3D graph in yt module

Question

could you help me with this code, please? I am trying to integrate the force line in the given point. I don't know where is a mistake - there is no streamline in the plot.

Data - dipole magnetic field are here

I tried this example with the change of data and the change of number of streamlines.

import numpy as np
import matplotlib.pyplot as plt
from numpy import array
import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D                 # 3d graph
from mpl_toolkits.mplot3d import proj3d                 # 3d graph
import math
from matplotlib import patches
import code
import yt
from yt import YTArray  # arrays in yt module
from yt.visualization.api import Streamlines  # force lines
import matplotlib.pylab as pl# Choose point in field
X_point = 0.007089085922957821
Y_point = 0.038439192046320805
Z_point = 0# Load data (dictionary)
try:
    import cPickle as pickle
except ImportError:  # python 3.x
    import picklewith open('data.p', 'rb') as fp:
    data = pickle.load(fp)Bx_d = data["Bx"]
By_d = data["By"]
Bz_d = data["Bz"]# 3d array of dipole magnetic field 
print(type(data))
bbox = np.array([[-0.15, 0.15], [0, 0.2], [-0.1, 0.1]]) # box, border
ds = yt.load_uniform_grid(data, Bx_d.shape, length_unit="Mpc", bbox=bbox, nprocs=100) # data, dimensionc = YTArray([X_point, Y_point, Z_point], 'm') # Define c: the center of the box, chosen point
c1 = ds.domain_center
print('c1', c1)
print(type(c1))
print('center',c)
N = 1 # N: the number of streamlines
scale = ds.domain_width[0] # scale: the spatial scale of the streamlines relative to the boxsize,
pos = c# Create streamlines of the 3D vector velocity and integrate them through
# the box defined above
streamlines = Streamlines(ds, pos, 'Bx', 'By', 'Bz', length=None) # length of integration
streamlines.integrate_through_volume()# Create a 3D plot, trace the streamlines through the 3D volume of the plot
fig=pl.figure()
ax = Axes3D(fig)
ax.scatter(X_point, Y_point, Z_point, marker = 'o', s=40, c='green')
print('tisk', streamlines.streamlines)for stream in streamlines.streamlines:
    stream = stream[np.all(stream != 0.0, axis=1)]
    ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1)# Save the plot to disk.
pl.savefig('streamlines.png')
plt.show()

Output:

Answer 1

Without knowing more about the data, as well as what the output of the print call is, it's not entirely clear what the error is. If the streamlines have meaningful values (i.e., the values of stream[:,0] etc are within the bounds of your Axes3D, it should produce results.

Options for debugging would start with examining the individual values, then proceeding to plotting them in 2D (using pairs of components of each stream -- (0,1), (1,2) and (0,2)), and then examining what happens if you allow Axes3D to autoscale the xyz axes. You may also experiment with the alpha value, to see if the lines are simply too light to see.

An example image that this produces would also help, so that it can be made clear a few things about the properties matplotlib assigns to the Axes3D object.