plotting a scatter plot in python using matplotlib

Question

I have a file with 3000 points in it. I have to plot a 3D scatter plot with those points.the points are as follows,

6.655597594660206395e-01,-5.205175889492101859e-01,4.583497554501108073e-01
3.357418723194116605e-02,-2.482341476533565849e+00,2.009030294705723030e+00
-1.398411818716352728e-01,-1.990250936356241063e+00,2.325394845551588929e+00

there are 3000 such points.

I have the code and it shows the error

TypeError: Cannot cast array data from dtype('float64') to dtype('<U32') according to the rule 'safe'

code I have written

from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np

x=[]
y=[]
z=[]

with open('3dpd.out') as f:
    lines = f.readlines()
    for line in lines :
        x.append(line.split(',')[0])
        y.append(line.split(',')[1])
        z.append(line.split(',')[2])


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

ax.set_title("Scatter Plot")
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')


ax.scatter(x, y, z, c='r')

plt.show()

guess that some of your data points are strings and not numbers, can you check data type of all points? — dejanmarich
– dejanmarich, Commented Oct 27, 2018 at 12:00

tom10 · Accepted Answer · 2018-10-27 16:18:00Z

1

When lines are read by readlines, they are read in as strings, so you need to convert these strings to numbers.

Also, note that I've separated each step into a different line in the code (eg, split, float, etc) which usually helps in debugging. (And you only need to call split once for each line.)

Here's an example that works:

from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np

x=[]
y=[]
z=[]

with open('3dpd.out') as f:
    lines = f.readlines()
    for line in lines :
        xs, ys, zs =  line.split(',')
        xv, yv, zv = [float(v) for v in (xs, ys, zs)]
        x.append(xv)
        y.append(yv)
        z.append(zv)

print type(xs)
print type(xv)

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

ax.set_title("Scatter Plot")
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')


ax.scatter(x, y, z, c='r')

plt.show()

edited Oct 27, 2018 at 16:18

answered Oct 27, 2018 at 14:47

tom10

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