Python - Writing numpy array data to a pipe opened with Popen

Question

I am trying to write a numpy array data to a pipe opened using subprocess.Popen in Python 3.4. Here is the code

import numpy
import subprocess

myArray = numpy.arange(10000).reshape([100,100])

fullCmd = "xpaset DS9Test array [xdim=100,bitpix=64,arch=littleendian,ydim=100]"

mp = subprocess.Popen(
    fullCmd, 
    shell = True, 
    stdin = subprocess.PIPE, 
    stdout = subprocess.PIPE, 
    stderr = subprocess.STDOUT,
    bufsize = 0
)

myArray.tofile(mp.stdin)

Unfortunately I am getting the following error:

  File "/Users/avigan/Work/HC-HR/FTS/test.py", line 25, in <module>
    myArray.tofile(mp.stdin)

OSError: first argument must be a string or open file

However, if I do:

print(mp.stdin)

<_io.FileIO name=71 mode='wb'>

I interpret this as a sign that the file descriptor is indeed open.

Anyone sees what wrong here?

Answer 1

Not exactly the solution what you ask for, but I had the same problem of wanting to redirect the numpy array to a PIPE so I could redirect it into feedgnuplot to build a histogram.

Instead, I ended up using a temporary file as follows:

import os
import tempfile

command = " | feedgnuplot --terminal 'dumb 160,40' --histogram 0 --with boxes --unset grid --exit"
with tempfile.NamedTemporaryFile('w+t', suffix=".txt") as f:
    np.savetxt(f, myArray, fmt='%.4f')
    f.seek(0)
    os.system("sudo more " + f.name + command)

While your usage requirement is probably different, you can still probably read back the temporary file for your own application.

HTH

Answer 2

According to the docs, this should be equivalent to tofile for writing binary data:

mp.stdin.write(myArray.tobytes())

See if it works.