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 -
get_path_values
(path)[source]¶ Takes a file path and returns values found for the following path keys:
sub- ses-
-
is_bids
(path)[source]¶ Checks if a file path appropriate for BIDS.
Main method of the validator. uses other class methods for checking different aspects of the file path.
Parameters: path (string) – A path of a file you want to check. Examples
>>> from bids.grabbids import BIDSValidator >>> validator = BIDSValidator() >>> validator.is_bids("/sub-01/ses-test/anat/sub-01_ses-test_rec-CSD_run-23_T1w.nii.gz") True >>> validator.is_bids("/sub-01/ses-test/sub-01_run-01_dwi.bvec") # missed session in the filename False
-