In-situ visualization #0: Make GLMakie available in 2D TreeMesh VisualizationCallback #2225

benegee · 2025-01-09T10:41:41Z

This is the first step in reintegrating @s6nistam's work on in-situ visualization.

As an alternative to Plots.jl it adds plotting with GLMakie for 2D TreeMesh setups.

github-actions · 2025-01-09T10:41:54Z

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Created with ❤️ by the Trixi.jl community.

codecov · 2025-01-12T13:13:29Z

Codecov Report

Attention: Patch coverage is 13.51351% with 32 lines in your changes missing coverage. Please review.

Project coverage is 96.34%. Comparing base (6149104) to head (72ac1cc).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
ext/TrixiMakieExt.jl	0.00%	27 Missing ⚠️
..._dgsem/elixir_advection_amr_visualization_makie.jl	0.00%	4 Missing ⚠️
src/callbacks_step/visualization.jl	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2225      +/-   ##
==========================================
- Coverage   96.42%   96.34%   -0.08%     
==========================================
  Files         487      488       +1     
  Lines       39345    39376      +31     
==========================================
  Hits        37935    37935              
- Misses       1410     1441      +31

Flag	Coverage Δ
unittests	`96.34% <13.51%> (-0.08%)`	⬇️

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sloede · 2025-01-16T12:44:34Z

Nice! Looking forward to this!

benegee · 2025-01-20T11:13:23Z

Ready for review @trixi-framework/developers .

This PR involves places I have not been before (visualization, packages extensions, ...). Any feedback or hints would be highly appreciated.

DanielDoehring · 2025-01-20T11:16:13Z

examples/tree_2d_dgsem/elixir_advection_amr_visualization_makie.jl

+visualization = VisualizationCallback(interval = 100, clims = (0, 1),
+                                      plot_creator = Trixi.show_plot_makie)


Since this is the first time this is used you could maybe explain the kwargs here (again)? Similar to

Trixi.jl/examples/tree_1d_dgsem/elixir_advection_basic.jl

Lines 13 to 29 in 6149104

coordinates_min = -1.0 # minimum coordinate

coordinates_max = 1.0 # maximum coordinate

# Create a uniformly refined mesh with periodic boundaries

mesh = TreeMesh(coordinates_min, coordinates_max,

initial_refinement_level = 4,

n_cells_max = 30_000) # set maximum capacity of tree data structure

# A semidiscretization collects data structures and functions for the spatial discretization

semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergence_test,

solver)

###############################################################################

# ODE solvers, callbacks etc.

# Create ODE problem with time span from 0.0 to 1.0

ode = semidiscretize(semi, (0.0, 1.0))

Thanks for catching this! We now use the correct arguments and added some comments.

DanielDoehring · 2025-01-20T11:18:09Z

src/callbacks_step/visualization.jl

+    # prevents anyone from using other packages, given that appropriate `plot_creator`s are
+    # passed.
+
+    # TODO: rest of this comment?


This should be resolved in the merged source code.

Yes, definitely!
I just need some explanation about the Requires.jl stuff.

@sloede It's been a while since you added this note. Could you help with updating it?

…ee/Trixi.jl into bg/makie-2d-visualization-callback

ranocha

Nice! I just had a quick look. This definitely should get an entry in NEWS.md

ext/TrixiGLMakieExt.jl

ranocha · 2025-01-20T14:04:51Z

src/callbacks_step/visualization.jl

@@ -166,7 +179,7 @@ function (visualization_callback::VisualizationCallback)(integrator)
 end

 """
-    show_plot(plot_data, variable_names;
+    show_plot(visualization_callback, plot_data, variable_names;


There are changes to documented API, so this is breaking. We should either enable the previous behavior again or include this only in a breaking release.

True!
In fact, I did not think about someone calling show_plot directly. For the callback it is only called internally.
Waiting for a breaking release would of course be fine.

I guess nobody is using it actively, but it's documented API.

ranocha · 2025-01-20T14:05:41Z

Project.toml

@@ -55,11 +55,13 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 [weakdeps]
 Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"


Does it need to be GLMakie.jl, or could it be also one of the other backends?

Having the 3D case in mind, it would be nice if you could interactively turn your plot around.

But I am not sufficiently familiar with Makie. Can you make the implementation independent of a certain backend?

Apparently that is how it is supposed to work. I feel amazed...

I now removed the GLMakie extension and moved its content to our existing Makie extension. For the added elixir both using GLMakie and using CairoMakie work (although the latter might not be too useful).

moved stuff to Makie extension

ranocha · 2025-01-21T12:28:45Z

I converted this to a draft PR so that nobody accidentally merges it.

s6nistam and others added 6 commits September 23, 2024 09:43

ParaviewCatalyst callback working except PlotData3D

6607023

Merge branch 'main' of github.com:benegee/Trixi.jl

44db6aa

Merge branch 'main' of github.com:benegee/Trixi.jl

88e35f7

Merge branch 'main' of github.com:benegee/Trixi.jl

46feed1

GLMakie 2D VisualizationCallback

d1a6122

delete extra files

034fa5a

benegee added 3 commits January 9, 2025 11:42

delete another file

716352e

wrong comment

a81e8dc

remove leftovers from testing

24fbffe

benegee added 3 commits January 16, 2025 17:48

types for Figure and Axis

d7540dc

use FigureAndAxes struct

9727d3f

format

2f0562b

benegee marked this pull request as ready for review January 20, 2025 11:09

Merge branch 'main' into bg/makie-2d-visualization-callback

5bd1c3a

DanielDoehring requested changes Jan 20, 2025

View reviewed changes

benegee added 3 commits January 20, 2025 12:56

pass plot_arguments to heatmap

4d0e9d3

explain kwargs

dab3337

Merge branch 'bg/makie-2d-visualization-callback' of github.com:beneg…

b5f8b52

…ee/Trixi.jl into bg/makie-2d-visualization-callback

ranocha requested changes Jan 20, 2025

View reviewed changes

benegee added 4 commits January 20, 2025 17:19

snake case

fda5f4f

import what is necessary only

4d401fa

removed GLMakie extensions

1fc1d92

moved stuff to Makie extension

format

72ac1cc

ranocha added visualization breaking labels Jan 21, 2025

ranocha mentioned this pull request Jan 17, 2025

Release v0.10 #2105

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ranocha marked this pull request as draft January 21, 2025 12:28

benegee mentioned this pull request Jan 23, 2025

Contours via Plots.jl are supported for TreeMesh #2230

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In-situ visualization #0: Make GLMakie available in 2D TreeMesh VisualizationCallback #2225

In-situ visualization #0: Make GLMakie available in 2D TreeMesh VisualizationCallback #2225

benegee commented Jan 9, 2025

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ranocha commented Jan 21, 2025

		visualization = VisualizationCallback(interval = 100, clims = (0, 1),
		plot_creator = Trixi.show_plot_makie)

	coordinates_min = -1.0 # minimum coordinate
	coordinates_max = 1.0 # maximum coordinate

	# Create a uniformly refined mesh with periodic boundaries
	mesh = TreeMesh(coordinates_min, coordinates_max,
	initial_refinement_level = 4,
	n_cells_max = 30_000) # set maximum capacity of tree data structure

	# A semidiscretization collects data structures and functions for the spatial discretization
	semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergence_test,
	solver)

	###############################################################################
	# ODE solvers, callbacks etc.

	# Create ODE problem with time span from 0.0 to 1.0
	ode = semidiscretize(semi, (0.0, 1.0))

In-situ visualization #0: Make GLMakie available in 2D TreeMesh VisualizationCallback #2225

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In-situ visualization #0: Make GLMakie available in 2D TreeMesh VisualizationCallback #2225

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benegee commented Jan 9, 2025

github-actions bot commented Jan 9, 2025

Review checklist

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