# guanaco
> Python library for doing 3D CTF correction
[](https://github.com/psf/black)
[](https://lgtm.com/projects/g/jmp1985/guanaco/context:python)
[](https://lgtm.com/projects/g/jmp1985/guanaco/alerts/)
[](https://github.com/rosalindfranklininstitute/guanaco/actions/workflows/python-package.yml)
[](https://github.com/rosalindfranklininstitute/guanaco/actions/workflows/python-publish.yml)
[](https://zenodo.org/badge/latestdoi/337997172)
## 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
```sh
export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install git+https://github.com/rosalindfranklininstitute/guanaco.git@master
```
To install from source, clone this repository. The repository has a submodule
for pybind11 so after cloning the repository run
```sh
git submodule update --init --recursive
```
Then do the following:
```sh
export CUDACXX=${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:
```sh
export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
python -m pip install .[test]
```
## Installation for developers
To install for development, clone this repository and then do the following:
```sh
export CUDACXX=${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:
```sh
pytest
```
## Usage
To do a tomographic reconstruction with no CTF correction do something do the following
```sh
guanaco -i images.mrc -o rec.mrc -d gpu
```
To correct all images with the same single defocus something do the following
```sh
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
```sh
guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7 --ndf=10
```
## Issues
Please use the [GitHub issue tracker](https://github.com/rosalindfranklininstitute/guanaco/issues) 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.
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