def create_cells(self, cellindex):
"""Create and layout N cells in the network."""
cells = {}
position_factor = 1e3
sim_params = hf.get_net_params(hf.get_tempdata_address())
mn_pos_x = sim_params[10]
mn_pos_y = sim_params[11]
mn_pos_z = sim_params[12]
cell = Mn()
'''cell.set_pos(mn_pos_x[0] + cellindex * position_factor,
mn_pos_y[0] + cellindex * position_factor,
mn_pos_z[0] + cellindex * position_factor)
'''
cell.set_pos(cellindex * position_factor,
cellindex * position_factor,
cellindex * position_factor)
cells.update({"Mn" : cell})
self.cellPositions['Mn'].append([cell.somapos[0], cell.somapos[1], cell.somapos[2]])
cell = Ia(n_nodes = hf.get_n_nodes_from_mat('E:\\Google Drive\\Github\\tempdata\\move_root_um_move_root_points_cs.mat',0))
cell.set_pos(cellindex * position_factor,
cellindex * position_factor,
cellindex * position_factor)
cells.update({"Ia" : cell})
self.cellPositions['Ia'].append([cell.somapos[0], cell.somapos[1], cell.somapos[2]])
cell = Ib(n_nodes = hf.get_n_nodes_from_mat('E:\\Google Drive\\Github\\tempdata\\move_root_um_move_root_points_cs.mat',1))
cell.set_pos(cellindex * position_factor,
cellindex * position_factor,
cellindex * position_factor)
cells.update({"Ib" : cell})
self.cellPositions['Ib'].append([cell.somapos[0], cell.somapos[1], cell.somapos[2]])
cell = IaInt()
cell.set_pos(cellindex * position_factor,
cellindex * position_factor,
cellindex * position_factor)
cells.update({"IaInt" : cell})
self.cellPositions['IaInt'].append([cell.somapos[0], cell.somapos[1], cell.somapos[2]])
cell = IbInt()
cell.set_pos(cellindex * position_factor,
cellindex * position_factor,
cellindex * position_factor)
cells.update({"IbInt" : cell})
self.cellPositions['IbInt'].append([cell.somapos[0], cell.somapos[1], cell.somapos[2]])
cell = Ren()
cell.set_pos(cellindex * position_factor,
cellindex * position_factor,
cellindex * position_factor)
cells.update({"Ren" : cell})
self.cellPositions['Ren'].append([cell.somapos[0], cell.somapos[1], cell.somapos[2]])
for key, value in cells.iteritems():
value.tstopms = self.cellParameters['tstopms']
return cells
def __init__(self, *args, **kwargs):
'''
class initialization
POPULATION_SIZE : int, number of cells
cellParameters : dict
populationParameters : dict
synapseParameters : dict
'''
super(Ia_network, self).__init__(*args, **kwargs)
self.cellPositions = {
'Mn' : [],
'Ia' : []
}
self.cellRotations = {
'Mn' : [],
'Ia' : []
}
sim_params = hf.get_net_params(hf.get_tempdata_address())
dummy_Ia = Ia(n_nodes = hf.get_n_nodes_from_mat('E:\\Google Drive\\Github\\tempdata\\move_root_um_move_root_points_cs.mat',0))
dummy_Mn = Mn()
self.cellMorphologies = {
'Mn' : dummy_Mn.morphology_address,
'Ia' : dummy_Ia.morphology_address
}
del dummy_Ia, dummy_Mn
def __init__(self, *args, **kwargs):
'''
class initialization
POPULATION_SIZE : int, number of cells
cellParameters : dict
populationParameters : dict
synapseParameters : dict
'''
super(Ia_network, self).__init__(*args, **kwargs)
self.cellPositions = {'Mn': [], 'Ia': []}
self.cellRotations = {'Mn': [], 'Ia': []}
sim_params = hf.get_net_params(hf.get_tempdata_address())
dummy_Ia = Ia(n_nodes=sim_params[0][0])
dummy_Mn = Mn()
self.cellMorphologies = {
'Mn': dummy_Mn.morphology_address,
'Ia': dummy_Ia.morphology_address
}
del dummy_Ia, dummy_Mn
def create_cells(self, cellindex):
"""Create and layout N cells in the network."""
cells = {}
position_factor = 1e3
sim_params = hf.get_net_params(hf.get_tempdata_address())
mn_pos_x = sim_params[10]
mn_pos_y = sim_params[11]
mn_pos_z = sim_params[12]
cell = Mn()
'''cell.set_pos(mn_pos_x[0] + cellindex * position_factor,
mn_pos_y[0] + cellindex * position_factor,
mn_pos_z[0] + cellindex * position_factor)
'''
cell.set_pos(cellindex * position_factor, cellindex * position_factor,
cellindex * position_factor)
cells.update({"Mn": cell})
self.cellPositions['Mn'].append(
[cell.somapos[0], cell.somapos[1], cell.somapos[2]])
cell = Ia(n_nodes=sim_params[0][0])
cell.set_pos(cellindex * position_factor, cellindex * position_factor,
cellindex * position_factor)
cells.update({"Ia": cell})
self.cellPositions['Ia'].append(
[cell.somapos[0], cell.somapos[1], cell.somapos[2]])
return cells
def __init__(self):
self.sim_params = hf.get_net_params(hf.get_tempdata_address())
self.n_nodes = self.sim_params[0][0]
self.diameter = self.sim_params[4][0]
self.inl = self.sim_params[5][0]
self.length = self.sim_params[4][0]
self.d_lambda = 0.1
super(Ia, self).__init__()
def __init__(self):
self.sim_params = hf.get_net_params(hf.get_tempdata_address())
self.n_nodes = self.sim_params[0][0]
self.diameter = self.sim_params[4][0]
self.inl = self.sim_params[5][0]
self.length = self.sim_params[4][0]
self.d_lambda = 0.1
super(Ia, self).__init__()
def create_cells(self, cellindex):
"""Create and layout N cells in the network."""
cells = {}
position_factor = 1e3
sim_params = hf.get_net_params(hf.get_tempdata_address())
mn_pos_x = sim_params[10]
mn_pos_y = sim_params[11]
mn_pos_z = sim_params[12]
if cellindex = self.populationParameters['size'] - 1:
cell = Mn(is_last_in_network = True)
def create_cells(self, N):
"""Create and layout N cells in the network."""
self.cells = []
r = 50 # Radius of cell locations from origin (0,0,0) in microns
N = self._N
position_factor = 5e3;
sim_params = hf.get_net_params(hf.get_tempdata_address())
mn_pos_x = sim_params[10]
mn_pos_y = sim_params[11]
mn_pos_z = sim_params[12]
for i in range(N):
cell = Mn()
cell.set_position(mn_pos_x[0]+i * position_factor,mn_pos_y[0]+i * position_factor,mn_pos_z[0]+i * position_factor)
self.cells.append(cell)
for i in range(N):
cell = Ia()
cell.set_position(i * position_factor,i * position_factor,i * position_factor)
self.cells.append(cell)
def create_cells(self, N):
"""Create and layout N cells in the network."""
self.cells = []
r = 50 # Radius of cell locations from origin (0,0,0) in microns
N = self._N
position_factor = 5e3
sim_params = hf.get_net_params(hf.get_tempdata_address())
mn_pos_x = sim_params[10]
mn_pos_y = sim_params[11]
mn_pos_z = sim_params[12]
for i in range(N):
cell = Mn()
cell.set_position(mn_pos_x[0] + i * position_factor,
mn_pos_y[0] + i * position_factor,
mn_pos_z[0] + i * position_factor)
self.cells.append(cell)
for i in range(N):
cell = Ia()
cell.set_position(i * position_factor, i * position_factor,
i * position_factor)
self.cells.append(cell)
from mpi4py import MPI
from matplotlib import pyplot
from neuronpy.graphics import spikeplot
import helper_functions as hf
from Ia_network_LFPy import Ia_network as Ia_net
os.chdir('E:\\Google Drive\\Github\\Spinal-Cord-Modeling\\Python')
tempdata_address = hf.get_tempdata_address()
mn_geom_address = hf.get_mn_geom_address()
Ia_geom_file = tempdata_address + "Ia_geometry"
mn_geom_file = mn_geom_address + "motoneuron_geometry"
mod_geom_file = tempdata_address + "model_tree.neu"
sim_params = hf.get_net_params(tempdata_address)
# sim_params[0] = n_nodes
# sim_params[1] = start_time
# sim_params[2] = dur_time
# sim_params[3] = interval_time
# sim_params[4] = diameter
# sim_params[5] = inl
# sim_params[6] = points_per_node
# sim_params[7] = ampstart
# sim_params[8] = stepsize
# sim_params[9] = ampmax
# sim_params[10]= coords_x
# sim_params[11]= coords_y
# sim_params[12]= coords_z
from neuronpy.graphics import spikeplot
import helper_functions as hf
from Ia_Clarke_LFPy import Ia_Clarke as Ia_net
import numpy as np
import cPickle as pickle
import scipy
os.chdir('E:\\Google Drive\\Github\\Spinal-Cord-Modeling\\Python')
tempdata_address = hf.get_tempdata_address()
mn_geom_address = hf.get_mn_geom_address()
Ib_geom_file = tempdata_address + "Ib_geometry"
mn_geom_file = mn_geom_address + "motoneuron_geometry"
mod_geom_file = tempdata_address + "model_tree.neu"
sim_params = hf.get_net_params(tempdata_address)
# sim_params[0] = n_nodes
# sim_params[1] = start_time
# sim_params[2] = dur_time
# sim_params[3] = interval_time
# sim_params[4] = diameter
# sim_params[5] = inl
# sim_params[6] = points_per_node
# sim_params[7] = ampstart
# sim_params[8] = stepsize
# sim_params[9] = ampmax
# sim_params[10]= coords_x
# sim_params[11]= coords_y
# sim_params[12]= coords_z