{
"info": {
"author": "Brian B. Avants and Nicholas Cullen",
"author_email": "stnava@gmail.com",
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"description": "\n\n# Advanced Normalization Tools in Python\n\n\n
\n\n[](https://circleci.com/gh/ANTsX/ANTsPy)\n[](https://travis-ci.org/ANTsX/ANTsPy)\n
\n\n 
\n\n\n[](https://mybinder.org/v2/gh/stnava/ANTsPyDocker/master)\n\n## About ANTsPy\n\nSearch [ANTsPy documentation at read the docs.](https://antspyx.readthedocs.io/en/latest/?badge=latest)\n\nANTsPy is a Python library which wraps the C++ biomedical image processing library [ANTs](https://github.com/ANTsX/ANTs),\nmatches much of the statistical capabilities of [ANTsR](https://github.com/ANTsX/ANTsR), and allows seamless integration\nwith numpy, scikit-learn, and the greater Python community.\n\nANTsPy includes blazing-fast IO (~40% faster than nibabel for loading Nifti images and\nconverting them to numpy arrays), registration, segmentation, statistical learning,\nvisualization, and other useful utility functions.\n\nANTsPy also provides a low-barrier opportunity for users to quickly wrap their ITK (or general C++)\ncode in Python without having to build an entire IO/plotting/wrapping code base from\nscratch - see [C++ Wrap Guide](tutorials/UsingITK.md) for a succinct tutorial.\n\nIf you want to contribute to ANTsPy or simply want to learn about the package architecture\nand wrapping process, please read the extensive [contributors guide](CONTRIBUTING.md).\n\nIf you have any questions or feature requests, feel free to open an issue or email Nick (ncullen at pennmedicine dot upenn dot edu).\n\n## Installation\n\nWe recommend that users install the latest pre-compiled binaries, which takes ~1 minute. Note\nthat ANTsPy is not currently tested for Python 2.7 support.\nCopy the following command and paste it into your bash terminal:\n\nFor MacOS:\n```bash\npip install https://github.com/ANTsX/ANTsPy/releases/download/Weekly/antspy-0.1.4-cp36-cp36m-macosx_10_7_x86_64.whl\n```\n\nFor Linux:\n```bash\npip install https://github.com/ANTsX/ANTsPy/releases/download/v0.1.4/antspy-0.1.4-cp36-cp36m-linux_x86_64.whl\n```\n\nIf the above doesn't work on your platform, then use:\n\n```\ngit clone https://github.com/ANTsX/ANTsPy\ncd ANTsPy\npython3 setup.py install\n```\nif you want more detailed instructions on installing ANTsPy, you can\nread the [installation tutorial](https://github.com/ANTsX/ANTsPy/blob/master/tutorials/InstallingANTsPy.md).\n\n------------------------------------------------------------------------------\n## ITK & VTK\n\n#### Insight Toolkit (ITK)\n\nBy default, ANTsPy will search for an existing ITK build by checking if the `ITK_DIR`\nenvironment variable is set. If that is not\nfound, it will build it for you. It does NOT require the Python wrappings for\nITK.\n\n#### Visualization Toolkit (VTK)\n\nBy default, ANTsPy will search for an existing VTK build by checking if the `VTK_DIR`\nenvironment variable is set. If that is not\nfound, it will build it for you. It does NOT require the Python wrappings for\nVTK. If you do not want VTK, then add the `--novtk` flag to setup (e.g. `python setup.py install --novtk`).\n\n## ANTsR Comparison\n\nHere is a quick example to show the similarity with ANTsR:\n\nANTsR code:\n```R\nlibrary(ANTsR)\nimg <- antsImageRead(getANTsRData(\"r16\"))\nimg <- resampleImage(img, c(64,64), 1, 0 )\nmask <- getMask(img)\nsegs1 <- atropos(a=img, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask )\n```\n\nANTsPy code:\n```python \nimport ants\nimg = ants.image_read(ants.get_data(\"r16\"))\nimg = ants.resample_image(img, (64,64), 1, 0 )\nmask = ants.get_mask(img)\nsegs1 = ants.atropos(a=img, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask )\n```\n\n## Tutorials\n\nWe provide numerous tutorials for new users: [https://github.com/ANTsX/ANTsPy/tree/master/tutorials](https://github.com/ANTsX/ANTsPy/tree/master/tutorials)\n\n[5 minute Overview](https://github.com/ANTsX/ANTsPy/blob/master/tutorials/tutorial_5min.md)\n\n[Nibabel Speed Comparison](https://github.com/ANTsX/ANTsPy/blob/master/tests/timings_io.py)\n\n[Composite registrations](https://github.com/ANTsX/ANTsPy/blob/master/tutorials/concatenateRegistrations.ipynb)\n\n## Build documentation\n\n```\ncd docs\nsphinx-apidoc -o source/ ../\nmake html\n```\n\n\n",
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