ITK external module to control topology of binary mask regions

These details have not been verified by PyPI

Project links

GitHub Statistics

View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery

Project description

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')

Closing holes in skull

Installation

To install the binary Python packages:

  python -m pip install itk-topologycontrol

Project details

These details have not been verified by PyPI

Project links

GitHub Statistics

View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery

Release history Release notifications | RSS feed

This version

1.1.0

Aug 6, 2023

1.0.1

Dec 22, 2022

1.0.0

Oct 6, 2022

0.9.0

Sep 29, 2022

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distributions

No source distribution files available for this release.See tutorial on generating distribution archives.

Built Distributions

itk_topologycontrol-1.1.0-cp311-cp311-win_amd64.whl (589.5 kB view hashes)

Uploaded Aug 6, 2023 CPython 3.11 Windows x86-64

itk_topologycontrol-1.1.0-cp311-cp311-manylinux_2_28_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.11 manylinux: glibc 2.28+ x86-64

itk_topologycontrol-1.1.0-cp311-cp311-macosx_10_9_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.11 macOS 10.9+ x86-64

itk_topologycontrol-1.1.0-cp310-cp310-win_amd64.whl (589.5 kB view hashes)

Uploaded Aug 6, 2023 CPython 3.10 Windows x86-64

itk_topologycontrol-1.1.0-cp310-cp310-manylinux_2_28_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.10 manylinux: glibc 2.28+ x86-64

itk_topologycontrol-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.10 macOS 10.9+ x86-64

itk_topologycontrol-1.1.0-cp39-cp39-win_amd64.whl (590.0 kB view hashes)

Uploaded Aug 6, 2023 CPython 3.9 Windows x86-64

itk_topologycontrol-1.1.0-cp39-cp39-manylinux_2_28_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.9 manylinux: glibc 2.28+ x86-64

itk_topologycontrol-1.1.0-cp39-cp39-macosx_10_9_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.9 macOS 10.9+ x86-64

itk_topologycontrol-1.1.0-cp38-cp38-win_amd64.whl (614.3 kB view hashes)

Uploaded Aug 6, 2023 CPython 3.8 Windows x86-64

itk_topologycontrol-1.1.0-cp38-cp38-manylinux_2_28_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.8 manylinux: glibc 2.28+ x86-64

itk_topologycontrol-1.1.0-cp38-cp38-macosx_10_9_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.8 macOS 10.9+ x86-64

itk_topologycontrol-1.1.0-cp37-cp37m-win_amd64.whl (614.0 kB view hashes)

Uploaded Aug 6, 2023 CPython 3.7m Windows x86-64

itk_topologycontrol-1.1.0-cp37-cp37m-manylinux_2_28_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.7m manylinux: glibc 2.28+ x86-64

itk_topologycontrol-1.1.0-cp37-cp37m-macosx_10_9_x86_64.whl (1.3 MB view hashes)

Uploaded Aug 6, 2023 CPython 3.7m macOS 10.9+ x86-64

Hashes for itk_topologycontrol-1.1.0-cp311-cp311-win_amd64.whl

Hashes for itk_topologycontrol-1.1.0-cp311-cp311-win_amd64.whl
Algorithm	Hash digest
SHA256	`2c2328936d9699dcc6b371eb4fb5a2d67872583d18429e04b5e7774702ab7fd6`
MD5	`702a876d4925cf8baef6ad83170db9fe`
BLAKE2b-256	`bac16a540b1dee18bb3c83c58d6d68e314fe4b45cfd008facde94ed7b9625112`

Hashes for itk_topologycontrol-1.1.0-cp311-cp311-manylinux_2_28_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp311-cp311-manylinux_2_28_x86_64.whl
Algorithm	Hash digest
SHA256	`091de6e0af2518a1a7d43b3acc3b86187967ed31535430157487b643dc3e8d80`
MD5	`d4556816d6d4bba4d7b245056252a69a`
BLAKE2b-256	`8ae3abf5ff6d0554eb9bbf9e316a23d45d3fd0315c8bdb5edb4758537f0fe7fe`

Hashes for itk_topologycontrol-1.1.0-cp311-cp311-macosx_10_9_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp311-cp311-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`3086a29a1a86260cfa8d6cf70c3876b1859e10a1f0dc45df754b46f08d22ee5a`
MD5	`af435c4c322a661e0177fcaa92512071`
BLAKE2b-256	`6db4808cb28815bb521d81f32dace21695ff7cbae042662c05b1c111d53e31f9`

Hashes for itk_topologycontrol-1.1.0-cp310-cp310-win_amd64.whl

Hashes for itk_topologycontrol-1.1.0-cp310-cp310-win_amd64.whl
Algorithm	Hash digest
SHA256	`56802f2010899ebf134c17f4b6f60901b6209727990829b6083a29cf20acc65f`
MD5	`9cd5d1627e7f7aeb30d148443d1d5d59`
BLAKE2b-256	`ee35099abed1d7f666b24e7053b731a934d52a598c3e8b3f4be49d01603088aa`

Hashes for itk_topologycontrol-1.1.0-cp310-cp310-manylinux_2_28_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp310-cp310-manylinux_2_28_x86_64.whl
Algorithm	Hash digest
SHA256	`c2661974a312781e422f23a559b950fa5d5198c7df2495a847140f43f5c77f12`
MD5	`a3eb85c214bd20a40377b5c4a60ba4b1`
BLAKE2b-256	`b48d6b2b68010bc4f43b18b16f732fa928091399748ead56239822dc2b992754`

Hashes for itk_topologycontrol-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`4aadfe26eb45ca9aaa1dbd17b757480befffe09352d30786c1075915a07c2066`
MD5	`f82fbed5a0076b0352b38c5633bdf522`
BLAKE2b-256	`e74773039d387b806064783409d307f937e1300835ce242e5cb465799c7a2cf8`

Hashes for itk_topologycontrol-1.1.0-cp39-cp39-win_amd64.whl

Hashes for itk_topologycontrol-1.1.0-cp39-cp39-win_amd64.whl
Algorithm	Hash digest
SHA256	`1966309b4b5080e5c8755ca02ed4cc0bdc990fcfa376ab154e5bfc217c8fa049`
MD5	`50f4293909c9345f2169c5a072cd3be2`
BLAKE2b-256	`18eb5f7263a1ba81b602c55602aec2c5bec305088cb98377c118bcef76ee58da`

Hashes for itk_topologycontrol-1.1.0-cp39-cp39-manylinux_2_28_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp39-cp39-manylinux_2_28_x86_64.whl
Algorithm	Hash digest
SHA256	`f2bc6922f3beebc4f52ffef11ba1b124839474f7e72491435332204dd8dc0de4`
MD5	`bad943d339c645f08803d1aea84a5456`
BLAKE2b-256	`56abab6ce012e4027539937723faba0cc9871a3affab0fbd7a760995414875a9`

Hashes for itk_topologycontrol-1.1.0-cp39-cp39-macosx_10_9_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`59ac98907366d88a2d9ea4aa25bcb5d194fa686e277942b1b4db5432cc400cab`
MD5	`f8efe4a62ead435dff7438554c0ef604`
BLAKE2b-256	`784b21a72060ccb7b90793e041e664f37c06036ae054401d8e9a8193be2f8267`

Hashes for itk_topologycontrol-1.1.0-cp38-cp38-win_amd64.whl

Hashes for itk_topologycontrol-1.1.0-cp38-cp38-win_amd64.whl
Algorithm	Hash digest
SHA256	`33eaa640c64194ea55cd2b15597cc7f3e576e100034192495e3bcf9f455d6ed7`
MD5	`5021e7361ae083061b2f67cb324ec1f3`
BLAKE2b-256	`95baef8cbdb162b63aadf97f655279fd38035540d026059921a125d787c25d70`

Hashes for itk_topologycontrol-1.1.0-cp38-cp38-manylinux_2_28_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp38-cp38-manylinux_2_28_x86_64.whl
Algorithm	Hash digest
SHA256	`e379c6d460c1076dec80fda7a1c6e4f1404ee3c78713214a27ba5902c8350209`
MD5	`26b1f3c38d78fc41a2682f4970a2c3b4`
BLAKE2b-256	`802263e40492dee85b194d6ec9fa9261e2d0d3dddc9c5228944c4f2f4f2feb49`

Hashes for itk_topologycontrol-1.1.0-cp38-cp38-macosx_10_9_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`81bc031f11ea5d5ecc8c3e3c040c675c257f0a997e48d30f4ede6bb1d478a840`
MD5	`c606f7ccea2afc1d4cb572aa83ee1104`
BLAKE2b-256	`200328de28453481ecb04b629de5f35802b978b8358e2cc2f7efa54c90c8c20b`

Hashes for itk_topologycontrol-1.1.0-cp37-cp37m-win_amd64.whl

Hashes for itk_topologycontrol-1.1.0-cp37-cp37m-win_amd64.whl
Algorithm	Hash digest
SHA256	`60c2ae316c2c6633593889b98726ad45b70ffbc16c849d9546490153071b6f32`
MD5	`11be421561867a0d2ec640e34fc08bfa`
BLAKE2b-256	`5dd304a3e556c01dba6762500a20faa2c893fcb88ff02e3340563dda7ae20be6`

Hashes for itk_topologycontrol-1.1.0-cp37-cp37m-manylinux_2_28_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp37-cp37m-manylinux_2_28_x86_64.whl
Algorithm	Hash digest
SHA256	`84a4a1f81242dc6f1654c65219407338e8b03cfb1b399ba16551695fd81010aa`
MD5	`beae80b685f6e81c31269a99a116e496`
BLAKE2b-256	`d8d0b28dabf56e4850e8b6ce1b31100a3094a6f14d9318896667ae65ee0294c8`

Hashes for itk_topologycontrol-1.1.0-cp37-cp37m-macosx_10_9_x86_64.whl

Hashes for itk_topologycontrol-1.1.0-cp37-cp37m-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`cc06bb524a73e3c030348a85a662ad8787bc567c61f22b3746614d24277d80c6`
MD5	`f951ebadfe4c2efea4136fc33cf0a510`
BLAKE2b-256	`ba38448b77237ab4f72d62905e17e9c00443efe8251e111e4b1ed353f1dc0ee1`