Update slicer and slicer surface toolbox

[jcfr]

Summary:

• Update Slicer from 5.3.0 to 5.9.0

• Update Slicer backporting SlicerSurfaceToolbox's module updates: Waiting that the proposed changes are integrated upstream, a fork of SlicerSurfaceToolbox has been added to the SlicerSALT GitHub organization. Related pull requests:

• ENH: Add MeshAligment Module Slicer/SlicerSurfaceToolbox#71

• ENH: Add MeshDataImprinter module Slicer/SlicerSurfaceToolbox#72

• ENH:Add SurfaceFeatureExtractor module Slicer/SlicerSurfaceToolbox#73

• ENH: Add SurfaceDistance Module Slicer/SlicerSurfaceToolbox#74

• ENH:Add AverageMesh module Slicer/SlicerSurfaceToolbox#75

Related forks:

• https://github.com/slicersalt/SlicerSurfaceToolbox
• https://github.com/slicersalt/Slicer

[vicory]

Getting this error when launching:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/work/salt/build_59/python-install/lib/python3.9/imp.py", line 169, in load_source
    module = _exec(spec, sys.modules[name])
  File "<frozen importlib._bootstrap>", line 613, in _exec
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/work/salt/build_59/Slicer-build/lib/SlicerSALT-5.9/qt-scripted-modules/WebServer.py", line 18, in <module>
    from WebServerLib.BaseRequestHandler import BaseRequestHandler, BaseRequestLoggingFunction
  File "/work/salt/build_59/Slicer-build/lib/SlicerSALT-5.9/qt-scripted-modules/WebServerLib/__init__.py", line 2, in <module>
    from .DICOMRequestHandler import DICOMRequestHandler
  File "/work/salt/build_59/Slicer-build/lib/SlicerSALT-5.9/qt-scripted-modules/WebServerLib/DICOMRequestHandler.py", line 2, in <module>
    import pydicom
ModuleNotFoundError: No module named 'pydicom'
loadSourceAsModule - Failed to load file "/work/salt/build_59/Slicer-build/lib/SlicerSALT-5.9/qt-scripted-modules/WebServer.py"  as module "WebServer" !
Fail to instantiate module  "WebServer"
The following modules failed to be instantiated:
   WebServer

@jcfr I don't think we're using the WebServer module for anything, so the easiest fix seems like it would be to just disable it for SALT. Do you agree?

[jcfr]

so the easiest fix seems like it would be to just disable it for SALT

Agreed. The module was just disabled. To move forward with local testing make sure to remove the WebServer module from your local build:

rm -rf /work/salt/build_59/Slicer-build/lib/SlicerSALT-5.9/qt-scripted-modules/WebServer*

[vicory]

As far as I can tell, all the existing modules are working as intended after this update.

[vicory]

@jcfr Anything else to do here or are we good to merge? Are we waiting for the upstream merges first?

[jcfr]

This has been rebased and is ready for final review & integration

Are we waiting for the upstream merges first?

Those pull request are for future reference only and not blocker for the SlicerSALT release