classconvergence
Plot the class distribution as a function of iteration from a Class2D or Class3D job from RELION.
This tool was tested with star files produced by RELION-3.1.0. Earlier versions of RELION are not supported.
Acknowledgments
I would not have been able to put this tool together without the
starfile library.
Installation
I recommend to install this tool in a dedicated conda environment. You can
create one like so (replace ENV_NAME with the name you want to give to this
environment):
$ conda deactivate
$ conda create --name ENV_NAME python=3.9
$ conda activate ENV_NAME
Once the conda environment is active, you can install the tool with the following command:
$ pip install classconvergence
Usage
$ classconvergence --help
Usage: classconvergence [OPTIONS] <job_directory>
Plot the class distribution as a function of iteration from a Class2D or
Class3D job from RELION.
Options:
-c, --count Plot particle counts per class (default, same effect as
not passing any option).
-p, --percent Plot percentages of particles per class (default:
counts).
-o, --output TEXT File name to save the plot (optional: with no file name,
simply display the plot on screen without saving it;
recommended file formats: .png, .pdf, .svg or any format
supported by matplotlib).
-h, --help Show this message and exit.
