# draw measurement points
ax.plot(PSET.foursphereParams['r'][:, 0],
PSET.foursphereParams['r'][:, 2],
'ko',
label='EEG/MEG sites')
for i, (x, y, z) in enumerate(PSET.foursphereParams['r']):
ax.text(x, z + 2500, r'{}'.format(i + 1), ha='center')
# dipole location
ax.plot([0],
[PSET.foursphereParams['radii'][0] + PSET.layer_data['center'][3]],
'k.',
label='dipole site')
ax.axis('equal')
ax.set_ylim(top=max(PSET.foursphereParams['radii']) + 5000)
ax.set_xticks(np.r_[-np.array(PSET.foursphereParams['radii']), 0,
PSET.foursphereParams['radii']])
ax.set_xticklabels([])
ax.legend(loc=(0.25, 0.05), frameon=False)
ax.text(-0.1,
1.05,
alphabet[5],
horizontalalignment='center',
verticalalignment='center',
fontsize=16,
fontweight='demibold',
# draw measurement points
ax3.plot(foursphereParams['r'][:, 0],
foursphereParams['r'][:, 2],
'ko',
label='EEG/MEG sites')
for i, (x, y, z) in enumerate(foursphereParams['r']):
# theta = np.arcsin(x / foursphereParams['radii'][-1])
# if x >= 0:
# ax3.text(x, z+5000, r'${}\pi$'.format(theta / np.pi))
# else:
# ax3.text(x, z+5000, r'${}\pi$'.format(theta / np.pi), ha='right')
ax3.text(x, z + 2500, r'{}'.format(i + 1), ha='center')
# dipole location
ax3.plot([0], [dipole_position[-1]], 'k.', label='dipole site')
ax3.axis('equal')
ax3.set_xticks(np.r_[-np.array(foursphereParams['radii']), 0,
foursphereParams['radii']])
ax3.set_xticklabels([])
ax3.legend(loc=(0.25, 0.15), frameon=False)
# four-sphere volume conductor
sphere = LFPy.FourSphereVolumeConductor(**foursphereParams)
phi_p = sphere.calc_potential(cell.current_dipole_moment, rz=dipole_position)
# import example_parallel_network_plotting as plotting
vlimround = draw_lineplot(
ax=ax4,
data=phi_p * 1E9,
unit=r'pV', #mV -> pV unit conversion
dt=cell.dt,
theta = np.linspace(0, np.pi, 31)
# draw some circles:
for i, r, label in zip(range(4), PSET.foursphereParams['radii'], ['brain', 'CSF', 'skull', 'scalp']):
ax.plot(np.cos(theta)*r, np.sin(theta)*r, 'C{}'.format(i), label=label + r', $r_%i=%i$ mm' % (i+1, r / 1000), clip_on=False)
# draw measurement points
ax.plot(PSET.foursphereParams['r'][:, 0], PSET.foursphereParams['r'][:, 2], 'ko', label='EEG/MEG sites')
for i, (x, y, z) in enumerate(PSET.foursphereParams['r']):
ax.text(x, z+2500, r'{}'.format(i+1), ha='center')
# dipole location
ax.plot([0], [PSET.foursphereParams['radii'][0] + PSET.layer_data['center'][3]], 'k.', label='dipole site')
ax.axis('equal')
ax.set_ylim(top=max(PSET.foursphereParams['radii']) + 5000)
ax.set_xticks(np.r_[-np.array(PSET.foursphereParams['radii']), 0, PSET.foursphereParams['radii']])
ax.set_xticklabels([])
ax.legend(loc=(0.25, 0.05), frameon=False)
ax.text(-0.1, 1.05, alphabet[5],
horizontalalignment='center',
verticalalignment='center',
fontsize=16, fontweight='demibold',
transform=ax.transAxes)
def plot_polarized_light(intensities,
deltaPhase=0,
fig=None,
show_components=False):
if fig is None:
fig = plt.figure(figsize=(20, 10))
X = np.linspace(0, 2 * np.pi)
Y = np.zeros_like(X)
Z = np.zeros_like(X)
V = intensities[0] * np.sin(X)
W = intensities[1] * np.sin(X - deltaPhase)
U = np.zeros_like(W)
ax = fig.add_subplot(121, projection='3d', azim=-25, elev=20)
ax.quiver(X, Y, Z, U, V, W, arrow_length_ratio=0.05, label="E")
if show_components:
ax.quiver(X,
Y,
Z,
U,
V,
np.zeros_like(W),
color=(1, 0, 0, 1),
arrow_length_ratio=0.05,
label="Ex")
ax.quiver(X,
Y,
Z,
U,
np.zeros_like(V),
W,
color=(0, 1, 0, 1),
arrow_length_ratio=0.05,
label="Ey")
ax.legend()
X_ax = np.array([-(1), 0, 0])
Y_ax = np.array([0, 1, 0])
Z_ax = np.array([0, 0, -1])
U_ax = np.array([5 + 2 * np.pi, 0, 0])
V_ax = np.array([0, -1.5, 0])
W_ax = np.array([0, 0, 1.5])
ax.quiver(X_ax,
Y_ax,
Z_ax,
U_ax,
V_ax,
W_ax,
arrow_length_ratio=0.01,
color=(0, 0, 0, 1))
for x, y, z, txt in zip(X_ax + U_ax, Y_ax + V_ax, Z_ax + W_ax,
["Z", "X", "Y"]):
ax.text(x - 0.1, y, z, txt, fontsize=16)
ax_2d = SubplotZero(fig, 122)
fig.add_subplot(ax_2d)
theta = np.linspace(0, 2 * np.pi, 1000)
ax_2d.plot(np.cos(theta), np.sin(theta), 'k--', linewidth=2)
# plt.annotate(s='Ey', xy=(0, -intensities[1]), xytext=(0, intensities[1]), horizontalalignment='center',
# verticalalignment='center',
# color='black', arrowprops=dict(arrowstyle='<->'),fontsize=18)
# verticalalignment='center',
# color='black', arrowprops=dict(arrowstyle='<->', shrinkA=0, shrinkB=0),
ax_2d.plot(V, W, 'b-', linewidth=5)
if intensities[0] > 1e-4:
ax_2d.arrow(-0.8 * intensities[0],
0,
1.8 * intensities[0],
0,
linewidth=0,
width=0.01,
color='black',
shape="full",
length_includes_head=True)
ax_2d.arrow(+0.8 * intensities[0],
0,
-1.8 * intensities[0],
0,
linewidth=0,
width=0.01,
color='black',
shape="full",
length_includes_head=True)
plt.annotate(s='Ex',
xy=(-0.9 * intensities[0], 0.03),
xytext=(0.9 * intensities[0], 0.02),
horizontalalignment='center',
fontsize=18,
color='black')
if intensities[1] > 1e-4:
ax_2d.arrow(0,
-0.8 * intensities[1],
0,
1.8 * intensities[1],
linewidth=0,
width=0.01,
color='black',
shape="full",
length_includes_head=True)
ax_2d.arrow(0,
+0.8 * intensities[1],
0,
-1.8 * intensities[1],
linewidth=0,
width=0.01,
color='black',
shape="full",
length_includes_head=True)
plt.annotate(s='Ey',
xy=(0.06, -0.9 * intensities[1]),
xytext=(0.06, 0.9 * intensities[1]),
horizontalalignment='center',
fontsize=18,
color='black')
# ax_2d.plot([0, 0],[0,intensities[1]],'k->', linewidth=4)
ax_2d.set_xlim([-1.1, 1.1])
ax_2d.set_ylim([-1.1, 1.1])
# # ax_2d.text(1,0,"X", fontsize=16)
# # ax_2d.text(0,1,"Y", fontsize=16)
plt.xticks([])
plt.yticks([])
ax_2d.axis('off')
# for direction in ["xzero", "yzero"]:
# ax_2d.axis[direction].set_axisline_style("-|>")
# ax_2d.axis[direction].set_visible(True)
for direction in ["left", "right", "bottom", "top"]:
ax_2d.axis[direction].set_visible(False)
ax.set_axis_off()
ax.set_xlim([0, 2 * np.pi])
ax.set_ylim([-0.4, 0.4])
ax.set_zlim([-0.4, 0.4])
fig.tight_layout()
plt.show()
for i, r, label in zip(range(4), foursphereParams['radii'], ['brain', 'CSF', 'skull', 'scalp']):
ax3.plot(np.cos(theta)*r, np.sin(theta)*r, 'C{}'.format(i), label=label + r', $r_%i=%i$ mm' % (i+1, r / 1000), clip_on=False)
# draw measurement points
ax3.plot(foursphereParams['r'][:, 0], foursphereParams['r'][:, 2], 'ko', label='EEG/MEG sites')
for i, (x, y, z) in enumerate(foursphereParams['r']):
# theta = np.arcsin(x / foursphereParams['radii'][-1])
# if x >= 0:
# ax3.text(x, z+5000, r'${}\pi$'.format(theta / np.pi))
# else:
# ax3.text(x, z+5000, r'${}\pi$'.format(theta / np.pi), ha='right')
ax3.text(x, z+2500, r'{}'.format(i + 1), ha='center')
# dipole location
ax3.plot([0], [dipole_position[-1]], 'k.', label='dipole site')
ax3.axis('equal')
ax3.set_xticks(np.r_[-np.array(foursphereParams['radii']), 0, foursphereParams['radii']])
ax3.set_xticklabels([])
ax3.legend(loc=(0.25, 0.15), frameon=False)
# four-sphere volume conductor
sphere = LFPy.FourSphereVolumeConductor(
**foursphereParams
)
phi_p = sphere.calc_potential(cell.current_dipole_moment, rz=dipole_position)
# import example_parallel_network_plotting as plotting
vlimround = draw_lineplot(ax=ax4, data=phi_p*1E9, unit=r'pV', #mV -> pV unit conversion
dt=cell.dt, ztransform=False,