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‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/

‎LICENSE‎

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MIT License
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Copyright (c) 2022 wiktorowski211
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# DEnse Displacement Sampling - deformable image registration
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This package provides Python wrapper around [DEEDS](https://github.com/mattiaspaul/deedsBCV), an efficient version for 3D discrete deformable image registration which is reaching the highest accuracy in several benchmarks [[1]](https://pubmed.ncbi.nlm.nih.gov/27254856/)[[2]](https://arxiv.org/abs/2109.11572) and serves as a good baseline for new solutions.
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## Referencing and citing
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If you use this implementation or parts of it please cite:
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>"MRF-Based Deformable Registration and Ventilation Estimation of Lung CT."
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by Mattias P. Heinrich, M. Jenkinson, M. Brady and J.A. Schnabel
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IEEE Transactions on Medical Imaging 2013, Volume 32, Issue 7, July 2013, Pages 1239-1248
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http://dx.doi.org/10.1109/TMI.2013.2246577
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and
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>"Multi-modal Multi-Atlas Segmentation using Discrete Optimisation and Self-Similarities"
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by Mattias P. Heinrich, Oskar Maier and Heinz Handels
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VISCERAL Challenge@ ISBI, Pages 27-30 2015
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http://ceur-ws.org/Vol-1390/visceralISBI15-4.pdf
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## Installation
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Current version requires an Unix-based system.
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```
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pip install git+https://github.com/wiktorowski211/deeds-registration
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```
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## Usage
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```
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from deeds import registration
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import SimpleITK as sitk
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fixed = sitk.ReadImage(PATH)
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moving = sitk.ReadImage(PATH)
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moved = registration(fixed, moving)
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```
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## Limitations
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Input images must:
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- have the same dimensions,
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- be a SimpleITK image object.

‎deeds/__init__.py‎

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from .registration import registration

‎deeds/libs/LICENSE‎

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MIT License
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Copyright (c) 2017 mattiaspaul
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎deeds/libs/__init__.py‎

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‎deeds/libs/deedsBCV.so‎

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‎deeds/registration.py‎

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import os
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import tempfile
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import subprocess
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try:
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import importlib.resources as pkg_resources
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except ImportError:
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# Try backported to PY<37 `importlib_resources`.
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import importlib_resources as pkg_resources
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from .utils import *
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def registration(fixed, moving, verbose=True):
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libs_path = pkg_resources.files('deeds.libs')
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deeds_path = os.path.join(libs_path, "deedsBCV.so")
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stdout = None if verbose else subprocess.DEVNULL
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# TODO: Use in-memory communication instead of the filesystem
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with tempfile.TemporaryDirectory() as tmp_dir:
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fixed_path = os.path.join(tmp_dir, "fixed.nii.gz")
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moving_path = os.path.join(tmp_dir, "moving.nii.gz")
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moved_path = os.path.join(tmp_dir, "moved")
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save_nifty(fixed, fixed_path)
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save_nifty(moving, moving_path)
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command = f"{deeds_path} -F {fixed_path} -M {moving_path} -O {moved_path}"
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subprocess.run(command.split(), stdout=stdout)
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moved_path = f"{moved_path}_deformed.nii.gz"
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moved = load_nifty(moved_path)
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return moved

‎deeds/tests/__init__.py‎

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‎deeds/tests/test_registration.py‎

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import unittest
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from ..registration import registration
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from ..utils import *
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class TestStringMethods(unittest.TestCase):
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def test_deeds_registration(self):
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fixed = load_nifty('samples/fixed.nii.gz')
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moving = load_nifty('samples/moving.nii.gz')
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moved = registration(fixed, moving)
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dice_before = compute_dice_score(fixed, moving)
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dice_after = compute_dice_score(fixed, moved)
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self.assertGreater(dice_after, dice_before)

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