Developer Manual

This 3D Slicer extension was developed within Python. The interface relies on Python Qt. The segmentation uses SimpleITK.

The following files can also run on command line independent of 3D Slicer:

• AutomaticContour/AutomaticContourLib/AutomaticContourCmd.py : generates masks
• CorticalBreakDetection/CorticalBreakDetectionLib/CorticalBreakDetectionCmd.py : implements Peters et al's cortical break detection algorithm
• CorticalBreakDetection/CorticalBreakDetectionLib/CBCTCorticalBreakDetectionLogic.py : implements a modified version of Peters et al's cortical break detection algorithm for CBCT images
• ErosionVolume/ErosionVolumeLib/ErosionVolumeCmd.py : segments erosions

Those scripts use the SimpleITK library. To run any of those scripts on command line, navigate to the corresponding directory in a conda prompt window. The command

python [filename.py] --help

will output what command line arguments are required by the script. Follow the instructions to run the script.

Developing in 3D Slicer

Enable developer mode in 3D Slicer to make creating and editing modules easier. Navigate to Edit -> Application Settings -> Developer and toggle on Enable Developer Mode

This provides an additional menu in each widget that allows you to reload the module after edits are made. Note that only the base .py file is reloaded (ie. ErosionVolume.py). Changes made to other scripts (ie. ErosionVolumeLogic.py) in the module resources require slicer to be restarted.

3D Slicer Doxygen

3D Slicer Doxygen documentation.

3D Slicer Discussion forum

An effective way to get help from the community.

3D Slicer FAQ

Set of common development questions/answers.

SimpleITK Doxygen

SimpleITK Doxygen documentation.