Out of memory when using Makie with large images

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1

Hi,
I’m having a problem with a big memory footprint when using CairoMakie to plot big images in the REPL. The code consists of loading four images with load and then plotting them using image! (no treatment whatsoever, so I did not include the code, but I can if necessary). If I run the plot code (with the images already loaded) once, it runs fine. But as I run it more times (say, for example, because I’m tweaking some attributes such as xlabel), julia eventually runs out of memory. I noticed a big memory footprint from my axes (1.4GB each!), although the output of varinfos() remains constant. Is there a kind of draft mode to reduce this footprint? (I know I could use GLMakie and tweak using Observables, but I find it more convenient to edit a vim buffer and execute its content with vim-slime).

Output of varinfo() for reference:

 julia --project
julia> varinfo()
  name                    size summary
  –––––––––––––––– ––––––––––– –––––––
  Base                         Module 
  Core                         Module 
  InteractiveUtils 519.661 KiB Module 
  Main                         Module 

# Loading images and modules...

julia> varinfo()
  name                   size summary                                                                        
  –––––––––––––––– –––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
  Base                        Module                                                                         
  Core                        Module                                                                         
  InteractiveUtils  1.184 MiB Module                                                                         
  Main                        Module                                                                         
  ans               2.095 KiB Markdown.MD                                                                    
  img_100nm        48.000 MiB 4096×4096 Array{RGB{N0f8},2} with eltype ColorTypes.RGB{FixedPointNumbers.N0f8}
  img_10nm          1.286 MiB 605×557 Array{RGBA{N0f8},2} with eltype ColorTypes.RGBA{FixedPointNumbers.N0f8}
  img_1um          48.000 MiB 4096×4096 Array{RGB{N0f8},2} with eltype ColorTypes.RGB{FixedPointNumbers.N0f8}
  img_pvktoa       48.000 MiB 4096×4096 Array{RGB{N0f8},2} with eltype ColorTypes.RGB{FixedPointNumbers.N0f8}

julia> 

# plotting once...

julia> varinfo()
  name                   size summary                                                                        
  –––––––––––––––– –––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
  Base                        Module                                                                         
  Core                        Module                                                                         
  InteractiveUtils  1.189 MiB Module                                                                         
  Main                        Module                                                                         
  ans               1.462 GiB Figure                                                                         
  ax_100nm          1.462 GiB Axis                                                                           
  ax_10nm           1.462 GiB Axis                                                                           
  ax_1um            1.462 GiB Axis                                                                           
  ax_toa            1.462 GiB Axis                                                                           
  f                 1.462 GiB Figure                                                                         
  img_100nm        48.000 MiB 4096×4096 Array{RGB{N0f8},2} with eltype ColorTypes.RGB{FixedPointNumbers.N0f8}
  img_10nm          1.286 MiB 605×557 Array{RGBA{N0f8},2} with eltype ColorTypes.RGBA{FixedPointNumbers.N0f8}
  img_1um          48.000 MiB 4096×4096 Array{RGB{N0f8},2} with eltype ColorTypes.RGB{FixedPointNumbers.N0f8}
  img_pvktoa       48.000 MiB 4096×4096 Array{RGB{N0f8},2} with eltype ColorTypes.RGB{FixedPointNumbers.N0f8}
2

After some investigation, it seems to be an issue with the internal type used by Makie (or Cairo?). The following test code (using fixed point numbers for the images):

using CairoMakie, Colors, FixedPointNumbers

CairoMakie.activate!(px_per_unit=3)

imgs = [rand(RGB{N0f8}, 4096, 4096) for _ in 1:4]

varinfo()

f = Figure()

axes = [Axis(f[i, j]) for i in 1:2, j in 1:2]

map(t->image!(t...), zip(axes, imgs))

varinfo()

yields

julia> varinfo()
  name                    size summary                            
  –––––––––––––––– ––––––––––– –––––––––––––––––––––––––––––––––––
  Base                         Module                             
  Core                         Module                             
  InteractiveUtils 866.682 KiB Module                             
  Main                         Module                             
  ans              192.000 MiB 4-element Vector{Matrix{RGB{N0f8}}}
  imgs             192.000 MiB 4-element Vector{Matrix{RGB{N0f8}}}

#plotting ...

julia> varinfo()
  name                    size summary                                                                                                                                             
  –––––––––––––––– ––––––––––– ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
  Base                         Module                                                                                                                                              
  Core                         Module                                                                                                                                              
  InteractiveUtils 871.404 KiB Module                                                                                                                                              
  Main                         Module                                                                                                                                              
  ans                1.955 GiB 4-element Vector{Image{Tuple{StepRangeLen{Float32, Float64, Float64, Int64}, StepRangeLen{Float32, Float64, Float64, Int64}, Matrix{RGB{Float32}}}}}
  axes               1.955 GiB 2×2 Matrix{Axis}                                                                                                                                    
  f                  1.955 GiB Figure                                                                                                                                              
  imgs             192.000 MiB 4-element Vector{Matrix{RGB{N0f8}}}

while if I use RGBf instead of RGB{N0f8} I get:

julia> varinfo()
  name                    size summary                                
  –––––––––––––––– ––––––––––– –––––––––––––––––––––––––––––––––––––––
  Base                         Module                                 
  Core                         Module                                 
  InteractiveUtils 866.635 KiB Module                                 
  Main                         Module                                 
  ans                1.000 GiB 4-element Vector{Matrix{RGBA{Float32}}}
  imgs               1.000 GiB 4-element Vector{Matrix{RGBA{Float32}}}

# Plotting ...

julia> varinfo()
  name                    size summary                                                                                                                                              
  –––––––––––––––– ––––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
  Base                         Module                                                                                                                                               
  Core                         Module                                                                                                                                               
  InteractiveUtils 871.311 KiB Module                                                                                                                                               
  Main                         Module                                                                                                                                               
  ans                1.018 GiB 4-element Vector{Image{Tuple{StepRangeLen{Float32, Float64, Float64, Int64}, StepRangeLen{Float32, Float64, Float64, Int64}, Matrix{RGBA{Float32}}}}}
  axes               1.018 GiB 2×2 Matrix{Axis}                                                                                                                                     
  f                  1.018 GiB Figure                                                                                                                                               
  imgs               1.000 GiB 4-element Vector{Matrix{RGBA{Float32}}}

Does Makie internally convert to RGBAf or something similar?

3

Makie does convert to RGBAf but still it seems weird that so much more memory is taken up than your actual images. I’d have to take a look where this happens, maybe something isn’t gc’ed correctly.

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