Related
This is a follow up to my question posted here. A network diagram is added as an inset in matplotlib figure.
import networkx as nx
import matplotlib.pyplot as plt
G = nx.gnm_random_graph(n=10, m=15, seed=1)
nxpos = nx.spring_layout(G, dim=3, seed=1)
nxpts = [nxpos[pt] for pt in sorted(nxpos)]
nx_lines = [(nxpts[i], nxpts[j]) for i, j in G.edges()]
# node values
values = [[1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[30, 80, 10, 79, 70, 60, 75, 78, 65, 10],
[1, .30, .10, .79, .70, .60, .75, .78, .65, .90]]
time = [0.0, 0.1, 0.2] # in seconds
fig, ax = plt.subplots()
ax.plot(
[1, 2, 3], [1, 2, 3],
'go-',
label='line 1',
linewidth=2
)
from mpl_toolkits.mplot3d import (Axes3D)
from matplotlib.transforms import Bbox
rect = [.6, 0, .5, .5]
bbox = Bbox.from_bounds(*rect)
inax = fig.add_axes(bbox, projection = '3d')
# inax.axis('off')
# set angle
angle = 25
inax.view_init(10, angle)
# hide axes, make transparent
# inax.set_facecolor('none')
inax.grid('off')
import numpy as np
# plot 3d
seen = set()
for i, j in G.edges():
x = np.stack((nxpos[i], nxpos[j]))
inax.plot(*x.T, color = 'k')
if i not in seen:
inax.scatter(*x[0], color = 'skyblue')
seen.add(i)
if j not in seen:
inax.scatter(*x[1], color = "skyblue")
seen.add(j)
fig.show()
I would like to change the grid properties i.e set the grid color to red and change line width. I tried inax.grid('on', color='r') but this doesn't change the color. Suggestions on how to change the settings will be really helpful.
You can do it like this:
inax.w_xaxis._axinfo.update({'grid' : {'color': 'red', 'linewidth': 0.8, 'linestyle': '-'}})
inax.w_yaxis._axinfo.update({'grid' : {'color': 'red', 'linewidth': 0.8, 'linestyle': '-'}})
inax.w_zaxis._axinfo.update({'grid' : {'color': 'red', 'linewidth': 0.8, 'linestyle': '-'}})
Output:
I've generated a network figure using vedo library and I'm trying to add this as an inset to a figure generated in matplotlib
import networkx as nx
import matplotlib.pyplot as plt
from vedo import *
from matplotlib.offsetbox import OffsetImage, AnnotationBbox
G = nx.gnm_random_graph(n=10, m=15, seed=1)
nxpos = nx.spring_layout(G, dim=3, seed=1)
nxpts = [nxpos[pt] for pt in sorted(nxpos)]
nx_lines = [(nxpts[i], nxpts[j]) for i, j in G.edges()]
pts = Points(nxpts, r=12)
edg = Lines(nx_lines).lw(2)
# node values
values = [[1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[30, 80, 10, 79, 70, 60, 75, 78, 65, 10],
[1, .30, .10, .79, .70, .60, .75, .78, .65, .90]]
time = [0.0, 0.1, 0.2] # in seconds
vplt = Plotter(N=1)
pts1 = pts.cmap('Blues', values[0])
vplt.show(
pts1, edg,
axes=False,
bg='white',
at=0,
interactive=False,
zoom=1.5
).screenshot("network.png")
ax = plt.subplot(111)
ax.plot(
[1, 2, 3], [1, 2, 3],
'go-',
label='line 1',
linewidth=2
)
arr_img = vplt.screenshot(returnNumpy=True, scale=1)
im = OffsetImage(arr_img, zoom=0.25)
ab = AnnotationBbox(im, (1, 0), xycoords='axes fraction', box_alignment=(1.1, -0.1), frameon=False)
ax.add_artist(ab)
plt.show()
ax.figure.savefig(
"output.svg",
transparent=True,
dpi=600,
bbox_inches="tight"
)
There resolution of the image in the inset is too low. Suggestions on how to add the inset without loss of resolution will be really helpful.
EDIT:
The answer posted below works for adding a 2D network, but I am still looking for ways that will be useful for adding a 3D network in the inset.
I am not familiar with vedo but the general procedure would be to create an inset_axis and plot the image with imshow. However, your code is using networkx which has matplotlib bindings and you can directly do this without vedo
EDIT: code edited for 3d plotting
import networkx as nx
import matplotlib.pyplot as plt
G = nx.gnm_random_graph(n=10, m=15, seed=1)
nxpos = nx.spring_layout(G, dim=3, seed=1)
nxpts = [nxpos[pt] for pt in sorted(nxpos)]
nx_lines = [(nxpts[i], nxpts[j]) for i, j in G.edges()]
# node values
values = [[1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[30, 80, 10, 79, 70, 60, 75, 78, 65, 10],
[1, .30, .10, .79, .70, .60, .75, .78, .65, .90]]
time = [0.0, 0.1, 0.2] # in seconds
fig, ax = plt.subplots()
ax.plot(
[1, 2, 3], [1, 2, 3],
'go-',
label='line 1',
linewidth=2
)
from mpl_toolkits.mplot3d import (Axes3D)
from matplotlib.transforms import Bbox
rect = [.6, 0, .5, .5]
bbox = Bbox.from_bounds(*rect)
inax = fig.add_axes(bbox, projection = '3d')
# inax = add_inset_axes(,
# ax_target = ax,
# fig = fig, projection = '3d')
# inax.axis('off')
# set angle
angle = 25
inax.view_init(10, angle)
# hide axes, make transparent
# inax.set_facecolor('none')
# inax.grid('off')
import numpy as np
# plot 3d
seen = set()
for i, j in G.edges():
x = np.stack((nxpos[i], nxpos[j]))
inax.plot(*x.T, color = 'k')
if i not in seen:
inax.scatter(*x[0], color = 'skyblue')
seen.add(i)
if j not in seen:
inax.scatter(*x[1], color = "skyblue")
seen.add(j)
fig.show()
I have a code for plotting a cone with some text and arrows like axes. How to change this code to get the bases of the cone looking like circles? Is the problem in the settings of margins? Or is it necessary to define circles in another way?
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits import mplot3d
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import proj3d
class Arrow3D(FancyArrowPatch):
def __init__(self, xs, ys, zs, *args, **kwargs):
FancyArrowPatch.__init__(self, (0, 0), (0, 0), *args, **kwargs)
self._verts3d = xs, ys, zs
def draw(self, renderer):
xs3d, ys3d, zs3d = self._verts3d
xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
self.set_positions((xs[0], ys[0]), (xs[1], ys[1]))
FancyArrowPatch.draw(self, renderer)
nn = 400 # number of points along circle's perimeter
theta = np.linspace(0, 2*np.pi, nn)
rho = np.ones(nn)
# (x,y) represents points on circle's perimeter
x = np.ravel(rho*np.cos(theta))
y = np.ravel(rho*np.sin(theta))
fig, ax = plt.subplots()
plt.rcParams["figure.figsize"] = [5, 5]
figsize = (5, 5)
ax = plt.axes(projection='3d') # set the axes for 3D plot
ax.azim = -88 # y rotation (default=270)
ax.elev = 13 # x rotation (default=0)
# Low, high values of z for plotting 2 circles at different elevation
loz, hiz = -15, 15
# Plot two circles
ax.plot(x, y, hiz)
ax.plot(x, y, loz)
# Set some indices to get proper (x,y) for line plotting
lo1,hi1 = 15, 15+nn//2
lo2,hi2 = lo1+nn//2-27, hi1-nn//2-27
# Plot 3d lines using coordinates of selected points
ax.plot([x[lo1], x[hi1]], [y[lo1], y[hi1]], [loz, hiz])
ax.plot([x[lo2], x[hi2]], [y[lo2], y[hi2]], [loz, hiz])
eps = 0.005
ax.plot([0, 0], [0, 0], [0, 20]) # extend in z direction
ax.plot([0-eps, 0], [0-eps, -5], [0-eps, 0]) # extend in y direction
ax.plot([0, 1.3], [0, 0], [0, 0]) # extend in x direction
ax.plot([0+eps, 0.6], [0+eps, -4], [0+eps, 16]) # v vector
ax.plot([0.63, 0.63], [-4, -4], [16, -0.005]) # vertical projection
ax.plot([0+eps, 0.6], [0+eps, -4], [0+eps, -0.005]) # to the beginning
ax.scatter(0, 0, 20, marker=(3, 0, 0), s=100, clip_on=False)
ax.scatter(0, -5, 0, marker=(3, 0, 43), s=100, clip_on=False)
ax.scatter(1.3, 0, 0, marker=(3, 0, 30), s=100, clip_on=False)
ax.scatter(0.6, -4, 16, marker=(3, 0, 80), s=100, clip_on=False)
ax.scatter(0.6, -4, -0.005, marker=(3, 0, 0), s=100, clip_on=False)
a2 = Arrow3D([0.14, -0.515], [-5.581, 1.358], [14.73, 4.983], mutation_scale=20, arrowstyle="-|>", color="k", connectionstyle="arc3,rad=0.3")
ax.add_artist(a2)
ax.text3D(0.23, -5.23, 23.33, r'$A$')
ax.text3D(1.41, 1.29, -2.7, r'$B$')
ax.text3D(-0.31, 1.46, -12.6, r'$C$')
ax.text3D(0.4, -5.48, 17, r'$D$')
ax.text3D(0.64, 1.57, -9.95, r'$E$')
ax.text3D(-0.2, -5.5, 15.73, r'$F$')
# Hide axes
ax._axis3don = False
# Save the figure (.pdf)
margins = { # vvv margin in inches
"left" : 1 / figsize[0],
"bottom" : -2.45 / figsize[1],
"right" : 1 - 0.5 / figsize[0],
"top" : 1 + 1.8 / figsize[1]
}
fig.subplots_adjust(**margins)
plt.savefig('output.pdf')
plt.show()
From this code I got the following output:
The desired output is bases looking like a circle.
This is the view from above:
It is not a circle but an ellipse.
Desired shape of the cone:
I have the following script:
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits import mplot3d
nn = 400 # number of points along circle's perimeter
theta = np.linspace(0, 2*np.pi, nn)
rho = np.ones(nn)
# (x,y) represents points on circle's perimeter
x = np.ravel(rho*np.cos(theta))
y = np.ravel(rho*np.sin(theta))
fig, ax = plt.subplots()
plt.rcParams["figure.figsize"] = [6, 10]
ax = plt.axes(projection='3d') # set the axes for 3D plot
ax.azim = -90 # y rotation (default=270)
ax.elev = 21 # x rotation (default=0)
# low, high values of z for plotting 2 circles at different elev.
loz, hiz = -15, 15
# Plot two circles
ax.plot(x, y, hiz)
ax.plot(x, y, loz)
# set some indices to get proper (x,y) for line plotting
lo1,hi1 = 15, 15+nn//2
lo2,hi2 = lo1+nn//2-27, hi1-nn//2-27
# plot 3d lines using coordinates of selected points
ax.plot([x[lo1], x[hi1]], [y[lo1], y[hi1]], [loz, hiz])
ax.plot([x[lo2], x[hi2]], [y[lo2], y[hi2]], [loz, hiz])
ax.plot([0, 0, 0], [0, 0, 10])
ax.plot([0, 0, 0], [9, 0, 0])
ax.plot([0, 0, 0], [0, 8, 0])
plt.show()
At the end of the script, I would like to plot three lines in three directions. How to do that? Why this:
ax.plot([0, 0, 0], [0, 0, 10])
ax.plot([0, 0, 0], [9, 0, 0])
ax.plot([0, 0, 0], [0, 8, 0])
gives the line in same direction?
And I have a second question, please. How to make the cone more narrower (the base more similar to circle)?
Output now:
ax.plot([0, 0, 0], [0, 0, 10]) is giving plot the x and y coordinates of 3 points, but you haven't given any coordinates in the z direction. Remember the inputs to plot are x, y, z, not, as you seem to have assumed, (x0,y0,z0), (x1,y1,z1)
So this is drawing 3 "lines" where two of them start and end at x=y=z=0, and one of them extends to y=10. The other two ax.plot calls you have are doing similar things.
To draw three lines that start at the origin and each extend along one of the x, y, or z directions, you perhaps meant to use:
ax.plot([0, 0], [0, 0], [0, 10]) # extend in z direction
ax.plot([0, 0], [0, 8], [0, 0]) # extend in y direction
ax.plot([0, 9], [0, 0], [0, 0]) # extend in x direction
Note that this also makes your circles look more like circles
After commenting the last 3 lines of your code, the image is the output I am getting
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits import mplot3d
nn = 400 # number of points along circle's perimeter
theta = np.linspace(0, 2*np.pi, nn)
rho = np.ones(nn)
# (x,y) represents points on circle's perimeter
x = np.ravel(rho*np.cos(theta))
y = np.ravel(rho*np.sin(theta))
fig, ax = plt.subplots()
plt.rcParams["figure.figsize"] = [6, 10]
ax = plt.axes(projection='3d') # set the axes for 3D plot
ax.azim = -90 # y rotation (default=270)
ax.elev = 21 # x rotation (default=0)
# low, high values of z for plotting 2 circles at different elev.
loz, hiz = -15, 15
# Plot two circles
ax.plot(x, y, hiz)
ax.plot(x, y, loz)
# set some indices to get proper (x,y) for line plotting
lo1,hi1 = 15, 15+nn//2
lo2,hi2 = lo1+nn//2-27, hi1-nn//2-27
# plot 3d lines using coordinates of selected points
ax.plot([x[lo1], x[hi1]], [y[lo1], y[hi1]], [loz, hiz])
ax.plot([x[lo2], x[hi2]], [y[lo2], y[hi2]], [loz, hiz])
#ax.plot([0, 0, 0], [0, 0, 10])
#ax.plot([0, 0, 0], [9, 0, 0])
#ax.plot([0, 0, 0], [0, 8, 0])
plt.show()
You can see that the base is almost a perfect circle. Because you are also plotting lines in your figure, it is giving an illusion that the base in not a circle.
And regarding the lines in 3 different directions. Since this part of code
ax.plot([0, 0, 0], [0, 0, 10])
ax.plot([0, 0, 0], [9, 0, 0])
ax.plot([0, 0, 0], [0, 8, 0])
has all zeroes in X-Axis, it is essentially plotting the lines on Y-Axis only.
When I give some values in the X-Axis part, like this
ax.plot([1, 0, 0], [0, 0, 10])
ax.plot([0, 0, 5], [9, 0, 0])
ax.plot([0, 8, 0], [0, 8, 0])
The output is
I hope this is what you were asking.
I would like to have names of axes as in the figure.
This could be a good starter. Try experiment with it.
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
fig = plt.figure(figsize=[8,8])
ax = fig.gca(projection = '3d')
# some settings
vleng = 4
aleng = vleng/3.
p = np.array([vleng, 0, 0])
q = np.array([0, vleng, 0])
r = np.array([0, 0, vleng])
ax.plot(*np.vstack([[0,0,0], p]).T, color='b')
ax.plot(*np.vstack([[0,0,0], q]).T, color='g')
ax.plot(*np.vstack([[0,0,0], r]).T, color='r')
# plotting arrow at terminal of the lines
ax.quiver(vleng, 0, 0, aleng, 0, 0, \
length=0.5, arrow_length_ratio=0.5, color='r')
ax.quiver(0, vleng, 0, 0, aleng, 0, \
length=0.5, arrow_length_ratio=0.5, color='m')
ax.quiver(0, 0, vleng, 0, 0, aleng, \
length=0.5, arrow_length_ratio=0.5, color='k')
ax.text3D(vleng+1.5, 0, 0, 'X')
ax.text3D(0, vleng+1.0, 0, 'y')
ax.text3D(0, 0, vleng+1.0, 'z')
ax.azim = 35 # y rotation (default=270)
ax.elev = 20 # x rotation (default=0)
ax.dist = 15 # zoom (define perspective)
ax.set_axis_off( ) # hide all grid
ax.set_aspect('equal')
# plot poly1
ax.plot3D( [3.5, 0.25, 2, 3.5], [1, 0.25, 2.5, 1], [1.9, 3.2, 3.8, 1.9], label = 'one line', color='pink' )
# projection of poly1 on xy-plane
ax.plot3D( [3.5, 0.25, 2, 3.5], [1, 0.25, 2.5, 1], [0, 0, 0, 0], label = 'one line', color='gray' )
#ax.legend()
plt.show()