In order to create a 3d plot using plot_surface and wireframe I wrote this (looking here around)
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from matplotlib import rc
from matplotlib.ticker import MultipleLocator
import matplotlib.ticker as mticker
import numpy as np
from matplotlib.ticker import FormatStrFormatter
def log_tick_formatter(val, pos=None):
return f"10$^{{{int(val)}}}$"
data=np.genfromtxt('jpdfomegal2_90.dat')
x_len= len(np.unique(data[:, 0]))
y_len= len(np.unique(data[:, 1]))
X = data[:, 0].reshape(x_len, y_len)
Y = data[:, 1].reshape(x_len, y_len)
Z = data[:, 2].reshape(x_len, y_len)
#identify lowest non-negative Z value Zmin>0
Zmin = np.where(Z > 0, Z, np.inf).min()
Zmax = Z.max()
#and substitute zero with a slightly lower value than Zmin
Z[Z==0] = 0.9 * Zmin
#log transformation because the conversion in 3D
#does not work well in matplotlib
Zlog = np.log10(Z)
rc('font',family='palatino')
rc('font',size=18)
fig = plt.figure(figsize=(12,8))
#ax = fig.add_subplot(projection='3d')
ax = Axes3D(fig)
ax.set_xlim3d(0,15)
ax.set_zlim3d(np.floor(np.log10(Zmin))-1, np.ceil(np.log10(10)))
ax.zaxis.set_major_formatter(mticker.FuncFormatter(log_tick_formatter))
ax.zaxis.set_major_locator(mticker.MaxNLocator(integer=True))
rc('font',family='palatino')
rc('font',size=18)
tmp_planes = ax.zaxis._PLANES
ax.zaxis._PLANES = ( tmp_planes[2], tmp_planes[3],
tmp_planes[0], tmp_planes[1],
tmp_planes[4], tmp_planes[5])
ax.set_xlabel('$\omega^2 /<\omega^2>$')
ax.xaxis.labelpad = 10
ax.yaxis.labelpad = 10
ax.set_ylabel('cos$(\omega,\lambda^2)$')
ax.zaxis.set_rotate_label(False) # disable automatic rotation
ax.zaxis.labelpad = 10
ax.set_zlabel('')
ax.view_init(elev=17, azim=-60)
ax.grid(False)
ax.xaxis.pane.set_edgecolor('black')
ax.yaxis.pane.set_edgecolor('black')
ax.zaxis.pane.set_edgecolor('black')
ax.xaxis.pane.fill = False
ax.yaxis.pane.fill = False
ax.zaxis.pane.fill = False
ax.xaxis.set_major_locator(MultipleLocator(2))
ax.yaxis.set_major_locator(MultipleLocator(0.2))
ax.zaxis.set_major_locator(MultipleLocator(1))
#not sure this axis scaling routine is really necessary
scale_x = 1
scale_y = 1
scale_z = 0.8
ax.get_proj = lambda: np.dot(Axes3D.get_proj(ax), np.diag([scale_x, scale_y, scale_z, 1]))
ax.contour(X, Y, np.log10(Z), 4, lw=0.1, colors="k", linestyles="--", offset=np.floor(np.log10(Zmin))-1)#-7)
surf = ax.plot_surface(X, Y, np.log10(Z), cmap="binary", lw=0.1,alpha=0.5)
ax.plot_wireframe(X, Y, np.log10(Z),linewidth=1,color='k')
ax.contour(X, Y, np.log10(Z), 4, lw=0.1, colors="k", linestyles="solid")
fig.colorbar(surf, shrink=0.5, aspect=20)
plt.tight_layout()
plt.savefig('jpdf_lambda2_90.png', bbox_inches='tight')
plt.show()
the problem is related to the "minorticks" along zaxis .. I obtain this :
but I would have this format and ticks in the axis
Does somebody clarify how to obtain it and as well I did not find a way to use the log scale in pyplot 3d
There's an open bug on log-scaling in 3D plots, and it looks like there won't be a fix any time soon.
You can use a matplotlib.ticker.FixedLocator to add the z-axis minor ticks, as shown below.
I didn't have your data, so I've plotted an arbitrary surface.
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from matplotlib import rc
from matplotlib.ticker import MultipleLocator, FixedLocator
import matplotlib.ticker as mticker
import numpy as np
from matplotlib.ticker import FormatStrFormatter
def log_tick_formatter(val, pos=None):
return f"10$^{{{int(val)}}}$"
x = np.linspace(1,15,15)
y = np.linspace(0,1,15)
X, Y = np.meshgrid(x, y)
Z = 1 + X**2 * Y**2
#identify lowest non-negative Z value Zmin>0
Zmin = np.where(Z > 0, Z, np.inf).min()
Zmax = Z.max()
#and substitute zero with a slightly lower value than Zmin
Z[Z==0] = 0.9 * Zmin
rc('font',family='palatino')
rc('font',size=18)
fig = plt.figure(figsize=(12,8))
ax = Axes3D(fig, auto_add_to_figure=False)
fig.add_axes(ax)
ax.set_xlim3d(0,15)
ax.set_zlim3d(np.floor(np.log10(Zmin))-1, np.ceil(np.log10(Zmax)))
ax.zaxis.set_major_formatter(mticker.FuncFormatter(log_tick_formatter))
tmp_planes = ax.zaxis._PLANES
ax.zaxis._PLANES = ( tmp_planes[2], tmp_planes[3],
tmp_planes[0], tmp_planes[1],
tmp_planes[4], tmp_planes[5])
ax.set_xlabel('$\omega^2 /<\omega^2>$')
ax.xaxis.labelpad = 10
ax.yaxis.labelpad = 10
ax.set_ylabel('cos$(\omega,\lambda^2)$')
ax.zaxis.set_rotate_label(False) # disable automatic rotation
ax.zaxis.labelpad = 10
ax.set_zlabel('')
ax.view_init(elev=17, azim=-60)
ax.grid(False)
ax.xaxis.pane.set_edgecolor('black')
ax.yaxis.pane.set_edgecolor('black')
ax.zaxis.pane.set_edgecolor('black')
ax.xaxis.pane.fill = False
ax.yaxis.pane.fill = False
ax.zaxis.pane.fill = False
ax.xaxis.set_major_locator(MultipleLocator(2))
ax.yaxis.set_major_locator(MultipleLocator(0.2))
ax.zaxis.set_major_locator(MultipleLocator(1))
# Z minor ticks
zminorticks = []
zaxmin, zaxmax = ax.get_zlim()
for zorder in np.arange(np.floor(zaxmin),
np.ceil(zaxmax)):
zminorticks.extend(np.log10(np.linspace(2,9,8)) + zorder)
ax.zaxis.set_minor_locator(FixedLocator(zminorticks))
#not sure this axis scaling routine is really necessary
scale_x = 1
scale_y = 1
scale_z = 0.8
ax.get_proj = lambda: np.dot(Axes3D.get_proj(ax), np.diag([scale_x, scale_y, scale_z, 1]))
ax.contour(X, Y, np.log10(Z), 4, colors="k", linestyles="--", offset=np.floor(np.log10(Zmin))-1)#-7)
surf = ax.plot_surface(X, Y, np.log10(Z), cmap="binary", lw=0.1,alpha=0.5)
ax.plot_wireframe(X, Y, np.log10(Z),linewidth=1,color='k')
ax.contour(X, Y, np.log10(Z), 4, colors="k", linestyles="solid")
fig.colorbar(surf, shrink=0.5, aspect=20)
# get a warning that Axes3D is incompatible with tight_layout()
# plt.tight_layout()
# for saving
# fig.savefig('log3d.png')
plt.show()
Related
I got some sort of a problem with a pendulum animation, I tried to display my animation (the pendulum's movement) next to a graph in two separate axes, but when I try my code, it barely works displaying two axes that overlap on one another... Here is what I tried:
PS: best would be that the circles I was intended to add at the end of my pendulum appear on the final animation, but I really have no idea how to put them only on a particular ax
from numpy import sin, cos, pi, array
import numpy as np
import scipy.integrate
import matplotlib.pyplot as plt
import matplotlib.animation as animation
g = 10
y0 = np.array([np.pi / 2.0, 0]) # angle, vitesse
j = 0.2
def f(y, t):
return np.array([y[1], -g * np.sin(y[0])-j*y[1]])
t = np.linspace(0, 100, 10000)
y = scipy.integrate.odeint(f, y0, t)
theta, thetadot = y[:, 0], y[:, 1]
fig, axs = plt.subplots(1,2)
axs[0] = fig.add_subplot(xlim=(-1.5, 1.5), ylim=(-1.5, 1.5))
axs[0].grid()
axs[0].set_box_aspect(1)
# anchor = plt.Circle((0, 0), 0.01, color='black')
# mass = plt.Circle((sin(y0[0]),-cos(y0[0])), 0.2, color='black')
pendulums = axs[0].plot((0, sin(y0[0])), (0, -cos(y0[0])), 'o-', color = 'black')
# plt.gca().add_patch(weight) # adding circles
# plt.gca().add_patch(attach)
phase = axs[1].plot(theta,thetadot)
def animate(i):
angle = theta[i]
x = (0, sin(angle))
y = (0, -cos(angle))
#mass.center = (x[1],y[1])
pendulums[0].set_data(x, y)
anim = animation.FuncAnimation(fig, animate, interval=10)
plt.show()
I am working with the following image:
from matplotlib import cbook
import matplotlib.patches as mpatches
from matplotlib.axes._base import _TransformedBoundsLocator
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import numpy as np
# a numpy array of 15x15
Z = cbook.get_sample_data("axes_grid/bivariate_normal.npy", np_load=True)
gs = GridSpec(2, 3)
fig = plt.figure(figsize=(3*3,2*3))
ax1 = fig.add_subplot(gs[:2, :2])
ax2 = fig.add_subplot(gs[1, 2])
Z2 = np.zeros((150, 150))
ny, nx = Z.shape
Z2[30:30+ny, 30:30+nx] = Z
ax1.imshow(Z2)
ax1.set_aspect("equal")
ax2.set_aspect("equal")
plt.tight_layout()
plt.show()
output:
As shown in the image, the x-axis of both plots are aligned. However, when I am adding a patch to the first plot the alignment becomes distorted:
Z = cbook.get_sample_data("axes_grid/bivariate_normal.npy", np_load=True)
gs = GridSpec(2, 3)
fig = plt.figure(figsize=(3*3,2*3))
ax1 = fig.add_subplot(gs[:2, :2])
ax2 = fig.add_subplot(gs[1, 2])
Z2 = np.zeros((150, 150))
ny, nx = Z.shape
Z2[30:30+ny, 30:30+nx] = Z
ax1.imshow(Z2)
x, y, width, height = 30, 30, 15, 15
ex, ey = (0,1)
xy_data = x + ex * width, y + ey * height
p = mpatches.ConnectionPatch(
xyA=(0,1), coordsA=ax2.transAxes,
xyB=xy_data, coordsB=ax1.transData)
ax1.add_patch(p)
ax1.set_aspect("equal")
ax2.set_aspect("equal")
plt.tight_layout()
plt.show()
output:
Why is this? How can I add a patch whilst retaining the original layout?
How to colour the base on y = 0.3 by the same color as the middle part of the cylinder have, please?
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d import proj3d
def data_for_cylinder_along_z(center_x,center_y,radius,height_z):
z = np.linspace(0, height_z, 200)
theta = np.linspace(0, 2*np.pi, 200)
theta_grid, z_grid=np.meshgrid(theta, z)
x_grid = radius*np.cos(theta_grid) + center_x
y_grid = radius*np.sin(theta_grid) + center_y
return x_grid,y_grid,z_grid
fig = plt.figure(figsize=[6,5])
ax = fig.add_subplot(111, projection='3d')
ax.azim = -39
ax.elev = 15
Xc,Zc,Yc = data_for_cylinder_along_z(0,0,0.05,0.3)
ax.plot_surface(Xc, Yc, Zc, alpha=0.4, color = 'grey')
plt.show()
import numpy as np
from matplotlib import pyplot as plt
data = np.random.normal(0,1,[100,3])
x = data[:,0]
y = data[:,1]
z = data[:,2]
plt.contour([x,y],z)
When I run this code with dummy data I get:
ValueError: Contour levels must be increasing
Do you have any idea what would this mean and how I could fix it?
plt.contour is a bit particular about its input, the z values must be on values on a rectangular 2D grid, see for example:
import matplotlib.pyplot as plt
import numpy as np
x = np.expand_dims(np.arange(1,11,1), axis=1)
y = np.expand_dims(np.arange(2,21,2), axis=0)
z = y * x
print(x.shape)
print(y.shape)
print(z.shape)
plt.figure()
plt.contour(z)
plt.show()
You can also provide x and y values for plt.contour by using np.meshgrid :
XX,YY = np.meshgrid(x,y)
plt.figure()
plt.contour(XX, YY, z)
plt.show()
If you have z-values with irregular values for x and y, you might use plt.tricontour, see the following example:
from matplotlib.tri import Triangulation
data = np.random.normal(0,1,[100,3])
x = data[:,0]
y = data[:,1]
#z = data[:,2]
z = x * y
tri = Triangulation(x,y)
plt.figure()
plt.tricontour(tri, z, )
plt.scatter(x,y, c=z)
plt.show()
Edit: from JohanC's comment i learned that this can be simplified without importing matplotlib.tri by:
plt.figure()
plt.tricontour(x,y,z)
plt.scatter(x,y, c=z)
plt.show()
I have a file 'mydata.tmp' which contains 3 colums like this:
3.81107 0.624698 0.000331622
3.86505 0.624698 0.000131237
3.91903 0.624698 5.15136e-05
3.97301 0.624698 1.93627e-05
1.32802 0.874721 1.59245
1.382 0.874721 1.542
1.43598 0.874721 1.572
1.48996 0.874721 4.27933
etc.
Then I want to make a heatmap color plot where the first two columns are coordinates, and the third column are the values of that coordinates.
Also, I would like to set the third column in log scale.
I have done this
import pandas as pd
import matplotlib.pyplot as plt
import scipy.interpolate
import numpy as np
import matplotlib.colors as colors
# import data
df = pd.read_csv('mydata.tmp', delim_whitespace=True,
comment='#',header=None,
names=['1','2','3'])
x = df['1']
y = df['2']
z = df['3']
spacing = 500
xi, yi = np.linspace(x.min(), x.max(), spacing), np.linspace(y.min(),
y.max(), spacing)
XI, YI = np.meshgrid(xi, yi)
rbf = scipy.interpolate.Rbf(x, y, z, function='linear')
ZI = rbf(XI, YI)
fig, ax = plt.subplots()
sc = ax.imshow(ZI, vmin=z.min(), vmax=z.max(), origin='lower',
extent=[x.min(), x.max(), y.min(),
y.max()], cmap="GnBu", norm=colors.LogNorm(vmin=ZI.min(),
vmax=ZI.max()))
fig.colorbar(sc, ax=ax, fraction=0.05, pad=0.01)
plt.show()
And I get this Image
which has all these empty pixels.
I am looking for something like this instead (I have done this other picture with GNUplot):
How can I do it?
You could use cmap.set_bad to define a color for the NaN values:
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import griddata
import matplotlib.colors as colors
from matplotlib import cm
import copy
# Some data
x = np.array([0, 1, 3, 0, 2, 4])
y = np.array([0, 0, 0, 1, 1, 1])
z = np.array([2, 2, 3, 2, 3, 4])
# Interpolation on a grid:
nrb_points = 101
xi = np.linspace(-.5, 4.5, nrb_points)
yi = np.linspace(-.5, 1.5, nrb_points)
XI, YI = np.meshgrid(xi, yi)
xy = np.vstack((x, y)).T
XY = (XI.ravel(), YI.ravel())
ZI = griddata(points, z, XY,
method='linear',
fill_value=np.nan) # Value used [for] points
# outside of the convex hull
# of the input points.
ZI = ZI.reshape(XI.shape)
# Color map:
cmap = copy.copy(cm.jet)
cmap.set_bad('grey', 1.)
# Graph:
plt.pcolormesh(xi, yi, ZI,
#norm=colors.LogNorm(),
cmap=cmap);
plt.colorbar(label='z');
plt.plot(x, y, 'ko');
plt.xlabel('x'); plt.ylabel('y');
the result is:
I would also use griddata instead of RBF method for the interpolation. Then, point outside the input data area (i.e. the convex hull) can be set to NaN.