From 172768723daccd8b1fe3d20f47a3414d22f1bb6d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Skukies?= <57703446+ReneSkukies@users.noreply.github.com> Date: Tue, 24 Oct 2023 16:42:08 +0200 Subject: [PATCH 1/4] Update README.md unify readme with unfold family --- README.md | 100 ++++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 82 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 498d2cde7..2da493118 100644 --- a/README.md +++ b/README.md @@ -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) @@ -22,33 +23,96 @@ The supportet visualizations are: - Topoplot series - Parallel Coordinates Plot +
+Click to see example plots + ![grafik](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/af2801e5-cd64-4932-b84d-9abc1d8470ee) -## Structure -### Code Notes +
+ +## Discover the Unfold-Family & Friends + +
+Click to expand + +| | 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) +
+ +## Install + +### Installing Julia + +
+Click to expand + +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 +
-### 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: -- 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 From d6ac6890dbe5bdbfaef0f857218abbfbd1e1bb91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Skukies?= <57703446+ReneSkukies@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:48:33 +0200 Subject: [PATCH 2/4] Update README.md Update unfold family table --- README.md | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 2da493118..df3b11200 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,9 @@ [![Build Status](https://github.com/unfoldtoolbox/UnfoldMakie.jl/workflows/CI/badge.svg)](https://github.com/unfoldtoolbox/UnfoldMakie.jl/actions) [![Coverage](https://codecov.io/gh/behinger/UnfoldMakie.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/behinger/UnfoldMakie.jl) +|rERP|EEG visualisation|EEG Simulations|BIDS pipeline|Decode EEG data|Statistical testing| +|---|---|---|---|---|---| +| | ||||| 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. @@ -30,22 +33,6 @@ The supportet visualizations are: -## Discover the Unfold-Family & Friends - -
-Click to expand - -| | 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) -
- ## Install ### Installing Julia From 23c0586175dc5e790832cc77878ae11f9921f156 Mon Sep 17 00:00:00 2001 From: Judith Schepers Date: Mon, 30 Oct 2023 10:54:08 +0100 Subject: [PATCH 3/4] Update README.md Updated/Corrected paths for adding documentation. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index df3b11200..50be91ce9 100644 --- a/README.md +++ b/README.md @@ -80,9 +80,9 @@ 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` +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 From ca2113c7407ec4ea592c49d4389433002fc5eb1e Mon Sep 17 00:00:00 2001 From: Benedikt Ehinger Date: Mon, 30 Oct 2023 11:09:20 +0100 Subject: [PATCH 4/4] Update README.md --- README.md | 48 ++++++++++++++++++++++++++---------------------- 1 file changed, 26 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index df3b11200..93ce54f7e 100644 --- a/README.md +++ b/README.md @@ -4,34 +4,35 @@ [![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) [![Coverage](https://codecov.io/gh/behinger/UnfoldMakie.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/behinger/UnfoldMakie.jl) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6531996.svg)](https://doi.org/10.5281/zenodo.6531996) |rERP|EEG visualisation|EEG Simulations|BIDS pipeline|Decode EEG data|Statistical testing| |---|---|---|---|---|---| | | ||||| -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. - -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`. - -The supportet visualizations are: - +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: + +- ![icon_erpplot_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/22c8472d-df78-46d7-afe8-e1e4e7b04313) +ERP plots +- ![icon_butterfly_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/30b86665-3705-4258-bffa-97abcd308235) +Butterfly plots +- ![icon_topoplot_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/ea91f14f-30df-4316-997b-56bc411c9276) +Topography plots +- ![icon_toposeries_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/eceab5d6-88c7-41ae-b0d8-5ca652e83b40) +Topography time series +- ![icon_erpgrid_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/83b42a21-439a-49fd-80bc-cd82872695e9) +ERP grid +- ![icon_erpimage_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/b45b0547-7333-4d28-9ac8-33a989b7c132) +ERP images +- ![icon_channelimage_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/7ea16a7a-879a-4dcc-aaab-bc97211910ba) +Channel images +- ![icon_parallel_20px](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/dab097c3-bcd6-4405-a44b-71cbe3e5fac9) +Parallel coordinates - Designmatrices -- Line Plots -- Butterfly Plots -- ERP Images with option for sorting -- Topo Plots -- Topoplot series -- Parallel Coordinates Plot - -
-Click to see example plots - -![grafik](https://github.com/unfoldtoolbox/UnfoldMakie.jl/assets/10183650/af2801e5-cd64-4932-b84d-9abc1d8470ee) -
## Install @@ -66,8 +67,11 @@ Pkg.add("UnfoldMakie") ```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) -# TBA +plot_erp(coeftable(m)) ``` ## Contributions