You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
120 lines
3.1 KiB
120 lines
3.1 KiB
2 years ago
|
"""
|
||
|
|
Create presynaptic and postsynaptic neurons, automatically connect them with
|
||
|
|
a synapse, stimulate the presynaptic cell, and analyze the resulting PSCs
|
||
|
|
in the postsynaptic cell.
|
||
|
|
"""
|
||
|
|
import faulthandler
|
||
|
|
|
||
|
|
faulthandler.enable()
|
||
|
|
import os, pickle, pprint
|
||
|
|
import numpy as np
|
||
|
|
import neuron
|
||
|
|
|
||
|
|
import cnmodel
|
||
|
|
import cnmodel.cells as cells
|
||
|
|
from cnmodel.util import UserTester
|
||
|
|
from cnmodel.protocols import SynapseTest
|
||
|
|
from cnmodel.util import reset
|
||
|
|
|
||
|
|
#
|
||
|
|
# Synapse tests
|
||
|
|
#
|
||
|
|
def test_sgc_bushy():
|
||
|
|
SynapseTester("sgc", "bushy")
|
||
|
|
|
||
|
|
|
||
|
|
def test_sgc_tstellate():
|
||
|
|
SynapseTester("sgc", "tstellate")
|
||
|
|
|
||
|
|
|
||
|
|
def test_sgc_tstellate2(): # again to test RNG stability
|
||
|
|
SynapseTester("sgc", "tstellate")
|
||
|
|
|
||
|
|
|
||
|
|
def test_sgc_dstellate():
|
||
|
|
SynapseTester("sgc", "dstellate")
|
||
|
|
|
||
|
|
|
||
|
|
def test_dstellate_bushy():
|
||
|
|
SynapseTester("dstellate", "bushy")
|
||
|
|
|
||
|
|
|
||
|
|
def test_dstellate_tstellate():
|
||
|
|
SynapseTester("dstellate", "tstellate")
|
||
|
|
|
||
|
|
|
||
|
|
def test_dstellate_dstellate():
|
||
|
|
SynapseTester("dstellate", "dstellate")
|
||
|
|
|
||
|
|
|
||
|
|
#
|
||
|
|
# Supporting functions
|
||
|
|
#
|
||
|
|
convergence = {
|
||
|
|
"sgc": {"bushy": 3, "tstellate": 6, "dstellate": 10, "dstellate_eager": 10},
|
||
|
|
"dstellate": {"bushy": 10, "tstellate": 15, "dstellate": 5},
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
def make_cell(typ):
|
||
|
|
if typ == "sgc":
|
||
|
|
cell = cells.SGC.create()
|
||
|
|
elif typ == "tstellate":
|
||
|
|
cell = cells.TStellate.create(debug=True, ttx=False)
|
||
|
|
elif (
|
||
|
|
typ == "dstellate"
|
||
|
|
): # Type I-II Rothman model, similiar excitability (Xie/Manis, unpublished)
|
||
|
|
cell = cells.DStellate.create(model="RM03", debug=True, ttx=False)
|
||
|
|
elif typ == "dstellate_eager": # From Eager et al.
|
||
|
|
cell = cells.DStellate.create(model="Eager", debug=True, ttx=False)
|
||
|
|
elif typ == "bushy":
|
||
|
|
cell = cells.Bushy.create(debug=True, ttx=False)
|
||
|
|
else:
|
||
|
|
raise ValueError("Unknown cell type '%s'" % typ)
|
||
|
|
return cell
|
||
|
|
|
||
|
|
|
||
|
|
class SynapseTester(UserTester):
|
||
|
|
def __init__(self, pre, post):
|
||
|
|
self.st = None
|
||
|
|
UserTester.__init__(self, "%s_%s" % (pre, post), pre, post)
|
||
|
|
|
||
|
|
def run_test(self, pre, post):
|
||
|
|
# Make sure no objects are left over from previous tests
|
||
|
|
reset(raiseError=False)
|
||
|
|
|
||
|
|
# seed random generator using the name of this test
|
||
|
|
seed = "%s_%s" % (pre, post)
|
||
|
|
|
||
|
|
pre_cell = make_cell(pre)
|
||
|
|
post_cell = make_cell(post)
|
||
|
|
|
||
|
|
n_term = convergence.get(pre, {}).get(post, None)
|
||
|
|
if n_term is None:
|
||
|
|
n_term = 1
|
||
|
|
st = SynapseTest()
|
||
|
|
st.run(pre_cell.soma, post_cell.soma, n_term, seed=seed)
|
||
|
|
if self.audit:
|
||
|
|
st.show_result()
|
||
|
|
|
||
|
|
info = dict(
|
||
|
|
rel_events=st.release_events(),
|
||
|
|
rel_timings=st.release_timings(),
|
||
|
|
open_prob=st.open_probability(),
|
||
|
|
event_analysis=st.analyze_events(),
|
||
|
|
)
|
||
|
|
self.st = st
|
||
|
|
|
||
|
|
# import weakref
|
||
|
|
# global last_syn
|
||
|
|
# last_syn = weakref.ref(st.synapses[0].terminal.relsi)
|
||
|
|
|
||
|
|
return info
|
||
|
|
|
||
|
|
def assert_test_info(self, *args, **kwds):
|
||
|
|
try:
|
||
|
|
super(SynapseTester, self).assert_test_info(*args, **kwds)
|
||
|
|
finally:
|
||
|
|
if self.st is not None:
|
||
|
|
self.st.hide()
|