Matplotlib plot 3d line on surface with shade

Question

Could anyone help me to plot such kind of figure, some lines on the 3d sphere, and such kind of coordinate?

Thanks.

Answer 1

The following is the code

# orintation
fig, axi = plt.subplots(figsize=figsize, dpi=dpi, subplot_kw={'projection': '3d'})
fig.patch.set_facecolor('white')
axorin = axi
ttheta = Table_theta[tidx][0]
tphi = Table_phi[tidx][0]
tpsi = Table_psi[tidx][0]
tnodes = get_ecoli_nodes_split_at(ttheta, tphi, tpsi, now_center=np.zeros(3), **problem_kwargs)
if trange_geo is None:
    tnode = np.vstack(tnodes)
    trange_geo = np.linalg.norm(tnode, axis=-1).max() * 0.8
# print('trange_geo=', trange_geo)
tmid = np.zeros(3)
axorin.set_xlim3d([tmid[0] - trange_geo, tmid[0] + trange_geo])
tticks = np.around(np.linspace(tmid[0] - trange_geo, tmid[0] + trange_geo, 21),
                   decimals=2)[1::6]
axorin.set_xticks(tticks)
axorin.set_xticklabels(tticks)
axorin.set_ylim3d([tmid[1] - trange_geo, tmid[1] + trange_geo])
tticks = np.around(np.linspace(tmid[1] - trange_geo, tmid[1] + trange_geo, 21),
                   decimals=2)[1::6]
axorin.set_yticks(tticks)
axorin.set_yticklabels(tticks)
axorin.set_zlim3d([tmid[2] - trange_geo, tmid[2] + trange_geo])
tticks = np.around(np.linspace(tmid[2] - trange_geo, tmid[2] + trange_geo, 21),
                   decimals=2)[1::6]
axorin.set_zticks(tticks)
axorin.set_zticklabels(tticks)
extFlow(axorin, trange_geo=trange_geo, **problem_kwargs)
# for tnodei in tnodes:
#     axorin.plot(tnodei[:, 0], tnodei[:, 1], tnodei[:, 2], 'dimgray')

# Jeffery sphere
u, v = np.mgrid[0:2*np.pi:100j, 0:np.pi:100j]
tr = np.linalg.norm(tnode, axis=-1).max()
x = np.cos(u) * np.sin(v) * tr
y = np.sin(u) * np.sin(v) * tr
z = np.cos(v) * tr
color1 = plt.get_cmap('gray')(np.linspace(0.2, 0.8, 256))
cmap = mcolors.LinearSegmentedColormap.from_list('my_colormap', color1)
axi.plot_surface(x, y, z, rstride=1, cstride=1, cmap=cmap, edgecolor='none', alpha=0.1)
# axi.plot(Table_P[tidx, 0] * tr, Table_P[tidx, 1] * tr, Table_P[tidx, 2] * tr, 'k', linewidth=3)
spf.colorline3d(Table_P[tidx] * tr, Table_t[tidx], show_project=show_project, ax0=axi, 
                tcl_lim=(tmin, tmax), tcl_fontsize=fontsize)
axi.scatter(Table_P[tidx, 0][0] * tr, Table_P[tidx, 1][0] * tr, Table_P[tidx, 2][0] * tr, 
            c='k', marker='s')
# clb = fig.axes[1]
# ticks = np.linspace(tmin, tmax, 5)
# clb.set_ticks(ticks)
# clb.ax.set_yticklabels(ticks, fontsize=30)
    
axi.set_xticklabels([])
axi.set_yticklabels([])
axi.set_zticklabels([])
axi.set_xlabel('$X_1$', fontsize=fontsize, labelpad=-5)
axi.set_ylabel('$X_2$', fontsize=fontsize, labelpad=-5)
axi.set_zlabel('$X_3$', fontsize=fontsize, labelpad=-5)

and the following is the output figure