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