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""" | ||
Definition of NativeElectrodeType class for NEST. | ||
""" | ||
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import numpy | ||
import nest | ||
from pyNN.standardmodels import electrodes, build_translations, StandardCurrentSource | ||
from pyNN.common import Population, PopulationView, Assembly | ||
from pyNN.parameters import ParameterSpace, Sequence | ||
from pyNN.nest.simulator import state | ||
from pyNN.nest.standardmodels.electrodes import NestCurrentSource | ||
from pyNN.models import BaseCellType | ||
from pyNN.nest.cells import NativeCellType | ||
from pyNN.nest.cells import get_receptor_types | ||
from pyNN.nest.cells import get_recordables | ||
from . import conversion | ||
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def get_defaults(model_name): | ||
valid_types = (int, float, Sequence) | ||
defaults = nest.GetDefaults(model_name) | ||
variables = defaults.get('recordables', []) | ||
ignore = ['archiver_length', 'available', 'Ca', 'capacity', 'elementsize', | ||
'frozen', 'instantiations', 'local', 'model', 'needs_prelim_update', | ||
'recordables', 'state', 't_spike', 'tau_minus', 'tau_minus_triplet', | ||
'thread', 'vp', 'receptor_types', 'events', 'global_id', | ||
'element_type', 'type', 'type_id', 'has_connections', 'n_synapses', | ||
'thread_local_id', 'node_uses_wfr', 'supports_precise_spikes', | ||
'synaptic_elements' | ||
] | ||
default_params = {} | ||
default_initial_values = {} | ||
for name, value in defaults.items(): | ||
if name in variables: | ||
default_initial_values[name] = value | ||
return default_params, default_initial_values | ||
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# Native model non standard | ||
def native_electrode_type(model_name): | ||
""" | ||
Return a new NativeElectrodeType subclass. | ||
""" | ||
assert isinstance(model_name, str) | ||
default_parameters, default_initial_values = get_defaults(model_name) | ||
receptor_types = get_receptor_types(model_name) # get_receptor_types imported from nest.cells.py | ||
return type(model_name, | ||
(NativeElectrodeType,), | ||
{'nest_model': model_name, | ||
'default_parameters': default_parameters, | ||
'default_initial_values': default_initial_values, | ||
'injectable': ("V_m" in default_initial_values), | ||
'nest_name': {"on_grid": model_name, "off_grid": model_name}, | ||
}) | ||
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# Should be usable with any NEST current generator | ||
class NativeElectrodeType(NestCurrentSource): | ||
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_is_computed = True | ||
_is_playable = True | ||
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def __init__(self, **parameters): | ||
self._device = nest.Create(self) | ||
self.cell_list = [] | ||
parameter_space = ParameterSpace(self.default_parameters, | ||
self.get_schema(), | ||
shape=(1,)) | ||
parameter_space.update(**parameters) | ||
self.set_native_parameters(parameter_space) | ||
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def get_native_electrode_type(self): | ||
# Call to the function native_electrode_type | ||
return nest.GetDefaults(self.nest_model)["native_electrode_type"][name] | ||
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def get_receptor_type(self, name): | ||
return nest.GetDefaults(self.nest_model)["receptor_types"][name] | ||
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def inject_into(self, cells): | ||
# Call to the function inject_into from NestCurrentSource | ||
super(NativeElectrodeType,self).inject_into([cells]) | ||
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def _generate(self): | ||
self.times = numpy.arange(self.start, self.stop, max(self.dt, simulator.state.dt)) | ||
self.times = numpy.append(self.times, self.stop) | ||
self.amplitudes = self.mean + self.stdev * numpy.random.randn(len(self.times)) | ||
self.amplitudes[-1] = 0.0 | ||
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def set_native_parameters(self, parameters): | ||
parameters.evaluate(simplify=True) | ||
for key, value in parameters.items(): | ||
if key == "amplitude_values": | ||
assert isinstance(value, Sequence) | ||
times = self._delay_correction(parameters["amplitude_times"].value) | ||
amplitudes = value.value | ||
ctr = next((i for i,v in enumerate(times) if v > state.dt), len(times)) - 1 | ||
if ctr >= 0: | ||
times[ctr] = state.dt | ||
times = times[ctr:] | ||
amplitudes = amplitudes[ctr:] | ||
for ind in range(len(times)): | ||
times[ind] = self._round_timestamp(times[ind], state.dt) | ||
nest.SetStatus(self._device, {key: amplitudes, | ||
'amplitude_times': times}) | ||
elif key in ("start", "stop"): | ||
nest.SetStatus(self._device, {key: self._delay_correction(value)}) | ||
#For NativeElectrodeType class | ||
if key == "start" and type(self).__name__ == "NativeElectrodeType": | ||
self._phase_correction(self.start, self.frequency, self.phase_given) | ||
elif key == "frequency": | ||
nest.SetStatus(self._device, {key: value}) | ||
self._phase_correction(self.start, self.frequency, self.phase_given) | ||
elif key == "phase": | ||
self.phase_given = value | ||
self._phase_correction(self.start, self.frequency, self.phase_given) | ||
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elif not key == "amplitude_times": | ||
nest.SetStatus(self._device, {key: value}) | ||
self.default_parameters[key] = value | ||
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