Internal:SlicerExtensions

PBNRR Extension

Repository: https://github.com/aangelos28/PBNRR

Status: UPLOADED

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  PBNRR running on the upcoming Slicer 4.9 release.

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  PBNRR running on the current Slicer 4.8.1 release (compiled with Qt 5 and VTK 9).

APBNRR Extension

Status: IMPLEMENTING LOCAL INTERMEDIARY MODULE LOGIC

Due to the conflict of ITKDev and the ITK version of Slicer, creating a locally executable APBNRR module for Slicer is not conventionally possible.

But I have figured out another way to do this. I will create a scriptable Python module for Slicer that will act as an intermediary between a portable (that statically links all dependencies) pre-compiled APBNRR executable. This will create the illusion that the user actually uses a traditional external module, which is not the case. The intermediary module will pass around data between the APBNRR executable and Slicer, and because of the deep integration of the Python environment with Slicer, results can instantly be displayed, similarly to a standard external module.

The skeleton of the intermediary module can also be reused for the remote execution module to save time, modified to accommodate remote execution and communicate via SSH.

Checklist

• [DONE] Create pre-compiled portable APBNRR executable.

 Statically Linked: ITK, VTK 6.1.0, BOOST 1.58.0, CGAL 4.0, PDM, CBC3D, GMP, MPFR
 Executable Size: 38 MB

 Note: Full portability may not be possible due to some system libraries like LIBC. If there are errors, the user can compile APBNRR themselves and the intermediary module should still work using it. I later plan to utilize the SuperBuild scripts I developed for the earlier design in this portion to create an automatic build system for APBNRR.

• Implement intermediary "executor" Python scriptable module in Slicer for local execution of APBNRR
  • [DONE] Design UI
  • [DONE] Implement UI
  • [IN PROGRESS] Implement logic
  • Test and debug
• Implement intermediary "executor" Python scriptable module in Slicer for remote execution of APBNRR and parameter optimization (reuse local module skeleton)
  • Design UI
  • Implement UI
  • Implement logic
  • Test and debug

Local Intermediary Module

Local Intermediary Module Logic

• Successful initial run
• Design will work

Checklist

• Implement external APBNRR execution from Slicer (required sanitized environment)
• Test external APBNRR execution
• Implement external APBNRR execution monitoring to pipe stdout to a Slicer window and detect when APBNRR has finished executing
• Implement constraints to prevent multiple executions of APBNRR simultaneously, and add a way to terminate APBNRR on demand.
• Implement automatic APBNRR output loading when APBNRR has finished

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  APBNRR Local Intermediary Module on Slicer 4.8 Successful Run

Local Intermediary Module UI

• Robust input validation via regular expressions and constraints
• Thread count limitation based on total threads available on running system
• Automatic file extensions for file dialogs
• Logical clustering of fields for easier memorization and emphasis
• Supports Slicer 4.8.x and 4.9

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  APBNRR Local Intermediary Module UI on Slicer 4.8 (a)

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  APBNRR Local Intermediary Module UI on Slicer 4.8 (b)

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  APBNRR Local Intermediary Module UI on Slicer 4.8 (c)