https://github.com/dyollb/itktopologycontrol

ITK external module to control topology of binary mask regions
https://github.com/dyollb/itktopologycontrol

cpp image-preprocessing itk itk-module python segmentation

Last synced: 12 months ago
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ITK external module to control topology of binary mask regions

• Host: GitHub
• URL: https://github.com/dyollb/itktopologycontrol
• Owner: dyollb
• License: apache-2.0
• Created: 2022-08-24T19:08:10.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-09-10T06:10:53.000Z (over 1 year ago)
• Last Synced: 2025-03-27T10:21:33.485Z (about 1 year ago)
• Topics: cpp, image-preprocessing, itk, itk-module, python, segmentation
• Language: C++
• Homepage:
• Size: 5.24 MB
• Stars: 1
• Watchers: 1
• Forks: 5
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# ITKTopologyControl

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[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://github.com/dyollb/ITKTopologyControl/blob/main/LICENSE)

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## Overview

This is a module for the Insight Toolkit ([ITK](https://github.com/InsightSoftwareConsortium/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.

```python

    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):

```python

    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')

```

![Closing holes in skull](https://raw.githubusercontent.com/dyollb/ITKTopologyControl/main/doc/close_holes_skull.gif)

## Installation

To install the binary Python packages:

```shell

  python -m pip install itk-topologycontrol

```