Merge pull request #79 from VEZY/compathelper/new_version/2024-10-18-…

…00-20-13-202-03192803601

CompatHelper: bump compat for Meshes to 0.52, (keep existing compat)

.gitignore

@@ -1,2 +1,3 @@
 /Manifest.toml
 /docs/build/
+test/Manifest.toml

Project.toml

@@ -8,6 +8,7 @@ ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 Meshes = "eacbb407-ea5a-433e-ab97-5258b1ca43fa"
 MultiScaleTreeGraph = "dd4a991b-8a45-4075-bede-262ee62d5583"
 Observables = "510215fc-4207-5dde-b226-833fc4488ee2"
@@ -19,18 +20,12 @@ TransformsBase = "28dd2a49-a57a-4bfb-84ca-1a49db9b96b8"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
-[weakdeps]
-Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-
-[extensions]
-PlantGeomMakie = "Makie"
-
 [compat]
 ColorSchemes = "3"
 Colors = "0.12"
 EzXML = "1"
 Makie = "0.21"
-Meshes = "0.44"
+Meshes = "0.52"
 MultiScaleTreeGraph = "0.14"
 Observables = "0.5"
 RecipesBase = "1"

ext/PlantGeomMakie.jl

@@ -15,11 +15,15 @@ import Unitful
 
 MeshesMakieExt = Base.get_extension(Meshes, :MeshesMakieExt)
 
-include("makie_recipes/RefMeshes_recipes.jl")
-include("makie_recipes/opf/plot_opf.jl")
-include("makie_recipes/opf_recipe.jl")
-include("makie_recipes/mtg_tree_recipe.jl")
-include("makie_recipes/colorbar.jl")
+if isnothing(MeshesMakieExt)
+    println("Couldn't import the MeshesMakieExt extension, please load the Meshes package before loading PlantGeom")
+else
+    include("makie_recipes/RefMeshes_recipes.jl")
+    include("makie_recipes/opf/plot_opf.jl")
+    include("makie_recipes/opf_recipe.jl")
+    include("makie_recipes/mtg_tree_recipe.jl")
+    include("makie_recipes/colorbar.jl")
+end
 
 export viz, viz!
 export colorbar

src/PlantGeom.jl

@@ -80,4 +80,15 @@ export colorbar
 
 export get_transformation_matrix
 
+
+# Code that should be moved to PlantGeomMakie:
+import Makie
+MeshesMakieExt = Base.get_extension(Meshes, :MeshesMakieExt)
+
+include("../ext/makie_recipes/RefMeshes_recipes.jl")
+include("../ext/makie_recipes/opf/plot_opf.jl")
+include("../ext/makie_recipes/opf_recipe.jl")
+include("../ext/makie_recipes/mtg_tree_recipe.jl")
+include("../ext/makie_recipes/colorbar.jl")
+
 end

src/helpers.jl

@@ -18,9 +18,7 @@ end
 
 function normals(mesh::RefMesh{S,ME,M,N,T}) where {S,ME<:Meshes.SimpleMesh,M,N,T}
     if length(mesh.normals) == 0
-        return SVector{length(Meshes.topology(mesh.mesh).connec)}(
-            Meshes.Point(Meshes.normal(Meshes.Triangle(Meshes.vertices(mesh.mesh)[[tri.indices...]]))) for tri in Meshes.topology(mesh.mesh).connec
-        )
+        return SVector{length(mesh.mesh)}(Meshes.normal(tri) for tri in mesh.mesh)
     else
         return mesh.normals
     end
@@ -38,23 +36,18 @@ Compute per vertex normals and return them as a `StaticArrays.SVector`.
 # https://stackoverflow.com/questions/45477806/general-method-for-calculating-smooth-vertex-normals-with-100-smoothness?noredirect=1&lq=1
 """
 function normals_vertex(mesh::RefMesh)
-    vertex_normals = fill(Meshes.Vec(0.0, 0.0, 0.0), Meshes.nvertices(mesh))
-    for (i, tri) in enumerate(Meshes.topology(mesh.mesh).connec)
-        vertex_normals[tri.indices[1]] = mesh.normals[i]
-        vertex_normals[tri.indices[2]] = mesh.normals[i]
-        vertex_normals[tri.indices[3]] = mesh.normals[i]
-    end
-
-    return SVector{length(vertex_normals)}(vertex_normals)
+    normals_vertex(mesh.mesh)
 end
 
 function normals_vertex(mesh::Meshes.SimpleMesh)
     vertex_normals = fill(Meshes.Vec(0.0, 0.0, 0.0), Meshes.nvertices(mesh))
-    for (i, tri) in enumerate(Meshes.topology(mesh).connec)
-        tri_norm = Meshes.normal(Meshes.Triangle(mesh.vertices[[tri.indices...]]...))
-        vertex_normals[tri.indices[1]] = tri_norm
-        vertex_normals[tri.indices[2]] = tri_norm
-        vertex_normals[tri.indices[3]] = tri_norm
+    tri_normals = [Meshes.normal(tri) for tri in mesh]
+
+    for (i, tri) in enumerate(Meshes.topology(mesh))
+        tri_indices = Meshes.indices(tri)
+        vertex_normals[tri_indices[1]] = tri_normals[i]
+        vertex_normals[tri_indices[2]] = tri_normals[i]
+        vertex_normals[tri_indices[3]] = tri_normals[i]
     end
 
     return SVector{length(vertex_normals)}(vertex_normals)

src/meshes/summary_coordinates.jl

@@ -37,5 +37,5 @@ Apply function `f` over the mesh coordinates `coord`.
 Values for `coord` can be 1 for x, 2 for y and 3 for z.
 """
 function map_coord(f, mesh, coord)
-    f([Meshes.to(i)[coord] for i in Meshes.vertices(mesh)])
+    f([Meshes.to(i)[coord] for i in Meshes.eachvertex(mesh)])
 end

src/opf/refmesh_to_mesh.jl

@@ -40,7 +40,7 @@ function refmesh_to_mesh(node)
 end
 
 function apply_transformation(transformation, ref_mesh)
-    Meshes.SimpleMesh([transformation(p) for p in Meshes.vertices(ref_mesh)], Meshes.topology(ref_mesh))
+    Meshes.SimpleMesh([transformation(p) for p in Meshes.eachvertex(ref_mesh)], Meshes.topology(ref_mesh))
 end
 
 function refmesh_to_mesh!(node)

src/opf/write_opf.jl

@@ -47,9 +47,9 @@ function write_opf(file, mtg)
         addelement!(
             mesh_elm,
             "points",
-            string("\n", join(Iterators.flatten(Unitful.ustrip.(Unitful.uconvert.(u"cm", Meshes.to(p))) for p in Meshes.vertices(mesh_.mesh)), "\t"), "\n")
+            string("\n", join(Iterators.flatten(Unitful.ustrip.(u"cm", Meshes.to(p)) for p in Meshes.eachvertex(mesh_.mesh)), "\t"), "\n")
         )
-
+        # p |> LengthUnit(u"cm")
         if length(mesh_.normals) == Meshes.nelements(mesh_) && length(mesh_.normals) != Meshes.nvertices(mesh_)
             # If the normals are per triangle, re-compute them per vertex:
             vertex_normals = normals_vertex(mesh_)
@@ -60,7 +60,7 @@ function write_opf(file, mtg)
         norm_elm = addelement!(
             mesh_elm,
             "normals",
-            string("\n", join(Iterators.flatten(Unitful.ustrip.(Unitful.uconvert.(u"cm", p)) for p in vertex_normals), "\t"), "\n")
+            string("\n", join(Iterators.flatten(Unitful.ustrip.(u"cm", p) for p in vertex_normals), "\t"), "\n")
         )
 
 
@@ -69,18 +69,19 @@ function write_opf(file, mtg)
             norm_elm = addelement!(
                 mesh_elm,
                 "textureCoords",
-                string("\n", join(Iterators.flatten(Unitful.ustrip.(Unitful.uconvert.(u"cm", Meshes.to(p))) for p in mesh_.texture_coords), "\t"), "\n")
+                string("\n", join(Iterators.flatten(Unitful.ustrip.(u"cm", Meshes.to(p)) for p in mesh_.texture_coords), "\t"), "\n")
             )
         end
 
         faces_elm = addelement!(mesh_elm, "faces")
 
+
         face_id = [0]
-        for i in firstindex(mesh_.mesh):lastindex(mesh_.mesh)
+        for tri in Meshes.elements(Meshes.topology(mesh_.mesh))
             face_elm = addelement!(
                 faces_elm,
                 "face",
-                string("\n", join(Meshes.topology(mesh_.mesh).connec[i].indices .- 1, "\t"), "\n")
+                string("\n", join(Meshes.indices(tri) .- 1, "\t"), "\n")
             )
             #? NB: we remove one because face index are 0-based in the opf
             face_elm["Id"] = face_id[1]
@@ -297,22 +298,22 @@ end
 
 function get_transformation_matrix(trans::Affine)
     A, b = parameters(trans)
-    b = Unitful.ustrip.(Unitful.uconvert.(u"cm", b))
+    b = Unitful.ustrip.(u"cm", b)
     vcat(hcat(A, b), [0 0 0 1])
 end
 
 function get_transformation_matrix(trans::Translate{3,T}) where {T}
-    x, y, z = Unitful.ustrip.(Unitful.uconvert.(u"cm", trans.offsets))
+    x, y, z = Unitful.ustrip.(u"cm", trans.offsets)
     [1.0 0.0 0.0 x; 0.0 1.0 0.0 y; 0.0 0.0 1.0 z; 0.0 0.0 0.0 1.0]
 end
 
 function get_transformation_matrix(trans::Translate{2,T}) where {T}
-    x, y = Unitful.ustrip.(Unitful.uconvert.(u"cm", trans.offsets))
+    x, y = Unitful.ustrip.(u"cm", trans.offsets)
     [1.0 0.0 0.0 x; 0.0 1.0 0.0 y; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0]
 end
 
 function get_transformation_matrix(trans::Translate{1,T}) where {T}
-    x = Unitful.ustrip.(Unitful.uconvert(u"cm", trans.offsets[1]))
+    x = Unitful.ustrip.(u"cm", trans.offsets[1])
     [1.0 0.0 0.0 x; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0]
 end
 

src/ops/write_ops.jl

@@ -40,8 +40,8 @@ write_ops("scene.ops", scene_dimensions, object_table)
 """
 function write_ops(file, scene_dimensions, object_table)
     dims = join([
-            Unitful.ustrip.(Unitful.uconvert.(u"m", Meshes.to(scene_dimensions[1])))...,
-            Unitful.ustrip.(Unitful.uconvert.(u"m", Meshes.to(scene_dimensions[2])))...
+            Unitful.ustrip.(u"m", Meshes.to(scene_dimensions[1]))...,
+            Unitful.ustrip.(u"m", Meshes.to(scene_dimensions[2]))...
         ][1:end-1], " ")
     ops_lines = vcat("# T xOrigin yOrigin zOrigin xSize ySize flat", string("T ", dims..., " flat"))
 
@@ -55,7 +55,7 @@ function write_ops(file, scene_dimensions, object_table)
                 "#[Archimed] $current_group",
                 "#sceneId plantId plantFileName x y z scale inclinationAzimut inclinationAngle stemTwist")
         end
-        x, y, z = Unitful.ustrip.(Unitful.uconvert.(u"m", Meshes.to(row.pos)))
+        x, y, z = Unitful.ustrip.(u"m", Meshes.to(row.pos))
         plant_scale = haskey(row, :scale) ? row.scale : 1.0
         plant_rotation = haskey(row, :rotation) ? row.rotation : 0.0
         plant_inclinationAzimut = haskey(row, :inclinationAzimut) ? row.inclinationAzimut : 0.0

src/structs.jl

@@ -80,7 +80,7 @@ RefMesh type. Stores all information about a Mesh:
 The reference meshes are then transformed on each node of the MTG using a transformation matrix
 to match the actual mesh.
 """
-struct RefMesh{S<:String,ME<:Meshes.Mesh{3},M<:Union{Material,Colorant},N<:AbstractVector,T<:Union{AbstractVector,Nothing}}
+struct RefMesh{S<:String,ME<:Meshes.Mesh{<:Meshes.𝔼{3}},M<:Union{Material,Colorant},N<:AbstractVector,T<:Union{AbstractVector,Nothing}}
     name::S
     mesh::ME
     normals::N