crashs-cbstools-bindings

Python bindings to select algorithms from cbstools-public (the CBS Tools Java library developed by Pierre-Louis Bazin and colleagues at the Max Planck Institute for Human Cognitive and Brain Sciences), used by CRASHS for its CRUISE-based cortical reconstruction pipeline.

Why this exists

CRASHS previously reached this code through NighRes, which wraps cbstools-public via JCC (compiling the Java to a jar and statically embedding a JVM into a compiled Python extension). That approach has never shipped a prebuilt PyPI wheel and requires a JDK/JCC/Python-headers build step at install time.

Instead, this package AOT-compiles the five cbstools-public classes CRASHS needs into a native shared library using GraalVM Native Image (no JVM at runtime), and exposes them to Python via ctypes. The result ships as an ordinary platform-specific binary wheel — no Java, JDK, or JVM is needed to install or use this package, only to build it from source.

This is split out from the crashs repo into its own package specifically because it changes rarely (only when the underlying cbstools-public algorithms need a bugfix or a new algorithm is added) while crashs itself changes often — bundling them together meant every crashs iteration paid for slow, large, multi-platform compiled-wheel builds it didn't need.

Installation

pip install crashs-cbstools-bindings

Building from source

Building from source requires a GraalVM JDK with the native-image component (GraalVM for JDK 21+ ships this by default) on PATH — only at build time, not at runtime.

git clone --recurse-submodules https://github.com/pyushkevich/crashs-cbstools-bindings
cd crashs-cbstools-bindings

# Build the native library once
bash native/scripts/build_native.sh macos-14   # or: ubuntu-latest, windows-2022

# Regular (non-editable) install picks up the native library correctly:
pip install .

Note: pip install -e . (editable install) does not work for this package, because the compiled native library is only copied into the installed package location, not back into the source tree that an editable install imports from. For local development, build once as above, then manually stage the artifact into the source tree before installing editable:

mkdir -p src/crashs_cbstools_bindings/_native_lib src/crashs_cbstools_bindings/_native_data
cp native/build/out/libcbstools_native.* src/crashs_cbstools_bindings/_native_lib/
cp -r native/data/topology_lut src/crashs_cbstools_bindings/_native_data/
pip install -e .

API

Five functions, one per wrapped cbstools-public algorithm, taking/returning numpy arrays (mirroring nighres's own function signatures and Fortran-order conventions):

  • topology_correction
  • cruise_cortex_extraction
  • levelset_to_mesh
  • surface_inflation
  • volumetric_layering

See src/crashs_cbstools_bindings/__init__.py for exact signatures, and tests/test_bindings.py for usage examples.

License and attribution

This repository's own code (the Java @CEntryPoint wrapper layer and the Python ctypes bindings) is MIT-licensed — see LICENSE. The compiled native library this package ships is a derivative work of cbstools-public and is additionally subject to cbstools-public's license, Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0). See THIRD_PARTY_LICENSES.md for full attribution details, the exact vendored commit, and what was and wasn't modified.

Project links

Data verified by PyPI on Sep 15, 2026
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Avatar for pyushkevich from gravatar.com pyushkevich

Credits

Author: Paul Yushkevich

GitHub Statistics

Data verified by PyPI on Sep 15, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License

Requires

Python >=3.8

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0.1.0

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