CHAP.saxswaxs package

PipelineItems unique to SAXSWAXS data processing workflows.

This module contains all the PipelineItems (Processors, Readers and Writers) that are unique to the SAXSWAXS workflow. Any of these PipelineItems can be used as items in a CHAP Pipeline or instantiated from a user Python script.

Note

Using the SAXSWAXS workflow pipeline items in a CHAP Pipeline and running it, requires a SAXSWAXS conda environent or access to the appropriate CHAP SAXSWAXS executable, see SAXS/WAXS module (CHAP.saxswaxs)

Submodules summary

processor

Processors unique to the SAXSWAXS workflow.

reader

Readers unique to the SAXSWAXS workflow.

writer

Writers unique to the SAXSWAXS workflow.

Subpackages

• CHAP.saxswaxs.server package
  • Submodules
  • CHAP.saxswaxs.server.chap module
  • CHAP.saxswaxs.server.logging_config module
    • StreamToLogFile
      • StreamToLogFile.encoding
      • StreamToLogFile.flush()
      • StreamToLogFile.isatty()
      • StreamToLogFile.write()
    • get_logger()
    • get_task_logger()
    • set_logdir()
    • task_log_context()
  • CHAP.saxswaxs.server.saxswaxs_to_chap module
    • VerboseSafeDumper
      • VerboseSafeDumper.ignore_aliases()
    • convert_configs()
    • make_pipeline()
    • saxswaxs_to_chap()
  • CHAP.saxswaxs.server.server module
  • CHAP.saxswaxs.server.slack module
  • CHAP.saxswaxs.server.task_queue module

Submodules

CHAP.saxswaxs.models module

CHAP.saxswaxs.processor module

CHAP.saxswaxs.reader module

Module for Readers unique to the SAXSWAXS workflow.

CHAP.saxswaxs.utils module

dict_to_zarr(tree, logger=None)

Create a Zarr group object based on a dictionary representing a Zarr tree of groups and arrays.

Parameters:

tree (dict[str, Any]) – Nested dictionary representing a Zarr tree of groups and arrays.

Returns:

Zarr group corresponding to the contents of tree.

Return type:

zarr.Group

CHAP.saxswaxs.writer module

Module for Writers unique to the SAXSWAXS workflow.