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Update README.md #85

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100 changes: 82 additions & 18 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# UnfoldMakie
# ![UnfoldMakie](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/57703446/26b770b3-afa0-4652-b654-82d2f737f42f)


[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://unfoldtoolbox.github.io/UnfoldMakie.jl/dev)
[![Build Status](https://github.com/unfoldtoolbox/UnfoldMakie.jl/workflows/CI/badge.svg)](https://github.com/unfoldtoolbox/UnfoldMakie.jl/actions)
Expand All @@ -22,33 +23,96 @@ The supportet visualizations are:
- Topoplot series
- Parallel Coordinates Plot
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Circular topoplots are missing

also the text above is suboptimal, we should remove the lines

The toolbox requires a Makie-Backend to be loaded, e.g. using CairoMakie
Some plotting functions require data-frames, with fields like :estimate or :time.

Or at least send them down to the quick start or something


<details>
<summary>Click to see example plots</summary>

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we need to update this plot @vladdez do we have a more exciting and more importantly, higher resolution plot?

We also shoudnt hide it, it is a plotting library. Maybe we can shrink it, and not show all plot types?

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Shrinking it would be nice, I hid it cause it was taking up a looooooot of space

![grafik](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/af2801e5-cd64-4932-b84d-9abc1d8470ee)

## Structure
### Code Notes
</details>

## Discover the Unfold-Family & Friends

<details>
<summary>Click to expand</summary>

| | Link to Toolbox|
|---|---|
Regression modeling of EEG data! | ![[Unfold.jl](https://github.com/unfoldtoolbox/Unfold.jl/tree/main)](https://github.com/unfoldtoolbox/Unfold.jl/assets/10183650/757575d0-aeb9-4d94-a5f8-832f13dcd2dd)
Simulate your own EEG data! | ![[UnfoldSim.jl](https://github.com/unfoldtoolbox/UnfoldSim.jl)](https://github.com/unfoldtoolbox/Unfold.jl/assets/10183650/328a4ccd-8860-4b13-9fb6-64d3df9e2091)
Easily load BIDS formatted EEG data! |![[UnfoldBIDS.jl](https://github.com/ReneSkukies/UnfoldBIDS.jl)](https://github.com/unfoldtoolbox/Unfold.jl/assets/10183650/2956ca20-9c48-4066-9e50-c5d25c50f0d1)
Decoding of EEG data made easy | ![[UnfoldDecode.jl](unfoldbids.com)](https://github.com/unfoldtoolbox/Unfold.jl/assets/10183650/802002c0-a1f2-4236-9123-562684d39dcf)
Statistically test your models! | ![[UnfoldStats.jl](unfoldstats.com)](https://github.com/unfoldtoolbox/Unfold.jl/assets/10183650/4c8f2b5a-ea84-4ee3-82f9-01ef05b4f4c6)
You are here | ![[UnfoldMakie.jl](unfoldmakie.com)](https://github.com/unfoldtoolbox/Unfold.jl/assets/10183650/37af35a0-c99c-4374-827b-40fc37de7c2b)
Julia interface to MNE-Python via PythonCall | [PyMNE.jl](https://github.com/beacon-biosignals/PyMNE.jl/tree/main)
</details>

## Install

### Installing Julia

<details>
<summary>Click to expand</summary>

The recommended way to install julia is [juliaup](https://github.com/JuliaLang/juliaup).
It allows you to, e.g., easily update Julia at a later point, but also test out alpha/beta versions etc.

TL:DR; If you dont want to read the explicit instructions, just copy the following command

#### Windows

AppStore -> JuliaUp, or `winget install julia -s msstore` in CMD

#### Mac & Linux

The code files can be found in the `src` folder.
`curl -fsSL https://install.julialang.org | sh` in any shell
</details>

### Documentation Notes
### Installing Unfold

The documentation can be found in the `doc` folder. We use `Documenter.jl` and plan to use `Literate.jl` for future usage.
In the `src` folder contained within it exists as "raw" `.md` files and in the `build` folder contained within it exists as `.html` after running the `make.jl` file.
These are specifically the "index" file with more files in sub folders.
```julia
using Pkg
Pkg.add("UnfoldMakie")
```

## Quickstart

```julia
using UnfoldMakie
using CairoMakie

# TBA
```

## Contributions

Contributions are very welcome. These could be typos, bugreports, feature-requests, speed-optimization, new solvers, better code, better documentation.

### How-to Contribute

You are very welcome to raise issues and start pull requests!

### Adding Documentation

1. We recommend to write a Literate.jl document and place it in `docs/_literate/FOLDER/FILENAME.jl` with `FOLDER` being `HowTo`, `Explanation`, `Tutorial` or `Reference` ([recommended reading on the 4 categories](https://documentation.divio.com/)).
2. Literate.jl converts the `.jl` file to a `.md` automatically and places it in `doc/src/_literate/FILENAME.jl`.
3. Edit [make.jl](https://github.com/unfoldtoolbox/Unfold.jl/blob/main/docs/make.jl) with a reference to `doc/src/_literate/FILENAME.jl`

## Citation
If you make use of theses visualizations, please cite [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6531996.svg)](https://doi.org/10.5281/zenodo.6531996)

## Authors
If you make use of theses visualizations, please cite:

It was authored by `Benedikt Ehinger` and has been worked upon by students and doctoral researchers within the context of a university project (`Fachpraktikum: Methods in Computational EEG`) at the University of Stuttgart.
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6531996.svg)](https://doi.org/10.5281/zenodo.6531996)

The student names are:
- Baumgartner, Daniel
- Döring, Sören
- Gärtner, Niklas
## Contributors (alphabetically)

Doctoral reserchers:
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you are a contributor too :)

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So far only because I updated the readme, no? Didn't think that would justify being on the list 👀

- Vladimir Mikheev
- **Daniel Baumgartner**
- **Benedikt Ehinger**
- **Sören Döring**
- **Niklas Gärtner**
- **Vladimir Mikheev**

## Acknowledgements

## Funding
Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project ID 251654672 – TRR 161 (project D05)

Funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy – EXC 2075 – 390740016
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