Unable to start python scripts from java code

Question

I've got java code to call a python script

Java

private void visualizeData() {
    try{
        Runtime.getRuntime().exec(“python pyScripts/visualize.py”)
    } catch (IOException e){
        e.printStackTrace();
    }
}

And this is my code for the visualize.py:

visualize.py

from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pylot as plt

f = open(“ecoli_data_transformed.txt”,”r”)

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

for line in f:
    (a, b, c) = line.split(“\t”)
    a = float(a)
    b = float(b)
    c = float(c)    

    ax.scatter(a,b,c)

ax.setxlabel(‘PCA1’)
ax.setylabel(‘PCA2’)
ax.setzlabel(‘PCA3’)

plt.show()

But it doesn't plot the data.

If I call the test.py script from the java code (test.py is in the same directory as visualize.py), it works:

test.py

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

np.random.seed(19680801)

def randrange(n, min, vmcx):
    return (vmax - vein)*np.random.rand(n) + vmin

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

n = 100

for c, m, slow, high in [(‘r’, ‘o’, -50, -25), (‘b’, ‘^’, -30, -5)]:
    xs = randrange(n, 23, 32)
    ys = randrange(n, 0, 100)
    zs = randrange(n, zlow, zhigh)
    ax.scatter(xs, ys, zs, c=c, marker=m)

ax.set_xlabel(‘X Label’)
ax.set_ylabel(‘Y Label’)
ax.set_zlabel(‘Z Label’)

plt.show()

What could be the problem?

*NOTE: Calling the visualize.py script from console by 'python visualize.py' works totally fine.

please paste the code in the question instead of attaching links of images. — Omar Einea
– Omar Einea, Commented Jan 4, 2018 at 14:11
To format as code, you should substitute your tabs for spaces in your editor, paste the code here, select it and use the code format tool available (which basically adds 4 spaces per line of code) — Leonardo Alves Machado
– Leonardo Alves Machado, Commented Jan 4, 2018 at 14:29
No, nothing. The code finishes, but the script's graph is never plotted. Not the case for test.py, everything works fine there. — Zafir Stojanovski
– Zafir Stojanovski, Commented Jan 4, 2018 at 15:25

hasbel · Accepted Answer · 2018-01-04 15:28:58Z

1

The relative path that you are passing to the open() command in your python script is probably the problem.

Your Java program is located in a different directory than the one your Python program is located in. When it starts the python script, the current path is still the path to the Java program.

This means that Python is unable to find the relative path to the file you are trying to open, ecoli_data_transformed.txt.

A work around would be to include the complete path to your .txt file:

f = open(“C:\\path\\to\\your\\file\\ecoli_data_transformed.txt”,”r”)

A better solution would be to determine it programatically:

import os

file_path = os.path.dirname(__file__)
f = open(file_path + "\\ecoli_data_transformed.txt”,”r”)

answered Jan 4, 2018 at 15:28

hasbel

263 bronze badges

Sign up to request clarification or add additional context in comments.

1 Comment

Zafir Stojanovski Over a year ago

OH MY GOD YES, THANK YOU! <3

Collectives™ on Stack Overflow

Unable to start python scripts from java code

1 Answer 1

1 Comment

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

1 Comment

Your Answer

Sign up or log in

Post as a guest

Related