delta.pipeline.Pipeline

class delta.pipeline.Pipeline(xpreader: xpreader, resfolder: Optional[Union[str, Path]] = None, on_the_fly: bool = False, reload: bool = False, verbose: int = 1)

Main Pipeline class to process all positions.

__init__(xpreader: xpreader, resfolder: Optional[Union[str, Path]] = None, on_the_fly: bool = False, reload: bool = False, verbose: int = 1)

Initialize Pipeline

Parameters

xpreaderobject

utilities xpreader object.

resfolderstr or Path, optional

Path to folder to save results to. The default is None.

on_the_flybool, optional

TODO

reloadbool, optional

Flag to reload previous position files from resfolder. The default is False.

verboseint, optional

Verbosity flag. The default is 1.

Returns

None.

Attributes

reader	Experiment reader object
positions	List of Position objects under current experiment
rotation_correction	Flag to perform rotation correction
drift_correction	Flag to perform XY drift correction
crop_windows	Flag to crop overlapping windows for segmentation
save_format	List of file save formats
daemon	Run the pipeline as a daemon process (not functional yet)
models	Dictionary of Tensorflow models

Methods

__init__(xpreader[, resfolder, on_the_fly, ...])	Initialize Pipeline
preprocess([positions, references, ROIs])	Pre-process positions (Rotation correction, identify ROIs, initialize drift correction)
process([positions, frames, features, clear])	Run pipeline.
run()	On-the-fly processor (not functional yet)