Source code for bluepyopt.ephys.recordings
"""Recording classes"""
"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by the Free Software Foundation.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
"""
import logging
from . import responses
logger = logging.getLogger(__name__)
[docs]
class Recording(object):
"""Class to represent object that record variables during simulations"""
def __init__(self, name=None):
"""Constructor
Args:
name (str): name of this object
"""
self.name = name
[docs]
class CompRecording(Recording):
"""Response to stimulus"""
def __init__(
self,
name=None,
location=None,
variable='v'):
"""Constructor
Args:
name (str): name of this object
location (Location): location in the model of the recording
variable (str): which variable to record from (e.g. 'v')
"""
super(CompRecording, self).__init__(
name=name)
self.location = location
self.variable = variable
self.varvector = None
self.tvector = None
self.time = None
self.voltage = None
self.instantiated = False
@property
def response(self):
"""Return recording response"""
if not self.instantiated:
return None
return responses.TimeVoltageResponse(self.name,
self.tvector.to_python(),
self.varvector.to_python())
[docs]
def instantiate(self, sim=None, icell=None):
"""Instantiate recording"""
logger.debug('Adding compartment recording of %s at %s',
self.variable, self.location)
self.varvector = sim.neuron.h.Vector()
seg = self.location.instantiate(sim=sim, icell=icell)
self.varvector.record(getattr(seg, '_ref_%s' % self.variable))
self.tvector = sim.neuron.h.Vector()
self.tvector.record(sim.neuron.h._ref_t) # pylint: disable=W0212
self.instantiated = True
[docs]
def destroy(self, sim=None):
"""Destroy recording"""
self.varvector = None
self.tvector = None
self.instantiated = False
def __str__(self):
"""String representation"""
return '%s: %s at %s' % (self.name, self.variable, self.location)
[docs]
class LFPRecording(Recording):
"""Extracellular electrode response to stimulus"""
location = "extracellular"
variable = "v"
def __init__(self, name=None):
"""Constructor
Args:
name (str): name of this object
"""
super(LFPRecording, self).__init__(name=name)
self.electrode = None
self.cell = None
self.tvector = None
self.time = None
self.sim = None
self.instantiated = False
@property
def response(self):
"""Return recording response"""
if not self.instantiated:
return None
self.tvector = self.cell.tvec
return responses.TimeLFPResponse(
self.name, self.tvector, self.electrode.data
)
def instantiate(self, sim=None, lfpy_cell=None, electrode=None):
import LFPy
"""Instantiate recording"""
logger.debug(
"Adding recording of %s at %s", self.variable, self.location
)
assert isinstance(
lfpy_cell, LFPy.Cell
), "LFPRecording is only available for LFPCellModel"
self.cell = lfpy_cell
self.tvector = None
self.electrode = electrode
self.sim = sim
self.instantiated = True
[docs]
def destroy(self, sim=None):
"""Destroy recording"""
self.electrode = None
self.LFP = None
self.tvector = None
self.electrode = None
self.cell = None
self.instantiated = False
def __str__(self):
"""String representation"""
return "%s: %s at %s" % (self.name, self.variable, self.location)