import numpy as np
from neuron import h
# from bmtk.simulator.bionet.modules.sim_module import SimulatorMod
from bmtk.simulator.bionet.io_tools import io
from bmtk.simulator.core.modules import iclamp
[docs]class AmpsReaderNRN(iclamp.AmpsReader):
[docs] def create_clamps(self, hobj):
clamps = []
for amp, delay, dur in zip(self.amps, self.delays, self.durations):
clamp = h.IClamp(hobj)
clamp.amp = amp
clamp.delay = delay
clamp.dur = dur
clamps.append(clamp)
return clamps
[docs]class CSVAmpReaderNRN(iclamp.CSVAmpReader):
def __init__(self, **args):
super().__init__(**args)
# NRN Vector.play function requires consistent
dts = np.unique(np.diff(self._inputs_df[self._ts_col].values))
if len(dts) > 1:
io.log_exception('{}: csv timestamps column ({}) must have a consistent intervals.'.format(
IClampMod.__name__, self._ts_col)
)
self._idt = dts[0]
self._istart = self.delays[0] # self._inputs_df[self._ts_col].values[0]
# self._amps_vals = self._inputs_df[self._amps_col].values
# self._ts_vals = self._inputs_df[self._ts_col].values
# The way NEURON's Vector.play([amps], dt) works is that it will access the [amps] at every dt interval (0.0,
# dt, 2dt, 3dt, ...) in ms regardless of when the IClamp starts. Thus if the initial onset stimuli is > 0.0 ms,
# we need to update the amps array so that the following occurs:
# 1. amps[0] is the injection current (usually 0.0mA) that occurs at the very start of the simulation.
# 2. the above _istart, and all other timestamps, is a multiple of dt.
# this may require decreasing dt which will require increasing the the amp array. eg:
# times: [200, 800, 1200, 1600] ==> [ 0, 200, 400, 800, 1000, 1200, 1400, 1600]
# amps: [0.1, 0.2, 0.3, 0.0] ==> [0.0, 0.1, 0.1, 0.2, 0.2, 0.3, 0.3, 0.0]
if self._istart < 0.0:
# Check in trying to start a current clamp before simulation starts
io.log_exception('{}: initial onset of stimulus ({}) cannot be a negative number.'.format(
IClampMod.__name__, self.delays)
)
elif self._istart > 0.0:
if self._istart - self._idt == 0.0:
# Simplist case initial onset time occurs at first dt after start of simulation, add a 0.0 current
# clamp at the very beginning of the simulation.
self.amps = np.concatenate(([0.0], self.amps))
self.delays = np.concatenate(([0.0], self.delays))
self._istart = 0.0
else:
warn_msg = '{}: initial onset of stimulus at {} does not occur at a {} timestep. Attempting to update' \
'timesteps and amp values'.format(IClampMod.__name__, self._istart, self._idt)
io.log_warning(warn_msg)
gcd = np.gcd(int(self._idt), int(self._istart))
amps = np.repeat(self.amps, int(self._idt)/gcd)
zero_curr = np.zeros(int(self._istart/gcd))
self.amps = np.concatenate((zero_curr, amps))
self.delays = np.concatenate(([0.0], self.delays))
self._idt = gcd
self._istart = 0.0
# Try to determine IClamp stop time (eg max duration)
if self.amps[-1] != 0:
self._istop = self.delays[-1] + self._idt
warn_msg = '{}: Stimulus of {} does not end with a 0.0, attempting to set turn off at time {}.'.format(
IClampMod.__name__, self._csv_path, self._istop)
io.log_warning(warn_msg)
else:
self._istop = self.delays[-1]
[docs] def create_clamps(self, hobj):
clamp = h.IClamp(hobj)
clamp.delay = self._istart
clamp.dur = self._istop
vect_stim = h.Vector(self.amps)
vect_stim.play(clamp._ref_amp, self._idt)
return [(vect_stim, clamp)]
[docs]class NWBReaderNRN(iclamp.NWBReader):
def __init__(self, **args):
super().__init__(**args)
self._istop = len(self.delays)*self._idt*1000.0
[docs] def create_clamps(self, hobj):
clamp = h.IClamp(hobj)
clamp.delay = self._offset
clamp.dur = self._istop
vect_stim = h.Vector(self.amps)
vect_stim.play(clamp._ref_amp, self._idt)
return [(vect_stim, clamp)]
[docs]class IClampMod(iclamp.IClampMod):
@property
def input2reader_map(self):
return {
'current_clamp': AmpsReaderNRN,
'csv': CSVAmpReaderNRN,
'file': CSVAmpReaderNRN,
'nwb': NWBReaderNRN,
'allen': NWBReaderNRN
}
def __init__(self, input_type, **mod_args):
super().__init__(input_type, **mod_args)
# Select location to place iclamp, if not specified use the center of the soma
self._section_name = mod_args.get('section_name', 'soma')
self._section_index = mod_args.get('section_index', 0)
self._section_dist = mod_args.get('section_dist', 0.5)
# IClamp objects need to be saved in memory otherwise NRN will try to garbage collect them
# prematurly
self._iclamps = []
[docs] def initialize(self, sim):
# Get select node gids, but only for those nodes that are on the current rank (if running on multiple cores)
select_gids = list(sim.net.get_node_set(self._node_set).gids())
gids_on_rank = list(set(select_gids) & set(select_gids))
for gid in gids_on_rank:
cell = sim.net.get_cell_gid(gid)
hobj_sec = getattr(cell.hobj, self._section_name)[self._section_index](self._section_dist)
self._iclamps.extend(self._amp_reader.create_clamps(hobj_sec))
