Interacting with external python

Support
1

I am trying to build on this example in:
https://www.slicer.org/wiki/Documentation/Nightly/Developers/Python_scripting#How_to_run_Python_script_using_a_non-Slicer_Python_environment

This

python_path = "C:/Users/amaga/AppData/Local/Continuum/anaconda3/python"
command_line = [python_path, "-c", "import pyRserve; conn = pyRserve.connect(); print(conn.eval('3 + 5'))"]
from subprocess import check_output
command_result = check_output(command_line, env=slicer.util.startupEnvironment())
print(command_result)

fails with error.

Traceback (most recent call last):
File "<console>", line 1, in <module>
File "C:\Program Files\Slicer 4.11.0-2018-11-02\lib\Python\Lib\subprocess.py", line 219, in check_output
raise CalledProcessError(retcode, cmd, output=output)
CalledProcessError: Command ‘[‘C:/Users/amaga/AppData/Local/Continuum/anaconda3/python’, ‘-c’, "import pyRserve; conn = pyRserve.connect(); print(conn.eval(‘3 + 5’))"]’ returned non-zero exit status 120

But in the interactive python console import pyRserve; conn = pyRserve.connect(); print(conn.eval(‘3 + 5’))
returns the correct value. So I know Rserve is working.

What is the correct way of passing bunch of commands to the external python in this context?

2

After first starting the R server from a separate R interpreter (details here), I wasn’t able to reproduce the issue.

3

himm,

On a different windows computer, I followed your updated pip install example and issued the command
"“c:\Program Files\Slicer 4.10.0\bin\PythonSlicer.exe” -m pip install pyRserve
as admin.
As far as I can tell, pyRserve installed correctly (although there was a warning about path (truncated output below)

Successfully built pyRserve
Installing collected packages: attrs, pluggy, scandir, pathlib2, funcsigs, colorama, atomicwrites, more-itertools, py, pytest, pyRserve
The scripts py.test.exe and pytest.exe are installed in ‘C:\Program Files\Slicer 4.10.0\lib\Python\Scripts’ which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed atomicwrites-1.2.1 attrs-18.2.0 colorama-0.4.1 funcsigs-1.0.2 more-itertools-4.3.0 pathlib2-2.3.2 pluggy-0.8.0 py-1.7.0 pyRserve-0.9.1 pytest-4.0.1 scandir-1.9.0

then I started the Rserve on my local R (3.5.0) and tested its connection with anaconda by issuing

import pyRserve; conn = pyRserve.connect(); print(conn.eval(‘3 + 5’))

and got the right result.

then I opened Slicer 4.10, and typed the script example above (path is slightly different on this machine).

python_path = “C:/Users/murat/anaconda3/python”
command_line = [python_path, “-c”, “import pyRserve; conn = pyRserve.connect(); print(conn.eval(‘3 + 5’))”]
from subprocess import check_output
command_result = check_output(command_line, env=slicer.util.startupEnvironment())
print(command_result)

and still got the exact error message as above.

Should I add the C:\Program Files\Slicer 4.10.0\lib\Python\Scripts’ to system path as suggested by install? I was wary of that messing up other things in Slicer. WHat else I might be missing?

4

Based on the snippet you are trying to execute, pyRserve should be installed within anaconda not within Slicer.

5

Right, there was no point in installing into Slicer (getting late here).
Nevertheless, it was installed in anaconda.

6

Whatever it was, it doesn’t matter anymore. Running it through Slicer’s pyRserve worked fine, which is more important anyways.
Thanks for the help!