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.
1 maintainer
Metadata
1 maintainer
Release files for guanaco 0.3.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| guanaco-0.3.4.tar.gz | 825.1 kB | With provenance | Details |
Release files / guanaco-0.3.4.tar.gz
| Download URL | guanaco-0.3.4.tar.gz |
|---|---|
| Size | 825.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
08749b407c30dd2955fc8447dc1e5f7d48edd8234a14c8581a5e7c862737e324
|
|
BLAKE2b-256 checksum How to use checksums |
677f6d23126b30a35473440b5fd690a2945e6d83956fa3188d310655a3634429
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Aug 7, 2025.
Transparency logSecurity for guanaco 0.3.4
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 1 file in this release has been uploaded with provenance metadata.
Attestation for guanaco-0.3.4.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Aug 7, 2025.
Transparency logA note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
