API Reference#

This section contains automatically generated documentation for the derotation package.

Modules

`derotation.analysis.bayesian_optimization`	Bayesian optimization to find the best center of rotation.
`derotation.analysis.blob_detection`	This module contains the BlobDetection class, which is used to detect the largest blob in each image of an image stack.
`derotation.analysis.fit_ellipse`	This module contains functions to fit an ellipse to the largest blob centers in each image of an image stack.
`derotation.analysis.full_derotation_pipeline`	`FullPipeline` is the main pipeline meant to be used for the full rotation protocol, which involves rotating the sample by 360 degrees at various speeds and directions.
`derotation.analysis.incremental_derotation_pipeline`	This module contains the `IncrementalPipeline` class, which is a child of the `FullPipeline` class.
`derotation.analysis.mean_images`	This module contains functions to calculate mean images in steps of 10 degrees.
`derotation.analysis.metrics`	This module contains functions to calculate metrics for the derotation analysis.
`derotation.config.load_config`
`derotation.derotate_batch`	This module contains the function derotate, which is used to run the full derotation pipeline on a single dataset.
`derotation.derotate_by_line`	This module contains the function `derotate_an_image_array_line_by_line`, which derotates an image stack line by line using the provided rotation angles.
`derotation.load_data.custom_data_loaders`	These functions are used to load data from the custom data format used in the experiments.
`derotation.plotting_hooks.for_derotation`	This module contains hooks for making plots while the derotation is running.
`derotation.sample_data`	Fetch and load sample datasets for derotation examples.
`derotation.simulate.line_scanning_microscope`	This module contains the `Rotator` class, which is used to simulate the acquisition of a rotated image stack as if for each line acquired, the sample was rotated at a given angle in a given center and plane of rotation.
`derotation.simulate.synthetic_data`	This module contains the `SyntheticData` class that generates synthetic data for testing and developing the derotation pipeline.