Mat file not saved properly in batch functions

A Python package that facilitates development and use of models of biological neural networks

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Vittorio
Posts: 5
Joined: Mon Aug 28, 2017 12:21 pm

Mat file not saved properly in batch functions

Post by Vittorio » Thu Feb 15, 2018 10:58 am

Hi, I have some issue saving mat files with the batch process.
When I save the mat files with the batch function (e.g. tutorial 8), the mat file doesn’t contain information about the neurons spikes/traces although it is indicated in the parameter file e.g.

Code: Select all

cfg.recordCells = ['all']  # which cells to record from
cfg.recordStim = True  # record spikes of cell stims
cfg.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}}  # Dict with traces to record
cfg.recordStep = 0.1 			# Step size in ms to save data (eg. V traces, LFP, etc)
cfg.saveFileStep = cfg.duration # step size in ms to save data to disk
cfg.savePickle = True # Whether or not to write spikes etc. to a .mat file
cfg.saveMat = True
I checked without batch function (by running the file separately via the init function) and the mat file created now contains all the information about neurons/spikes. Am I missing something?

Thanks,
Vittorio

salvadord
Posts: 70
Joined: Tue Aug 18, 2015 3:49 pm

Re: Mat file not saved properly in batch functions

Post by salvadord » Thu Feb 15, 2018 11:30 am

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

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