TPS2TOPAS with Phase Space Scoring

[jsheetz1]

• Added Phase space scoring capabilities
• Added file path conversion for WSL users
• GTV selection for phase space scoring
• added example input file and updated the current input file template to reflect my changes. Example is included to avoid any confusion in formatting

[JoseRamosMendez]

Hi there!
Thanks for adding phase-space scoring and WSL support. Before we can merge this, please address the following:

• Update your branch with the latest changes from develop and resolve the conflicting files (input_handling and write_PCF).

• The script currently fails to run because it cannot find wslPath. Please include this dependency or, better, replace it with built-in Python path handling tool.

• Use the same capitalization for PhaseSpace everywhere. Some parts currently use PhaseSpace, while others use (lowercase) phasespace.

• Please check the WSL file-copy command. Code running inside WSL normally uses cp, not the Windows copy command.

• Selection of ROI based on numbers starts at 1 and expects a certain order (in ChooseROIs for ROI_List[i+1]), but this might not be a warranty in all DICOM RTSTRUCT files. You could loop through the elements instead.

• Fix the ROI file-writing code. Some lines format the filename after writing the text, this could cause the program to crash.

• Check that an input file has enough lines before reading values from it (e.g., before accessing inputInfo[9]). A short or incomplete file can currently cause an unexpected error.

• Please avoid breaking existing input files. The new operating-system line makes the older format unusable. Add protection to continue supporting the old format, and add to the README how users must update their files.

• Add tests for the new features in ./tests/, including phase-space scoring, multiple ROIs, WSL paths, incomplete input files, and older input files.

• After updating the branch, please run:

  python3 -m pytest -q
  python3 -m py_compile *.py

Cheers!