-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #85 from unfoldtoolbox/better-read-me
Update README.md
- Loading branch information
Showing
1 changed file
with
86 additions
and
31 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,109 @@ | ||
| # UnfoldMakie | ||
| #  | ||
|
|
||
|
|
||
| [](https://unfoldtoolbox.github.io/UnfoldMakie.jl/dev) | ||
| [](https://github.com/unfoldtoolbox/UnfoldMakie.jl/actions) | ||
| [](https://codecov.io/gh/behinger/UnfoldMakie.jl) | ||
| [](https://doi.org/10.5281/zenodo.6531996) | ||
|
|
||
| |rERP|EEG visualisation|EEG Simulations|BIDS pipeline|Decode EEG data|Statistical testing| | ||
| |---|---|---|---|---|---| | ||
| | <a href="https://github.com/unfoldtoolbox/Unfold.jl/tree/main"><img src="https://github-production-user-asset-6210df.s3.amazonaws.com/10183650/277623787-757575d0-aeb9-4d94-a5f8-832f13dcd2dd.png"></a> | <a href="https://github.com/unfoldtoolbox/UnfoldMakie.jl"><img src="https://github-production-user-asset-6210df.s3.amazonaws.com/10183650/277623793-37af35a0-c99c-4374-827b-40fc37de7c2b.png"></a>|<a href="https://github.com/unfoldtoolbox/UnfoldSim.jl"><img src="https://github-production-user-asset-6210df.s3.amazonaws.com/10183650/277623795-328a4ccd-8860-4b13-9fb6-64d3df9e2091.png"></a>|<a href="https://github.com/unfoldtoolbox/UnfoldBIDS.jl"><img src="https://github-production-user-asset-6210df.s3.amazonaws.com/10183650/277622460-2956ca20-9c48-4066-9e50-c5d25c50f0d1.png"></a>|<a href="https://github.com/unfoldtoolbox/UnfoldDecode.jl"><img src="https://github-production-user-asset-6210df.s3.amazonaws.com/10183650/277622487-802002c0-a1f2-4236-9123-562684d39dcf.png"></a>|<a href="https://github.com/unfoldtoolbox/UnfoldStats.jl"><img src="https://github-production-user-asset-6210df.s3.amazonaws.com/10183650/277623799-4c8f2b5a-ea84-4ee3-82f9-01ef05b4f4c6.png"></a>| | ||
|
|
||
| A toolbox for visualizations of EEG/ERP data and Unfold.jl models. | ||
| Building on the [Unfold](https://github.com/unfoldtoolbox/unfold.jl/) and [Makie](https://makie.juliaplots.org/stable/), it grants users high performance, and highly customizable plots. | ||
|
|
||
| We currently support: | ||
| <img src="https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/af2801e5-cd64-4932-b84d-9abc1d8470ee" width="300" align="right"> | ||
| -  | ||
| ERP plots | ||
| -  | ||
| Butterfly plots | ||
| -  | ||
| Topography plots | ||
| -  | ||
| Topography time series | ||
| -  | ||
| ERP grid | ||
| -  | ||
| ERP images | ||
| -  | ||
| Channel images | ||
| -  | ||
| Parallel coordinates | ||
| - Designmatrices | ||
|
|
||
|
|
||
| UnfoldMakie allows many visualizations for ERP and "Unfolded"-models. | ||
| Building on the [Unfold](https://github.com/unfoldtoolbox/unfold.jl/) and [Makie](https://makie.juliaplots.org/stable/), it grants users highly customizable plots. | ||
| ## Install | ||
|
|
||
| The toolbox requires a Makie-Backend to be loaded, e.g. `using CairoMakie` | ||
| ### Installing Julia | ||
|
|
||
| Some plotting functions require data-frames, with fields like `:estimate` or `:time`. | ||
| <details> | ||
| <summary>Click to expand</summary> | ||
|
|
||
| The supportet visualizations are: | ||
| 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. | ||
|
|
||
| - Designmatrices | ||
| - Line Plots | ||
| - Butterfly Plots | ||
| - ERP Images with option for sorting | ||
| - Topo Plots | ||
| - Topoplot series | ||
| - Parallel Coordinates Plot | ||
| 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 | ||
|
|
||
| `curl -fsSL https://install.julialang.org | sh` in any shell | ||
| </details> | ||
|
|
||
| ### Installing Unfold | ||
|
|
||
|  | ||
| ```julia | ||
| using Pkg | ||
| Pkg.add("UnfoldMakie") | ||
| ``` | ||
|
|
||
| ## Structure | ||
| ### Code Notes | ||
| ## Quickstart | ||
|
|
||
| The code files can be found in the `src` folder. | ||
| ```julia | ||
| using UnfoldMakie | ||
| using CairoMakie | ||
| data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true) | ||
| times = range(0, step = 1 / 100, length = size(data, 2)) | ||
| m= fit(UnfoldModel,@formula(0~1+condition),evts,data,times) | ||
|
|
||
| ### Documentation Notes | ||
| plot_erp(coeftable(m)) | ||
| ``` | ||
|
|
||
| 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. | ||
| ## 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 `docs/src/generated/FOLDER/FILENAME.md`. | ||
| 3. Edit [make.jl](https://github.com/unfoldtoolbox/Unfold.jl/blob/main/docs/make.jl) with a reference to `docs/src/generated/FOLDER/FILENAME.md`. | ||
|
|
||
| ## Citation | ||
| If you make use of theses visualizations, please cite [](https://doi.org/10.5281/zenodo.6531996) | ||
|
|
||
| ## Authors | ||
| If you make use of theses visualizations, please cite: | ||
|
|
||
| [](https://doi.org/10.5281/zenodo.6531996) | ||
|
|
||
| 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. | ||
| ## Contributors (alphabetically) | ||
|
|
||
| The student names are: | ||
| - Baumgartner, Daniel | ||
| - Döring, Sören | ||
| - Gärtner, Niklas | ||
| - **Daniel Baumgartner** | ||
| - **Benedikt Ehinger** | ||
| - **Sören Döring** | ||
| - **Niklas Gärtner** | ||
| - **Vladimir Mikheev** | ||
|
|
||
| Doctoral reserchers: | ||
| - 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 |