def hh_cell(name):
cell = Cell(name=f"cell_{name}")
soma = cell.add_sec("soma", diam=20, l=20, nseg=10)
cell.add_sec("apic", diam=2, l=50, nseg=100)
cell.insert("hh")
cell.connect_secs(child="apic", parent="soma", child_loc=0, parent_loc=1)
cell.make_spike_detector(soma(0.5))
return cell
def test_remove_new_cell_with_no_ref(self):
"""
deletion of cell, when all its sections have no reference outside - deletes all its
sections as well
"""
cell = Cell(name="cell")
soma = cell.add_sec("soma")
dend1 = cell.add_sec("dend1")
dend2 = cell.add_sec("dend2")
cell.connect_secs(child=dend1, parent=soma, child_loc=0, parent_loc=0.1)
cell.connect_secs(child=dend2, parent=soma, child_loc=0, parent_loc=0.9)
soma = None
dend1 = None
dend2 = None
self.assertEqual(6, _get_secs())
cell.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def get_cell_with_iclamps_as_synapses(warmup, dur, name, input_size, low=0.08, high=0.1):
# Create cell
cell = Cell(name=name)
soma = cell.add_sec("soma", diam=10, l=10, nseg=5)
dend = cell.add_sec("dend", diam=5, l=100, nseg=50)
cell.connect_secs(child=dend, parent=soma)
cell.insert("hh")
# Make synapses
iclamp_syns = []
for i in range(input_size):
iclamp = IClamp(segment=dend(np.random.rand()))
syn = iclamp.stim(delay=warmup, dur=dur, amp=UniformDist(low=low, high=high))
iclamp_syns.append(syn)
# Make recording
rec = Record(elements=soma(0.5), variables='v')
cell.make_spike_detector(seg=soma(0.5))
return cell, iclamp_syns, rec
def test_remove_new_cell_with_remove_immediate(self):
"""
remove immediate removes each section immediate only if there is no reference to the HOC
object of this section outside the Sec object.
"""
cell = Cell(name="cell")
soma = cell.add_sec("soma")
dend1 = cell.add_sec("dend1")
dend2 = cell.add_sec("dend2")
cell.connect_secs(child=dend1, parent=soma, child_loc=0, parent_loc=0.1)
cell.connect_secs(child=dend2, parent=soma, child_loc=0, parent_loc=0.9)
self.assertEqual(6, _get_secs())
soma.remove_immediate_from_neuron()
dend1.remove_immediate_from_neuron()
dend2.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
cell.remove_immediate_from_neuron()
def test_remove_new_cell_with_del_ref(self):
"""
deletion of cell, when all its outside references are deletes - deletes all its
sections as well. But deletion of single soma won't delete section soma since its reference
is still in Cell
"""
cell = Cell(name="cell")
soma = cell.add_sec("soma")
dend1 = cell.add_sec("dend1")
dend2 = cell.add_sec("dend2")
cell.connect_secs(child=dend1, parent=soma, child_loc=0, parent_loc=0.1)
cell.connect_secs(child=dend2, parent=soma, child_loc=0, parent_loc=0.9)
del soma
del dend1
del dend2
self.assertEqual(6, _get_secs())
cell.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
class TestSection(unittest.TestCase):
def setUp(self):
self.cell = Cell(name="cell")
self.soma = self.cell.add_sec("soma", diam=10, l=10, nseg=10)
self.dend1 = self.cell.add_sec("dend1", diam=1, l=10, nseg=10)
self.dend2 = self.cell.add_sec("dend2", diam=1, l=10, nseg=10)
self.cell.connect_secs(child=self.dend1, parent=self.soma, child_loc=0, parent_loc=0.1)
self.cell.connect_secs(child=self.dend2, parent=self.soma, child_loc=0, parent_loc=0.9)
def tearDown(self):
self.soma.remove_immediate_from_neuron()
self.dend1.remove_immediate_from_neuron()
self.dend2.remove_immediate_from_neuron()
self.cell.remove_immediate_from_neuron()
all_sec_num = _get_secs()
if all_sec_num != 0:
raise RuntimeError("Not all section have been removed after teardown. "
"Sections left: %s" % all_sec_num)
def test_remove_synapse(self):
"""
Removal of the parent section doesn't remove child sections
"""
dend3 = self.cell.add_sec("dend3", diam=1, l=10, nseg=10)
self.cell.connect_secs(child=dend3, parent=self.soma, child_loc=0, parent_loc=0.5)
syn = self.cell.add_synapse(source=None, mod_name="Exp2Syn", seg=dend3(0.5))
dend3 = None
self.assertEqual(4, _get_secs())
syn.remove_immediate_from_neuron()
self.assertEqual(4, _get_secs())
def test_remove_point_process(self):
"""
Immediate removal of Point Process in outside reference makes
that Point Process inside synapse also delete
"""
syn = self.cell.add_synapse(source=None, mod_name="Exp2Syn", seg=self.dend2(0.5))
syn.point_process.remove_immediate_from_neuron()
self.assertEqual(0, len(self.cell.syns[0].point_process.__dict__))
def test_remove_synapse2(self):
"""
Remove outside reference and inside (Cell's) reference deletes section from NEURON
"""
dend3 = self.cell.add_sec("dend3", diam=1, l=10, nseg=10)
self.cell.connect_secs(child=dend3, parent=self.soma, child_loc=0, parent_loc=0.5)
dend3 = None
self.assertEqual(4, _get_secs())
self.cell.secs = self.cell.secs[:3]
self.assertEqual(3, len(self.cell.secs))
self.assertEqual(3, _get_secs())
def test_remove_synapse3(self):
"""
Remove outside reference and inside (Cell's) reference doesn't delete section if it has
reference inside the synapse
"""
dend3 = self.cell.add_sec("dend3", diam=1, l=10, nseg=10)
self.cell.connect_secs(child=dend3, parent=self.soma, child_loc=0, parent_loc=0.5)
syn = self.cell.add_synapse(source=None, mod_name="Exp2Syn", seg=dend3(0.5))
dend3 = None
self.assertEqual(4, _get_secs())
self.cell.secs = self.cell.secs[:3]
self.assertEqual(3, len(self.cell.secs))
self.assertEqual(4, _get_secs())
syn.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def test_remove_soma(self):
"""
Removal of the parent section doesn't remove child sections
"""
self.soma.remove_immediate_from_neuron()
self.assertEqual(2, _get_secs())
def test_removal_sec_from_cell_object(self):
"""
removal section by cell object - removes it from the cell object's self.secs list
"""
self.cell.add_sec("dend3", diam=10, l=10, nseg=10)
self.cell.remove_secs("dend3")
self.assertEqual(3, _get_secs())
self.assertEqual(3, len(self.cell.secs))
def test_removal_sec_outside_cell_object(self):
"""
removal section by itself - removes it from the cell object's self.secs list
"""
dend3 = self.cell.add_sec("dend3", diam=10, l=10, nseg=10)
dend3.remove_immediate_from_neuron()
self.assertEqual(4, len(self.cell.secs))
def test_removal_sec_outside_cell_object_clear_secs_manual(self):
"""
removal section from secs clear also the object dend3
"""
dend3 = self.cell.add_sec("dend3", diam=10, l=10, nseg=10)
self.cell.secs.remove(dend3)
self.assertEqual(3, len(self.cell.secs))
def test_remove_dend1(self):
"""
Removal of the parent section doesn't remove child sections
"""
self.dend1.remove_immediate_from_neuron()
self.assertEqual(2, _get_secs())
def test_remove_dend1_soma(self):
"""
Removal of the parent section doesn't remove child sections
"""
self.soma.remove_immediate_from_neuron()
self.dend1.remove_immediate_from_neuron()
self.assertEqual(1, _get_secs())
def test_remove_cell(self):
"""
Removal of cell only doesn't remove any sections since their references are valid
"""
self.cell.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def test_remove_sec_with_hoc_ref(self):
"""
Immediate removal of Section doesn't remove it from NEURON if there is outside reference to
the HOC object that Point Process inside synapse also delete
"""
hoc_soma = self.soma.hoc
self.soma.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def test_remove_new_cell_with_no_ref(self):
"""
deletion of cell, when all its sections have no reference outside - deletes all its
sections as well
"""
cell = Cell(name="cell")
soma = cell.add_sec("soma")
dend1 = cell.add_sec("dend1")
dend2 = cell.add_sec("dend2")
cell.connect_secs(child=dend1, parent=soma, child_loc=0, parent_loc=0.1)
cell.connect_secs(child=dend2, parent=soma, child_loc=0, parent_loc=0.9)
soma = None
dend1 = None
dend2 = None
self.assertEqual(6, _get_secs())
cell.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def test_remove_new_cell_with_del_ref(self):
"""
deletion of cell, when all its outside references are deletes - deletes all its
sections as well. But deletion of single soma won't delete section soma since its reference
is still in Cell
"""
cell = Cell(name="cell")
soma = cell.add_sec("soma")
dend1 = cell.add_sec("dend1")
dend2 = cell.add_sec("dend2")
cell.connect_secs(child=dend1, parent=soma, child_loc=0, parent_loc=0.1)
cell.connect_secs(child=dend2, parent=soma, child_loc=0, parent_loc=0.9)
del soma
del dend1
del dend2
self.assertEqual(6, _get_secs())
cell.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def test_remove_new_cell_with_remove_immediate(self):
"""
remove immediate removes each section immediate only if there is no reference to the HOC
object of this section outside the Sec object.
"""
cell = Cell(name="cell")
soma = cell.add_sec("soma")
dend1 = cell.add_sec("dend1")
dend2 = cell.add_sec("dend2")
cell.connect_secs(child=dend1, parent=soma, child_loc=0, parent_loc=0.1)
cell.connect_secs(child=dend2, parent=soma, child_loc=0, parent_loc=0.9)
self.assertEqual(6, _get_secs())
soma.remove_immediate_from_neuron()
dend1.remove_immediate_from_neuron()
dend2.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
cell.remove_immediate_from_neuron()
def test_removal_sec_after_synapse_remove(self):
"""
Removing synapse allows to remove section as well
"""
dend3 = self.cell.add_sec("dend3", diam=10, l=10, nseg=10)
syn = self.cell.add_synapse(source=None, mod_name="Exp2Syn", seg=dend3(0.5))
syn.remove_immediate_from_neuron()
self.soma.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
def test_removal_sec_as_part_of_synapse(self):
"""
Removal of Sec which is a part of a Synapse won't delete the Section in NEURON as long as
Synapse exists.
"""
dend3 = self.cell.add_sec("dend3", diam=10, l=10, nseg=10)
syn = self.cell.add_synapse(source=None, mod_name="Exp2Syn", seg=dend3(0.5))
dend3.remove_immediate_from_neuron()
self.assertEqual(4, _get_secs())
def test_removal_sec_before_synapse_remove(self):
"""
Removing section before removing synapse - makes that section is not removed. It is because
we remove dend3 section, but self.cell still holds the reference to the synapse.
"""
dend3 = self.cell.add_sec("dend3", diam=10, l=10, nseg=10)
self.cell.add_synapse(source=None, mod_name="Exp2Syn", seg=dend3(0.5))
dend3.remove_immediate_from_neuron()
self.assertEqual(4, _get_secs())
def test_removal_cell_before_synapse_remove(self):
"""
Removing whole cell after none of its content's reference is stored out of the cell - makes
all its content and synapses removal.
"""
cell2 = Cell(name="cell2")
dend3 = cell2.add_sec("dend3", diam=10, l=10, nseg=10)
cell2.add_synapse(source=None, mod_name="Exp2Syn", seg=dend3(0.5))
dend3 = None
cell2.remove_immediate_from_neuron()
self.assertEqual(3, _get_secs())
class TestSection(unittest.TestCase):
def setUp(self):
self.cell = Cell(name="cell")
def tearDown(self):
self.cell.remove_immediate_from_neuron()
l = len(list(h.allsec()))
if len(list(h.allsec())) != 0:
raise RuntimeError("Not all section have been removed after teardown. "
"Sections left: %s" % l)
def test_default_name(self):
"""
If the name exists it will add a number starting from 2 to the proposed name.
"""
pat = re.compile("[1-9]")
for i in range(10):
self.cell.add_sec("dend")
for i, dend in enumerate(self.cell.filter_secs(name="dend")):
res = pat.search(dend.name)
if i == 0:
self.assertIsNone(res)
else:
self.assertEqual(i + 1, int(dend.name.replace("dend", "")))
dend.remove_immediate_from_neuron()
def test_regex_search(self):
for i in range(10):
self.cell.add_sec("dend")
for i, dend in enumerate(self.cell.filter_secs("regex:dend[1-9]")):
self.assertEqual(i + 2, int(dend.name.replace("dend", "")))
for d in self.cell.secs:
d.remove_immediate_from_neuron()
def test_connections(self):
soma = self.cell.add_sec(name="soma", l=10, nseg=10)
dend = self.cell.add_sec(name="dend", l=100, nseg=10)
self.cell.connect_secs(child=dend, parent=soma, child_loc=0, parent_loc=0.7)
self.assertEqual(0, dend.orientation)
self.assertEqual(0.7, dend.parent_loc)
self.assertIsNone(soma.parent_loc)
def test_allseg(self):
soma = self.cell.add_sec(name="soma", diam=1, l=10, nseg=20)
dend = self.cell.add_sec(name="dend", diam=1, l=100, nseg=200)
self.assertEqual(22, len(soma.segs))
self.assertEqual(202, len(dend.segs))
def test_area1(self):
soma = self.cell.add_sec(name="soma", diam=1, l=10, nseg=20)
dend = self.cell.add_sec(name="dend", diam=1, l=100, nseg=200)
self.assertEqual(0, soma.segs[0].area)
self.assertEqual(0, soma.segs[-1].area)
self.assertEqual(0, dend.segs[0].area)
self.assertEqual(0, dend.segs[-1].area)
for s in soma.segs[1:-1]:
self.assertEqual(1.5708, round(s.area, 4))
for s in dend.segs[1:-1]:
self.assertEqual(1.5708, round(s.area, 4))
def test_area2(self):
apic = self.cell.add_sec(name="apic", diam=10, l=10, nseg=4)
for s in apic.segs[1:-1]:
self.assertEqual(78.5398, round(s.area, 4))
from neuronpp.utils.simulation import Simulation
from neuronpp.cells.cell import Cell
from neuronpp.utils.record import Record
from neuronpp.core.cells.netstim_cell import NetStimCell
path = os.path.dirname(os.path.abspath(__file__))
model_path1 = os.path.join(path, "..", "commons/mods/ebner2019")
model_path2 = os.path.join(path, "..", "commons/morphologies/swc/my.swc")
# Prepare cell
cell = Cell(name="cell", compile_paths=model_path1)
cell.load_morpho(filepath=model_path2)
cell.add_sec("dend[1]", diam=10, l=10, nseg=10)
cell.connect_secs(source="dend[1]", target="soma")
cell.insert("pas")
cell.insert("hh")
# Two examples of synapses with NetStim:
stim_cell = NetStimCell("stim_cell")
stim = stim_cell.make_netstim(start=250, number=30, interval=1)
soma = cell.filter_secs("soma")
# 1) Hoc-style synapse
pp = cell.add_point_process(mod_name="ExpSyn", seg=soma(0.5))
cell.add_netcon(source=stim, point_process=pp, netcon_weight=0.01, delay=1)
# 2) Recommended synapse
syn1 = cell.add_synapse(source=stim,
seg=soma(0.5),
from neuronpp.utils.simulation import Simulation
from neuronpp.cells.cell import Cell
from neuronpp.utils.record import Record
from neuronpp.core.cells.netstim_cell import NetStimCell
path = os.path.dirname(os.path.abspath(__file__))
model_path1 = os.path.join(path, "..", "commons/mods/ebner2019")
model_path2 = os.path.join(path, "..", "commons/morphologies/swc/my.swc")
# Prepare cell
cell = Cell(name="cell", compile_paths=model_path1)
cell.load_morpho(filepath=model_path2)
cell.add_sec("dend[1]", diam=10, l=10, nseg=10)
cell.connect_secs(child="dend[1]", parent="soma")
cell.insert("pas")
cell.insert("hh")
# Two examples of synapses with NetStim:
stim_cell = NetStimCell("stim_cell")
stim = stim_cell.add_netstim(start=250, number=30, interval=1)
soma = cell.filter_secs("soma")
# 1) Hoc-style synapse
pp = cell.add_point_process(mod_name="ExpSyn", seg=soma(0.5))
cell.add_netcon(source=stim, point_process=pp, netcon_weight=0.01, delay=1)
# 2) Recommended synapse
syn1 = cell.add_synapse(source=stim,
seg=soma(0.5),
