def setupOptions(model, **kwargs):
'''Can be called with no arguments except model. This will use the defaults
in param_sim.py param_model_defaults.py and apply no overrides.
Optionally, can pass any keyword arguments that are parameter names in
param_sim (e.g. fname, plotcomps, logging_level, etc.) to override them.
This function also handles any command line arguments. When run from command
line, any command line options will take precedence over param_sim and
param_model_defaults.
Function is wrapped with a function that counts calls to enable checking if
options have already been set up.
'''
# Warn if overwriting prior setupOptions
if setupOptions.calls > 1:
model.log.warning('''setupOptions has already been called. Overwriting
prior call with new options''')
# Get the option_parsers
param_sim_parser, model_parser = standard_options.standard_options()
param_sim = model.param_sim
###### apply any kwargs that are param_sim overrides. #####
# Find set of all kwargs that match param_sim variables
param_sim_overrides = set(set(kwargs.keys()) & set(vars(param_sim).keys()))
# Override each param_sim parameter in kwargs and pop item from kwargs
for k in param_sim_overrides:
setattr(param_sim, k, kwargs.pop(k))
# Command line args should have precedence--call here to update param_sim
# with any command line options after applying param_sim_overrides above
# Passing existing namespace into parse_known_args will only set attributes
# for command line arguments that are explicitly passed; no defaults are set
param_sim, unknown_args = param_sim_parser.parse_known_args(namespace = param_sim)
# parsing model params separately for setting spineYN, calYN, etc. from command line
model, _ = model_parser.parse_known_args(unknown_args, namespace = model)
# Pass param_sim to overrides and return model, plotcomps, and param_sim
model, param_sim = standard_options.overrides(param_sim, model)
# Any additional kwarg handling for kwargs not in param_sim can be added here:
# Setup logging level
log = setupLogging(model, level = param_sim.logging_level)
# Set fname to default if is None in param_sim:
if param_sim.fname is None:
param_sim.fname = (model.param_stim.Stimulation.Paradigm.name + '_' +
#model.param_stim.location.stim_dendrites[0])
#change to (after checking with Dan)
model.param_stim.Stimulation.StimLoc.stim_dendrites[0])
######### Add any new code here to parse additional possible kwargs.
######### Be sure to pop any parsed kwarg from kwargs dictionary.
######### Now kwargs should be empty, if not we passed an invalid kwarg
if len(kwargs) > 0:
log.warning("Passed invalid keyword arguments {} to setupOptions",
kwargs)
return model # Not necessary to return
def option_parser():
p = standard_options.standard_options(
default_injection_delay=0.2,
default_injection_width=0.4,
default_injection_current=[-0.15e-9, 0.15e-9, 0.35e-9],
default_simulation_time=.9,
default_plot_vm=None,
)
p.add_argument('--morph-file')
p.add_argument('--baseline', type=real)
p.add_argument('--model', required=True)
p.add_argument('--neuron-type', required=True)
p.add_argument('--RA', type=real)
p.add_argument('--RM', type=real)
p.add_argument('--CM', type=real)
p.add_argument('--Erest', type=real)
p.add_argument('--Eleak', type=real)
p.add_argument('--Kir-offset', type=real)
p.add_argument('--cond', default=[], nargs='+', type=cond_setting, action=standard_options.AppendFlat)
p.add_argument('--save-vm')
return p
def parse_args(commandline, do_exit):
parser, _ = standard_options.standard_options()
parser.add_argument("--cond",
'-c',
type=str,
help='give exper name, for example: GABAosc')
#these control synaptic strength and should start with GABA for ctrl, POST-HFS or POST-NoDa
parser.add_argument(
"--syn",
'-syn',
type=str,
default='non',
help='optional: synapse type of special input, omit or non for none')
parser.add_argument(
"--freq",
'-f',
type=int,
default=0,
help="optional: frequency of special input, omit or 0 for non")
#could change this to type list to provide a range of frequencies
parser.add_argument("--trials", '-n', type=int, help="number of trials")
parser.add_argument("--stpYN",
'-stp',
type=int,
choices=[1, 0],
help="1 for yes, 0 for no short term plas")
parser.add_argument("--ttGPe",
'-tg',
type=str,
default='',
help="name of tt files for GPe")
parser.add_argument("--ttstr",
'-ts',
type=str,
default='',
help="name of tt files for Str")
parser.add_argument("--ttSTN",
'-tn',
type=str,
default='',
help="name of tt files for STN")
try:
args = parser.parse_args(
commandline
) # maps arguments (commandline) to choices, and checks for validity of choices.
except SystemExit:
if do_exit:
raise # raise the exception above (SystemExit)
else:
raise ValueError('invalid ARGS')
return args
def parse_args(commandline,do_exit):
parser, _ = standard_options.standard_options()
parser.add_argument("--stoptask", type=standard_options.parse_boolean, default=False, help="True to provide stop signal input")
parser.add_argument("--fb_npas", type=int, default=3, help = "weight for npas feedback to SPNs")
parser.add_argument("--fb_lhx",type=int, default=4, help="weight for lhx6 feedback to FSIs")
parser.add_argument("--trials",type=int, help="number of trials")
parser.add_argument("--pulsedur",'-dur', type=float, default=0,help="duration of stn pulse inputs during stop task")
parser.add_argument("--stnfreq",'-stn', type=str, help="frequency of stn inputs to GPe")
parser.add_argument("--rampdur",'-ramp', type=float, default=0,help="duration of ctx ramp inputs to striatum")
parser.add_argument("--ctxfreq",'-ctx', type=str, help="frequency of ctx inputs to striatum")
parser.add_argument("--FSI",'-FSI', type=str, default='11', help="2 bit string controlling FSI inputs, first bit=0 deletes inputs to FSI, 2nd bit=0 deletes inputs to SPNs")
try:
args = parser.parse_args(commandline) # maps arguments (commandline) to choices, and checks for validity of choices.
except SystemExit:
if do_exit:
raise # raise the exception above (SystemExit)
else:
raise ValueError('invalid ARGS')
return args
def option_parser():
''' Extends moose_nerp.prototypes.standard_options by defining additional
console arguments simulation.
'''
p, _ = standard_options.standard_options(
default_injection_delay=0.2,
default_injection_width=0.4,
default_injection_current=[-0.15e-9, 0.15e-9, 0.35e-9],
default_simulation_time=.9,
default_plot_vm=None,
)
p.add_argument('--morph-file')
p.add_argument('--baseline', type=real)
p.add_argument('--model', required=True)
p.add_argument('--neuron-type', required=True)
p.add_argument('--RA', type=real)
p.add_argument('--RM', type=real)
p.add_argument('--CM', type=real)
p.add_argument('--Erest', type=real)
p.add_argument('--Eleak', type=real)
p.add_argument('--Kir-offset', type=real)
p.add_argument('--cond',
default=[],
nargs='+',
type=cond_setting,
action=standard_options.AppendFlat)
p.add_argument('--save-vm')
p.add_argument('--chan',
default=[],
nargs='+',
type=chan_setting,
action=standard_options.AppendFlat)
p.add_argument('--CaPoolTauDend', type=real)
p.add_argument('--CaPoolTauSoma', type=real)
p.add_argument('--CaPoolBDend', type=real)
p.add_argument('--CaPoolBSoma', type=real)
return p
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
from pprint import pprint
import moose
from moose_nerp.prototypes import (cell_proto, calcium, clocks, inject_func,
tables, plasticity_test, logutil, util,
standard_options, constants)
from moose_nerp import ca1
from moose_nerp.graph import plot_channel, neuron_graph, spine_graph
option_parser = standard_options.standard_options(
default_injection_current=[200e-12])
param_sim = option_parser.parse_args()
param_sim.save = 0
plotcomps = [ca1.param_cond.NAME_SOMA]
######## adjust the model settings if specified by command-line options and retain model defaults otherwise
#These assignment statements are required because they are not part of param_sim namespace.
if param_sim.calcium is not None:
ca1.calYN = param_sim.calcium
if param_sim.spines is not None:
ca1.spineYN = param_sim.spines
if param_sim.stim_paradigm is not None:
ca1.param_stim.Stimulation.Paradigm = ca1.param_stim.paradigm_dict[
param_sim.stim_paradigm]
if param_sim.stim_loc is not None:
from moose_nerp.prototypes import (cell_proto,
calcium,
clocks,
inject_func,
tables,
plasticity_test,
logutil,
util,
standard_options,
constants)
from moose_nerp import d1d2
from moose_nerp.graph import plot_channel, neuron_graph, spine_graph
#two examples of calling option_parser - one overrides the defaults and is useful when running from python window
option_parser = standard_options.standard_options()
option_parser = standard_options.standard_options(default_calcium=True, default_spines=False,default_injection_current=[-0.5e-9],default_stim='inject',default_stim_loc='soma')
#,default_simulation_time=0.01)
param_sim = option_parser.parse_args()
param_sim.save=1
plotcomps=[d1d2.param_cond.NAME_SOMA]
param_sim.hsolve=0
######## adjust the model settings if specified by command-line options and retain model defaults otherwise
#These assignment statements are required because they are not part of param_sim namespace.
if param_sim.calcium is not None:
d1d2.calYN = param_sim.calcium
if param_sim.spines is not None:
d1d2.spineYN = param_sim.spines
if param_sim.stim_paradigm is not None:
d1d2.param_stim.Stimulation.Paradigm=d1d2.param_stim.paradigm_dict[param_sim.stim_paradigm]
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
from pprint import pprint
import moose
from moose_nerp.prototypes import (cell_proto, calcium, clocks, inject_func,
tables, plasticity_test, logutil, util,
standard_options, constants)
from moose_nerp import ep
from moose_nerp.graph import plot_channel, neuron_graph, spine_graph
option_parser = standard_options.standard_options(
default_injection_current=[-200e-12, -100e-12, 150e-12, 50e-12],
default_simulation_time=0.6,
default_injection_width=0.3,
default_injection_delay=0.1,
default_plotdt=0.0001)
param_sim = option_parser.parse_args()
param_sim.hsolve = 1
plotcomps = [ep.param_cond.NAME_SOMA]
######## adjust the model settings if specified by command-line options and retain model defaults otherwise
#These assignment statements are required because they are not part of param_sim namespace.
if param_sim.calcium is not None:
ep.calYN = param_sim.calcium
if param_sim.spines is not None:
ep.spineYN = param_sim.spines
if param_sim.stim_paradigm is not None:
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
from pprint import pprint
import moose
from moose_nerp.prototypes import (cell_proto, calcium, clocks, inject_func,
tables, plasticity_test, logutil, util,
standard_options, constants)
from moose_nerp import gp
from moose_nerp.graph import plot_channel, neuron_graph, spine_graph
option_parser = standard_options.standard_options(
default_injection_current=[25e-12], #[-100e-12, -50e-12, 25e-12,75e-12],
default_simulation_time=0.6,
default_injection_width=0.4,
default_plotdt=0.0001)
#,default_stim='PSP_1')
# Issue with stimulation needs fixing:
#Line 83: st, spines, pg = inject_func.ConnectPreSynapticPostSynapticStimulation(gp,ntype)
#File "moose_nerp/prototypes/inject_func.py", line 227, in ConnectPreSynapticPostSynapticStimulation
#stim_spines.update(new_spines)
#TypeError: 'NoneType' object is not iterable
#same error with or without spines
param_sim = option_parser.parse_args()
plotcomps = [gp.param_cond.NAME_SOMA]
######## adjust the model settings if specified by command-line options and retain model defaults otherwise
