Analysis And Assess

Notes

  • User requested an analysis of neurongraph.cpp and an assessment of its documentation.
  • The file uses Doxygen-style comments for most functions and methods.
  • Some referenced methods (e.g., setSoma, removeSomaSegment) are not present in neurongraph.cpp; may be implemented elsewhere or missing.
  • removeSomaSegment is implemented in neuronoperations.cpp.
  • User requested analysis and documentation generation for neuronoperations.cpp methods.
  • All methods in neuronoperations.cpp are now documented with Doxygen-style comments.
  • User requested analysis and documentation generation for bindings.cpp methods.
  • All methods in bindings.cpp are now documented with Doxygen-style and inline comments.
  • User requested analysis and documentation generation for neurontrunks.cpp methods.
  • All methods in neurontrunks.cpp are now documented with Doxygen-style comments.
  • Function declaration syntax issues (dot vs. scope resolution operator) were found in neurontrunks.cpp and are being addressed.
  • Doxygen documentation is being (re)added to all methods in neurontrunks.cpp per user request; several methods are now complete.
  • User requested documentation for neuronugx.cpp.
  • File-level and method-level Doxygen documentation has been added to neuronugx.cpp (writeToFileUGX, readFromFileUGX).
  • User requested documentation for utils.cpp.
  • File-level and method-level Doxygen documentation has been added to utils.cpp.
  • User requested documentation for callbacks.cpp.
  • File-level and method-level Doxygen documentation has been added to callbacks.cpp.
  • User requested documentation for draw_utils.cpp.
  • File-level and method-level Doxygen documentation has been added to draw_utils.cpp.
  • User requested documentation for globals.cpp and opgl_utils.cpp.
  • File-level Doxygen documentation has been added to globals.cpp.
  • File-level and method-level Doxygen documentation has been added to opgl_utils.cpp.
  • User requested documentation for all header files in include/project and include/viewer directories.
  • Documentation for neurongraph.h in include/project has been added.
  • Documentation for utils.h in include/project has been added.
  • Documentation for draw_utils.h in include/viewer has been added.
  • Documentation for callbacks.h in include/viewer has been added.
  • Documentation for globals.h in include/viewer has been added.
  • Documentation for opgl_utils.h in include/viewer has been added.
  • User reported a possible bug: radius information appears magnified in neuronviewer.cpp; investigation into how radius is handled/scaled is required.
  • Radius scaling bug fixed: drawSimpleSphere now uses node.radius in renderSWC, so spheres now reflect actual SWC radii.
  • New issue: soma node (id 1, pid -1) appears too large; need to investigate if special handling or scaling for soma nodes is required.

Task List

  • Analyze neurongraph.cpp file structure and content
  • Assess the quality and completeness of documentation in neurongraph.cpp
    • Check for missing or undocumented methods referenced in comments
  • Analyze neuronoperations.cpp file structure and content
  • Generate annotation/documentation for all methods in neuronoperations.cpp
  • Analyze bindings.cpp file structure and content
  • Generate annotation/documentation for all methods in bindings.cpp
  • Analyze neurontrunks.cpp file structure and content
  • Generate annotation/documentation for all methods in neurontrunks.cpp
    • Document getNeighborMap
    • Document getTrunks
    • Document assembleTrunks (basic version)
    • Document allLinearSplineResampledTrunks
    • Document allCubicSplineResampledTrunks
    • Document linearSplineResampleTrunk
    • Document cubicSplineResampleTrunk
    • Document generateRefinements
  • Analyze neuronugx.cpp file structure and content
  • Generate annotation/documentation for all methods in neuronugx.cpp
  • Analyze utils.cpp file structure and content
  • Generate annotation/documentation for all methods in utils.cpp
  • Analyze callbacks.cpp file structure and content
  • Generate annotation/documentation for all methods in callbacks.cpp
  • Analyze draw_utils.cpp file structure and content
  • Generate annotation/documentation for all methods in draw_utils.cpp
  • Analyze globals.cpp file structure and content
  • Generate annotation/documentation for all methods in globals.cpp
  • Analyze opgl_utils.cpp file structure and content
  • Generate annotation/documentation for all methods in opgl_utils.cpp
  • Document neurongraph.h in include/project
  • Document utils.h in include/project
  • Document draw_utils.h in include/viewer
  • Document callbacks.h in include/viewer
  • Document globals.h in include/viewer
  • Document opgl_utils.h in include/viewer
  • Document all header files in include/viewer
  • Investigate radius scaling/handling in neuronviewer.cpp and related headers
    • Fix drawSimpleSphere to use node.radius
    • Investigate and correct soma node (id 1) rendering/size

Current Goal

  • Investigate and correct soma node rendering/size