def _ion_register(self):
charge = self._charge
if self._name is not None:
ion_type = h.ion_register(self._name, charge)
if ion_type == -1:
raise RxDException('Unable to register species: %s' %
self._name)
# insert the species if not already present
regions = self._regions if hasattr(self._regions,
'__len__') else [self._regions]
for r in regions:
if r.nrn_region in ('i', 'o'):
for s in r.secs:
try:
ion_forms = [
self._name + 'i', self._name + 'o',
'i' + self._name, 'e' + self._name
]
for i in ion_forms:
# this throws an exception if one of the ion forms is missing
temp = s.__getattribute__(self._name + 'i')
except:
s.insert(self._name + '_ion')
# set to recalculate reversal potential automatically
# the last 1 says to set based on global initial concentrations
# e.g. nai0_na_ion, etc...
h.ion_style(self._name + '_ion', 3, 2, 1, 1, 1, sec=s)
def _ion_register(self):
"""modified from neuron.rxd.species.Species._ion_register"""
ion_type = h.ion_register(self._species, self._charge)
if ion_type == -1:
raise RxDException('Unable to register species: %s' % self._species)
# insert the species if not already present
ion_forms = [self._species + 'i', self._species + 'o', 'i' + self._species, 'e' + self._species]
for s in h.allsec():
try:
for i in ion_forms:
# this throws an exception if one of the ion forms is missing
temp = s.__getattribute__(i)
except:
s.insert(self._species + '_ion')
# set to recalculate reversal potential automatically
# the last 1 says to set based on global initial concentrations
# e.g. nao0_na_ion, etc...
# TODO: this is happening GLOBALLY even to sections that aren't inside the extracellular domain (FIX THIS)
h.ion_style(self._species + '_ion', 3, 2, 1, 1, 1, sec=s)
def _ion_register(self):
charge = self._charge
if self._name is not None:
ion_type = h.ion_register(self._name, charge)
if ion_type == -1:
raise RxDException('Unable to register species: %s' % self._name)
# insert the species if not already present
regions = self._regions if hasattr(self._regions, '__len__') else [self._regions]
for r in regions:
if r.nrn_region in ('i', 'o'):
for s in r.secs:
try:
ion_forms = [self._name + 'i', self._name + 'o', 'i' + self._name, 'e' + self._name]
for i in ion_forms:
# this throws an exception if one of the ion forms is missing
temp = s.__getattribute__(self._name + 'i')
except:
s.insert(self._name + '_ion')
# set to recalculate reversal potential automatically
# the last 1 says to set based on global initial concentrations
# e.g. nai0_na_ion, etc...
h.ion_style(self._name + '_ion', 3, 2, 1, 1, 1, sec=s)
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."""
# TODO: if a list of sections is passed in, make that one region
# _species_count is used to create a unique _real_name for the species
global _species_count
# TODO: check about the 0<x<1 problem alluded to in the documentation
h.define_shape()
self._name = name
if name is not None:
if not isinstance(name, str):
raise Exception('Species name must be a string')
if name in _defined_species and _defined_species[name]() is not None:
raise Exception('Species "%s" previously defined: %r' % (name, _defined_species[name]()))
else:
name = _species_count
self._id = _species_count
_species_count += 1
_defined_species[name] = weakref.ref(self)
if regions is None:
raise Exception('Must specify region where species is present')
if hasattr(regions, '__len__'):
regions = list(regions)
else:
regions = list([regions])
if not all(isinstance(r, region.Region) for r in regions):
raise Exception('regions list must consist of Region objects only')
self._regions = regions
self._real_name = name
self.initial = initial
self._charge = charge
self._d = d
# at this point self._name is None if unnamed or a string == name if
# named
if self._name is not None:
ion_type = h.ion_register(name, charge)
if ion_type == -1:
raise Exception('Unable to register species: %s' % species)
# insert the species if not already present
for r in regions:
if r.nrn_region in ('i', 'o'):
for s in r.secs:
try:
ion_forms = [name + 'i', name + 'o', 'i' + name, 'e' + name]
for i in ion_forms:
# this throws an exception if one of the ion forms is missing
temp = s.__getattribute__(name + 'i')
except:
s.insert(name + '_ion')
# set to recalculate reversal potential automatically
# the last 1 says to set based on global initial concentrations
# e.g. nai0_na_ion, etc...
h.ion_style(name + '_ion', 3, 2, 1, 1, 1, sec=s)
self._real_secs = region._sort_secs(sum([r.secs for r in regions], []))
# TODO: at this point the sections are sorted within each region, but for
# tree solver (which not currently using) would need sorted across
# all regions if diffusion between multiple regions
self._secs = [Section1D(self, sec, d, r) for r in regions for sec in r.secs]
if self._secs:
self._offset = self._secs[0]._offset
else:
self._offset = 0
self._has_adjusted_offsets = False
self._assign_parents()
self._update_region_indices()
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."""
# TODO: if a list of sections is passed in, make that one region
# _species_count is used to create a unique _real_name for the species
global _species_count
# TODO: check about the 0<x<1 problem alluded to in the documentation
h.define_shape()
self._name = name
if name is not None:
if not isinstance(name, str):
raise Exception('Species name must be a string')
if name in _defined_species and _defined_species[name](
) is not None:
raise Exception('Species "%s" previously defined: %r' %
(name, _defined_species[name]()))
else:
name = _species_count
self._id = _species_count
_species_count += 1
_defined_species[name] = weakref.ref(self)
if regions is None:
raise Exception('Must specify region where species is present')
if hasattr(regions, '__len__'):
regions = list(regions)
else:
regions = list([regions])
if not all(isinstance(r, region.Region) for r in regions):
raise Exception('regions list must consist of Region objects only')
self._regions = regions
self._real_name = name
self.initial = initial
self._charge = charge
self._d = d
# at this point self._name is None if unnamed or a string == name if
# named
if self._name is not None:
ion_type = h.ion_register(name, charge)
if ion_type == -1:
raise Exception('Unable to register species: %s' % species)
# insert the species if not already present
for r in regions:
if r.nrn_region in ('i', 'o'):
for s in r.secs:
try:
ion_forms = [
name + 'i', name + 'o', 'i' + name, 'e' + name
]
for i in ion_forms:
# this throws an exception if one of the ion forms is missing
temp = s.__getattribute__(name + 'i')
except:
s.insert(name + '_ion')
# set to recalculate reversal potential automatically
# the last 1 says to set based on global initial concentrations
# e.g. nai0_na_ion, etc...
h.ion_style(name + '_ion', 3, 2, 1, 1, 1, sec=s)
self._real_secs = region._sort_secs(sum([r.secs for r in regions], []))
# TODO: at this point the sections are sorted within each region, but for
# tree solver (which not currently using) would need sorted across
# all regions if diffusion between multiple regions
self._secs = [
Section1D(self, sec, d, r) for r in regions for sec in r.secs
]
if self._secs:
self._offset = self._secs[0]._offset
else:
self._offset = 0
self._has_adjusted_offsets = False
self._assign_parents()
self._update_region_indices()