Issue #7

anaIFernst · anaIFernst · commit 9e3df982e72c · 2024-01-16T16:29:45.000+01:00
- In all tutorials w/ trees&gt; in treeparams swtiched the leaf_angle and branch_angle, change Node to TreeNode
    - Tree tutorial, done!
    - Forest, done!
    - Growth forest, done!
        - Notes:
            - if 50 daily steps are used, the forest is bushy, maybe due to low #daily steps? Let’s increase!
            - if 70 daily steps are used, the forest is still bush, even bushier! The internodes are smaller than leaves and some of the leaves and branches are growing into the soil layer.
            - if 100 daily steps are used, Makie crashes, ups
    - Ray-traced forest, done!
- create_sky updated in ray-traced forest!
    - Need to release new version, else make a note to remind the user to update to master version
diff --git a/docs/src/tutorials/from_tree_forest/forest.md b/docs/src/tutorials/from_tree_forest/forest.md
@@ -1,11 +1,11 @@
 # Forest
 
-Alejandro Morales
+Alejandro Morales and Ana Ernst
 
 Centre for Crop Systems Analysis - Wageningen University
 
 > ## TL;DR
-> Similar in functionality to [Tree]() tutorial with separate graphs for each tree 
+> Similar in functionality to [Tree](https://virtualplantlab.com/dev/tutorials/from_tree_forest/tree/) tutorial with separate graphs for each tree 
 > - Modify tree parameters for each tree
 > - Multithreaded simulation (grow trees in parallel)
 > - Scene customization (e.g., add soil)
@@ -28,8 +28,8 @@ module TreeTypes
     struct Meristem <: VirtualPlantLab.Node end
     # Bud
     struct Bud <: VirtualPlantLab.Node end
-    # Node
-    struct Node <: VirtualPlantLab.Node end
+    # TreeNode
+    struct TreeNode <: VirtualPlantLab.Node end
     # BudNode
     struct BudNode <: VirtualPlantLab.Node end
     # Internode (needs to be mutable to allow for changes over time)
@@ -46,8 +46,8 @@ module TreeTypes
         growth::Float64 = 0.1
         budbreak::Float64 = 0.25
         phyllotaxis::Float64 = 140.0
-        leaf_angle::Float64 = 30.0
-        branch_angle::Float64 = 45.0
+        leaf_angle::Float64 = 45.0
+        branch_angle::Float64 = 30.0
     end
 end
 
@@ -93,7 +93,7 @@ end
 Rules for meristem and branches:
 
 ````julia
-meristem_rule = Rule(TreeTypes.Meristem, rhs = mer -> TreeTypes.Node() +
+meristem_rule = Rule(TreeTypes.Meristem, rhs = mer -> TreeTypes.TreeNode() +
                                               (TreeTypes.Bud(), TreeTypes.Leaf()) +
                                          TreeTypes.Internode() + TreeTypes.Meristem())
 
@@ -179,13 +179,13 @@ We may assume that the initial orientation is uniformly distributed between 0 an
 orientations = [rand()*360.0 for i = 1:2.0:20.0, j = 1:2.0:20.0]
 ````
 
-For the `growth` and `budbreak` parameters we will assumed that they follow a
+For the `growth` and `budbreak` parameters we will be assumed to follow a
 LogNormal and Beta distribution, respectively. We can generate random
 values from these distributions using the `Distributions` package. For the
 relative growth rate:
 
 ````julia
-growths = rand(LogNormal(-2, 0.3), 10, 10)
+growths = rand(LogNormal(-2, 0.2), 10, 10)
 histogram(vec(growths))
 ````
 
@@ -200,7 +200,7 @@ Now we can create our forest by calling the `create_tree` function we defined ea
 with the correct inputs per tree:
 
 ````julia
-forest = vec(create_tree.(origins, growths, budbreaks, orientations));
+forest = vec(create_tree.(origins, growths, budbreaks, orientations))
 ````
 
 By vectorizing `create_tree()` over the different arrays, we end up with an array
@@ -217,7 +217,7 @@ We can simulate the growth of each tree by applying the method `simulate` to eac
 tree, creating a new version of the forest (the code below is an array comprehension)
 
 ````julia
-newforest = [simulate(tree, getInternode, 2) for tree in forest];
+newforest = [simulate(tree, getInternode, 2) for tree in forest]
 ````
 
 And we can render the forest with the function `render` as in the binary tree
@@ -273,7 +273,7 @@ geometric element it is best to combine all these geometries in a `GLScene` obje
 with the `newforest` generated in the above:
 
 ````julia
-scene = Scene(newforest);
+scene = Scene(newforest)
 ````
 
 We can create the soil tile directly, without having to create a graph. The simplest approach is two use
diff --git a/docs/src/tutorials/from_tree_forest/growthforest.md b/docs/src/tutorials/from_tree_forest/growthforest.md
@@ -57,7 +57,7 @@ module TreeTypes
     # Bud
     struct Bud <: VirtualPlantLab.Node end
     # Node
-    struct Node <: VirtualPlantLab.Node end
+    struct TreeNode <: VirtualPlantLab.Node end
     # BudNode
     struct BudNode <: VirtualPlantLab.Node end
     # Internode (needs to be mutable to allow for changes over time)
@@ -92,8 +92,8 @@ module TreeTypes
         plastochron::Int64 = 5 ## Number of days between phytomer production
         leaf_expansion::Float64 = 15.0 ## Number of days that a leaf expands
         phyllotaxis::Float64 = 140.0
-        leaf_angle::Float64 = 30.0
-        branch_angle::Float64 = 45.0
+        leaf_angle::Float64 = 45.0
+        branch_angle::Float64 = 30.0
     end
 end
 
@@ -145,7 +145,7 @@ internodes and will only be triggered every X days, where X is the plastochron.
 function create_meristem_rule(vleaf, vint)
     meristem_rule = Rule(TreeTypes.Meristem,
                         lhs = mer -> mod(data(mer).age, graph_data(mer).plastochron) == 0,
-                        rhs = mer -> TreeTypes.Node() +
+                        rhs = mer -> TreeTypes.TreeNode() +
                                      (TreeTypes.Bud(),
                                      TreeTypes.Leaf(biomass = vleaf.biomass,
                                                     length  = vleaf.length,
@@ -178,7 +178,7 @@ function prob_break(bud)
             child = children(child)[1]
             data_child = data(child)
         # If we encounter a node, extract the next internode
-        elseif data_child isa TreeTypes.Node
+        elseif data_child isa TreeTypes.TreeNode
                 child = filter(x -> data(x) isa TreeTypes.Internode, children(child))[1]
                 data_child = data(child)
         else
diff --git a/docs/src/tutorials/from_tree_forest/raytracedforest.md b/docs/src/tutorials/from_tree_forest/raytracedforest.md
@@ -1,20 +1,19 @@
 # Ray-traced forest
 
-Alejandro Morales
+Alejandro Morales and Ana Ernst
 
 Centre for Crop Systems Analysis - Wageningen University
 
 > ## TL;DR
 > Now we want to forest growth model that PAR interception and introduces user to the ray-tracer.
-> - Include material as a property for each object
-> - Create sky for specific conditions and locations
+> - Include [material](https://virtualplantlab.com/dev/manual/Raytracer/#Materials) as a property for each object
+> - Create sky for specific conditions and locations using [SkyDomes](https://virtualplantlab.com/dev/VPLVerse/SkyDomes/)
 > - Layer different types of radiation in sky domes (e.g., direct and diffuse)
 > - Combine graph and sky with a ray-tracer
-> - Compute growth and biomass production according to PAR interception and RUE
+> - Compute growth and biomass production according to PAR interception and RUE 
 > 
 
-In this example we extend the forest growth model to include PAR interception and
-radiation use efficiency to compute the daily growth rate.
+In this example we extend the [Growth Forest](https://virtualplantlab.com/dev/tutorials/from_tree_forest/growthforest/) model to include PAR interception and radiation use efficiency to compute the daily growth rate.
 
 The following packages are needed:
 
@@ -50,8 +49,8 @@ module TreeTypes
     end
     # Bud
     struct Bud <: VirtualPlantLab.Node end
-    # Node
-    struct Node <: VirtualPlantLab.Node end
+    # TreeNode
+    struct TreeNode <: VirtualPlantLab.Node end
     # BudNode
     struct BudNode <: VirtualPlantLab.Node end
     # Internode (needs to be mutable to allow for changes over time)
@@ -89,8 +88,8 @@ module TreeTypes
         plastochron::Int64 = 5 ## Number of days between phytomer production
         leaf_expansion::Float64 = 15.0 ## Number of days that a leaf expands
         phyllotaxis::Float64 = 140.0
-        leaf_angle::Float64 = 30.0
-        branch_angle::Float64 = 45.0
+        leaf_angle::Float64 = 45.0
+        branch_angle::Float64 = 30.0
     end
 end
 
@@ -142,7 +141,7 @@ internodes and will only be triggered every X days, where X is the plastochron.
 function create_meristem_rule(vleaf, vint)
     meristem_rule = Rule(TreeTypes.Meristem,
                         lhs = mer -> mod(data(mer).age, graph_data(mer).plastochron) == 0,
-                        rhs = mer -> TreeTypes.Node() +
+                        rhs = mer -> TreeTypes.TreeNode() +
                                      (TreeTypes.Bud(),
                                      TreeTypes.Leaf(biomass = vleaf.biomass,
                                                     length  = vleaf.length,
@@ -175,11 +174,11 @@ function prob_break(bud)
             child = children(child)[1]
             data_child = data(child)
         # If we encounter a node, extract the next internode
-        elseif data_child isa TreeTypes.Node
+        elseif data_child isa TreeTypes.TreeNode
                 child = filter(x -> data(x) isa TreeTypes.Internode, children(child))[1]
                 data_child = data(child)
         else
-            error("Should be Internode, Node or Meristem")
+            error("Should be Internode, TreeNode or Meristem")
         end
     end
     # Compute the probability of bud break as function of distance and
@@ -221,6 +220,7 @@ function create_soil()
     VirtualPlantLab.translate!(soil, Vec(0.0, 10.5, 0.0)) ## Corner at (0,0,0)
     return soil
 end
+
 function create_scene(forest)
     # These are the trees
     scene = Scene(vec(forest))
@@ -251,10 +251,12 @@ function create_sky(;scene, lat = 52.0*π/180.0, DOY = 182)
     dec = declination(DOY)
     DL = day_length(lat, dec)*3600
     # Compute solar irradiance
-    temp = [clear_sky(lat = lat, DOY = DOY, f = f) for f in fs] # W/m2
+    temp = [clear_sky(lat = lat, DOY = DOY, f = f) for f in fs] # W m2
     Ig   = getindex.(temp, 1)
     Idir = getindex.(temp, 2)
     Idif = getindex.(temp, 3)
+    theta = getindex.(temp, 4)
+    phi = getindex.(temp, 5)
     # Conversion factors to PAR for direct and diffuse irradiance
     f_dir = waveband_conversion(Itype = :direct,  waveband = :PAR, mode = :power)
     f_dif = waveband_conversion(Itype = :diffuse, waveband = :PAR, mode = :power)
@@ -268,8 +270,11 @@ function create_sky(;scene, lat = 52.0*π/180.0, DOY = 182)
                   nrays_dif = 1_000_000, ## Total number of rays for diffuse solar radiation
                   sky_model = StandardSky, ## Angular distribution of solar radiation
                   dome_method = equal_solid_angles, ## Discretization of the sky dome
+                  # Angles
                   ntheta = 9, ## Number of discretization steps in the zenith angle
-                  nphi = 12) ## Number of discretization steps in the azimuth angle
+                  theta_dir = theta, ## Direction of the zenith angle
+                  nphi = 12, ## Number of discretization steps in the azimuth angle
+                  phi_dir = phi) ## Direction of 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])
@@ -514,7 +519,7 @@ histogram(vec(orientations))
 origins = [Vec(i,j,0) for i = 1:2.0:20.0, j = 1:2.0:20.0];
 ````
 
-The following initalizes a tree based on the origin, orientation and RUE:
+The following initializes a tree based on the origin, orientation and RUE:
 
 ````julia
 function create_tree(origin, orientation, RUE)
diff --git a/docs/src/tutorials/from_tree_forest/tree.md b/docs/src/tutorials/from_tree_forest/tree.md
@@ -1,6 +1,6 @@
 # Tree
 
-Alejandro Morales
+Alejandro Morales and Ana Ernst
 
 Centre for Crop Systems Analysis - Wageningen University
 
@@ -14,17 +14,17 @@ In this example we build a 3D representation of a binary TreeTypes. Although thi
 
 The model requires five types of nodes:
 
-*Meristem*: These are the nodes responsible for growth of new organs in our binary TreeTypes. They contain no data or geometry (i.e. they are a point in the 3D structure).
+- *Meristem*: These are the nodes responsible for growth of new organs in our binary TreeTypes. They contain no data or geometry (i.e. they are a point in the 3D structure).
 
-*Internode*: The result of growth of a branch, between two nodes. Internodes are represented by cylinders with a fixed width but variable length.
+- *Internode*: The result of growth of a branch, between two nodes. Internodes are represented by cylinders with a fixed width but variable length.
 
-*Node*: What is left after a meristem produces a new organ (it separates internodes). They contain no data or geometry (so also a point) but are required to keep the branching structure of the tree as well as connecting leaves.
+- *TreeNode*: What is left after a meristem produces a new organ (it separates internodes). They contain no data or geometry (so also a point) but are required to keep the branching structure of the tree as well as connecting leaves.
 
-*Bud*: These are dormant meristems associated to tree nodes. When they are activated, they become an active meristem that produces a branch. They contain no data or geometry, but they change the orientation of the turtle.
+- *Bud*: These are dormant meristems associated to tree nodes. When they are activated, they become an active meristem that produces a branch. They contain no data or geometry, but they change the orientation of the turtle.
 
-*BudNode*: The node left by a bud after it has been activated. They contain no data or geometry, but they change the orientation of the turtle.
+- *BudNode*: The node left by a bud after it has been activated. They contain no data or geometry, but they change the orientation of the turtle.
 
-*Leaf*: These are the nodes associated to leaves in the TreeTypes. They are represented by ellipses with a particular orientation and insertion angle. The insertion angle is assumed constant, but the orientation angle varies according to an elliptical phyllotaxis rule.
+- *Leaf*: These are the nodes associated to leaves in the TreeTypes. They are represented by ellipses with a particular orientation and insertion angle. The insertion angle is assumed constant, but the orientation angle varies according to an elliptical phyllotaxis rule.
 
 In this first simple model, only internodes grow over time according to a relative growth rate, whereas leaves are assumed to be of fixed sized determined at their creation. For simplicity, all active meristems will produce a phytomer (combination of node, internode, leaves and buds) per time step. Bud break is assumed stochastic, with a probability that increases proportional to the number of phytomers from the apical meristem (up to 1). In the following tutorials, these assumptions are replaced by more realistic models of light interception, photosynthesis, etc.
 
@@ -41,8 +41,8 @@ module TreeTypes
     struct Meristem <: VirtualPlantLab.Node end
     # Bud
     struct Bud <: VirtualPlantLab.Node end
-    # Node
-    struct Node <: VirtualPlantLab.Node end
+    # TreeNode
+    struct TreeNode <: VirtualPlantLab.Node end
     # BudNode
     struct BudNode <: VirtualPlantLab.Node end
     # Internode (needs to be mutable to allow for changes over time)
@@ -59,8 +59,8 @@ module TreeTypes
         growth::Float64 = 0.1
         budbreak::Float64 = 0.25
         phyllotaxis::Float64 = 140.0
-        leaf_angle::Float64 = 30.0
-        branch_angle::Float64 = 45.0
+        leaf_angle::Float64 = 45.0
+        branch_angle::Float64 = 30.0
     end
 end
 ````
@@ -99,9 +99,9 @@ end
 The growth rule for a branch within a tree is simple: a phytomer (or basic unit of morphology) is composed of a node, a leaf, a bud node, an internode and an active meristem at the end. Each time step, the meristem is replaced by a new phytomer, allowing for the development within a branch.
 
 ````julia
-meristem_rule = Rule(TreeTypes.Meristem, rhs = mer -> TreeTypes.Node() +
+meristem_rule = Rule(TreeTypes.Meristem, rhs = mer -> TreeTypes.TreeNode() +
                                               (TreeTypes.Bud(), TreeTypes.Leaf()) +
-                                         TreeTypes.Internode() + TreeTypes.Meristem())
+                                               TreeTypes.Internode() + TreeTypes.Meristem())
 ````
 
 In addition, every step of the simulation, each bud may break, creating a new branch. The probability of bud break is proportional to the number of phytomers from the apical meristem (up to 1), which requires a relational rule to count the number of internodes in the graph up to reaching a meristem. When a bud breaks, it is replaced by a bud node, an internode and a new meristem. This new meristem becomes the apical meristem of the new branch, such that `meristem_rule` would apply. Note how we create an external function to compute whether a bud breaks or not. This is useful to keep the `branch_rule` rule simple and readable, while allow for a relatively complex bud break model. It also makes it easier to debug the bud break model, since it can be tested independently of the graph rewriting.
