plotRatePSD
Posted: Tue Dec 05, 2017 11:39 am
Hi,
I'm having some trouble getting plotRatePSD to work. I create a network with the following populations:
netParams.popParams['PY'] = {'cellType': 'sPY','gridSpacing': netParams.sizeX / numcorticalcells, 'zRange':[0.95,1.0], 'yRange':[0.95,1.0], 'cellModel':'HH'}
netParams.popParams['IN'] = {'cellType': 'sIN','gridSpacing': netParams.sizeX / numcorticalcells, 'zRange':[0.95,1.0],'yRange':[49.95,50.0], 'cellModel':'HH'}
netParams.popParams['RE'] = {'cellType': 'sRE','gridSpacing': netParams.sizeX / numthalamiccells, 'zRange':[0.95,1.0],'yRange':[99.95,100.0], 'cellModel':'HH'}
netParams.popParams['TC'] = {'cellType': 'sTC','gridSpacing': netParams.sizeX / numthalamiccells, 'zRange':[0.95,1.0],'yRange':[149.95,150.0], 'cellModel':'HH'}
Then there's some code to finish setting up the network which I've omitted. I try to make spectral density plot of firing rates with the following line:
simConfig.analysis['plotRatePSD'] = {'include':['PY']}
When I call sim.analyze(), I get the following error:
Plotting firing rate power spectral density (PSD) ...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "absence.py", line 134, in <module>
sim.analyze()
File "C:\ProgramData\Anaconda2\lib\site-packages\netpyne\wrappers.py", line 52, in analyze
sim.analysis.plotData() # gather spiking data and cell info from each node
File "C:\ProgramData\Anaconda2\lib\site-packages\netpyne\analysis.py", line 43, in plotData
out = func(**kwargs) # call function with user arguments
File "C:\ProgramData\Anaconda2\lib\site-packages\netpyne\analysis.py", line 1207, in plotRatePSD
color = popColors[subset] if subset in popColors else colorList[iplot%len(colorList)]
TypeError: argument of type 'NoneType' is not iterable
Do I have the right idea about how to set up the plotRatePSD call? Is a providing a color dictionary in the call manditory? Or is there something else going on here?
Also, if you would like the complete python file, let me know.
Thanks,
Andrew
I'm having some trouble getting plotRatePSD to work. I create a network with the following populations:
netParams.popParams['PY'] = {'cellType': 'sPY','gridSpacing': netParams.sizeX / numcorticalcells, 'zRange':[0.95,1.0], 'yRange':[0.95,1.0], 'cellModel':'HH'}
netParams.popParams['IN'] = {'cellType': 'sIN','gridSpacing': netParams.sizeX / numcorticalcells, 'zRange':[0.95,1.0],'yRange':[49.95,50.0], 'cellModel':'HH'}
netParams.popParams['RE'] = {'cellType': 'sRE','gridSpacing': netParams.sizeX / numthalamiccells, 'zRange':[0.95,1.0],'yRange':[99.95,100.0], 'cellModel':'HH'}
netParams.popParams['TC'] = {'cellType': 'sTC','gridSpacing': netParams.sizeX / numthalamiccells, 'zRange':[0.95,1.0],'yRange':[149.95,150.0], 'cellModel':'HH'}
Then there's some code to finish setting up the network which I've omitted. I try to make spectral density plot of firing rates with the following line:
simConfig.analysis['plotRatePSD'] = {'include':['PY']}
When I call sim.analyze(), I get the following error:
Plotting firing rate power spectral density (PSD) ...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "absence.py", line 134, in <module>
sim.analyze()
File "C:\ProgramData\Anaconda2\lib\site-packages\netpyne\wrappers.py", line 52, in analyze
sim.analysis.plotData() # gather spiking data and cell info from each node
File "C:\ProgramData\Anaconda2\lib\site-packages\netpyne\analysis.py", line 43, in plotData
out = func(**kwargs) # call function with user arguments
File "C:\ProgramData\Anaconda2\lib\site-packages\netpyne\analysis.py", line 1207, in plotRatePSD
color = popColors[subset] if subset in popColors else colorList[iplot%len(colorList)]
TypeError: argument of type 'NoneType' is not iterable
Do I have the right idea about how to set up the plotRatePSD call? Is a providing a color dictionary in the call manditory? Or is there something else going on here?
Also, if you would like the complete python file, let me know.
Thanks,
Andrew