adding 3D subplot to the set of 2D - python

I would like to add 3D plot in matplotlib 1.5.1 to the existing set of 2D plots (subplots). 2D plots work fine w/o 3D, but when I add 3D I'm getting an error that 'module' object has no attribute 'plot_surface'. I'd like to keep the code simple so I apply all commands to plt without creating new figure(there is also a way of adding labels with set_xlabel) which makes things ambiguous. The first 3 plots are simple 2D plots and the last is 3D.
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import axes3d
y1 = u.nodes.concentration
x1 = u.nodes.x
plt.figure(figsize=(20, 10))
plt.subplot(221)
plt.title('Profile')
plt.xlabel('Range')
plt.ylabel('Concentration')
plt.plot(x1, y1, '-b')
# Inhibitor plt
y2 = z.nodes.concentration
x2 = z.nodes.x
plt.subplot(222)
plt.title('Profile')
plt.xlabel('Range')
plt.ylabel('Concentration')
plt.plot(x2, y2, '-r')
# Modulator plt
y3 = v.nodes.concentration
x3 = v.nodes.x
plt.subplot(223)
plt.title('Profile')
plt.xlabel('Range')
plt.ylabel('Concentration')
plt.plot(x3, y3, '-g')
#3D plot
plt.subplot(224, projection='3d')
# Grab data.
xx = u_fft_x_norm
yy = [i*time_period for i in xrange(1, times)]
zz = u_timespace
XX, YY = np.meshgrid(xx, yy)
ZZ = zz
# Plot a basic wireframe.
plt.plot_surface(XX, YY, ZZ, rstride=20, cstride=20)
plt.xlabel('Space')
plt.ylabel('Time')
plt.zlabel('Value')
plt.title('Profile')

I guess the error is self-explanatory. pyplot does not have a plot_surface command. There is also no indication that it should. Looking at all examples you find, plot_surface is an attribute of an axes.
ax = plt.subplot(224, projection='3d')
ax.plot_surface(X, Y, Z, cmap=cm.coolwarm, linewidth=0, antialiased=False)

Related

3D wireframe plot with 2D projections: Spatial organiszation & frequency of projection

I'm working on a 3D plot displayed by a wireframe, where 2D plots are projected on the x, y, and z surface, respectively. Below you can find a minimum example.
I have 2 questions:
With contourf, the 2D plots for every x=10, x=20,... or y=10, y=20,... are displayed on the plot walls. Is there a possibility to define for which x or y, respectively, the contour plots are displayed? For example, in case I only want to have the xz contour plot for y = 0.5 mirrored on the wall?
ADDITION: To display what I mean with "2D plots", I changed "contourf" in the code to "contour" and added the resulting plot to this question. Here you can see now the xz lines for different y values, all offset to y=90. What if I do not want to have all the lines, but only two of them for defined y values?
3D_plot_with_2D_contours
As you can see in the minimum example, the 2D contour plot optically covers the wireframe 3D plot. With increasing the transparency with alpha=0.5 I can increase the transparency of the 2D contours to at least see the wireframe, but it is still optically wrong. Is it possible to sort the objects correctly?
import matplotlib.pyplot as plt,numpy as np
import pylab as pl
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt,numpy as np
plt.clf()
fig = plt.figure(1,figsize=(35,17),dpi=600,facecolor='w',edgecolor='k')
fig.set_size_inches(10.5,8)
ax = fig.gca(projection='3d')
X, Y, Z = axes3d.get_test_data(0.05)
Xnew = X + 50
Ynew = Y + 50
cset = ax.contourf(Xnew, Ynew, Z, zdir='z', offset=-100, cmap=plt.cm.coolwarm, alpha=0.5)
cset = ax.contourf(Xnew, Ynew, Z, zdir='x', offset=10, cmap=plt.cm.coolwarm, alpha=0.5)
cset = ax.contourf(Xnew, Ynew, Z, zdir='y', offset=90, cmap=plt.cm.coolwarm, alpha = 0.5)
ax.plot_wireframe(Xnew, Ynew, Z, rstride=5, cstride=5, color='black')
Z=Z-Z.min()
Z=Z/Z.max()
from scipy.ndimage.interpolation import zoom
Xall=zoom(Xnew,5)
Yall=zoom(Ynew,5)
Z=zoom(Z,5)
ax.set_xlim(10, 90)
ax.set_ylim(10, 90)
ax.set_zlim(-100, 100)
ax.tick_params(axis='z', which='major', pad=10)
ax.set_xlabel('X',labelpad=10)
ax.set_ylabel('Y',labelpad=10)
ax.set_zlabel('Z',labelpad=17)
ax.view_init(elev=35., azim=-70)
fig.tight_layout()
plt.show()
ADDITION 2: Here is the actual code I'm working with. However, the original data are hidden in the csv files which are too big to be included in the minimal example. That's why was initially replacing them by the test data. However, maybe the actual code helps nevertheless.
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt,numpy as np
import pylab as pl
from matplotlib.markers import MarkerStyle
import csv
with open("X.csv", 'r') as f:
X = list(csv.reader(f, delimiter=";"))
import numpy as np
X = np.array(X[1:], dtype=np.float)
import csv
with open("Z.csv", 'r') as f:
Z = list(csv.reader(f, delimiter=";"))
import numpy as np
Z = np.array(Z[1:], dtype=np.float)
Y = [[7,7.1,7.2,7.3,7.4,7.5,7.6,7.7,7.8,7.9,8,8.1,8.2,8.3,8.4,8.5,8.6,8.7,8.8,8.9,9]]
Xall = np.repeat(X[:],21,axis=1)
Yall = np.repeat(Y[:],30,axis=0)
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt,numpy as np
plt.clf()
fig = plt.figure(1,figsize=(35,17),dpi=600,facecolor='w',edgecolor='k')
fig.set_size_inches(10.5,8)
ax = fig.gca(projection='3d')
cset = ax.contourf(Xall, Yall, Z, 2, zdir='x', offset=0, cmap=plt.cm.coolwarm, shade = False, edgecolor='none', alpha=0.5)
cset = ax.contourf(Xall, Yall, Z, 2, zdir='y', offset=9, cmap=plt.cm.coolwarm, shade = False, edgecolor='none', alpha=0.5)
ax.plot_wireframe(Xall, Yall, Z, rstride=1, cstride=1, color='black')
Z=Z-Z.min()
Z=Z/Z.max()
from scipy.ndimage.interpolation import zoom
Xall=zoom(Xall,5)
Yall=zoom(Yall,5)
Z=zoom(Z,5)
cset = ax.plot_surface(Xall, Yall, np.zeros_like(Z)-0,facecolors=plt.cm.coolwarm(Z),shade=False,alpha=0.5,linewidth=False)
ax.set_xlim(-0.5, 31)
ax.set_ylim(6.9, 9.1)
ax.set_zlim(0, 500)
labelsx = [item.get_text() for item in ax.get_xticklabels()]
empty_string_labelsx = ['']*len(labelsx)
ax.set_xticklabels(empty_string_labelsx)
labelsy = [item.get_text() for item in ax.get_yticklabels()]
empty_string_labelsy = ['']*len(labelsy)
ax.set_yticklabels(empty_string_labelsy)
labelsz = [item.get_text() for item in ax.get_zticklabels()]
empty_string_labelsz = ['']*len(labelsz)
ax.set_zticklabels(empty_string_labelsz)
import matplotlib.ticker as ticker
ax.xaxis.set_major_locator(ticker.MultipleLocator(5))
ax.xaxis.set_minor_locator(ticker.MultipleLocator(1))
ax.yaxis.set_major_locator(ticker.MultipleLocator(0.5))
ax.yaxis.set_minor_locator(ticker.MultipleLocator(0.25))
ax.zaxis.set_major_locator(ticker.MultipleLocator(100))
ax.zaxis.set_minor_locator(ticker.MultipleLocator(50))
ax.tick_params(axis='z', which='major', pad=10)
ax.set_xlabel('X',labelpad=5,fontsize=15)
ax.set_ylabel('Y',labelpad=5,fontsize=15)
ax.set_zlabel('Z',labelpad=5,fontsize=15)
ax.view_init(elev=35., azim=-70)
fig.tight_layout()
plt.show()
Alternate possible answer.
This code demonstrates
A plot of a surface and its correponding wireframe
The creation of data and its plot of 3d lines (draped on the surface in 1) at specified values of x and y
Projections of the 3d lines (in 2) on to the frame walls
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from scipy import interpolate
import numpy as np
# use the test data for plotting
fig = plt.figure(1, figsize=(6,6), facecolor='w', edgecolor='gray')
ax = fig.gca(projection='3d')
X, Y, Z = axes3d.get_test_data(0.1) #get 3d data at appropriate density
# create an interpolating function
# can take a long time if data is too large
f1 = interpolate.interp2d(X, Y, Z, kind='linear')
# in general, one can use a set of other X,Y,Z that cover a surface
# preferably, (X,Y) are in grid arrangement
# make up a new set of 3d data to plot
# ranges of x1, and y1 will be inside (X,Y) of the data obtained above
# related grid, x1g,y1g,z1g will be obtained from meshgrid and the interpolated function
x1 = np.linspace(-15,15,10)
y1 = np.linspace(-15,15,10)
x1g, y1g = np.meshgrid(x1, y1)
z1g = f1(x1, y1) #dont use (x1g, y1g)
# prep data for 3d line on the surface (X,Y,Z) at x=7.5
n = 12
x_pf = 7.5
x5 = x_pf*np.ones(n)
y5 = np.linspace(-15, 15, n)
z5 = f1(x_pf, y5)
# x5,y5,z5 can be used to plot 3d line on the surface (X,Y,Z)
# prep data for 3d line on the surface (X,Y,Z) at y=6
y_pf = 6
x6 = np.linspace(-15, 15, n)
y6 = x_pf*np.ones(n)
z6 = f1(x6, y_pf)
# x6,y6,z6 can be used to plot 3d line on the surface (X,Y,Z)
ax = fig.gca(projection='3d')
ax.plot_surface(x1g, y1g, z1g, alpha=0.25)
ax.plot_wireframe(x1g, y1g, z1g, rstride=2, cstride=2, color='black', zorder=10, alpha=1, lw=0.8)
# 3D lines that follow the surface
ax.plot(x5,y5,z5.flatten(), color='red', lw=4)
ax.plot(x6,y6,z6.flatten(), color='green', lw=4)
# projections of 3d curves
# project red and green lines to the walls
ax.plot(-15*np.ones(len(y5)), y5, z5.flatten(), color='red', lw=4, linestyle=':', alpha=0.6)
ax.plot(x6, 15*np.ones(len(x6)), z6.flatten(), color='green', lw=4, linestyle=':', alpha=0.6)
# projections on other sides (become vertical lines)
# change to if True, to plot these
if False:
ax.plot(x5, 15*np.ones(len(x5)), z5.flatten(), color='red', lw=4, alpha=0.3)
ax.plot(-15*np.ones(len(x6)), y6, z6.flatten(), color='green', lw=4, alpha=0.3)
ax.set_title("Projections of 3D lines")
# set limits
ax.set_xlim(-15, 15.5)
ax.set_ylim(-15.5, 15)
plt.show();
(Answer to question 1) To plot the intersections between the surface and the specified planes (y=-20, and y=20), one need to find what Y[?]=-20 and 20. By inspection, I found that Y[100]=20, Y[20]=-20.
The relevant code to plot the lines of intersection:
# By inspection, Y[100]=20, Y[20]=-20
ax.plot3D(X[100], Y[100], Z[100], color='red', lw=6) # line-1 at y=20
ax.plot3D(X[20], Y[20], Z[20], color='green', lw=6) # line-2 at y=-20
# Project them on Z=-100 plane
ax.plot3D(X[100], Y[100], -100, color='red', lw=3) # projection of Line-1
ax.plot3D(X[20], Y[20], -100, color='green', lw=3) # projection of Line-2
The output plot:
(Answer to question 2) To get better plot with the wireframe standout from the surface plot. The surface plot must be partially transparent, which is achieved by setting option alpha=0.6. The relevant code follows.
Z1 = Z-Z.min()
Z1 = Z1/Z.max()
Xall = zoom(X,3)
Yall = zoom(Y,3)
Zz = zoom(Z1, 3)
surf = ax.plot_surface(Xall, Yall, Zz, rstride=10, cstride=10,
facecolors = cm.jet(Zz/np.amax(Zz)),
linewidth=0, antialiased=True,
alpha= 0.6)
# Wireframe
ax.plot_wireframe(X, Y, Z, rstride=5, cstride=5, color='black', alpha=1, lw=0.8)
The plot is:

2D line not showing clearly along with surface on 3D plot

I am trying to plot a 1D line along with a 2D surface in matplotlib with Axes3D:
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(-1., 1.1, 0.1)
y = x.copy()
X, Y = np.meshgrid(x, y)
Z = np.abs(X) + np.abs(Y)
plt.close('all')
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.plot(np.zeros_like(y), y, 1, color='k')
ax.plot(x, np.zeros_like(x), 1, color='k')
surf = ax.plot_surface(X, Y, Z, color='w')
plt.show(block=False)
but the 2D plot somehow hides the lines:
If I comment the surf = plot_surface(...) code line, the 1D lines show correctly:
How can I have the lines showing correctly along with the surface?
Axes3D.plot_surface() apparently accepts a transparency (alpha) argument, which actually gets forwarded to a base class, Poly3DCollection.
And of course the line plot() calls accept a linewidth argument.
So if you render the line plots with thicker lines and you render the surface with some transparency, you should be able to find a combination of settings which let you see both the lines and the surface in a balanced way.
https://matplotlib.org/tutorials/toolkits/mplot3d.html#mpl_toolkits.mplot3d.Axes3D.plot_surface
https://matplotlib.org/api/_as_gen/mpl_toolkits.mplot3d.art3d.Poly3DCollection.html#mpl_toolkits.mplot3d.art3d.Poly3DCollection
You can also achieve this by using the zorder in the plot_surface and plot commands to make the lines sit on top of the surface. E.g.
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np
x = np.arange(-1., 1.1, 0.1)
y = x.copy()
X, Y = np.meshgrid(x, y)
Z = np.abs(X) + np.abs(Y)
plt.close('all')
fig = plt.figure()
ax = fig.gca(projection='3d')
surf = ax.plot_surface(X, Y, Z, color='w', zorder=1)
ax.plot(np.zeros_like(y), y, 1, color='k', zorder=10)
ax.plot(x, np.zeros_like(x), 1, color='k', zorder=11)
plt.show(block=False)

Plotting streamlines in a Matplotlib 3Dplot?

I'm trying to plot streamlines on a plane in a 3D plot using Matplotlib. For the streamlines, I'd like to use the function streamplot(), because of its simplicity. Here's a MWE that I modified from the gallery (to attempt the streamplot() call):
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from matplotlib import cm
X, Y, Z = axes3d.get_test_data(0.05)
fig = plt.figure()
ax = fig.gca()
plt.streamplot(X, Y, X, Y)
plt.show()
fig = plt.figure()
ax = fig.gca(projection='3d')
cset = ax.contour(X, Y, Z, zdir='z', offset=-10, cmap=cm.coolwarm)
ax.set_zlim(-100, 100)
plt.show()
fig = plt.figure()
ax = fig.gca(projection='3d')
cset = ax.streamplot(X, Y, X, Y, zdir='z', offset=-10, cmap=cm.coolwarm)
ax.set_zlim(-100, 100)
plt.show()
The first and second examples work as intended, however, the third example gives me this error:
TypeError: streamplot() got an unexpected keyword argument 'zdir'
which hints to the possibility of this not being implemented. If I check Axes3D, the function streamplot() I get:
In [28]: Axes3D.streamplot
Out[28]: <function matplotlib.axes._axes.Axes.streamplot>
From which we get that streamplot() is the 2D version, and hence can't be directly used in 3D plots.
Is there a way to circumvent this and get a streamlines plane in a 3D plot?

Filling between two lines with Matplotlib with 2 restrictions

I would like to fill the area between the curve y1=x^3 and then line y2=3x-2.
Below is code I have that will do this, however, I want to place the restriction that y1 < y2 (which I have done with the where option of fill_between) and that x<1.
The problem that occurs with the code below is that the area between the curve is filled for x>1. I would like to plot these graphs on the range [-2.5,2.5]. How do I get matplotlib to stop filling between the curves for x>1?
My code:
import matplotlib.pyplot as plot
import numpy as np
x = np.linspace(-2.5, 2.5, 100)
y1 = np.array([i**3 for i in x])
y2 = np.array([3*i-2 for i in x])
fig = plot.figure()
ax = fig.add_subplot(1,1,1)
ax.plot(x, y1, label=r"$y=x^3$")
ax.plot(x, y2, label=r"$y=3x-2$")
ax.spines['left'].set_position('center')
ax.spines['right'].set_color('none')
ax.spines['bottom'].set_position('center')
ax.spines['top'].set_color('none')
ax.spines['left'].set_smart_bounds(True)
ax.spines['bottom'].set_smart_bounds(True)
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
ax.fill_between(x, y1, y2, where=y2<y1, facecolor='green')
ax.legend()
plot.show()
I got it. The easiest fix is to define 3 new variables, u,v, and w, where u holds the x values for v and w, and v = x^3, w=3x-2.
u=x[x<1]
v=y1[y1<1]
w=y2[y2<1]
Then plot these values with fill_between:
ax.fill_between(u, v, w, where=w<v, facecolor='green')

Matplotlib 2d Plot on Faces of 3d Plot

I am producing plots of a spacecraft's trajectory at a specific point in its orbit.
I have a piece of code which produces a 3d line plot in 3dMatplotlib (a part of mycode and figure is shown here (I have drastically reduced the number of points within X,Y,Z to ~20 per array to make it easier to simply copy and paste as the principle is the same):
#
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.axes3d import Axes3D
from numpy import *
XdS=[14.54156005, 14.53922242, 14.53688586, 14.53454823, 14.5322106 , 14.52987297, 14.52753426, 14.52519555, 14.52285792, 14.52051922, 14.51818051, 14.51584073, 14.51350095, 14.51116117, 14.5088214 , 14.50648162, 14.50414076, 14.50179991, 14.49945906, 14.49711821]
YdS=[31.13035144, 31.12920087, 31.12805245, 31.12690188, 31.12575131, 31.12460073, 31.12345016, 31.12229745, 31.12114473, 31.11999201, 31.1188393 , 31.11768443, 31.11652957, 31.11537471, 31.11421984, 31.11306283, 31.11190582, 31.11074882, 31.10959181, 31.1084348]
ZdS=[3.94109446, 3.94060316, 3.94011186, 3.93962083, 3.93912926, 3.93863796, 3.93814639, 3.93765482, 3.93716325, 3.93667169, 3.93617985, 3.93568828, 3.93519618, 3.93470434, 3.9342125 , 3.9337204 , 3.93322829, 3.93273592, 3.93224382, 3.93175144]
fig=plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.plot(XdS,YdS,ZdS,c='black',linewidth=2)
ax.set_xlabel('XKSM (Saturn Radii)')
ax.set_ylabel('YKSM (Saturn Radii)')
ax.set_zlabel('ZKSM (Saturn Radii)')
plt.show()
#
What I want to do is be able to plot the 2d plots X vs Y, X vs Z, and Y vs Z on the edges/planes of this plot i.e. show what the 3d trajectory looks like looking at it in the 3 2d planes and display them at each axis of the current plot. (It isn’t actually as complicated as it might sound, as I already have the X,Y,Z, values for the trajectory). Here I found a similar example which achieves this, however utilising all 3d plot functions, available at: http://matplotlib.org/1.3.1/examples/mplot3d/contour3d_demo3.html : If you check out check out the link it will show the type of image i am trying to achieve.
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from matplotlib import cm
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y, Z = axes3d.get_test_data(0.05)
ax.plot_surface(X, Y, Z, rstride=8, cstride=8, alpha=0.3)
cset = ax.contour(X, Y, Z, zdir='z', offset=-100, cmap=cm.coolwarm)
cset = ax.contour(X, Y, Z, zdir='x', offset=-40, cmap=cm.coolwarm)
cset = ax.contour(X, Y, Z, zdir='y', offset=40, cmap=cm.coolwarm)
ax.set_xlabel('X')
ax.set_xlim(-40, 40)
ax.set_ylabel('Y')
ax.set_ylim(-40, 40)
ax.set_zlabel('Z')
ax.set_zlim(-100, 100)
plt.show()
This is in theory exactly what I need, in the way it takes sort of a planar view of the 3d situation. However I cannot implement a 2d line plot on a 3d axis nor can I use the offset command in a 2d plot (getting the error: TypeError: There is no line property "offset").
Is there a 2d equivalent to the 3d “offset” command and Is it possible to plot the 2d values on the planes of the 3d plot as I desire? Also is there a way to plot 2d lines having initialised a 3d projection? Can anyone offer any ideas/point me in any direction in general to help me achieve this?
My sincere thanks in advance and apologies if any part of this post is out of order, this is my first one!
Try this:
xmin = min(XdS)
ymax = max(YdS)
zmin = min(ZdS)
length_of_array = len(XdS)
xmin_array = [xmin] * length_of_array
ymax_array = [ymax] * length_of_array
zmin_array = [zmin] * length_of_array
fig=plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.plot(XdS,YdS,ZdS,zdir='z', c='r')
ax.plot(XdS,YdS,zmin_array, zdir='z', c='g')
ax.plot(xmin_array, YdS, ZdS, 'y')
ax.plot(XdS,ymax_array,ZdS,'b')
ax.set_xlabel('XKSM (Saturn Radii)')
ax.set_ylabel('YKSM (Saturn Radii)')
ax.set_zlabel('ZKSM (Saturn Radii)')
plt.show()

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