Point process not located in a section

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Krishna Chaitanya
Posts: 67
Joined: Wed Jan 18, 2012 12:25 am
Location: University of Pavia

Point process not located in a section

Post by Krishna Chaitanya » Tue Nov 20, 2018 6:35 am

Hi,

When I use integrate and fire model template in NetPyNE through importing class, and when I try to simulate it, I get an error "Point process not located in a section".

This typically happens during association of gid to a pointer i.e., NetCon(pointer, None).

However, I used to do the same in NEURON using h.NetCon(pointer, None, sec=<sec>). There's no error in this case.

I do not understand why NetPyNE throws an error when using the same template.

salvadord
Posts: 76
Joined: Tue Aug 18, 2015 3:49 pm

Re: Point process not located in a section

Post by salvadord » Thu Nov 22, 2018 1:41 pm

Hi Krishna,

Could you please share your code so we can look at the details? If it's not too long you can post it here. Alternatively you can share the link to a repo (eg. in Github) or send it to me by email (salvadordura@gmail.com).

Thanks

Krishna Chaitanya
Posts: 67
Joined: Wed Jan 18, 2012 12:25 am
Location: University of Pavia

Re: Point process not located in a section

Post by Krishna Chaitanya » Fri Nov 23, 2018 10:37 am

Hello,

Here's the script I used to simulate

Code: Select all

from netpyne import specs, sim

# Network parameters
netParams = specs.NetParams()  # object of class NetParams to store the network parameters


netParams.popParams['Izhi03a_pop'] = {'cellType': 'PYR', 'numCells': 100, 'cellModel': 'Izhike'}



cellRule = netParams.importCellParams(label='PYR_Izhi03a_rule', conds={'cellType': 'PYR', 'cellModel':'Izhike'},
	fileName='GrCTemp.py', cellName='granule')
netParams.renameCellParamsSec('PYR_Izhi03a_rule', 'sec', 'soma')  # rename imported section 'sec' to 'soma'
cellRule['secs']['soma']['pointps']['Granule_0']['vref'] = 'vv' # specify that uses its own voltage V


# Stimulation parameters
netParams.stimSourceParams['bkg'] = {'type': 'NetStim', 'rate': 50, 'noise': 0.1}

netParams.stimTargetParams['bg2'] = {'source': 'bkg', 'conds': {'cellType': 'PYR', 'cellModel': ['Izhike']}, 
									'weight': 9, 'delay': 5, 'sec': 'soma'}


## Connectivity params		


# Simulation options
simConfig = specs.SimConfig()					# object of class SimConfig to store simulation configuration
simConfig.duration = 1*1e3 			# Duration of the simulation, in ms
simConfig.dt = 0.025 				# Internal integration timestep to use
simConfig.verbose = 0			# Show detailed messages
simConfig.threshold=-42 
simConfig.recordTraces = {'V_soma':{'sec':'soma', 'loc':0.5, 'var':'vv'}}  # Dict with traces to record
simConfig.recordStep = 0.1 			# Step size in ms to save data (eg. V traces, LFP, etc)
simConfig.filename = 'model_output'  # Set file output name
simConfig.savePickle = True		# Save params, network and sim output to pickle file

simConfig.analysis['plotRaster'] = True#{True, 'saveFig': 'tut_import_raster.png'}			# Plot a raster
simConfig.analysis['plotTraces'] = {'include': [1], 'saveFig':'plotvoltage.png'} 			# Plot recorded traces for this list of cells
My model has a internal threshold of -42, which means if the voltage crosses the threshold -42, it should generate a spike.

After simulation, the raster plot doesn't show anything because there are no spikes recorded.

I don't understand where I am going wrong.

Kindly let me know if there are any errors in the script I have used.

Thank you.

salvadord
Posts: 76
Joined: Tue Aug 18, 2015 3:49 pm

Re: Point process not located in a section

Post by salvadord » Thu Nov 29, 2018 11:26 am

Thanks Krishna. I need the GrCTemp.py to actually test the model. You can paste it here or email to salvadordura@gmail.com

Krishna Chaitanya
Posts: 67
Joined: Wed Jan 18, 2012 12:25 am
Location: University of Pavia

Re: Point process not located in a section

Post by Krishna Chaitanya » Fri Nov 30, 2018 1:46 am

Hi,

I have sent an email with the cell template.

The template is for a detailed model. Is there a possibility to export cell positions from hdf5 and set it in the model? I have predefined cell positions in hdf5.

Kindly let me know.

Thank you.

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