"""
Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
"""
import os
import posixpath
import sys
import pickle
import numpy as np
import neuron
from LFPy import Cell, RecExtElectrode
from LFPy.run_simulation import _run_simulation, _run_simulation_with_electrode
class TemplateCell(Cell):
"""
class LFPy.TemplateCell
This class allow using NEURON templates with some limitations.
This takes all the same parameters as the Cell class, but requires three
more template related parameters
Parameters
----------
morphology : str
path to morphology file
templatefile : str
File with cell template definition(s)
templatename : str
Cell template-name used for this cell object
templateargs : str
Parameters provided to template-definition
v_init : float
Initial membrane potential. Default to -65.
Ra : float
axial resistance. Defaults to 150.
cm : float
membrane capacitance. Defaults to 1.0
passive : bool
Passive mechanisms are initialized if True. Defaults to True
passive_parameters : dict
parameter dictionary with values for the passive membrane mechanism in
NEURON ('pas'). The dictionary must contain keys 'g_pas' and 'e_pas',
like the default: passive_parameters=dict(g_pas=0.001, e_pas=-70)
extracellular : bool
switch for NEURON's extracellular mechanism. Defaults to False
dt: float
Simulation time step. Defaults to 2**-4
tstart : float
initialization time for simulation <= 0 ms. Defaults to 0.
tstop : float
stop time for simulation > 0 ms. Defaults to 100.
nsegs_method : 'lambda100' or 'lambda_f' or 'fixed_length' or None
nseg rule, used by NEURON to determine number of compartments.
Defaults to 'lambda100'
max_nsegs_length : float or None
max segment length for method 'fixed_length'. Defaults to None
lambda_f : int
AC frequency for method 'lambda_f'. Defaults to 100
d_lambda : float
parameter for d_lambda rule. Defaults to 0.1
delete_sections : bool
delete pre-existing section-references. Defaults to True
custom_code : list or None
list of model-specific code files ([.py/.hoc]). Defaults to None
custom_fun : list or None
list of model-specific functions with args. Defaults to None
custom_fun_args : list or None
list of args passed to custom_fun functions. Defaults to None
pt3d : bool
use pt3d-info of the cell geometries switch. Defaults to False
celsius : float or None
Temperature in celsius. If nothing is specified here
or in custom code it is 6.3 celcius
verbose : bool
verbose output switch. Defaults to False
Examples
--------
>>> import LFPy
>>> cellParameters = {
>>> 'morphology' : '<path to morphology.hoc>',
>>> 'templatefile' : '<path to template_file.hoc>'
>>> 'templatename' : 'templatename'
>>> 'templateargs' : None
>>> 'v_init' : -65,
>>> 'cm' : 1.0,
>>> 'Ra' : 150,
>>> 'passive' : True,
>>> 'passive_parameters' : {'g_pas' : 0.001, 'e_pas' : -65.},
>>> 'dt' : 2**-3,
>>> 'tstart' : 0,
>>> 'tstop' : 50,
>>> }
>>> cell = LFPy.TemplateCell(**cellParameters)
>>> cell.simulate()
"""
def __init__(self,
templatefile='LFPyCellTemplate.hoc',
templatename='LFPyCellTemplate',
templateargs=None,
verbose=False,
**kwargs):
"""
Initialization of the Template Cell object.
"""
if "win32" in sys.platform and type(templatefile) is str:
templatefile = templatefile.replace(os.sep, posixpath.sep)
self.templatefile = templatefile
self.templatename = templatename
self.templateargs = templateargs
self.verbose = verbose
if not hasattr(neuron.h, 'd_lambda'):
neuron.h.load_file('stdlib.hoc', 'String') #NEURON std. library
neuron.h.load_file('import3d.hoc') #import 3D morphology lib
#load the cell template specification
#check if templatename exist in neuron.h namespace:
if hasattr(neuron.h, self.templatename):
if self.verbose:
print('template %s exist already' % self.templatename)
else:
if type(self.templatefile) == str:
neuron.h.load_file(self.templatefile)
elif type(self.templatefile) == list:
for template in self.templatefile:
if "win32" in sys.platform:
template = template.replace(os.sep, posixpath.sep)
neuron.h.load_file(template)
#initialize the cell object
Cell.__init__(self, **kwargs)
def _load_geometry(self):
"""Load the morphology-file in NEURON"""
try:
neuron.h.sec_counted = 0
except LookupError:
neuron.h('sec_counted = 0')
#the python cell object we are loading the morphology into:
self.template = getattr(neuron.h, self.templatename)(self.templateargs)
#perform a test if the morphology is already loaded:
seccount = 0
for sec in self.template.all:
seccount += 1
if seccount == 0:
#import the morphology, try and determine format
fileEnding = self.morphology.split('.')[-1]
if not fileEnding == 'hoc' or fileEnding == 'HOC':
#create objects for importing morphologies of different formats
if fileEnding == 'asc' or fileEnding == 'ASC':
Import = neuron.h.Import3d_Neurolucida3()
if not self.verbose:
Import.quiet = 1
elif fileEnding == 'swc' or fileEnding == 'SWC':
Import = neuron.h.Import3d_SWC_read()
elif fileEnding == 'xml' or fileEnding == 'XML':
Import = neuron.h.Import3d_MorphML()
else:
raise ValueError('%s is not a recognised morphology file format! ').with_traceback('Should be either .hoc, .asc, .swc, .xml!' \
% self.morphology)
#assuming now that morphology file is the correct format
try:
Import.input(self.morphology)
except:
if not hasattr(neuron, 'neuroml'):
raise Exception('Can not import, try and copy the ' + \
'nrn/share/lib/python/neuron/neuroml ' + \
'folder into %s' % neuron.__path__[0])
else:
raise Exception('something wrong with file, see output')
try:
imprt = neuron.h.Import3d_GUI(Import, 0)
except:
raise Exception('See output, try to correct the file')
#instantiate the cell object
if fileEnding == 'xml' or fileEnding == 'XML':
#can not currently assign xml to cell template
try:
imprt.instantiate(self.template)
except:
raise Exception("this xml file is not supported")
else:
imprt.instantiate(self.template)
else:
neuron.h.execute("xopen(\"%s\")" % self.morphology, self.template)
#set shapes and create sectionlists
neuron.h.define_shape()
self._create_sectionlists()
def _create_sectionlists(self):
"""Create section lists for different kinds of sections"""
self.allsecnames = []
for sec in self.template.all:
self.allsecnames.append(sec.name())
self.allseclist = self.template.all
#list of soma sections, assuming it is named on the format "soma*"
self.nsomasec = 0
self.somalist = neuron.h.SectionList()
for sec in self.allseclist:
if 'soma' in sec.name():
self.somalist.append(sec=sec)
self.nsomasec += 1