Slicer Processing Module

This module defines some processing functions for use in (and requiring) 3DSlicer. As such, these functions must be imported manually when desired, using

import ablinfer.slicer.processing

Currently, two processing functions are provided.

"render_3d"

This function takes a single parameter, "smoothing", and renders the target segmentation in 3D.

"seged"

This function provides complete access to the 3DSlicer Segmentation Editor, though it’s not particularly friendly.The actions correspond to the active effects of the segmentation editor using the same names: the string action is passed directly to the segmentation editor. Typically, determining the parameter names will require some searching and some trials. The best place to look is likely the Slicer Segment Editor Python modules; the SegmentEditor*Effect.py files are relatively friendly. The action is usually found in the __init__ method as scriptedEffect.name and the default values/available parameters are usually in the setMRMLDefaults method.

For example, to remove all islands but the largest from all segments, the processing section in the model specification would be (note the capitalization in action and params):

{
    "name": "Island Removal",
    "...",
    "operation": "seged",
    "action": "Islands",
    "targets": [],
    "params": {
        "Operation": "KEEP_LARGEST_ISLAND",
        "MinimumSize": 1
    }
}

(NB: despite MinimumSize being uneditable in Slicer [at the time of this writing], it does actually impact island removal).