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Added 3D Shepp-Logan and array type modification #154

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Added 3D Shepp-Logan and array type modification #154

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ebce189
added 3D Shepp-Logan support
hzarei4 May 30, 2024
ae70d26
optimized 3D shepp-logan
hzarei4 Jun 10, 2024
c965784
added type modification
hzarei4 Jun 11, 2024
2fac621
N, M size correction
hzarei4 Jun 11, 2024
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4 changes: 3 additions & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,18 @@ ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
NDTools = "98581153-e998-4eef-8d0d-5ec2c052313d"
OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
StringDistances = "88034a9c-02f8-509d-84a9-84ec65e18404"

[compat]
AxisArrays = "0.3, 0.4"
ColorTypes = "0.8, 0.9, 0.10, 0.11"
FileIO = "1"
ImageIO = "0.3, 0.4, 0.5, 0.6"
ImageMagick = "1"
FileIO = "1"
OffsetArrays = "1"
StringDistances = "0.10, 0.11"
julia = "1.3"
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78 changes: 54 additions & 24 deletions src/TestImages.jl
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Expand Up @@ -4,6 +4,8 @@ using Pkg.Artifacts
using StringDistances
using ColorTypes
using ColorTypes.FixedPointNumbers
using NDTools: reorient
using StaticArrays
const artifacts_toml = abspath(joinpath(@__DIR__, "..", "Artifacts.toml"))

export testimage, testimage_dip3e
Expand Down Expand Up @@ -197,14 +199,22 @@ MRI version [2] is calculated.

[3] Jain, Anil K. Fundamentals of digital image processing. _Prentice-Hall, Inc._, (1989): 439.
"""
function shepp_logan(N::Int, M::Int; high_contrast::Bool=true, highContrast=nothing)
function shepp_logan(::Type{T}, N::Int, M::Int, O::Int; high_contrast::Bool=true, highContrast=nothing) where {T}
#println("shepp_logan function called")
if !isnothing(highContrast)
# compatbitity to Images.shepp_logan
# remove this when we remove Images.shepp_logan
Base.depwarn("keyword `highContrast` is deprecated, use `high_contrast` instead.", :shepp_logan)
end
x = Array(range(-1, stop=1, length=M)')
y = Array(range(1, stop=-1, length=N))
x = reorient(Array(range(-1, stop=1, length=N)), Val(1))
y = reorient(Array(range(-1, stop=1, length=M)), Val(2))
if O == 1
z = [0.0]
else
z = reorient(Array(range(-1, stop=1, length=O)), Val(3))
#println("z: ", z)
end
#z = Array(range(-1, stop=1, length=O))

# follow the notation in [2]
A = high_contrast ?
Expand All @@ -215,36 +225,56 @@ function shepp_logan(N::Int, M::Int; high_contrast::Bool=true, highContrast=noth
# [3] p.439 uses the following setting for the CT version
# and is used by MATLAB's built-in `phantom` with method `Shepp-Logan`
# (1.0 , -0.98 , -0.02 , -0.02 , 0.01, 0.01 , 0.01 , 0.01 , 0.01 , 0.01 )
x₀ = (0.0 , 0.0 , 0.22 , -0.22 , 0.0 , 0.0 , 0.0 , -0.08 , 0.0 , 0.06 )
y₀ = (0.0 , -0.0184, 0.0 , 0.0 , 0.35, 0.1 , -0.1 , -0.605, -0.605, -0.605)
a = (0.69, 0.6624, 0.11 , 0.16 , 0.21, 0.046, 0.046, 0.046, 0.023, 0.023)
b = (0.92, 0.874 , 0.31 , 0.41 , 0.25, 0.046, 0.046, 0.023, 0.023, 0.046)
ϕ = (0.0 , 0.0 , -18.0 , 18.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 )

function _ellipse(dx, dy, a, b, sin_ϕ, cos_ϕ)
tx = cos_ϕ * dx + sin_ϕ * dy
ty = sin_ϕ * dx - cos_ϕ * dy
abs2(tx * b) + abs2(ty * a) < (a * b)^2
x₀ = (0.0 , 0.0 , 0.22 , -0.22 , 0.0 , 0.0 , 0.0 , -0.08 , 0.0 , 0.06 )
y₀ = (0.0 , -0.0184, 0.0 , 0.0 , 0.35 , 0.1 , -0.1 , -0.605, -0.605, -0.605)
z₀ = (0.0 , 0.0 , 0.0 , 0.0 , -0.15 , 0.25 , 0.25 , 0.0 , 0.0 , 0.0)
a = (0.69, 0.6624, 0.11 , 0.16 , 0.21 , 0.046, 0.046, 0.046, 0.023, 0.023)
b = (0.92, 0.874 , 0.31 , 0.41 , 0.25 , 0.046, 0.046, 0.023, 0.023, 0.046)
c = (0.81, 0.780 , 0.22 , 0.28 , 0.41 , 0.050, 0.050, 0.050, 0.020, 0.020)
ϕ = (0.0 , 0.0 , -18.0 , 18.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 )
θ = (0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 )
ψ = (0.0 , 0.0 , 10.0 , 10.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 )

@inline function mat_mul(t::SVector{N, T}, matrix_c::SMatrix{N,N,T})::SVector{N,T} where {N,T}
return matrix_c * t
end

@inline function mat_div(t::SVector{N, T}, v::SVector{N, T})::SVector{N,T} where {N,T}
return t ./ v
end
function _ellipse(dx, dy, a, b)
# a faster case when ϕ == 0.0
abs2(dx * b) + abs2(dy * a) < (a * b)^2
@inline function sum_abs2(t::SVector{N, T})::T where {N,T}
return sum(abs2.(t))
end

P = zeros(Gray{Float64}, N, M)
P = zeros(T, N, M, O)
for l = 1:length(ϕ)
if ϕ[l] == 0.0
@. P = gray(P) + A[l] * _ellipse(x - x₀[l], y - y₀[l], a[l], b[l])
if ϕ[l] == 0.0 && θ[l] == 0.0 && ψ[l] == 0.0

R = SMatrix{3, 3, Float64}([
1.0 0.0 0.0;
0.0 1.0 0.0;
0.0 0.0 1.0
])
else
sin_ϕ, cos_ϕ = sincosd(ϕ[l])
@. P = gray(P) + A[l] * _ellipse(x - x₀[l], y - y₀[l], a[l], b[l], sin_ϕ, cos_ϕ)
sinϕ, cosϕ = sincosd(ϕ[l])
sinθ, cosθ = sincosd(θ[l])
sinψ, cosψ = sincosd(ψ[l])

R = SMatrix{3, 3, Float64}([
(cosψ*cosϕ-cosθ*sinψ*sinϕ) (cosψ*sinϕ+cosθ*sinψ*cosϕ) (sinψ*sinθ);
(-sinψ*cosϕ-cosθ*cosψ*sinϕ) (-sinψ*sinϕ+cosθ*cosψ*cosϕ) (cosψ*sinθ);
(sinθ*sinϕ) (-sinθ*cosϕ) (cosθ)
])

end
end
P .+= T(A[l]) .* (sum_abs2.(mat_div.(mat_mul.(SVector{3, Float64}.(x .- x₀[l], y .- y₀[l], z .- z₀[l]), Ref(R)) , Ref(SVector{3, Float64}(a[l], b[l], c[l])))) .<= 1.0)

end
return P
end
shepp_logan(N::Integer, M::Integer; kwargs...) = shepp_logan(Int(N), Int(M); kwargs...)
shepp_logan(N::Integer; kwargs...) = shepp_logan(Int(N), Int(N); kwargs...)
shepp_logan(N::Integer, M::Integer, O::Integer; kwargs...) = shepp_logan(Gray{Float64}, Int(N), Int(M), Int(O); kwargs...)
shepp_logan(N::Integer, M::Integer; kwargs...) = shepp_logan(Gray{Float64}, Int(N), Int(M), 1; kwargs...)[:, :, 1]
shepp_logan(N::Integer; kwargs...) = shepp_logan(Gray{Float64}, Int(N), Int(N), 1; kwargs...)[:, :, 1]

function _precompile_()
ccall(:jl_generating_output, Cint, ()) == 1 || return nothing
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