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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: 2 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 (about 4 years ago)
Default Branch: master
Last Pushed: 2024-06-17T16:03:24.000Z (7 months ago)
Last Synced: 2024-10-13T19:39:37.841Z (3 months ago)
Topics: fspm, graphs, julia, plants
Language: Julia
Homepage: https://vezy.github.io/MultiScaleTreeGraph.jl/stable
Size: 2.98 MB
Stars: 10
Watchers: 4
Forks: 1
Open Issues: 20
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.bib

Awesome Lists containing this project

README

        # MultiScaleTreeGraph

[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://VEZY.github.io/MultiScaleTreeGraph.jl/stable)

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://VEZY.github.io/MultiScaleTreeGraph.jl/dev)

[![Build Status](https://github.com/VEZY/MultiScaleTreeGraph.jl/workflows/CI/badge.svg)](https://github.com/VEZY/MultiScaleTreeGraph.jl/actions)

[![Coverage](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl)

[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)

[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5654676.svg)](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)