config

The "config" file is a main configuration defining the experiment and is applicable to all parts of processing: beamline preprocessing, standard preprocessing, phasing, and beamline visualization.

Parameters

  • working_dir

Mandatory, root directory of the experiment files.
working_dir = "/path/to/the/experiment/"

  • experiment_id

Mandatory, a string identifying the experiment.
experiment_id = "ab"

  • scan

Optional (but typically needed), string type encapsulating a single number, a range, or combination of numbers and ranges separated by comma, defining scans that will be read and combined to create data file. This parameter should not be set when running multi-peak case.
scan = "54"
scan = "2-7"
scan = "2-7, 10, 15, 20-22"

  • beamline

Optional, beamline where the experiment was conducted. If not configured, the beamline preprocessing and beamline visualization scripts are not available.
beamline = "aps_34idc"

  • multipeak

Optional, boolean parameter indicating whether it is multi-peak case. Defaults to False.
multipeak = True

  • separate_scans

Optional, deafults to False. In typical scenario the data from all scans in experiment are combined. If specified as separate scans, each scan will be processed separately and will have sub-experiment name containing scan index ex. "scan_9", where 9 is scan index.
separate_scans = False

  • separate_scan_ranges

Optional, defaults to False. In typical scenario the data from all scans in experiment are combined. If specified as separate scan ranges, each scan or scan range in the experiment will be processed separately and will have sub-experiment name containing scan index, or scan index range, ex. "scan_9", where 9 is scan index, or "scan_10-15", where 10-15 is the scan range. The scans and scan ranges are defined in main configuration "config" file as scan parameter, and are part of experiment name.
separate_scan_ranges = True

  • converter_ver

Mandatory after cohere ver 3.0. If not configured, it will be auto-updated by scripts to match the latest converter version.
converter_ver = 3