PyIGTL in Docker: Trouble with

Support
1

Hello, would this be the right place to post this?

I am trying to run a python script that communicates with a 3d slicer extension using the pyigtl library.

However, I am struggling to get the script to communicate with slicer. which is outside the container.

The docker Image is the python:3.10-slim-bullseye, but the same errors occur with the nvidia/cuda:12.3.0-base-ubuntu22.04 image.

Basically, the script runs :

text_server = pyigtl.OpenIGTLinkServer(port=18945, local_server=True)

the code will stall on the next part:

string_message = pyigtl.StringMessage(f, device_name="TextMessage")
text_server.send_message(string_message)

Attempting to set local server to false like so:

text_server = pyigtl.OpenIGTLinkServer(port=18945, local_server=False, iface="0.0.0.0".encode('utf-8'))

reuslts in this error:

Traceback (most recent call last):
  File "/app/server/server.py", line 174, in <module>
    asyncio.run(main())
  File "/usr/lib/python3.10/asyncio/runners.py", line 44, in run
  File "/app/server/server.py", line 170, in main
    await tmsserver.run_server()
  File "/app/server/server.py", line 43, in run_server
    servertms = pyigtl.OpenIGTLinkServer(port=18944, local_server=False, iface="0.0.0.0".encode('utf-8'))
  File "/usr/local/lib/python3.10/dist-packages/pyigtl/comm.py", line 178, in __init__
    self.host = socket.inet_ntoa(fcntl.ioctl(soc.fileno(), 0x8915, struct.pack('256s', ifname[:15]))[20:24])
struct.error: argument for 's' must be a bytes object

the same error occurs if the iface var is set to wifi0 and wlan0 and eth0 stalls like the local version

For added context the script is SlicerTMS/server/server.py in the SlicerTMS github page

2

Maybe it’s as simple as making sure the port is mapped from the docker instance?

3

I run the docker containers with
`` bash
docker run -it -p 18944:18944 -p 18945:18945 test
```

and expose both ports in the docker file with

EXPOSE 18944
EXPOSE 18945

but that does not change the errors I am experiencing

was there anything I need to do for port mapping?

would it help if I changed the ports used by the python script?

Thanks

4

I suggest getting the communication working with pyigtl outside of docker with simple test cases and then try those test cases inside docker to debug.

5

I have been able to get the same script running in a dev environment on my windows 11 PC,

doing that it connects fine and doesn’t cause any problems.

Otherwise, I will looking into getting simpler test cases running, likely sometime next week

Thanks

6

Also, forgot to mention a weird bit, I got 3d slicer and the python script to run in the same container and had the same issue

7

We used OpenIGTLink between Slicer instances in linux docker containers and it worked well.

This is supposed to stall until a client is connected. You can attach a debugger to confirm that indeed the server is waiting on a client to connect.

Do you run pyigtl in Slicer application’s Python environment or in a different Python executable?
In Slicer, you need to use the OpenIGTLinkIF module instead of pyigtl.

8

HI, Thanks for all the help.

It works now, after uninstalling and reinstalling the OpenIGTLinkIF extension, I could connect using

text_server = pyigtl.OpenIGTLinkServer(port=18945, local_server=False, iface="eth0".encode('utf-8'))
string_message = pyigtl.StringMessage(f, device_name="TextMessage")
text_server.send_message(string_message)

I don’t really know what changed when it was reinstalled but it now showed this connection when on the OpenIGTLinkIF menu.

As for the development environment from before, it was a separate environment to the one associated with the slicer application.

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