From 8bbff87612fcc045676d9e48650120e2dbd991ec Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 18 Mar 2020 15:31:45 +0000
Subject: [PATCH] RF,ENH: Rewrite gifti.relatedFiles to support BIDS-style
naming conventions
---
fsl/data/gifti.py | 121 +++++++++++++++++++++++++++++++++++++---------
1 file changed, 98 insertions(+), 23 deletions(-)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 4f8cc2f91..7dc0eca30 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -25,12 +25,14 @@ are available:
import glob
+import re
import os.path as op
import numpy as np
import nibabel as nib
import fsl.utils.path as fslpath
+import fsl.utils.bids as bids
import fsl.data.constants as constants
import fsl.data.mesh as fslmesh
@@ -45,6 +47,15 @@ EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI file']
"""A description for each of the :data:`ALLOWED_EXTENSIONS`. """
+VERTEX_DATA_EXTENSIONS = ['.func.gii',
+ '.shape.gii',
+ '.label.gii',
+ '.time.gii']
+"""File suffixes which are interpreted as GIFTI vertex data files,
+containing data values for every vertex in the mesh.
+"""
+
+
class GiftiMesh(fslmesh.Mesh):
"""Class which represents a GIFTI surface image. This is essentially
just a 3D model made of triangles.
@@ -262,7 +273,7 @@ def prepareGiftiVertexData(darrays, filename=None):
vertices.
"""
- intents = set([d.intent for d in darrays])
+ intents = {d.intent for d in darrays}
if len(intents) != 1:
raise ValueError('{} contains multiple (or no) intents'
@@ -301,45 +312,109 @@ def relatedFiles(fname, ftypes=None):
directory which appear to be related with the given one. Files which
share the same prefix are assumed to be related to the given file.
+ This function assumes that the GIFTI files are named according to a
+ standard convention - the following conventions are supported:
+ - HCP-style, i.e.: ``<subject>.<hemi>.<type>.<space>.<ftype>.gii``
+ - BIDS-style, i.e.:
+ ``<source_prefix>_hemi-<hemi>[_space-<space>]*_<suffix>.<ftype>.gii``
+
+ If the files are not named according to one of these conventions, this
+ function will return an empty list.
+
:arg fname: Name of the file to search for related files for
:arg ftype: If provided, only files with suffixes in this list are
- searched for. Defaults to files which contain vertex data.
+ searched for. Defaults to :attr:`VERTEX_DATA_EXTENSIONS`.
"""
if ftypes is None:
- ftypes = ['.func.gii', '.shape.gii', '.label.gii', '.time.gii']
+ ftypes = VERTEX_DATA_EXTENSIONS
- # We want to return all files in the same
- # directory which have the following name:
+ path = op.abspath(fname)
+ dirname, fname = op.split(path)
+ # We want to identify all files in the same
+ # directory which are associated with the
+ # given file. We assume that the files are
+ # named according to one of the following
+ # conventions:
#
- # [subj].[hemi].[type].*.[ftype]
+ # - HCP style:
+ # <subject>.<hemi>.<type>.<space>.<ftype>.gii
#
-
- # where
- # - [subj] is the subject ID, and matches fname
+ # - BIDS style:
+ # <source_prefix>_hemi-<hemi>[_space-<space>]*.<ftype>.gii
#
- # - [hemi] is the hemisphere, and matches fname
+ # We cannot assume consistent ordering of
+ # the entities (key-value pairs) within a
+ # BIDS style filename, so we cannot simply
+ # use a regular expression or glob pattern.
+ # Instead, for each style we define:
#
- # - [type] defines the file contents
+ # - a "matcher" function, which tests
+ # whether the file matches the style,
+ # and returns the important elements
+ # from the file name.
#
- # - suffix is func, shape, label, time, or `ftype`
-
- path = op.abspath(fname)
- dirname, fname = op.split(path)
-
- # get the [subj].[hemi] prefix
- try:
- subj, hemi, _ = fname.split('.', 2)
- prefix = '.'.join((subj, hemi))
- except Exception:
+ # - a "searcher" function, which takes
+ # the elements of the input file
+ # that were extracted by the matcher,
+ # and searches for other related files
+
+ # HCP style - extract "<subject>.<hemi>"
+ # and "<space>".
+ def matchhcp(f):
+ pat = r'^(.*\.[LR])\..*\.(.*)\..*\.gii$'
+ match = re.match(pat, f)
+ if match:
+ return match.groups()
+ else:
+ return None
+
+ def searchhcp(match, ftype):
+ prefix, space = match
+ template = '{}.*.{}{}'.format(prefix, space, ftype)
+ return glob.glob(op.join(dirname, template))
+
+ # BIDS style - extract all entities (kv
+ # pairs), ignoring specific irrelevant
+ # ones.
+ def matchbids(f):
+ try: match = bids.BIDSFile(f)
+ except ValueError: return None
+ match.entities.pop('desc', None)
+ return match
+
+ def searchbids(match, ftype):
+ allfiles = glob.glob(op.join(dirname, '*{}'.format(ftype)))
+ for f in allfiles:
+ try: bf = bids.BIDSFile(f)
+ except ValueError: continue
+ if bf.match(match, False):
+ yield f
+
+ # find the first style that matches
+ matchers = [matchhcp, matchbids]
+ searchers = [searchhcp, searchbids]
+ for matcher, searcher in zip(matchers, searchers):
+ match = matcher(fname)
+ if match:
+ break
+
+ # Give up if the file does
+ # not match any known style.
+ else:
return []
+ # Build a list of files in the same
+ # directory and matching the template
related = []
-
for ftype in ftypes:
- hits = glob.glob(op.join(dirname, '{}*{}'.format(prefix, ftype)))
+
+ hits = searcher(match, ftype)
+
+ # eliminate dupes
related.extend([h for h in hits if h not in related])
+ # exclude the file itself
return [r for r in related if r != path]
--
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