The aim of this package is to provide real-time 3D visualization in Python for specifically, but not limited to, biomedical data. The library is based on LibCarna.
See libcarna.readthedocs.io for examples and documentation.
- Only 8bit and 16bit volume data are supported at the moment.
- Only a subset of rendering stages is exposed to Python yet.
- Build process is currently limited to Linux-based systems.
General dependencies are listed in environment.yml. Further dependencies for testing are listed in test/requirements.txt, and those for the documentation in docs/requirements.txt.
The easiest way to install and use the library is to use one of the binary Conda packages:
conda install bioconda::libcarna-pythonIf you encounter an error that looks like below,
Failed expression: pimpl->eglDpy != EGL_NO_DISPLAY
then you must install the EGL implementation suitable for your rendering hardware (e.g., sudo apt install libegl1
installs a meta package that automatically chooses the right implementation, or libegl-mesa0 for software rendering).
There is a build script for Ubuntu Linux which builds a wheel file:
LIBCARNA_PYTHON_BUILD_DOCS=1 LIBCARNA_PYTHON_BUILD_TESTS=1 ./linux_build.bashAdaption to other distributions should be self-explanatory.
After building the wheel file, it can be installed using:
pip install --force-reinstall build/dist/libcarna_python-*.whlTo build against a development version of LibCarna, install it locally via
LIBCARNA_SRC_PREFIX="../LibCarna" ./install_libcarna_dev.bashwhere you make LIBCARNA_SRC_PREFIX point to the source directory.
This will create a local directory .libcarna-dev. The build process will give precedence to LibCarna from this directory over other versions. Simply remove .libcarna-dev to stop building agaisnt the development version of LibCarna.