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...
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
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