Hi all, I try to use subprocess.call to run an external application in the python interactor of 3D Slicer but failed! Error message is “terminate called after throwing an instance of ‘H5::DataSpaceIException’” However, when I run the python in the terminal and input the same command, the applicati…

yes I did installation again and the path was changed. I didnt check updated the path. now its running. Thanks all

[image] wpgao: Is there any difference between the two pythons? Yes, Slicer’s python is embedded . subprocess.call should generally work, however, it will block Slicer (GUI will freeze) until the call completes (you can use Popen or Slicer’s CLI infrastructure instead for asynchronous calls).…

The crash is probably because your application tries to use Slicer’s ITK, VTK, HDF5, etc. libraries. If you want to use the default system environment, you can retrieve it using slicer.util.startupEnvironment(). from subprocess import check_output check_output( ["/usr/bin/python3", "-c", "print('…

@ihnorton Thanks for your reply. I just try to call a function of ANTs for image registration! @lassoan Thanks! It works according to your suggestion. In addition, shell should be set True. Otherwise, it does not work. I don’t know why and there is no any information output to the terminal!

Hi andras, I am extactly doing the same but getting error. Traceback (most recent call last): File "<console>", line 1, in <module> File "C:\Program Files\Slicer 4.10.2\lib\Python\Lib\subprocess.py", line 212, in check_output process = Popen(stdout=PIPE, *popenargs, **kwargs) File "C:\Pr…

The message indicates that the path to the executable is incorrect. So that we can better understand the problem, could you share the code leading to this exception ?

I am simply checking it with print statement. command_line = [r"F:\anaconda3\python3.exe","-c","print('helo')"] from subprocess import check_output command_result = check_output(command_line, env = slicer.util.startupEnvironment())

Hi, Why am I unable to run the code below command_line=["F:\anaconda3\python.exe","-c", "print('hola')"] from subprocess import run command_result = run(command_line, env = slicer.util.startupEnvironment()) print(command_result) Traceback (most recent call last): File "F:\Slicer 4.11.0-2019-07-…

You should do this instead: command_line=["F:/anaconda3/python.exe", "-c", "print('hola')"] from subprocess import run command_result = run(command_line, env=slicer.util.startupEnvironment()) print(command_result)

[image] jcfr: command_line=[“F:/anaconda3/python.exe”, “-c”, “print(‘hola’)”] from subprocess import run command_result = run(command_line, env=slicer.util.startupEnvironment()) print(command_result) the error remain the same I am unable to understand. It could not find the file.

@Saima I get the error you are getting when the python path that you are targeting doesn’t actually exist. Can you confirm that "F:\anaconda3\python.exe" actually exists?

Subprocess.call does not work!

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Subprocess.call does not work!

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