https://github.com/vezy/multiscaletreegraph.jl
Read, analyse, compute, write and convert MTG files
https://github.com/vezy/multiscaletreegraph.jl
fspm graphs julia plants
Last synced: 4 months ago
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Read, analyse, compute, write and convert MTG files
- Host: GitHub
- URL: https://github.com/vezy/multiscaletreegraph.jl
- Owner: VEZY
- License: mit
- Created: 2020-10-06T17:46:08.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2025-03-14T17:13:11.000Z (4 months ago)
- Last Synced: 2025-03-14T17:22:31.607Z (4 months ago)
- Topics: fspm, graphs, julia, plants
- Language: Julia
- Homepage: https://vezy.github.io/MultiScaleTreeGraph.jl/stable
- Size: 3.11 MB
- Stars: 10
- Watchers: 3
- Forks: 1
- Open Issues: 23
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.bib
Awesome Lists containing this project
README
# MultiScaleTreeGraph
[](https://VEZY.github.io/MultiScaleTreeGraph.jl/stable)
[](https://VEZY.github.io/MultiScaleTreeGraph.jl/dev)
[](https://github.com/VEZY/MultiScaleTreeGraph.jl/actions)
[](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl)
[](https://github.com/invenia/BlueStyle)
[](https://github.com/SciML/ColPrac)
[](https://doi.org/10.5281/zenodo.5654676)
The goal of MultiScaleTreeGraph.jl is to read, write, analyse and plot MTG (Multi-scale Tree Graph) files. These files describe the plant topology (*i.e.* structure) along with some attributes for each node (*e.g.* geometry, colors, state...).
> The package is under intensive development and is in a very early version. The functions may heavily change from one version to another until a more stable version is released.
## 1. Installation
You can install the latest stable version of MultiScaleTreeGraph.jl using this command:
```julia
] add MultiScaleTreeGraph
```
Or if you prefer the development version:
```julia
using Pkg
Pkg.add(url="https://github.com/VEZY/MultiScaleTreeGraph.jl", rev="master")
```
## 2. Example
Read a simple MTG file:
```julia
using MultiScaleTreeGraph
file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.mtg")
mtg = read_mtg(file)
```
Then you can compute new variables in the MTG using a `DataFrame.jl`'s alike syntax:
```julia
transform!(mtg, :Length => (x -> x * 1000.) => :length_mm)
```
And then write the MTG back to disk:
```julia
write_mtg("test.mtg",mtg)
```
## 3. Conversion
You can convert an MTG into a DataFrame and select the variables you need:
```julia
DataFrame(mtg, [:length_mm, :XX])
```
Or convert it to a [MetaGraph](https://juliagraphs.org/MetaGraphsNext.jl/dev/):
```julia
MetaGraph(mtg)
```
## 4. Compatibility
We can plot the MTG using the companion package [`PlantGeom.jl`](https://github.com/VEZY/PlantGeom.jl).
`MultiScaleTreeGraph.jl` trees are compatible with the [AbstractTrees.jl](https://github.com/JuliaCollections/AbstractTrees.jl) package, which means you can use all functions from that package, *e.g.*:
```julia
using AbstractTrees
node = get_node(mtg, 4)
nodevalue(node)
parent(node)
nextsibling(node)
prevsibling(nextsibling(node))
childrentype(node)
childtype(node)
childstatetype(node)
getdescendant(mtg, (1, 1, 1, 2))
collect(PreOrderDFS(mtg))
collect(PostOrderDFS(mtg))
collect(Leaves(mtg))
collect(nodevalues(PreOrderDFS(mtg)))
print_tree(mtg)
```
You can learn more about `MultiScaleTreeGraph.jl` in the [documentation of the package](https://vezy.github.io/MultiScaleTreeGraph.jl/dev/).
## 3. Acknowledgments
Several tree-related functions in use are adapted from [DataTrees.jl](https://github.com/vh-d/DataTrees.jl/).
This package is heavily inspired by [OpenAlea's MTG](https://github.com/openalea/mtg) implementation in Python.
## 4. Similar packages
- [MultiScaleArrays.jl](https://github.com/SciML/MultiScaleArrays.jl)
- [MultilayerGraphs.jl](https://github.com/JuliaGraphs/MultilayerGraphs.jl)