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Examples

This page illustrates the Julia package MIRTjim.

This page comes from a single Julia file: 1-examples.jl.

You can access the source code for such Julia documentation using the 'Edit on GitHub' link in the top right. You can view the corresponding notebook in nbviewer here: 1-examples.ipynb, or open it in binder here: 1-examples.ipynb.

Setup

Packages needed here.

using MIRTjim: jim, prompt, mid3
using AxisArrays: AxisArray
using ColorTypes: RGB
using OffsetArrays: OffsetArray
using Unitful
using Unitful: μm, s
import Plots
using InteractiveUtils: versioninfo

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);

Simple 2D image

The simplest example is a 2D array. Note that jim is designed to show a function f(x,y) sampled as an array z[x,y] so the 1st index is horizontal direction.

x, y = 1:9, 1:7
f(x,y) = x * (y-4)^2
z = f.(x, y') # 9 × 7 array
jim(z ; xlabel="x", ylabel="y", title="f(x,y) = x * (y-4)^2")
Example block output

Compare with Plots.heatmap to see the differences (transpose, color, wrong aspect ratio, distractingly many ticks):

Plots.heatmap(z, title="heatmap")
Example block output
isinteractive() && prompt();

Images often should include a title, so title = is optional.

jim(z, "hello")
Example block output

OffsetArrays

jim displays the axes naturally.

zo = OffsetArray(z, (-3,-1))
jim(zo, "OffsetArray example")
Example block output

3D arrays

jim automatically makes 3D arrays into a mosaic.

f3 = reshape(1:(9*7*6), (9, 7, 6))
jim(f3, "3D"; size=(600, 300))
Example block output

One can specify how many images per row or column for such a mosaic.

x11 = reshape(1:(5*6*11), (5, 6, 11))
jim(x11, "nrow=3"; nrow=3)
Example block output
jim(x11, "ncol=6"; ncol=6, size=(600, 200))
Example block output

Central slices with mid3

The mid3 function shows the central x-y, y-z, and x-z slices (axial, coronal, sagittal) planes. Making useful xticks and yticks in this case takes some fiddling.

x,y,z = -20:20, -10:10, 1:30
xc = reshape(x, :, 1, 1)
yc = reshape(y, 1, :, 1)
zc = reshape(z, 1, 1, :)
rx = reshape(range(2, 19, length(z)), size(zc))
ry = reshape(range(2, 9, length(z)), size(zc))
cone = @. abs2(xc / rx) + abs2(yc / ry) < 1
jim(mid3(cone); color=:cividis, title="mid3")
xticks = ([1, length(x), length(x)+length(z)],
 ["$(x[begin])", "$(x[end]), $(z[begin])", "$(z[end])"])
yticks = ([1, length(y), length(y)+length(z)],
 ["$(y[begin])", "$(y[end]), $(z[begin])", "$(z[end])"])
Plots.plot!(;xticks , yticks)
Example block output

Arrays of images

jim automatically makes arrays of images into a mosaic.

z3 = reshape(1:(9*7*6), (7, 9, 6))
z4 = [z3[:,:,(j-1)*3+i] for i=1:3, j=1:2]
jim(z4, "Arrays of images")
Example block output

Units

jim supports units, with axis and colorbar units appended naturally.

x = 0.1*(1:9)u"m/s"
y = (1:7)u"s"
zu = x * y'
jim(x, y, zu, "units" ;
    clim=(0,7).*u"m", xlabel="rate", ylabel="time", colorbar_title="distance")
Example block output

Note that aspect_ratio reverts to :auto when axis units differ.

Image spacing is appropriate even for non-square pixels if Δx and Δy have matching units.

x = range(-2,2,201) * 1u"m"
y = range(-1.2,1.2,150) * 1u"m" # Δy ≢ Δx
z = @. sqrt(x^2 + (y')^2) ≤ 1u"m"
jim(x, y, z, "Axis units with unequal spacing"; color=:cividis, size=(600,350))
Example block output

Units are also supported for 3D arrays, but the z-axis is ignored for plotting.

x = (2:9) * 1μm
y = (3:8) * 1/s
z = (4:7) * 1μm * 1s
f3d = rand(8, 6, 4) # * s^2
jim(x, y, z, f3d, "3D with axis units")
Example block output

One can use a tuple for the axes instead; only the x and y axes are used.

jim((x, y, z), f3d, "axes tuple")
Example block output

AxisArrays

jim displays the axes (names and units) naturally by default:

x = (1:9)μm
y = (1:7)μm/s
za = AxisArray(x * y'; x, y)
jim(za, "AxisArray")
Example block output

Color images

jim(rand(RGB{Float32}, 8, 6); title="RGB image")
Example block output

Options

See the docstring for jim for its many options. Here are some defaults.

jim(:defs)
Dict{Symbol, Any} with 22 entries:
  :colorbar     => :legend
  :nrow         => 0
  :line3plot    => true
  :clim         => nothing
  :ncol         => 0
  :ylabel       => nothing
  :title        => ""
  :yflip        => nothing
  :abswarn      => false
  :mosaic_npad  => 1
  :fft0         => false
  :prompt       => false
  :yreverse     => nothing
  :tickdigit    => 1
  :xlabel       => nothing
  :aspect_ratio => :infer
  :line3type    => :yellow
  :padval       => nothing
  :color        => :grays
  ⋮             => ⋮

One can set "global" defaults using appropriate keywords from above list. Use :push! and :pop! for such changes to be temporary.

jim(:push!) # save current defaults
jim(:colorbar, :none) # disable colorbar for subsequent figures
jim(:yflip, false) # have "y" axis increase upward
jim(rand(9,7), "rand", color=:viridis) # kwargs... passed to heatmap()
Example block output
jim(:pop!); # restore

Layout

One can use jim just like plot with a layout of subplots. The gui=true option is useful when you want a figure to appear even when other code follows. Often it is used with the prompt=true option (not shown here). The size option helps avoid excess borders.

p1 = jim(rand(5,7); prompt=false)
p2 = jim(rand(6,8); color=:viridis, prompt=false)
p3 = jim(rand(9,7); color=:cividis, title="plot 3", prompt=false)
jim(p1, p2, p3; layout=(1,3), gui=true, size = (600,200))
Example block output

Reproducibility

This page was generated with the following version of Julia:

using InteractiveUtils: versioninfo
io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
12-element Vector{SubString{String}}:
 "Julia Version 1.10.3"
 "Commit 0b4590a5507 (2024-04-30 10:59 UTC)"
 "Build Info:"
 "  Official https://julialang.org/ release"
 "Platform Info:"
 "  OS: Linux (x86_64-linux-gnu)"
 "  CPU: 4 × AMD EPYC 7763 64-Core Processor"
 "  WORD_SIZE: 64"
 "  LIBM: libopenlibm"
 "  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)"
 "Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)"
 ""

And with the following package versions

import Pkg; Pkg.status()
Status `~/work/MIRTjim.jl/MIRTjim.jl/docs/Project.toml`
  [39de3d68] AxisArrays v0.4.7
  [3da002f7] ColorTypes v0.11.5
  [e30172f5] Documenter v1.4.1
⌃ [9ee76f2b] ImageGeoms v0.10.0
⌃ [71a99df6] ImagePhantoms v0.8.0
  [98b081ad] Literate v2.18.0
  [170b2178] MIRTjim v0.25.0 `~/work/MIRTjim.jl/MIRTjim.jl`
  [6fe1bfb0] OffsetArrays v1.14.0
  [91a5bcdd] Plots v1.40.4
  [1986cc42] Unitful v1.20.0
  [b77e0a4c] InteractiveUtils
Info Packages marked with ⌃ have new versions available and may be upgradable.

This page was generated using Literate.jl.