NeuroMorpho.Org ID : NMO_09365 ''' from netpyne.support import morphology from netpyne import sim from neuron import h import matplotlib.pyplot as plt from mpl_toolkits import mplot3d import platform import neuron as nrn #load cell as mycell #def getmorph(self): myCell = morphology.Cell() morphology.load(filename=os.path.join(wdir, 'MN3_morphology.swc'), cell=myCell) #plot loaded cell fig = plt.figure() ax = plt.axes(projection='3d') morphology.shapeplot(h, ax, color='r') #get the sections from the cell secs = list(h.allsec()) secs_all = secs soma = [] axon = [] dend = [] #get the sections fro soma, axon and dend #def getset(self):
import matplotlib.pyplot as plt
from mpl_toolkits import mplot3d
import platform
import neuron as nrn
if platform.system() == 'Windows':
nrn.load_mechanisms(os.path.join(wdir + 'Morph_practice', 'modfiles'))
import sys
sys.path.append('C:', 'nrn', 'lib', 'python')
sys.path.append('D:', 'Okinawa', 'Python')
sys.path.append(wdir + 'Morph_practice', 'modfiles')
#class TC_cell():
#load cell as mycell
myCell = morphology.Cell()
morphology.load(filename=os.path.join(wdir, 'SWC', 'AA_0266.swc'), cell=myCell)
#plot loaded cell
fig = plt.figure()
ax = plt.axes(projection='3d')
morphology.shapeplot(h, ax)
#get the sections from the cell
secs = list(h.allsec())
secs_all = secs
soma = []
axon = []
dend = []
#get the sections fro soma, axon and dend
for sec in secs:
import os
wdir = os.getcwd()
from netpyne.support import morphology
from netpyne import sim
from neuron import h
import matplotlib.pyplot as plt
import matplotlib.cm
from mpl_toolkits import mplot3d
import platform
import neuron as nrn
#load cell as mycell
# def getmorph(self):
myCell_1 = morphology.Cell()
morphology.load(filename=os.path.join(wdir, 'MN1_morphology.swc'),
cell=myCell_1)
cell1_secs = list(h.allsec())
lenght_1 = len(cell1_secs)
myCell_2 = morphology.Cell()
morphology.load(filename=os.path.join(wdir, 'MN2_morphology.swc'),
cell=myCell_2)
cell2_secs = list(h.allsec())
del cell2_secs[0:lenght_1]
lenght_2 = len(cell2_secs)
myCell_3 = morphology.Cell()
def importCell(fileName, cellName, cellArgs = None, cellInstance = False):
"""
Function for/to <short description of `netpyne.conversion.neuronPyHoc.importCell`>
Parameters
----------
fileName : <type>
<Short description of fileName>
**Default:** *required*
cellName : <type>
<Short description of cellName>
**Default:** *required*
cellArgs : <``None``?>
<Short description of cellArgs>
**Default:** ``None``
**Options:** ``<option>`` <description of option>
cellInstance : bool
<Short description of cellInstance>
**Default:** ``False``
**Options:** ``<option>`` <description of option>
"""
h.initnrn()
varList = mechVarList() # list of properties for all density mechanisms and point processes
origGlob = getGlobals(list(varList['mechs'].keys())+list(varList['pointps'].keys()))
origGlob['v_init'] = -65 # add by hand since won't be set unless load h.load_file('stdrun')
if cellArgs is None: cellArgs = [] # Define as empty list if not otherwise defined
if fileName.endswith('.hoc') or fileName.endswith('.tem'):
h.load_file(fileName)
if not cellInstance:
if isinstance(cellArgs, dict):
cell = getattr(h, cellName)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(h, cellName)(*cellArgs) # create cell using template, passing list with args
else:
try:
cell = getattr(h, cellName)
except:
cell = None
elif fileName.endswith('.py'):
filePath,fileNameOnly = os.path.split(fileName) # split path from filename
if filePath not in sys.path: # add to path if not there (need to import module)
sys.path.insert(0, filePath)
removeFilePath = True
else:
removeFilePath = False
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
tempModule = importlib.import_module(moduleName)
modulePointer = tempModule
if isinstance(cellArgs, dict):
cell = getattr(modulePointer, cellName)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(modulePointer, cellName)(*cellArgs) # create cell using template, passing list with args
if removeFilePath: sys.path.remove(filePath)
elif fileName.endswith('.swc'):
from netpyne.support.morphology import load
cell = load(fileName)
else:
print("File name should end in '.hoc', '.py', or '.swc'")
return
secDic, secListDic, synMechs, globs = getCellParams(cell, varList, origGlob)
if fileName.endswith('.py'):
_delete_module(moduleName)
_delete_module('tempModule')
del modulePointer
elif fileName.endswith('.hoc'):
for sec in h.allsec():
try:
if h.cas()!=sec: sec.push()
h.delete_section()
h.pop_section()
except:
pass
h.initnrn()
setGlobals(origGlob) # restore original globals
return secDic, secListDic, synMechs, globs