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)