bids.layout.BIDSValidator

class BIDSValidator(index_associated=True)[source]

An object for BIDS (Brain Imaging Data Structure) verification in a data.

The main method of this class is is_bids(). You should use it for checking whether a file path compatible with BIDS.

Parameters

index_associated (bool, default: True) – Specifies if an associated data should be checked. If it is true then any file paths in directories code/, derivatives/, sourcedata/ and stimuli/ will pass the validation, else they won’t.

Examples

>>> from bids.grabbids import BIDSValidator
>>> validator = BIDSValidator()
>>> filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz",
>>> "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe", #wrong extension
>>> "/participants.tsv"]
>>> for filepath in filepaths:
>>>     print( validator.is_bids(filepath) )
True
False
True

Methods

get_path_values(path)

Takes a file path and returns values found for the following path keys: sub- ses-

is_associated_data(path)

Check if file is appropriate associated data.

is_bids(path)

Checks if a file path appropriate for BIDS.

is_file(path)

Check if file is phenotypic data.

is_phenotypic(path)

Check if file is phenotypic data.

is_session_level(path)

Check if the file has appropriate name for a session level.

is_subject_level(path)

Check if the file has appropriate name for a subject level.

is_top_level(path)

Check if the file has appropriate name for a top-level file.

conditional_match

get_regular_expressions

__init__(index_associated=True)[source]

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__([index_associated])

Initialize self.

conditional_match(expression, path)

get_path_values(path)

Takes a file path and returns values found for the following path keys: sub- ses-

get_regular_expressions(fileName)

is_associated_data(path)

Check if file is appropriate associated data.

is_bids(path)

Checks if a file path appropriate for BIDS.

is_file(path)

Check if file is phenotypic data.

is_phenotypic(path)

Check if file is phenotypic data.

is_session_level(path)

Check if the file has appropriate name for a session level.

is_subject_level(path)

Check if the file has appropriate name for a subject level.

is_top_level(path)

Check if the file has appropriate name for a top-level file.