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
1 maintainer
Metadata
1 maintainer
Release files for itk-topologycontrol 1.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 38.0 MB
Release files / itk_topologycontrol-1.2.0-cp311-abi3-win_amd64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-win_amd64.whl |
|---|---|
| Size | 596.6 kB |
| Tags | CPython 3.11 Windows x86-64 abi3 |
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Release files / itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_28_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_28_x86_64.whl |
|---|---|
| Size | 2.4 MB |
| Tags | CPython 3.11 Linux glibc 2.28+ x86-64 abi3 |
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Release files / itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_28_aarch64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_28_aarch64.whl |
|---|---|
| Size | 2.2 MB |
| Tags | CPython 3.11 Linux glibc 2.28+ ARM64 abi3 |
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Release files / itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_17_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_17_x86_64.whl |
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| Size | 880.5 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 abi3 |
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Release files / itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 2.4 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 abi3 |
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Release files / itk_topologycontrol-1.2.0-cp311-abi3-macosx_11_0_arm64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-macosx_11_0_arm64.whl |
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| Size | 534.9 kB |
| Tags | CPython 3.11 abi3 macOS 11.0+ ARM64 |
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Release files / itk_topologycontrol-1.2.0-cp311-abi3-macosx_10_9_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp311-abi3-macosx_10_9_x86_64.whl |
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| Size | 654.4 kB |
| Tags | CPython 3.11 abi3 macOS 10.9+ x86-64 |
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Release files / itk_topologycontrol-1.2.0-cp310-cp310-win_amd64.whl
| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-win_amd64.whl |
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| Size | 597.1 kB |
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Release files / itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_28_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_28_x86_64.whl |
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| Size | 2.4 MB |
| Tags | CPython 3.10 Linux glibc 2.28+ x86-64 |
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Release files / itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_28_aarch64.whl
| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_28_aarch64.whl |
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| Size | 2.2 MB |
| Tags | CPython 3.10 Linux glibc 2.28+ ARM64 |
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Release files / itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_17_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_17_x86_64.whl |
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| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 2.4 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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Release files / itk_topologycontrol-1.2.0-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-macosx_11_0_arm64.whl |
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| Size | 534.1 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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Release files / itk_topologycontrol-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl |
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| Size | 653.3 kB |
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Release files / itk_topologycontrol-1.2.0-cp39-cp39-win_amd64.whl
| Download URL | itk_topologycontrol-1.2.0-cp39-cp39-win_amd64.whl |
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| Size | 597.8 kB |
| Tags | CPython 3.9 Windows x86-64 |
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| Download URL | itk_topologycontrol-1.2.0-cp39-cp39-manylinux_2_28_x86_64.whl |
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| Size | 2.4 MB |
| Tags | CPython 3.9 Linux glibc 2.28+ x86-64 |
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| Download URL | itk_topologycontrol-1.2.0-cp39-cp39-manylinux_2_28_aarch64.whl |
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Release files / itk_topologycontrol-1.2.0-cp39-cp39-manylinux_2_17_x86_64.whl
| Download URL | itk_topologycontrol-1.2.0-cp39-cp39-manylinux_2_17_x86_64.whl |
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| Size | 883.8 kB |
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| Download URL | itk_topologycontrol-1.2.0-cp39-cp39-macosx_11_0_arm64.whl |
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| Download URL | itk_topologycontrol-1.2.0-cp38-cp38-win_amd64.whl |
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| Size | 624.7 kB |
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| Download URL | itk_topologycontrol-1.2.0-cp38-cp38-manylinux_2_28_x86_64.whl |
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| Download URL | itk_topologycontrol-1.2.0-cp38-cp38-manylinux_2_28_aarch64.whl |
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| Tags | CPython 3.8 Linux glibc 2.28+ ARM64 |
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| Download URL | itk_topologycontrol-1.2.0-cp38-cp38-manylinux_2_17_x86_64.whl |
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| Size | 883.8 kB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
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| Size | 2.4 MB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
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Release files / itk_topologycontrol-1.2.0-cp38-cp38-macosx_10_9_x86_64.whl
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