bids.reports.BIDSReport

class BIDSReport(layout, config=None)[source]

Generates publication-quality data acquisition methods section from BIDS dataset.

Parameters:
  • layout (bids.layout.BIDSLayout) – Layout object for a BIDS dataset.
  • config (str or dict, optional) –

    Configuration info for methods generation. Can be a path to a file (str), a dictionary, or None. If None, loads and uses default configuration information. Keys in the dictionary include:

    ’dir’: a dictionary for converting encoding direction strings
    (e.g., j-) to descriptions (e.g., anterior to posterior)
    ’seq’: a dictionary of sequence abbreviations (e.g., EP) and
    corresponding names (e.g., echo planar)
    ’seqvar’: a dictionary of sequence variant abbreviations
    (e.g., SP) and corresponding names (e.g., spoiled)

Methods

generate(**kwargs) Generate the methods section.
generate(**kwargs)[source]

Generate the methods section.

Parameters:task_converter (dict, optional) – A dictionary with information for converting task names from BIDS filename format to human-readable strings.
Returns:counter – A dictionary of unique descriptions across subjects in the dataset, along with the number of times each pattern occurred.
Return type:collections.Counter

Examples

>>> from os.path import join
>>> from bids.layout import BIDSLayout
>>> from bids.reports import BIDSReport
>>> from bids.tests import get_test_data_path
>>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
>>> report = BIDSReport(layout)
>>> counter = report.generate(session='01')
>>> counter.most_common()[0][0]