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nabu.stitching.utils.post_processing

source module nabu.stitching.utils.post_processing

Classes

  • StitchingPostProcAggregation — for remote stitching each process will stitch a part of the volume or projections. Then once all are finished we want to aggregate them all to a final volume or NXtomo.

  • SlurmStitchingFollowerContext — Util class to provide user feedback from stitching done on slurm

  • SlurmStitchingFollowerThread — Thread to check progression of stitching slurm job(s) Read slurm jobs .out file each 'delay time' and look for a tqdm line at the end. If it exists then deduce progress from it.

source class StitchingPostProcAggregation(stitching_config: SingleAxisStitchingConfiguration, futures: Optional[tuple] = None, existing_objs_ids: Optional[tuple] = None, progress_bars: Optional[dict] = None)

for remote stitching each process will stitch a part of the volume or projections. Then once all are finished we want to aggregate them all to a final volume or NXtomo.

This is the goal of this class. Please be careful with API. This is already inheriting from a tomwer class

:param stitching_config: configuration of the stitching configuration :param futures: futures that just run :param existing_objs: futures that just run :param progress_bars: tqdm progress bars for each jobs

Methods

source property StitchingPostProcAggregation.futures

source property StitchingPostProcAggregation.progress_bars: dict

source method StitchingPostProcAggregation.retrieve_tomo_objects() → tuple

Return tomo objects to be stitched together. Either from future or from existing_objs

Raises

  • RuntimeError

source method StitchingPostProcAggregation.dump_stitching_config_as_nx_process(file_path: str, data_path: str, overwrite: bool, process_name: str)

source property StitchingPostProcAggregation.stitching_config: SingleAxisStitchingConfiguration

source method StitchingPostProcAggregation.process() → None

main function

Raises

  • TypeError

  • RuntimeError

source method StitchingPostProcAggregation.follow_progress() → AbstractContextManager

source class SlurmStitchingFollowerContext(output_files_to_progress_bars: dict)

Bases : AbstractContextManager

Util class to provide user feedback from stitching done on slurm

source class SlurmStitchingFollowerThread(file_to_progress_bar: dict, delay_time: float = 0.5)

Bases : Thread

Thread to check progression of stitching slurm job(s) Read slurm jobs .out file each 'delay time' and look for a tqdm line at the end. If it exists then deduce progress from it.

file_to_progress_bar provide for each slurm .out file the progress bar to update

Attributes

  • name — A string used for identification purposes only.

  • ident — Thread identifier of this thread or None if it has not been started.

  • native_id — Native integral thread ID of this thread, or None if it has not been started.

  • daemon — A boolean value indicating whether this thread is a daemon thread.

Methods

source property SlurmStitchingFollowerThread.file_to_progress_bar: dict

source method SlurmStitchingFollowerThread.run() → None

source method SlurmStitchingFollowerThread.join(timeout: Union[float, None] = None) → None

source staticmethod SlurmStitchingFollowerThread.cast_progress_line_from_log(line: str) → Optional[float]

Try to retrieve from a line from log the advancement (in percentage)