Frequently Asked Questions¶
Can I have a version of pipeline without all the notes?¶
Yes! all the tutorial cells in the pipeline are tagged with “tutorial”.
We can use nbconvert to obtain a copy of the notebook with all those cells removed.
For example, the following command will give you a clean pipeline:
jupyter nbconvert pipeline.ipynb \
--TagRemovePreprocessor.enabled=True \
--TagRemovePreprocessor.remove_cell_tags="tutorial" \
--to notebook \
--output pipeline_clean.ipynb
Just note that since this is a different copy of the pipeline, there might be extra work if you want to merge you edits on this clean copy with updates in the default pipeline notebook.
KilledWorker dammit, what do I do?¶
Short answer: sometimes all you need is to try again.
If that doesn’t work or if that’s getting annoying, then increasing memory_limit of the cluster would most likely fix it.
See Dealing with KilledWorker for more detail.
What do I do with the output of MiniAn?¶
Hopefully the tutorials in the pipeline would give you an idea of how to interprete each variable.
Then if you’re happy to work with xarray, then you will feel right at home once you do open_minian.
See Saving to other formats for details on converting the output to other formats.