organoid_tracker.imaging.file_loader module

An abstract file loader that can open certain file types (images, tracking data) and load them into an experiment. The program ships with several built-in file loaders, which just wrap functions like organoid_tracker.imaging.io.load_data_file(…). It’s fine to call those functions directly. But using this system, the GUI can track which file formats are supported (for the dialogs or drag-and-drop), and plugins can add support for additional file formats.

class organoid_tracker.imaging.file_loader.FileLoader

Bases: ABC

A file handler that can open certain file types (images, tracking data) and load them into an experiment.

abstract get_file_patterns() → set[str]: Returns a set of file patterns (like “*.tif”) that this handler can open. Patterns should be in lower case.

abstract get_name() → str: Returns the name of this file handler, for example “TIFF image sequence”.

abstract get_type() → FileLoaderType: Returns the type of file that this handler can open.

abstract load_file_interactive(file_path: str, *, into: LoadInto) → bool

Loads the file at the given path and adds its contents into the given experiment. This method is allowed to interact with the user, for example by showing a dialog to ask for additional information.

If a file loader wants to add extra tabs to the GUI (for example, when loading multiple image sequences), those can be added to the create_extra_tabs list. This list should start empty, and any Experiment instances added to it will be shown in extra tabs.

Returns whether loading was successful. If loading was cancelled or failed, return False.

Note: if you’re replacing the image loader, make sure to call experiment.images.close_image_loader() first, to avoid a memory and file handler leak.

class organoid_tracker.imaging.file_loader.FileLoaderType(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

The type of file that a FileHandler can open.

This influences a few things in the GUI: - In which loading button the handler shows up (image loading button vs tracking data button). - For tracking data, a warning is shown first if there were any unsaved changes.

When you’re loading a file format that contains both images and tracking data, prefer TRACKING. Alternatively, you can register two loaders, one that only loads the image data from the file, and one that only loads the tracking data.

IMAGE = 1

TRACKING = 2

class organoid_tracker.imaging.file_loader.LoadInto(experiment: Experiment)

Bases: object

When loading a file, there will always be one open experiment already. In addition, you can create extra experiments, which will be shown in extra tabs added to the GUI.

allow_extra_tabs: bool = True

experiment: Experiment

extra_experiments: List[Experiment]

next_experiment() → Experiment: First time this method is called, it returns the main experiment. Subsequent calls create new experiments, add those to the self.extra_tabs list, and then return them.