Update to VPL 0.0.7

Author: AleMorales

Project.toml

@@ -1,7 +1,7 @@
 name = "VPLDocs"
 uuid = "19246b20-85cd-4f94-a989-28bb6828320f"
 authors = ["Alejandro Morales Sierra <alejandro.moralessierra@wur.nl> and contributors"]
-version = "0.0.6"
+version = "0.0.7"
 
 [deps]
 Ecophys = "19467474-d12d-47c9-939f-3e50fbfd93ad"
@@ -16,12 +16,12 @@ VirtualPlantLab = "b977ecfa-1b9a-418d-909d-4ebe565736ce"
 
 [compat]
 Ecophys = "0.1.0"
-PlantGeomPrimitives = "0.0.3"
-PlantGeomTurtle = "0.0.4"
-PlantGraphs = "0.0.2"
-PlantRayTracer = "0.0.6"
+PlantGeomPrimitives = "0.0.5"
+PlantGeomTurtle = "0.0.6"
+PlantGraphs = "0.0.3"
+PlantRayTracer = "0.0.8"
 PlantSimEngine = "0.9"
-PlantViz = "0.0.6"
-SkyDomes = "0.1.6"
-VirtualPlantLab = "0.0.6"
-julia = "1.9"
+PlantViz = "0.0.8"
+SkyDomes = "0.1.8"
+VirtualPlantLab = "0.0.7"
+julia = "1.11"

docs/Project.toml

@@ -13,12 +13,12 @@ VirtualPlantLab = "b977ecfa-1b9a-418d-909d-4ebe565736ce"
 
 [compat]
 Ecophys = "0.1.0"
-PlantGeomPrimitives = "0.0.3"
-PlantGeomTurtle = "0.0.4"
-PlantGraphs = "0.0.2"
-PlantRayTracer = "0.0.6"
+PlantGeomPrimitives = "0.0.5"
+PlantGeomTurtle = "0.0.6"
+PlantGraphs = "0.0.3"
+PlantRayTracer = "0.0.8"
 PlantSimEngine = "0.9"
-PlantViz = "0.0.6"
-SkyDomes = "0.1.6"
-VirtualPlantLab = "0.0.6"
-julia = "1.9"
+PlantViz = "0.0.8"
+SkyDomes = "0.1.8"
+VirtualPlantLab = "0.0.7"
+julia = "1.11"

docs/src/howto/Coordinates.md

@@ -183,7 +183,7 @@ function simulate(n)
     for i in 1:n
         growth!(tree)
     end
-    Scene(tree) # Generate the scene to trigger feed!() methods
+    Mesh(tree) # Generate the mesh to trigger feed!() methods
     heights, angles = leaf_info(tree)
     return tree, heights, angles
 end
@@ -199,7 +199,7 @@ tree, heights, angles = simulate(25);
 We can check how the final tree looks like:
 
 ```julia
-render(Scene(tree))
+render(Mesh(tree))
 ```
 
 And we can plot the distribtuion of leaf heights and angles:
@@ -270,7 +270,7 @@ tree, heights2, angles2 = simulate(25);
 And confirm that we get the same tree:
 
 ```julia
-render(Scene(tree))
+render(Mesh(tree))
 length(angles) == length(angles2)
 ```
 

docs/src/howto/GridCloner.md

@@ -89,65 +89,65 @@ end
 tiles = vec([create_tile(origin, dx, dy) for origin in origins]);
 ```
 
-Now we can combine the plants and tiles into a single scene. We randomize the color of each
+Now we can combine the plants and tiles into a single mesh. We randomize the color of each
 tile to help identify them in the visualization:
 
 ```julia
-plant_scene = Scene(vec(plants));
-soil_scene = Scene()
+plant_mesh = Mesh(vec(plants));
+soil_mesh = Mesh()
 for tile in tiles
-    add!(soil_scene, mesh = tile, colors = RGB(rand(), rand(), rand()))
+    add!(soil_mesh, tile, colors = RGB(rand(), rand(), rand()))
 end
-scene = Scene([plant_scene, soil_scene]);
-render(scene)
+mesh = Mesh([plant_mesh, soil_mesh]);
+render(mesh)
 ```
 
-We can also visualize the bounding boxes of a scene (and any clone). If we just want the
-box for the original scene, we can create a grid with no clones. The build the acceleration
+We can also visualize the bounding boxes of a mesh (and any clone). If we just want the
+box for the original mesh, we can create a grid with no clones. The build the acceleration
 object (which includes the grid cloner) and add it to the 3D rendering:
 
 ```julia
 rt_settings = RTSettings(nx = 0, ny = 0)
-acc_one = accelerate(scene, settings = rt_settings);
-render(scene)
+acc_one = accelerate(mesh, settings = rt_settings);
+render(mesh)
 render!(acc_one.grid)
 ```
 
 We can see that bounding box extends to the tips of the leaves, as they grow beyond the soil
-area allocated to the plant. If we now create multiple clones of this scene, we should
+area allocated to the plant. If we now create multiple clones of this mesh, we should
 displace them by a distance of `10dx` along the x-axis and `10dy` along the y-axis. This
 will ensure that the soil tiles of clones do not overlap but the plants will. In other words,
 we emulate additional rows and plants within rows while respecting the same spacing between
 them:
 
 ```julia
 rt_settings = RTSettings(nx = 1, ny = 1, dx = 10dx, dy = 10dy)
-acc = accelerate(scene, settings = rt_settings);
+acc = accelerate(mesh, settings = rt_settings);
 ```
 
-We can now add all the bounding boxes of the clones to the scene:
+We can now add all the bounding boxes of the clones to the mesh:
 
 ```julia
-render(scene)
+render(mesh)
 render!(acc.grid)
 ```
 
 We can see that the bounding boxes of the clones overlap, as expected. Currently there is no
 way in VPL to visualize the actual clones (since that additional geometry is never actually
 generated, see details about *instancing* above). We can do this manually by manually changing
-the meshes of the scene using the method `VirtualPlantLab.translate!`. We add the bounding
-box of the original scene too:
+the meshes of the mesh using the method `VirtualPlantLab.translate!`. We add the bounding
+box of the original mesh too:
 
 ```julia
-scenes = Scene[]
+meshes = Mesh[]
 for i in -10:10
     for j in -10:10
-        new_scene = deepcopy(scene)
-        VirtualPlantLab.translate!(new_scene.mesh, Vec(i*10dx, j*10dy, 0.0))
-        push!(scenes, new_scene)
+        new_mesh = deepcopy(mesh)
+        VirtualPlantLab.translate!(new_mesh, Vec(i*10dx, j*10dy, 0.0))
+        push!(meshes, new_mesh)
     end
 end
-render(Scene(scenes), axes = false)
+render(Mesh(meshes), axes = false)
 render!(acc_one.grid, alpha = 0.8)
 ```
 

docs/src/howto/LightSources.md

@@ -132,31 +132,31 @@ creating multiple sensors below the light source and measuring the light intensi
 sensor.
 
 ```julia
-scene = Scene()
+mesh = Mesh()
 sensors = [Sensor(1) for _ in 1:400]
 c = 1
 for i in 1:20
     for j in 1:20
         r = Rectangle(length = 0.05, width = 0.05)
         rotatey!(r, π/2) ## To put it in the XY plane
         VirtualPlantLab.translate!(r, Vec((i - 1)*0.05, (j - 1)*0.05 + 0.025, 0.0))
-        add!(scene, mesh = r, materials = sensors[c], colors = rand(RGB))
+        add!(mesh, r, materials = sensors[c], colors = rand(RGB))
         c += 1
     end
 end
 ```
 
 ```julia
 import GLMakie
-render(scene)
+render(mesh)
 ```
 
 We can now create a ray tracing object without a grid cloner (note that since all the
 surfaces are sensors we can just set `maxiter = 1`):
 
 ```julia
 settings = RTSettings(pkill = 0.9, maxiter = 1, parallel = true)
-rtobj = RayTracer(scene, source, settings = settings);
+rtobj = RayTracer(mesh, source, settings = settings);
 trace!(rtobj)
 ```
 
@@ -185,7 +185,7 @@ Let's test this by creating a new light source and tracing the rays again.
 ```julia
 source = Source(PointSource(Vec(0.5, 0.5, 1.0)), GaussianSource(X(), Y(), -Z(), 1.0), 1.0, 1_000_000)
 settings = RTSettings(pkill = 0.9, maxiter = 1, parallel = true)
-rtobj = RayTracer(scene, source, settings = settings);
+rtobj = RayTracer(mesh, source, settings = settings);
 trace!(rtobj)
 ```
 

docs/src/howto/Materials.md

@@ -65,7 +65,7 @@ the calculations of absorbed irradiance.
 
 ```julia
 g = Graph(axiom = RA(90.0) +  Tile(1.0, 1.0, 40));
-sc = Scene(g);
+sc = Mesh(g);
 source = DirectionalSource(sc, θ = π/4, Φ = π/2, radiosity = 1.0, nrays = 5_000_000);
 nothing #hide
 ```
@@ -97,11 +97,10 @@ renderer to get the exact colors we specify.
 
 ```julia
 tile.colors = RGB.(0.0, α, 0.0)
-sc = Scene(g)
+sc = Mesh(g)
 render(sc, wireframe = true, shading = GLMakie.NoShading)
 ```
 
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-

docs/src/howto/Message.md

@@ -158,20 +158,20 @@ For a visualization of both leaves and internodes we can actually leave the mess
 given how the code above is structured:
 
 ```julia
-scene = Scene(newtree);
-render(scene, axes = false)
+mesh = Mesh(newtree);
+render(mesh, axes = false)
 ```
 
 For only leaves:
 
 ````julia
-scene = Scene(newtree, message = "leaves");
-render(scene, axes = false)
+mesh = Mesh(newtree, message = "leaves");
+render(mesh, axes = false)
 ````
 
 And for only internodes:
 
 ````julia
-scene = Scene(newtree, message = "internodes");
-render(scene, axes = false)
+mesh = Mesh(newtree, message = "internodes");
+render(mesh, axes = false)
 ````