Source code for bids.layout.layout

"""BIDSLayout class."""
import os
import json
import re
from collections import defaultdict
from io import open
from functools import partial
from itertools import chain
import copy
import warnings
import sqlite3
import enum
from pathlib import Path

import sqlalchemy as sa
from sqlalchemy.orm import joinedload
from bids_validator import BIDSValidator

from ..utils import listify, natural_sort, make_bidsfile
import inflect
from .writing import build_path, write_contents_to_file
from .models import (Base, Config, BIDSFile, Entity, Tag)
from .index import BIDSLayoutIndexer
from .. import config as cf

try:
    from os.path import commonpath
except ImportError:
    def commonpath(paths):
        prefix = os.path.commonprefix(paths)
        if not os.path.isdir(prefix):
            prefix = os.path.dirname(prefix)
        return prefix

__all__ = ['BIDSLayout']


[docs]def parse_file_entities(filename, entities=None, config=None, include_unmatched=False): """Parse the passed filename for entity/value pairs. Parameters ---------- filename : str The filename to parse for entity values entities : list or None, optional An optional list of Entity instances to use in extraction. If passed, the config argument is ignored. Default is None. config : str or :obj:`bids.layout.models.Config` or list or None, optional One or more :obj:`bids.layout.models.Config` objects or names of configurations to use in matching. Each element must be a :obj:`bids.layout.models.Config` object, or a valid :obj:`bids.layout.models.Config` name (e.g., 'bids' or 'derivatives'). If None, all available configs are used. Default is None. include_unmatched : bool, optional If True, unmatched entities are included in the returned dict, with values set to None. If False (default), unmatched entities are ignored. Returns ------- dict Keys are Entity names and values are the values from the filename. """ # Load Configs if needed if entities is None: if config is None: config = ['bids', 'derivatives'] config = [Config.load(c) if not isinstance(c, Config) else c for c in listify(config)] # Consolidate entities from all Configs into a single dict entities = {} for c in config: entities.update(c.entities) entities = entities.values() # Extract matches bf = make_bidsfile(filename) ent_vals = {} for ent in entities: match = ent.match_file(bf) if match is not None or include_unmatched: ent_vals[ent.name] = match return ent_vals
[docs]def add_config_paths(**kwargs): """Add to the pool of available configuration files for BIDSLayout. Parameters ---------- kwargs : dict Dictionary specifying where to find additional config files. Keys are names, values are paths to the corresponding .json file. Examples -------- > add_config_paths(my_config='/path/to/config') > layout = BIDSLayout('/path/to/bids', config=['bids', 'my_config']) """ for k, path in kwargs.items(): if not os.path.exists(path): raise ValueError( 'Configuration file "{}" does not exist'.format(k)) if k in cf.get_option('config_paths'): raise ValueError('Configuration {!r} already exists'.format(k)) kwargs.update(**cf.get_option('config_paths')) cf.set_option('config_paths', kwargs)
[docs]class BIDSLayout(object): """Layout class representing an entire BIDS dataset. Parameters ---------- root : str The root directory of the BIDS dataset. validate : bool, optional If True, all files are checked for BIDS compliance when first indexed, and non-compliant files are ignored. This provides a convenient way to restrict file indexing to only those files defined in the "core" BIDS spec, as setting validate=True will lead files in supplementary folders like derivatives/, code/, etc. to be ignored. absolute_paths : bool, optional If True, queries always return absolute paths. If False, queries return relative paths (for files and directories). derivatives : bool or str or list, optional Specifies whether and/or which derivatives to to index. If True, all pipelines found in the derivatives/ subdirectory will be indexed. If a str or list, gives the paths to one or more derivatives directories to index. If False or None, the derivatives/ directory is ignored during indexing, and derivatives will have to be added manually via add_derivatives(). Note: derivatives datasets MUST contain a dataset_description.json file in order to be indexed. config : str or list or None, optional Optional name(s) of configuration file(s) to use. By default (None), uses 'bids'. sources : :obj:`bids.layout.BIDSLayout` or list or None, optional Optional BIDSLayout(s) from which the current BIDSLayout is derived. ignore : str or SRE_Pattern or list Path(s) to exclude from indexing. Each path is either a string or a SRE_Pattern object (i.e., compiled regular expression). If a string is passed, it must be either an absolute path, or be relative to the BIDS project root. If an SRE_Pattern is passed, the contained regular expression will be matched against the full (absolute) path of all files and directories. By default, indexing ignores all files in 'code/', 'stimuli/', 'sourcedata/', 'models/', and any hidden files/dirs beginning with '.' at root level. force_index : str or SRE_Pattern or list Path(s) to forcibly index in the BIDSLayout, even if they would otherwise fail validation. See the documentation for the ignore argument for input format details. Note that paths in force_index takes precedence over those in ignore (i.e., if a file matches both ignore and force_index, it *will* be indexed). Note: NEVER include 'derivatives' here; use the derivatives argument (or :obj:`bids.layout.BIDSLayout.add_derivatives`) for that. config_filename : str Optional name of filename within directories that contains configuration information. regex_search : bool Whether to require exact matching (True) or regex search (False, default) when comparing the query string to each entity in .get() calls. This sets a default for the instance, but can be overridden in individual .get() requests. database_path : str Optional path to directory containing SQLite database file index for this BIDS dataset. If a value is passed and the folder already exists, indexing is skipped. By default (i.e., if None), an in-memory SQLite database is used, and the index will not persist unless .save() is explicitly called. reset_database : bool If True, any existing directory specified in the database_path argument is deleted, and the BIDS dataset provided in the root argument is reindexed. If False, indexing will be skipped and the existing database file will be used. Ignored if database_path is not provided. index_metadata : bool If True, all metadata files are indexed at initialization. If False, metadata will not be available (but indexing will be faster). """ _default_ignore = ("code", "stimuli", "sourcedata", "models", re.compile(r'^\.'))
[docs] def __init__(self, root, validate=True, absolute_paths=True, derivatives=False, config=None, sources=None, ignore=None, force_index=None, config_filename='layout_config.json', regex_search=False, database_path=None, database_file=None, reset_database=False, index_metadata=True): """Initialize BIDSLayout.""" self.root = root self.validate = validate self.absolute_paths = absolute_paths self.derivatives = {} self.sources = sources self.regex_search = regex_search self.config_filename = config_filename # Store original init arguments as dictionary self._init_args = self._sanitize_init_args( root=root, validate=validate, absolute_paths=absolute_paths, derivatives=derivatives, ignore=ignore, force_index=force_index, index_metadata=index_metadata, config=config) if database_path is None and database_file is not None: database_path = database_file warnings.warn( 'In pybids 0.10 database_file argument was deprecated in favor' ' of database_path, and will be removed in 0.12. ' 'For now, treating database_file as a directory.', DeprecationWarning) if database_path: database_path = str(Path(database_path).absolute()) self.session = None index_dataset = self._init_db(database_path, reset_database) # Do basic BIDS validation on root directory self._validate_root() if ignore is None: ignore = self._default_ignore # Instantiate after root validation to ensure os.path.join works self.ignore = [os.path.abspath(os.path.join(self.root, patt)) if isinstance(patt, str) else patt for patt in listify(ignore or [])] self.force_index = [os.path.abspath(os.path.join(self.root, patt)) if isinstance(patt, str) else patt for patt in listify(force_index or [])] # Initialize the BIDS validator and examine ignore/force_index args self._validate_force_index() if index_dataset: # Create Config objects if config is None: config = 'bids' config = [Config.load(c, session=self.session) for c in listify(config)] self.config = {c.name: c for c in config} # Missing persistence of configs to the database for config_obj in self.config.values(): self.session.add(config_obj) self.session.commit() # Index files and (optionally) metadata indexer = BIDSLayoutIndexer(self) indexer.index_files() if index_metadata: indexer.index_metadata() else: # Load Configs from DB self.config = {c.name: c for c in self.session.query(Config).all()} # Add derivatives if any are found if derivatives: if derivatives is True: derivatives = os.path.join(root, 'derivatives') self.add_derivatives( derivatives, parent_database_path=database_path, validate=validate, absolute_paths=absolute_paths, derivatives=None, sources=self, ignore=ignore, config=None, force_index=force_index, config_filename=config_filename, regex_search=regex_search, index_metadata=index_metadata, reset_database=index_dataset or reset_database )
def __getattr__(self, key): """Dynamically inspect missing methods for get_<entity>() calls and return a partial function of get() if a match is found.""" if key.startswith('get_'): ent_name = key.replace('get_', '') entities = self.get_entities() # Use inflect to check both singular and plural forms if ent_name not in entities: sing = inflect.engine().singular_noun(ent_name) if sing in entities: ent_name = sing else: raise AttributeError( "'get_{}' can't be called because '{}' isn't a " "recognized entity name.".format(ent_name, ent_name)) return partial(self.get, return_type='id', target=ent_name) # Spit out default message if we get this far raise AttributeError("%s object has no attribute named %r" % (self.__class__.__name__, key)) def __repr__(self): """Provide a tidy summary of key properties.""" # TODO: Replace each nested list comprehension with a single DB query n_sessions = len([session for isub in self.get_subjects() for session in self.get_sessions(subject=isub)]) n_runs = len([run for isub in self.get_subjects() for run in self.get_runs(subject=isub)]) n_subjects = len(self.get_subjects()) root = self.root[-30:] s = ("BIDS Layout: ...{} | Subjects: {} | Sessions: {} | " "Runs: {}".format(root, n_subjects, n_sessions, n_runs)) return s def _set_session(self, database_file): if database_file is not None: # https://docs.sqlalchemy.org/en/13/dialects/sqlite.html # When a file-based database is specified, the dialect will use # NullPool as the source of connections. This pool closes and # discards connections which are returned to the pool immediately. # SQLite file-based connections have extremely low overhead, so # pooling is not necessary. The scheme also prevents a connection # from being used again in a different thread and works best # with SQLite's coarse-grained file locking. from sqlalchemy.pool import NullPool engine = sa.create_engine( 'sqlite:///{dbfilepath}'.format(dbfilepath=database_file), connect_args={'check_same_thread': False}, poolclass=NullPool) else: # https://docs.sqlalchemy.org/en/13/dialects/sqlite.html # Using a Memory Database in Multiple Threads # To use a :memory: database in a multithreaded scenario, the same # connection object must be shared among # threads, since the database exists only within the scope of that # connection. The StaticPool implementation will maintain a single # connection globally, and the check_same_thread flag can be passed # to Pysqlite as False: from sqlalchemy.pool import StaticPool engine = sa.create_engine( 'sqlite://', # In memory database connect_args={'check_same_thread': False}, poolclass=StaticPool) # Note that using a :memory: database in multiple threads requires # a recent version of SQLite. def regexp(expr, item): """Regex function for SQLite's REGEXP.""" reg = re.compile(expr, re.I) return reg.search(item) is not None conn = engine.connect() # Do not remove this decorator!!! An in-line create_function call will # work when using an in-memory SQLite DB, but fails when using a file. # For more details, see https://stackoverflow.com/questions/12461814/ @sa.event.listens_for(engine, "begin") def do_begin(conn): conn.connection.create_function('regexp', 2, regexp) self.session = sa.orm.sessionmaker(bind=engine)() @staticmethod def _make_db_paths(database_path): if database_path is not None: database_path = Path(database_path) database_file = database_path / 'layout_index.sqlite' database_sidecar = database_path / 'layout_args.json' database_path.mkdir(exist_ok=True, parents=True) else: database_file = None database_sidecar = None return database_file, database_sidecar @staticmethod def _sanitize_init_args(**kwargs): """ Prepare initalization arguments for serialization """ # Make ignore and force_index serializable for k in ['ignore', 'force_index']: kwargs[k] = [ str(a) for a in kwargs[k] if a is not None] \ if kwargs[k] is not None else None kwargs['root'] = str(Path(kwargs['root']).absolute()) # Get abspaths if isinstance(kwargs['derivatives'], list): kwargs['derivatives'] = [ str(Path(der).absolute()) for der in listify(kwargs['derivatives']) ] return kwargs def _init_db(self, database_path=None, reset_database=False): database_file, database_sidecar = self._make_db_paths(database_path) # Reset database if needed and return whether or not it was reset # determining if the database needs resetting must be done prior # to setting the session (which creates the empty database file) reset_database = ( reset_database or # Manual Request not database_file or # In memory transient db not database_file.exists() # New file based db created ) self._set_session(database_file) if not reset_database: saved_args = json.loads(database_sidecar.read_text()) for k, v in saved_args.items(): if self._init_args[k] != v: raise ValueError( "Initialization argument ('{}') does not match " "for database_path: {}.\n" "Saved value: {}.\n" "Current value: {}.".format( k, database_path, v, self._init_args[k]) ) else: engine = self.session.get_bind() Base.metadata.drop_all(engine) Base.metadata.create_all(engine) if database_sidecar: database_sidecar.write_text(json.dumps(self._init_args)) return True return False def _validate_root(self): # Validate root argument and make sure it contains mandatory info try: self.root = str(self.root) except: raise TypeError("root argument must be a string (or a type that " "supports casting to string, such as " "pathlib.Path) specifying the directory " "containing the BIDS dataset.") self.root = os.path.abspath(self.root) if not os.path.exists(self.root): raise ValueError("BIDS root does not exist: %s" % self.root) target = os.path.join(self.root, 'dataset_description.json') if not os.path.exists(target): if self.validate: raise ValueError( "'dataset_description.json' is missing from project root." " Every valid BIDS dataset must have this file.") else: self.description = None else: with open(target, 'r', encoding='utf-8') as desc_fd: self.description = json.load(desc_fd) if self.validate: for k in ['Name', 'BIDSVersion']: if k not in self.description: raise ValueError("Mandatory '%s' field missing from " "dataset_description.json." % k) def _validate_force_index(self): # Derivatives get special handling; they shouldn't be indexed normally if self.force_index is not None: for entry in self.force_index: condi = (isinstance(entry, str) and os.path.normpath(entry).startswith('derivatives')) if condi: msg = ("Do not pass 'derivatives' in the force_index " "list. To index derivatives, either set " "derivatives=True, or use add_derivatives().") raise ValueError(msg) def _in_scope(self, scope): """Determine whether current BIDSLayout is in the passed scope. Parameters ---------- scope : str or list The intended scope(s). Each value must be one of 'all', 'raw', 'derivatives', or a pipeline name. """ scope = listify(scope) if 'all' in scope: return True # We assume something is a BIDS-derivatives dataset if it either has a # defined pipeline name, or is applying the 'derivatives' rules. pl_name = self.description.get("PipelineDescription", {}).get("Name") is_deriv = bool(pl_name or ('derivatives' in self.config)) return ((not is_deriv and 'raw' in scope) or (is_deriv and ('derivatives' in scope or pl_name in scope))) def _get_layouts_in_scope(self, scope): """Return all layouts in the passed scope.""" if scope == 'self': return [self] def collect_layouts(layout): """Recursively build a list of layouts.""" children = list(layout.derivatives.values()) layouts = [collect_layouts(d) for d in children] return [layout] + list(chain(*layouts)) layouts = [l for l in collect_layouts(self) if l._in_scope(scope)] return list(set(layouts)) def _sanitize_query_dtypes(self, entities): """Automatically convert entity query values to correct dtypes.""" entities = entities.copy() names = list(entities.keys()) ents = {e.name: e for e in self.session.query(Entity) .filter(Entity.name.in_(names)).all()} # Fail silently because the DB may still know how to reconcile # type differences. for name, val in entities.items(): if isinstance(val, enum.Enum): continue try: if isinstance(val, (list, tuple)): entities[name] = [ents[name]._astype(v) for v in val] else: entities[name] = ents[name]._astype(val) except: pass return entities @property def entities(self): """Get the entities.""" return self.get_entities() @property def files(self): """Get the files.""" return self.get_files()
[docs] @classmethod def load(cls, database_path): """ Load index from database path. Initalization parameters are set to those found in database_path JSON sidecar. Parameters ---------- database_path : str The path to the desired database folder. By default, uses .db_cache. If a relative path is passed, it is assumed to be relative to the BIDSLayout root directory. """ database_file, database_sidecar = cls._make_db_paths(database_path) init_args = json.loads(database_sidecar.read_text()) return cls(database_path=database_path, **init_args)
[docs] def save(self, database_path, replace_connection=True): """Save the current index as a SQLite3 DB at the specified location. Note: This is only necessary if a database_path was not specified at initalization, and the user now wants to save the index. If a database_path was specified originally, there is no need to re-save using this method. Parameters ---------- database_path : str The path to the desired database folder. By default, uses .db_cache. If a relative path is passed, it is assumed to be relative to the BIDSLayout root directory. replace_connection : bool, optional If True, the newly created database will be used for all subsequent connections. This means that any changes to the index made after the .save() call will be reflected in the database file. If False, the previous database will continue to be used, and any subsequent changes will not be reflected in the new file unless save() is explicitly called again. """ database_file, database_sidecar = self._make_db_paths(database_path) new_db = sqlite3.connect(str(database_file)) old_db = self.session.get_bind().connect().connection with new_db: for line in old_db.iterdump(): if line not in ('BEGIN;', 'COMMIT;'): new_db.execute(line) new_db.commit() if replace_connection: self._set_session(str(database_file)) # Dump instance arguments to JSON database_sidecar.write_text(json.dumps(self._init_args)) # Recursively save children for pipeline_name, der in self.derivatives.items(): der.save(os.path.join( database_path, pipeline_name))
[docs] def get_entities(self, scope='all', metadata=None): """Get entities for all layouts in the specified scope. Parameters ---------- scope : str The scope of the search space. Indicates which BIDSLayouts' entities to extract. See :obj:`bids.layout.BIDSLayout.get` docstring for valid values. metadata : bool or None By default (None), all available entities are returned. If True, only entities found in metadata files (and not defined for filenames) are returned. If False, only entities defined for filenames (and not those found in JSON sidecars) are returned. Returns ------- dict Dictionary where keys are entity names and values are Entity instances. """ # TODO: memoize results layouts = self._get_layouts_in_scope(scope) entities = {} for l in layouts: query = l.session.query(Entity) if metadata is not None: query = query.filter_by(is_metadata=metadata) results = query.all() entities.update({e.name: e for e in results}) return entities
[docs] def get_files(self, scope='all'): """Get BIDSFiles for all layouts in the specified scope. Parameters ---------- scope : str The scope of the search space. Indicates which BIDSLayouts' entities to extract. See :obj:`bids.layout.BIDSLayout.get` docstring for valid values. Returns: A dict, where keys are file paths and values are :obj:`bids.layout.BIDSFile` instances. """ # TODO: memoize results layouts = self._get_layouts_in_scope(scope) files = {} for l in layouts: results = l.session.query(BIDSFile).all() files.update({f.path: f for f in results}) return files
[docs] def clone(self): """Return a deep copy of the current BIDSLayout.""" return copy.deepcopy(self)
[docs] def parse_file_entities(self, filename, scope='all', entities=None, config=None, include_unmatched=False): """Parse the passed filename for entity/value pairs. Parameters ---------- filename : str The filename to parse for entity values scope : str or list, optional The scope of the search space. Indicates which BIDSLayouts' entities to extract. See :obj:`bids.layout.BIDSLayout.get` docstring for valid values. By default, extracts all entities. entities : list or None, optional An optional list of Entity instances to use in extraction. If passed, the scope and config arguments are ignored, and only the Entities in this list are used. config : str or :obj:`bids.layout.models.Config` or list or None, optional One or more :obj:`bids.layout.models.Config` objects, or paths to JSON config files on disk, containing the Entity definitions to use in extraction. If passed, scope is ignored. include_unmatched : bool, optional If True, unmatched entities are included in the returned dict, with values set to None. If False (default), unmatched entities are ignored. Returns ------- dict Dictionary where keys are Entity names and values are the values extracted from the filename. """ # If either entities or config is specified, just pass through if entities is None and config is None: layouts = self._get_layouts_in_scope(scope) config = chain(*[list(l.config.values()) for l in layouts]) config = list(set(config)) return parse_file_entities(filename, entities, config, include_unmatched)
[docs] def add_derivatives(self, path, parent_database_path=None, **kwargs): """Add BIDS-Derivatives datasets to tracking. Parameters ---------- path : str or list One or more paths to BIDS-Derivatives datasets. Each path can point to either a derivatives/ directory containing one more more pipeline directories, or to a single pipeline directory (e.g., derivatives/fmriprep). parent_database_path : str If not None, use the pipeline name from the dataset_description.json file as the database folder name to nest within the parent database folder name to write out derivatie index to. kwargs : dict Optional keyword arguments to pass on to BIDSLayout() when initializing each of the derivative datasets. Notes ----- Every derivatives directory intended for indexing MUST contain a valid dataset_description.json file. See the BIDS-Derivatives specification for details. """ paths = listify(path) deriv_dirs = [] # Collect all paths that contain a dataset_description.json def check_for_description(bids_dir): dd = os.path.join(bids_dir, 'dataset_description.json') return os.path.exists(dd) for p in paths: p = os.path.abspath(p) if os.path.exists(p): if check_for_description(p): deriv_dirs.append(p) else: subdirs = [d for d in os.listdir(p) if os.path.isdir(os.path.join(p, d))] for sd in subdirs: sd = os.path.join(p, sd) if check_for_description(sd): deriv_dirs.append(sd) if not deriv_dirs: warnings.warn("Derivative indexing was requested, but no valid " "datasets were found in the specified locations " "({}). Note that all BIDS-Derivatives datasets must" " meet all the requirements for BIDS-Raw datasets " "(a common problem is to fail to include a " "dataset_description.json file in derivatives " "datasets).".format(paths)) for deriv in deriv_dirs: dd = os.path.join(deriv, 'dataset_description.json') with open(dd, 'r', encoding='utf-8') as ddfd: description = json.load(ddfd) pipeline_name = description.get( 'PipelineDescription', {}).get('Name') if pipeline_name is None: raise ValueError("Every valid BIDS-derivatives dataset must " "have a PipelineDescription.Name field set " "inside dataset_description.json.") if pipeline_name in self.derivatives: raise ValueError("Pipeline name '%s' has already been added " "to this BIDSLayout. Every added pipeline " "must have a unique name!") # Default config and sources values kwargs['config'] = kwargs.get('config') or ['bids', 'derivatives'] kwargs['sources'] = kwargs.get('sources') or self if parent_database_path: child_database_path = os.path.join( parent_database_path, pipeline_name) kwargs['database_path'] = child_database_path self.derivatives[pipeline_name] = BIDSLayout(deriv, **kwargs)
[docs] def to_df(self, metadata=False, **filters): """Return information for BIDSFiles tracked in Layout as pd.DataFrame. Parameters ---------- metadata : bool, optional If True, includes columns for all metadata fields. If False, only filename-based entities are included as columns. filters : dict, optional Optional keyword arguments passed on to get(). This allows one to easily select only a subset of files for export. Returns ------- :obj:`pandas.DataFrame` A pandas DataFrame, where each row is a file, and each column is a tracked entity. NaNs are injected whenever a file has no value for a given attribute. """ try: import pandas as pd except ImportError: raise ImportError('Missing dependency: "pandas"') # TODO: efficiency could probably be improved further by joining the # BIDSFile and Tag tables and running a single query. But this would # require refactoring the below to use _build_file_query, which will # in turn likely require generalizing the latter. files = self.get(**filters) file_paths = [f.path for f in files] query = self.session.query(Tag).filter(Tag.file_path.in_(file_paths)) if not metadata: query = query.join(Entity).filter(Entity.is_metadata == False) tags = query.all() tags = [[t.file_path, t.entity_name, t.value] for t in tags] data = pd.DataFrame(tags, columns=['path', 'entity', 'value']) data = data.pivot('path', 'entity', 'value') # Add in orphaned files with no Tags. Maybe make this an argument? orphans = list(set(file_paths) - set(data.index)) for o in orphans: data.loc[o] = pd.Series() return data.reset_index()
[docs] def get(self, return_type='object', target=None, scope='all', regex_search=False, absolute_paths=None, drop_invalid_filters=True, **filters): """Retrieve files and/or metadata from the current Layout. Parameters ---------- return_type : str, optional Type of result to return. Valid values: 'object' (default): return a list of matching BIDSFile objects. 'file' or 'filename': return a list of matching filenames. 'dir': return a list of directories. 'id': return a list of unique IDs. Must be used together with a valid target. target : str, optional Optional name of the target entity to get results for (only used if return_type is 'dir' or 'id'). scope : str or list, optional Scope of the search space. If passed, only nodes/directories that match the specified scope will be searched. Possible values include: 'all' (default): search all available directories. 'derivatives': search all derivatives directories 'raw': search only BIDS-Raw directories 'self': search only the directly called BIDSLayout <PipelineName>: the name of a BIDS-Derivatives pipeline regex_search : bool or None, optional Whether to require exact matching (False) or regex search (True) when comparing the query string to each entity. absolute_paths : bool, optional Optionally override the instance-wide option to report either absolute or relative (to the top of the dataset) paths. If None, will fall back on the value specified at BIDSLayout initialization. filters : dict Any optional key/values to filter the entities on. Keys are entity names, values are regexes to filter on. For example, passing filters={'subject': 'sub-[12]'} would return only files that match the first two subjects. In addition to ordinary data types, the following enums are defined (in the Query class): * Query.NONE: The named entity must not be defined. * Query.ANY: the named entity must be defined, but can have any value. Returns ------- list of :obj:`bids.layout.BIDSFile` or str A list of BIDSFiles (default) or strings (see return_type). Notes ----- * In pybids 0.9.0, the 'extensions' argument has been removed in favor of the 'extension' entity. """ if 'extensions' in filters: filters['extension'] = filters.pop('extensions') warnings.warn("In pybids 0.9.0, the 'extensions' filter was " "deprecated in favor of 'extension'. The former will" " stop working in 0.11.0.", DeprecationWarning) layouts = self._get_layouts_in_scope(scope) entities = self.get_entities() # For consistency with past versions where "extensions" was a # hard-coded argument, allow leading periods if 'extension' in filters: exts = listify(filters['extension']) filters['extension'] = [x.lstrip('.') for x in exts] if drop_invalid_filters: invalid_filters = set(filters.keys()) - set(entities.keys()) if invalid_filters: for inv_filt in invalid_filters: filters.pop(inv_filt) # Provide some suggestions if target is specified and invalid. if target is not None and target not in entities: import difflib potential = list(entities.keys()) suggestions = difflib.get_close_matches(target, potential) if suggestions: message = "Did you mean one of: {}?".format(suggestions) else: message = "Valid targets are: {}".format(potential) raise ValueError(("Unknown target '{}'. " + message) .format(target)) results = [] for l in layouts: query = l._build_file_query(filters=filters, regex_search=regex_search) # Eager load associations, because mixing queries from different # DB sessions causes objects to detach query = query.options(joinedload(BIDSFile.tags) .joinedload(Tag.entity)) results.extend(query.all()) # Convert to relative paths if needed if absolute_paths is None: # can be overloaded as option to .get absolute_paths = self.absolute_paths if not absolute_paths: for i, fi in enumerate(results): fi = copy.copy(fi) fi.path = os.path.relpath(fi.path, self.root) results[i] = fi if return_type.startswith('file'): results = natural_sort([f.path for f in results]) elif return_type in ['id', 'dir']: if target is None: raise ValueError('If return_type is "id" or "dir", a valid ' 'target entity must also be specified.') results = [x for x in results if target in x.entities] if return_type == 'id': results = list(set([x.entities[target] for x in results])) results = natural_sort(results) elif return_type == 'dir': template = entities[target].directory if template is None: raise ValueError('Return type set to directory, but no ' 'directory template is defined for the ' 'target entity (\"%s\").' % target) # Construct regex search pattern from target directory template template = self.root + template to_rep = re.findall(r'{(.*?)\}', template) for ent in to_rep: patt = entities[ent].pattern template = template.replace('{%s}' % ent, patt) template += r'[^\%s]*$' % os.path.sep matches = [ f.dirname if absolute_paths else os.path.relpath(f.dirname, self.root) # noqa: E501 for f in results if re.search(template, f.dirname) ] results = natural_sort(list(set(matches))) else: raise ValueError("Invalid return_type specified (must be one " "of 'tuple', 'filename', 'id', or 'dir'.") else: results = natural_sort(results, 'path') return results
[docs] def get_file(self, filename, scope='all'): """Return the BIDSFile object with the specified path. Parameters ---------- filename : str The path of the file to retrieve. Must be either an absolute path, or relative to the root of this BIDSLayout. scope : str or list, optional Scope of the search space. If passed, only BIDSLayouts that match the specified scope will be searched. See :obj:`BIDSLayout.get` docstring for valid values. Default is 'all'. Returns ------- :obj:`bids.layout.BIDSFile` or None File found, or None if no match was found. """ filename = os.path.abspath(os.path.join(self.root, filename)) for layout in self._get_layouts_in_scope(scope): result = layout.session.query( BIDSFile).filter_by(path=filename).first() # noqa: E501 if result: return result return None
def _build_file_query(self, **kwargs): query = self.session.query(BIDSFile).filter_by(is_dir=False) filters = kwargs.get('filters') # Entity filtering if filters: query = query.join(BIDSFile.tags) regex = kwargs.get('regex_search', False) filters = self._sanitize_query_dtypes(filters) for name, val in filters.items(): if isinstance(val, (list, tuple)) and len(val) == 1: val = val[0] if val is None or isinstance(val, enum.Enum): name_clause = query.filter(BIDSFile.tags.any(entity_name=name)) if val == Query.ANY: query = name_clause else: query = query.except_(name_clause) continue if regex: if isinstance(val, (list, tuple)): val_clause = sa.or_(*[Tag._value.op('REGEXP')(str(v)) for v in val]) else: val_clause = Tag._value.op('REGEXP')(str(val)) else: if isinstance(val, (list, tuple)): val_clause = Tag._value.in_(val) else: val_clause = Tag._value == val subq = sa.and_(Tag.entity_name == name, val_clause) query = query.filter(BIDSFile.tags.any(subq)) return query
[docs] def get_collections(self, level, types=None, variables=None, merge=False, sampling_rate=None, skip_empty=False, **kwargs): """Return one or more variable Collections in the BIDS project. Parameters ---------- level : {'run', 'session', 'subject', 'dataset'} The level of analysis to return variables for. Must be one of 'run', 'session','subject', or 'dataset'. types : str or list Types of variables to retrieve. All valid values reflect the filename stipulated in the BIDS spec for each kind of variable. Valid values include: 'events', 'physio', 'stim', 'scans', 'participants', 'sessions', and 'regressors'. Default is None. variables : list Optional list of variables names to return. If None, all available variables are returned. merge : bool If True, variables are merged across all observations of the current level. E.g., if level='subject', variables from all subjects will be merged into a single collection. If False, each observation is handled separately, and the result is returned as a list. sampling_rate : int or str If level='run', the sampling rate to pass onto the returned :obj:`bids.variables.kollekshuns.BIDSRunVariableCollection`. skip_empty : bool Whether or not to skip empty Variables (i.e., where there are no rows/records in a file after applying any filtering operations like dropping NaNs). kwargs Optional additional arguments to pass onto :obj:`bids.variables.io.load_variables`. Returns ------- list of :obj:`bids.variables.kollekshuns.BIDSVariableCollection` or :obj:`bids.variables.kollekshuns.BIDSVariableCollection` A list if merge=False; a single :obj:`bids.variables.kollekshuns.BIDSVariableCollection` if merge=True. """ from bids.variables import load_variables index = load_variables(self, types=types, levels=level, skip_empty=skip_empty, **kwargs) return index.get_collections(level, variables, merge, sampling_rate=sampling_rate)
[docs] def get_metadata(self, path, include_entities=False, scope='all'): """Return metadata found in JSON sidecars for the specified file. Parameters ---------- path : str Path to the file to get metadata for. include_entities : bool, optional If True, all available entities extracted from the filename (rather than JSON sidecars) are included in the returned metadata dictionary. scope : str or list, optional The scope of the search space. Each element must be one of 'all', 'raw', 'self', 'derivatives', or a BIDS-Derivatives pipeline name. Defaults to searching all available datasets. Returns ------- dict A dictionary of key/value pairs extracted from all of the target file's associated JSON sidecars. Notes ----- A dictionary containing metadata extracted from all matching .json files is returned. In cases where the same key is found in multiple files, the values in files closer to the input filename will take precedence, per the inheritance rules in the BIDS specification. """ for layout in self._get_layouts_in_scope(scope): query = (layout.session.query(Tag) .join(BIDSFile) .filter(BIDSFile.path == path)) if not include_entities: query = query.join(Entity).filter(Entity.is_metadata == True) results = query.all() if results: return {t.entity_name: t.value for t in results} return {}
[docs] def get_dataset_description(self, scope='self', all_=False): """Return contents of dataset_description.json. Parameters ---------- scope : str The scope of the search space. Only descriptions of BIDSLayouts that match the specified scope will be returned. See :obj:`bids.layout.BIDSLayout.get` docstring for valid values. Defaults to 'self' --i.e., returns the dataset_description.json file for only the directly-called BIDSLayout. all_ : bool If True, returns a list containing descriptions for all matching layouts. If False (default), returns for only the first matching layout. Returns ------- dict or list of dict a dictionary or list of dictionaries (depending on all_). """ layouts = self._get_layouts_in_scope(scope) if not all_: return layouts[0].get_file('dataset_description.json').get_dict() return [l.get_file('dataset_description.json').get_dict() for l in layouts]
[docs] def get_nearest(self, path, return_type='filename', strict=True, all_=False, ignore_strict_entities='extension', full_search=False, **filters): """Walk up file tree from specified path and return nearest matching file(s). Parameters ---------- path (str): The file to search from. return_type (str): What to return; must be one of 'filename' (default) or 'tuple'. strict (bool): When True, all entities present in both the input path and the target file(s) must match perfectly. When False, files will be ordered by the number of matching entities, and partial matches will be allowed. all_ (bool): When True, returns all matching files. When False (default), only returns the first match. ignore_strict_entities (str, list): Optional entity/entities to exclude from strict matching when strict is True. This allows one to search, e.g., for files of a different type while matching all other entities perfectly by passing ignore_strict_entities=['type']. Ignores extension by default. full_search (bool): If True, searches all indexed files, even if they don't share a common root with the provided path. If False, only files that share a common root will be scanned. filters : dict Optional keywords to pass on to :obj:`bids.layout.BIDSLayout.get`. """ path = os.path.abspath(path) # Make sure we have a valid suffix if not filters.get('suffix'): f = self.get_file(path) if 'suffix' not in f.entities: raise ValueError( "File '%s' does not have a valid suffix, most " "likely because it is not a valid BIDS file." % path ) filters['suffix'] = f.entities['suffix'] # Collect matches for all entities entities = {} for ent in self.get_entities(metadata=False).values(): m = ent.regex.search(path) if m: entities[ent.name] = ent._astype(m.group(1)) # Remove any entities we want to ignore when strict matching is on if strict and ignore_strict_entities is not None: for k in listify(ignore_strict_entities): entities.pop(k, None) # Get candidate files results = self.get(**filters) # Make a dictionary of directories --> contained files folders = defaultdict(list) for f in results: folders[f.dirname].append(f) # Build list of candidate directories to check search_paths = [] while True: if path in folders and folders[path]: search_paths.append(path) parent = os.path.dirname(path) if parent == path: break path = parent if full_search: unchecked = set(folders.keys()) - set(search_paths) search_paths.extend(path for path in unchecked if folders[path]) def count_matches(f): # Count the number of entities shared with the passed file f_ents = f.entities keys = set(entities.keys()) & set(f_ents.keys()) shared = len(keys) return [shared, sum([entities[k] == f_ents[k] for k in keys])] matches = [] for path in search_paths: # Sort by number of matching entities. Also store number of # common entities, for filtering when strict=True. num_ents = [[f] + count_matches(f) for f in folders[path]] # Filter out imperfect matches (i.e., where number of common # entities does not equal number of matching entities). if strict: num_ents = [f for f in num_ents if f[1] == f[2]] num_ents.sort(key=lambda x: x[2], reverse=True) if num_ents: for f_match in num_ents: matches.append(f_match[0]) if not all_: break matches = [match.path if return_type.startswith('file') else match for match in matches] return matches if all_ else matches[0] if matches else None
[docs] def get_bvec(self, path, **kwargs): """Get bvec file for passed path.""" result = self.get_nearest(path, extension='bvec', suffix='dwi', all_=True, **kwargs) return listify(result)[0]
[docs] def get_bval(self, path, **kwargs): """Get bval file for passed path.""" result = self.get_nearest(path, suffix='dwi', extension='bval', all_=True, **kwargs) return listify(result)[0]
[docs] def get_fieldmap(self, path, return_list=False): """Get fieldmap(s) for specified path.""" fieldmaps = self._get_fieldmaps(path) if return_list: return fieldmaps else: if len(fieldmaps) == 1: return fieldmaps[0] elif len(fieldmaps) > 1: raise ValueError("More than one fieldmap found, but the " "'return_list' argument was set to False. " "Either ensure that there is only one " "fieldmap for this image, or set the " "'return_list' argument to True and handle " "the result as a list.") else: # len(fieldmaps) == 0 return None
def _get_fieldmaps(self, path): sub = self.parse_file_entities(path)['subject'] fieldmap_set = [] suffix = '(phase1|phasediff|epi|fieldmap)' files = self.get(subject=sub, suffix=suffix, regex_search=True, extension=['nii.gz', 'nii']) for file in files: metadata = self.get_metadata(file.path) if metadata and "IntendedFor" in metadata.keys(): intended_for = listify(metadata["IntendedFor"]) if any([path.endswith(_suff) for _suff in intended_for]): cur_fieldmap = {} if file.entities['suffix'] == "phasediff": cur_fieldmap = {"phasediff": file.path, "magnitude1": file.path.replace( "phasediff", "magnitude1"), "suffix": "phasediff"} magnitude2 = file.path.replace( "phasediff", "magnitude2") if os.path.isfile(magnitude2): cur_fieldmap['magnitude2'] = magnitude2 elif file.entities['suffix'] == "phase1": cur_fieldmap["phase1"] = file.path cur_fieldmap["magnitude1"] = \ file.path.replace("phase1", "magnitude1") cur_fieldmap["phase2"] = \ file.path.replace("phase1", "phase2") cur_fieldmap["magnitude2"] = \ file.path.replace("phase1", "magnitude2") cur_fieldmap["suffix"] = "phase" elif file.entities['suffix'] == "epi": cur_fieldmap["epi"] = file.path cur_fieldmap["suffix"] = "epi" elif file.entities['suffix'] == "fieldmap": cur_fieldmap["fieldmap"] = file.path cur_fieldmap["magnitude"] = \ file.path.replace("fieldmap", "magnitude") cur_fieldmap["suffix"] = "fieldmap" fieldmap_set.append(cur_fieldmap) return fieldmap_set
[docs] def get_tr(self, derivatives=False, **filters): """Return the scanning repetition time (TR) for one or more runs. Parameters ---------- derivatives : bool If True, also checks derivatives images. filters : dict Optional keywords used to constrain the selected runs. Can be any arguments valid for a .get call (e.g., BIDS entities or JSON sidecar keys). Returns ------- float A single float. Notes ----- Raises an exception if more than one unique TR is found. """ # Constrain search to functional images filters.update(suffix='bold', datatype='func') scope = 'all' if derivatives else 'raw' images = self.get(extension=['nii', 'nii.gz'], scope=scope, **filters) if not images: raise ValueError("No functional images that match criteria found.") all_trs = set() for img in images: md = self.get_metadata(img.path) all_trs.add(round(float(md['RepetitionTime']), 5)) if len(all_trs) > 1: raise ValueError("Unique TR cannot be found given filters {!r}" .format(filters)) return all_trs.pop()
[docs] def build_path(self, source, path_patterns=None, strict=False, scope='all', validate=True): """Construct a target filename for a file or dictionary of entities. Parameters ---------- source : str or :obj:`bids.layout.BIDSFile` or dict The source data to use to construct the new file path. Must be one of: - A BIDSFile object - A string giving the path of a BIDSFile contained within the current Layout. - A dict of entities, with entity names in keys and values in values path_patterns : list Optional path patterns to use to construct the new file path. If None, the Layout-defined patterns will be used. Entities should be represented by the name surrounded by curly braces. Optional portions of the patterns should be denoted by square brackets. Entities that require a specific value for the pattern to match can pass them inside carets. Default values can be assigned by specifying a string after the pipe operator. E.g., (e.g., {type<image>|bold} would only match the pattern if the entity 'type' was passed and its value is "image", otherwise the default value "bold" will be used). Example: 'sub-{subject}/[var-{name}/]{id}.csv' Result: 'sub-01/var-SES/1045.csv' strict : bool, optional If True, all entities must be matched inside a pattern in order to be a valid match. If False, extra entities will be ignored so long as all mandatory entities are found. scope : str or list, optional The scope of the search space. Indicates which BIDSLayouts' path patterns to use. See BIDSLayout docstring for valid values. By default, uses all available layouts. If two or more values are provided, the order determines the precedence of path patterns (i.e., earlier layouts will have higher precedence). validate : bool, optional If True, built path must pass BIDS validator. If False, no validation is attempted, and an invalid path may be returned (e.g., if an entity value contains a hyphen). """ # 'is_file' is a crude check for Path objects if isinstance(source, str) or hasattr(source, 'is_file'): source = str(source) if source not in self.files: source = os.path.join(self.root, source) source = self.get_file(source) if isinstance(source, BIDSFile): source = source.entities if path_patterns is None: layouts = self._get_layouts_in_scope(scope) path_patterns = [] seen_configs = set() for l in layouts: for c in l.config.values(): if c in seen_configs: continue if c.default_path_patterns is not None: path_patterns.extend(c.default_path_patterns) seen_configs.add(c) built = build_path(source, path_patterns, strict) if built is None: raise ValueError( "Unable to construct build path with source {}".format(source)) to_check = os.path.join(os.path.sep, built) if not validate or BIDSValidator().is_bids(to_check): return built raise ValueError("Built path {} is not a valid BIDS filename. Please " "make sure all provided entity values are " "spec-compliant.".format(built))
[docs] def copy_files(self, files=None, path_patterns=None, symbolic_links=True, root=None, conflicts='fail', **kwargs): """Copy BIDSFile(s) to new locations. The new locations are defined by each BIDSFile's entities and the specified `path_patterns`. Parameters ---------- files : list Optional list of BIDSFile objects to write out. If none provided, use files from running a get() query using remaining **kwargs. path_patterns : str or list Write patterns to pass to each file's write_file method. symbolic_links : bool Whether to copy each file as a symbolic link or a deep copy. root : str Optional root directory that all patterns are relative to. Defaults to current working directory. conflicts : str Defines the desired action when the output path already exists. Must be one of: 'fail': raises an exception 'skip' does nothing 'overwrite': overwrites the existing file 'append': adds a suffix to each file copy, starting with 1 kwargs : dict Optional key word arguments to pass into a get() query. """ _files = self.get(**kwargs) if files: _files = list(set(files).intersection(_files)) for f in _files: f.copy(path_patterns, symbolic_link=symbolic_links, root=self.root, conflicts=conflicts)
[docs] def write_contents_to_file(self, entities, path_patterns=None, contents=None, link_to=None, content_mode='text', conflicts='fail', strict=False, validate=True): """Write arbitrary data to a file defined by the passed entities and path patterns. Parameters ---------- entities : dict A dictionary of entities, with Entity names in keys and values for the desired file in values. path_patterns : list Optional path patterns to use when building the filename. If None, the Layout-defined patterns will be used. contents : object Contents to write to the generate file path. Can be any object serializable as text or binary data (as defined in the content_mode argument). link_to : str Optional path with which to create a symbolic link to. Used as an alternative to and takes priority over the contents argument. conflicts : str Defines the desired action when the output path already exists. Must be one of: 'fail': raises an exception 'skip' does nothing 'overwrite': overwrites the existing file 'append': adds a suffix to each file copy, starting with 1 strict : bool If True, all entities must be matched inside a pattern in order to be a valid match. If False, extra entities validate : bool If True, built path must pass BIDS validator. If False, no validation is attempted, and an invalid path may be returned (e.g., if an entity value contains a hyphen). """ path = self.build_path(entities, path_patterns, strict, validate=validate) if path is None: raise ValueError("Cannot construct any valid filename for " "the passed entities given available path " "patterns.") write_contents_to_file(path, contents=contents, link_to=link_to, content_mode=content_mode, conflicts=conflicts, root=self.root)
class Query(enum.Enum): """Enums for use with BIDSLayout.get().""" NONE = 1 # Entity must not be present ANY = 2 # Entity must be defined, but with an arbitrary value