3D Plot with Matplotlib: Hide axes but keep axis-labels?

Question

I am using Matplotlib to visualize three-dimensional arrays. I got it almost the way I want it, apart from a minor snag... see the illustration and the description below of what I can get it to do and what I want it to do...

Show a bunch of cubes with labels, but also a bunch of other stuff.
Show a bunch of cubes but no axis-labels.
This is what I want but cannot get it to do... I want to display a bunch of cubes WITH axis-labels but nothing else.

enter image description here

I hope you guys can help me out :) See the source below.

from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from matplotlib import rcParams
import numpy as np
rcParams['axes.labelsize'] = 14
rcParams['axes.titlesize'] = 16
rcParams['xtick.labelsize'] = 14
rcParams['ytick.labelsize'] = 14
rcParams['legend.fontsize'] = 14
rcParams['font.family'] = 'serif'
rcParams['font.serif'] = ['Computer Modern Roman']
rcParams['text.usetex'] = True
rcParams['grid.alpha'] = 0.0

def make_cube():
    """ A Cube consists of a bunch of planes..."""

    planes = {
        "top"    : ( [[0,1],[0,1]], [[0,0],[1,1]], [[1,1],[1,1]] ),
        "bottom" : ( [[0,1],[0,1]], [[0,0],[1,1]], [[0,0],[0,0]] ),
        "left"   : ( [[0,0],[0,0]], [[0,1],[0,1]], [[0,0],[1,1]] ),
        "right"  : ( [[1,1],[1,1]], [[0,1],[0,1]], [[0,0],[1,1]] ),
        "front"  : ( [[0,1],[0,1]], [[0,0],[0,0]], [[0,0],[1,1]] ),
        "back"   : ( [[0,1],[0,1]], [[1,1],[1,1]], [[0,0],[1,1]] )
    }
    return planes

def render_array(ary, highlight):
    fig = plt.figure()
    ax = fig.add_subplot(111, projection='3d')

    cube = make_cube()

    for space in xrange(0, ary.shape[0]):
        for column in xrange(0, ary.shape[1]):
            for row in xrange(0, ary.shape[2]):
                alpha = 0.01
                if highlight[space,column,row] == 1:
                    alpha = 1
                for side in cube:
                    (Xs, Ys, Zs) = (
                        np.asarray(cube[side][0])+space+space*0.2,
                        np.asarray(cube[side][2])+row+row*0.2,
                        np.asarray(cube[side][3])+column+column*0.2
                    )
                    ax.plot_surface(Xs, Ys, Zs, rstride=1, cstride=1, alpha=alpha)

    highest = 0                         # Make it look cubic
    for size in ary.shape:
        if size > highest:
            highest = size
    ax.set_xlim((0,highest))
    ax.set_ylim((0,highest))
    ax.set_zlim((0,highest))


    ax.set_xlabel('Third dimension' )   # Meant to visualize ROW-MAJOR ordering 
    ax.set_ylabel('Row(s)')
    ax.set_zlabel('Column(s)')

    #plt.axis('off')    # This also removes the axis labels... i want those...
    #ax.set_axis_off()  # this removes too much (also the labels)

    # So I try this instead...
    ax.set_xticks([])          # removes the ticks... great now the rest of it
    ax.set_yticks([])
    ax.set_zticks([])
    #ax.grid(False)             # this does nothing....
    #ax.set_frame_on(False)     # this does nothing....
    plt.show()

def main():

    subject = np.ones((3,4,3))

    highlight = np.zeros(subject.shape) # Highlight a row
    highlight[1,1,:] = 1

    render_array(subject, highlight)    # Show it

if __name__ == "__main__":
    main()

Update, thanks to the answer, here is what I was missing:

# Get rid of the panes                          
ax.w_xaxis.set_pane_color((1.0, 1.0, 1.0, 0.0)) 
ax.w_yaxis.set_pane_color((1.0, 1.0, 1.0, 0.0)) 
ax.w_zaxis.set_pane_color((1.0, 1.0, 1.0, 0.0)) 

# Get rid of the spines                         
ax.w_xaxis.line.set_color((1.0, 1.0, 1.0, 0.0)) 
ax.w_yaxis.line.set_color((1.0, 1.0, 1.0, 0.0)) 
ax.w_zaxis.line.set_color((1.0, 1.0, 1.0, 0.0))

Which will, together with:

# Get rid of the ticks                          
ax.set_xticks([])                               
ax.set_yticks([])                               
ax.set_zticks([])

Hide everything but the labels, as illustrated in 3).

UPDATE

I've cleaned and got the code into a working state and made it available here: https://github.com/safl/ndarray_plot

Along with a couple of additional examples here: http://nbviewer.ipython.org/github/safl/ndarray_plot/blob/master/nb/ndap.ipynb

Just a note to let you know - explicitly including an unusual (i.e. cool) use case is really helpful to others later on! — uhoh
– uhoh, Commented Jul 21, 2016 at 9:24

nicoguaro · Accepted Answer · 2015-03-15 07:23:16Z

12

I tried to run your code, but it is not working in my computer.

Below you can see a solution for plotting a sphere. Basically, I turned the color of the panes and spines to alpha=0 by hand and make the ticks to be empty lists (as you pointed out).

from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from matplotlib import rcParams
import numpy as np
rcParams['axes.labelsize'] = 18
rcParams['font.family'] = 'serif'
rcParams['font.serif'] = ['Computer Modern Roman']
rcParams['text.usetex'] = True

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

u = np.linspace(0, 2 * np.pi, 100)
v = np.linspace(0, np.pi, 100)

x = 10 * np.outer(np.cos(u), np.sin(v))
y = 10 * np.outer(np.sin(u), np.sin(v))
z = 10 * np.outer(np.ones(np.size(u)), np.cos(v))
ax.plot_surface(x, y, z,  rstride=4, cstride=4, color='b')

# Get rid of the panes
ax.w_xaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
ax.w_yaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
ax.w_zaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))

# Get rid of the spines
ax.w_xaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
ax.w_yaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
ax.w_zaxis.line.set_color((1.0, 1.0, 1.0, 0.0))

# Get rid of the ticks
ax.set_xticks([]) 
ax.set_yticks([]) 
ax.set_zticks([])

# Add the labels
ax.set_xlabel('Third dimension' )
ax.set_ylabel('Row(s)')
ax.set_zlabel('Column(s)')
plt.show()

And here is my output

enter image description here

answered Mar 15, 2015 at 7:23

nicoguaro

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3 Comments

safl Over a year ago

Thanks @nicoguaro, I was missing: "ax.w_xaxis.set_pane_color" and "ax.w_xaxis.line.set_color".

nicoguaro Over a year ago

Not a problem. Can you fix your code? I'm interested in running it... Maybe I can use it for visualization of tensors later.

safl Over a year ago

I've cleaned it up and made it available here: github.com/safl/ndarray_plot

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