CAREamics copier template

The CAREamics copier template helps you build CAREamics scripts using intuitive prompting in the console. The output is Python script that you can run to train and predict on your own data.

At the end of the process, you will have created the following files:

my_project_name/
└── experiment_name/
    ├── experiment_name.py
    └── config.yaml

Where experiment_name.py is the main script that you can run to train and predict on your data. The config.yaml file contains the configuration for the experiment, which you can reuse in other contexts (e.g. with similar data).

How to use CAREamics copier template

1. Install CAREamics in an environment.
2. Install copier and black.

   pip install copier black

3. Run copier with the CAREamics template.

   copier copy gh:CAREamics/careamics-copier my_project_name

Run the generated script

If your paths are correct, you can simply run the generated script with:

python my_project_name/experiment_name/experiment_name.py

Where my_project_name is the name you provided when running copier, and experiment_name is the name of the experiment you entered during the prompting process.

The script does not work, what should I do?

First and foremost, make sure that the paths to your data are correct in the python script. You can modify them after the script has been generated.

If you encounter any issues with the generated script, please open an issue.