def test_cell_distort_geometry_01(self):
cell0 = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
factors = [-0.2, 0.1, 0., 0.1, 0.2]
nus = [-0.5, 0., 0.5]
for factor in factors:
for nu in nus:
for axis in 'xyz':
cell1 = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(
LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
cell1.distort_geometry(factor=factor, nu=nu, axis=axis)
for attr in ['start', 'mid', 'end']:
for ax in 'xyz'.replace(axis, ''):
np.testing.assert_allclose(
getattr(cell0, ax + attr) * (1 + factor * nu),
getattr(cell1, ax + attr))
np.testing.assert_allclose(
getattr(cell0, axis + attr) * (1 - factor),
getattr(cell1, axis + attr))
def generate_LFP_for_single_neuron(electrode, cell_name, params):
cwd = os.getcwd()
neuron.h.load_file('stdrun.hoc')
neuron.h.load_file('import3d.hoc')
#Loading the neuron models of interest
neuron_model = '/home/baran/Desktop/neuron_models/' + cell_name
load_mechanisms_from_neuron_model(cell_name)
templatename = load_cell_properties(cell_name)
os.chdir(neuron_model)
morphologyfile = glob(os.path.join('morphology', '*'))[0]
add_synapses = False
cell = LFPy.TemplateCell(morphology=morphologyfile,
templatefile=(os.path.join(
neuron_model, 'template.hoc')),
templatename=templatename,
templateargs=1 if add_synapses else 0,
tstop=params['tstop'],
dt=params['dt'],
nsegs_method=None,
pt3d=True,
verbose=True)
#Add stimulation electrode
pointProcess = LFPy.StimIntElectrode(cell, **params['PointProcParams'])
cell.simulate(electrode=electrode)
os.chdir(cwd)
return electrode, cell
def test_cell_chiral_morphology_02(self):
'''test LFPy.TemplateCell.chiral_morphology()'''
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
xstarts = cell.xstart.copy()
xmids = cell.xmid.copy()
xends = cell.xend.copy()
ystarts = cell.ystart.copy()
ymids = cell.ymid.copy()
yends = cell.yend.copy()
zstarts = cell.zstart.copy()
zmids = cell.zmid.copy()
zends = cell.zend.copy()
# test rotation 180 deg around z-axis
cell.chiral_morphology(axis='z')
# assert that y- and z-coordinates are inverted, using absolute
# tolerances
np.testing.assert_allclose(cell.xstart, xstarts, atol=1e-07)
np.testing.assert_allclose(cell.xmid, xmids, atol=1e-07)
np.testing.assert_allclose(cell.xend, xends, atol=1e-07)
np.testing.assert_allclose(cell.ystart, ystarts, atol=1e-07)
np.testing.assert_allclose(cell.ymid, ymids, atol=1e-07)
np.testing.assert_allclose(cell.yend, yends, atol=1e-07)
np.testing.assert_allclose(cell.zstart, -zstarts, atol=1e-07)
np.testing.assert_allclose(cell.zmid, -zmids, atol=1e-07)
np.testing.assert_allclose(cell.zend, -zends, atol=1e-07)
def return_cell(self):
self.model_path = join(root_path+'TC_neuron')
neuron.load_mechanisms(self.model_path)
cell_parameters = {
'morphology': join(self.model_path, 'soma.hoc'),
'passive':False,
'v_init' : -60,
'extracellular':False,
'nsegs_method': 'none',
# 'timeres_NEURON':0.1,
# 'timeres_python':0.1,
'dt' : 0.1,
'tstop':2000,
'tstart':0,
'templatefile': join(self.model_path, 'TC_GH2.hoc'),
'templatename':'sTC',
'templateargs':None,
'delete_sections':False
}
cell = LFPy.TemplateCell(**cell_parameters)
return cell
def test_cell_set_rotation_05(self):
'''test LFPy.TemplateCell.set_rotation()'''
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
pt3d=True)
xstarts = cell.xstart.copy()
xmids = cell.xmid.copy()
xends = cell.xend.copy()
ystarts = cell.ystart.copy()
ymids = cell.ymid.copy()
yends = cell.yend.copy()
# test rotation 180 deg around z-axis
cell.set_rotation(z=np.pi)
# assert that y- and z-coordinates are inverted, using absolute
# tolerances
np.testing.assert_allclose(cell.xstart, -xstarts, atol=1e-07)
np.testing.assert_allclose(cell.xmid, -xmids, atol=1e-07)
np.testing.assert_allclose(cell.xend, -xends, atol=1e-07)
np.testing.assert_allclose(cell.ystart, -ystarts, atol=1e-07)
np.testing.assert_allclose(cell.ymid, -ymids, atol=1e-07)
np.testing.assert_allclose(cell.yend, -yends, atol=1e-07)
def return_cell(self):
self.model_path = join(root_path+'cortex_neurons')
neuron.load_mechanisms(self.model_path)
cell_parameters = {
'morphology': join(self.model_path, 'soma.hoc'),
'passive':False,
'v_init' : -70,
'extracellular':False,
'nsegs_method': 'lambda_f',
'lambda_f': 50,
#'timeres_NEURON':0.1,
#'timeres_python':0.1,
'dt' : 0.1,
'tstop':2000,
'tstart':0,
'templatefile': join(self.model_path, 'sPY_template'),
'templatename':'sPY',
'templateargs':None,
'custom_fun': None,
'delete_sections':False
}
cell = LFPy.TemplateCell(**cell_parameters)
cell.set_rotation(x=-1.57, y=0.0, z=0.0)
return cell
def simulate(cell_parameters, synapse_parameters, grid_electrode_parameters, syninds, x_rot=0, y_rot=0, z_rot=0, active=False):
"""set synapse location. simulate cell, synapse and electrodes for input synapse location"""
# create cell with parameters in dictionary
if not active:
cell = LFPy.Cell(**cell_parameters)
else:
cell = LFPy.TemplateCell(**cell_parameters)
# rotate cell
cell.set_rotation(x=x_rot)
cell.set_rotation(y=y_rot)
cell.set_rotation(z=z_rot)
# insert synapses
if type(syninds) == int:
syninds = [syninds]
for idx in syninds:
synapse_parameters['idx'] = idx
synapse = LFPy.Synapse(cell, **synapse_parameters)
synapse.set_spike_times(np.array([20.]))
# simulate cell
cell.simulate(rec_imem = True,
rec_vmem = True,
rec_current_dipole_moment=True)
#create grid electrodes
grid_electrode = LFPy.RecExtElectrode(cell, **grid_electrode_parameters)
grid_electrode.calc_lfp()
return cell, synapse, grid_electrode
def test_cell_set_pos_00(self):
'''test LFPy.TemplateCell.set_pos'''
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
np.testing.assert_allclose(cell.somapos, [0, 0, 0])
def create_cell(cell_parameters, active=False, x_rot=0, y_rot=0, z_rot=0):
# create cell with parameters in dictionary
if not active:
cell = LFPy.Cell(**cell_parameters)
else:
cell = LFPy.TemplateCell(**cell_parameters)
cell.set_rotation(x=x_rot)
cell.set_rotation(y=y_rot)
cell.set_rotation(z=z_rot)
return cell
def test_cell_get_rand_prob_area_norm_from_idx_00(self):
'''test LFPy.TemplateCell.get_rand_prob_area_norm()'''
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
p = cell.get_rand_prob_area_norm_from_idx(idx=np.array([0]))
np.testing.assert_equal(p, np.array([1.]))
def test_cell_get_idx_parent_children_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
np.testing.assert_array_equal(
cell.get_idx_parent_children(parent='soma[0]'),
cell.get_idx(section=['soma[0]', 'dend[0]']))
def stickSimulationTesttvec(**kwargs):
stick = LFPy.TemplateCell(morphology=os.path.join(LFPy.__path__[0], 'test',
'stick.hoc'),
verbose=False,
templatefile=os.path.join(
LFPy.__path__[0], 'test',
'stick_template.hoc'),
templatename='stick_template',
templateargs=None,
**kwargs)
stick.simulate(rec_imem=False)
return stick.tvec
def test_cell_simulate_current_dipole_moment_01(self):
stickParams = {
'morphology':
os.path.join(LFPy.__path__[0], 'test', 'stick.hoc'),
'templatefile':
os.path.join(LFPy.__path__[0], 'test', 'stick_template.hoc'),
'templatename':
'stick_template',
'templateargs':
None,
'cm':
1,
'Ra':
150,
'v_init':
-65,
'passive':
True,
'passive_parameters': {
'g_pas': 1. / 30000,
'e_pas': -65
},
'tstart':
-100,
'tstop':
100,
'dt':
2**-4,
'nsegs_method':
'lambda_f',
'lambda_f':
100,
}
stimParams = {
'pptype': 'SinSyn',
'delay': 0.,
'dur': 1000.,
'pkamp': 1.,
'freq': 100.,
'phase': 0,
'bias': 0.,
'record_current': False
}
for idx in range(31): #31 segments
if idx != 15: # no net dipole moment because of stick symmetry
stick = LFPy.TemplateCell(**stickParams)
synapse = LFPy.StimIntElectrode(stick, idx=idx, **stimParams)
stick.simulate(rec_imem=True, rec_current_dipole_moment=True)
p = np.dot(stick.imem.T, np.c_[stick.xmid, stick.ymid,
stick.zmid])
np.testing.assert_allclose(p, stick.current_dipole_moment)
def test_cell_strip_hoc_objects_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
cell.strip_hoc_objects()
for attribute in dir(cell):
self.assertNotEqual(str(type(getattr(cell, attribute))),
'hoc.HocObject')
def test_cell_get_rand_prob_area_norm_from_idx(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
p = cell.get_rand_prob_area_norm_from_idx(idx=cell.get_idx(
section='allsec'))
self.assertListEqual(cell.get_rand_prob_area_norm().tolist(),
p.tolist())
def test_cell_get_idx_name_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
np.testing.assert_array_equal(
cell.get_idx_name(idx=np.array([0])),
np.array([[0, 'ball_and_stick_template[0].soma[0]', 0.5]],
dtype=object))
def test_cell_simulate_current_dipole_moment_02(self):
stickParams = {
'morphology':
os.path.join(LFPy.__path__[0], 'test', 'stick.hoc'),
'templatefile':
os.path.join(LFPy.__path__[0], 'test', 'stick_template.hoc'),
'templatename':
'stick_template',
'templateargs':
None,
'cm':
1,
'Ra':
150,
'v_init':
-65,
'passive':
True,
'passive_parameters': {
'g_pas': 1. / 30000,
'e_pas': -65
},
'tstart':
-100,
'tstop':
100,
'dt':
2**-4,
'nsegs_method':
'lambda_f',
'lambda_f':
100,
}
stimParams = {
'e': 0, # reversal potential
'syntype': 'Exp2Syn', # synapse type
'tau1': 0.1, # syn. time constant
'tau2': 2., # syn. time constant
'weight': 0.01,
}
for idx in range(31): #31 segments
if idx != 15: # no net dipole moment because of stick symmetry
stick = LFPy.TemplateCell(**stickParams)
synapse = LFPy.Synapse(stick, idx=idx, **stimParams)
synapse.set_spike_times(np.array([10., 20., 30., 40., 50.]))
stick.simulate(rec_imem=True, rec_current_dipole_moment=True)
p = np.dot(stick.imem.T, np.c_[stick.xmid, stick.ymid,
stick.zmid])
np.testing.assert_allclose(p, stick.current_dipole_moment)
def test_cell_get_closest_idx_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
nsegs_method=None)
self.assertEqual(cell.get_closest_idx(x=0, y=0, z=0),
cell.get_idx(section='soma')[0])
self.assertEqual(cell.get_closest_idx(x=-25, y=0, z=175),
cell.get_idx(section='dend[1]')[0])
def test_cell_get_rand_prob_area_norm_00(self):
'''test LFPy.TemplateCell.get_rand_prob_area_norm()'''
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
p = cell.get_rand_prob_area_norm()
self.assertAlmostEqual(p.sum(), 1.)
self.assertTrue(p.min() >= 0.)
self.assertTrue(p.max() <= 1.)
def test_cell_get_intersegment_distance_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
idx0 = 0
idx1 = 1
distance = cell.get_intersegment_distance(idx0=idx0, idx1=idx1)
vector = cell.get_intersegment_vector(idx0=idx0, idx1=idx1)
self.assertEqual(np.sqrt(np.array(vector)**2).sum(), distance)
def cellsim_w_HH(stim_I=0.2,
gnabar_hh=0.12,
gkbar_hh=0.036,
gl_hh=0.0003,
el_hh=-54.3):
#LFPy.TemplateCell params
cell_params = dict(
morphology='soma.hoc',
templatefile='LFPyCellTemplate.hoc',
templatename='LFPyCellTemplate',
passive=False,
nsegs_method=None,
tstartms=0,
tstopms=1000,
extracellular=False,
)
#LFPy.StimIntElectrode params
stim_params = {
'idx': 0,
'pptype': 'IClamp',
'delay': 100.,
'dur': 800.,
'amp': stim_I,
}
#Why templatecell - Hay2011 is one, see LFPy examples using it.
cell = LFPy.TemplateCell(**cell_params)
#throw on some HH channels
for sec in cell.allseclist:
sec.insert('hh')
#These are important, basically the DOFs were attempting to fit
for seg in sec:
seg.hh.gnabar = gnabar_hh
seg.hh.gkbar = gkbar_hh
seg.hh.gl = gl_hh
seg.hh.el = el_hh
#set stimulus
stim = LFPy.StimIntElectrode(cell, **stim_params)
#run the sim
cell.simulate()
#return data
return cell.tvec, cell.somav
def test_cell_get_intersegment_vector_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
idx0 = 0
idx1 = 1
vector = cell.get_intersegment_vector(idx0=idx0, idx1=idx1)
self.assertListEqual(vector, [
cell.xmid[idx1] - cell.xmid[idx0], cell.ymid[idx1] -
cell.ymid[idx0], cell.zmid[idx1] - cell.zmid[idx0]
])
def test_cell_set_point_process_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
cell.set_point_process(idx=0,
pptype='IClamp',
record_current=False,
**dict(delay=1., amp=1.))
self.assertEqual(cell.stimlist[0].hname(), 'IClamp[0]')
self.assertEqual(len(cell.stimlist), 1)
self.assertEqual(cell.stimlist[0].delay, 1.)
self.assertEqual(cell.stimlist[0].amp, 1.)
def test_cell_cellpickler_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
cell_pickle = cell.cellpickler(filename=None, pickler=pickle.dumps)
pickled_cell = pickle.loads(cell_pickle)
for attribute in dir(cell):
if attribute.startswith('__') or attribute.startswith('_'):
pass
else:
self.assertEqual(type(getattr(cell, attribute)),
type(getattr(pickled_cell, attribute)))
def test_cell_get_idx_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
nsegs_method=None)
self.assertListEqual(cell.get_idx(section='soma').tolist(), [0])
self.assertListEqual(cell.get_idx(section='soma[0]').tolist(), [0])
self.assertListEqual(cell.get_idx(section='dend[0]').tolist(), [1])
self.assertListEqual(cell.get_idx(section='dend[1]').tolist(), [2])
self.assertListEqual(cell.get_idx(section='dend[2]').tolist(), [3])
self.assertListEqual(cell.get_idx(section='dend').tolist(), [1, 2, 3])
self.assertListEqual(
cell.get_idx(section='allsec').tolist(), [0, 1, 2, 3])
self.assertListEqual(
cell.get_idx(section=['soma', 'dend']).tolist(), [0, 1, 2, 3])
self.assertListEqual(cell.get_idx(section='apic').tolist(), [])
def return_cell(self):
self.model_path = join(root_path+'Geir2011')
neuron.load_mechanisms(self.model_path)
cell_parameters = {
# 5 dendrites
#'morphology': join(self.model_path, 'ballnsticks.hoc'),
# 4 dendrites
'morphology': join(self.model_path, 'ballnsticks2.hoc'),
'passive':True,
'v_init' : -63,
'extracellular':False,
'nsegs_method': 'lambda_f',
'lambda_f': 50,
# 'timeres_NEURON':0.1,
# 'timeres_python':0.1,
'dt':0.1,
'tstop':2000,
'tstart':0,
'templatefile': join(self.model_path, 'LFPyCellTemplate.hoc'),
'templatename':'LFPyCellTemplate',
'templateargs':None,
'custom_fun': [insertChannels.active_declarations],
'custom_fun_args': [{'arg1': 'arg1'}],
'delete_sections':False,
# passive mechanisms
# 'passive_parameters': dict(g_pas=1/22000, e_pas=-67.5, Ra=113, cm=1.1)
'passive_parameters':dict(g_pas=1/22000, e_pas=-67.5, Ra = 113, cm = 1.1)
# 'e_pas' : -67.5,
# 'Ra' : 113,
# 'rm' : 22000,
# 'cm' : 1.1
}
cell = LFPy.TemplateCell(**cell_parameters)
cell.set_rotation(x=-1.57, y=0.0, z=0.0)
# self.cell = cell
return cell
def test_cell_set_synapse_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
cell.set_synapse(idx=0,
syntype='ExpSyn',
record_curret=False,
record_potential=False,
weight=1.,
**dict(e=10., tau=2.))
self.assertTrue('ExpSyn' in cell.synlist[0].hname())
self.assertEqual(len(cell.synlist), 1)
self.assertEqual(len(cell.netconlist), 1)
self.assertEqual(len(cell.netstimlist), 1)
self.assertEqual(cell.synlist[0].e, 10.)
self.assertEqual(cell.synlist[0].tau, 2.)
self.assertEqual(cell.netconlist[0].weight[0], 1.)
def test_cell_set_rotation_06(self):
'''test LFPy.TemplateCell.set_rotation()'''
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test', 'stick.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
xstarts = cell.xstart.copy()
xmids = cell.xmid.copy()
xends = cell.xend.copy()
ystarts = cell.ystart.copy()
ymids = cell.ymid.copy()
yends = cell.yend.copy()
zstarts = cell.zstart.copy()
zmids = cell.zmid.copy()
zends = cell.zend.copy()
# test rotation: 90 deg around x-axis, 90 deg around y-axis, 90 deg around z-axis
cell.set_rotation(x=np.pi / 2., y=np.pi, z=np.pi / 4.)
# revert rotation: -90 deg around x-axis, -90 deg around y-axis, -90 deg around z-axis, rotation_order='zyx'
cell.set_rotation(x=-np.pi / 2.,
y=-np.pi,
z=-np.pi / 4.,
rotation_order='zyx')
# assert that x-, y- and z-coordinates are same as beginning, using absolute
# tolerances
np.testing.assert_allclose(cell.xstart, xstarts, atol=1e-07)
np.testing.assert_allclose(cell.xmid, xmids, atol=1e-07)
np.testing.assert_allclose(cell.xend, xends, atol=1e-07)
np.testing.assert_allclose(cell.ystart, ystarts, atol=1e-07)
np.testing.assert_allclose(cell.ymid, ymids, atol=1e-07)
np.testing.assert_allclose(cell.yend, yends, atol=1e-07)
np.testing.assert_allclose(cell.zstart, zstarts, atol=1e-07)
np.testing.assert_allclose(cell.zmid, zmids, atol=1e-07)
np.testing.assert_allclose(cell.zend, zends, atol=1e-07)
def test_cell_get_rand_idx_area_norm_00(self):
cell = LFPy.TemplateCell(
morphology=os.path.join(LFPy.__path__[0], 'test',
'ball_and_sticks_w_lists.hoc'),
templatefile=os.path.join(LFPy.__path__[0], 'test',
'ball_and_stick_template.hoc'),
templatename='ball_and_stick_template',
templateargs=None,
)
idx = cell.get_rand_idx_area_norm(nidx=1000000)
# compute histogram and correlate with segment area
bins = np.arange(cell.totnsegs + 1)
hist, bin_edges = np.histogram(idx, bins=bins)
# compute Pearson correlation coefficients between area and histogram
# reporting success if within 5 decimal places
self.assertAlmostEqual(np.corrcoef(cell.area, hist)[0, 1],
1.,
places=5)
# check if min and max is in the range of segment indices
self.assertEqual(idx.min(), 0)
self.assertEqual(idx.max(), cell.totnsegs - 1)
print("biophysics loaded")
if not hasattr(neuron.h, templatename):
# Load main cell template
neuron.h.load_file(1, "template.hoc")
add_synapses = False
morphologyfile = glob(os.path.join('morphology', '*'))
LFPy.cell.neuron.init()
cell = LFPy.TemplateCell(morphology=morphologyfile[0],
templatefile=posixpth(
os.path.join(NRN, 'template.hoc')),
templatename=templatename,
templateargs=1 if add_synapses else 0,
tstop=tstop,
dt=dt,
extracellular=True,
nsegs_method=None,
passive=False)
# Set Position and Rotation
cell.set_rotation(x=np.pi / 2, z=np.pi / 2)
if np.max(cell.zend) > 0:
cell.set_pos(z=-np.max(cell.zend) - 50)
source_amps = bisc.currents
positions_x = np.zeros(
bisc.get_electrodes_number()) # to replace, use in built mea function