def test_cell_distort_geometry_01(self):
cell0 = LFPy.NetworkCell(
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.NetworkCell(
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 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.NetworkCell(**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_chiral_morphology_02(self):
'''test LFPy.NetworkCell.chiral_morphology()'''
cell = LFPy.NetworkCell(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 test_cell_set_rotation_06(self):
'''test LFPy.NetworkCell.set_rotation()'''
cell = LFPy.NetworkCell(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_set_rotation_05(self):
'''test LFPy.NetworkCell.set_rotation()'''
cell = LFPy.NetworkCell(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 test_cell_tstart_00(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},
'dt' : 2**-4,
'nsegs_method' : 'lambda_f',
'lambda_f' : 100,
}
stimParams = {
'pptype' : 'SinSyn',
'dur' : 1000.,
'pkamp' : 1.,
'freq' : 100.,
'bias' : 0.,
'record_current' : False
}
stick0 = LFPy.NetworkCell(tstart=0, tstop=200, **stickParams)
synapse0 = LFPy.StimIntElectrode(stick0,
stick0.get_closest_idx(0, 0, 1000),
delay=0, phase=0.,
**stimParams)
stick0.simulate(rec_imem=True, rec_vmem=True, rec_current_dipole_moment=True)
stick1 = LFPy.NetworkCell(tstart=-100, tstop=100, **stickParams)
synapse1 = LFPy.StimIntElectrode(stick1,
stick1.get_closest_idx(0, 0, 1000),
delay=-100, phase=0.,
**stimParams)
stick1.simulate(rec_imem=True, rec_vmem=True, rec_current_dipole_moment=True)
inds = stick0.tvec >= 100
np.testing.assert_allclose(stick0.vmem[:, inds], stick1.vmem)
np.testing.assert_allclose(stick0.imem[:, inds], stick1.imem)
np.testing.assert_allclose(stick0.current_dipole_moment[inds, :],
stick1.current_dipole_moment)
def test_cell_get_rand_prob_area_norm_from_idx(self):
cell = LFPy.NetworkCell(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_set_pos_00(self):
'''test LFPy.NetworkCell.set_pos'''
cell = LFPy.NetworkCell(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 stickSimulationTesttvec(**kwargs):
stick = LFPy.NetworkCell(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_get_rand_prob_area_norm_from_idx_00(self):
'''test LFPy.NetworkCell.get_rand_prob_area_norm()'''
cell = LFPy.NetworkCell(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_name_00(self):
cell = LFPy.NetworkCell(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_get_idx_parent_children_00(self):
cell = LFPy.NetworkCell(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 test_cell_strip_hoc_objects_00(self):
cell = LFPy.NetworkCell(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_00(self):
'''test LFPy.NetworkCell.get_rand_prob_area_norm()'''
cell = LFPy.NetworkCell(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_closest_idx_00(self):
cell = LFPy.NetworkCell(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_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.NetworkCell(**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_set_point_process_00(self):
cell = LFPy.NetworkCell(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_get_intersegment_distance_00(self):
cell = LFPy.NetworkCell(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 test_cell_get_intersegment_vector_00(self):
cell = LFPy.NetworkCell(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_with_recextelectrode_00(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' : 0,
'tstop' : 100,
'dt' : 2**-4,
'nsegs_method' : 'lambda_f',
'lambda_f' : 100,
}
electrodeParams = {
'sigma' : 0.3,
'x' : np.ones(11) * 100.,
'y' : np.zeros(11),
'z' : np.linspace(1000, 0, 11),
'method' : 'pointsource'
}
stimParams = {
'pptype' : 'SinSyn',
'delay' : 0.,
'dur' : 1000.,
'pkamp' : 1.,
'freq' : 100.,
'phase' : 0,
'bias' : 0.,
'record_current' : False
}
stick = LFPy.NetworkCell(**stickParams)
synapse = LFPy.StimIntElectrode(stick, stick.get_closest_idx(0, 0, 1000),
**stimParams)
electrode = LFPy.RecExtElectrode(**electrodeParams)
stick.simulate(electrode, rec_imem=True)
electrode1 = LFPy.RecExtElectrode(cell=stick, **electrodeParams)
electrode1.calc_lfp()
np.testing.assert_allclose(electrode.LFP, electrode1.LFP)
def test_cell_cellpickler_00(self):
cell = LFPy.NetworkCell(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.NetworkCell(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 test_cell_set_synapse_00(self):
cell = LFPy.NetworkCell(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_get_rand_idx_area_norm_00(self):
cell = LFPy.NetworkCell(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)
