Improve RefMeshes API

Project.toml

@@ -12,6 +12,7 @@ Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 Meshes = "eacbb407-ea5a-433e-ab97-5258b1ca43fa"
 MultiScaleTreeGraph = "dd4a991b-8a45-4075-bede-262ee62d5583"
 Observables = "510215fc-4207-5dde-b226-833fc4488ee2"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -28,6 +29,7 @@ Makie = "0.21"
 Meshes = "0.52"
 MultiScaleTreeGraph = "0.14"
 Observables = "0.5"
+OrderedCollections = "1.7.0"
 RecipesBase = "1"
 Rotations = "1"
 StaticArrays = "1"

README.md

@@ -16,7 +16,7 @@ The package provides different functionalities, the main ones being:
 - plotting using `viz` and `viz!`, optionally using coloring by attribute;
 - mesh transformations using `transform_mesh!`
 
-Note that `:geometry` is a reserved attribute in nodes (*e.g.* organs) used for the 3D geometry. It is stored as a special structure (`geometry`).
+Note that `:geometry` is a reserved attribute in nodes (*e.g.* organs) used for the 3D geometry. It is stored as a special structure (`Geometry`).
 
 ## Example usage
 

docs/src/index.md

@@ -14,7 +14,7 @@ The package provides different functionalities, the main ones being:
 - plotting using `viz` and `viz!`, optionally using coloring by attribute;
 - mesh transformations using [`transform_mesh!`](@ref)
 
-Note that PlantGeom reserves the `:geometry` attribute in the nodes (*e.g.* organs). It uses it to store the 3D geometry as a special structure ([`geometry`](@ref)).
+Note that PlantGeom reserves the `:geometry` attribute in the nodes (*e.g.* organs). It uses it to store the 3D geometry as a special structure ([`Geometry`](@ref)).
 
 ```@setup animation
 using CairoMakie, Meshes, PlantGeom, MultiScaleTreeGraph # Note: CairoMakie must be loaded before PlantGeom to access the extensions
@@ -63,7 +63,7 @@ opf = read_opf(joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simp
 transform!(opf, refmesh_to_mesh!)
 # And compute the max z of each node based on their mesh:
 transform!(opf, zmax => :z_node, ignore_nothing = true)
-# Or the z coordinate of each vertez of each node mesh:
+# Or the z coordinate of each vertex of each node mesh:
 transform!(opf, :geometry => (x -> [Meshes.coords(i)z for i in Meshes.vertices(x.mesh)]) => :z_vertex, ignore_nothing = true)
 
 

docs/src/makie_3d.md

@@ -114,18 +114,18 @@ We can get the default color of each reference mesh by using:
 get_ref_meshes_color(ref_meshes)
 ```
 
-Now we know the first reference mesh is the cylinder (it is brown) and the second one is the leaf (it is green).
+Now we know there are two reference meshes, one for a cylinder called "Mesh0" colored in brown, and a second one for the leaf that is green.
 
-To update their colors we can simply pass the new colors as a dictionary mapping colors to reference meshes like so:
+To update their colors we can simply pass the new colors as a dictionary mapping colors to the names of the reference meshes like so:
 
 ```@example 2
-viz(mtg, color = Dict(1 => :gray87, 2 => "#42A25ABD"))
+viz(mtg, color = Dict("Mesh0" => :gray87, "Mesh1" => "#42A25ABD"))
 ```
 
 If we want to update the second reference mesh only (the leaves), we would do:
 
 ```@example 2
-viz(mtg, color = Dict(2 => "#42A25ABD"))
+viz(mtg, color = Dict("Mesh1" => "#42A25ABD"))
 ```
 
 ### Map color to attributes

ext/makie_recipes/RefMeshes_recipes.jl

@@ -1,8 +1,8 @@
-Makie.plottype(::RefMeshes) = MeshesMakieExt.Viz{<:Tuple{RefMeshes}}
-Makie.args_preferred_axis(::RefMeshes) = Makie.LScene
+Makie.plottype(::Vector{RefMesh}) = MeshesMakieExt.Viz{<:Tuple{Vector{RefMesh}}}
+Makie.args_preferred_axis(::Vector{RefMesh}) = Makie.LScene
 
 # Documentation is in opf_recipe.jl
-function Makie.plot!(plot::MeshesMakieExt.Viz{<:Tuple{RefMeshes}})
+function Makie.plot!(plot::MeshesMakieExt.Viz{<:Tuple{Vector{RefMesh}}})
     # Mesh list:
     p = PlantGeom.align_ref_meshes(plot[:object][])
 
@@ -18,7 +18,7 @@ function Makie.plot!(plot::MeshesMakieExt.Viz{<:Tuple{RefMeshes}})
             # see here for default value in MeshViz:
             # https://github.com/JuliaGeometry/MeshViz.jl/blob/6e37908c78c06212f09229e3e8d92483535ffa16/src/MeshViz.jl#L50
             ref_colors = get_ref_meshes_color(plot[:object][])
-            colorant = Observables.Observable(Dict(zip(1:n_meshes, ref_colors)))
+            colorant = Observables.Observable(ref_colors)
         else
             colorant = Makie.lift(x -> Dict(zip(keys(p), repeat([x], n_meshes))), color)
         end
@@ -34,7 +34,7 @@ function Makie.plot!(plot::MeshesMakieExt.Viz{<:Tuple{RefMeshes}})
     end
 
     # Parsing the colors in the dictionary into Colorants:
-    new_color = Dict{Int,Union{Colorant,Vector{<:Colorant}}}([k => isa(v, AbstractArray) ? parse.(Colorant, v) : parse(Colorant, v) for (k, v) in colorant[]])
+    new_color = Dict{String,Union{Colorant,Vector{<:Colorant}}}([k => isa(v, AbstractArray) ? parse.(Colorant, v) : parse(Colorant, v) for (k, v) in colorant[]])
 
     if length(colorant[]) != n_meshes
         ref_cols = get_ref_meshes_color(plot[:object][])
@@ -44,7 +44,7 @@ function Makie.plot!(plot::MeshesMakieExt.Viz{<:Tuple{RefMeshes}})
         end
     end
 
-    for (key, value) in enumerate(p)
-        MeshesMakieExt.viz!(plot, value, color=new_color[key], segmentcolor=plot[:segmentcolor], showsegments=plot[:showsegments], colormap=plot[:colormap])
+    for (name, refmesh) in p
+        MeshesMakieExt.viz!(plot, refmesh, color=new_color[name], segmentcolor=plot[:segmentcolor], showsegments=plot[:showsegments], colormap=plot[:colormap])
     end
 end

ext/makie_recipes/opf/plot_opf.jl

@@ -72,9 +72,6 @@ function plot_opf(plot)
     link = hasproperty(plot, :link) ? plot[:link][] : nothing
 
     plot_opf(colorant, plot, f, symbol, scale, link)
-    #? NB: implement scale / symbol / link / filter_fun filtering to be able to plot only
-    #? a subset of the plant/scene. This will be especially usefull when we have different
-    #? kind of geometries at different scales of representation.
 end
 
 # Case where the color is a colorant (e.g. `:red`, or `RGB(0.1,0.5,0.1)`):
@@ -106,14 +103,12 @@ function plot_opf(colorant::Observables.Observable{T}, plot, f, symbol, scale, l
 
     opf = plot[:object]
 
-    ref_meshes = get_ref_meshes(opf[])
-
     any_node_selected = Ref(false)
     # Make the plot, case where the color is a color for each reference mesh:
     MultiScaleTreeGraph.traverse!(opf[]; filter_fun=f, symbol=symbol, scale=scale, link=link) do node
         any_node_selected[] = true
 
-        node[color_attr_name] = Makie.@lift color_from_refmeshes($colorant, node, ref_meshes)
+        node[color_attr_name] = Makie.@lift color_from_refmeshes($colorant, node)
         MeshesMakieExt.viz!(
             plot,
             node[:geometry].mesh === nothing ? refmesh_to_mesh(node) : node[:geometry].mesh,
@@ -128,8 +123,12 @@ function plot_opf(colorant::Observables.Observable{T}, plot, f, symbol, scale, l
     any_node_selected[] || error("No corresponding node found for the selection given as the combination of `symbol`, `scale`, `link` and `filter_fun` arguments. ")
 end
 
-function color_from_refmeshes(color::Union{RefMeshColorant,DictRefMeshColorant,DictVertexRefMeshColorant}, node, ref_meshes)
-    color.colors[PlantGeom.get_ref_mesh_index!(node, ref_meshes)]
+function color_from_refmeshes(color::RefMeshColorant, node)
+    material_single_color(node.geometry.ref_mesh.material)
+end
+
+function color_from_refmeshes(color::Union{DictRefMeshColorant,DictVertexRefMeshColorant}, node)
+    get(color.colors, get_ref_mesh_name(node), material_single_color(node.geometry.ref_mesh.material))
 end
 
 # Case where the color is an attribute of the MTG:

src/PlantGeom.jl

@@ -29,6 +29,7 @@ import StaticArrays: SMatrix, SVector
 import LinearAlgebra: I, UniformScaling, Diagonal # Used for geometry parsing in OPF
 import RecipesBase
 import Base
+import OrderedCollections
 
 # For random name of the color attribute for caching:
 import UUIDs
@@ -52,6 +53,7 @@ include("colors/colors.jl")
 include("colors/get_mtg_color.jl")
 include("opf/mtg_recipe_helpers.jl")
 include("opf/diagram.jl")
+include("deprecated.jl")
 
 # function viz2 end
 # function viz2! end
@@ -71,7 +73,7 @@ export xmax, ymax, zmax, xmin, ymin, zmin
 export refmesh_to_mesh!
 export transform_mesh!
 export Material, Phong
-export RefMesh, RefMeshes
+export RefMesh
 export (==), names
 export get_color, get_colormap
 

src/colors/get_mtg_color.jl

@@ -1,17 +1,15 @@
-struct RefMeshColorant
-    colors::Vector{Colorant}
-end
+struct RefMeshColorant end
 
 struct AttributeColorant
     color::Symbol
 end
 
 struct DictRefMeshColorant
-    colors::Dict{Int64,Colorant}
+    colors::Dict{String,Colorant}
 end
 
 struct DictVertexRefMeshColorant
-    colors::Dict{Int64,Union{Colorant,Vector{<:Colorant}}}
+    colors::Dict{String,Union{Colorant,Vector{<:Colorant}}}
 end
 
 struct VectorColorant
@@ -52,7 +50,7 @@ function get_mtg_color(color, opf)
 end
 
 function get_mtg_color(::Type{RefMeshColorantType}, color, opf)
-    return RefMeshColorant(get_ref_meshes_color(get_ref_meshes(opf)))
+    return RefMeshColorant()
 end
 
 function get_mtg_color(::Type{AttributeColorantType}, color, opf)
@@ -64,42 +62,12 @@ function get_mtg_color(::Type{T}, color, opf) where {T<:Symbol}
 end
 
 function get_mtg_color(::Type{DictRefMeshColorantType}, color, opf)
-    ref_meshes = get_ref_meshes(opf)
-
     # Parsing the colors in the dictionary into Colorants:
-    new_color = Dict{Int,Colorant}([k => parse(Colorant, v) for (k, v) in color])
-
-    # If color is a dictionary, it should have the same length as number of RefMeshes, or
-    # if not, we provide the missing values from the reference mesh color:
-    if length(color) != length(ref_meshes.meshes)
-        ref_cols = get_ref_meshes_color(ref_meshes)
-        missing_mesh_input = setdiff(collect(keys(ref_cols)), collect(keys(color)))
-        for i in missing_mesh_input
-            push!(new_color, i => ref_cols[i])
-        end
-    end
-
+    new_color = Dict{String,Colorant}([k => parse(Colorant, v) for (k, v) in color])
     return DictRefMeshColorant(new_color)
 end
 
 function get_mtg_color(::Type{DictVertexRefMeshColorantType}, color, opf)
-    ref_meshes = get_ref_meshes(opf)
-
-    # If color is a dictionary, it should have the same length as number of RefMeshes, or
-    # if not, we provide the missing values from the reference mesh color:
-    if length(color) != length(ref_meshes.meshes)
-        # Parsing the colors in the dictionary into Colorants:
-        new_color = Dict{Int,Union{Colorant,Vector{<:Colorant}}}(
-            [k => (isa(v, AbstractVector) ? parse.(Colorant, v) : parse(Colorant, v)) for (k, v) in color]
-        )
-        ref_cols = get_ref_meshes_color(ref_meshes)
-        missing_mesh_input = setdiff(collect(keys(ref_cols)), collect(keys(color)))
-        for i in missing_mesh_input
-            push!(new_color, i => ref_cols[i])
-        end
-        color = new_color
-    end
-
     return DictVertexRefMeshColorant(color)
 end
 

src/deprecated.jl

@@ -0,0 +1 @@
+@deprecate geometry(; ref_mesh, ref_mesh_index=nothing, transformation=Identity(), dUp=1.0, dDwn=1.0, mesh=nothing) Geometry(; ref_mesh, transformation=Identity(), dUp=1.0, dDwn=1.0, mesh=nothing)

src/equality.jl

@@ -13,24 +13,12 @@ function Base.:(==)(a::T, b::T) where {T<:RefMesh}
 end
 
 """
-    ==(a::RefMeshes, b::RefMeshes)
+    ==(a::Geometry, b::Geometry)
 
-Test RefMeshes equality.
-"""
-function Base.:(==)(a::T, b::T) where {T<:RefMeshes}
-    isequal(names(a), names(b)) &&
-        all([isequal(a.meshes[i], b.meshes[i]) for i in 1:length(a.meshes)])
-end
-
-
-"""
-    ==(a::geometry, b::geometry)
-
-Test RefMeshes equality.
+Test RefMesh equality.
 """
-function Base.:(==)(a::T, b::T) where {T<:geometry}
+function Base.:(==)(a::T, b::T) where {T<:Geometry}
     isequal(a.ref_mesh, b.ref_mesh) &&
-        isequal(a.ref_mesh_index, b.ref_mesh_index) &&
         isequal(a.transformation(Meshes.Point(1, 2, 3)), b.transformation(Meshes.Point(1, 2, 3))) &&
         # NB: transform a point here because transformations can't be compared directly
         isequal(a.dUp, b.dUp) &&

src/helpers.jl

@@ -8,7 +8,7 @@ function Meshes.nvertices(mesh::RefMesh)
 end
 
 """
-    nelements(meshes::RefMeshes)
+    nelements(meshes::RefMesh)
 
 Return the number of elements of a reference mesh
 """
@@ -51,24 +51,4 @@ function normals_vertex(mesh::Meshes.SimpleMesh)
     end
 
     return SVector{length(vertex_normals)}(vertex_normals)
-end
-
-"""
-    nvertices(meshes::RefMeshes)
-
-Return the number of vertices for each reference mesh as a vector of nvertices
-"""
-function Meshes.nvertices(meshes::RefMeshes)
-    [Meshes.nvertices(i) for i in meshes.meshes]
-    # TODO: Implement for RefMesh with GeometryBasics
-end
-
-"""
-    nelements(meshes::RefMeshes)
-
-Return the number of elements for each reference mesh as a vector of nelements
-"""
-function Meshes.nelements(meshes::RefMeshes)
-    [Meshes.nelements(i) for i in meshes.meshes]
-    # TODO: Implement for RefMesh with GeometryBasics
-end
+end

src/meshes/transformations.jl

@@ -73,10 +73,4 @@ end
 
 function apply(t, x::RefMesh)
     RefMesh(x.name, apply(t, x.mesh), x.normals, x.texture_coords, x.material, x.taper)
-end
-
-function apply(t, x::RefMeshes)
-    for i in eachindex(x)
-        x[i] = apply(t, x[i])
-    end
 end

src/opf/read_opf.jl

@@ -415,9 +415,8 @@ function parse_opf_topology!(node, mtg, features, attr_type, mtg_type, ref_meshe
 
                 push!(
                     attrs,
-                    Symbol(elem.name) => geometry(
-                        ref_meshes.meshes[geom[:shapeIndex]],
-                        geom[:shapeIndex],
+                    Symbol(elem.name) => Geometry(
+                        ref_meshes[geom[:shapeIndex]],
                         transformation,
                         geom[:dUp],
                         geom[:dDwn],