All of the examples can be found in Jupyter notebook form here.

Tomography

Tomography is the process of reconstructing a density distribution from given integrals over sections of the distribution. In our example, we will work with tomography on black and white images. Suppose $x$ be the vector of $n$ pixel densities, with $x_j$ denoting how white pixel $j$ is. Let $y$ be the vector of $m$ line integrals over the image, with $y_i$ denoting the integral for line $i$. We can define a matrix $A$ to describe the geometry of the lines. Entry $A_{ij}$ describes how much of pixel $j$ is intersected by line $i$. Assuming our measurements of the line integrals are perfect, we have the relationship that

\[ y = Ax\]

However, anytime we have measurements, there are usually small errors that occur. Therefore it makes sense to try to minimize

\[ \|y - Ax\|_2^2.\]

This is simply an unconstrained least squares problem; something we can readily solve!

using Convex, ECOS, DelimitedFiles, SparseArrays
aux(str) = joinpath(@__DIR__, "aux_files", str) # path to auxiliary files
line_mat_x = readdlm(aux("tux_sparse_x.txt"))
summary(line_mat_x)

line_mat_y = readdlm(aux("tux_sparse_y.txt"))
summary(line_mat_y)

line_mat_val = readdlm(aux("tux_sparse_val.txt"))
summary(line_mat_val)

line_vals = readdlm(aux("tux_sparse_lines.txt"))
summary(line_vals)
"3300×1 Array{Float64,2}"

Form the sparse matrix from the data Image is 50 x 50

img_size = 50
50

The number of pixels in the image

num_pixels = img_size * img_size

line_mat = spzeros(length(line_vals), num_pixels)

num_vals = length(line_mat_val)

for i in 1:num_vals
  x = Int(line_mat_x[i])
  y = Int(line_mat_y[i])
  line_mat[x + 1, y + 1] = line_mat_val[i]
end

pixel_colors = Variable(num_pixels)
# line_mat * pixel_colors should be close to the line_integral_values
# to reflect that, we minimize a norm
objective = sumsquares(line_mat * pixel_colors - line_vals)
problem = minimize(objective)
solve!(problem, () -> ECOS.Optimizer(verbose=0))

rows = zeros(img_size*img_size)
cols = zeros(img_size*img_size)
for i = 1:img_size
  for j = 1:img_size
    rows[(i-1)*img_size + j] = i
    cols[(i-1)*img_size + j] = img_size + 1 - j
  end
end

Plot the image using the pixel values obtained!

using Plots
image = reshape(evaluate(pixel_colors), img_size, img_size)
heatmap(image, yflip=true, aspect_ratio=1, colorbar=nothing, color=:grays)

This page was generated using Literate.jl.