Cohort selector

Select participants based on any field.

CohortSelector

 CohortSelector (base_path:str='nbs/examples/', cohort:str=None,
                 errors:str='warn', **kwargs)

*Class for selecting a subset of a cohort’s data based on a query.

Args:

base_path (str, optional): Base path of the datasets. Defaults to DATASETS_PATH.
cohort (str, optional): Name of the cohort. Defaults to COHORT.
errors (str, optional): Error action. Defaults to ERROR_ACTION.
**kwargs: Additional keyword arguments.

Attributes:

cohort (str): Name of the cohort.
base_path (str): Base path of the datasets.
errors (str): Error action.
kwargs: Additional keyword arguments.
ml (MetaLoader): MetaLoader object for loading metadata and data.*

cs = CohortSelector()

You may use the CohortSelector to select participants based on any fields. The selector will return a DataFrame with the selected sub-cohort, along with the fields that were used in the query.

For example, the following query selects participants who have moderate obstructive sleep apnea (AHI > 15) based on recordings of at least 4 hours of sleep.

ml = MetaLoader()

cs.select('15 < ahi < 20 & total_sleep_time > 4*3600')

				ahi	total_sleep_time
participant_id	cohort	research_stage	array_index
9	10k	02_00_visit	2	18.39	23748.0
15	10k	00_00_visit	0	19.54	19230.0
30	10k	00_00_visit	0	18.52	25111.0
42	10k	00_00_visit	1	17.84	24966.0
49	10k	02_00_visit	0	17.58	21980.0
...	...	...	...	...	...
902	10k	02_00_visit	2	19.78	24162.0
914	10k	02_00_visit	2	17.54	26479.0
936	10k	00_00_visit	1	17.43	20865.0
941	10k	00_00_visit	0	17.82	17606.0
965	10k	00_00_visit	2	15.38	24390.0

77 rows × 2 columns

You may also use the selector to filter on dates. Here we filter on dates of image collection in the fundus imaging dataset.

In addition, we may load additional fields that are not part of the query.

cs.select('fundus/collection_date > "2022-01-01"', add_fields='fundus_image_left')

				fundus_image_left	collection_date
participant_id	cohort	research_stage	array_index
0	10k	00_00_visit	0	/path/to/file	2022-11-16
1	10k	00_00_visit	0	/path/to/file	2022-06-30
3	10k	00_00_visit	0	/path/to/file	2022-04-26