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_correctioncruise_cortex_extractionlevelset_to_meshsurface_inflationvolumetric_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.
1 maintainer
Metadata
1 maintainer
Release files for crashs-cbstools-bindings 0.1.1
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