guanaco

Python library for doing 3D CTF correction

Installation

In order to build this package, the following dependencies are required:

• The CUDA toolkit
• FFTW

To install from the github repository do the following

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install git+https://github.com/rosalindfranklininstitute/guanaco.git@master

To install from source, clone this repository. The repository has a submodule for pybind11 so after cloning the repository run

git submodule update --init --recursive

Then do the following:

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install .

If you would like to run the tests then, clone this repository and then do the following:

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install .[test]

Installation for developers

To install for development, clone this repository and then do the following:

export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install -e .

Testing

To run the tests, follow the installation instructions for developers and then do the following:

pytest

Usage

To do a tomographic reconstruction with no CTF correction do something do the following

guanaco -i images.mrc -o rec.mrc -d gpu

To correct all images with the same single defocus something do the following

guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7

To correct all images with the same defocus range something do the following

guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7 --ndf=10

Issues

Please use the GitHub issue tracker to submit bugs or request features.

License

Copyright Diamond Light Source and Rosalind Franklin Institute, 2021

Distributed under the terms of the GPLv3 license, guanaco is free and open source software.