Source code for emodelrunner.stimuli

"""Stimulus class."""

# Copyright 2020-2022 Blue Brain Project / EPFL

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

#     http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from bluepyopt.ephys.stimuli import Stimulus


# inspired by bluepyemodel.ecode.sAHP

[docs]
class Pulse(Stimulus):
    """Train pulse.

    Attributes:
        delay (float): delay after which the stimuli begin (ms)
        duration (float): duration of the stimuli (ms)
        amp (float): amplitude of the stimuli (nA)
        tpulse (float): time between two pulse starts (ms)
        width (float): width of the step stimuli (ms)
        total_duration (float): total duration (delay + duration) (ms)
        location (Location): location of stimulus
        iclamp (neuron IClamp): clamp to inject the stimulus into the cell
        current_vec (neuron Vector): current to inject to the cell
        time_vec (neuron Vector): times at which to play the current
    """

    def __init__(self, location, delay, duration, amp, frequency, width):
        """Constructor.

        Args:
            location (Location): location of stimulus
            delay (float): delay after which the stimuli begin (ms)
            duration (float): duration of the stimuli (ms)
            amp (float): amplitude of the stimuli (nA)
            frequency (float): frequency of the pulse stimuli (1/s)
            width (float): width of the step stimuli (ms)
        """
        self.delay = delay
        self.duration = duration
        self.amp = amp
        self.tpulse = 1000.0 / frequency
        self.width = width
        self.total_duration = self.delay + self.duration

        self.location = location

        self.iclamp = None
        self.current_vec = None
        self.time_vec = None

        super().__init__()


[docs]
    def instantiate(self, sim=None, icell=None):
        """Instantiate stimulus.

        Args:
            sim (bluepyopt.ephys.NrnSimulator): neuron simulator
            icell (neuron cell): cell instantiation in simulator
        """
        # adaptation from TStim.hoc proc train from neurodamus

        icomp = self.location.instantiate(sim=sim, icell=icell)

        self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
        self.iclamp.dur = self.total_duration

        self.current_vec = sim.neuron.h.Vector()
        self.time_vec = sim.neuron.h.Vector()

        if self.width > self.tpulse:
            # one long pulse
            self.time_vec.append(self.delay)
            self.current_vec.append(0)

            self.time_vec.append(self.delay)
            self.current_vec.append(self.amp)

            self.time_vec.append(self.total_duration)
            self.current_vec.append(self.amp)

            self.time_vec.append(self.total_duration)
            self.current_vec.append(0)

        else:
            # repeated pulse injections
            remtime = self.duration
            next_pulse = self.delay

            while remtime > 0:
                if self.width < remtime:
                    self.time_vec.append(next_pulse)
                    self.current_vec.append(0)

                    self.time_vec.append(next_pulse)
                    self.current_vec.append(self.amp)

                    self.time_vec.append(next_pulse + self.width)
                    self.current_vec.append(self.amp)

                    self.time_vec.append(next_pulse + self.width)
                    self.current_vec.append(0)
                else:
                    self.time_vec.append(next_pulse)
                    self.current_vec.append(0)

                    self.time_vec.append(next_pulse)
                    self.current_vec.append(self.amp)

                    self.time_vec.append(self.total_duration)
                    self.current_vec.append(self.amp)

                    self.time_vec.append(self.total_duration)
                    self.current_vec.append(0)

                next_pulse += self.tpulse
                remtime -= self.tpulse

        self.time_vec.append(self.total_duration)
        self.current_vec.append(0)

        self.iclamp.delay = 0
        self.current_vec.play(
            self.iclamp._ref_amp,  # pylint:disable=W0212
            self.time_vec,
            1,
            sec=icomp.sec,
        )



[docs]
    def destroy(self, sim=None):  # pylint:disable=W0613
        """Destroy stimulus.

        Args:
            sim (bluepyopt.ephys.NrnSimulator): neuron simulator
        """
        self.iclamp = None
        self.time_vec = None
        self.current_vec = None




# inspired by bluepyemodel.ecode.sAHP

[docs]
class MultipleSteps(Stimulus):
    """Multiple steps protocol at custom times.

    Attributes:
        starts (list): times at which each step occurs (ms)
        amp (float): amplitude of the stimuli (nA)
        width (float): width of the step stimuli (ms)
        total_duration (float): total duration (ms)
        location (Location): location of stimulus
        iclamp (neuron IClamp): clamp to inject the stimulus into the cell
        current_vec (neuron Vector): current to inject to the cell
        time_vec (neuron Vector): times at which to play the current
    """

    def __init__(self, location, starts, amp, width):
        """Constructor.

        Args:
            location (Location): location of stimulus
            starts (list): times at which each step occurs (ms)
            amp (float): amplitude of the stimuli (nA)
            width (float): width of the step stimuli (ms)
        """
        self.starts = starts
        self.amp = amp
        self.width = width
        self.total_duration = self.starts[-1] + self.width

        self.location = location

        self.iclamp = None
        self.current_vec = None
        self.time_vec = None

        super().__init__()


[docs]
    def instantiate(self, sim=None, icell=None):
        """Instantiate stimulus.

        Args:
            sim (bluepyopt.ephys.NrnSimulator): neuron simulator
            icell (neuron cell): cell instantiation in simulator
        """
        # adaptation from TStim.hoc proc train from neurodamus

        icomp = self.location.instantiate(sim=sim, icell=icell)

        self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
        self.iclamp.dur = self.total_duration

        self.current_vec = sim.neuron.h.Vector()
        self.time_vec = sim.neuron.h.Vector()

        for start in self.starts:
            self.time_vec.append(start)
            self.current_vec.append(0)

            self.time_vec.append(start)
            self.current_vec.append(self.amp)

            self.time_vec.append(start + self.width)
            self.current_vec.append(self.amp)

            self.time_vec.append(start + self.width)
            self.current_vec.append(0)

        self.time_vec.append(self.total_duration)
        self.current_vec.append(0)

        self.iclamp.delay = 0
        self.current_vec.play(
            self.iclamp._ref_amp,  # pylint:disable=W0212
            self.time_vec,
            1,
            sec=icomp.sec,
        )



[docs]
    def destroy(self, sim=None):  # pylint:disable=W0613
        """Destroy stimulus.

        Args:
            sim (bluepyopt.ephys.NrnSimulator): neuron simulator
        """
        self.iclamp = None
        self.time_vec = None
        self.current_vec = None