diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8d0ae06b614a8dbebd0c3c9b7a483ba596a600c9..49beaf83d423cd3a0e784b2af0bb8cebd2a745c7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -134,7 +134,7 @@ variables:
rules:
- if: $SKIP_TESTS != null
when: never
- - if: $CI_COMMIT_MESSAGE =~ /skip-tests/
+ - if: $CI_COMMIT_MESSAGE =~ /\[skip-tests\]/
when: never
- if: $CI_PIPELINE_SOURCE == "merge_request_event"
when: on_success
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index aeaf86356c9bd85834b13a825c8ecb20a2658fa8..b9fab5d092b766e33361a50ee96fb52c1f921953 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.15.0 (Under development)
+--------------------------
+
+
+Changed
+^^^^^^^
+
+
+* All metadata stored in GIfTI files is now copied by :class:`.GiftiMesh`
+ instances into their :class:`.Meta` store (!416).
+
3.14.1 (Thursday 31st August 2023)
----------------------------------
diff --git a/fsl/data/cifti.py b/fsl/data/cifti.py
index ecd193eb9854b2c3198954852f8f9cfc76706bf0..08f67f3688a01a3cdaa2ab45ad2f647279a42eba 100644
--- a/fsl/data/cifti.py
+++ b/fsl/data/cifti.py
@@ -440,11 +440,12 @@ class BrainStructure(object):
secondary_str = 'AnatomicalStructureSecondary'
primary = "other"
secondary = None
- for meta in [gifti_obj] + gifti_obj.darrays:
- if primary_str in meta.meta.metadata:
- primary = meta.meta.metadata[primary_str]
- if secondary_str in meta.meta.metadata:
- secondary = meta.meta.metadata[secondary_str]
+
+ for obj in [gifti_obj] + gifti_obj.darrays:
+ if primary_str in obj.meta:
+ primary = obj.meta[primary_str]
+ if secondary_str in obj.meta:
+ secondary = obj.meta[secondary_str]
anatomy = cls.from_string(primary, issurface=True)
anatomy.secondary = None if secondary is None else secondary.lower()
return anatomy
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 077b7c4e14eea3c84064b45d9d69f9253a5ed742..0ff4c8dd5848e78dd7704a01d6e6db9474ffaca4 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -101,9 +101,24 @@ class GiftiMesh(fslmesh.Mesh):
for i, v in enumerate(vertices):
if i == 0: key = infile
- else: key = '{}_{}'.format(infile, i)
+ else: key = f'{infile}_{i}'
self.addVertices(v, key, select=(i == 0), fixWinding=fixWinding)
- self.setMeta(infile, surfimg)
+ self.meta[infile] = surfimg
+
+ # Copy all metadata entries for the GIFTI image
+ for k, v in surfimg.meta.items():
+ self.meta[k] = v
+
+ # and also for each GIFTI data array - triangles
+ # are stored under "faces", and pointsets are
+ # stored under "vertices"/[0,1,2...] (as there may
+ # be multiple pointsets in a file)
+ self.meta['vertices'] = {}
+ for i, arr in enumerate(surfimg.darrays):
+ if arr.intent == constants.NIFTI_INTENT_POINTSET:
+ self.meta['vertices'][i] = dict(arr.meta)
+ elif arr.intent == constants.NIFTI_INTENT_TRIANGLE:
+ self.meta['faces'] = dict(arr.meta)
if vdata is not None:
self.addVertexData(infile, vdata)
@@ -130,7 +145,7 @@ class GiftiMesh(fslmesh.Mesh):
continue
self.addVertices(vertices[0], sfile, select=False)
- self.setMeta(sfile, surfimg)
+ self.meta[sfile] = surfimg
def loadVertices(self, infile, key=None, *args, **kwargs):
@@ -154,10 +169,10 @@ class GiftiMesh(fslmesh.Mesh):
for i, v in enumerate(vertices):
if i == 0: key = infile
- else: key = '{}_{}'.format(infile, i)
+ else: key = f'{infile}_{i}'
vertices[i] = self.addVertices(v, key, *args, **kwargs)
- self.setMeta(infile, surfimg)
+ self.meta[infile] = surfimg
return vertices
@@ -221,12 +236,12 @@ def loadGiftiMesh(filename):
vdata = [d for d in gimg.darrays if d.intent not in (pscode, tricode)]
if len(triangles) != 1:
- raise ValueError('{}: GIFTI surface files must contain '
- 'exactly one triangle array'.format(filename))
+ raise ValueError(f'{filename}: GIFTI surface files must '
+ 'contain exactly one triangle array')
if len(pointsets) == 0:
- raise ValueError('{}: GIFTI surface files must contain '
- 'at least one pointset array'.format(filename))
+ raise ValueError(f'{filename}: GIFTI surface files must '
+ 'contain at least one pointset array')
vertices = [ps.data for ps in pointsets]
indices = np.atleast_2d(triangles[0].data)
@@ -276,14 +291,14 @@ def prepareGiftiVertexData(darrays, filename=None):
intents = {d.intent for d in darrays}
if len(intents) != 1:
- raise ValueError('{} contains multiple (or no) intents'
- ': {}'.format(filename, intents))
+ raise ValueError(f'{filename} contains multiple '
+ f'(or no) intents: {intents}')
intent = intents.pop()
if intent in (constants.NIFTI_INTENT_POINTSET,
constants.NIFTI_INTENT_TRIANGLE):
- raise ValueError('{} contains surface data'.format(filename))
+ raise ValueError(f'{filename} contains surface data')
# Just a single array - return it as-is.
# n.b. Storing (M, N) data in a single
@@ -298,8 +313,8 @@ def prepareGiftiVertexData(darrays, filename=None):
vdata = [d.data for d in darrays]
if any([len(d.shape) != 1 for d in vdata]):
- raise ValueError('{} contains one or more non-vector '
- 'darrays'.format(filename))
+ raise ValueError(f'{filename} contains one or '
+ 'more non-vector darrays')
vdata = np.vstack(vdata).T
vdata = vdata.reshape(vdata.shape[0], -1)
@@ -374,7 +389,7 @@ def relatedFiles(fname, ftypes=None):
def searchhcp(match, ftype):
prefix, space = match
- template = '{}.*.{}{}'.format(prefix, space, ftype)
+ template = f'{prefix}.*.{space}{ftype}'
return glob.glob(op.join(dirname, template))
# BIDS style - extract all entities (kv
diff --git a/fsl/tests/__init__.py b/fsl/tests/__init__.py
index edd0f7b46b276ba03af3766973e0d5a9ec9b4a67..c96143037145baea9b2c0d177555120794580d28 100644
--- a/fsl/tests/__init__.py
+++ b/fsl/tests/__init__.py
@@ -147,6 +147,8 @@ def testdir(contents=None, suffix=""):
shutil.rmtree(self.testdir)
return ctx(contents)
+testdir.__test__ = False
+
def make_dummy_files(paths):
"""Creates dummy files for all of the given paths. """
diff --git a/fsl/tests/test_meta.py b/fsl/tests/test_meta.py
index 791f1873b0b070e8b3a61c78aa0e8ae58917f541..a8221b2af6a15c35b36e474883a7a5b2ea8a8d04 100644
--- a/fsl/tests/test_meta.py
+++ b/fsl/tests/test_meta.py
@@ -19,6 +19,8 @@ def test_meta():
for k, v in data.items():
assert m.getMeta(k) == v
+ assert m.meta == data
+
assert list(data.keys()) == list(m.metaKeys())
assert list(data.values()) == list(m.metaValues())
assert list(data.items()) == list(m.metaItems())
diff --git a/fsl/utils/meta.py b/fsl/utils/meta.py
index 30d18a567021f014f9ae41fcbcb381f43b47155d..2eccff01ea2cf36b070f1839f6f8a69494f14be4 100644
--- a/fsl/utils/meta.py
+++ b/fsl/utils/meta.py
@@ -7,12 +7,9 @@
"""This module provides the :class:`Meta` class. """
-import collections
-
-
-class Meta(object):
- """The ``Meta`` class is intended to be used as a mixin for other classes. It
- is simply a wrapper for a dictionary of key-value pairs.
+class Meta:
+ """The ``Meta`` class is intended to be used as a mixin for other classes.
+ It is simply a wrapper for a dictionary of key-value pairs.
It has a handful of methods allowing you to add and access additional
metadata associated with an object.
@@ -20,6 +17,7 @@ class Meta(object):
.. autosummary::
:nosignatures:
+ meta
metaKeys
metaValues
metaItems
@@ -32,11 +30,17 @@ class Meta(object):
"""Initialises a ``Meta`` instance. """
new = super(Meta, cls).__new__(cls)
- new.__meta = collections.OrderedDict()
+ new.__meta = {}
return new
+ @property
+ def meta(self):
+ """Return a reference to the metadata dictionary. """
+ return self.__meta
+
+
def metaKeys(self):
"""Returns the keys contained in the metadata dictionary
(``dict.keys``).