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112 lines
3.0 KiB
112 lines
3.0 KiB
2 years ago
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# -*- encoding: utf-8 -*-
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from neuron import h
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import pyqtgraph as pg
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import cnmodel.util as util
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from .protocol import Protocol
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from .. import cells
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class SimpleSynapseTest(Protocol):
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def reset(self):
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super(SimpleSynapseTest, self).reset()
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def run(
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self,
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pre_sec,
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post_sec,
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temp=34.0,
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dt=0.025,
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vclamp=-65.0,
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iterations=1,
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tstop=200.0,
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stim_params=None,
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**kwds
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):
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"""
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"""
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Protocol.run(self, **kwds)
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pre_cell = cells.cell_from_section(pre_sec)
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post_cell = cells.cell_from_section(post_sec)
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synapse = pre_cell.connect(post_cell, type="simple")
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self.synapse = synapse
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self.pre_sec = synapse.terminal.section
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self.post_sec = synapse.psd.section
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self.pre_cell = pre_cell
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self.post_cell = post_cell
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#
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# voltage clamp the target cell
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#
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vccontrol = h.VClamp(0.5, sec=post_cell.soma)
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vccontrol.dur[0] = tstop
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vccontrol.amp[0] = vclamp
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# vccontrol.dur[1] = 100.0
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# vccontrol.amp[1] = clampV
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# vccontrol.dur[2] = 20.0
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# vccontrol.amp[2] = clampV
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#
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# set up stimulation of the presynaptic axon/terminal
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#
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istim = h.iStim(0.5, sec=pre_cell.soma)
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stim = {
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"NP": 10,
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"Sfreq": 100.0,
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"delay": 10.0,
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"dur": 0.5,
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"amp": 10.0,
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"PT": 0.0,
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"dt": dt,
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}
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if stim_params is not None:
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stim.update(stim_params)
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(secmd, maxt, tstims) = util.make_pulse(stim)
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self.stim = stim
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if tstop is None:
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tstop = len(secmd) * dt
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istim.delay = 0
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istim.dur = 1e9 # these actually do not matter...
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istim.iMax = 0.0
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# istim current pulse train
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i_stim_vec = h.Vector(secmd)
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i_stim_vec.play(istim._ref_i, dt, 0)
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#
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# Run simulation
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#
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h.tstop = tstop # duration of a run
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h.celsius = temp
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h.dt = dt
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self.temp = temp
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self.dt = dt
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for nrep in list(range(iterations)): # could do multiple runs....
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self.reset()
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self["v_pre"] = pre_cell.soma(0.5)._ref_v
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self["t"] = h._ref_t
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self["v_soma"] = post_cell.soma(0.5)._ref_v
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self["i_soma"] = vccontrol._ref_i
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util.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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self.win.resize(800, 800)
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t = self["t"]
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p1 = self.win.addPlot(title=self.pre_cell.status["name"])
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p1.setLabels(left="V pre (mV)", bottom="Time (ms)")
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p1.plot(t, self["v_pre"])
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self.win.nextRow()
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p2 = self.win.addPlot(title=self.post_cell.status["name"])
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p2.plot(t[1:], self["i_soma"][1:], pen=pg.mkPen("w", width=2))
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p2.setLabels(left="I post (nA)", bottom="Time (ms)")
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p2.setXLink(p1)
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