def parse_templates_json(templates_json="templates.json",
ignore_chans = [],
save_example_files=False,
verbose=False):
with open(templates_json, "r") as templates_json_file:
json_cells = json.load(templates_json_file)
concentrationModels = ''
for firing_type_u in json_cells:
if verbose: print("\n --------------- %s "%(firing_type_u))
firing_type = str(firing_type_u)
cell_dict = json_cells[firing_type]
nml_doc = neuroml.NeuroMLDocument(id=firing_type)
# Membrane properties
#
included_channels[firing_type] = []
channel_densities = []
channel_density_nernsts = []
channel_density_non_uniform_nernsts = []
channel_density_non_uniforms = []
species = []
for section_list in cell_dict['forsecs']:
for parameter_name in cell_dict['forsecs'][section_list]:
value = cell_dict['forsecs'][section_list][parameter_name]
if verbose: print(" --- %s, %s: %s "%(section_list,parameter_name,value))
if parameter_name == 'g_pas':
channel = 'pas'
arguments = {}
cond_density = "%s S_per_cm2" % value
if verbose: print(' - Adding %s with %s'%(channel, cond_density))
channel_nml2_file = "%s.channel.nml"%channel
if channel_nml2_file not in included_channels[firing_type]:
nml_doc.includes.append(
neuroml.IncludeType(
href="../../NeuroML2/%s" %
channel_nml2_file))
included_channels[firing_type].append(channel_nml2_file)
erev = cell_dict['forsecs'][section_list]['e_pas']
erev = "%s mV" % erev
arguments["cond_density"] = cond_density
arguments['ion_channel'] = channel
arguments["ion"] = "non_specific"
arguments["erev"] = erev
arguments["id"] = "%s_%s" % (section_list, parameter_name)
channel_class = 'ChannelDensity'
density = getattr(neuroml, channel_class)(**arguments)
channel_densities.append(density)
for section_list in cell_dict['parameters']:
for parameter_name in cell_dict['parameters'][section_list]:
if parameter_name != 'e_pas' and 'CaDynamics_E2' not in parameter_name:
parameter_dict = cell_dict['parameters'][section_list][parameter_name]
if verbose: print(" --- %s, %s: %s "%(section_list,parameter_name,parameter_dict))
channel = parameter_dict['channel']
if channel not in ignore_chans:
arguments = {}
cond_density = None
variable_parameters = None
if parameter_dict['distribution']['disttype'] == "uniform":
value = float(parameter_dict['distribution']['value'])
if channel in density_scales:
value = value * density_scales[channel]
cond_density = "%s S_per_cm2" % value
else:
new_expr = '1e4 * (%s)'%parameter_dict['distribution']['value'].replace('x','p').replace('epp','exp')
iv = neuroml.InhomogeneousValue(inhomogeneous_parameters="PathLengthOver_%s"%section_list,
value=new_expr)
variable_parameters = [
neuroml.VariableParameter(
segment_groups=section_list,
parameter='condDensity',
inhomogeneous_value=iv)]
channel_name = channel
if channel_substitutes.has_key(channel):
channel_name = channel_substitutes[channel]
channel_nml2_file = "%s.channel.nml"%channel_name
if channel_nml2_file not in included_channels[firing_type]:
nml_doc.includes.append(
neuroml.IncludeType(
href="../../NeuroML2/%s" %
channel_nml2_file))
included_channels[firing_type].append(channel_nml2_file)
arguments['ion'] = channel_ions[channel]
erev = ion_erevs[arguments["ion"]]
channel_class = 'ChannelDensity'
if erev == "nernst":
erev = None
channel_class = 'ChannelDensityNernst'
elif erev == "pas":
erev = cell_dict['parameters'] \
[section_list]['e_pas']['distribution']\
['value']
erev = "%s mV" % erev
arguments["ion"] = "non_specific"
if variable_parameters is not None:
channel_class += 'NonUniform'
else:
arguments["segment_groups"] = section_list
if erev is not None:
arguments["erev"] = erev
arguments["id"] = "%s_%s" % (section_list, parameter_name)
if cond_density is not None:
arguments["cond_density"] = cond_density
arguments['ion_channel'] = channel_name
if variable_parameters is not None:
arguments['variable_parameters'] = variable_parameters
density = getattr(neuroml, channel_class)(**arguments)
if channel_class == "ChannelDensityNernst":
channel_density_nernsts.append(density)
elif channel_class == "ChannelDensityNernstNonUniform":
channel_density_non_uniform_nernsts.append(density)
elif channel_class == "ChannelDensityNonUniform":
channel_density_non_uniforms.append(density)
else:
channel_densities.append(density)
elif 'gamma_CaDynamics_E2' in parameter_name:
parameter_dict = cell_dict['parameters'][section_list][parameter_name]
model = 'CaDynamics_E2_NML2__%s_%s'%(firing_type,section_list)
value = parameter_dict['distribution']['value']
concentrationModels+='<concentrationModel id="%s" ion="ca" '%model +\
'type="concentrationModelHayEtAl" minCai="1e-4 mM" ' +\
'gamma="%s" '%value
elif 'decay_CaDynamics_E2' in parameter_name:
# calcium_model = \
# neuroml.DecayingPoolConcentrationModel(ion='ca')
model = 'CaDynamics_E2_NML2__%s_%s'%(firing_type,section_list)
species.append(neuroml.Species(
id='ca',
ion='ca',
initial_concentration='5.0E-11 mol_per_cm3',
initial_ext_concentration='2.0E-6 mol_per_cm3',
concentration_model=model,
segment_groups=section_list))
channel_nml2_file = 'CaDynamics_E2_NML2.nml'
if channel_nml2_file not in included_channels[firing_type]:
included_channels[firing_type].append(channel_nml2_file)
parameter_dict = cell_dict['parameters'][section_list][parameter_name]
value = parameter_dict['distribution']['value']
concentrationModels+='decay="%s ms" depth="0.1 um"/> <!-- For group %s in %s-->\n\n'%(value,section_list,firing_type)
capacitance_overwrites = {}
for section_list in cell_dict['forsecs']:
for parameter_name in cell_dict['forsecs'][section_list]:
if parameter_name == "cm" and section_list != 'all':
value = cell_dict['forsecs'][section_list][parameter_name]
capacitance_overwrites[
section_list] = "%s uF_per_cm2" % value
specific_capacitances = []
for section_list in default_capacitances:
if section_list in capacitance_overwrites:
capacitance = capacitance_overwrites[section_list]
else:
capacitance = default_capacitances[section_list]
specific_capacitances.append(
neuroml.SpecificCapacitance(value=capacitance,
segment_groups=section_list))
init_memb_potentials = [neuroml.InitMembPotential(
value="-80 mV", segment_groups='all')]
membrane_properties = neuroml.MembraneProperties(
channel_densities=channel_densities,
channel_density_nernsts=channel_density_nernsts,
channel_density_non_uniform_nernsts=channel_density_non_uniform_nernsts,
channel_density_non_uniforms=channel_density_non_uniforms,
specific_capacitances=specific_capacitances,
init_memb_potentials=init_memb_potentials)
# Intracellular Properties
#
resistivities = []
resistivities.append(neuroml.Resistivity(
value="100 ohm_cm", segment_groups='all'))
intracellular_properties = neuroml.IntracellularProperties(
resistivities=resistivities,
species=species)
# Cell construction
#
biophysical_properties = \
neuroml.BiophysicalProperties(id="biophys",
intracellular_properties=
intracellular_properties,
membrane_properties=
membrane_properties)
biophysical_properties_vs_types[firing_type] = biophysical_properties
if save_example_files:
cell = neuroml.Cell(id=firing_type,
notes="\n*************************\nThis is not a physiologically constrained cell model!!\n"+\
"It is only for testing formatting of the biophysicalProperties extracted from templates.json\n*************************\n",
biophysical_properties=biophysical_properties)
nml_doc.cells.append(cell)
cell.morphology = neuroml.Morphology(id="morph")
cell.morphology.segments.append(neuroml.Segment(id='0',
name='soma',
proximal=neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=10),
distal=neuroml.Point3DWithDiam(x=0,y=20,z=0,diameter=10)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="soma",
neuro_lex_id="sao864921383",
members=[neuroml.Member("0")]))
cell.morphology.segments.append(neuroml.Segment(id='1',
name='axon',
parent=neuroml.SegmentParent(segments='0',fraction_along="0"),
proximal=neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=2),
distal=neuroml.Point3DWithDiam(x=0,y=-50,z=0,diameter=2)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="axon",
neuro_lex_id="sao864921383",
members=[neuroml.Member("1")]))
cell.morphology.segments.append(neuroml.Segment(id='2',
name='basal_dend',
parent=neuroml.SegmentParent(segments='0'),
proximal=neuroml.Point3DWithDiam(x=0,y=20,z=0,diameter=3),
distal=neuroml.Point3DWithDiam(x=50,y=20,z=0,diameter=3)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="basal_dend",
neuro_lex_id="sao864921383",
members=[neuroml.Member("2")]))
cell.morphology.segments.append(neuroml.Segment(id='3',
name='apical_dend1',
parent=neuroml.SegmentParent(segments='0'),
proximal=neuroml.Point3DWithDiam(x=0,y=20,z=0,diameter=3),
distal=neuroml.Point3DWithDiam(x=0,y=120,z=0,diameter=3)))
cell.morphology.segments.append(neuroml.Segment(id='4',
name='apical_dend2',
parent=neuroml.SegmentParent(segments='0'),
proximal=neuroml.Point3DWithDiam(x=0,y=120,z=0,diameter=3),
distal=neuroml.Point3DWithDiam(x=0,y=220,z=0,diameter=3)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="apical_dend",
neuro_lex_id="sao864921383",
members=[neuroml.Member("3"),neuroml.Member("4")]))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="somatic",includes=[neuroml.Include("soma")]))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="axonal", includes=[neuroml.Include("axon")]))
sg = neuroml.SegmentGroup(id="basal", includes=[neuroml.Include("basal_dend")])
sg.inhomogeneous_parameters.append(neuroml.InhomogeneousParameter(id="PathLengthOver_"+"basal",
variable="x",
metric="Path Length from root",
proximal=neuroml.ProximalDetails(translation_start="0")))
cell.morphology.segment_groups.append(sg)
sg = neuroml.SegmentGroup(id="apical", includes=[neuroml.Include("apical_dend")])
sg.inhomogeneous_parameters.append(neuroml.InhomogeneousParameter(id="PathLengthOver_"+"apical",
variable="x",
metric="Path Length from root",
proximal=neuroml.ProximalDetails(translation_start="0")))
cell.morphology.segment_groups.append(sg)
nml_filename = 'test/%s.cell.nml' % firing_type
neuroml.writers.NeuroMLWriter.write(nml_doc, nml_filename)
logging.debug("Written cell file to: %s", nml_filename)
neuroml.utils.validate_neuroml2(nml_filename)
conc_mod_file = open('test/concentrationModel.txt','w')
conc_mod_file.write(concentrationModels)
conc_mod_file.close()
def create_GoC(runid):
### ---------- Load Params
noPar = True
pfile = Path('cellparams_file.pkl')
keepFile = open('useParams_FI_14_25.pkl', 'rb')
runid = pkl.load(keepFile)[runid]
keepFile.close()
print('Running morphology for parameter set = ', runid)
if pfile.exists():
print('Reading parameters from file:')
file = open('cellparams_file.pkl', 'rb')
params_list = pkl.load(file)
if len(params_list) > runid:
p = params_list[runid]
file.close()
if noPar:
p = icp.get_channel_params(runid)
# Creating document for cell
gocID = 'Golgi_040408_C1_' + format(runid, '05d')
goc = nml.Cell(id=gocID) #--------simid
cell_doc = nml.NeuroMLDocument(id=gocID)
cell_doc.cells.append(goc)
### Load morphology
morpho_fname = 'Golgi_040408_C1.cell.nml'
morpho_file = pynml.read_neuroml2_file(morpho_fname)
morpho = morpho_file.cells[0].morphology
cell_doc.includes.append(nml.IncludeType(href=morpho_fname))
goc.morphology = morpho
### ---------- Channels
na_fname = 'Golgi_Na.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=na_fname))
nar_fname = 'Golgi_NaR.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=nar_fname))
nap_fname = 'Golgi_NaP.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=nap_fname))
ka_fname = 'Golgi_KA.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=ka_fname))
sk2_fname = 'Golgi_SK2.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=sk2_fname))
km_fname = 'Golgi_KM.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=km_fname))
kv_fname = 'Golgi_KV.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=kv_fname))
bk_fname = 'Golgi_BK.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=bk_fname))
cahva_fname = 'Golgi_CaHVA.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=cahva_fname))
calva_fname = 'Golgi_CaLVA.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=calva_fname))
hcn1f_fname = 'Golgi_HCN1f.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=hcn1f_fname))
hcn1s_fname = 'Golgi_HCN1s.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=hcn1s_fname))
hcn2f_fname = 'Golgi_HCN2f.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=hcn2f_fname))
hcn2s_fname = 'Golgi_HCN2s.channel.nml'
cell_doc.includes.append(nml.IncludeType(href=hcn2s_fname))
leak_fname = 'Golgi_lkg.channel.nml'
#leak_ref = nml.IncludeType( href=leak_fname)
cell_doc.includes.append(nml.IncludeType(href=leak_fname))
calc_fname = 'Golgi_CALC.nml'
cell_doc.includes.append(nml.IncludeType(href=calc_fname))
calc = pynml.read_neuroml2_file(
calc_fname).decaying_pool_concentration_models[0]
calc2_fname = 'Golgi_CALC2.nml'
cell_doc.includes.append(nml.IncludeType(href=calc2_fname))
goc_2pools_fname = 'GoC_2Pools.cell.nml'
### ------Biophysical Properties
biophys = nml.BiophysicalProperties(id='biophys_' + gocID)
goc.biophysical_properties = biophys
# Inproperties
'''
res = nml.Resistivity( p["ra"] ) # --------- "0.1 kohm_cm"
ca_species = nml.Species( id="ca", ion="ca", concentration_model=calc.id, initial_concentration ="5e-5 mM", initial_ext_concentration="2 mM" )
ca2_species = nml.Species( id="ca2", ion="ca2", concentration_model="Golgi_CALC2", initial_concentration ="5e-5 mM", initial_ext_concentration="2 mM" )
intracellular = nml.IntracellularProperties( )
intracellular.resistivities.append( res )
intracellular.species.append( ca_species )
'''
intracellular = pynml.read_neuroml2_file(goc_2pools_fname).cells[
0].biophysical_properties.intracellular_properties
biophys.intracellular_properties = intracellular
# Membrane properties ------- cond
memb = nml.MembraneProperties()
biophys.membrane_properties = memb
#pynml.read_neuroml2_file(leak_fname).ion_channel[0].id -> can't read ion channel passive
chan_leak = nml.ChannelDensity(ion_channel="LeakConductance",
cond_density=p["leak_cond"],
erev="-55 mV",
ion="non_specific",
id="Leak")
memb.channel_densities.append(chan_leak)
chan_na = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(na_fname).ion_channel[0].id,
cond_density=p["na_cond"],
erev="87.39 mV",
ion="na",
id="Golgi_Na_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_na)
chan_nap = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(nap_fname).ion_channel[0].id,
cond_density=p["nap_cond"],
erev="87.39 mV",
ion="na",
id="Golgi_NaP_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_nap)
chan_nar = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(nar_fname).ion_channel[0].id,
cond_density=p["nar_cond"],
erev="87.39 mV",
ion="na",
id="Golgi_NaR_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_nar)
chan_ka = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(ka_fname).ion_channel[0].id,
cond_density=p["ka_cond"],
erev="-84.69 mV",
ion="k",
id="Golgi_KA_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_ka)
chan_sk = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(sk2_fname).ion_channel_kses[0].id,
cond_density=p["sk2_cond"],
erev="-84.69 mV",
ion="k",
id="Golgi_KAHP_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_sk)
chan_kv = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(kv_fname).ion_channel[0].id,
cond_density=p["kv_cond"],
erev="-84.69 mV",
ion="k",
id="Golgi_KV_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_kv)
chan_km = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(km_fname).ion_channel[0].id,
cond_density=p["km_cond"],
erev="-84.69 mV",
ion="k",
id="Golgi_KM_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_km)
chan_bk = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(bk_fname).ion_channel[0].id,
cond_density=p["bk_cond"],
erev="-84.69 mV",
ion="k",
id="Golgi_BK_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_bk)
chan_h1f = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(hcn1f_fname).ion_channel[0].id,
cond_density=p["hcn1f_cond"],
erev="-20 mV",
ion="h",
id="Golgi_hcn1f_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_h1f)
chan_h1s = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(hcn1s_fname).ion_channel[0].id,
cond_density=p["hcn1s_cond"],
erev="-20 mV",
ion="h",
id="Golgi_hcn1s_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_h1s)
chan_h2f = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(hcn2f_fname).ion_channel[0].id,
cond_density=p["hcn2f_cond"],
erev="-20 mV",
ion="h",
id="Golgi_hcn2f_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_h2f)
chan_h2s = nml.ChannelDensity(
ion_channel=pynml.read_neuroml2_file(hcn2s_fname).ion_channel[0].id,
cond_density=p["hcn2s_cond"],
erev="-20 mV",
ion="h",
id="Golgi_hcn2s_soma_group",
segment_groups="soma_group")
memb.channel_densities.append(chan_h2s)
chan_hva = nml.ChannelDensityNernst(
ion_channel=pynml.read_neuroml2_file(cahva_fname).ion_channel[0].id,
cond_density=p["cahva_cond"],
ion="ca",
id="Golgi_Ca_HVA_soma_group",
segment_groups="soma_group")
memb.channel_density_nernsts.append(chan_hva)
chan_lva = nml.ChannelDensityNernst(
ion_channel=pynml.read_neuroml2_file(calva_fname).ion_channel[0].id,
cond_density=p["calva_cond"],
ion="ca2",
id="Golgi_Ca_LVA_soma_group",
segment_groups="soma_group")
memb.channel_density_nernsts.append(chan_lva)
memb.spike_threshes.append(nml.SpikeThresh("0 mV"))
memb.specific_capacitances.append(
nml.SpecificCapacitance("1.0 uF_per_cm2"))
memb.init_memb_potentials.append(nml.InitMembPotential("-60 mV"))
goc_filename = '{}.cell.nml'.format(gocID)
pynml.write_neuroml2_file(cell_doc, goc_filename)
return True
cd_k = neuroml.ChannelDensity(id="k_chan",
segment_groups="all",
ion="k",
ion_channel="K_BC",
erev="-90 mV",
cond_density="30 mS_per_cm2")
channel_densities.append(cd_k)
specific_capacitances = []
specific_capacitances.append(
neuroml.SpecificCapacitance(value='1.0 uF_per_cm2', segment_groups='all'))
init_memb_potentials = [
neuroml.InitMembPotential(value="-80 mV", segment_groups='all')
]
membrane_properties = neuroml.MembraneProperties(
channel_densities=channel_densities,
channel_density_non_uniforms=channel_density_non_uniforms,
specific_capacitances=specific_capacitances,
init_memb_potentials=init_memb_potentials)
# Intracellular Properties
#
resistivities = []
resistivities.append(
neuroml.Resistivity(value="100 ohm_cm", segment_groups='all'))
intracellular_properties = neuroml.IntracellularProperties(