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Incoroporate py_igtlink code into slicelet #51

Closed tdowrick closed 3 years ago

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Mar 21, 2019, 10:53

We are currently running a bk_openigtlink.py script to acquire the BK image data. This script should be put somewhere sensible in the file hierearchy, and called from the slicelet.

tdowrick commented 3 years ago

In GitLab by @AnastasisGeorgoulas on Mar 25, 2019, 09:55

If it's not too hard to change in the scikit-surgerybk package, it might be better to expose a method there that creates the server. We could then include the package in our dependencies and use it as a library, rather than copying the script here and running it.

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Mar 26, 2019, 10:09

mentioned in merge request !7

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Mar 26, 2019, 10:09

created merge request !7 to address this issue

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Mar 26, 2019, 10:11

Yes - good idea. I have open an issue in the bk library to address this.

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Mar 26, 2019, 10:41

We'll need to check the performance of running the pyigtlink code in a thread once we have it set up. We've cuurrently been running it in a separate process, which in principle should be faster than running a separate thread inside the main code.

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Mar 27, 2019, 09:33

I have added a class that will start the pyIGTLink server sending data from the BK to bk5000.py (https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgerybk/blob/master/sksurgerybk/interface/bk5000.py#L369)

It can also be launched from the command line using python bk5000.py 1

tdowrick commented 3 years ago

In GitLab by @AnastasisGeorgoulas on Mar 27, 2019, 10:40

Great, thanks!

tdowrick commented 3 years ago

In GitLab by @AnastasisGeorgoulas on Apr 3, 2019, 15:36

Note that for this to work we will first need to install scikit-surgerybk for Slicer's Python to find it. Installing it via pip should work - I have just tried it and packages persist within Slicer sessions as you'd expect. There are two ways to do this:

  1. Use the pip module from within the Slicer interpreter
  2. Run the PythonSlicer executable that comes with Slicer
tdowrick commented 3 years ago

In GitLab by @AnastasisGeorgoulas on Apr 3, 2019, 17:49

mentioned in commit 48fd57d66e8c26904e085ece6a93d4f093194e17

tdowrick commented 3 years ago

In GitLab by @ThomasDowrick on Apr 25, 2019, 07:43

closed

tdowrick commented 3 years ago

In GitLab by @AnastasisGeorgoulas on May 7, 2019, 10:15

mentioned in commit 6d8e8807e882a360ab1e98dbabfa38f0a01781e9