Develop Reference

How to relate size parameter of .scatter() with radius?

I want to draw some circles using `ax3.scatter(x1, y1, s=r1 , facecolors='none', edgecolors='r'), where:
x1 and y1 are the coordinates of these circles
r1 is the radius of these circles
I thought typing s = r1 I would get the correct radius, but that's not the case.
How can I fix this?

If you change the value of 'r' (now 5) to your desired radius, it works. This is adapted from the matplotlib.org website, "Scatter Plots With a Legend". Should be scatter plots with attitude!
import numpy as np
import matplotlib.pyplot as plt
np.random.seed(19680801)
fig, ax = plt.subplots()
for color in ['tab:blue', 'tab:orange', 'tab:green']:
r = 5 #radius
n = 750 #number of circles
x, y = np.random.rand(2, n)
#scale = 200.0 * np.random.rand(n)
scale = 3.14159 * r**2 #CHANGE r
ax.scatter(x, y, c=color, s=scale, label=color,
alpha=0.3, edgecolors='none')
ax.legend()
ax.grid(True)
plt.show()

Make 3D triangle lines more visible in pyplot

I'd like to make a triangle plot in matplotlib with a mostly-transparent surface. I'm running the example code at https://matplotlib.org/mpl_examples/mplot3d/trisurf3d_demo.py:
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np
n_radii = 8
n_angles = 36
# Make radii and angles spaces (radius r=0 omitted to eliminate duplication).
radii = np.linspace(0.125, 1.0, n_radii)
angles = np.linspace(0, 2*np.pi, n_angles, endpoint=False)
# Repeat all angles for each radius.
angles = np.repeat(angles[..., np.newaxis], n_radii, axis=1)
# Convert polar (radii, angles) coords to cartesian (x, y) coords.
# (0, 0) is manually added at this stage, so there will be no duplicate
# points in the (x, y) plane.
x = np.append(0, (radii*np.cos(angles)).flatten())
y = np.append(0, (radii*np.sin(angles)).flatten())
# Compute z to make the pringle surface.
z = np.sin(-x*y)
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.plot_trisurf(x, y, z, linewidth=0.2, antialiased=True)
plt.show()
I can set
ax.plot_trisurf(x, y, z, linewidth=0.2, alpha = 0.2, antialiased=True)
to set the opacity to 0.2, but then the lines disappear. Furthermore, when I change the linewidth, even without the alpha, I see no change in the thickness of the lines between the points. How can I have a triangle plot where the faces are mostly transparent and the lines are clearly visible?

How to order ax.scatter and ax.quiver in Python 3D plot?

I want to draw a spin systems. I have the picture below. However, I want the quivers to be INSIDE the scatter circles and the "Main arrow" to be a bright one. Thus, how can I order three plots?
Thank You in advance!
Here is the code:
import matplotlib.pyplot as plt
from matplotlib import cm, colors
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
############################## A sphere #################################
r = 4
pi = np.pi
cos = np.cos
sin = np.sin
phi, theta = np.mgrid[0.0:pi:100j, 0.0:2.0*pi:100j]
x = r*sin(phi)*cos(theta)
y = r*sin(phi)*sin(theta)
z = r*cos(phi)
#Set colours and render
fig = plt.figure(figsize=(10,10))
ax = fig.add_subplot(111, projection='3d')
ax.plot_surface(x, y, z, rstride=1, cstride=1, color='red', alpha=0.6, linewidth=0)
############################ One arrow ########################
x1 = 0
y1 = 0
z1 = 0
dx1 = 0
dy1 = 0
dz1 = 2
ax.quiver(x1, y1, z1, dx1, dy1, dz1, pivot='middle', color="blue", linewidths=5.0,length=1.4)
ax.scatter(0, 0, 0,color="blue", s=800)
############################ Array of arrows ############################################
ax.set_xlim([-4,4])
ax.set_ylim([-4,4])
ax.set_zlim([-4,4])
ax.set_aspect("equal")
plt.tight_layout()
N = 5 # number of points - 5x5x5
scale = 0.4 # scale for the increment of an arrow
ax = fig.gca(projection='3d')
xx = np.linspace(-3.5, 3.5, N)
yy = np.linspace(-3.5, 3.5, N)
zz = np.linspace(-3.5, 3.5, N)
dxx = scale*np.random.rand(N)
dyy = scale*np.random.rand(N)
dzz = scale*np.random.rand(N)
x, y, z = np.meshgrid(yy, zz, xx)
dx, dy, dz = np.meshgrid(dxx, dyy, dzz)
ax.scatter(x, y, z,color="orange", s=200)
ax.quiver(x, y, z, dx, dy, dz, pivot='middle', length=1.6, color="blue")
plt.show()

fix graphic isometric figure

I Have the following code taken from Here, in this code a figure of height two is generated by two cubes (upper and bottom), I want generate the figure of height two by a only one figure, likewise the figure of height 3,4,5,...
import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import matplotlib.pyplot as plt
def cuboid_data(center, N, size=(1,1,1)):
# code taken from
# https://stackoverflow.com/questions/30715083/python-plotting-a-wireframe-3d-cuboid?noredirect=1&lq=1
# suppose axis direction: x: to left; y: to inside; z: to upper
# get the (left, outside, bottom) point
o = [a - b / 2 for a, b in zip(center, size)]
l, w, h = size
x = [[o[0], o[0] + l, o[0] + l, o[0], o[0]], # x coordinate of points in bottom surface
[o[0], o[0] + l, o[0] + l, o[0], o[0]], # x coordinate of points in upper surface
[o[0], o[0] + l, o[0] + l, o[0], o[0]], # x coordinate of points in outside surface
[o[0], o[0] + l, o[0] + l, o[0], o[0]]] # x coordinate of points in inside surface
y = [[o[1], o[1], o[1] + w, o[1] + w, o[1]], # y coordinate of points in bottom surface
[o[1], o[1], o[1] + w, o[1] + w, o[1]], # y coordinate of points in upper surface
[o[1], o[1], o[1], o[1], o[1]], # y coordinate of points in outside surface
[o[1] + w, o[1] + w, o[1] + w, o[1] + w, o[1] + w]] # y coordinate of points in inside surface
z = [[0,0,0,0,0],
[N,N,N,N,N],
[0, 0, N,N, 0],
[0, 0, N, N, 0]]
return x, y, z
def plotCubeAt(pos=(0,0), N=0, ax=None):
# Plotting N cube elements at position pos
if ax !=None:
if N > 0:
#for n in range(N):
X, Y, Z = cuboid_data( (pos[0],pos[1],N),N )
ax.plot_surface(X, Y, Z, color='y', rstride=1, cstride=1)#,linewidth=0)
def plotIsoMatrix(ax, matrix):
# plot a Matrix
# where matrix[i,j] cubes are added at position (i,j)
for i in range(matrix.shape[0]):
for j in range(matrix.shape[1]):
plotCubeAt(pos=(i,j), N=matrix[i,j], ax=ax)
l = max(matrix.shape[0], matrix.shape[1], matrix.max())
#bb = np.array([(0,0,0), (0,l,0), (l,0,0), (l,l,0),(0,0,l), (0,l,l), (l,0,l), (l,l,l)])
#ax.plot(bb[:,0], bb[:,1], bb[:,2], "w", alpha=0.0)
if __name__ == '__main__':
fig = plt.figure()
ax = fig.gca(projection='3d')
#ax.set_aspect('equal')
matrix = np.array([[2,2],[1,2]])
plotIsoMatrix(ax, matrix)
#ax.set_axis_off()
plt.ion()
plt.show()
This generate the following figure:
I want to generate the following figure:
How fix this ?
Thanks

Solution usiing matplotlib
First of all, if you do not want to have single cubes, but cuboids, there is a much simpler solution - using matplotlib bar3d.
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.set_aspect('equal')
matrix = np.array([[2,2],[1,2]])
xpos, ypos = np.meshgrid(np.arange(matrix.shape[0]),np.arange(matrix.shape[1]) )
xpos = xpos.flatten('F')
ypos = ypos.flatten('F')
zpos = np.zeros_like(xpos)
dx = np.ones_like(zpos)
dy = dx.copy()
dz = matrix.flatten()
ax.bar3d(xpos, ypos, zpos, dx, dy, dz, color='y', zsort='average', linewidth=0)
l = max(matrix.shape[0], matrix.shape[1], matrix.max())
bb = np.array([(0,0,0), (0,l,0), (l,0,0), (l,l,0),(0,0,l), (0,l,l), (l,0,l), (l,l,l)])
ax.plot(bb[:,0], bb[:,1], bb[:,2], "w", alpha=0.0)
ax.set_axis_off()
plt.show()
Concerning the overlapping faces of the cuboids, there is no solution in matplotlib. I think this behaviour is commonly considered to be an unresolvable bug, as is also described in the Matplotlib 3D FAQ. Also, manually setting zorder will not work. The good news is, however, that this overlapping is angle dependent. So you will always find a viewing angle (rotate the plot with the mouse) where it looks good.
Solution using mayavi
Using Mayavi, one does not have the problem of overlapping faces at all. Also the barchart in mayavi is much more convenient, making this only 5 lines of code:
import numpy as np
import mayavi.mlab as mlab
mlab.figure(bgcolor=(1,1,1))
matrix = np.array([[2,2],[1,2]])
mlab.barchart(matrix, color=(1.,0.86, 0.12), lateral_scale=1.0)
mlab.show()

How do you create a 3D surface plot with missing values matplotlib?

I am trying to create a 3D surface energy diagram where an x,y position on a grid contains an associated z level. The issue is that the grid is not uniform (ie, there is not a z component for every x,y position). Is there a way to refrain from plotting those values by calling them NaN in the corresponding position in the array?
Here is what I have tried so far:
import numpy as np
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import pylab
from matplotlib import cm
#Z levels
energ = np.array([0,3.5,1,-0.3,-1.5,-2,-3.4,-4.8])
#function for getting x,y associated z values?
def fun(x,y,array):
return array[x]
#arrays for grid
x = np.arange(0,7,0.5)
y = np.arange(0,7,0.5)
#create grid
X, Y = np.meshgrid(x,y)
zs = np.array([fun(x,y,energ) for x in zip(np.ravel(X))])
Z = zs.reshape(X.shape)
plt3d = plt.figure().gca(projection='3d')
#gradients now with respect to x and y, but ideally with respect to z only
Gx, Gz = np.gradient(X * Y)
G = (Gx ** 2 + Gz ** 2) ** .5 # gradient magnitude
N = G / G.max() # normalize 0..1
plt3d.plot_surface(X, Y, Z, rstride=1, cstride=1,
facecolors=cm.jet(N), edgecolor='k', linewidth=0, antialiased=False, shade=False)
plt.show()
I cannot post image here of this plot but if you run the code you will see it
But I would like to not plot certain x,y pairs, so the figure should triangle downward to the minimum. Can this be accomplished by using nan values? Also would like spacing between each level, to be connected by lines.
n = np.NAN
#energ represents the z levels, so the overall figure should look like a triangle.
energ = np.array([[0,0,0,0,0,0,0,0,0,0,0,0,0],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,2.6,n,2.97,n,2.6,n,2.97,n,2.6,n,3.58,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,1.09,n,1.23,n,1.09,n,1.23,n,1.7,n,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,-0.65,n,-0.28,n,-0.65,n,0.33,n,n,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,n,-2.16,n,-2.02,n,-1.55,n,n,n,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,n,n,-3.9,n,-2.92,n,n,n,n,n,],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,n,n,n,-4.8,n,n,n,n,n,n,]])
plt3d = plt.figure().gca(projection='3d')
Gx, Gz = np.gradient(X * energ) # gradients with respect to x and z
G = (Gx ** 2 + Gz ** 2) ** .5 # gradient magnitude
N = G / G.max() # normalize 0..1
x = np.arange(0,13,1)
y = np.arange(0,13,1)
X, Y = np.meshgrid(x,y)
#but the shapes don't seem to match up
plt3d.plot_surface(X, Y, energ, rstride=1, cstride=1,
facecolors=cm.jet(N), edgecolor='k',
linewidth=0, antialiased=False, shade=False
)
Using masked arrays generates the following error: local Python[7155] : void CGPathCloseSubpath(CGMutablePathRef): no current point.
n = np.NAN
energ = np.array([[0,0,0,0,0,0,0,0,0,0,0,0,0],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,2.6,n,2.97,n,2.6,n,2.97,n,2.6,n,3.58,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,1.09,n,1.23,n,1.09,n,1.23,n,1.7,n,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,-0.65,n,-0.28,n,-0.65,n,0.33,n,n,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,n,-2.16,n,-2.02,n,-1.55,n,n,n,n],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,n,n,-3.9,n,-2.92,n,n,n,n,n,],[n,n,n,n,n,n,n,n,n,n,n,n,n],[n,n,n,n,n,n,-4.8,n,n,n,n,n,n,]])
x = np.arange(0,13,1)
y = np.arange(0,13,1)
X, Y = np.meshgrid(x,y)
#create masked arrays
mX = ma.masked_array(X, mask=[[0,0,0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,0,1,0,1,0,1,0,1,0,1,0,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,0,1,0,1,0,1,0,1,0,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,0,1,0,1,0,1,0,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,0,1,0,1,0,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,0,1,0,1,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,1,0,1,1,1,1,1,1]])
mY = ma.masked_array(Y, mask=[[0,0,0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,0,1,0,1,0,1,0,1,0,1,0,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,0,1,0,1,0,1,0,1,0,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,0,1,0,1,0,1,0,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,0,1,0,1,0,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,0,1,0,1,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,1,0,1,1,1,1,1,1]])
m_energ = ma.masked_array(energ, mask=[[0,0,0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,0,1,0,1,0,1,0,1,0,1,0,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,0,1,0,1,0,1,0,1,0,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,0,1,0,1,0,1,0,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,0,1,0,1,0,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,0,1,0,1,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,1,0,1,1,1,1,1,1]])
plt3d = plt.figure().gca(projection='3d')
plt3d.plot_surface(mX, mY, m_energ, rstride=1, cstride=1, edgecolor='k', linewidth=0, antialiased=False, shade=False)
plt.show()

I was playing around with the code from this forum post, and I was able to make the graph have missing values. You can try the code yourself! I got it to work using float("nan") for the missing values.
import plotly.graph_objects as go
import numpy as np
x = np.arange(0.1,1.1,0.1)
y = np.linspace(-np.pi,np.pi,10)
#print(x)
#print(y)
X,Y = np.meshgrid(x,y)
#print(X)
#print(Y)
result = []
for i,j in zip(X,Y):
result.append(np.log(i)+np.sin(j))
result[0][0] = float("nan")
upper_bound = np.array(result)+1
lower_bound = np.array(result)-1
fig = go.Figure(data=[
go.Surface(z=result),
go.Surface(z=upper_bound, showscale=False, opacity=0.3,colorscale='purp'),
go.Surface(z=lower_bound, showscale=False, opacity=0.3,colorscale='purp')])
fig.show()