""" The contents of a BIDS dataset. """
import os
import json
from hed.schema.hed_schema import HedSchema
from hed.schema.hed_schema_io import load_schema_version
from hed.schema.hed_schema_group import HedSchemaGroup
from hed.tools.bids.bids_file_group import BidsFileGroup
LIBRARY_URL_BASE = "https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/"
[docs]class BidsDataset:
""" A BIDS dataset representation primarily focused on HED evaluation.
Attributes:
root_path (str): Real root path of the BIDS dataset.
schema (HedSchema or HedSchemaGroup): The schema used for evaluation.
tabular_files (dict): A dictionary of BidsTabularDictionary objects containing a given type.
"""
[docs] def __init__(self, root_path, schema=None, tabular_types=None,
exclude_dirs=['sourcedata', 'derivatives', 'code', 'stimuli']):
""" Constructor for a BIDS dataset.
Parameters:
root_path (str): Root path of the BIDS dataset.
schema (HedSchema or HedSchemaGroup): A schema that overrides the one specified in dataset.
tabular_types (list or None): List of strings specifying types of tabular types to include.
If None or empty, then ['events'] is assumed.
exclude_dirs=['sourcedata', 'derivatives', 'code']:
"""
self.root_path = os.path.realpath(root_path)
with open(os.path.join(self.root_path, "dataset_description.json"), "r") as fp:
self.dataset_description = json.load(fp)
if schema:
self.schema = schema
else:
self.schema = load_schema_version(self.dataset_description.get("HEDVersion", None))
self.exclude_dirs = exclude_dirs
self.tabular_files = {"participants": BidsFileGroup(root_path, suffix="participants", obj_type="tabular")}
if not tabular_types:
self.tabular_files["events"] = BidsFileGroup(root_path, suffix="events", obj_type="tabular",
exclude_dirs=exclude_dirs)
else:
for suffix in tabular_types:
self.tabular_files[suffix] = BidsFileGroup(root_path, suffix=suffix, obj_type="tabular",
exclude_dirs=exclude_dirs)
[docs] def get_tabular_group(self, obj_type="events"):
""" Return the specified tabular file group.
Parameters:
obj_type (str): Suffix of the BidsFileGroup to be returned.
Returns:
BidsFileGroup or None: The requested tabular group.
"""
if obj_type in self.tabular_files:
return self.tabular_files[obj_type]
else:
return None
[docs] def validate(self, types=None, check_for_warnings=True):
""" Validate the specified file group types.
Parameters:
types (list): A list of strings indicating the file group types to be validated.
check_for_warnings (bool): If True, check for warnings.
Returns:
list: List of issues encountered during validation. Each issue is a dictionary.
"""
if not types:
types = list(self.tabular_files.keys())
issues = []
for tab_type in types:
files = self.tabular_files[tab_type]
issues += files.validate_sidecars(self.schema, check_for_warnings=check_for_warnings)
issues += files.validate_datafiles(self.schema, check_for_warnings=check_for_warnings)
return issues
[docs] def get_summary(self):
""" Return an abbreviated summary of the dataset. """
summary = {"dataset": self.dataset_description['Name'],
"hed_schema_versions": self.schema.get_schema_versions(),
"file_group_types": f"{str(list(self.tabular_files.keys()))}"}
return summary