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249 lines
8.5 KiB
249 lines
8.5 KiB
2 years ago
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"""
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test_sgc_input_phaselocking.py
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Test phase locking from an input sgc to a target cell type. Runs simulations
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with AN input, and plots the results, including PSTH and phase histogram.
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Usage: python test_sgc_input_phaselocking.py celltype stimulus species
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where:
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celltype is one of [bushy, tstellate, octopus, dstellate] (default: bushy)
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stimulus is one of [tone, SAM, clicks] (default: tone)
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species is one of [guineapig, mouse] (default: guineapig)
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"""
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import sys
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import numpy as np
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import pyqtgraph as pg
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from neuron import h
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from cnmodel.protocols import Protocol
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from cnmodel import cells
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from cnmodel.util import sound
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import cnmodel.util.pynrnutilities as PU
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from cnmodel import data
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class SGCInputTestPL(Protocol):
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def set_cell(self, cell="bushy"):
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self.cell = cell
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def run(
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self, temp=34.0, dt=0.025, seed=575982035, stimulus="tone", species="mouse"
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):
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assert stimulus in ["tone", "SAM", "clicks"] # cases available
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if self.cell == "bushy":
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postCell = cells.Bushy.create(species=species)
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elif self.cell == "tstellate":
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postCell = cells.TStellate.create(species=species)
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elif self.cell == "octopus":
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postCell = cells.Octopus.create(species=species)
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elif self.cell == "dstellate":
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postCell = cells.DStellate.create(species=species)
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else:
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raise ValueError(
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"cell %s is not yet implemented for phaselocking" % self.cell
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)
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self.post_cell = postCell
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self.stimulus = stimulus
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self.run_duration = 1.0 # in seconds
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self.pip_duration = 0.8 # in seconds
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self.pip_start = [0.02] # in seconds
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self.Fs = 100e3 # in Hz
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self.f0 = 4000.0 # stimulus in Hz
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self.cf = 4000.0 # SGCs in Hz
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self.fMod = 100.0 # mod freq, Hz
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self.dMod = 50.0 # % mod depth, Hz
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self.dbspl = 60.0
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if self.stimulus == "SAM":
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self.stim = sound.SAMTone(
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rate=self.Fs,
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duration=self.run_duration,
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f0=self.f0,
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fmod=self.fMod,
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dmod=self.dMod,
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dbspl=self.dbspl,
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ramp_duration=2.5e-3,
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pip_duration=self.pip_duration,
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pip_start=self.pip_start,
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)
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if self.stimulus == "tone":
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self.f0 = 1000.0
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self.cf = 1000.0
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self.stim = sound.TonePip(
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rate=self.Fs,
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duration=self.run_duration,
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f0=self.f0,
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dbspl=self.dbspl,
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ramp_duration=2.5e-3,
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pip_duration=self.pip_duration,
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pip_start=self.pip_start,
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)
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if self.stimulus == "clicks":
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self.click_rate = 0.020 # msec
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self.stim = sound.ClickTrain(
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rate=self.Fs,
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duration=self.run_duration,
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f0=self.f0,
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dbspl=self.dbspl,
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click_start=0.010,
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click_duration=100.0e-6,
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click_interval=self.click_rate,
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nclicks=int((self.run_duration - 0.01) / self.click_rate),
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ramp_duration=2.5e-3,
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)
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n_sgc = data.get(
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"convergence", species=species, post_type=postCell.type, pre_type="sgc"
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)[0]
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self.n_sgc = int(np.round(n_sgc))
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self.pre_cells = []
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self.synapses = []
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j = 0
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for k in range(self.n_sgc):
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seed = seed + k
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preCell = cells.DummySGC(cf=self.cf, sr=2)
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synapse = preCell.connect(postCell)
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for i in range(synapse.terminal.n_rzones):
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self["xmtr%03d" % j] = synapse.terminal.relsite._ref_XMTR[i]
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j = j + 1
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synapse.terminal.relsite.Dep_Flag = False
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preCell.set_sound_stim(self.stim, seed=seed)
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self.pre_cells.append(preCell)
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self.synapses.append(synapse)
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self["vm"] = postCell.soma(0.5)._ref_v
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# self['prevm'] = preCell.soma(0.5)._ref_v
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self["t"] = h._ref_t
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postCell.cell_initialize()
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h.tstop = 1e3 * self.run_duration # duration of a run
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h.celsius = temp
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h.dt = dt
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self.custom_init()
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h.run()
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def show(self):
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self.win = pg.GraphicsWindow()
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p1 = self.win.addPlot(title="stim", row=0, col=0)
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p1.plot(self.stim.time * 1000, self.stim.sound)
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p1.setXLink(p1)
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p2 = self.win.addPlot(title="AN spikes", row=1, col=0)
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vt = pg.VTickGroup(self.pre_cells[0]._spiketrain)
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p2.addItem(vt)
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p2.setXLink(p1)
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p3 = self.win.addPlot(title="%s Spikes" % self.cell, row=2, col=0)
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bspk = PU.findspikes(self["t"], self["vm"], -30.0)
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bspktick = pg.VTickGroup(bspk)
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p3.addItem(bspktick)
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p3.setXLink(p1)
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p4 = self.win.addPlot(title="%s Vm" % self.cell, row=3, col=0)
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p4.plot(self["t"], self["vm"])
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p4.setXLink(p1)
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p5 = self.win.addPlot(title="xmtr", row=0, col=1)
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j = 0
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for k in range(self.n_sgc):
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synapse = self.synapses[k]
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for i in range(synapse.terminal.n_rzones):
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p5.plot(self["t"], self["xmtr%03d" % j], pen=(i, 15))
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j = j + 1
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p5.setXLink(p1)
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p6 = self.win.addPlot(title="AN phase", row=1, col=1)
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phasewin = [
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self.pip_start[0] + 0.25 * self.pip_duration,
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self.pip_start[0] + self.pip_duration,
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]
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prespk = self.pre_cells[0]._spiketrain # just sample one...
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spkin = prespk[np.where(prespk > phasewin[0] * 1e3)]
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spikesinwin = spkin[np.where(spkin <= phasewin[1] * 1e3)]
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print("\nCell type: %s" % self.cell)
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print("Stimulus: ")
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# set freq for VS calculation
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if self.stimulus == "tone":
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f0 = self.f0
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print(
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"Tone: f0=%.3f at %3.1f dbSPL, cell CF=%.3f"
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% (self.f0, self.dbspl, self.cf)
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)
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if self.stimulus == "SAM":
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f0 = self.fMod
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print(
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(
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"SAM Tone: f0=%.3f at %3.1f dbSPL, fMod=%3.1f dMod=%5.2f, cell CF=%.3f"
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% (self.f0, self.dbspl, self.fMod, self.dMod, self.cf)
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)
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)
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if self.stimulus == "clicks":
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f0 = 1.0 / self.click_rate
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print(
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"Clicks: interval %.3f at %3.1f dbSPL, cell CF=%.3f "
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% (self.click_rate, self.dbspl, self.cf)
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)
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vs = PU.vector_strength(spikesinwin, f0)
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print(
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"AN Vector Strength at %.1f: %7.3f, d=%.2f (us) Rayleigh: %7.3f p = %.3e n = %d"
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% (f0, vs["r"], vs["d"] * 1e6, vs["R"], vs["p"], vs["n"])
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)
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(hist, binedges) = np.histogram(vs["ph"])
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p6.plot(
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binedges, hist, stepMode=True, fillBrush=(100, 100, 255, 150), fillLevel=0
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)
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p6.setXRange(0.0, 2 * np.pi)
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p7 = self.win.addPlot(title="%s phase" % self.cell, row=2, col=1)
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spkin = bspk[np.where(bspk > phasewin[0] * 1e3)]
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spikesinwin = spkin[np.where(spkin <= phasewin[1] * 1e3)]
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vs = PU.vector_strength(spikesinwin, f0)
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print(
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"%s Vector Strength: %7.3f, d=%.2f (us) Rayleigh: %7.3f p = %.3e n = %d"
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% (self.cell, vs["r"], vs["d"] * 1e6, vs["R"], vs["p"], vs["n"])
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)
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(hist, binedges) = np.histogram(vs["ph"])
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p7.plot(
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binedges, hist, stepMode=True, fillBrush=(100, 100, 255, 150), fillLevel=0
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)
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p7.setXRange(0.0, 2 * np.pi)
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p7.setXLink(p6)
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self.win.show()
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if __name__ == "__main__":
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if len(sys.argv) > 1 and sys.argv[1] in ["help", "-h", "--help"]:
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print(
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"\nUsage: python test_sgc_input_phaselocking.py\n celltype [bushy, tstellate, octopus, dstellate] (default: bushy)"
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)
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print(" stimulus [tone, SAM, clicks] (default: tone)")
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print(" species [guineapig mouse] (default: guineapig)\n")
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exit(0)
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if len(sys.argv) > 1:
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cell = sys.argv[1]
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else:
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cell = "bushy"
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if len(sys.argv) > 2:
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stimulus = sys.argv[2]
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else:
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stimulus = "tone"
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if len(sys.argv) > 3:
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species = sys.argv[3]
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else:
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species = "guineapig"
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print("cell type: ", cell)
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prot = SGCInputTestPL()
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prot.set_cell(cell)
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prot.run(stimulus=stimulus, species=species)
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prot.show()
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import sys
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if sys.flags.interactive == 0:
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pg.QtGui.QApplication.exec_()
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