Custom

Beyond the built-in step types described previously, pytribeam also enables users to create their own custom scripts to run during an acquisition experiment. This can be useful for prototyping new workflows, or performing unique operations that are specific to the user's instrument or configuation. pytribeam offers this adapter for advanced users that are comfortable with creating their own automation workflows, either with the lower-level functionality of pytribeam package, which is described in API documentation, or through any other executable package the users have access to.

All custom scripts are executed as a subprocess via the main python loop. To assist in various operations that may be of interest to users of the Custom step type, pytribeam creates a .yml file prior to the execution of the subprocess called slice_info.yml that is saved in the user-defined experimental directory. This file is automatically deleted after sucessfull execution of the subprocess and contains the following information: - exp_dir: The experimental directory as a string - slice_number: The current active slice number as an integer

Additional information could be included in the .yml file upon request for future releases.

The Custom step type takes the following parameters:

• script_path (str): The path of the script the user intends to run. The file must exist, and does not necessarilly have to a python file (see below)

• executable_path (str): The path to any valid executable installed on the machine. The executable must exist, and should be able to run the script_path as an argument from the command line.

As Custom scripts were generally designed for python scripts using the subprocess module, users should expect the following to be executable from the command line while using a Custom script:

path/to/exectuable.exe path/to/script.file_extension