Source code for bids.layout.layout

"""BIDSLayout class."""
import re
from collections import defaultdict
from functools import partial, lru_cache
from itertools import chain
import json
import copy
import enum
import difflib
from pathlib import Path
import warnings
from typing import Hashable

import sqlalchemy as sa
from sqlalchemy.orm import aliased
from sqlalchemy.sql.expression import cast
from bids_validator import BIDSValidator

from ..utils import listify, natural_sort
from ..external import inflect
from ..exceptions import (
    BIDSDerivativesValidationError,
    BIDSEntityError,
    BIDSValidationError,
    NoMatchError,
    TargetError,
)

from .validation import (validate_root, validate_derivative_path,
                         absolute_path_deprecation_warning,
                         indexer_arg_deprecation_warning,
                         EXAMPLE_DERIVATIVES_DESCRIPTION)
from .writing import build_path, write_to_file
from .models import (Config, BIDSFile, DerivativeDatasets, Entity, Tag)
from .index import BIDSLayoutIndexer
from .db import ConnectionManager
from .utils import (BIDSMetadata, parse_file_entities)

__all__ = ['BIDSLayout']


[docs] class BIDSLayout: """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 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. 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. indexer: BIDSLayoutIndexer or callable An optional BIDSLayoutIndexer instance to use for indexing, or any callable that takes a BIDSLayout instance as its only argument. If None, a new indexer with default parameters will be implicitly created. is_derivative: bool Index dataset as a derivative dataset. This can be enabled along with validate=False to index derivatives without dataset_description.json. If validate=True, the dataset must have a dataset_description.json with DatasetType=derivative and GeneratedBy indexer_kwargs: dict Optional keyword arguments to pass onto the newly created BIDSLayoutIndexer. Valid keywords are 'ignore', 'force_index', 'index_metadata', and 'config_filename'. Ignored if indexer is not None. """
[docs] def __init__(self, root=None, validate=True, absolute_paths=True, derivatives=False, config=None, sources=None, regex_search=False, database_path=None, reset_database=False, indexer=None, is_derivative=False, **indexer_kwargs): if not absolute_paths: absolute_path_deprecation_warning() ind_args = {'force_index', 'ignore', 'index_metadata', 'config_filename'} if ind_args & set(indexer_kwargs.keys()): indexer_arg_deprecation_warning() # Load from existing database file load_db = (database_path is not None and reset_database is False and ConnectionManager.exists(database_path)) if load_db: self.connection_manager = ConnectionManager(database_path) info = self.connection_manager.layout_info # Overwrite init args with values in DB root = info.root absolute_paths = info.absolute_paths derivatives = info.derivatives config = info.config # Validate that a valid BIDS project exists at root root, description = validate_root(root, validate) if any([ is_derivative, description and description.get("DatasetType") == "derivative" ]): try: self.source_pipeline = validate_derivative_path(root) except BIDSValidationError as err: if validate: raise err self.source_pipeline = None default_config = ["bids", "derivatives"] self.is_derivative = True else: self.source_pipeline = None default_config = ["bids"] self.is_derivative = False self._root = root # type: Path self.description = description self.absolute_paths = absolute_paths self.derivatives = DerivativeDatasets() self.sources = sources self.regex_search = regex_search # Initialize a completely new layout and index the dataset if not load_db: # If config supplied from user or loaded from db, use it. Otherwise, fall # back to a default config = listify(config if config else default_config) init_args = dict(root=root, absolute_paths=absolute_paths, derivatives=derivatives, config=config) self.connection_manager = ConnectionManager( database_path, reset_database, config, init_args) # Do not overwrite indexer variable, so the same configuration is passed to # add_derivatives() below _indexer = indexer or BIDSLayoutIndexer( validate=validate and not is_derivative, **indexer_kwargs ) _indexer(self) # Add derivatives if any are found if derivatives: if derivatives is True: derivatives = root / 'derivatives' self.add_derivatives( derivatives, parent_database_path=database_path, validate=validate, absolute_paths=absolute_paths, derivatives=None, sources=self, config=None, regex_search=regex_search, reset_database=reset_database, indexer=indexer, **indexer_kwargs)
@property def root(self): return str(self._root) 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 BIDSEntityError( "'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.""" n_subjects = len( [s.value for s in self.session.query(Tag).filter_by( entity_name='subject').group_by(Tag._value)] ) n_sessions = len( set( (t.value, t.file.entities.get('subject')) for t in self.session.query(Tag).filter_by(entity_name='session') if t.file.entities.get('subject') ) ) n_runs = len( set( (t.value, t.file.entities.get('subject')) for t in self.session.query(Tag).filter_by(entity_name='run') if isinstance(t.value, int) and t.file.entities.get('subject') ) ) root = self.root[-30:] s = ("BIDS Layout: ...{} | Subjects: {} | Sessions: {} | " "Runs: {}".format(root, n_subjects, n_sessions, n_runs)) return s 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.source_pipeline return any([ 'raw' in scope and not self.is_derivative, ('derivatives' in scope or pl_name in scope) and self.is_derivative ]) 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] = [ v if isinstance(v, Query) else ents[name]._astype(v) for v in val ] else: entities[name] = ents[name]._astype(val) except Exception: pass return entities @property def session(self): return self.connection_manager.session @property @lru_cache() def config(self): return {c.name: c for c in self.session.query(Config).all()} @property def entities(self): """Get the entities.""" return self.get_entities() @property def files(self): """Get the files.""" return self.get_files() @classmethod def load(cls, database_path): """ Load index from database path. Initialization parameters are set to those found in database_path JSON sidecar. Parameters ---------- database_path : str, Path The path to the desired database folder. If a relative path is passed, it is assumed to be relative to the BIDSLayout root directory. """ return cls(database_path=database_path) 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 initialization, 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_path = Path(database_path) self.connection_manager = self.connection_manager.save_database( database_path, replace_connection) # Recursively save children for pipeline_name, der in self.derivatives.items(): der.save(database_path / pipeline_name) 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.join(Tag).filter_by(is_metadata=metadata) results = query.all() entities.update({e.name: e for e in results}) return entities 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 def clone(self): """Return a deep copy of the current BIDSLayout.""" return copy.deepcopy(self) 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) def _get_derivative_dirs(self, paths): for path in paths: p = Path(path).absolute() base = p.name if Path.exists(p / "dataset_description.json"): yield (base, p) else: yield from ( (f"{base}/{dd.parent.name}", dd.parent) for dd in p.glob("*/dataset_description.json") ) 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 or more pipeline directories, or to a single pipeline directory (e.g., derivatives/fmriprep). parent_database_path : str or Path 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 derivative 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) if parent_database_path: parent_database_path = Path(parent_database_path) deriv_paths = list(self._get_derivative_dirs(paths)) if not deriv_paths: 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).\n".format(paths) + "Example contents of 'dataset_description.json':\n%s" % json.dumps(EXAMPLE_DERIVATIVES_DESCRIPTION)) # Default config and sources values kwargs['sources'] = kwargs.get('sources') or self for name, path in deriv_paths: if parent_database_path: child_database_path = parent_database_path / name kwargs['database_path'] = child_database_path if name in self.derivatives: raise BIDSDerivativesValidationError( f"Pipeline name {name} ({path!s}) has already been added to this " "BIDSLayout. Every added pipeline must have a unique name!" ) self.derivatives[name] = BIDSLayout(path, is_derivative=True, **kwargs) 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(Tag.is_metadata == False) # noqa: E712 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(index='path', columns='entity', values='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(dtype=float) return data.reset_index() def get(self, return_type='object', target=None, scope='all', regex_search=False, absolute_paths=None, invalid_filters='error', **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. invalid_filters (str): Controls behavior when named filters are encountered that don't exist in the database (e.g., in the case of a typo like subbject='0.1'). Valid values: 'error' (default): Raise an explicit error. 'drop': Silently drop invalid filters (equivalent to not having passed them as arguments in the first place). 'allow': Include the invalid filters in the query, resulting in no results being returned. 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). """ if absolute_paths is False: absolute_path_deprecation_warning() layouts = self._get_layouts_in_scope(scope) entities = self.get_entities() # error check on users accidentally passing in filters if isinstance(filters.get('filters'), dict): raise RuntimeError('You passed in filters as a dictionary named ' 'filters; please pass the keys in as named ' 'keywords to the `get()` call. For example: ' '`layout.get(**filters)`.') # Ensure leading periods if extensions were passed if 'extension' in filters and 'bids' in self.config: filters['extension'] = ['.' + x.lstrip('.') if isinstance(x, str) else x for x in listify(filters['extension'])] if invalid_filters != 'allow': bad_filters = set(filters.keys()) - set(entities.keys()) if bad_filters: if invalid_filters == 'drop': for bad_filt in bad_filters: filters.pop(bad_filt) elif invalid_filters == 'error': first_bad = list(bad_filters)[0] msg = "'{}' is not a recognized entity. ".format(first_bad) ents = list(entities.keys()) suggestions = difflib.get_close_matches(first_bad, ents) if suggestions: msg += "Did you mean {}? ".format(suggestions) raise ValueError(msg + "If you're sure you want to impose " "this constraint, set " "invalid_filters='allow'.") # Provide some suggestions if target is specified and invalid. if target is not None and target not in entities: 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 TargetError(("Unknown target '{}'. " + message) .format(target)) results = [] for l in layouts: query = l._build_file_query(filters=filters, regex_search=regex_search) # NOTE: The following line, when uncommented, eager loads # associations. This was introduced in order to prevent sessions # from randomly detaching. It should be fixed by setting # expire_on_commit at session creation, but let's leave this here # for another release or two to make sure we don't have any further # problems. # 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 = str(fi._path.relative_to(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 TargetError('If return_type is "id" or "dir", a valid ' 'target entity must also be specified.') if return_type == 'id': results = list(dict.fromkeys( res.entities[target] for res in results if target in res.entities and isinstance(res.entities[target], Hashable) )) 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 # On Windows, the regex won't compile if, e.g., there is a folder starting with "U" on the path. # Converting to a POSIX path with forward slashes solves this. template = self._root.as_posix() + template to_rep = re.findall(r'{(.*?)\}', template) for ent in to_rep: patt = entities[ent].pattern template = template.replace('{%s}' % ent, patt) # Avoid matching subfolders. We are working with POSIX paths here, so we explicitly use "/" # as path separator. template += r'[^/]*$' matches = [ f.dirname if absolute_paths else str(f._dirname.relative_to(self._root)) # noqa: E501 for f in results if re.search(template, f._dirname.as_posix()) ] 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 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 = self._root.joinpath(filename).absolute() for layout in self._get_layouts_in_scope(scope): result = layout.session.query( BIDSFile).filter_by(path=str(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: regex = kwargs.get('regex_search', False) filters = self._sanitize_query_dtypes(filters) for name, val in filters.items(): tag_alias = aliased(Tag) val_list = list(listify(val)) if val is not None else [None] if not val_list: continue if Query.OPTIONAL in val_list: continue none = required = False if None in val_list: none = True val_list.remove(None) if Query.NONE in val_list: none = True val_list.remove(Query.NONE) if Query.REQUIRED in val_list: required = True val_list.remove(Query.REQUIRED) if none and required: # Always true, apply no filter continue # Baseline, use join, start accumulating clauses join_method = query.join val_clauses = [] # NONE and REQUIRED get special treatment if none: join_method = query.outerjoin val_clauses.append(tag_alias._value.is_(None)) if required: val_clauses.append(tag_alias._value.isnot(None)) # Any remaining values if regex: val_clauses.extend([tag_alias._value.op('REGEXP')(str(v)) for v in val_list]) elif val_list: _value = tag_alias._value if isinstance(val_list[0], int): _value = cast(tag_alias._value, sa.Integer) val_clauses.append(_value.in_(val_list)) # Looking for intersection with list of vals, so use OR val_clause = sa.or_(*val_clauses) if len(val_clauses) > 1 else val_clauses[0] query = join_method( tag_alias, sa.and_( BIDSFile.path == tag_alias.file_path, tag_alias.entity_name == name ), ) query = query.filter(val_clause) query = query.group_by(BIDSFile.path) return query 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.collections.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.collections.BIDSVariableCollection` or :obj:`bids.variables.collections.BIDSVariableCollection` A list if merge=False; a single :obj:`bids.variables.collections.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) 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. """ md = BIDSMetadata(str(path)) for layout in self._get_layouts_in_scope(scope): query = (layout.session.query(Tag) .join(BIDSFile) .filter(BIDSFile.path == str(path))) if not include_entities: query = query.join(Entity).filter(Tag.is_metadata == True) # noqa: E712 results = query.all() if results: md.update({t.entity_name: t.value for t in results}) return md return md 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] 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 = Path(path).absolute() # Make sure we have a valid suffix if not filters.get('suffix'): f = self.get_file(path) if 'suffix' not in f.entities: raise BIDSValidationError( "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(str(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 = path.parent 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 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] 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] 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): path = str(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"]) # path uses local os separators while _suff read from json likely uses author's os separators, so we # convert _suff to use local separators. if any([path.endswith(str(Path(_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 Path(magnitude2).is_file(): 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 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 NoMatchError("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 NoMatchError("Unique TR cannot be found given filters {!r}" .format(filters)) return all_trs.pop() def build_path(self, source, path_patterns=None, strict=False, scope='all', validate=True, absolute_paths=None): """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 angle brackets. 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). 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. """ # '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 = 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 = Path('/').joinpath(built).as_posix() if validate and not BIDSValidator().is_bids(to_check): raise BIDSValidationError( "Built path {} is not a valid BIDS filename. " "Please make sure all provided entity values are " "spec-compliant.".format(built)) # Convert to absolute paths if needed if absolute_paths is None: absolute_paths = self.absolute_paths if absolute_paths: built = self._root / built # type: pathlib.Path # convert into a posix path for consistency with `writing.build_path` built = built.as_posix() # type: str return built 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 dataset root. 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. """ root = self.root if root is None else root _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=root, conflicts=conflicts) def write_to_file(self, entities, path_patterns=None, contents=None, link_to=None, copy_from=None, content_mode='text', conflicts='fail', strict=False, validate=True): """Write data to a file defined by the passed entities and 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 will be ignored so long as all mandatory entities are found. 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_to_file(path, contents=contents, link_to=link_to, copy_from=copy_from, 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 REQUIRED = ANY = 2 # Entity must be defined, but with an arbitrary value OPTIONAL = 3 # Entity may or may not be defined