From dedb67a0b741322bae73e3cc5451472787916609 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 30 Oct 2019 06:29:23 +0000
Subject: [PATCH] ENH: New bids metadata reader.
---
fsl/data/bids.py | 204 ++++++++++++++++++++++++++++++++++++++++++++++
fsl/data/image.py | 5 +-
2 files changed, 206 insertions(+), 3 deletions(-)
create mode 100644 fsl/data/bids.py
diff --git a/fsl/data/bids.py b/fsl/data/bids.py
new file mode 100644
index 000000000..46595141d
--- /dev/null
+++ b/fsl/data/bids.py
@@ -0,0 +1,204 @@
+#!/usr/bin/env python
+#
+# 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
+
+
+.. 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
+
+
+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.)
+ """
+
+
+ def __init__(self, filename):
+ """Create a ``BIDSFile``. """
+ entities, suffix = parseFilename(filename)
+ self.filename = op.abspath(filename)
+ self.entities = entities
+ self.suffix = suffix
+
+
+ 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
+
+
+def parseFilename(filename):
+ """Parses a BIDS-like file name. The file name is assumed to 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, or ``None`` if there is no suffix.
+ """
+
+ 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('-'))
+
+ part = parts[-1].split('-')
+
+ if len(part) == 1: suffix = part[0]
+ else: entities.append(part.split('-'))
+
+ entities = dict(entities)
+
+ return entities, suffix
+
+
+def isBIDSDir(dirname):
+ """Returns ``True`` if ``dirname`` is the root directory of a BIDS dataset.
+ """
+ return op.exists(op.join(dirname, 'dataset_description.json'))
+
+
+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
+
+
+def isBIDSFile(filename):
+ """Returns ``True`` if ``filename`` looks like a BIDS image or JSON file.
+ """
+
+ filename = op.basename(filename)
+ pattern = r'([a-z0-9]+-[a-z0-9]+_)*([a-z0-9])+\.(nii|nii\.gz|json)'
+ flags = re.ASCII | re.IGNORECASE
+
+ return inBIDSDir(filename) and re.fullmatch(pattern, filename, flags)
+
+
+@memoize.memoize
+def loadMetadataFile(filename):
+ """Load ``filename`` (assumed to be JSON), returning its contents. """
+ with open(filename, 'rt') as f:
+ return json.load(f)
+
+
+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
+ files = 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
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 188167b9a..a31ab3173 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -61,8 +61,8 @@ log = logging.getLogger(__name__)
ALLOWED_EXTENSIONS = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.hdr.gz']
"""The file extensions which we understand. This list is used as the default
-if the ``allowedExts`` parameter is not passed to any of the functions
-below.
+if the ``allowedExts`` parameter is not passed to any of the ``*Ext``
+functions, or the :func:`looksLikeImage` function.
"""
@@ -246,7 +246,6 @@ class Nifti(notifier.Notifier, meta.Meta):
if not isinstance(header, nib.analyze.AnalyzeHeader):
raise ValueError('Unrecognised header: {}'.format(header))
- header = header
origShape, shape, pixdim = Nifti.determineShape(header)
voxToWorldMat = Nifti.determineAffine(header)
affines, isneuro = Nifti.generateAffines(voxToWorldMat,
--
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