DCNmodel/cnmodel/protocols/population_test.py

from __future__ import print_function
import numpy as np
import pyqtgraph as pg

from neuron import h

import cnmodel.util as util
from .protocol import Protocol
from ..util import custom_init
from cnmodel.util import sound


class PopulationTest(Protocol):
    def reset(self):
        super(PopulationTest, self).reset()

    def run(
        self, pops, cf=16e3, temp=34.0, dt=0.025, stim="sound", simulator="cochlea"
    ):
        """ 
        1. Connect pop1 => pop2
        2. Instantiate a single cell in pop2
        3. Automatically generate presynaptic cells and synapses from pop1
        4. Stimulate presynaptic cells and record postsynaptically
        """

        pre_pop, post_pop = pops
        pre_pop.connect(post_pop)
        self.pre_pop = pre_pop
        self.post_pop = post_pop

        # start with one cell, selected from the user-selected population, that has
        # a cf close to the center CF
        post_cell_ind = post_pop.select(1, cf=cf, create=True)[0]
        post_cell = post_pop.get_cell(post_cell_ind)
        post_pop.resolve_inputs(depth=1)
        post_sec = post_cell.soma
        self.post_cell_ind = post_cell_ind
        self.post_cell = post_cell

        pre_cell_inds = post_pop.cell_connections(post_cell_ind)[pre_pop]
        pre_cells = [pre_pop.get_cell(i) for i in pre_cell_inds]
        pre_secs = [cell.soma for cell in pre_cells]
        self.pre_cells = pre_cells
        self.pre_cell_inds = pre_cell_inds
        self.stim = sound.TonePip(
            rate=100e3,
            duration=0.1,
            f0=cf,
            dbspl=60,
            ramp_duration=2.5e-3,
            pip_duration=0.05,
            pip_start=[0.02],
        )

        ##
        ## voltage clamp the target cell
        ##
        # clampV = 40.0
        # vccontrol = h.VClamp(0.5, sec=post_cell.soma)
        # vccontrol.dur[0] = 10.0
        # vccontrol.amp[0] = clampV
        # vccontrol.dur[1] = 100.0
        # vccontrol.amp[1] = clampV
        # vccontrol.dur[2] = 20.0
        # vccontrol.amp[2] = clampV

        #
        # set up stimulation of the presynaptic cells
        #
        self.stim_params = []
        self.istim = []
        for i, pre_cell in enumerate(pre_cells):
            if stim == "sound":
                pre_cell.set_sound_stim(self.stim, seed=i, simulator=simulator)
                amp = 0.0
            else:
                amp = 3.0
                istim = h.iStim(0.5, sec=pre_cell.soma)
                stim = {}
                stim["NP"] = 10
                stim["Sfreq"] = 100.0  # stimulus frequency
                stim["delay"] = 10.0
                stim["dur"] = 0.5
                stim["amp"] = amp
                stim["PT"] = 0.0
                stim["dt"] = dt
                (secmd, maxt, tstims) = util.make_pulse(stim)
                self.stim_params.append(stim)

                # istim current pulse train
                i_stim_vec = h.Vector(secmd)
                i_stim_vec.play(istim._ref_i, dt, 0, pre_cell.soma(0.5))
                self.istim.append((istim, i_stim_vec))
                self["istim"] = istim._ref_i

            # record presynaptic Vm
            self["v_pre%d" % i] = pre_cell.soma(0.5)._ref_v

        self["t"] = h._ref_t
        self["v_post"] = post_cell.soma(0.5)._ref_v

        #
        # Run simulation
        #
        h.dt = dt
        self.dt = dt
        h.celsius = post_cell.status["temperature"]
        self.temp = h.celsius
        post_cell.cell_initialize()  # proper initialization.
        h.dt = self.dt
        custom_init(v_init=post_cell.vm0)
        h.t = 0.0
        h.tstop = 200.0
        while h.t < h.tstop:
            h.fadvance()

    def show(self):
        print(
            "Connected %d presynaptic cells to 1 postsynaptic cell."
            % len(self.pre_cell_inds)
        )
        print("Postsynaptic CF = %0.2f" % self.post_pop.cells[self.post_cell_ind]["cf"])
        print("Presynaptic CF = %s" % self.pre_pop.cells[self.pre_cell_inds]["cf"])

        self.win = pg.GraphicsWindow()
        self.win.resize(1000, 1000)

        cmd_plot = self.win.addPlot(title="Stim")
        try:
            cmd_plot.plot(self["t"], self["istim"])
        except:
            pass

        self.win.nextRow()
        pre_plot = self.win.addPlot(title=self.pre_cells[0].type + " Vm")
        for i in range(len(self.pre_cells)):
            pre_plot.plot(
                self["t"],
                self["v_pre%d" % i],
                pen=pg.mkPen(
                    pg.intColor(i, len(self.pre_cells)),
                    hues=len(self.pre_cells),
                    width=1.0,
                ),
            )

        self.win.nextRow()
        post_plot = self.win.addPlot(title="Post Cell: %s" % self.post_cell.type)
        post_plot.plot(self["t"], self["v_post"])