ENH/BUG: Update optical CT gel dosimetry workflow for Slicer 5.8 and add a user-defined sampling axis

[gslle924]

This PR updates the GelDosimetryAnalysis extension to be compatible with Slicer 5.8 and later and adds a user-defined sampling axis for dose calibration.

[gslle924]

Line Profile module is now part of Slicer core, therefore line profile computation should be removed from this extension and the module in Slicer core should be used.

[gslle924]

I have pushed the latest updates to my repository. Once the Slicelet module is available in the latest version of 3D Slicer, I can update the line profile functionality using Slicer’s built-in Line Profile module. @Sunderlandkyl @lassoan @cpinter

[cpinter]

Sorry for the wait. It seems that none of us has time for a thorough code review. Can you please do the following to facilitate the integration process?

• Confirm it works with the latest Slicer (5.12.3 and also the preview)
• Provide a video showing end-to-end flow

Also, the diff shows that basically every line has been changed although they do not seem to be. Please double check end of line character (\n or \r\n), and make sure it does not change.

Thank you very much!

[gslle924]

Sorry for the wait. It seems that none of us has time for a thorough code review. Can you please do the following to facilitate the integration process?

• Confirm it works with the latest Slicer (5.12.3 and also the preview)
• Provide a video showing end-to-end flow

Also, the diff shows that basically every line has been changed although they do not seem to be. Please double check end of line character (\n or \r\n), and make sure it does not change.

Thank you very much!

Hi @cpinter,

Both the optical CT and MR-based gel dosimetry workflows work with the latest stable version of Slicer as well as the current preview version.

I have uploaded videos demonstrating the complete end-to-end workflow. The optical CT workflow was demonstrated using Slicer 5.12.3, while the MR-based workflow was demonstrated using Slicer 5.13 Preview. The code is organized into two separate branches: master for the optical CT workflow and mr-workflow for the MR-based workflow.

In addition, I made the following updates:

• Confirmed that the code uses CRLF line endings so that the end-of-line format remains unchanged.
• Updated the module titles to Optical CT Gel Dosimetry Analysis and MR Gel Dosimetry Analysis, allowing them to be integrated as two separate modules within the Slicelet.
• Updated the line profile tool so that both workflows use the Line Profile module built in Slicer.

Both modules are now ready to be added to Slicer.

Thank you!

[gslle924]

I’ve restructured the extension to resolve the loading conflicts between the MR and optical CT modules and allow both workflows to run independently within the same extension. The main changes are:

• Renamed all the MR workflow's classes and files (GelDosimetryAnalysisMR, GelDosimetryAnalysisMRWidget, GelDosimetryAnalysisMRLogic, etc.) so they don't clash with the optical CT module.
• Restructured the repo so optical CT (GelDosimetryAnalysis/) and MR (GelDosimetryAnalysisMR/) now sit as two fully separate, independently loadable modules within the same extension, each with its own CMakeLists.txt.
• Updated the top-level CMakeLists.txt so both modules get built together.
• Tested this in Slicer 5.12.3 by pointing Application Settings > Modules > Additional Module Paths at each module's own subfolder, and confirmed both load and run side by side (screenshot attached).
• Everything's now consolidated on the master branch, so both modules can be pulled/installed together going forward.