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  • Nov 25 2022 16:47

    cedricrommel on master

    Implement ATCNet Create ATCNet test Update api.rst and whats_new.rst and 15 more (compare)

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robintibor
@robintibor
you accepted that invitation before
you joining?
have time?
Maciej Sliwowski
@sliwy
I'll be in 2 minutes, sorry
robintibor
@robintibor
@sliwy
robintibor
@robintibor
maziek
@sliwy
are you here?
gemeinl
@gemeinl
robintibor
@robintibor
I like the last part @gemeinl
i wonder if you could reverse the order in that tutorial, like first show the last part saying this is how you get a braindecode-dataset from this mne, and then saying ok now let's look into each step in detail
also, if we already had mne epochs, would there also be a clear way atm? is this not intended atm? how is it?
but ya also @sliwy maybe you can say how you find it in terms of understand dataset structure? it seems quite helpful to me!
I also added my current naming preference here: braindecode/braindecode#59
Maciej Sliwowski
@sliwy
@gemeinl I really like the dataset tutorial, great thing! I agree with @robintibor to start with the last cell - just quickly show how to read mne data. It looks simple and straightforward, you do not have to spend time to figure out where to start and what you need. It may be the first part - basic and usual application. The second part may describe more advanced usage e.g. with splitting (looks really interesting, I didn't know we have this functionality) and any other cool stuff is inside braindecode.
Maciej Sliwowski
@sliwy
One thing that may help to understand, it may be dividing this notebook into sections (like in the beginning) to focus attention, e.g "Dataset splitting" or "Creating windows"
It really helps a lot in understanding the dataset structures!
gemeinl
@gemeinl
Sure, I can easily swap the order. I just wanted to give this to you guys as fast as possible. I will make a proper plot_....py out of it.

also, if we already had mne epochs, would there also be a clear way atm? is this not intended atm? how is it?

I will see to this next. It could become a bit more tricky, though. The WindowsDataset gives x, y, ind, where y and ind are read from the metadata pandas.DataFrame from the mne.Epochs objects. If it is not there, you have to manually add it. I have never tried it, will see how it can be done.

gemeinl
@gemeinl
There is still the CroppedXyDataset but this should not be used, right? If I remember correctly, you wanted this to be removed @robintibor
robintibor
@robintibor
If we have very simple way to go from X y directly to windows dataset, then this could be removed, yes
like dataset = create_from_X_y(X,y)
with dataset being windows dataset
gemeinl
@gemeinl
such a function does not exsist yet, but i think this would be the way to go: https://gist.github.com/gemeinl/1220413cb4418a94c48b71c5014bb390#file-braindecode_xy_data_example-ipynb
Both examples i now sent would benefit from removing pandas import, i believe. We could do this by changing description argument of BaseDataset from pandas.Series to dict and cast it internally. What do you think abou this?
robintibor
@robintibor
ya why not, you could also support both as argument if there is something you may need to supply as series sometimes, i am not deep inside to judge
x y looks great, would be super to make it into single function
gemeinl
@gemeinl
I agree, making a function and removing XyDataset would be great :)
robintibor
@robintibor
@sliwy will work today more, is it fine if I take over your pull request at some point if necessary?
Maciej Sliwowski
@sliwy
@robintibor yeah, feel free to review/improve it. I did almost everything, no point in holding it back.
robintibor
@robintibor
great
robintibor
@robintibor
now starting some extensive refactorings
Alexandre Gramfort
@agramfort
robintibor
@robintibor
deploy of docs failed multiple times with some error about read-only SSH key, so I added a User key under https://app.circleci.com/settings/project/github/braindecode/braindecode/ssh?return-to=https%3A%2F%2Fapp.circleci.com%2Fpipelines%2Fgithub%2Fbraindecode%2Fbraindecode @agramfort
here circleci code is indeed read-only, I don't know if that is a problem: https://github.com/braindecode/braindecode/settings/keys
robintibor
@robintibor
image.png
if you asked about touching something before, them I am not aware of it. the screenshot above shows something visible under https://github.com/braindecode/braindecode/settings/keys , which I do not know why it happened
Alexandre Gramfort
@agramfort
ok something was changed
one needs to have read write keys in sync between circle ci and github
robintibor
@robintibor
on master it seemed to work again after I added this user key
Alexandre Gramfort
@agramfort
great !
anhnguyenducminh
@anhnguyenducminh
anhnguyenducminh
@anhnguyenducminh
Hi all, we are a team of students in Singapore investigating the relationship between environment, physiological measurement and electroencephalography. Currently, we are using deep learning to connect EEG measurement and other data types. We currently intend to use EEG data as input for our regression model to predict other measurements. As we have never used deep learning on EEG data before we do not know how to start. We are using OpenBCI cyton so the EEG data that we stored are in txt file – which can be made into numpy array. We are intending to use Braindecode, we did manage to store our data as MNE raw arrays and after reading the documentation, we managed to create a BaseConcatDataset (we are not sure if we set the parameters for create_from_X_y correctly, I am still not sure on the meaning of window in the structure). After that we are not what preprocessing method and regression parameters to use. Thank you very much for your help.
robintibor
@robintibor
Hi
anhnguyenducminh
@anhnguyenducminh
Thank you for the link, I have finished most of it, and got the model to start running but when there are multiple targets in the regression model ( I follow the regression example in braindecode.org), I encounter this error: