Source code for LFPy.templatecell

#!/usr/bin/env python
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
GNU General Public License for more details.


import os
import posixpath
import sys
import neuron
from LFPy import Cell

[docs]class TemplateCell(Cell): """ ``LFPy.Cell`` like class allowing use of NEURON templates with some limitations. This takes all the same parameters as the Cell class, but requires three more template related parameters ``templatefile``, ``templatename`` and ``templateargs`` 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 segments. 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() See also -------- Cell NetworkCell """ def __init__(self, templatefile='LFPyCellTemplate.hoc', templatename='LFPyCellTemplate', templateargs=None, verbose=False, **kwargs): if "win32" in sys.platform and isinstance(templatefile, 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 isinstance(self.templatefile, str): neuron.h.load_file(self.templatefile) elif isinstance(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 parent Cell object super().__init__(**kwargs) def _load_geometry(self): """Load the morphology-file in NEURON""" # 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 not a recognised morphology format' % self.morphology).with_traceback( 'Should be either .hoc, .asc, .swc, .xml') # assuming now that morphology file is the correct format try: Import.input(self.morphology) except BaseException: 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 BaseException: 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 BaseException: 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( 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 self.somalist.append(sec=sec) self.nsomasec += 1