diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 0be39e4..6f646ad 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-28T16:53:34","documenter_version":"1.8.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-28T17:01:29","documenter_version":"1.8.0"}} \ No newline at end of file diff --git a/dev/API/index.html b/dev/API/index.html index 2104ede..464d763 100644 --- a/dev/API/index.html +++ b/dev/API/index.html @@ -1,5 +1,5 @@ -API · PlantGeom.jl
GitHub

API

PlantGeom.Phong — Type

Data structure for a mesh material that is used to describe the light components of a Phong reflection type model. All data is stored as RGBα for Red, Green, Blue and transparency.

source
PlantGeom.RefMesh — Type
RefMesh(
+API · PlantGeom.jl
GitHub
API
PlantGeom.Phong — Type
Data structure for a mesh material that is used to describe the light components of a Phong reflection type model. All data is stored as RGBα for Red, Green, Blue and transparency.
source
PlantGeom.RefMesh — Type
RefMesh(
     name::S
     mesh::SimpleMesh
     normals::N
@@ -8,7 +8,7 @@
     taper::Bool
 )
 
-RefMesh(name, mesh, material = RGB(220 / 255, 220 / 255, 220 / 255))
RefMesh type. Stores all information about a Mesh:
  • name::S: the mesh name
  • mesh::SimpleMesh: the actual mesh information -> points and topology
  • normals::Vector{Float64}: the normals, given as a vector of x1,y1,z1,x2,y2,z2...
  • texture_coords::Vector{Float64}: the texture coordinates (not used yet), idem, a vector
  • material::M: the material, used to set the shading
  • taper::Bool: true if tapering is enabled
The reference meshes are then transformed on each node of the MTG using a transformation matrix to match the actual mesh.
source
PlantGeom.geometry — Type
geometry(; ref_mesh<:RefMesh, ref_mesh_index=nothing, transformation=Identity(), dUp=1.0, dDwn=1.0, mesh::Union{SimpleMesh,Nothing}=nothing)
A Node geometry with the reference mesh, its transformation (as a function) and optionnally the index of the reference mesh in the reference meshes data base (see notes) and the resulting mesh (optional to save memory).
Note
The refmesh usually points to a RefMesh stored in the `:refmeshes` attribute of the root node of the MTG.
Although optional, storing the index of the reference mesh (ref_mesh_index) in the database allows a faster writing of the MTG as an OPF to disk.
The transformation field should be a TransformsBase.Transform, such as TransformsBase.Identity, or the ones implemented in  Meshes.jl, e.g. Translate, Scale... If you already have the transformation matrix, you can pass it to Meshes.Affine(). 
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Base.:== — Method
==(a::geometry, b::geometry)
Test RefMeshes equality.
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Base.:== — Method
==(a::RefMesh, b::RefMesh)
Test RefMesh equality.
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Base.:== — Method
==(a::RefMeshes, b::RefMeshes)
Test RefMeshes equality.
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Meshes.nelements — Method
nelements(meshes::RefMeshes)
Return the number of elements for each reference mesh as a vector of nelements
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Meshes.nelements — Method
nelements(meshes::RefMeshes)
Return the number of elements of a reference mesh
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Meshes.nvertices — Method
nvertices(meshes::RefMeshes)
Return the number of vertices for each reference mesh as a vector of nvertices
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Meshes.viz — Function
viz(opf::MultiScaleTreeGraph.Node; kwargs...)
+RefMesh(name, mesh, material = RGB(220 / 255, 220 / 255, 220 / 255))
RefMesh type. Stores all information about a Mesh:
  • name::S: the mesh name
  • mesh::SimpleMesh: the actual mesh information -> points and topology
  • normals::Vector{Float64}: the normals, given as a vector of x1,y1,z1,x2,y2,z2...
  • texture_coords::Vector{Float64}: the texture coordinates (not used yet), idem, a vector
  • material::M: the material, used to set the shading
  • taper::Bool: true if tapering is enabled
The reference meshes are then transformed on each node of the MTG using a transformation matrix to match the actual mesh.
source
PlantGeom.geometry — Type
geometry(; ref_mesh<:RefMesh, ref_mesh_index=nothing, transformation=Identity(), dUp=1.0, dDwn=1.0, mesh::Union{SimpleMesh,Nothing}=nothing)
A Node geometry with the reference mesh, its transformation (as a function) and optionnally the index of the reference mesh in the reference meshes data base (see notes) and the resulting mesh (optional to save memory).
Note
The refmesh usually points to a RefMesh stored in the `:refmeshes` attribute of the root node of the MTG.
Although optional, storing the index of the reference mesh (ref_mesh_index) in the database allows a faster writing of the MTG as an OPF to disk.
The transformation field should be a TransformsBase.Transform, such as TransformsBase.Identity, or the ones implemented in  Meshes.jl, e.g. Translate, Scale... If you already have the transformation matrix, you can pass it to Meshes.Affine(). 
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Base.:== — Method
==(a::geometry, b::geometry)
Test RefMeshes equality.
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Base.:== — Method
==(a::RefMesh, b::RefMesh)
Test RefMesh equality.
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Base.:== — Method
==(a::RefMeshes, b::RefMeshes)
Test RefMeshes equality.
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Meshes.nelements — Method
nelements(meshes::RefMeshes)
Return the number of elements for each reference mesh as a vector of nelements
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Meshes.nelements — Method
nelements(meshes::RefMeshes)
Return the number of elements of a reference mesh
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Meshes.nvertices — Method
nvertices(meshes::RefMeshes)
Return the number of vertices for each reference mesh as a vector of nvertices
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Meshes.viz — Function
viz(opf::MultiScaleTreeGraph.Node; kwargs...)
 viz!(opf::MultiScaleTreeGraph.Node; kwargs...)
Vizualise the 3D geometry of an MTG (usually read from an OPF). This function search for the :geometry attribute in each node of the MTG, and build the vizualisation using the mesh field, or the reference meshes and the associated transformation matrix if missing.
The :geometry attribute is usually added by the refmesh_to_mesh! function first, which can be called with the transform! function. See the examples below.
Arguments
  • opf: The MTG to be vizualised.
  • kwargs: Additional arguments to be passed to viz!, wich includes: 
    • color: The color to be used for the plot. Can be a colorant, an attribute of the MTG (given as a Symbol), or a dictionary of colors for each reference mesh.
    • colormap: The colorscheme to be used for the plot. Can be a Symbol or a ColorScheme. 
    • segmentcolor: The color to be used for the facets. Should be a colorant or a symbol of color.
    • showsegments: A boolean indicating whether the facets should be shown or not.
    • color_missing: The color to be used for missing values. Should be a colorant or a symbol of color.
    • color_vertex: A boolean indicating whether the values in color (if colored by attributes) are defined for each vertex of the mesh, or for each mesh.
    • index: An integer giving the index of the attribute value to be vizualised. This is useful when the attribute is a vector of values for e.g. each timestep.
    • color_cache_name: The name of the color cache. Should be a string (default to a random string).
Note that color_vertex is set to false by default.
Examples
using MultiScaleTreeGraph, PlantGeom, GLMakie
 
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
@@ -62,7 +62,7 @@
 # Or just changing the color of some:
 viz(meshes, color = Dict(1 => :burlywood4, 3 => :burlywood4))
 # One color for each vertex of the refmesh 0:
-viz(meshes, color = Dict(2 => 1:nvertices(meshes)[2]))
source
Meshes.viz! — Function
viz(opf::MultiScaleTreeGraph.Node; kwargs...)
+viz(meshes, color = Dict(2 => 1:nvertices(meshes)[2]))
source
Meshes.viz! — Function
viz(opf::MultiScaleTreeGraph.Node; kwargs...)
 viz!(opf::MultiScaleTreeGraph.Node; kwargs...)
Vizualise the 3D geometry of an MTG (usually read from an OPF). This function search for the :geometry attribute in each node of the MTG, and build the vizualisation using the mesh field, or the reference meshes and the associated transformation matrix if missing.
The :geometry attribute is usually added by the refmesh_to_mesh! function first, which can be called with the transform! function. See the examples below.
Arguments
  • opf: The MTG to be vizualised.
  • kwargs: Additional arguments to be passed to viz!, wich includes: 
    • color: The color to be used for the plot. Can be a colorant, an attribute of the MTG (given as a Symbol), or a dictionary of colors for each reference mesh.
    • colormap: The colorscheme to be used for the plot. Can be a Symbol or a ColorScheme. 
    • segmentcolor: The color to be used for the facets. Should be a colorant or a symbol of color.
    • showsegments: A boolean indicating whether the facets should be shown or not.
    • color_missing: The color to be used for missing values. Should be a colorant or a symbol of color.
    • color_vertex: A boolean indicating whether the values in color (if colored by attributes) are defined for each vertex of the mesh, or for each mesh.
    • index: An integer giving the index of the attribute value to be vizualised. This is useful when the attribute is a vector of values for e.g. each timestep.
    • color_cache_name: The name of the color cache. Should be a string (default to a random string).
Note that color_vertex is set to false by default.
Examples
using MultiScaleTreeGraph, PlantGeom, GLMakie
 
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
@@ -116,7 +116,7 @@
 # Or just changing the color of some:
 viz(meshes, color = Dict(1 => :burlywood4, 3 => :burlywood4))
 # One color for each vertex of the refmesh 0:
-viz(meshes, color = Dict(2 => 1:nvertices(meshes)[2]))
source
PlantGeom.color_type — Method
color_type(color, opf)
Return the type of the color, whether it is an attribute, a colorant, or a RefMeshColorant.
Arguments
  • color: The color to be checked.
  • opf: The MTG to be plotted.
Returns
  • RefMeshColorant: If the color is :slategray3, then it is the default color given by Meshes,
so we assume nothing was passed by the user and color by reference mesh instead.
  • AttributeColorant: If the color is an attribute of the MTG, then we color by that attribute.
  • T: If the color is a colorant, then we color everything by that color.
Examples
using MultiScaleTreeGraph, PlantGeom, Colors
+viz(meshes, color = Dict(2 => 1:nvertices(meshes)[2]))
source
PlantGeom.color_type — Method
color_type(color, opf)
Return the type of the color, whether it is an attribute, a colorant, or a RefMeshColorant.
Arguments
  • color: The color to be checked.
  • opf: The MTG to be plotted.
Returns
  • RefMeshColorant: If the color is :slategray3, then it is the default color given by Meshes,
so we assume nothing was passed by the user and color by reference mesh instead.
  • AttributeColorant: If the color is an attribute of the MTG, then we color by that attribute.
  • T: If the color is a colorant, then we color everything by that color.
Examples
using MultiScaleTreeGraph, PlantGeom, Colors
 
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 
@@ -133,10 +133,10 @@
 color_type(:slategray3, opf)
 
 # Dict of colors:
-color_type(Dict(1=>RGB(0.1,0.5,0.1), 2=>RGB(0.5,0.1,0.1)), opf)
source
PlantGeom.colorbar — Method
colorbar(parent, plotobject, kwargs...)
Add a colorbar based on the attribute chose to color the plot. plotobject must be a plot of an MTG colored by an attribute. Use Makie.Colorbar for any other use case instead.
Arguments
  • parent: parent scene
  • plotobject: plot object to add the colorbar to
  • kwargs: keyword arguments to pass to Makie.Colorbar, e.g. label="Length (m)"
Example
```julia using GLMakie, MultiScaleTreeGraph, PlantGeom file = joinpath(dirname(dirname(pathof(PlantGeom))), "test", "files", "simpleplant.opf") opf = readopf(file)
f, ax, p = viz(opf, color=:Length) colorbar(f[1, 2], p) f
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PlantGeom.coordinates! — Method
coordinates!(mtg; angle = 45; force = false)
Compute dummy 3d coordinates for the mtg nodes using an alterning phyllotaxy. Used when coordinates are missing. Coordinates are just node attributes with reserved names: :XX, :YY and :ZZ.
Returns
Nothing, mutates the mtg in-place (adds :XX, :YY and :ZZ to nodes).
Examples
file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.mtg")
+color_type(Dict(1=>RGB(0.1,0.5,0.1), 2=>RGB(0.5,0.1,0.1)), opf)
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PlantGeom.colorbar — Method
colorbar(parent, plotobject, kwargs...)
Add a colorbar based on the attribute chose to color the plot. plotobject must be a plot of an MTG colored by an attribute. Use Makie.Colorbar for any other use case instead.
Arguments
  • parent: parent scene
  • plotobject: plot object to add the colorbar to
  • kwargs: keyword arguments to pass to Makie.Colorbar, e.g. label="Length (m)"
Example
```julia using GLMakie, MultiScaleTreeGraph, PlantGeom file = joinpath(dirname(dirname(pathof(PlantGeom))), "test", "files", "simpleplant.opf") opf = readopf(file)
f, ax, p = viz(opf, color=:Length) colorbar(f[1, 2], p) f
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PlantGeom.coordinates! — Method
coordinates!(mtg; angle = 45; force = false)
Compute dummy 3d coordinates for the mtg nodes using an alterning phyllotaxy. Used when coordinates are missing. Coordinates are just node attributes with reserved names: :XX, :YY and :ZZ.
Returns
Nothing, mutates the mtg in-place (adds :XX, :YY and :ZZ to nodes).
Examples
file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.mtg")
 mtg = read_mtg(file)
 coordinates!(mtg)
-DataFrame(mtg, [:XX, :YY, :ZZ])
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PlantGeom.diagram — Function
diagram(opf::MultiScaleTreeGraph.Node; kwargs...)
+DataFrame(mtg, [:XX, :YY, :ZZ])
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PlantGeom.diagram — Function
diagram(opf::MultiScaleTreeGraph.Node; kwargs...)
 diagram!(opf::MultiScaleTreeGraph.Node; kwargs...)
Make a diagram of the MTG tree using a Makie.jl backend.
Danger
This function is an extension to the package. It is only available if you imported a Makie backend (e.g. using GLMakie) prior to using PlantGeom.
The main attributes are:
  • color: the color of the nodes
  • colormap: the colormap used if the color uses an attribute. By default it uses viridis.
Must be a ColorScheme from ColorSchemes or a Symbol with its name.
Examples
using GLMakie, PlantGeom
 
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
@@ -151,7 +151,7 @@
 diagram(opf, color = :red)
 
 # Or colouring by opf attribute, *e.g.* using the nodes Z coordinates:
-diagram(opf, color = :ZZ)
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PlantGeom.diagram! — Function
diagram(opf::MultiScaleTreeGraph.Node; kwargs...)
 diagram!(opf::MultiScaleTreeGraph.Node; kwargs...)
Make a diagram of the MTG tree using a Makie.jl backend.
Danger
This function is an extension to the package. It is only available if you imported a Makie backend (e.g. using GLMakie) prior to using PlantGeom.
The main attributes are:
  • color: the color of the nodes
  • colormap: the colormap used if the color uses an attribute. By default it uses viridis.
Must be a ColorScheme from ColorSchemes or a Symbol with its name.
Examples
using GLMakie, PlantGeom
 
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
@@ -166,8 +166,8 @@
 diagram(opf, color = :red)
 
 # Or colouring by opf attribute, *e.g.* using the nodes Z coordinates:
-diagram(opf, color = :ZZ)
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PlantGeom.get_color — Method
get_color(var <: AbstractArray, range_var, colormap=colorschemes[:viridis])
-get_color(var, range_var, colormap=colorschemes[:viridis])
Map value(s) to colors from a colormap based on a range of values
Arguments
  • var: value(s) to map to colors
  • range_var: range of values to map to colors
  • colormap: colormap to use
Returns
  • color: color(s) corresponding to var
Examples
```julia using Colors
getcolor(1, 1:2, colormap = colorschemes[:viridis]) # returns RGB{N0f8}(0.267004,0.00487433,0.329415) getcolor(1:2, 1:10, colormap = colorschemes[:viridis]) # returns RGB{N0f8}(0.267004,0.00487433,0.329415) get_color(1:2, 1:10, 1, colormap = colorschemes[:viridis]) # returns RGB{N0f8}(0.267004,0.00487433,0.329415)
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PlantGeom.get_mtg_color — Method
get_mtg_color(color, opf)
Return the color to be used for the plot.
Arguments
  • color: The color to be checked.
  • opf: The MTG to be plotted.
Returns
The color to be used for the plot.
Examples
using MultiScaleTreeGraph, PlantGeom, Colors
+diagram(opf, color = :ZZ)
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PlantGeom.get_color — Method
get_color(var <: AbstractArray, range_var, colormap=colorschemes[:viridis])
+get_color(var, range_var, colormap=colorschemes[:viridis])
Map value(s) to colors from a colormap based on a range of values
Arguments
  • var: value(s) to map to colors
  • range_var: range of values to map to colors
  • colormap: colormap to use
Returns
  • color: color(s) corresponding to var
Examples
```julia using Colors
getcolor(1, 1:2, colormap = colorschemes[:viridis]) # returns RGB{N0f8}(0.267004,0.00487433,0.329415) getcolor(1:2, 1:10, colormap = colorschemes[:viridis]) # returns RGB{N0f8}(0.267004,0.00487433,0.329415) get_color(1:2, 1:10, 1, colormap = colorschemes[:viridis]) # returns RGB{N0f8}(0.267004,0.00487433,0.329415)
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PlantGeom.get_mtg_color — Method
get_mtg_color(color, opf)
Return the color to be used for the plot.
Arguments
  • color: The color to be checked.
  • opf: The MTG to be plotted.
Returns
The color to be used for the plot.
Examples
using MultiScaleTreeGraph, PlantGeom, Colors
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 opf = read_opf(file)
 
@@ -176,28 +176,28 @@
 get_mtg_color(:Length, opf)
 get_mtg_color(:slategray3, opf)
 get_mtg_color(Dict(1=>RGB(0.1,0.5,0.1), 2=>RGB(0.1,0.1,0.5)), opf)
-get_mtg_color(Dict(1 => :burlywood4, 2 => :springgreen4), opf)
source
PlantGeom.get_ref_mesh_index — Function
get_ref_mesh_index!(node, ref_meshes = get_ref_meshes(node))
-get_ref_mesh_index(node, ref_meshes = get_ref_meshes(node))
Get the index of the reference mesh used in the current node.
Notes
Please use the ref_meshes argument preferably as not giving it make the function visit the root node each time otherwise, and it can become a limitation when traversing a big MTG.
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PlantGeom.get_ref_mesh_index! — Function
get_ref_mesh_index!(node, ref_meshes = get_ref_meshes(node))
-get_ref_mesh_index(node, ref_meshes = get_ref_meshes(node))
Get the index of the reference mesh used in the current node.
Notes
Please use the ref_meshes argument preferably as not giving it make the function visit the root node each time otherwise, and it can become a limitation when traversing a big MTG.
source
PlantGeom.get_ref_meshes — Method
get_ref_meshes(mtg)
Get all reference meshes from an mtg, usually from an OPF.
Examples
using PlantGeom
+get_mtg_color(Dict(1 => :burlywood4, 2 => :springgreen4), opf)
source
PlantGeom.get_ref_mesh_index — Function
get_ref_mesh_index!(node, ref_meshes = get_ref_meshes(node))
+get_ref_mesh_index(node, ref_meshes = get_ref_meshes(node))
Get the index of the reference mesh used in the current node.
Notes
Please use the ref_meshes argument preferably as not giving it make the function visit the root node each time otherwise, and it can become a limitation when traversing a big MTG.
source
PlantGeom.get_ref_mesh_index! — Function
get_ref_mesh_index!(node, ref_meshes = get_ref_meshes(node))
+get_ref_mesh_index(node, ref_meshes = get_ref_meshes(node))
Get the index of the reference mesh used in the current node.
Notes
Please use the ref_meshes argument preferably as not giving it make the function visit the root node each time otherwise, and it can become a limitation when traversing a big MTG.
source
PlantGeom.get_ref_meshes — Method
get_ref_meshes(mtg)
Get all reference meshes from an mtg, usually from an OPF.
Examples
using PlantGeom
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 opf = read_opf(file)
 meshes = get_ref_meshes(opf)
 
 using GLMakie
-viz(meshes)
source
PlantGeom.get_ref_meshes_color — Method
get_ref_meshes_color(meshes::RefMeshes)
Get the reference meshes colors (only the diffuse part for now).
Examples
using MultiScaleTreeGraph, PlantGeom
+viz(meshes)
source
PlantGeom.get_ref_meshes_color — Method
get_ref_meshes_color(meshes::RefMeshes)
Get the reference meshes colors (only the diffuse part for now).
Examples
using MultiScaleTreeGraph, PlantGeom
 file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.opf")
 opf = read_opf(file)
 meshes = get_ref_meshes(opf)
-PlantGeom.get_ref_meshes_color(meshes)
source
PlantGeom.map_coord — Method
map_coord(f, mesh, coord)
Apply function f over the mesh coordinates coord. Values for coord can be 1 for x, 2 for y and 3 for z.
source
PlantGeom.map_coord — Method
map_coord(f, mesh, coord)
Apply function f over the mesh coordinates coord. Values for coord can be 1 for x, 2 for y and 3 for z.
source
PlantGeom.meshBDD_to_meshes — Method
meshBDD_to_meshes(x)
Examples
using MultiScaleTreeGraph
 file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.opf")
 opf = read_opf(file)
-meshBDD_to_meshes(opf[:meshBDD])
source
PlantGeom.mtg_coordinates_df — Function
mtg_coordinates_df(mtg, attr; force = false)
-mtg_coordinates_df!(mtg, attr; force = false)
Extract the coordinates of the nodes of the mtg and the coordinates of their parents (:XXfrom, :YYfrom, :ZZ_from) and output a DataFrame. Optionally you can also provide an attribute to add to the output DataFrame too by passing its name as a symbol to attr.
The coordinates are computed using coordinates! if missing, or if force = true.
source
PlantGeom.mtg_to_opf_link — Method
mtg_to_opf_link(link)
Takes an MTG link as input ("/", "<" or "+") and outputs its corresponding link as declared in the OPF format ("decomp", "follow" or "branch")
source
PlantGeom.mtg_topology_to_xml! — Function
mtg_topology_to_xml!(node, xml_parent)
Write the MTG topology, attributes and geometry into XML format. This function is used to write the "topology" section of the OPF.
source
PlantGeom.normals_vertex — Method
normals_vertex(mesh::Meshes.SimpleMesh)
Compute per vertex normals and return them as a StaticArrays.SVector.
#! This is a naive approach because I have no time right know. #! We just put the face mesh as a vertex mesh (and ovewritting values for common points)
TODO: Use a real computation instead. See e.g.:
https://stackoverflow.com/questions/45477806/general-method-for-calculating-smooth-vertex-normals-with-100-smoothness?noredirect=1&lq=1
source
PlantGeom.parse_opf_array — Function
Parse an array of values from the OPF into a Julia array (Arrays in OPFs are not following XML recommendations)
source
PlantGeom.parse_opf_elements! — Method
Generic parser for OPF elements.
Arguments
  • opf::OrderedDict: the opf Dict (using [XMLDict.xml_dict])
  • elem_types::Array: the target types of the element (e.g. "[String, Int64]")
Details
elem_types should be of the same length as the number of elements found in each item of the subchild. elem_types = [Float64, Float64, Float64, Float64, Float64, Float64]
source
PlantGeom.parse_opf_topology! — Function
parse_opf_topology!(node, mtg, features, attr_type, mtg_type, ref_meshes, id_set=Set{Int}())
Parser of the OPF topology.
Arguments
  • node::ElementNode: the XML node to parse.
  • mtg::Union{Nothing,Node}: the parent MTG node.
  • features::Dict: the features of the OPF.
  • attr_type::DataType: the type of the attributes to use.
  • mtg_type::DataType: the type of the MTG to use.
  • ref_meshes::Dict: the reference meshes.
  • read_id::Bool: whether to read the ID from the OPF or recompute it on the fly.
  • max_id::RefValue{Int64}=Ref(1): the ID of the first node, if read_id==false.
Note
The transformation matrices in geometry are 3*4.
source
PlantGeom.plot_opf — Method
plot_opf(plot)
Actual workhorse function for plotting an OPF / MTG with geometry.
Arguments
  • plot: The plot object.
The plot object can have the following optional arguments:
  • color: The color to be used for the plot. Can be a colorant, an attribute of the MTG, or a dictionary of colors for each reference mesh.
  • alpha: The alpha value to be used for the plot. Should be a float between 0 and 1.
  • colormap: The colorscheme to be used for the plot. Can be a Symbol or a ColorScheme.
  • colorrange: The range of values to be used for the colormap. Should be a tuple of floats (optionally with units if e.g. z position).
  • segmentcolor: The color to be used for the facets. Should be a colorant or a symbol of color.
  • showsegments: A boolean indicating whether the facets should be shown or not.
  • segmentsize: The size of the segments. Should be a float.
  • showpoints: A boolean indicating whether the points should be shown or not.
  • color_missing: The color to be used for missing values. Should be a colorant or a symbol of color.
  • color_vertex: A boolean indicating whether the values in color (if colored by attributes) are defined for each vertex of the mesh, or for each mesh.
  • pointsize: The size of the points. Should be a float.
  • index: An integer giving the index of the attribute value to be vizualised. This is useful when the attribute is a vector of values for e.g. each timestep.
  • color_cache_name: The name of the color cache. Should be a string (default to a random string).
Examples
```julia using MultiScaleTreeGraph, PlantGeom, Colors
file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
opf = read_opf(file)
f, a, plot = viz(opf) plot_opf(p)
f, a, plot = viz(opf, color=:red) plot_opf(plot)
f, a, plot = viz(opf, color=:Length) plot_opf(plot)
plot_opf(opf; color=Dict(1=>RGB(0.1,0.5,0.1), 2=>RGB(0.1,0.1,0.5)))
plot_opf(opf; color=:red, colormap=:viridis)
plot_opf(opf; color=:red, colormap=:viridis, segmentcolor=:red, showsegments=true)
source
PlantGeom.read_opf — Method
read_opf(file; attr_type = Dict, mtg_type = MutableNodeMTG)
Read an OPF file, and returns an MTG.
Arguments
  • file::String: The path to the opf file.
  • attr_type::DataType = Dict: the type used to hold the attribute values for each node.
  • mtg_type = MutableNodeMTG: the type used to hold the mtg encoding for each node (i.e.
link, symbol, index, scale). See details section below.
  • read_id::Bool = true: whether to read the ID from the OPF or recompute it on the fly.
  • max_id::RefValue{Int64}=Ref(1): the ID of the first node, if read_id==false.
Details
attr_type should be:
  • NamedTuple if you don't plan to modify the attributes of the mtg, e.g. to use them for
plotting or computing statistics...
  • MutableNamedTuple if you plan to modify the attributes values but not adding new attributes
very often, e.g. recompute an attribute value...
  • Dict or similar (e.g. OrderedDict) if you plan to heavily modify the attributes, e.g.
adding/removing attributes a lot
The MultiScaleTreeGraph package provides two types for mtg_type, one immutable (NodeMTG), and one mutable (MutableNodeMTG). If you're planning on modifying the mtg encoding of some of your nodes, you should use MutableNodeMTG, and if you don't want to modify  anything, use NodeMTG instead as it should be faster.
Note
See the documentation of the MTG format from the MTG package documentation for further details, e.g. The MTG concept.
Returns
The MTG root node.
Examples
using PlantGeom
+meshBDD_to_meshes(opf[:meshBDD])
source
PlantGeom.mtg_coordinates_df — Function
mtg_coordinates_df(mtg, attr; force = false)
+mtg_coordinates_df!(mtg, attr; force = false)
Extract the coordinates of the nodes of the mtg and the coordinates of their parents (:XXfrom, :YYfrom, :ZZ_from) and output a DataFrame. Optionally you can also provide an attribute to add to the output DataFrame too by passing its name as a symbol to attr.
The coordinates are computed using coordinates! if missing, or if force = true.
source
PlantGeom.mtg_to_opf_link — Method
mtg_to_opf_link(link)
Takes an MTG link as input ("/", "<" or "+") and outputs its corresponding link as declared in the OPF format ("decomp", "follow" or "branch")
source
PlantGeom.mtg_topology_to_xml! — Function
mtg_topology_to_xml!(node, xml_parent)
Write the MTG topology, attributes and geometry into XML format. This function is used to write the "topology" section of the OPF.
source
PlantGeom.normals_vertex — Method
normals_vertex(mesh::Meshes.SimpleMesh)
Compute per vertex normals and return them as a StaticArrays.SVector.
#! This is a naive approach because I have no time right know. #! We just put the face mesh as a vertex mesh (and ovewritting values for common points)
TODO: Use a real computation instead. See e.g.:
https://stackoverflow.com/questions/45477806/general-method-for-calculating-smooth-vertex-normals-with-100-smoothness?noredirect=1&lq=1
source
PlantGeom.parse_opf_array — Function
Parse an array of values from the OPF into a Julia array (Arrays in OPFs are not following XML recommendations)
source
PlantGeom.parse_opf_elements! — Method
Generic parser for OPF elements.
Arguments
  • opf::OrderedDict: the opf Dict (using [XMLDict.xml_dict])
  • elem_types::Array: the target types of the element (e.g. "[String, Int64]")
Details
elem_types should be of the same length as the number of elements found in each item of the subchild. elem_types = [Float64, Float64, Float64, Float64, Float64, Float64]
source
PlantGeom.parse_opf_topology! — Function
parse_opf_topology!(node, mtg, features, attr_type, mtg_type, ref_meshes, id_set=Set{Int}())
Parser of the OPF topology.
Arguments
  • node::ElementNode: the XML node to parse.
  • mtg::Union{Nothing,Node}: the parent MTG node.
  • features::Dict: the features of the OPF.
  • attr_type::DataType: the type of the attributes to use.
  • mtg_type::DataType: the type of the MTG to use.
  • ref_meshes::Dict: the reference meshes.
  • read_id::Bool: whether to read the ID from the OPF or recompute it on the fly.
  • max_id::RefValue{Int64}=Ref(1): the ID of the first node, if read_id==false.
Note
The transformation matrices in geometry are 3*4.
source
PlantGeom.plot_opf — Method
plot_opf(plot)
Actual workhorse function for plotting an OPF / MTG with geometry.
Arguments
  • plot: The plot object.
The plot object can have the following optional arguments:
  • color: The color to be used for the plot. Can be a colorant, an attribute of the MTG, or a dictionary of colors for each reference mesh.
  • alpha: The alpha value to be used for the plot. Should be a float between 0 and 1.
  • colormap: The colorscheme to be used for the plot. Can be a Symbol or a ColorScheme.
  • colorrange: The range of values to be used for the colormap. Should be a tuple of floats (optionally with units if e.g. z position).
  • segmentcolor: The color to be used for the facets. Should be a colorant or a symbol of color.
  • showsegments: A boolean indicating whether the facets should be shown or not.
  • segmentsize: The size of the segments. Should be a float.
  • showpoints: A boolean indicating whether the points should be shown or not.
  • color_missing: The color to be used for missing values. Should be a colorant or a symbol of color.
  • color_vertex: A boolean indicating whether the values in color (if colored by attributes) are defined for each vertex of the mesh, or for each mesh.
  • pointsize: The size of the points. Should be a float.
  • index: An integer giving the index of the attribute value to be vizualised. This is useful when the attribute is a vector of values for e.g. each timestep.
  • color_cache_name: The name of the color cache. Should be a string (default to a random string).
Examples
```julia using MultiScaleTreeGraph, PlantGeom, Colors
file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
opf = read_opf(file)
f, a, plot = viz(opf) plot_opf(p)
f, a, plot = viz(opf, color=:red) plot_opf(plot)
f, a, plot = viz(opf, color=:Length) plot_opf(plot)
plot_opf(opf; color=Dict(1=>RGB(0.1,0.5,0.1), 2=>RGB(0.1,0.1,0.5)))
plot_opf(opf; color=:red, colormap=:viridis)
plot_opf(opf; color=:red, colormap=:viridis, segmentcolor=:red, showsegments=true)
source
PlantGeom.read_opf — Method
read_opf(file; attr_type = Dict, mtg_type = MutableNodeMTG)
Read an OPF file, and returns an MTG.
Arguments
  • file::String: The path to the opf file.
  • attr_type::DataType = Dict: the type used to hold the attribute values for each node.
  • mtg_type = MutableNodeMTG: the type used to hold the mtg encoding for each node (i.e.
link, symbol, index, scale). See details section below.
  • read_id::Bool = true: whether to read the ID from the OPF or recompute it on the fly.
  • max_id::RefValue{Int64}=Ref(1): the ID of the first node, if read_id==false.
Details
attr_type should be:
  • NamedTuple if you don't plan to modify the attributes of the mtg, e.g. to use them for
plotting or computing statistics...
  • MutableNamedTuple if you plan to modify the attributes values but not adding new attributes
very often, e.g. recompute an attribute value...
  • Dict or similar (e.g. OrderedDict) if you plan to heavily modify the attributes, e.g.
adding/removing attributes a lot
The MultiScaleTreeGraph package provides two types for mtg_type, one immutable (NodeMTG), and one mutable (MutableNodeMTG). If you're planning on modifying the mtg encoding of some of your nodes, you should use MutableNodeMTG, and if you don't want to modify  anything, use NodeMTG instead as it should be faster.
Note
See the documentation of the MTG format from the MTG package documentation for further details, e.g. The MTG concept.
Returns
The MTG root node.
Examples
using PlantGeom
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 # file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","coffee.opf")
-opf = read_opf(file)
source
PlantGeom.read_ops — Method
read_ops(file; attr_type=Dict{String,Any}, mtg_type=MutableNodeMTG)
Reads an OPS file and returns the content as a MultiScaleTreeGraph.
Arguments
  • file::String: Path of the .ops file to read.
  • attr_type::Type=Dict{Symbol,Any}: Type of the attributes to use.
  • mtg_type::Type: Type of the MTG to use, e.g. NodeMTG or MutableNodeMTG.
Returns
A MultiScaleTreeGraph of the scene, with the OPFs as children of the scene node. The dimension of the scene is available in the scene_dimensions attribute of the scene node. Each root node of the OPFs has a scene_transformation attribute that stores the transformation applied to the OPF by the scene. It allows updating the scene transformations and write the scene back to disk. The OPF root node also has the following attributes:
  • sceneID::Int: Scene ID.
  • plantID::Int: Plant ID.
  • filePath::String: Path to the original .opf file.
  • pos::Meshes.Point: Position of the object.
  • scale::Float64: Scale of the object.
  • inclinationAzimut::Float64: Inclination azimut of the object.
  • inclinationAngle::Float64: Inclination angle of the object.
  • rotation::Float64: Rotation of the object.
  • functional_group::String: Functional group of the object.
Details
Node IDs of the OPFs are recomputed at import to ensure their uniqueness in the larger scene MTG.
Example
using CairoMakie, PlantGeom
-joinpath(pathof(PlantGeom) |> dirname |> dirname, "test", "files", "scene.ops") |> read_ops |> viz
source
PlantGeom.read_ops_file — Method
read_ops_file(file)
Read the content of an .ops file and return a tuple with the scene dimensions and the object table.
Arguments
  • file::String: Path of the .ops file to read.
Returns
The scene dimensions and the object table as a tuple. The scene dimensions are a tuple of two Meshes.Point with the origin point and opposite point of the scene.  The object table is an array of NamedTuple with the following fields:
  • sceneID::Int: Scene ID.
  • plantID::Int: Plant ID.
  • filePath::String: Path to the .opf file.
  • pos::Meshes.Point: Position of the object.
  • scale::Float64: Scale of the object.
  • inclinationAzimut::Float64: Inclination azimut of the object.
  • inclinationAngle::Float64: Inclination angle of the object.
  • rotation::Float64: Rotation of the object.
  • functional_group::String: Functional group of the object.
source
PlantGeom.read_ops — Method
read_ops(file; attr_type=Dict{String,Any}, mtg_type=MutableNodeMTG)
Reads an OPS file and returns the content as a MultiScaleTreeGraph.
Arguments
  • file::String: Path of the .ops file to read.
  • attr_type::Type=Dict{Symbol,Any}: Type of the attributes to use.
  • mtg_type::Type: Type of the MTG to use, e.g. NodeMTG or MutableNodeMTG.
Returns
A MultiScaleTreeGraph of the scene, with the OPFs as children of the scene node. The dimension of the scene is available in the scene_dimensions attribute of the scene node. Each root node of the OPFs has a scene_transformation attribute that stores the transformation applied to the OPF by the scene. It allows updating the scene transformations and write the scene back to disk. The OPF root node also has the following attributes:
  • sceneID::Int: Scene ID.
  • plantID::Int: Plant ID.
  • filePath::String: Path to the original .opf file.
  • pos::Meshes.Point: Position of the object.
  • scale::Float64: Scale of the object.
  • inclinationAzimut::Float64: Inclination azimut of the object.
  • inclinationAngle::Float64: Inclination angle of the object.
  • rotation::Float64: Rotation of the object.
  • functional_group::String: Functional group of the object.
Details
Node IDs of the OPFs are recomputed at import to ensure their uniqueness in the larger scene MTG.
Example
using CairoMakie, PlantGeom
+joinpath(pathof(PlantGeom) |> dirname |> dirname, "test", "files", "scene.ops") |> read_ops |> viz
source
PlantGeom.read_ops_file — Method
read_ops_file(file)
Read the content of an .ops file and return a tuple with the scene dimensions and the object table.
Arguments
  • file::String: Path of the .ops file to read.
Returns
The scene dimensions and the object table as a tuple. The scene dimensions are a tuple of two Meshes.Point with the origin point and opposite point of the scene.  The object table is an array of NamedTuple with the following fields:
  • sceneID::Int: Scene ID.
  • plantID::Int: Plant ID.
  • filePath::String: Path to the .opf file.
  • pos::Meshes.Point: Position of the object.
  • scale::Float64: Scale of the object.
  • inclinationAzimut::Float64: Inclination azimut of the object.
  • inclinationAngle::Float64: Inclination angle of the object.
  • rotation::Float64: Rotation of the object.
  • functional_group::String: Functional group of the object.
source
PlantGeom.refmesh_to_mesh — Function
refmesh_to_mesh!(node)
 refmesh_to_mesh(node)
Compute a node mesh based on the reference mesh, the transformation matrix and the tapering. The mutating version adds the new mesh to the mesh field of the geometry attribute of the node.
Examples
using PlantGeom
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 opf = read_opf(file)
@@ -207,7 +207,7 @@
 new_mesh = refmesh_to_mesh(node)
 
 using GLMakie
-viz(new_mesh)
source
PlantGeom.refmesh_to_mesh! — Function
refmesh_to_mesh!(node)
 refmesh_to_mesh(node)
Compute a node mesh based on the reference mesh, the transformation matrix and the tapering. The mutating version adds the new mesh to the mesh field of the geometry attribute of the node.
Examples
using PlantGeom
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 opf = read_opf(file)
@@ -217,7 +217,7 @@
 new_mesh = refmesh_to_mesh(node)
 
 using GLMakie
-viz(new_mesh)
source
PlantGeom.taper — Method
Returns a tapered mesh using dDwn and dUp based on the geometry of an input mesh. Tapering a mesh transforms it into a tapered version (i.e. pointy) or enlarged object, e.g. make a cone from a cylinder.
source
PlantGeom.transform_mesh! — Method
transform_mesh!(node::Node, transformation)
Add a new transformation to the node geometry transformation field.  The transformation is composed with the previous transformation if any.
transformation must be a function.
It is also possible to invert a transformation using revert from Meshes.jl.
Examples
using PlantGeom, MultiScaleTreeGraph, GLMakie, Rotations, Meshes
+viz(new_mesh)
source
PlantGeom.taper — Method
Returns a tapered mesh using dDwn and dUp based on the geometry of an input mesh. Tapering a mesh transforms it into a tapered version (i.e. pointy) or enlarged object, e.g. make a cone from a cylinder.
source
PlantGeom.transform_mesh! — Method
transform_mesh!(node::Node, transformation)
Add a new transformation to the node geometry transformation field.  The transformation is composed with the previous transformation if any.
transformation must be a function.
It is also possible to invert a transformation using revert from Meshes.jl.
Examples
using PlantGeom, MultiScaleTreeGraph, GLMakie, Rotations, Meshes
 
 file = joinpath(dirname(dirname(pathof(PlantGeom))), "test", "files", "simple_plant.opf")
 opf = read_opf(file)
@@ -255,24 +255,24 @@
 
 # Plot the result:
 viz(opf)
-viz!(opf4)
source
PlantGeom.write_opf — Method
write_opf(file, opf)
Write an MTG with explicit geometry to disk as an OPF file.
Notes
Node attributes :ref_meshes and :geometry are treated as reserved keywords and should not be used without knowing their meaning:
  • :ref_meshes: a RefMeshes structure that holds the MTG reference meshes.
  • :geometry: a geometry instance
Examples
using PlantGeom
+viz!(opf4)
source
PlantGeom.write_opf — Method
write_opf(file, opf)
Write an MTG with explicit geometry to disk as an OPF file.
Notes
Node attributes :ref_meshes and :geometry are treated as reserved keywords and should not be used without knowing their meaning:
  • :ref_meshes: a RefMeshes structure that holds the MTG reference meshes.
  • :geometry: a geometry instance
Examples
using PlantGeom
 file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
 opf = read_opf(file)
 write_opf("test.opf", opf)
 opf2 = read_opf("test.opf")
-viz(opf2)
source
PlantGeom.write_ops — Method
write_ops(file, scene_dimensions, object_table)
Write a scene file (.ops), with the given dimensions and object table.
Arguments
  • file::String: Path of the .ops file to write.
  • scene_dimensions::Tuple{Meshes.Point{3,T},Meshes.Point{3,T}}: Dimensions of the scene.
  • object_table: Table with the objects to write in the .ops file. The table may have the following columns:
    • sceneID::Int: Scene ID (mandatory).
    • plantID::Int: Plant ID (mandatory).
    • filePath::String: Path to the .opf file (mandatory).
    • pos::Meshes.Point{3,T}: Position of the object (mandatory).
    • functional_group::String: Functional group of the object, used to map the object to the models (mandatory).
    • scale::T: Scale of the object (optional, 0.0 as default).
    • inclinationAzimut::T: Inclination azimut of the object (optional, 0.0 as default).
    • inclinationAngle::T: Inclination angle of the object (optional, 0.0 as default).
    • rotation::T: Rotation of the object (optional, 0.0 as default).
Details
object_table can be of any format that implement the Tables.jl interface, e.g. an array of NamedTuples, a DataFrame...
Example
```julia using Meshes using Tables using PlantGeom
scenedimensions = (Meshes.Point(0.0, 0.0, 0.0), Meshes.Point(100.0, 100.0, 100.0)) positions = [Meshes.Point(50.0, 50.0, 50.0), Meshes.Point(60.0, 60.0, 60.0), Meshes.Point(70.0, 70.0, 70.0)] objecttable = [     (sceneID=1, plantID=p, filePath="opf/plantp.opf", pos=positions[p], functionalgroup="plant", rotation=0.1) for p in 1:3 ]
writeops("scene.ops", scenedimensions, object_table)
source
PlantGeom.write_ops — Method
write_ops(file, scene_dimensions, object_table)
Write a scene file (.ops), with the given dimensions and object table.
Arguments
  • file::String: Path of the .ops file to write.
  • scene_dimensions::Tuple{Meshes.Point{3,T},Meshes.Point{3,T}}: Dimensions of the scene.
  • object_table: Table with the objects to write in the .ops file. The table may have the following columns:
    • sceneID::Int: Scene ID (mandatory).
    • plantID::Int: Plant ID (mandatory).
    • filePath::String: Path to the .opf file (mandatory).
    • pos::Meshes.Point{3,T}: Position of the object (mandatory).
    • functional_group::String: Functional group of the object, used to map the object to the models (mandatory).
    • scale::T: Scale of the object (optional, 0.0 as default).
    • inclinationAzimut::T: Inclination azimut of the object (optional, 0.0 as default).
    • inclinationAngle::T: Inclination angle of the object (optional, 0.0 as default).
    • rotation::T: Rotation of the object (optional, 0.0 as default).
Details
object_table can be of any format that implement the Tables.jl interface, e.g. an array of NamedTuples, a DataFrame...
Example
```julia using Meshes using Tables using PlantGeom
scenedimensions = (Meshes.Point(0.0, 0.0, 0.0), Meshes.Point(100.0, 100.0, 100.0)) positions = [Meshes.Point(50.0, 50.0, 50.0), Meshes.Point(60.0, 60.0, 60.0), Meshes.Point(70.0, 70.0, 70.0)] objecttable = [     (sceneID=1, plantID=p, filePath="opf/plantp.opf", pos=positions[p], functionalgroup="plant", rotation=0.1) for p in 1:3 ]
writeops("scene.ops", scenedimensions, object_table)
source
PlantGeom.xmax — Function
xmax(x)
 ymax(x)
-zmax(x)
Get the maximum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.xmin — Function
xmin(x)
+zmax(x)
Get the maximum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.xmin — Function
xmin(x)
 ymin(x)
-zmin(x)
Get the minimum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.ymax — Function
xmax(x)
+zmin(x)
Get the minimum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.ymax — Function
xmax(x)
 ymax(x)
-zmax(x)
Get the maximum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.ymin — Function
xmin(x)
+zmax(x)
Get the maximum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.ymin — Function
xmin(x)
 ymin(x)
-zmin(x)
Get the minimum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.zmax — Function
xmax(x)
+zmin(x)
Get the minimum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.zmax — Function
xmax(x)
 ymax(x)
-zmax(x)
Get the maximum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.zmin — Function
xmin(x)
+zmax(x)
Get the maximum x, y or z coordinates of a mesh or a Node.
source
PlantGeom.zmin — Function
xmin(x)
 ymin(x)
-zmin(x)
Get the minimum x, y or z coordinates of a mesh or a Node.
source
RecipesBase.plot — Function
plot(opf::MultiScaleTreeGraph.Node; kwargs...)
+zmin(x)
Get the minimum x, y or z coordinates of a mesh or a Node.
source
RecipesBase.plot — Function
plot(opf::MultiScaleTreeGraph.Node; kwargs...)
 plot!(opf::MultiScaleTreeGraph.Node; kwargs...)
Make a diagram of the MTG tree, paired with a Plots.jl backend.
See also diagram for the same plot with a Makie.jl backend.
Attributes
  • mode = "2d": The mode for plotting, either "2d" or "3d"
  • node_color = :black: the node color, can be a color or any MTG attribute
  • edge_color = node_color: same as node_color, but for the edges
  • colormap = :viridis: the colormap used for coloring
  • color_missing = RGBA(0, 0, 0, 0.3): The color used for missing values
Examples
# import Pkg; Pkg.add("PlotlyJS")
 using Plots, PlantGeom
 plotlyjs()
@@ -282,7 +282,7 @@
 
 opf = read_opf(file)
 
-plot(opf, node_color = :Length)
source
RecipesBase.plot! — Function
plot(opf::MultiScaleTreeGraph.Node; kwargs...)
+plot(opf, node_color = :Length)
source
RecipesBase.plot! — Function
plot(opf::MultiScaleTreeGraph.Node; kwargs...)
 plot!(opf::MultiScaleTreeGraph.Node; kwargs...)
Make a diagram of the MTG tree, paired with a Plots.jl backend.
See also diagram for the same plot with a Makie.jl backend.
Attributes
  • mode = "2d": The mode for plotting, either "2d" or "3d"
  • node_color = :black: the node color, can be a color or any MTG attribute
  • edge_color = node_color: same as node_color, but for the edges
  • colormap = :viridis: the colormap used for coloring
  • color_missing = RGBA(0, 0, 0, 0.3): The color used for missing values
Examples
# import Pkg; Pkg.add("PlotlyJS")
 using Plots, PlantGeom
 plotlyjs()
@@ -292,4 +292,4 @@
 
 opf = read_opf(file)
 
-plot(opf, node_color = :Length)
source

+plot(opf, node_color = :Length)
source
diff --git a/dev/index.html b/dev/index.html index bb088b4..a9ca44b 100644 --- a/dev/index.html +++ b/dev/index.html @@ -31,4 +31,4 @@ # And making a little animation out of it: CairoMakie.record(f, "plant_animation.mp4", 1:120) do frame ax2.azimuth[] = 0.3π + 0.3 * sin(2π * frame / 120) -end +end diff --git a/dev/makie_3d/index.html b/dev/makie_3d/index.html index cda1a1c..4c055a9 100644 --- a/dev/makie_3d/index.html +++ b/dev/makie_3d/index.html @@ -3,25 +3,25 @@ Page(exportable=true, offline=true)

Then we can plot our interactive 3D plant:

using PlantGeom, WGLMakie
 mtg = read_opf(joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf"))
 viz(mtg)
-
+
- +
-
+
@@ -43,12 +43,12 @@ width="50mm" height="25mm" viewBox="0 0 2 1" stroke="none" preserveAspectRatio="none" shape-rendering="crispEdges"> - - + @@ -67,4 +67,4 @@ record(f, "coffee_steps.mp4", 1:12, framerate=2) do timestep p.index[] = timestep -end
"coffee_steps.mp4"

+end
"coffee_steps.mp4"

diff --git a/dev/plot_diagram/makie_diagram/index.html b/dev/plot_diagram/makie_diagram/index.html index e8ab0c5..dad4d24 100644 --- a/dev/plot_diagram/makie_diagram/index.html +++ b/dev/plot_diagram/makie_diagram/index.html @@ -5,4 +5,4 @@ PlantGeom.coordinates!(opf, force = true) # Then we plot the MTG using the newly created ZZ attribute: diagram(opf, color = :YY)Example block output

We can also color the edges differently, e.g. using the XX attribute computed using coordinates!:

PlantGeom.coordinates!(opf, force = true)
-diagram(opf, color = :YY, edge_color = :XX)
Example block output

Attributes used for coloring may have missing values. In this case you can choose their color using color_missing, e.g.:

diagram(opf, color = :Length, edge_color = :Width, color_missing = :red)
+diagram(opf, color = :YY, edge_color = :XX)Example block output

Attributes used for coloring may have missing values. In this case you can choose their color using color_missing, e.g.:

diagram(opf, color = :Length, edge_color = :Width, color_missing = :red)
diff --git a/dev/plot_diagram/mtgplot.html b/dev/plot_diagram/mtgplot.html index 8625ce6..da47a5f 100644 --- a/dev/plot_diagram/mtgplot.html +++ b/dev/plot_diagram/mtgplot.html @@ -1,7 +1,7 @@ -
+
+