ITKTopologyControl

Overview

This is a module for the Insight Toolkit (ITK). The module includes a filter called FixTopologyCarveOutside which works like morphological closing, except that in the "erode" phase topological constraints are enforced to avoid re-opening holes. It is able to close holes in thin layers (e.g. skull) with a minimal thickness.

    import itk
    skull_mask = itk.imread('path/to/skull_with_holes.mha').astype(itk.US)

    ImageType = type(skull_mask)
    MaskType = itk.Image[itk.UC, 3]

    top_control = itk.FixTopologyCarveOutside[ImageType, ImageType, MaskType].New()
    top_control.SetInput(skull_mask)
    top_control.SetRadius(5)
    top_control.Update()
    skull_mask_closed = top_control.GetOutput()

    itk.imwrite(skull_mask_closed, 'skull_mask_closed.mha')

Or using a custom mask (e.g. a sphere around a hole):

    import itk
    custom_mask = itk.imread('path/to/custom_mask.mha').astype(itk.UC)
    skull_mask = itk.imread('path/to/skull_with_holes.mha').astype(itk.US)
    skull_mask_closed = itk.fix_topology_carve_outside(skull_mask, MaskImage=custom_mask, Radius=5)
    itk.imwrite(skull_mask_closed, 'skull_mask_closed.mha')

Installation

To install the binary Python packages:

  python -m pip install itk-topologycontrol