Add SlicerSPECTRecon extension

[ObedDzik]

New extension

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[lukepolson]

@lassoan let us know if there's anything you want us to add before merging ☺

[ObedDzik]

@lassoan hi team, we wanted to know if there is anything else to be done on our part for the successful merging of this extension.

[lukepolson]

@lassoan @pieper

[lassoan]

Thank you for your excellent contribution and sorry for the long delay, we had a long backlog of extensions work through.
The extension looks great, there is just one significant issue about how the required Python packages are installed, and a few minor tweaks:

• Slicer startup after installing the extension appears to be hanging. Most users would force stop Slicer and conclude that the extension is broken. Actually, what's happening is that the extension installs Python packages at startup, which can take several minutes, and by the user aborting the installation the result is some incompletely installed Python packages, which actually do not work. All subsequent Slicer application starts are very slow, too (2-3x longer than usual) because the module spends a lot of time checking these packages and importing them. The solution is to not install any Python packages and refrain from importing any non-trivial packages in the main module .py at the file scope. Installing/importing packages inside functions - when actually needed - is OK. Installing/importing packages at the file scope in additional .py files (e.g., those in the Logic folder) is OK.
• Fix project name and image URLs in CMakeLists.txt (see Update CMakeLists.txt PyTomography/SlicerSPECTRecon#36)
• Change repository name to Slicer, which in this case is SlicerSPECTRecon
• Rename the module name to SPECTRecon (we don't want each module name to start with Slicer), preferably change the module title to human-readable, such as SPECT reconstruction
• Make link to the excellent user manual much more visible! I almost gave up on trying the extension when I accidentally noticed a little text mentioning User_Manual.md. It was not even a link that I could click. Make it big and bold and maybe show it at multiple places.
• User interface section: mention the module name that should be opened, add a link to the user manual
• It would be nice to have a very simple, basic non-video tutorial (just a few bullet points and screenshots). Having a video tutorial is great for some people, but many people will refuse to watch a 30-minute tutorial. Also, you can ensure that a text-based tutorial is always up-to-date, but it is practically impossible to update video tutorials up-to-date, so they will always be somewhat inaccurate.

[lukepolson]

Hi @lassoan ,

Thanks for the kind words about the extension and sorry for the late reply. I believe I have now addressed all the issues you raised above in the main repository https://github.com/PyTomography/Slicer/tree/main

I just need @ObedDzik to change the commit from this link to match the new title. Obed I made a pull request here, Andras can you also confirm that these are the required changes based on what you mentioned above?

Also @lassoan , I've changed the repository name here to be "Slicer". Is that what you meant?

[lassoan]

Thank you, I'll review the updates tomorrow. To just quickly respond to the repository and extension name: The repository name should start with Slicer followed by the extension's name. Sorry, I missed the "start" word in my comment. So, please rename the repository from Slicer to SlicerSPECTRecon or SlicerSPECTReconstruction.

[lukepolson]

Thanks @lassoan , and don't hesitate to ask if there's anything else that would help improve the module : ). It's been a real pleasure working/learning with slicer

[lukepolson]

Hi @lassoan , any updates on this?

[lukepolson]

Hi @jamesobutler @lassoan , anything else we can do?

[lukepolson]

@lassoan any advice for what went wrong with the checks? Apologies for for messaging so much, but there's a couple groups interested in using the extension for some of their own recons : )

[lukepolson]

@lassoan @jamesobutler please let us know the next steps

[lassoan]

Thanks for your patience. When installing the extension into a fresh Slicer installation (that does not have pytomography installed) I get this error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\D\S4R\python-install\Lib\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 "C:/D/S4R/Slicer-build/slicer.org/Extensions-33204/SPECTRecon/lib/Slicer-5.7/qt-scripted-modules/SPECTRecon.py", line 49, in <module>
    from Logic.SPECTReconLogic import SPECTReconLogic
  File "C:\D\S4R\Slicer-build\slicer.org\Extensions-33204\SPECTRecon\lib\Slicer-5.7\qt-scripted-modules\Logic\SPECTReconLogic.py", line 8, in <module>
    from pytomography.io.SPECT import dicom
ModuleNotFoundError: No module named 'pytomography'
[Qt] loadSourceAsModule - Failed to load file "C:/D/S4R/Slicer-build/slicer.org/Extensions-33204/SPECTRecon/lib/Slicer-5.7/qt-scripted-modules/SPECTRecon.py"  as module "SPECTRecon" !
[Qt] Fail to instantiate module  "SPECTRecon"
[Qt] The following modules failed to be instantiated:
[Qt]    SPECTRecon

You can fix this by making sure you don't import anything in the main scope of the module (e.g., move from Logic.SPECTReconLogic import SPECTReconLogic into the functions where you actually need to use SPECTReconLogic.

[lukepolson]

@lassoan I just pushed an update to the main repo, do the tests need to rerun?