Mesh Plotting #218

hervasa2 · 2021-09-16T16:36:39Z

Added mesh plotting for ConeMantle. Supported in pyplot() and gr(). Note that the only way to do this in gr() is using st = :mesh3d which is "experimental". Previously st = :surface was able to properly color the face of a triangle in gr(), now it needs 5 or more points to work, and no longer respects the boundaries set by the points. Therefore :mesh3d must be used. For consistency when surface() or equivalently plot(; st = :surface) is called, pyplot() uses :surface and gr() uses :mesh3d to produce a visually equivalent result. The experimental :mesh3d gives the warning (directly from GR, not from SSD) GR: mesh3d is experimental (no face colors) for each element in the series. As stated, there are no face colors yet, and therefore it will look like a dense wireframe for now.

To achieve the desired plot mesh(cm::ConeMantle{T}) is called. This will return a Mesh{T}. A plot recipe for Mesh is provided. Its fields are 3 matrices, which pyplot() :surface takes as input.
With, gr() this does not work. So we turn to :mesh3d. However, :mesh3d takes arrays as inputs: a list of points just like :path3d. The keyword connections is used to tell how these points assemble into triangles (whose faces will be filled - someday). The function polymesh is provided to turn a Mesh{T} into a PolyMesh{T,4} whose fields are arrays of 4 points. Mesh{T} naturally deconstructs into quadrangels instead of triangles and therefore PolyMesh{T,4} is used. In the future PolyMesh{T,3} will be useful for other meshes which deconstruct more naturally into triangles.

3 examples follow

T = Float64
cylindermantle = CSG.ConeMantle{T,Tuple{T,T},Nothing,:outwards}((1,1),nothing,1,CartesianPoint{T}(0,0,0),RotX(0))
conemantle_tranformed = CSG.ConeMantle{T,Tuple{T,T},Nothing,:outwards}((1,2),nothing,1,CartesianPoint{T}(1,0,0),RotY(π/2))
conemantle_partial = CSG.ConeMantle{T,Tuple{T,T},Tuple{T,T},:outwards}((3,2),(0,3π/2),1,CartesianPoint{T}(0,0,0),RotX(0))

pyplot(); surface(cylindermantle)

gr(); surface(cylindermantle)

pyplot(); surface(conemantle_tranformed)

gr(); surface(conemantle_tranformed)

pyplot(); surface(conemantle_partial)

gr(); surface(conemantle_partial)

src/ConstructiveSolidGeometry/plotting/SurfacePrimitives/ConeMantle.jl

fhagemann · 2021-09-16T19:17:43Z

src/ConstructiveSolidGeometry/plotting/Meshing.jl

+struct PolyMesh{T,N}
+    x::Vector{SVector{N,T}}
+    y::Vector{SVector{N,T}}
+    z::Vector{SVector{N,T}}
 end


Just to clarify: PolyMesh is an auxiliary struct for plotting using mesh3d in GR?

For now this it is its only purpose. However, I will need PolyMesh{T,3} for when I plot surfaces for which I cannot write a analytical mesh. These arbitrary meshes will be generated by the JuliaGeometry/VoronoiDelaunay.jl package and then stored in a PolyMesh{T,3} (which contains vectors of triangle vertices. PolyMesh{T,4} contains vectors of quadrangle vertices). Note that pyplot() understands PolyMesh{T} aswell. So in theory we do not need to check for the backend and can always pass a PolyMesh. But we save time by not doing this in pyplot(). Another reason to use Mesh{T} is that pyplot() looks really nice with this structure.

This all is very annoying... I don't mean you implementation but this whole Plots.jl, GR/PyPlot stuff for 3D plots...

Meshes.jl actually seems to make really nice progress and provides a mesh struct we can use.

using Plots using Meshes T = Float64 p0 = Point3([0,0,0]) px = Point3([1,0,0]) py = Point3([0,1,0]) pz = Point3([0,0,1]) # mesh of three triangles, just as an example mesh = SimpleMesh([p0, px, py, pz], [connect((1, 2, 3)), connect((1, 2, 4))]) plot(mesh)

This produces a wireframe in GR. With PyPlot it throws an error....
I would favor to use the mesh from Meshes.jl and, as they also provide already plot recipes for Plots.jl
(even though they plot usually with MeshViz.jl), talk to them regarding your workaround for plotting nice surfaces via PyPlot to their package. They suggest to contact them via https://julialang.zulipchat.com/#narrow/stream/275558-meshes.2Ejl before making issues on GitHub. Maybe we could also improve/contribute to Plots.jl directly.
And we might talk to Josef Heinen regarding face support from GR.jl.

I know this will increase the time until everything is through, but I think this is the better way and will reduce the amount of code in our package as we would only need to implement the connections for the vertices of our volume primitives to create the meshes.

src/ConstructiveSolidGeometry/plotting/SurfacePrimitives/ConeMantle.jl

fhagemann · 2021-09-16T19:22:22Z

src/ConstructiveSolidGeometry/plotting/SurfacePrimitives/ConeMantle.jl

        end
    end
-     if !haskey(plotattributes, :show_normal) || plotattributes[:show_normal]
+    if !haskey(plotattributes, :show_normal) || plotattributes[:show_normal]


is !haskey intended, i.e. default to plot it if not specified?
I would personally prefer haskey and only plot it if explicitly specified.

This line is not my code, but I agree

Yes, we should set the default to false.

src/ConstructiveSolidGeometry/SurfacePrimitives/ConeMantle.jl

fhagemann · 2021-09-17T05:55:06Z

Will this PR introduce mesh plotting only for ConeMantle or are you planning to add mesh methods for all other primitives in this PR as well?

hervasa2 · 2021-09-17T11:49:14Z

Will this PR introduce mesh plotting only for ConeMantle or are you planning to add mesh methods for all other primitives in this PR as well?

This PR is meant to add mesh methods for all surface primitives. However, I started it with only one, to see if you liked the way its implemented before I proceed

hervasa2 · 2021-09-19T15:15:06Z

Meshing methods for all instances of all surface primitives. This includes 2D meshing for the arbitrary Polygon{N,T}. Support for gr() and pyplot()
in(p::Polygon{4,T}) is now generalized for to in(p::Polygon{N,T}).

The current status of plotting now is:

plot(s::SurfacePrimitive) relies on method lines(s). lines(s) is not available for all instances of a given SurfacePrimitive. eg: no method matching lines(::SolidStateDetectors.ConstructiveSolidGeometry.TorusMantle{Float64, Nothing, Tuple{Float64, Float64}, :outwards})
surface(s::SurfacePrimitive) relies on methods mesh(s) or trimesh(s). It should be complete for all instances of all SurfacePrimitives. Pending review.
scatter(s::SurfacePrimitive) will rely on method sample(s). Previously implemented as SSD_style = :samplesurface. Not started.

Some pyplot() examples follow. All of them have also been tested to work in gr().

src/ConstructiveSolidGeometry/SurfacePrimitives/Plane.jl

lmh91

I think we really should talk to the Plots.jl, GR.jl & PyPlot.jl people and make this right.
Even if this needs some time.
But there seems plenty of other people wanting this feature. So it would be a really nice contribution to the Julia Ecosystem. And it would reduce the amount of code we have to maintain.

lmh91 · 2021-09-20T09:37:24Z

Project.toml

@@ -30,6 +30,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+VoronoiDelaunay = "72f80fcb-8c52-57d9-aff0-40c1a3526986"


I do not see the reason why we would need this dependency.

It also does not seem to be really maintained. Last commit in January and the last release is almost one year old. Also the last issues did not received any comments.

src/ConstructiveSolidGeometry/SurfacePrimitives/Plane.jl

src/ConstructiveSolidGeometry/SurfacePrimitives/Polygon.jl

lmh91 · 2021-09-20T10:11:55Z

src/ConstructiveSolidGeometry/plotting/Meshing.jl

+struct PolyMesh{T,N}
+    x::Vector{SVector{N,T}}
+    y::Vector{SVector{N,T}}
+    z::Vector{SVector{N,T}}
 end


This all is very annoying... I don't mean you implementation but this whole Plots.jl, GR/PyPlot stuff for 3D plots...

Meshes.jl actually seems to make really nice progress and provides a mesh struct we can use.

using Plots using Meshes T = Float64 p0 = Point3([0,0,0]) px = Point3([1,0,0]) py = Point3([0,1,0]) pz = Point3([0,0,1]) # mesh of three triangles, just as an example mesh = SimpleMesh([p0, px, py, pz], [connect((1, 2, 3)), connect((1, 2, 4))]) plot(mesh)

This produces a wireframe in GR. With PyPlot it throws an error....
I would favor to use the mesh from Meshes.jl and, as they also provide already plot recipes for Plots.jl
(even though they plot usually with MeshViz.jl), talk to them regarding your workaround for plotting nice surfaces via PyPlot to their package. They suggest to contact them via https://julialang.zulipchat.com/#narrow/stream/275558-meshes.2Ejl before making issues on GitHub. Maybe we could also improve/contribute to Plots.jl directly.
And we might talk to Josef Heinen regarding face support from GR.jl.

I know this will increase the time until everything is through, but I think this is the better way and will reduce the amount of code in our package as we would only need to implement the connections for the vertices of our volume primitives to create the meshes.

lmh91 · 2021-09-20T10:13:11Z

src/ConstructiveSolidGeometry/plotting/SurfacePrimitives/ConeMantle.jl

        end
    end
-     if !haskey(plotattributes, :show_normal) || plotattributes[:show_normal]
+    if !haskey(plotattributes, :show_normal) || plotattributes[:show_normal]


Yes, we should set the default to false.

lmh91 · 2021-09-22T16:06:04Z

I added mesh plotting via the seriestype :mesh3d into Plots.jl: JuliaPlots/Plots.jl#3835

So, once Plots.jl makes a new release we can remove the special case for the PyPlot backend and do not have to write backend dependent code.
Locally, I just commented out those cases and was able to reproduce your plot pyplot(); surface(cylindermantle) with
pyplot(); surface(cylindermantle, linewidth = 0).

I am in contact with Josef Heinen (GR.jl) to get support of filled faces also in GR.
I will add this into Plots.jl as well as soon as it is in GR.jl.

oschulz · 2021-09-23T10:15:43Z

Awesome!

lmh91 · 2021-10-07T14:48:20Z

Okay, so now it is (will be) also supported by GR :)

JuliaPlots/Plots.jl#3868

lmh91 · 2021-10-08T07:55:13Z

So (once the PR in Plots.jl is through) we only need one struct for a mesh:

I would suggest this:

struct mesh{T}
    x::Array{T}
    y::Array{T}
    z::Array{T}
    connections::Vector{Vector{T}} # We probably could also use `VectorOfVectors` from `ArraysOfArrays.jl`
end

so we can use a recipe like

@recipe function f(m::Mesh)
     seriestype := :mesh3d
     connections =: m.connections
     m.x, m.y, m.z
end

Regarding the structure of connections (They can be given in different ways, see):
It is a Vector{Vector{T}}. Each element (::Vector{T}) describes one Polygon. So we are not limited to triangles:

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))
connections = [ # Pyramide
     [1, 2, 4, 3], # Quadrangle 
     [1, 2, 5], # Triangle
     [2, 4, 5], # Triangle
     [4, 3, 5], # Triangle
     [3, 1, 5]  # Triangle
]

hervasa2 · 2021-10-11T16:42:51Z

Backend independent meshing implementation using development branch of Plots (https://github.com/lmh91/Plots.jl/tree/gr_mesh3d) by @lmh91.

Now there is only one mesh struct used by both pyplot and gr.
Ugly rotations of vertical surfaces is no longer needed.
gr now provides face colors
The connections field of Mesh{T} contains the indices of the points which will form a polygon in the mesh. All meshes use quadrilaterals except Polygon which uses itself.

conemantle_tranformed = CSG.ConeMantle{T,Tuple{T,T},Nothing,:outwards}((1,2),nothing,1,CartesianPoint{T}(1,0,0),RotY(π/2))
es = CSG.EllipticalSurface{T,Tuple{T,T},Nothing}((1,2),nothing, zero(CartesianPoint{T}), RotX(π/6))

n = 6
polygon = CSG.Polygon{n,T}([RotX(π/4)*Pt(cos(i), sin(i),0) for i in 0:2π/n:2π-2π/n])
 
em = CSG.EllipsoidMantle{T,T,Tuple{T,T},Tuple{T,T},:ouwards}(1,(0,3π/2),(0,π/2), zero(CartesianPoint{T}), RotX(0))
 
tm = CSG.TorusMantle{T,Tuple{T,T},Tuple{T,T},:outwards}(2,1,(0,3π/2),(0,3π/2),CartesianPoint{T}(1,1,1), RotX(π/4))

lmh91

Very nice! Just some minor things, see comments.

src/ConstructiveSolidGeometry/plotting/Meshing.jl

lmh91 · 2021-10-13T09:55:38Z

The PR in Plots.jl it through and the release v1.22.6 is on its way.
It should be available soon.

fhagemann · 2021-10-14T14:34:12Z

I tried this out but it didn't work (my Plots was not up to date).
We should somehow adapt the requirements such that the needed version of Plots is loaded.
Any ideas how to do this?

lmh91 · 2021-10-14T14:57:49Z

I tried this out but it didn't work (my Plots was not up to date). We should somehow adapt the requirements such that the needed version of Plots is loaded. Any ideas how to do this?

I asked in the Julia Plotting channel on Slack about this. Maybe there is a way.

fhagemann · 2021-10-14T18:53:06Z

How do I plot the detector using meshes?

fhagemann · 2021-10-14T19:01:08Z

src/ConstructiveSolidGeometry/SurfacePrimitives/SurfacePrimitives.jl

+function _get_n_points_in_arc_φ(p::AbstractSurfacePrimitive, n::Int64)::Int64
+    φMin, φMax = get_φ_limits(p)
+    f = (φMax - φMin)/(2π)
+    Int(ceil(n*f))
+end
+
+function _get_n_points_in_arc_θ(p::AbstractSurfacePrimitive, n::Int64)::Int64
+    θMin, θMax = get_θ_limits(p)
+    f = (θMax - θMin)/(2π)
+    Int(ceil(n*f))
+end


I am getting an error that these functions are not defined when trying to plot a detector.
I guess they need to go before all the includes in this file.

Seems to be on your side. I was just able to plot a detector locally.
Also, the docs build went through where a detector is plotted.
I used:

using Plots, SolidStateDetectors T = Float32 sim = Simulation{T}(SSD_examples[:InvertedCoax]) plot(sim.detector)

mesh plotting for ConeMantle

a983cc5

hervasa2 requested review from lmh91 and fhagemann September 16, 2021 16:36

fhagemann reviewed Sep 16, 2021

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hervasa2 added 6 commits September 17, 2021 13:50

Corrections from Felix

e349314

EllipticalSurface meshing

39c6544

EllipticalSurface mesh transformations

b6b12e8

EllipsoidMantle meshing

7cb0223

TorusMantle meshing

c4acae2

Polygon meshing and mesh changes

cfd85e8

hervasa2 commented Sep 19, 2021

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src/ConstructiveSolidGeometry/SurfacePrimitives/Plane.jl Show resolved Hide resolved

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lmh91 reviewed Sep 20, 2021

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hervasa2 added 2 commits September 20, 2021 15:06

Removed VoronoiDelaunay dep

f8c708d

show_normal defaulted to false

a9fc903

hervasa2 added 2 commits October 8, 2021 13:30

single mesh struct conemantle mesh

82c54de

surface primitives meshing and connections

1e9e087

lmh91 requested changes Oct 13, 2021

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src/ConstructiveSolidGeometry/plotting/Meshing.jl Outdated Show resolved Hide resolved

hervasa2 added 3 commits October 14, 2021 13:31

connections and vertices functions for all surface primitives

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top level plot recipes

e151626

n => n_arc

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lmh91 approved these changes Oct 14, 2021

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lmh91 merged commit 418da02 into JuliaPhysics:v0.7 Oct 14, 2021

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Mesh Plotting #218

Mesh Plotting #218

hervasa2 commented Sep 16, 2021

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Mesh Plotting #218

Mesh Plotting #218

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