This page explains the mask aspects of the Julia package
ImageGeoms.
Packages needed here.
using ImageGeoms: ImageGeom, MaskCircle, MaskAllButEdge
using ImageGeoms: maskit, embed, embed!, getindex! # +jim +size
using ImageGeoms: mask_outline
using MIRTjim: jim, prompt
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);
In tomographic image reconstruction, patients are usually more "round"
than "square" so often we only want to estimate the pixels inside some
support mask: a Bool array indicating which pixels are to be estimated.
(The rest are constrained to be zero.)
The ImageGeom struct has an entry to store this mask.
The default is Trues(dims) which is a "lazy" Bool AbstractArray
from the FillArrays package that is conceptually similar to trues(dims)
but requires O(1) storage. So there is essentially no memory penalty
to storing this entry in the ImageGeom for users who do not want
to think about a mask.
For users who do want a mask, fortunately Julia uses a special BitArray
type to store Bool arrays, so the storage is 8× less than using bytes
in most other languages.
Often we use a "circle inscribed in the square" as a generic support mask, and one of the built-in constructors can generate such a circular mask:
ig = ImageGeom(MaskCircle() ; dims=(40,32), deltas=(1mm,1mm))
That last line shows that 716 of 1280=40*32 mask pixels are nonzero.
jim(ig)
Note that jim displays the axes with the units naturally;
see MIRTjim.jl.
A 3D mask can be hard to visualize, so there is a mask_or method
that collapses it to 2D:
ig = ImageGeom(MaskAllButEdge() ; dims=(32,32,16))
jim(ig)
Often we need to extract the pixel values within a mask:
ig = ImageGeom(MaskAllButEdge() ; dims=(6,4))
x = 1:size(ig,1)
y = 1:size(ig,2)
ramp = x .+ 10*y'
ig.mask
core = ramp[ig.mask]
Or equivalently:
maskit(ramp, ig.mask)
Conversely, we can embed that list of pixels back into an array:
array = embed(core, ig.mask)
There are in-place versions of these two operations:
core = Array{Float32}(undef, sum(ig.mask))
getindex!(core, ramp, ig.mask)
array = collect(zeros(Float16, ig))
embed!(array, core, ig.mask)
Sometimes we need the outline of the mask.
ig = ImageGeom(MaskCircle() ; dims=(40,32))
outline = mask_outline(ig.mask)
jim(
jim(ig.mask, "Mask"; prompt=false),
jim(outline, "Outline"; prompt=false),
)
This notebook was generated using Literate.jl.