.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Gauss2, phantom, radon, spectrum
+using ImagePhantoms: gauss2, phantom, radon, spectrum
 import ImagePhantoms as IP
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt
@@ -56,7 +56,7 @@ using physical units.
 =#
 
 width = (50mm, 20mm) # full-width at half-maximum (FHWM)
-ob = Gauss2((20mm, 30mm), width, π/6, 1.0f0)
+ob = gauss2((20mm, 30mm), width, π/6, 1.0f0)
 
 
 # ### Phantom image using `phantom`
@@ -176,5 +176,5 @@ The good agreement between the analytical spectra (solid lines)
 and the DFT samples (disks)
 validates that `phantom`, `radon`, and `spectrum`
 are all self consistent
-for this `Gauss2` object.
+for this `Gauss2` shape.
 =#

docs/lit/examples/05-triangle.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Triangle, phantom, radon, spectrum
+using ImagePhantoms: triangle, phantom, radon, spectrum
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt
 using FFTW: fft, fftshift
@@ -48,7 +48,7 @@ for constructing 2D digital image phantoms.
 The basic shape here is an equilateral triangle
 whose base is [-1/2,1/2] along the x axis,
 pointing upwards along the y axis.
-When defining such a `Triangle` object one can specify
+When defining such a `Triangle` shape one can specify
 its center, widths, angle and value.
 All of the methods in `ImagePhantoms` support physical units,
 so we use such units throughout this example.
@@ -59,7 +59,7 @@ using physical units.
 =#
 
 width = (20mm, 80mm)
-ob = Triangle((40mm, 30mm), width, π/6, 1.0f0)
+ob = triangle((40mm, 30mm), width, π/6, 1.0f0)
 
 
 # ### Phantom image using `phantom`
@@ -180,7 +180,7 @@ The good agreement between the analytical spectra (solid lines)
 and the DFT samples (disks)
 validates that `phantom`, `radon`, and `spectrum`
 are all self consistent
-for this `Triangle` object.
+for this `Triangle` shape.
 =#
 
 

docs/lit/examples/07-shepp.jl

@@ -25,7 +25,9 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms
+using ImagePhantoms: shepp_logan, SouthPark
+using ImagePhantoms: SheppLoganToft, SheppLoganEmis, SheppLoganBrainWeb
+using ImagePhantoms: ellipse_parameters, ellipse, phantom
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt
 using Unitful: g, cm
@@ -159,7 +161,7 @@ to have the middle ellipses be non-overlapping:
 
 ob = ellipse_parameters(SheppLoganBrainWeb(), disjoint=true)
 ob[:,end] = 1:10
-ob = Ellipse(ob)
+ob = ellipse(ob)
 x = LinRange(-0.4, 0.4, 206)
 y = LinRange(-0.5, 0.5, 256)
 oversample = 3

docs/lit/examples/09-disk.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Ellipse, phantom, disk_phantom_params
+using ImagePhantoms: ellipse, phantom, disk_phantom_params
 using ImageGeoms: ImageGeom
 using MIRTjim: jim, prompt
 using Plots # @animate, gif
@@ -57,7 +57,7 @@ function disk_phantom(title::String)
     x = (-M÷2:M÷2-1) * dx
     y = (-N÷2:N÷2-1) * dy
     params = disk_phantom_params( ; rhead = () -> rand(100:105))
-    objects = Ellipse(params) # vector of Ellipse objects
+    objects = ellipse(params) # vector of Object{Ellipse}
     oversample = 3
     img = phantom(x, y, objects, oversample)
     jim(x, y, img; title, clim=(0,1300))

docs/lit/examples/10-mri-sense.jl

@@ -27,7 +27,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: ellipse_parameters, SheppLoganBrainWeb, Ellipse
+using ImagePhantoms: ellipse_parameters, SheppLoganBrainWeb, ellipse
 using ImagePhantoms: phantom, mri_smap_fit, mri_spectra
 using FFTW: fft, fftshift
 using ImageGeoms: embed
@@ -42,9 +42,9 @@ using Unitful: mm
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
-# ### Overview
-
 #=
+### Overview
+
 Modern MRI scanners use multiple receive coils
 each of which has its own "sensitivity map" (or "coil profile").
 Realistic MRI simulations should account for the effects of those
@@ -82,14 +82,16 @@ dx, dy = fovs ./ (nx,ny)
 x = (-(nx÷2):(nx÷2-1)) * dx
 y = (-(ny÷2):(ny÷2-1)) * dy
 
-# Define Shepp-Logan phantom object,
-# with random complex phases
-# to make it a bit more realistic.
+#=
+Define Shepp-Logan phantom object,
+with random complex phases
+to make it a bit more realistic.
+=#
 
 oa = ellipse_parameters(SheppLoganBrainWeb() ; disjoint=true, fovs)
 seed!(0)
 oa[:,end] = [1; randn(ComplexF32, 9)] # random phases
-oa = Ellipse(oa)
+oa = ellipse(oa)
 oversample = 3
 image0 = phantom(x, y, oa, oversample)
 cfun = z -> cat(dims = ndims(z)+1, real(z), imag(z))

docs/lit/examples/30-3d.jl

@@ -26,17 +26,17 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms
-using ImageGeoms: ImageGeom, axesf
-using MIRTjim: jim, prompt
-using UnitfulRecipes
-using Unitful: mm
-using InteractiveUtils: versioninfo
+#src using ImagePhantoms
+#src using ImageGeoms: ImageGeom, axesf
+#src using MIRTjim: jim, prompt
+#src using UnitfulRecipes
+#src using Unitful: mm
 
-# 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 # The following line is helpful when running this file as a script;
+#src # this way it will prompt user to hit a key after each figure is displayed.
+
+#src isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
 #=
@@ -115,15 +115,3 @@ For example projection views,
 see the Ellipsoid examples.
 
 =#
-
-
-# ## 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()

docs/lit/examples/32-ellipsoid.jl

@@ -25,7 +25,8 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Ellipsoid, phantom, radon, spectrum
+using ImagePhantoms: ellipsoid, phantom, radon, spectrum
+using ImagePhantoms: Object, Ellipsoid
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt, mid3
 using FFTW: fft, fftshift
@@ -53,17 +54,18 @@ All of the methods in `ImagePhantoms` support physical units,
 so we use such units throughout this example.
 (Using units is recommended but not required.)
 
-Here are 3 ways to define an ellipsoid object,
+Here are 4 ways to define an `Object{Ellipsoid}`,
 using physical units.
 =#
 
 center = (20mm, 10mm, 5mm)
 radii = (25mm, 35mm, 15mm)
 ϕ0s = :(π/6) # symbol version for nice plot titles
 angles = (eval(ϕ0s), 0)
-Ellipsoid([20mm, 10mm, 5mm, 25mm, 35mm, 15mm, π/6, 0, 1.0f0]) # Vector{Number}
-Ellipsoid( 20mm, 10mm, 5mm, 25mm, 35mm, 15mm, π/6, 0, 1.0f0 ) # 9 arguments
-ob = Ellipsoid(center, radii, angles, 1.0f0) # tuples (recommended use)
+Object(Ellipsoid(), center, radii, angles, 1.0f0) # top-level constructor
+ellipsoid([20mm, 10mm, 5mm, 25mm, 35mm, 15mm, π/6, 0, 1.0f0]) # Vector{Number}
+ellipsoid( 20mm, 10mm, 5mm, 25mm, 35mm, 15mm, π/6, 0, 1.0f0 ) # 9 arguments
+ob = ellipsoid(center, radii, angles, 1.0f0) # tuples (recommended use)
 
 
 #=

docs/lit/examples/33-cuboid.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Cuboid, phantom, radon, spectrum
+using ImagePhantoms: cuboid, phantom, radon, spectrum
 import ImagePhantoms as IP
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt, mid3
@@ -54,7 +54,7 @@ All of the methods in `ImagePhantoms` support physical units,
 so we use such units throughout this example.
 (Using units is recommended but not required.)
 
-Here are 3 ways to define a 3D cuboid object,
+Here are 3 ways to define a 3D `Object{Cuboid}`,
 using physical units.
 =#
 
@@ -63,9 +63,9 @@ width = (35mm, 25mm, 15mm)
 ϕ0s = :(π/6) # symbol version for nice plot titles
 ϕ0 = eval(ϕ0s)
 angles = (ϕ0, 0)
-Cuboid([10mm, 8mm, 6mm, 35mm, 25mm, 15mm, π/6, 0, 1.0f0]) # Vector{Number}
-Cuboid( 10mm, 8mm, 6mm, 35mm, 25mm, 15mm, π/6, 0, 1.0f0 ) # 9 arguments
-ob = Cuboid(center, width, angles, 1.0f0) # tuples (recommended use)
+cuboid([10mm, 8mm, 6mm, 35mm, 25mm, 15mm, π/6, 0, 1.0f0]) # Vector{Number}
+cuboid( 10mm, 8mm, 6mm, 35mm, 25mm, 15mm, π/6, 0, 1.0f0 ) # 9 arguments
+ob = cuboid(center, width, angles, 1.0f0) # tuples (recommended use)
 
 
 #=

docs/lit/examples/34-gauss3.jl

@@ -25,7 +25,7 @@ This page was generated from a single Julia file:
 
 # Packages needed here.
 
-using ImagePhantoms: Gauss3, phantom, radon, spectrum
+using ImagePhantoms: gauss3, phantom, radon, spectrum
 import ImagePhantoms as IP
 using ImageGeoms: ImageGeom, axesf
 using MIRTjim: jim, prompt, mid3
@@ -54,17 +54,17 @@ All of the methods in `ImagePhantoms` support physical units,
 so we use such units throughout this example.
 (Using units is recommended but not required.)
 
-Here are 3 ways to define a 3D gaussian object,
+Here are 3 ways to define a 3D `Object{Gauss3}`,
 using physical units.
 =#
 
 center = (20mm, 10mm, 5mm)
 width = (25mm, 35mm, 15mm)
 ϕ0s = :(π/6) # symbol version for nice plot titles
 angles = (eval(ϕ0s), 0)
-Gauss3([40mm, 20mm, 2mm, 25mm, 35mm, 12mm, π/6, 0, 1.0f0]) # Vector{Number}
-Gauss3(20mm, 20mm, 2mm, 25mm, 35mm, 12mm, π/6, 0, 1.0f0) # 9 arguments
-ob = Gauss3(center, width, angles, 1.0f0) # tuples (recommended use)
+gauss3([40mm, 20mm, 2mm, 25mm, 35mm, 12mm, π/6, 0, 1.0f0]) # Vector{Number}
+gauss3(20mm, 20mm, 2mm, 25mm, 35mm, 12mm, π/6, 0, 1.0f0) # 9 arguments
+ob = gauss3(center, width, angles, 1.0f0) # tuples (recommended use)
 
 
 #=