Merge pull request #18 from VirtualPlantLab/update_0.1.0

update primitives and raytraced forest to 0.1.0

Author: anaIFernst

Project.toml

@@ -1,27 +1,33 @@
 name = "VPLDocs"
 uuid = "19246b20-85cd-4f94-a989-28bb6828320f"
 authors = ["Alejandro Morales Sierra <[email protected]> and contributors"]
-version = "0.0.7"
+version = "0.1.0"
 
 [deps]
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Ecophys = "19467474-d12d-47c9-939f-3e50fbfd93ad"
+FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
 PlantGeomPrimitives = "7eef3cc5-4580-4ff0-8f6f-933507db6664"
 PlantGeomTurtle = "7d6e2781-1c99-4c66-97ec-106669f3e96e"
 PlantGraphs = "615ad455-9aac-4340-9247-71ef610f781a"
 PlantRayTracer = "78485975-e4aa-407d-b3bb-ded5a4265d05"
 PlantSimEngine = "9a576370-710b-4269-adf9-4f603a9c6423"
 PlantViz = "358bd95d-d12c-439f-94b7-04b17e500c7f"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 SkyDomes = "1838625c-7cf7-40c6-898b-904883e4b556"
 VirtualPlantLab = "b977ecfa-1b9a-418d-909d-4ebe565736ce"
 
 [compat]
+Distributions = "0.25.120"
 Ecophys = "0.1.0"
-PlantGeomPrimitives = "0.0.5"
-PlantGeomTurtle = "0.0.6"
-PlantGraphs = "0.0.3"
-PlantRayTracer = "0.0.8"
+FastGaussQuadrature = "1.0.2"
+PlantGeomPrimitives = "0.1.0"
+PlantGeomTurtle = "0.1.0"
+PlantGraphs = "0.1.0"
+PlantRayTracer = "0.1.0"
 PlantSimEngine = "0.9"
-PlantViz = "0.0.8"
-SkyDomes = "0.1.8"
-VirtualPlantLab = "0.0.7"
+PlantViz = "0.1.0"
+Plots = "1.40.17"
+SkyDomes = "0.1.9"
+VirtualPlantLab = "0.1.0"
 julia = "1.11"

docs/src/manual/Geometry/Primitives.md

@@ -39,94 +39,115 @@ to ensure that the transparency is enabled when rendering the mesh.
 
 ## Triangle
 ```julia
-p = Triangle(length = 1.0, width = 1.0)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = Triangle!(turtle; length = 1.0, width = 1.0, colors = rand(RGBA))    
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Rectangle
 ```julia
-p = Rectangle(length = 1.0, width = 1.0)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = Rectangle!(turtle; length = 1.0, width = 1.0, colors = rand(RGBA)) 
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Trapezoid
 ```julia
-p = Trapezoid(length = 1.0, width = 1.0, ratio = 0.5)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = Trapezoid!(turtle; length = 1.0, width = 1.0, ratio = 0.5, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Ellipse
 ```julia
-p = Ellipse(length = 1.0, width = 1.0, n = 30)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = Ellipse!(turtle; length = 1.0, width = 1.0, n = 30, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Axis-aligned bounding box
 ```julia
+turtle = Turtle()
 p = BBox(Vec(0.0, 0.0, 0.0), Vec(1.0, 1.0, 1.0))
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+Mesh!(turtle, p, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Cube
 
 Solid version
 
 ```julia
-p = SolidCube(length = 1.0, width = 1.0, height = 1.0)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = SolidCube!(turtle; length = 1.0, width = 1.0, height = 1.0, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 Hollow version
 
 ```julia
-p = HollowCube(length = 1.0, width = 1.0, height = 1.0)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = HollowCube!(turtle; length = 1.0, width = 1.0, height = 1.0, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)e)
 ```
 
+
+## Primitives with (semi-)circular bases
+
+The following primitive types share a parameter n, which is the number of triangles to discretize the cylinder into.
+The lower is number n, cicle base shape will be more rough (e.g., n = 20, base shape is a pentagon).
+The higher is number n, cicle base shape will be more smooth (e.g., n = 80, base shape is a circle).
+
 ## Cylinder
 
 Solid version
 
 ```julia
-p = SolidCylinder(length = 1.0, width = 1.0, height = 1.0, n = 80)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = SolidCylinder!(turtle; length = 1.0, width = 1.0, height = 1.0, n = 80, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 Hollow version
 
 ```julia
-p = HollowCylinder(length = 1.0, width = 1.0, height = 1.0, n = 40)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = HollowCylinder!(turtle; length = 1.0, width = 1.0, height = 1.0, n = 80, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Frustum
 
 Solid version
 
 ```julia
-p = SolidFrustum(length = 1.0, width = 1.0, height = 1.0, ratio = 0.5, n = 80)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = SolidFrustum!(turtle; length = 1.0, width = 1.0, height = 1.0, ratio = 0.5, n = 80, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 Hollow version
 
 ```julia
-p = HollowFrustum(length = 1.0, width = 1.0, height = 1.0, ratio = 0.5, n = 40)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = HollowFrustum!(turtle; length = 1.0, width = 1.0, height = 1.0, ratio = 0.5, n = 80, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 ## Cone
 
 Solid version
 
 ```julia
-p = SolidCone(length = 1.0, width = 1.0, height = 1.0, n = 40)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = SolidCone!(turtle; length = 1.0, width = 1.0, height = 1.0, n = 80, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```
 
 Hollow version
 
 ```julia
-p = HollowCone(length = 1.0, width = 1.0, height = 1.0, n = 20)
-render(p, wireframe = true, normals = true, color = RGBA(0,1,0,0.5), transparency = true)
+turtle = Turtle()
+p = HollowCone!(turtle; length = 1.0, width = 1.0, height = 1.0, n = 80, colors = rand(RGBA))
+render(Mesh(turtle), wireframe = true)
 ```

docs/src/tutorials/from_tree_forest/raytracedforest.md

@@ -247,7 +247,7 @@ function `sky()` (this last step requires the 3D scene as input in order to plac
 the light sources adequately).
 
 ```julia
-function create_sky(;scene, lat = 52.0*π/180.0, DOY = 182)
+function create_sky(;mesh, lat = 52.0*π/180.0, DOY = 182)
     # Fraction of the day and day length
     fs = collect(0.1:0.1:0.9)
     dec = declination(DOY)
@@ -264,7 +264,7 @@ function create_sky(;scene, lat = 52.0*π/180.0, DOY = 182)
     Idir_PAR = f_dir.*Idir
     Idif_PAR = f_dif.*Idif
     # Create the dome of diffuse light
-    dome = sky(scene,
+    dome = sky(mesh,
                   Idir = 0.0, ## No direct solar radiation
                   Idif = sum(Idir_PAR)/10*DL, ## Daily Diffuse solar radiation
                   nrays_dif = 1_000_000, ## Total number of rays for diffuse solar radiation
@@ -274,7 +274,7 @@ function create_sky(;scene, lat = 52.0*π/180.0, DOY = 182)
                   nphi = 12) ## Number of discretization steps in the azimuth angle
     # Add direct sources for different times of the day
     for I in Idir_PAR
-        push!(dome, sky(scene, Idir = I/10*DL, nrays_dir = 100_000, Idif = 0.0)[1])
+        push!(dome, sky(mesh, Idir = I/10*DL, nrays_dir = 100_000, Idif = 0.0)[1])
     end
     return dome
 end
@@ -299,10 +299,9 @@ for details). The acceleration structure allows speeding up the ray tracing
 by avoiding testing all rays against all objects in the scene.
 
 ```julia
-function create_raytracer(mesh, sources)
+function create_raytracer(acc_mesh, sources)
     settings = RTSettings(pkill = 0.9, maxiter = 4, nx = 5, ny = 5, parallel = true)
-    RayTracer(mesh, sources, settings = settings, acceleration = BVH,
-                     rule = SAH{3}(5, 10));
+    RayTracer(acc_mesh, sources, settings = settings);
 end
 ```
 
@@ -314,8 +313,9 @@ the `Material` objects (see `feed!()` above):
 ```julia
 function run_raytracer!(forest; DOY = 182)
     mesh   = create_scene(forest)
-    sources = create_sky(mesh = mesh, DOY = DOY)
-    rtobj   = create_raytracer(mesh, sources)
+    acc_mesh = accelerate(mesh, acceleration = BVH, rule = SAH{3}(5, 10))
+    sources = create_sky(mesh = acc_mesh, DOY = DOY)
+    rtobj   = create_raytracer(acc_mesh, sources)
     trace!(rtobj)
     return nothing
 end
@@ -393,7 +393,7 @@ plot(0:1:50, x -> sink_strength(TreeTypes.Leaf(age = x), TreeTypes.treeparams())
      xlabel = "Age", ylabel = "Sink strength", label = "Leaf")
 
 sink_strength(int) = pdf(int.sink, int.age)
-plot!(0:1:50, x -> sink_strength(TreeTypes.Leaf(age = x)), label = "Internode")
+plot!(0:1:50, x -> sink_strength(TreeTypes.Internode(age = x)), label = "Internode")
 ```
 
 Now we need a function that updates the biomass of the tree, allocates it to the