utils#

init_sample_manager_and_processors(folder='', configs=None)[source]#

Bootstrap a SampleManager and core pipeline processors for a given experiment folder.

This is a convenience factory for headless / script usage (no GUI, no ExperimentController). It builds a SampleManager from the folder’s config files, then instantiates and sets up the StitchingProcessor and RegistrationProcessor so they are ready for immediate use.

Deprecated since version 3.1: The configs parameter is deprecated and will be removed in a future version. Provide a folder path instead.

Parameters:

  • folder (str | Path) – Path to the experiment directory containing the sample and pipeline config files. Must be non-empty.

  • configs (Any, optional) – Deprecated. Previously accepted pre-loaded config objects. Passing a non-None value raises a DeprecationWarning.

Returns

dict[str, SampleManager | StitchingProcessor | RegistrationProcessor]

A dictionary with the following keys:

  • 'sample_manager'SampleManager

    Fully initialised sample manager with workspace and channel metadata.

  • 'stitcher'StitchingProcessor

    Stitching processor, set up and ready to run stitching steps.

  • 'registration_processor'RegistrationProcessor

    Registration processor, set up and ready to run alignment steps.

Raises:

  • ValueError – If folder is empty or falsy.

  • DeprecationWarning – If configs is not None (legacy call-site).