diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index ea17df9c9056ce0f4add92d35bc52ed3611a32b7..371404bc22438c8526386453de3d99183daaf155 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,29 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+2.9.0 (Under development)
+-------------------------
+
+
+Added
+^^^^^
+
+
+* New ``firstDot`` option to the :func:`.path.getExt`,
+ :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
+ rudimentary support for double-barrelled filenames.
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.gifti.relatedFiles` function now supports files with
+ BIDS-style naming conventions.
+* The :mod:`.bids` module has been updated to support files with any
+ extension, not just those in the core BIDS specification (``.nii``,
+ ``.nii.gz``, ``.json``, ``.tsv``).
+
2.8.4 (Monday 2nd March 2020)
-----------------------------
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 2d1f3856d5ddae797b271a4cf79c4b14a12faf8b..7dc0eca309468ff9692c902f09ebbd1b4b8d8985 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.
@@ -102,8 +113,11 @@ class GiftiMesh(fslmesh.Mesh):
# as the specfiied one.
if loadAll:
+ # Only attempt to auto-load sensibly
+ # named gifti files (i.e. *.surf.gii,
+ # rather than *.gii).
+ surfFiles = relatedFiles(infile, [ALLOWED_EXTENSIONS[0]])
nvertices = vertices[0].shape[0]
- surfFiles = relatedFiles(infile, ALLOWED_EXTENSIONS)
for sfile in surfFiles:
@@ -259,7 +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'
@@ -298,45 +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]
diff --git a/fsl/utils/bids.py b/fsl/utils/bids.py
index 40bab3a04990d6cff53f55310cc378b581a75dcc..cae75cb4f61a806faa7de5a7d83dc04cb44e7f83 100644
--- a/fsl/utils/bids.py
+++ b/fsl/utils/bids.py
@@ -9,6 +9,7 @@
.. autosummary::
:nosignatures:
+ BIDSFile
isBIDSDir
inBIDSDir
isBIDSFile
@@ -57,20 +58,34 @@ class BIDSFile(object):
self.suffix = suffix
- def match(self, other):
+ def __str__(self):
+ """Return a strimg representation of this ``BIDSFile``. """
+ return 'BIDSFile({})'.format(self.filename)
+
+
+ def __repr__(self):
+ """Return a strimg representation of this ``BIDSFile``. """
+ return str(self)
+
+
+ def match(self, other, suffix=True):
"""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.
+ :arg other: ``BIDSFile`` to compare
+
+ :arg suffix: Defaults to ``True``. If ``False``, the comparison
+ is made solely on the entity values.
+
+ :returns: ``True`` if ``self.suffix == other.suffix`` (unless
+ ``suffix`` is ``False``) and if all of the entities in
+ ``other`` are present in ``self``, ``False`` otherwise.
"""
- suffix = self.suffix == other.suffix
+ suffix = (not suffix) or (self.suffix == other.suffix)
entities = True
for key, value in other.entities.items():
- entities = entities and self.entities.get(key, None) == value
+ entities = entities and (self.entities.get(key, None) == value)
return suffix and entities
@@ -83,7 +98,11 @@ def parseFilename(filename):
sub-01_ses-01_task-stim_bold.nii.gz
- has suffix ``bold``, and entities ``sub=01``, ``ses=01`` and ``task=stim``.
+ has suffix ``bold``, entities ``sub=01``, ``ses=01`` and ``task=stim``, and
+ extension ``.nii.gz``.
+
+ .. note:: This function assumes that no period (``.``) characters occur in
+ the body of a BIDS filename.
:returns: A tuple containing:
- A dict containing the entities
@@ -97,7 +116,7 @@ def parseFilename(filename):
suffix = None
entities = []
filename = op.basename(filename)
- filename = fslpath.removeExt(filename, ['.nii', '.nii.gz', '.json'])
+ filename = fslpath.removeExt(filename, firstDot=True)
parts = filename.split('_')
for part in parts[:-1]:
@@ -148,7 +167,7 @@ def isBIDSFile(filename, strict=True):
"""
name = op.basename(filename)
- pattern = r'([a-z0-9]+-[a-z0-9]+_)*([a-z0-9])+\.(nii|nii\.gz|json)'
+ pattern = r'([a-z0-9]+-[a-z0-9]+_)*([a-z0-9])+\.(.+)'
flags = re.ASCII | re.IGNORECASE
match = re.fullmatch(pattern, name, flags) is not None
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index e45f82213f0b44495bd1c6e4573bb5ab169b7c1d..8d312bef5f7e427debeb6fde27ce30501220c3f6 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -218,37 +218,61 @@ def addExt(prefix,
return allPaths[0]
-def removeExt(filename, allowedExts=None):
+def removeExt(filename, allowedExts=None, firstDot=False):
"""Returns the base name of the given file name. See :func:`splitExt`. """
- return splitExt(filename, allowedExts)[0]
+ return splitExt(filename, allowedExts, firstDot)[0]
-def getExt(filename, allowedExts=None):
+def getExt(filename, allowedExts=None, firstDot=False):
"""Returns the extension of the given file name. See :func:`splitExt`. """
- return splitExt(filename, allowedExts)[1]
+ return splitExt(filename, allowedExts, firstDot)[1]
-def splitExt(filename, allowedExts=None):
+def splitExt(filename, allowedExts=None, firstDot=False):
"""Returns the base name and the extension from the given file name.
- If ``allowedExts`` is ``None``, this function is equivalent to using::
+ If ``allowedExts`` is ``None`` and ``firstDot`` is ``False``, this
+ function is equivalent to using::
os.path.splitext(filename)
- If ``allowedExts`` is provided, but the file does not end with an allowed
- extension, a tuple containing ``(filename, '')`` is returned.
+ If ``allowedExts`` is ``None`` and ``firstDot`` is ``True``, the file
+ name is split on the first period that is found, rather than the last
+ period. For example::
+
+ splitExt('image.nii.gz') # -> ('image.nii', '.gz')
+ splitExt('image.nii.gz', firstDot=True) # -> ('image', '.nii.gz')
+
+ If ``allowedExts`` is provided, ``firstDot`` is ignored. In this case, if
+ the file does not end with an allowed extension, a tuple containing
+ ``(filename, '')`` is returned.
:arg filename: The file name to split.
:arg allowedExts: Allowed/recognised file extensions.
+
+ :arg firstDot: Split the file name on the first period, rather than the
+ last period. Ignored if ``allowedExts`` is specified.
"""
- # If allowedExts is not specified,
- # we just use op.splitext
+ # If allowedExts is not specified
+ # we split on a period character
if allowedExts is None:
- return op.splitext(filename)
+
+ # split on last period - equivalent
+ # to op.splitext
+ if not firstDot:
+ return op.splitext(filename)
+
+ # split on first period
+ else:
+ idx = filename.find('.')
+ if idx == -1:
+ return filename, ''
+ else:
+ return filename[:idx], filename[idx:]
# Otherwise, try and find a suffix match
extMatches = [filename.endswith(ext) for ext in allowedExts]
diff --git a/tests/test_bids.py b/tests/test_bids.py
index 58bb08f516554d1c58d85991a75ee4d9c38f7bb9..a5facaf8ea2727a23e89471bc13e57dee25745f4 100644
--- a/tests/test_bids.py
+++ b/tests/test_bids.py
@@ -19,7 +19,7 @@ import fsl.utils.bids as fslbids
def test_parseFilename():
with pytest.raises(ValueError):
- fslbids.parseFilename('bad.txt')
+ fslbids.parseFilename('bad_file.txt')
tests = [
('sub-01_ses-01_t1w.nii.gz',
@@ -62,12 +62,12 @@ def test_isBIDSFile():
Path('sub-01_ses-01_t1w.nii'),
Path('sub-01_ses-01_t1w.json'),
Path('a-1_b-2_c-3_d-4_e.nii.gz'),
+ Path('sub-01_ses-01_t1w.txt'),
]
badfiles = [
Path('sub-01_ses-01.nii.gz'),
Path('sub-01_ses-01_t1w'),
Path('sub-01_ses-01_t1w.'),
- Path('sub-01_ses-01_t1w.txt'),
Path('sub_ses-01_t1w.nii.gz'),
Path('sub-01_ses_t1w.nii.gz'),
]
diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index f5e798377e5e45dff555c2aa90d2b41fa5ae3ed9..d4cc1bec5ede307776f8f22d5857b692e67c01e6 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -711,6 +711,16 @@ def test_splitExt():
print(filename, '==', (outbase, outext))
assert fslpath.splitExt(filename, allowed) == (outbase, outext)
+ # firstDot=True
+ tests = [
+ ('blah', ('blah', '')),
+ ('blah.blah', ('blah', '.blah')),
+ ('blah.one.two', ('blah', '.one.two')),
+ ('blah.one.two.three', ('blah', '.one.two.three')),
+ ]
+
+ for f, exp in tests:
+ assert fslpath.splitExt(f, firstDot=True) == exp
def test_getFileGroup_imageFiles_shouldPass():
diff --git a/tests/test_gifti.py b/tests/test_gifti.py
index 835655b1e7da240484101ec7aa4a2b44dbf7490e..6d23e665e105f24e4756148ec896ea6c86436ff4 100644
--- a/tests/test_gifti.py
+++ b/tests/test_gifti.py
@@ -47,9 +47,9 @@ def test_GiftiMesh_create_loadAll():
with tempdir() as td:
- vertSets = [op.join(td, 'prefix.L.1.surf.gii'),
- op.join(td, 'prefix.L.2.surf.gii'),
- op.join(td, 'prefix.L.3.surf.gii')]
+ vertSets = [op.join(td, 'prefix.L.1.space.surf.gii'),
+ op.join(td, 'prefix.L.2.space.surf.gii'),
+ op.join(td, 'prefix.L.3.space.surf.gii')]
for vs in vertSets:
shutil.copy(testfile, vs)
@@ -154,82 +154,122 @@ def test_loadGiftiVertexData():
assert isinstance(gimg, nib.gifti.GiftiImage)
assert tuple(data.shape) == (642, 10)
-
-def test_relatedFiles():
-
- listing = [
- 'subject.L.ArealDistortion_FS.32k_fs_LR.shape.gii',
- 'subject.L.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
- 'subject.L.BA.32k_fs_LR.label.gii',
- 'subject.L.MyelinMap.32k_fs_LR.func.gii',
- 'subject.L.MyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.L.SmoothedMyelinMap.32k_fs_LR.func.gii',
- 'subject.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.L.aparc.32k_fs_LR.label.gii',
- 'subject.L.aparc.a2009s.32k_fs_LR.label.gii',
- 'subject.L.atlasroi.32k_fs_LR.shape.gii',
- 'subject.L.corrThickness.32k_fs_LR.shape.gii',
- 'subject.L.curvature.32k_fs_LR.shape.gii',
- 'subject.L.flat.32k_fs_LR.surf.gii',
- 'subject.L.inflated.32k_fs_LR.surf.gii',
- 'subject.L.midthickness.32k_fs_LR.surf.gii',
- 'subject.L.pial.32k_fs_LR.surf.gii',
- 'subject.L.sphere.32k_fs_LR.surf.gii',
- 'subject.L.sulc.32k_fs_LR.shape.gii',
- 'subject.L.thickness.32k_fs_LR.shape.gii',
- 'subject.L.very_inflated.32k_fs_LR.surf.gii',
- 'subject.L.white.32k_fs_LR.surf.gii',
- 'subject.R.ArealDistortion_FS.32k_fs_LR.shape.gii',
- 'subject.R.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
- 'subject.R.BA.32k_fs_LR.label.gii',
- 'subject.R.MyelinMap.32k_fs_LR.func.gii',
- 'subject.R.MyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.R.SmoothedMyelinMap.32k_fs_LR.func.gii',
- 'subject.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.R.aparc.32k_fs_LR.label.gii',
- 'subject.R.aparc.a2009s.32k_fs_LR.label.gii',
- 'subject.R.atlasroi.32k_fs_LR.shape.gii',
- 'subject.R.corrThickness.32k_fs_LR.shape.gii',
- 'subject.R.curvature.32k_fs_LR.shape.gii',
- 'subject.R.flat.32k_fs_LR.surf.gii',
- 'subject.R.inflated.32k_fs_LR.surf.gii',
- 'subject.R.midthickness.32k_fs_LR.surf.gii',
- 'subject.R.pial.32k_fs_LR.surf.gii',
- 'subject.R.sphere.32k_fs_LR.surf.gii',
- 'subject.R.sulc.32k_fs_LR.shape.gii',
- 'subject.R.thickness.32k_fs_LR.shape.gii',
- 'subject.R.very_inflated.32k_fs_LR.surf.gii',
- 'subject.R.white.32k_fs_LR.surf.gii',
- 'badly-formed-filename.surf.gii'
- ]
-
- lsurfaces = [l for l in listing if (l.startswith('subject.L') and
- l.endswith('surf.gii'))]
- lrelated = [l for l in listing if (l.startswith('subject.L') and
- not l.endswith('surf.gii'))]
-
- rsurfaces = [l for l in listing if (l.startswith('subject.R') and
- l.endswith('surf.gii'))]
- rrelated = [l for l in listing if (l.startswith('subject.R') and
- not l.endswith('surf.gii'))]
+hcp_listing = [
+ 'subject.L.ArealDistortion_FS.32k_fs_LR.shape.gii',
+ 'subject.L.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
+ 'subject.L.BA.32k_fs_LR.label.gii',
+ 'subject.L.MyelinMap.32k_fs_LR.func.gii',
+ 'subject.L.MyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.L.SmoothedMyelinMap.32k_fs_LR.func.gii',
+ 'subject.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.L.aparc.32k_fs_LR.label.gii',
+ 'subject.L.aparc.a2009s.32k_fs_LR.label.gii',
+ 'subject.L.atlasroi.32k_fs_LR.shape.gii',
+ 'subject.L.corrThickness.32k_fs_LR.shape.gii',
+ 'subject.L.curvature.32k_fs_LR.shape.gii',
+ 'subject.L.flat.32k_fs_LR.surf.gii',
+ 'subject.L.inflated.32k_fs_LR.surf.gii',
+ 'subject.L.midthickness.32k_fs_LR.surf.gii',
+ 'subject.L.pial.32k_fs_LR.surf.gii',
+ 'subject.L.sphere.32k_fs_LR.surf.gii',
+ 'subject.L.sulc.32k_fs_LR.shape.gii',
+ 'subject.L.thickness.32k_fs_LR.shape.gii',
+ 'subject.L.very_inflated.32k_fs_LR.surf.gii',
+ 'subject.L.white.32k_fs_LR.surf.gii',
+ 'subject.R.ArealDistortion_FS.32k_fs_LR.shape.gii',
+ 'subject.R.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
+ 'subject.R.BA.32k_fs_LR.label.gii',
+ 'subject.R.MyelinMap.32k_fs_LR.func.gii',
+ 'subject.R.MyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.R.SmoothedMyelinMap.32k_fs_LR.func.gii',
+ 'subject.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.R.aparc.32k_fs_LR.label.gii',
+ 'subject.R.aparc.a2009s.32k_fs_LR.label.gii',
+ 'subject.R.atlasroi.32k_fs_LR.shape.gii',
+ 'subject.R.corrThickness.32k_fs_LR.shape.gii',
+ 'subject.R.curvature.32k_fs_LR.shape.gii',
+ 'subject.R.flat.32k_fs_LR.surf.gii',
+ 'subject.R.inflated.32k_fs_LR.surf.gii',
+ 'subject.R.midthickness.32k_fs_LR.surf.gii',
+ 'subject.R.pial.32k_fs_LR.surf.gii',
+ 'subject.R.sphere.32k_fs_LR.surf.gii',
+ 'subject.R.sulc.32k_fs_LR.shape.gii',
+ 'subject.R.thickness.32k_fs_LR.shape.gii',
+ 'subject.R.very_inflated.32k_fs_LR.surf.gii',
+ 'subject.R.white.32k_fs_LR.surf.gii'
+]
+
+bids_listing = [
+ 'sub-001_ses-001_hemi-L_desc-corr_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-L_desc-drawem_space-T2w_dparc.label.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_desc-medialwall_mask.shape.gii',
+ 'sub-001_ses-001_hemi-L_desc-smoothed_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_curv.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_inflated.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_midthickness.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_pial.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_sphere.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_sulc.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_veryinflated.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_wm.surf.gii',
+ 'sub-001_ses-001_hemi-R_desc-corr_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-R_desc-drawem_space-T2w_dparc.label.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_desc-medialwall_mask.shape.gii',
+ 'sub-001_ses-001_hemi-R_desc-smoothed_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_curv.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_inflated.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_midthickness.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_pial.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_sphere.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_sulc.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_veryinflated.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_wm.surf.gii'
+]
+
+
+def test_relatedFiles_hcp(): _test_relatedFiles(hcp_listing)
+def test_relatedFiles_bids(): _test_relatedFiles(bids_listing)
+def _test_relatedFiles(listing):
+
+ listing = list(listing)
+ listing.append('badly-formed-filename.surf.gii')
+
+ def ishemi(f, hemi):
+ return ('hemi-{}'.format(hemi) in f) or \
+ ('.{}.' .format(hemi) in f)
+
+ def issurf(f):
+ return f.endswith('surf.gii')
+
+ def isrelated(f):
+ return not issurf(f)
+
+ lsurfaces = [l for l in listing if issurf( l) and ishemi(l, 'L')]
+ lrelated = [l for l in listing if isrelated(l) and ishemi(l, 'L')]
+ rsurfaces = [l for l in listing if issurf( l) and ishemi(l, 'R')]
+ rrelated = [l for l in listing if isrelated(l) and ishemi(l, 'R')]
with tempdir() as td:
+ listing = [op.join(td, f) for f in listing]
+ lsurfaces = [op.join(td, f) for f in lsurfaces]
+ rsurfaces = [op.join(td, f) for f in rsurfaces]
+ lrelated = [op.join(td, f) for f in lrelated]
+ rrelated = [op.join(td, f) for f in rrelated]
+
for l in listing:
- with open(op.join(td, l), 'wt') as f:
+ with open(l, 'wt') as f:
f.write(l)
- badname = op.join(op.join(td, 'badly-formed-filename'))
+ badname = op.join(td, 'badly-formed-filename.surf.gii')
assert len(gifti.relatedFiles(badname)) == 0
assert len(gifti.relatedFiles('nonexistent')) == 0
- llisting = [op.join(td, f) for f in listing]
- lsurfaces = [op.join(td, f) for f in lsurfaces]
- rsurfaces = [op.join(td, f) for f in rsurfaces]
- lrelated = [op.join(td, f) for f in lrelated]
- rrelated = [op.join(td, f) for f in rrelated]
-
for s in lsurfaces:
result = gifti.relatedFiles(s)
assert sorted(lrelated) == sorted(result)
@@ -237,12 +277,13 @@ def test_relatedFiles():
result = gifti.relatedFiles(s)
assert sorted(rrelated) == sorted(result)
- exp = lsurfaces + lrelated
+ exp = lsurfaces
exp = [f for f in exp if f != lsurfaces[0]]
result = gifti.relatedFiles(lsurfaces[0],
- ftypes=gifti.ALLOWED_EXTENSIONS)
+ ftypes=[gifti.ALLOWED_EXTENSIONS[0]])
assert sorted(exp) == sorted(result)
+
TEST_VERTS = np.array([
[0, 0, 0],
[1, 0, 0],