Issues with Kachery

[MaitreyiJ]

Hi!
I have been attempting to use spike forest for some spike sorting benchmarking .
I was able to clone the repo and I also downloaded the dependency Kachery-but I am having the following error when I attempt to run one of the examples in this repo(running spykingCircus sorter)

with ka.config(fr='default_readonly'): (Error in this line)
AttributeError: module 'kachery' has no attribute 'config'

I have tried to set the environment variable -kachery storage to some folder for temp files storage and I am not too sure how to set the password for the environment variable kachery_password.

I also attempted to run the test files in the kachery repo and I get the error-Permission denied.

I am suspecting that there is some issue with the kachery dependency.
Any help/instructions will be highly helpful.

Regards
Maitreyi

[magland]

Hi Maitreyi. Could you please confirm that you are using the right version of kachery? Did you install using pip install kachery? Try pip list to see which version is installed.

Then try a basic:

with ka.config(fr='default_readonly'):
    pass

[MaitreyiJ]

Yes I tried running the command, this time it doesn't fail, but gives a warning
Warning: unable to load preset configurations from: https://raw.githubusercontent.com/flatironinstitute/kachery/config/config/config_2019a.json

[magland]

Okay, we will look into this tomorrow, thanks for the report.

[MaitreyiJ]

Hi !
I have been able to run the sorter now-successfully (given in the example) but there is a specific directory structure I had to follow-in terms of placing the dependencies.(kachery files)

I am currently trying to read the output files generated by the example( the Jason files) with the help of widgets/ sh links.

Thanks for the support.

[magland]

What do you mean by widgets/ sh links? Do you need help with this?

…

On Thu, May 14, 2020 at 4:12 PM MaitreyiJ ***@***.***> wrote: Hi ! I have been able to run the sorter now-successfully (given in the example) but there is a specific directory structure I had to follow-in terms of placing the dependencies.(kachery files) I am currently trying to read the output files generated by the example( the Jason files) with the help of widgets/ sh links. Thanks for the support. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA4CIQFRMMRDX7XIVEDOCTTRRRGCFANCNFSM4M657QKQ> .

[MaitreyiJ]

Yes, I think you can help me out with this.
The following screenshot was taken after running the python script example_spykingcircus.py
Running the script opens the command prompt and suuccefully runs the sorter (spykingCircus) on the data-set. However the command prompt closes immediately once the spike sorting is complete and the following output is recorded in the python shell.

I am unable to understand how I should go about viewing the output files. As per the documentation , a single Jason file will contain the output . But I cant locate that file or any putput produced by the sorter.

This is what I see in the shell(in case the screenshot doesn't load properly)
===== Hither: finished [spykingcircus] with status finished after 117.37312245368958 sec
Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json
Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json
Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json
Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json
hither.File(C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905)

[magland]

It appears that you are on windows. We haven't tested anything on windows. One thing you could do is to make a virtual linux machine.

…

On Thu, May 14, 2020 at 4:35 PM MaitreyiJ ***@***.***> wrote: Yes, I think you can help me out with this. The following screenshot was taken after running the python script example_spykingcircus.py Running the script opens the command prompt and suuccefully runs the sorter (spykingCircus) on the data-set. However the command prompt closes immediately once the spike sorting is complete and the following output is recorded in the python shell. I am unable to understand how I should go about viewing the output files. As per the documentation , a single Jason file will contain the output . But I cant locate that file or any putput produced by the sorter. [image: OutputDebuggingIssues] <https://user-images.githubusercontent.com/59170109/81983061-bfc8dd80-9600-11ea-947e-b88934e55e74.png> This is what I see in the shell(in case the screenshot doesn't load properly) ===== Hither: finished [spykingcircus] with status finished after 117.37312245368958 sec Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json Warning: problem writing .record.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\e5\7d\75\e57d75df9b97b4c275976cbdaa43f101da393c99.record.json Warning: problem writing .hints.json file: C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905.hints.json hither.File(C:\Users\Maitreyi\CareerDevelopmentoversumeer\SummerResearch2020\spikeforest2.kachery-storage\sha1\41\31\da\4131da62e3189a45b3844e5d699c96e492034905) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA4CIQFCS4LWOISWFSOLMLLRRRI2XANCNFSM4M657QKQ> .