derotation.derotate_batch#

This module contains the function derotate, which is used to run the full derotation pipeline on a single dataset. It can be called externally from the command line or from a script to run multiple datasets in parallel. Configurations are generated based on the provided dataset folder and output folder.

Functions

derotate(dataset_folder, output_folder, ...)

Run the derotation pipeline on a single dataset.
derotation.derotate_batch.derotate(dataset_folder, output_folder, path_to_stimulus_randperm, glob_naming_pattern_tif, glob_naming_pattern_bin, folder_suffix='full')[source]#

Run the derotation pipeline on a single dataset. This function is responsible for loading the configuration, updating the paths, the pipeline choice, and running the pipeline.

Parameters:

  • dataset_folder (Path) – The path to the dataset folder.

  • output_folder (str) – The path to the output folder in which to save the results.

  • path_to_stimulus_randperm (str) – The path to the stimulus random permutation file.

  • glob_naming_pattern_tif (str) – The glob naming pattern for the tif file.

  • glob_naming_pattern_bin (str) – The glob naming pattern for the bin file.

  • folder_suffix (str, optional) – The suffix to append to the output folder name, by default “full”. This is used to differentiate between full and incremental pipelines.

Raises:

Exception – If the pipeline fails.

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