Source code for fsl.utils.bids

#
# bids.py - Simple BIDS metadata reader.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides a few functions for working with BIDS data sets.

.. autosummary::
   :nosignatures:

   isBIDSDir
   inBIDSDir
   isBIDSFile
   loadMetadata

All of the other functions in this module should not be considered part of the
public API.


.. note::  The `pybids <https://bids-standard.github.io/pybids/>`_ library is
           a more suitable choice if you are after a more robust and featured
           interface for working with BIDS datasets.
"""


import os.path   as op
import itertools as it
import              re
import              glob
import              json

import fsl.utils.memoize as memoize
import fsl.utils.path    as fslpath


[docs]class BIDSFile(object): """The ``BIDSFile`` class parses and stores the entities and suffix contained in a BIDS file. See the :func:`parseFilename` function. The :meth:`match` method can be used to compare two ``BIDSFile`` instances. The following attributes are available on a ``BIDSFile`` instance: - ``filename``: Absolute path to the file - ``entities``: Dict of ``key : value`` pairs, the entities that are present in the file name (e.g. ``{'sub' : '01}``) - ``suffix``: File suffix (e.g. ``T1w``, ``bold``, etc.) """
[docs] def __init__(self, filename): """Create a ``BIDSFile``. """ entities, suffix = parseFilename(filename) self.filename = op.abspath(filename) self.entities = entities self.suffix = suffix
[docs] def match(self, other): """Compare this ``BIDSFile`` to ``other``. :arg other: ``BIDSFile`` to compare :returns: ``True`` if ``self.suffix == other.suffix`` and if all of the entities in ``other`` are present in ``self``, ``False`` otherwise. """ suffix = self.suffix == other.suffix entities = True for key, value in other.entities.items(): entities = entities and self.entities.get(key, None) == value return suffix and entities
[docs]def parseFilename(filename): """Parses a BIDS-like file name. The file name must consist of zero or more "entities" (alpha-numeric ``name-value`` pairs), a "suffix", all separated by underscores, and a regular file extension. For example, the following file:: sub-01_ses-01_task-stim_bold.nii.gz has suffix ``bold``, and entities ``sub=01``, ``ses=01`` and ``task=stim``. :returns: A tuple containing: - A dict containing the entities - The suffix """ if not isBIDSFile(filename, strict=False): raise ValueError('Does not look like a BIDS ' 'file: {}'.format(filename)) suffix = None entities = [] filename = op.basename(filename) filename = fslpath.removeExt(filename, ['.nii', '.nii.gz', '.json']) parts = filename.split('_') for part in parts[:-1]: entities.append(part.split('-')) suffix = parts[-1] entities = dict(entities) return entities, suffix
[docs]def isBIDSDir(dirname): """Returns ``True`` if ``dirname`` is the root directory of a BIDS dataset. """ return op.exists(op.join(dirname, 'dataset_description.json'))
[docs]def inBIDSDir(filename): """Returns ``True`` if ``filename`` looks like it is within a BIDS dataset directory, ``False`` otherwise. """ dirname = op.abspath(op.dirname(filename)) inBIDS = False while True: if isBIDSDir(dirname): inBIDS = True break prevdir = dirname dirname = op.dirname(dirname) # at filesystem root if prevdir == dirname: break return inBIDS
[docs]def isBIDSFile(filename, strict=True): """Returns ``True`` if ``filename`` looks like a BIDS image or JSON file. :arg filename: Name of file to check :arg strict: If ``True`` (the default), the file must be within a BIDS dataset directory, as defined by :func:`inBIDSDir`. """ name = op.basename(filename) pattern = r'([a-z0-9]+-[a-z0-9]+_)*([a-z0-9])+\.(nii|nii\.gz|json)' flags = re.ASCII | re.IGNORECASE match = re.fullmatch(pattern, name, flags) is not None return ((not strict) or inBIDSDir(filename)) and match
@memoize.memoize def loadMetadataFile(filename): """Load ``filename`` (assumed to be JSON), returning its contents. """ with open(filename, 'rt') as f: return json.load(f)
[docs]def loadMetadata(filename): """Load all of the metadata associated with ``filename``. :arg filename: Path to a data file in a BIDS dataset. :returns: A dict containing all of the metadata associated with ``filename`` """ filename = op.realpath(op.abspath(filename)) bfile = BIDSFile(filename) dirname = op.dirname(filename) prevdir = filename metafiles = [] metadata = {} # Walk up the directory tree until # we hit the BIDS dataset root, or # the filesystem root while True: # Gather all json files in this # directory with matching entities # and suffix, sorted alphabetically # and reversed, so that earlier # ones take precedence files = reversed(sorted(glob.glob(op.join(dirname, '*.json')))) files = [BIDSFile(f) for f in files if isBIDSFile(f)] files = [f.filename for f in files if bfile.match(f)] # build a list of all files metafiles.append(files) # move to the next dir up prevdir = dirname dirname = op.dirname(dirname) # stop when we hit the dataset or filesystem root if isBIDSDir(prevdir) or dirname == prevdir: break # Load in each json file, from # shallowest to deepest, so entries # in deeper files take precedence # over shallower ones. for f in it.chain(*reversed(metafiles)): # assuming here that every file contains a dict metadata.update(loadMetadataFile(f)) return metadata