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espenhgn / ViSAPy

Python package for generating benchmark data for evaluating spike sorting methods
GNU General Public License v2.0
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Failed to generate the sample dataset #5

Open AkiHase opened 4 years ago

AkiHase commented 4 years ago

hello, I downloaded and installed ViSAPy.Then try running "example_in_vivo_tetrode.py" to generate dataset. Unfortunately, the program seems to break down in the middle of the process.The interrupt is in the following position:

...... creating new database file savedata_tetrode_Mon_Mar_2_16_21_25_2020_4040335fbe0f408f847b24c6b424c0cd/non_stat_spikes.db Inserts took 114.618 seconds. Indexed db in 34.9237 seconds. setting up spike_generator connecting non-stationary poisson times (program stopped after this line)

Do you know why? I guess it is because my computer is not equipped enough, so could you please offer the recommended computer configuration? Or if it's convenient for you, can you just provide the download of the sample datasets you mentioned in the paper? I am a college student and want to use data to do some study and research. I will sincerely thank you!

espenhgn commented 4 years ago

Hi @AkiHase, Thanks for your interest in ViSAPy. Unfortunately it hasn't been maintained much if at all in recent times. Before you give it up, perhaps try and use the ViSAPy dev branch as well as the newest version of LFPy (v2.0.4) from either PyPi, conda-forge or github.com/LFPy/LFPy. No guaranties, but that may work for you. The calculations are still quite memory hungry though, and you may simply run out of RAM on your machine.

As an alternative which is more lightweight and also faster, I can point you to the MEArec package by @alejoe91 at https://github.com/alejoe91/MEArec, described in this paper: https://www.biorxiv.org/content/biorxiv/early/2019/07/03/691642.full.pdf

At the moment, my datasets are not easily accessible in the cloud.

AkiHase commented 4 years ago

@espenhgn Thank you for your very timely reply, Anyway, your reply is very helpful to me. Sincerely thank you again!

alejoe91 commented 4 years ago

@AkiHase we are updating and improving MEArec in these days. It should be done by tomorrow with a new version. Let me know if you end up using it and if you have any problems.