Add `:mesh3d` seriesstyle for PyPlot backend #3835

lmh91 · 2021-09-21T09:34:39Z

I added the support for the seriestype :mesh3d for the PyPlot backend.

The inputs are the vertices of a mesh and the connections have to be specified via the connections keyword
similar to https://docs.juliaplots.org/latest/generated/plotlyjs/#plotlyjs-ref47.
However, there is a difference in the syntax of how the connections are specified.
Here, it takes ::Vector{Vector{Ints}} where each element of the outer vector defines a single polygon.
Combinations of different polygons are possible as it is shown in the following example:

    using Plots
    pyplot()
    T = Float64
    p0 = T[0,0,0]
    p1 = T[1,0,0]
    p2 = T[0,1,0]
    p3 = T[1,1,0]
    p4 = T[1/2,1/2,1]
    pts = [p0, p1, p2, p3, p4]
    x, y, z = broadcast(i -> getindex.(pts, i), (1,2,3))

    plot(x, y, z, # [x[i],y[i],z[i]] is the i-th vertix of the mesh
        st=:mesh3d, 
        connections = [
            [1, 2, 4, 3], # Quadrangle 
            [1, 2, 5], # Triangle
            [2, 4, 5], # Triangle
            [4, 3, 5], # Triangle
            [3, 1, 5]  # Triangle
        ], 
        linecolor = :black,
        fillcolor = :blue,
        linewidth = 2,
        legend = true,
        label = "Pyramide",
        fillalpha = 0.2
    )

I hope I did everything correct and please let me know if something should be implemented in a different way.

via `Poly3DCollection`.

t-bltg · 2021-09-21T09:45:07Z

I'm wondering if we can unify all backends on the connections keyword, maybe not draw only triangles as with

Plots.jl/src/utils.jl

Line 1184 in 5a48002

function mesh3d_triangles(x, y, z, cns)

, but arbitrary polygons.

BTW, could you add the connections kw to the backends supporting mesh3d (GR, Gaston, others ?) in src/backends.jl: it seems they are missing and they now pop up as a warning because of #3816.

Please also update the Pyplot examples by removing #47 in the list of skipped examples:

Plots.jl/src/examples.jl

Line 1238 in 4d40bae

:pyplot => [2, 25, 30, 31, 47, 49, 55],

for the docs.

Otherwise LGTM at first glance.

codecov · 2021-09-21T09:51:20Z

Codecov Report

Merging #3835 (2b4e74c) into master (0cd8124) will decrease coverage by 0.25%.
The diff coverage is 9.37%.

@@            Coverage Diff             @@
##           master    #3835      +/-   ##
==========================================
- Coverage   63.50%   63.25%   -0.26%     
==========================================
  Files          28       28              
  Lines        7464     7489      +25     
==========================================
- Hits         4740     4737       -3     
- Misses       2724     2752      +28

Impacted Files	Coverage Δ
src/backends.jl	`63.47% <ø> (ø)`
src/backends/pgfplotsx.jl	`61.17% <0.00%> (-0.38%)`	⬇️
src/examples.jl	`61.97% <ø> (ø)`
src/utils.jl	`52.85% <11.11%> (-1.93%)`	⬇️
src/args.jl	`73.46% <0.00%> (-0.58%)`	⬇️
src/backends/unicodeplots.jl	`75.00% <0.00%> (ø)`
src/backends/gr.jl	`89.42% <0.00%> (+0.08%)`	⬆️
src/colorbars.jl	`92.72% <0.00%> (+1.81%)`	⬆️

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for the backends which support `:mesh3d` as series type.

lmh91 · 2021-09-21T10:41:48Z

Thanks for the feedback.

I removed #47 for pyplot from the list of skipping examples and added the :connections kw to the backends which have :mesh3d in their list of supported seriestypes.

Hmm, I could add a method for mesh3d_triangles which dispatch on cns. I should be able to add support of the current syntax for only triangles to the pyplot backend.

lmh91 · 2021-09-21T11:39:59Z

Okay, I did not add a new method but added the support of the current (only-triangle) syntax for :connections
directly in src/backends/pyplot.jl under st ==:mesh3d.

The example from the docs https://docs.juliaplots.org/latest/generated/plotlyjs/#plotlyjs-ref47
works now also with pyplot. I just added an alpha value here such that the structure becomes visible.

x = [0, 1, 2, 0]
y = [0, 0, 1, 2]
z = [0, 2, 0, 1]
i = [0, 0, 0, 1]
j = [1, 2, 3, 2]
k = [2, 3, 1, 3]

mesh3d(x, y, z; connections = (i, j, k), 
    title = "triangles", xlabel = "x", ylabel = "y", zlabel = "z", 
    legend = :none, margin = 2 * Plots.mm, alpha = 0.2)

I am not fan of that syntax though as it uses 0-based indexing...

t-bltg · 2021-09-21T11:55:51Z

I am not fan of that syntax though as it uses 0-based indexing...

Yep, I don't know who chose this (one argument maybe is that most meshing libraries are written in C/C++/Python, hence the 0 based).

It bothers me a little to have 0 based indexing for triangles and 1 based for arbitrary polygons. What is the Matlab indexing based on for the triangulation in https://www.mathworks.com/help/matlab/ref/trimesh.html ? I think it's 1 based (https://mathworks.com/help/matlab/ref/delaunayn.html).

If it were me, I'd vote to unify this to 1 based indexing ...

for PyPlot

lmh91 · 2021-09-21T11:57:03Z

Sorry for the force push. I forgot to delete one debugging line in the first place.

t-bltg · 2021-09-21T11:59:00Z

Sorry for the force push. I forgot to delete one debugging line in the first place.

No worries, I also use (and certainly abuse) the force push 😆 .

lmh91 · 2021-09-21T12:31:04Z

I would also vote for 1 and I would prefer Vector{NTuple{N, Int}} (length M) or Matrix{Int} (size = NxM)
so one would have a similar syntax for meshes only containing quadrangles.

As this would be a breaking change we could leave the 0-based syntax with a deprecation warning and add the new 1-based synatx in parallel. Since we could dispatch on NTuple{3, Vector{Int}} (current syntax) and Vector{NTuple{N,Int} or Matrix{Int} for meshes with only one type of polygon.

t-bltg · 2021-09-21T12:38:12Z

I would also vote for 1 and I would prefer Vector{NTuple{N, Int}} (length M) or Matrix{Int} (size = NxM)
so one would have a similar syntax for meshes only containing quadrangles.

As this would be a breaking change we could leave the 0-based syntax with a deprecation warning and add the new 1-based synatx in parallel. Since we could dispatch on NTuple{3, Vector{Int}} (current syntax) and Vector{NTuple{N,Int} or Matrix{Int} for meshes with only one type of polygon.

This looks reasonable, but it'd be better if we had complementary opinions on this matter.
Maybe @BeastyBlacksmith knows the reason behind 0 based indexing ?

BeastyBlacksmith · 2021-09-21T12:46:45Z

mesh3d was started in #2909, so the answer to the indexing is probabably: because plotly does (pgfplots also IIRC)

lmh91 · 2021-09-22T11:27:08Z

I would really suggest to use the 1-based julia way for the standard array types.

As Julia supports the definition of Array types which are 0-based (or actually any starting index),
one who would like to use 0-based indexing for the connections can do so, but would have to wrap his coordinate vectors x,
y and z into the 0-based array types. And internally the connections are anyhow increase with .+1
to setup the points for the plotly backend in mesh3d_triangles.

But I am open to implement it in any way. Just tell my :)

BeastyBlacksmith · 2021-09-22T11:41:04Z

As this would be a breaking change we could leave the 0-based syntax with a deprecation warning and add the new 1-based synatx in parallel. Since we could dispatch on NTuple{3, Vector{Int}} (current syntax) and Vector{NTuple{N,Int} or Matrix{Int} for meshes with only one type of polygon.

I am okay with this. There is no need for users to wrap their coordinate vectors though, we can do the neccessary +/-1 internally.

lmh91 · 2021-09-22T13:35:49Z

Okay, I added the 1-based syntax for :connections via dispatching on AbstractVector{NTuple{3,T}}.
The 0-based syntax still works with :connections <: Tuple{Array,Array,Array}.
I hope I did it for all backends which support :mesh3d correctly. I was not able to test all of them on my system.

I also updated the example #47.

t-bltg · 2021-09-22T13:56:27Z

I was not able to test all of them on my system.

I've modified your post, could you tick which backends you have tested ? (GR is automagically tested in the CI).

lmh91 · 2021-09-22T14:36:30Z

I changed the system and was able to test all (comparing the plots produced by the two different syntax) successfully.

BeastyBlacksmith · 2021-09-22T15:15:48Z

Thanks a lot. I would appreciate, if you can have a look into #3503 to see, if your information is correct.

j-fu · 2021-09-22T20:19:46Z

Hi, great work! I have seen this with the update to 1.22.2 . Is there a way to do Gouraud shading based on a vector of point colors or a colormap ? Can triangle colors be specified ? I am asking specifically for the GR backend, because it's fast, and OpenGL supports all this.

t-bltg · 2021-09-22T20:44:50Z

Hi, great work! I have seen this with the update to 1.22.2 . Is there a way to do Gouraud shading based on a vector of point colors or a colormap ? Can triangle colors be specified ? I am asking specifically for the GR backend, because it's fast, and OpenGL supports all this.

Not yet (it was evoked when I wrote #3612), but it shouldn't be too hard to implement if GR supports this ...

lmh91 · 2021-09-22T20:47:26Z

I am actually in contact with Josef Heinen (GR.jl) regarding face colors. I hope we can add this soon.

j-fu · 2021-09-23T09:43:07Z

I am actually in contact with Josef Heinen (GR.jl) regarding face colors. I hope we can add this soon.

As I said, two modi would be interesting: node-wise coloring with color interpolation (Gouraud shading)
and face-wise coloring (flat shading). There is also Phong shading which interpolates normal. I find this less relevant as it would smooth out/hide discretization details, but that's a matter of taste.

With this functionality I could complete the Plots backend for GridVisualize.jl...

lmh91 · 2021-09-23T10:05:58Z

I will communicate it to him.

BTW, for the PyPlot backend we could maybe also add some shading option which I found for Poly3DCollections:
https://stackoverflow.com/questions/56864378/how-to-light-and-shade-a-poly3dcollection
via mesh.set_facecolor(rgbNew) where rgbNew can be an vector of colors for each face.

j-fu · 2021-09-23T10:14:22Z

I will communicate it to him.

BTW, for the PyPlot backend we could maybe also add some shading option which I found for Poly3DCollections:
https://stackoverflow.com/questions/56864378/how-to-light-and-shade-a-poly3dcollection
via mesh.set_facecolor(rgbNew) where rgbNew can be an vector of colors for each face.

See also here: https://github.com/j-fu/GridVisualize.jl/blob/main/src/pyplot.jl#L497
So this is flat shading. I did not find Gouraud shading for this case.

OTOH pyplot is a bit overloaded performance-wise for this purpose, and the visual quality of the plots not that good (of course I could have missed some tricks here..).

Add :mesh3d seriesstyle for PyPlot backend

c9d8ac1

via `Poly3DCollection`.

t-bltg added the extension new behaviour label Sep 21, 2021

lmh91 added 2 commits September 21, 2021 12:35

Add :connections to lists of supported keywords

7951523

for the backends which support `:mesh3d` as series type.

Remove JuliaPlots#47 from list of skipping examples for PyPlot

20c5288

Add support for only-triangle syntax for :connections kw

3051adf

for PyPlot

lmh91 force-pushed the poly_mesh_3d branch from 263c96a to 3051adf Compare September 21, 2021 11:56

lmh91 added 3 commits September 22, 2021 15:28

Add 1-based indexing syntax for connections kw in :mesh3d

88351f3

Update description for example JuliaPlots#47 (:mesh3d)

2a0aa0f

Hotfix 1-based indexing for mesh3d in pgfplotsx

2b4e74c

t-bltg approved these changes Sep 22, 2021

View reviewed changes

BeastyBlacksmith merged commit 866cb0c into JuliaPlots:master Sep 22, 2021

BeastyBlacksmith mentioned this pull request Sep 22, 2021

Feature Request: trisurf_plot aka mesh3d #392

Closed

lmh91 mentioned this pull request Sep 22, 2021

Mesh Plotting JuliaPhysics/SolidStateDetectors.jl#218

Merged

lmh91 mentioned this pull request Oct 7, 2021

Use GR.polygonmesh3d for :mesh3d seriestype #3868

Merged

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Add `:mesh3d` seriesstyle for PyPlot backend #3835

Add `:mesh3d` seriesstyle for PyPlot backend #3835

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Add :mesh3d seriesstyle for PyPlot backend #3835

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Add `:mesh3d` seriesstyle for PyPlot backend #3835

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