def __init__(self, regions=None, d=0, name=None, charge=0, initial=None):
"""s = rxd.Species(regions, d = 0, name = None, charge = 0, initial = None)
Declare a species.
Parameters:
regions -- a Region or list of Region objects containing the species
d -- the diffusion constant of the species (optional; default is 0, i.e. non-diffusing)
name -- the name of the Species; used for syncing with HOC (optional; default is none)
charge -- the charge of the Species (optional; default is 0)
initial -- the initial concentration or None (if None, then imports from HOC if the species is defined at finitialize, else 0)
Note:
charge must match the charges specified in NMODL files for the same ion, if any."""
import neuron
import ctypes
from . import rxd
# if there is a species, then rxd is being used, so we should register
# this function may be safely called many times
rxd._do_nbs_register()
# TODO: check if "name" already defined elsewhere (if non-None)
# if so, make sure other fields consistent, expand regions as appropriate
self._allow_setting = True
self.regions = regions
self.d = d
self.name = name
self.charge = charge
self.initial = initial
_all_species.append(weakref.ref(self))
# declare an update to the structure of the model (the number of differential equations has changed)
neuron.nrn_dll_sym('structure_change_cnt', ctypes.c_int).value += 1
# initialize self if the rest of rxd is already initialized
if initializer.is_initialized():
if _has_3d:
if isinstance(regions, region.Region) and not regions._secs1d:
pass
elif hasattr(regions, '__len__') and all(not r._secs1d
for r in regions):
pass
else:
# TODO: remove this limitation
# one strategy would be to just redo the whole thing; what are the implications of that?
# (pointers would be invalid; anything else?)
raise RxDException(
'Currently cannot add species containing 1D after 3D species defined and initialized. To work-around: reorder species definition.'
)
self._do_init()
def __init__(self, secs=None, nrn_region=None, geometry=None, dimension=None, dx=None, name=None):
"""
In NEURON 7.4+, secs is optional at initial region declaration, but it
must be specified before the reaction-diffusion model is instantiated.
.. note:: dimension and dx will be deprecated in a future version
"""
self._allow_setting = True
self.secs = secs
self.nrn_region = nrn_region
self.geometry = geometry
if dimension is not None:
warnings.warn(
"dimension argument was a development feature only; use set_solve_type instead... the current version sets all the sections to your requested dimension, but this will override any previous settings"
)
import neuron
neuron.rxd.set_solve_type(secs, dimension=dimension)
self._name = name
self.dx = dx
_all_regions.append(weakref.ref(self))
# initialize self if the rest of rxd is already initialized
if initializer.is_initialized():
self._do_init()
def __init__(self,
secs=None,
nrn_region=None,
geometry=None,
dimension=None,
dx=None,
name=None):
"""
In NEURON 7.4+, secs is optional at initial region declaration, but it
must be specified before the reaction-diffusion model is instantiated.
.. note:: dimension and dx will be deprecated in a future version
"""
self._allow_setting = True
self.secs = secs
self.nrn_region = nrn_region
self.geometry = geometry
if dimension is not None:
warnings.warn(
'dimension argument was a development feature only; use set_solve_type instead... the current version sets all the sections to your requested dimension, but this will override any previous settings'
)
import neuron
neuron.rxd.set_solve_type(secs, dimension=dimension)
self._name = name
self.dx = dx
_all_regions.append(weakref.ref(self))
# initialize self if the rest of rxd is already initialized
if initializer.is_initialized():
self._do_init()
def __init__(self, regions=None, d=0, name=None, charge=0, initial=None):
"""s = rxd.Species(regions, d = 0, name = None, charge = 0, initial = None)
Declare a species.
Parameters:
regions -- a Region or list of Region objects containing the species
d -- the diffusion constant of the species (optional; default is 0, i.e. non-diffusing)
name -- the name of the Species; used for syncing with HOC (optional; default is none)
charge -- the charge of the Species (optional; default is 0)
initial -- the initial concentration or None (if None, then imports from HOC if the species is defined at finitialize, else 0)
Note:
charge must match the charges specified in NMODL files for the same ion, if any."""
import neuron
import ctypes
from . import rxd
# if there is a species, then rxd is being used, so we should register
# this function may be safely called many times
rxd._do_nbs_register()
# TODO: check if "name" already defined elsewhere (if non-None)
# if so, make sure other fields consistent, expand regions as appropriate
self._allow_setting = True
self.regions = regions
self.d = d
self.name = name
self.charge = charge
self.initial = initial
_all_species.append(weakref.ref(self))
# declare an update to the structure of the model (the number of differential equations has changed)
neuron.nrn_dll_sym('structure_change_cnt', ctypes.c_int).value += 1
# initialize self if the rest of rxd is already initialized
if initializer.is_initialized():
if _has_3d:
if isinstance(regions, region.Region) and not regions._secs1d:
pass
elif hasattr(regions, '__len__') and all(not r._secs1d for r in regions):
pass
else:
# TODO: remove this limitation
# one strategy would be to just redo the whole thing; what are the implications of that?
# (pointers would be invalid; anything else?)
raise RxDException('Currently cannot add species containing 1D after 3D species defined and initialized. To work-around: reorder species definition.')
self._do_init()
