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Merge additions from work leading to Conference submission #18

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Merge additions from work leading to Conference submission #18

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@scott-huberty scott-huberty commented Aug 28, 2024 •
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@christian-oreilly this PR aims to take the 1st step to integrating the changes we made during our paper write-up (on the slurm branch) into main. All this PR does is make some organizational changes to the files we added. Mainly, on the slurm branch, All the files we added during our analysis blitz were placed into the slurm subfolder, including py files, images, data files, etc.

Now these files are placed in respective data, images, notebooks, scripts, and scripts/slurm subfolders. In cases where the scripts/notebooks/images were very specific to our paper, I placed them into a paper subfolder.

The proposed notebook structure looks like this:

eog-learn/
├─ data/
│  ├─ paper/
│  │  ├─ eeg_signals.netcdf
│  │  ├─ et_signals.netcdf
│  │  ├─ topo_erp.netcdf
├─ eoglearn/
│  ├─ io
│  ├─ viz
├─ images/
│  ├─ sensitivity_specificity.png
│  ├─ topo_ica.png
│  ├─ topo_model.png
├─ notebooks/
│  ├─ eog_model.ipynb
│  ├─ paper/
│  │  ├─ LSTM_compute_xr.ipynb
│  │  ├─ Pytorch_EOG_LSTM_analysis.ipynb
├─ scripts/
│  ├─ run_eog_lstm_ica_mp.py
│  ├─ run_eog_lstm_regression.py
│  ├─ run_eog_lstm_regression_mp.py
|  ├─ slurm/
│     ├─ run_eog_lstm.sbatch

Wheres on the slurm branch, it looked like this:

eog-learn/
├─ eoglearn/
│  ├─ io
│  ├─ viz
├─ notebooks/
│  ├─ eog_model.ipynb
├─ slurm/
│  ├─ run_eog_lstm.sbatch
│  ├─ eeg_signals.netcdf
│  ├─ et_signals.netcdf
│  ├─ topo_erp.netcdf
│  ├─ LSTM_compute_xr.ipynb
│  ├─ Pytorch_EOG_LSTM_analysis.ipynb
│  ├─ run_eog_lstm_ica_mp.py
│  ├─ run_eog_lstm_regression.py
│  ├─ run_eog_lstm_regression_mp.py
|  ├─ images/
│      ├─ sensitivity_specificity.png
│      ├─ topo_ica.png
│      ├─ topo_model.png

What do you think?

Note

I did not actually commit the data files we generated to this repository (i.e. eeg_signals.netcdf) because of how large they are. I did add a .gitkeep file into data/paper so that this directory structure is preserved. But each of us is assumed to have a copy of those files in their local repo.

@scott-huberty scott-huberty marked this pull request as draft August 28, 2024 17:43
@scott-huberty scott-huberty marked this pull request as ready for review August 28, 2024 21:15
@scott-huberty scott-huberty mentioned this pull request Aug 29, 2024
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@scott-huberty @christian-oreilly