API

Geometry(; ref_mesh<:RefMesh, 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 the resulting mesh (optional, may be lazily computed).

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().

A material for the illumination model (e.g. Phong illumination).

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.

RefMesh(
    name::S
    mesh::SimpleMesh
    normals::N
    texture_coords::T
    material::M
    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.

==(a::Geometry, b::Geometry)

Test RefMesh equality.

==(a::RefMesh, b::RefMesh)

Test RefMesh equality.

nelements(meshes::RefMesh)

Return the number of elements of a reference mesh

nvertices(meshes::RefMesh)

Return the number of vertices of a reference mesh

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).
  • filter_fun: A function to filter the nodes to be plotted. Should be a function taking a node as argument and returning a boolean.
  • symbol: Plot only nodes with this symbol. Should be a String or a vector of.
  • scale: Plot only nodes with this scale. Should be an Int or a vector of.
  • link: Plot only nodes with this link. Should be a String or a vector of.

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")
# file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","coffee.opf")

opf = read_opf(file)
viz(opf)

# If you need to plot the opf several times, you better cache the mesh in the node geometry
# like so:
transform!(opf, refmesh_to_mesh!)

# Then plot it again like before, and it will be faster:
viz(opf)

# We can also color the 3d plot with several options:
# With one shared color:
viz(opf, color = :red)
# One color per reference mesh:
viz(opf, color = Dict(1 => :burlywood4, 2 => :springgreen4, 3 => :burlywood4))

# Or just changing the color of some:
viz(opf, color = Dict(1 => :burlywood4))

# Or coloring by opf attribute, e.g. using the mesh max Z coordinates (NB: need to use
# `refmesh_to_mesh!` before, see above):
transform!(opf, zmax => :z_max, ignore_nothing = true)
viz(opf, color = :z_max)

# One color for each vertex of the refmesh 1:
using Meshes
vertex_color = get_color(1:nvertices(get_ref_meshes(opf))[1], [1,nvertices(get_ref_meshes(opf))[1]])
viz(opf, color = Dict(1 => vertex_color))

# Or even coloring by the value of the Z coordinates of each vertex:
transform!(opf, :geometry => (x -> [Meshes.coords(i).z for i in Meshes.vertices(x.mesh)]) => :z, ignore_nothing = true)
viz(opf, color = :z, showsegments = true)

f,a,p = viz(opf, color = :z, showsegments = true)
p[:color] = :Length

viz!(ref_meshes; kwargs...)

Plot all reference meshes in a single 3d plot using Makie.

Examples

using PlantGeom, GLMakie

file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
opf = read_opf(file)
meshes = get_ref_meshes(opf)

viz(meshes)
# With one shared color:
viz(meshes, color = :green)
# One color per reference mesh:
viz(meshes, color = Dict(1 => :burlywood4, 2 => :springgreen4, 3 => :burlywood4))
# 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]))

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).
  • filter_fun: A function to filter the nodes to be plotted. Should be a function taking a node as argument and returning a boolean.
  • symbol: Plot only nodes with this symbol. Should be a String or a vector of.
  • scale: Plot only nodes with this scale. Should be an Int or a vector of.
  • link: Plot only nodes with this link. Should be a String or a vector of.

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")
# file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","coffee.opf")

opf = read_opf(file)
viz(opf)

# If you need to plot the opf several times, you better cache the mesh in the node geometry
# like so:
transform!(opf, refmesh_to_mesh!)

# Then plot it again like before, and it will be faster:
viz(opf)

# We can also color the 3d plot with several options:
# With one shared color:
viz(opf, color = :red)
# One color per reference mesh:
viz(opf, color = Dict(1 => :burlywood4, 2 => :springgreen4, 3 => :burlywood4))

# Or just changing the color of some:
viz(opf, color = Dict(1 => :burlywood4))

# Or coloring by opf attribute, e.g. using the mesh max Z coordinates (NB: need to use
# `refmesh_to_mesh!` before, see above):
transform!(opf, zmax => :z_max, ignore_nothing = true)
viz(opf, color = :z_max)

# One color for each vertex of the refmesh 1:
using Meshes
vertex_color = get_color(1:nvertices(get_ref_meshes(opf))[1], [1,nvertices(get_ref_meshes(opf))[1]])
viz(opf, color = Dict(1 => vertex_color))

# Or even coloring by the value of the Z coordinates of each vertex:
transform!(opf, :geometry => (x -> [Meshes.coords(i).z for i in Meshes.vertices(x.mesh)]) => :z, ignore_nothing = true)
viz(opf, color = :z, showsegments = true)

f,a,p = viz(opf, color = :z, showsegments = true)
p[:color] = :Length

viz!(ref_meshes; kwargs...)

Plot all reference meshes in a single 3d plot using Makie.

Examples

using PlantGeom, GLMakie

file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")
opf = read_opf(file)
meshes = get_ref_meshes(opf)

viz(meshes)
# With one shared color:
viz(meshes, color = :green)
# One color per reference mesh:
viz(meshes, color = Dict(1 => :burlywood4, 2 => :springgreen4, 3 => :burlywood4))
# 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]))

align_ref_meshes(meshes::Vector{RefMesh})

Align all reference meshes along the X axis. Used for visualisation only.

attributes_to_xml(node, xml_parent)

Write an MTG node into an XML node.

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")

opf = read_opf(file)

# Colors:
color_type(:red, opf)
color_type(RGB(0.1,0.5,0.1), opf)

# Attributes:
color_type(:Length, opf)

# Default color:
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)

colorant_to_string(x)

Parse a geometry material for OPF writing.

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

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])

diagram(opf::MultiScaleTreeGraph.Node; kwargs...)
diagram!(opf::MultiScaleTreeGraph.Node; kwargs...)

Make a diagram of the MTG tree using a Makie.jl backend.

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")
# file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","coffee.opf")

opf = read_opf(file)

diagram(opf)

# We can also color the 3d plot with several options:
# With one shared color:
diagram(opf, color = :red)

# Or colouring by opf attribute, *e.g.* using the nodes Z coordinates:
diagram(opf, color = :ZZ)

diagram(opf::MultiScaleTreeGraph.Node; kwargs...)
diagram!(opf::MultiScaleTreeGraph.Node; kwargs...)

Make a diagram of the MTG tree using a Makie.jl backend.

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")
# file = joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","coffee.opf")

opf = read_opf(file)

diagram(opf)

# We can also color the 3d plot with several options:
# With one shared color:
diagram(opf, color = :red)

# Or colouring by opf attribute, *e.g.* using the nodes Z coordinates:
diagram(opf, color = :ZZ)

Add a new point after (x1,y1) using same direction and length relative to it

Get the attributes types in Julia DataType.

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)

get_colormap(colormap)

Get the colormap as a ColorScheme if it is a named color or ColorScheme

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)

get_mtg_color(:red, opf)
get_mtg_color(RGB(0.1,0.5,0.1), opf)
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)

get_ref_mesh_name(node)

Get the name of the reference mesh used for the current node.

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)

get_ref_meshes_color(meshes::Vector{RefMesh})

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)

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.

Parse a material in opf format to a Phong material.

material_to_opf_string(material::Phong)
material_to_opf_string(material::Colorant)

Format a material into a Dict for OPF writting.

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])

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.

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")

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.

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

Parse the geometry element of the OPF.

Note

The transformation matrix is 3*4. elem = elem.content

Parse the materialBDD using parse_opf_elements!

Parse the meshBDD using parse_opf_array

Parse an array of values from the OPF into a Julia array (Arrays in OPFs are not following XML recommendations)

Parse the opf attributes as a Dict.

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]

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.

parse_ref_meshes(mtg)

Parse the reference meshes of an OPF into RefMeshes.

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).
• filter_fun: A function to filter the nodes to be plotted. Should be a function taking a node as argument and returning a boolean.
• symbol: Plot only nodes with this symbol. Should be a String or a vector of.
• scale: Plot only nodes with this scale. Should be an Int or a vector of.
• link: Plot only nodes with this link. Should be a String or a vector of.

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)

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)

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

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.

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)

node = opf[1][1][1]

new_mesh = refmesh_to_mesh(node)

using GLMakie
viz(new_mesh)

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)

node = opf[1][1][1]

new_mesh = refmesh_to_mesh(node)

using GLMakie
viz(new_mesh)

Rotate a point (x1,y1) around (x0, y0) with angle.

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.

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)

# Visualize the mesh as is:
viz(opf)

# Copy the OPF, and translate the whole plant by 15 in the y direction (this is in cm, the mesh comes from XPlo):
opf2 = deepcopy(opf)
transform!(opf2, x -> transform_mesh!(x, Translate(0, 15, 0)))
viz!(opf2) # Visualize it again in the same figure

# Same but rotate the whole plant around the X axis:
opf3 = deepcopy(opf)
transform!(opf3, x -> transform_mesh!(x, Rotate(RotX(0.3))))
# NB: we use Rotations.jl's RotX here. Input in radian, use rad2deg and deg2rad if needed.
viz!(opf3)

# Same but rotate only the second leaf around the Z axis:
opf4 = deepcopy(opf)
# Build the meshes from the reference meshes (need it because we want the coordinates of the parent):
transform!(opf4, refmesh_to_mesh!)

# Get the second leaf in the OPF:
leaf_node = get_node(opf4, 8)

# Get the parent node (internode) Z coordinates:
parent_zmax = zmax(leaf_node.parent)

# Define a rotation of the mesh around the Z axis defined by the parent node max Z:
transformation = recenter(Rotate(RotZ(1.0)), Point(0.0, 0.0, parent_zmax))

# Update the transformation matrix of the leaf and its mesh:
transform_mesh!(leaf_node, transformation)

# Plot the result:
viz(opf)
viz!(opf4)

write_opf(file, opf)

Write an MTG with explicit geometry to disk as an OPF file.

Notes

Node attribute :geometry is treated as a reserved keyword and should not be used without knowing their meaning.

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)

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

using Meshes
using Tables
using PlantGeom

scene_dimensions = (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)]
object_table = [
    (sceneID=1, plantID=p, filePath="opf/plant_$p.opf", pos=positions[p], functional_group="plant", rotation=0.1) for p in 1:3
]

write_ops("scene.ops", scene_dimensions, object_table)

xmax(x)
ymax(x)
zmax(x)

Get the maximum x, y or z coordinates of a mesh or a Node.

xmin(x)
ymin(x)
zmin(x)

Get the minimum x, y or z coordinates of a mesh or a Node.

xmax(x)
ymax(x)
zmax(x)

Get the maximum x, y or z coordinates of a mesh or a Node.

xmin(x)
ymin(x)
zmin(x)

Get the minimum x, y or z coordinates of a mesh or a Node.

xmax(x)
ymax(x)
zmax(x)

Get the maximum x, y or z coordinates of a mesh or a Node.

xmin(x)
ymin(x)
zmin(x)

Get the minimum x, y or z coordinates of a mesh or a Node.

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()

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)

plot(opf, node_color = :Length)

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()

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)

plot(opf, node_color = :Length)