for i_amp, amp in enumerate(amp_spread):
dis = distance[0]
loop = 0
spiked = True # artificially set to True, to engage the loop, but anyway tested for distance = 0
print("debug01 loop {} rank {} amp {} distance {}".format(
loop, RANK, amp, dis))
while spiked and loop < len(distance):
# displacement, amp, loop, PROBLEM
dis = distance[loop]
print("debug001 loop {} rank {} amp {} distance {}".format(
loop, RANK, amp, dis))
source_amps = np.multiply(polarity, amp)
ExtPot = utils.ImposedPotentialField(
source_amps, positions[0],
positions[1] + displacement_source,
positions[2] + dura_height, sigma)
# LFPy.cell.neuron.init()
cell = LFPy.TemplateCell(
morphology=morphologyfile,
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)
# set view as in most other examples
cell.set_rotation(x=np.pi / 2)
n_stim_amp = -stim_amp / 4
source_geometry = np.array(
[-stim_amp / 4, -stim_amp / 4, -stim_amp / 4, -stim_amp / 4, stim_amp])
source_zs = np.ones(len(source_xs)) * cortical_surface_height
# Stimulation Parameters:
max_current = -100000. # mA
current_resolution = 100
# amp_range = np.exp(np.linspace(1, np.log(max_current), current_resolution))
amp_range = np.linspace(1, max_current, current_resolution)
amp = amp_range[0]
for loop in range(current_resolution):
# loop for various geometries
source_amps = source_geometry * amp_range[loop]
ExtPot = utils.ImposedPotentialField(source_amps, source_xs, source_ys,
source_zs, sigma)
plot_field_length = 500
v_field_ext_xz = np.zeros((100, 100))
xf = np.linspace(-plot_field_length, plot_field_length, 100)
zf = np.linspace(-plot_field_length, cortical_surface_height, 100)
for xidx, x in enumerate(xf):
for zidx, z in enumerate(zf):
v_field_ext_xz[xidx, zidx] = ExtPot.ext_field(x, 0, z)
vmin = -1000
vmax = 1000
logthresh = 0
fig = plt.figure(figsize=[18, 7])
fig.suptitle('CURRENT = {0} mA'.format((amp_range[loop]) / 1000.))
fig.subplots_adjust(wspace=.6)
# source_geometry = np.array([-stim_amp, 0, stim_amp, 0, 0]) # dipole
# source_geometry = np.array([-stim_amp / 4, -stim_amp / 4, -stim_amp / 4, -stim_amp / 4, stim_amp])
# source_geometry = np.array([stim_amp, stim_amp, stim_amp, stim_amp, -stim_amp])
# source_geometry = np.array([-1, -1, 1, 1, 1, 1, -1, -1])
name_shape_ecog = 'twosquare'
polarity, n_elec, positions = utils.create_array_shape(name_shape_ecog, 25)
amp = (200. * 10**3) / n_elec # uA
voltage = 5000
cortical_surface_height = 20
source_amps = np.multiply(polarity, amp)
ExtPot = utils.ImposedPotentialField(source_amps, positions[0], positions[1],
positions[2] + cortical_surface_height,
sigma)
x_extent = 500
z_extent = 1000
y_extent = 500
space_resolution = 500
depth_check = -350
# v_field_ext_xz = np.zeros((space_resolution, space_resolution))
# v_field_ext_xy2 = np.zeros((space_resolution, space_resolution))
# xf = np.linspace(-x_extent, x_extent, space_resolution)
# zf = np.linspace(-x_extent * 2, cortical_surface_height, space_resolution)
# for xidx, x in enumerate(xf):
# for zidx, z in enumerate(zf):
# v_field_ext_xz[xidx, zidx] = ExtPot.ext_field(x, 0, z)
# # v_field_ext_xz[xidx, zidx] = ExtPot.ext_field(0, x, z)
# v_clr = lambda z: plt.cm.jet(1.0 * (z - np.min(zs)) / (np.max(zs) - np.min(zs)))
# v_clr = lambda z: plt.cm.jet(1.0 * (z - np.min(cell.zend)) / (np.max(np.abs(cell.zmid) - np.min(np.abs(cell.zmid)))))
# WHILE/FOR
click = 0
# is_spike = np.zeros(n_cells)
is_spike = False
for depth in distance:
while amp < max_current and not is_spike:
amp = amp_range[click]
source_amps = np.multiply(polarity, amp)
ExtPot = utils.ImposedPotentialField(source_amps, positions[0], positions[1], positions[2] + dura_height, sigma)
# source_amps = source_geometry * amp
# ExtPot = utils.ImposedPotentialField(source_amps, source_xs, source_ys, source_zs, sigma)
# Find external potential field at all cell positions as a function of time
# v_field_ext_stick = np.zeros((len(zs), n_tsteps))
# v_field_ext_stick = ext_field(zs).reshape(len(zs), 1) * pulse.reshape(1, n_tsteps)
# v_field_ext_stick = v_cell_ext[v_idxs]
# Insert external potential at cell
if cell_id == 1:
cell = LFPy.Cell(**cell_parameters)
cell.set_rotation(x=np.pi / 2.)
else:
