Search found 67 matches

by salvadord
Sat May 05, 2018 5:37 pm
Forum: NetPyNE
Topic: Import json format of morphology to NetPyNE
Replies: 2
Views: 125

Re: Import json format of morphology to NetPyNE

Hi Javad, Thanks for your question. So the file format is .json but what is the data structure that the morphology is stored in? e.g is it a dictionary of sections with 3d pts, does it follow a similar structure to swc? Perhaps you can share the file to get a better idea. NetPyNE can import morpholo...
by salvadord
Tue Apr 24, 2018 12:53 pm
Forum: NetPyNE
Topic: Slow speed to save sim results
Replies: 2
Views: 117

Re: Slow speed to save sim results

Hi Stefano, Sorry to hear the saving is taking so long. The independence of num of cores is normal, since data is gathered on the master node and then saved. The similar speed with SSD drives might indicate that what's taking longer could be the internal conversion to Matlab format (prior to saving ...
by salvadord
Sat Apr 21, 2018 5:59 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 12
Views: 7690

Re: VERSION RELEASES

# Version 0.7.8 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.8 - Added netParams.rotateCellsRandomly option to rotate cells randomly around y-axis - Added netParams.defineCellShapes option to convert stylized cell geometries to 3d points - Added 'histogram' option to plotSpikeStats - Im...
by salvadord
Sat Mar 24, 2018 8:28 pm
Forum: NetPyNE
Topic: Field names are restricted to 31 characters
Replies: 2
Views: 115

Re: Field names are restricted to 31 characters

Hi Stefano, I have never encountered this error but yes, it is related to the scipy savemat function, which has a limit of 31 chars per field: https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.savemat.html There seems to be an option to increase it to 64: long_field_names = True hope thi...
by salvadord
Wed Mar 21, 2018 6:20 pm
Forum: NetPyNE
Topic: plotLFP
Replies: 2
Views: 142

Re: plotLFP

Hi Andrew, Sorry for the delay responding -- unfortunately the email alerts for this forum are not working. I have fixed a few minor bugs (including this one) since the release of this feature, so please try the github "development" version and let me know if it works; instructions to install here: ...
by salvadord
Sat Feb 24, 2018 8:18 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 12
Views: 7690

Re: VERSION RELEASES

# Version 0.7.7 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.7 - Added LFP recording at arbitrary 3D locations - Added plotting of LFP time series, PSD, freq vs time and electrode locations - Updates to NeuroML conversion code. - ShapePlot now shows segment diameters as linewidths (Pyth...
by salvadord
Thu Feb 15, 2018 11:30 am
Forum: NetPyNE
Topic: Mat file not saved properly in batch functions
Replies: 1
Views: 134

Re: Mat file not saved properly in batch functions

Hi Vittorio,

Thanks for pointing this out, the issue was related to a bug in the "scipy" package — see https://github.com/scipy/scipy/issues/3487.

I found a workaround in netpyne and pushed to the GitHub ‘development' branch — it now works ok.

Thanks
Salva
by salvadord
Thu Feb 08, 2018 12:41 pm
Forum: NetPyNE
Topic: Gap junction support - parallel simulation?
Replies: 3
Views: 171

Re: Gap junction support - parallel simulation?

I fixed the bug that was preventing gap junctions to work with multiple cores. It will be released in the next version but you can try it now using the 'development' version of NetPyNE -- see instructions here: http://neurosimlab.org/netpyne/install.html#install-via-pip-development-version let me kn...
by salvadord
Mon Feb 05, 2018 5:01 pm
Forum: NetPyNE
Topic: Gap junction support - parallel simulation?
Replies: 3
Views: 171

Re: Gap junction support - parallel simulation?

Yes, it did originally, but I just tested it and seems some change introduced in a later version has broken mpi support -- I will post a message here once I fix it.

thanks for your message
by salvadord
Mon Jan 15, 2018 11:05 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 12
Views: 7690

Re: VERSION RELEASES

# Version 0.7.6 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.6 - Added option to order raster spike trains by multipe tags (eg. ['pop', 'y']) - Enable providing a 2D list of spike times to VecStim populations - Added exception handling to analysis functions - Updated saveLoadV1 examples...
by salvadord
Wed Dec 13, 2017 10:26 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1522

Re: Netpyne on clusters

try adding this at the top of the main script you are calling:

Code: Select all

import matplotlib; matplotlib.use('Agg')
by salvadord
Tue Dec 12, 2017 10:37 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1522

Re: Netpyne on clusters

Seems like there is some issue with matplotlib -- can you import it by itself outside of netpyne?

You can use the command line option '-nogui' (this sets netpyne.__gui__ to False) to avoid importing graphic-related modules -- but you won't be able to use the most analysis functions.
by salvadord
Tue Dec 12, 2017 10:33 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 4681

Re: Spike source and target sections

Where exactly did you change the label 'soma' to 'soma_C''? in the original imported file? in the netpyne netParams? I just tried replacing 'soma' with 'soma_C' in another example, and worked ok. So it might be that you are not replacing the label consistently, or some other bug. Feel free to send m...
by salvadord
Tue Dec 12, 2017 10:11 am
Forum: NetPyNE
Topic: Bug in plasticity option
Replies: 1
Views: 1205

Re: Bug in plasticity option

You can find the stdp.mod file here: https://github.com/Neurosim-lab/netpyne ... m/stdp.mod

let me know if that works
by salvadord
Wed Dec 06, 2017 3:19 pm
Forum: NetPyNE
Topic: plotRatePSD
Replies: 1
Views: 2325

Re: plotRatePSD

Andrew, The issue was due to a bug introduced in a recent change to plotRatePSD(). I have fixed it and pushed to the 'development' github branch of netpyne. It will be released in next version. You can use it now by cloning this github branch. Alternatively, you can just pass a dict with the color f...