def test_very_small(self):
spine_density = 0.0001
out = get_spine_number(self.soma, spine_density, False)
self.assertTrue(out in [0, 1])
def test_length_density(self):
spine_density = 0.1
out = get_spine_number(self.soma, spine_density, False)
self.assertEqual(out, 10)
def test_area_density(self):
spine_density = 0.01
out = get_spine_number(self.soma, spine_density, True)
expected = np.pi * spine_density * self.soma.hoc.L * self.soma.hoc.diam
self.assertEqual(out, int(np.ceil(expected)))
def add_spines_by_density(self,
secs: List[Sec],
spine_density,
spine_type="generic",
**spine_params):
"""
Add spines with specified linear density (per 1 um) to specified
secions (compartments). Spines can have
a predifined type (stubby, thin, mushroom) or, alternatively, their
dimentions (head_diam, head_len, neck_diam, neck_len) can be specified
in spine_params.
:param secs:
Section that will have spines
:param spine_density:
spine density in spines/1um
:param spine_type:
Spine type. There are four predifined types: thin, stubby,
mushroom and other.
:param **spine_params:
See below
Keyword arguments:
:spine_tag:
String attached to name of every head and neck
:head_diam:
Spine head diameter
:head_len:
Length of the spine head
:neck_diam:
Spine neck diameter
:neck_len:
Length of the spine neck
:area_densisty:
if False spine_density is treated as linear spine density [um]
if True spine_density is treated as area density [um2]
:u_random: None
seed for the random number generator used for picking out
spine positions
:spine_g_pas:
pas conductance. By default g_pas of the parent section
will be used.
:spine_E_pas:
pas reversal potential. By default pas reversal potential
of the parent section will be used.
:spine_rm:
membrane resistivity. By default 1/pas conductance of the
parent section will be used.
:spine_ra:
axial resistivity. By default axial resistivity of the parent
section will be used.
:area_densisty:
if False spine_density is treated as linear spine density [um]
if True spine_density is treated as area density [um2]
:add_pas:
add passive mechanism
:return:
TODO change this to list of objects
list target location
TODO: add spines with a distribution of head dimensions and
neck dimensions
"""
try:
spine_dimensions = SPINE_DIMENSIONS[spine_type]
except KeyError:
spine_dimensions = SPINE_DIMENSIONS["generic"]
spine_tag = spine_params.pop("spine_tag", spine_type)
head_diam = spine_params.pop("head_diam",
spine_dimensions["head_diam"])
head_len = spine_params.pop("head_len", spine_dimensions["head_len"])
neck_diam = spine_params.pop("neck_diam",
spine_dimensions["neck_diam"])
neck_len = spine_params.pop("neck_len", spine_dimensions["neck_len"])
# If Falde
spine_E_pas = spine_params.pop("spine_E_pas", None)
spine_g_pas = spine_params.pop("spine_g_pas", None)
spine_rm = spine_params.pop("spine_rm", None)
spine_ra = spine_params.pop("spine_ra", None)
spine_cm = spine_params.pop("spine_cm", None)
add_pas = spine_params.pop("add_pas", False)
if isinstance(spine_rm, int) or isinstance(spine_rm, float):
spine_g_pas = 1 / spine_rm
area_density = spine_params.pop("area_density", False)
seed = spine_params.pop("u_random", None)
if seed is not None:
np.random.seed(seed)
all_target_locations = []
for sec in secs:
spine_number = get_spine_number(sec=sec,
density=spine_density,
area_density=area_density)
E_pas, g_pas, ra, cm = establish_electric_properties(
sec, spine_E_pas, spine_g_pas, spine_ra, spine_cm)
if not add_pas:
E_pas = None
g_pas = None
if isinstance(seed, int):
target_locations = np.random.uniform(0., 1.,
spine_number).tolist()
else:
target_locations = np.linspace(0., .99, spine_number).tolist()
self._add_spines_to_section(sec,
spine_tag,
target_locations,
head_diam,
head_len,
neck_diam,
neck_len,
E_pas,
g_pas,
ra,
cm,
add_pas=add_pas)
all_target_locations.append(target_locations)
return all_target_locations
