netpyne.network.network

Module defining Network class and methods

Classes:

Network([params])

Class for/to <short description of netpyne.network.network.Network>

class netpyne.network.network.Network(params=None)

Bases: object

Class for/to <short description of netpyne.network.network.Network>

Methods:

setParams(params)
createPops()
createCells()
addStims()	Internal function to add stims specified in specs.NetParams Usage: Creates and attaches stims to targets via CompartCell.addstim() based on entries in the specs.NetParams sub- dictionaries -- specs.NetParams.stimSourceParams and specs.NetParams.stimTargetParams (see below) NetParams.stimSourceParams entries contain key-value pairs to describe NEURON point processes specified by the 'type' entry (i.e. 'IClamp', 'VClamp', 'SEClamp', 'AlphaSynapse', 'VecStim') NetParams.stimTargetParams entries contain key-value pairs to describe the post-synaptic connections for a stimSourceParam entry specified by the 'source' entry, including a 'sec' and 'loc' entry (describing section and location) for where the post-synaptic connection will exist and a 'conds' entry with a dictionary specifying the cell criteria for the post-synaptic connections: (i.e. 'x', 'y', 'z' or 'xnorm', 'ynorm', 'znorm' specifying cell criteria by location, 'cellList' specifying cell criteria by specific gid, or arbitrary 'key': 'value' tags. For 'VecStim' point processes, it may be more convenient to create an artificial cell (i.e.netParams.popParams see: netpyne/cell/pointCell.py) which allows pattern generation ('rhythmic', 'evoked', 'poisson', 'gauss') by key-value entries in a 'spikePattern' dictionary.
connectCells()	Function for/to <short description of netpyne.network.conn.connectCells>
fullConn(preCellsTags, postCellsTags, connParam)	Function for/to <short description of netpyne.network.conn.fullConn>
generateRandsPrePost(pre, post)	Function for/to <short description of netpyne.network.conn.generateRandsPrePost>
probConn(preCellsTags, postCellsTags, connParam)	Function for/to <short description of netpyne.network.conn.probConn>
randUniqueInt(r, N, vmin, vmax)	Function for/to <short description of netpyne.network.conn.randUniqueInt>
convConn(preCellsTags, postCellsTags, connParam)	Function for/to <short description of netpyne.network.conn.convConn>
divConn(preCellsTags, postCellsTags, connParam)	Function for/to <short description of netpyne.network.conn.divConn>
fromListConn(preCellsTags, postCellsTags, ...)	Function for/to <short description of netpyne.network.conn.fromListConn>
pathDistance(to_segment)	Compute the path distance between two points on a neuron based on h.distance()
posFromLoc(x)	Compute absolute 3D position of given section at location x
subcellularConn(allCellTags, allPopTags)	Function for/to <short description of netpyne.network.subconn.subcellularConn>
addRxD([nthreads])	Function for/to <short description of netpyne.network.netrxd.addRxD>
calcSegCoords()	Function for/to <short description of netpyne.network.shape.calcSegCoords>
defineCellShapes()	Function for/to <short description of netpyne.network.shape.defineCellShapes>
modifyCells(params[, updateMasterAllCells])	Function for/to <short description of netpyne.network.modify.modifyCells>
modifySynMechs(params[, updateMasterAllCells])	Function for/to <short description of netpyne.network.modify.modifySynMechs>
modifyConns(params[, updateMasterAllCells])	Function for/to <short description of netpyne.network.modify.modifyConns>
modifyStims(params[, updateMasterAllCells])	Function for/to <short description of netpyne.network.modify.modifyStims>

setParams(params)

createPops()

createCells()

addStims()

Internal function to add stims specified in specs.NetParams Usage:

Creates and attaches stims to targets via CompartCell.addstim() based on entries in the specs.NetParams sub- dictionaries – specs.NetParams.stimSourceParams and specs.NetParams.stimTargetParams (see below) NetParams.stimSourceParams entries contain key-value pairs to describe NEURON point processes specified by the ‘type’ entry (i.e. ‘IClamp’, ‘VClamp’, ‘SEClamp’, ‘AlphaSynapse’, ‘VecStim’) NetParams.stimTargetParams entries contain key-value pairs to describe the post-synaptic connections for a stimSourceParam entry specified by the ‘source’ entry, including a ‘sec’ and ‘loc’ entry (describing section and location) for where the post-synaptic connection will exist and a ‘conds’ entry with a dictionary specifying the cell criteria for the post-synaptic connections: (i.e. ‘x’, ‘y’, ‘z’ or ‘xnorm’, ‘ynorm’, ‘znorm’ specifying cell criteria by location, ‘cellList’ specifying cell criteria by specific gid, or arbitrary ‘key’: ‘value’ tags. For ‘VecStim’ point processes, it may be more convenient to create an artificial cell (i.e.netParams.popParams see: netpyne/cell/pointCell.py) which allows pattern generation (‘rhythmic’, ‘evoked’, ‘poisson’, ‘gauss’) by key-value entries in a ‘spikePattern’ dictionary.

Parameters:

self (<type>) – <Short description of self> Default: required

connectCells()

Function for/to <short description of netpyne.network.conn.connectCells>

Parameters:

self (<type>) – <Short description of self> Default: required

fullConn(preCellsTags, postCellsTags, connParam)

Function for/to <short description of netpyne.network.conn.fullConn>

Parameters:

• self (<type>) – <Short description of self> Default: required

• preCellsTags (<type>) – <Short description of preCellsTags> Default: required

• postCellsTags (<type>) – <Short description of postCellsTags> Default: required

• connParam (<type>) – <Short description of connParam> Default: required

generateRandsPrePost(pre, post)

Function for/to <short description of netpyne.network.conn.generateRandsPrePost>

Parameters:

• self (<type>) – <Short description of self> Default: required

• pre (<type>) – <Short description of pre> Default: required

• post (<type>) – <Short description of post> Default: required

probConn(preCellsTags, postCellsTags, connParam)

Function for/to <short description of netpyne.network.conn.probConn>

Parameters:

• self (<type>) – <Short description of self> Default: required

• preCellsTags (<type>) – <Short description of preCellsTags> Default: required

• postCellsTags (<type>) – <Short description of postCellsTags> Default: required

• connParam (<type>) – <Short description of connParam> Default: required

randUniqueInt(r, N, vmin, vmax)

Function for/to <short description of netpyne.network.conn.randUniqueInt>

Parameters:

• self (<type>) – <Short description of self> Default: required

• r (<type>) – <Short description of r> Default: required

• N (<type>) – <Short description of N> Default: required

• vmin (<type>) – <Short description of vmin> Default: required

• vmax (<type>) – <Short description of vmax> Default: required

convConn(preCellsTags, postCellsTags, connParam)

Function for/to <short description of netpyne.network.conn.convConn>

Parameters:

• self (<type>) – <Short description of self> Default: required

• preCellsTags (<type>) – <Short description of preCellsTags> Default: required

• postCellsTags (<type>) – <Short description of postCellsTags> Default: required

• connParam (<type>) – <Short description of connParam> Default: required

divConn(preCellsTags, postCellsTags, connParam)

Function for/to <short description of netpyne.network.conn.divConn>

Parameters:

• self (<type>) – <Short description of self> Default: required

• preCellsTags (<type>) – <Short description of preCellsTags> Default: required

• postCellsTags (<type>) – <Short description of postCellsTags> Default: required

• connParam (<type>) – <Short description of connParam> Default: required

fromListConn(preCellsTags, postCellsTags, connParam)

Function for/to <short description of netpyne.network.conn.fromListConn>

Parameters:

• self (<type>) – <Short description of self> Default: required

• preCellsTags (<type>) – <Short description of preCellsTags> Default: required

• postCellsTags (<type>) – <Short description of postCellsTags> Default: required

• connParam (<type>) – <Short description of connParam> Default: required

pathDistance(to_segment)

Compute the path distance between two points on a neuron based on h.distance()

Parameters:

• from_segment (<type>) – <Short description of origin_segment> Default: required

• to_segment (<type>) – <Short description of to_segment> Default: required

posFromLoc(x)

Compute absolute 3D position of given section at location x

Parameters:

• sec (dict) – <Short description of origin_segment> Default: required

• x (float) – <Short description of to_segment> Default: required

subcellularConn(allCellTags, allPopTags)

Function for/to <short description of netpyne.network.subconn.subcellularConn>

Parameters:

• self (<type>) – <Short description of self> Default: required

• allCellTags (<type>) – <Short description of allCellTags> Default: required

• allPopTags (<type>) – <Short description of allPopTags> Default: required

addRxD(nthreads=None)

Function for/to <short description of netpyne.network.netrxd.addRxD>

Parameters:

self (<type>) – <Short description of self> Default: required

calcSegCoords()

Function for/to <short description of netpyne.network.shape.calcSegCoords>

Parameters:

self (<type>) – <Short description of self> Default: required

defineCellShapes()

Function for/to <short description of netpyne.network.shape.defineCellShapes>

Parameters:

self (<type>) – <Short description of self> Default: required

modifyCells(params, updateMasterAllCells=False)

Function for/to <short description of netpyne.network.modify.modifyCells>

Parameters:

• self (<type>) – <Short description of self> Default: required

• params (<type>) – <Short description of params> Default: required

• updateMasterAllCells (bool) – <Short description of updateMasterAllCells> Default: False Options: <option> <description of option>

modifySynMechs(params, updateMasterAllCells=False)

Function for/to <short description of netpyne.network.modify.modifySynMechs>

Parameters:

• self (<type>) – <Short description of self> Default: required

• params (<type>) – <Short description of params> Default: required

• updateMasterAllCells (bool) – <Short description of updateMasterAllCells> Default: False Options: <option> <description of option>

modifyConns(params, updateMasterAllCells=False)

Function for/to <short description of netpyne.network.modify.modifyConns>

Parameters:

• self (<type>) – <Short description of self> Default: required

• params (<type>) – <Short description of params> Default: required

• updateMasterAllCells (bool) – <Short description of updateMasterAllCells> Default: False Options: <option> <description of option>

modifyStims(params, updateMasterAllCells=False)

Function for/to <short description of netpyne.network.modify.modifyStims>

Parameters:

• self (<type>) – <Short description of self> Default: required

• params (<type>) – <Short description of params> Default: required

• updateMasterAllCells (bool) – <Short description of updateMasterAllCells> Default: False Options: <option> <description of option>