diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index b792deadc8444062fbfc6f81e12555ba3901982f..ae032ca0801613df43503e37426aaf164d1a272e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -23,6 +23,8 @@ Changed
* Minimum required version of ``nibabel`` is now 2.3.
* The :class:`.Image` class now fully delegates to ``nibabel`` for managing
file handles.
+* The :class:`.GiftiMesh` class can now load surface files which contain
+ vertex data.
Removed
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index b0b018c20e5c1955597fb75f6c740fc796ba861e..c4d8ce9c79b8062b413fceaf14a5581b68503437 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -19,6 +19,7 @@ are available:
GiftiMesh
loadGiftiMesh
loadGiftiVertexData
+ prepareGiftiVertexData
relatedFiles
"""
@@ -34,15 +35,13 @@ import fsl.data.constants as constants
import fsl.data.mesh as fslmesh
-# We include '.gii' here because not all surface
-# GIFTIs follow the file suffix convention.
ALLOWED_EXTENSIONS = ['.surf.gii', '.gii']
"""List of file extensions that a file containing Gifti surface data
is expected to have.
"""
-EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI file']
+EXTENSION_DESCRIPTIONS = ['GIFTII surface file', 'GIFTI file']
"""A description for each of the :data:`ALLOWED_EXTENSIONS`. """
@@ -60,7 +59,8 @@ class GiftiMesh(fslmesh.Mesh):
"""Load the given GIFTI file using ``nibabel``, and extracts surface
data using the :func:`loadGiftiMesh` function.
- :arg infile: A GIFTI surface file (``*.surf.gii``).
+ :arg infile: A GIFTI file (``*..gii``) which contains a surface
+ definition.
:arg fixWinding: Passed through to the :meth:`addVertices` method
for the first vertex set.
@@ -76,34 +76,42 @@ class GiftiMesh(fslmesh.Mesh):
name = fslpath.removeExt(op.basename(infile), ALLOWED_EXTENSIONS)
infile = op.abspath(infile)
- surfimg, vertices, indices = loadGiftiMesh(infile)
-
+ surfimg, indices, vertices, vdata = loadGiftiMesh(infile)
fslmesh.Mesh.__init__(self,
indices,
name=name,
dataSource=infile)
- self.addVertices(vertices, infile, fixWinding=fixWinding)
+ for i, v in enumerate(vertices):
+ if i == 0: key = infile
+ else: key = '{} [{}]'.format(infile, i)
+ self.addVertices(v, key, select=(i == 0), fixWinding=fixWinding)
self.setMeta(infile, surfimg)
+ if vdata is not None:
+ self.addVertexData(infile, vdata)
+
# Find and load all other
# surfaces in the same directory
# as the specfiied one.
if loadAll:
- nvertices = vertices.shape[0]
+ nvertices = vertices[0].shape[0]
surfFiles = relatedFiles(infile, ALLOWED_EXTENSIONS)
for sfile in surfFiles:
- surfimg, vertices, _ = loadGiftiMesh(sfile)
+ try:
+ surfimg, _, vertices, _ = loadGiftiMesh(sfile)
+ except Exception:
+ continue
- if vertices.shape[0] != nvertices:
+ if vertices[0].shape[0] != nvertices:
continue
- self.addVertices(vertices, sfile, select=False)
- self.setMeta( sfile, surfimg)
+ self.addVertices(vertices[0], sfile, select=False)
+ self.setMeta(sfile, surfimg)
def loadVertices(self, infile, key=None, *args, **kwargs):
@@ -123,7 +131,7 @@ class GiftiMesh(fslmesh.Mesh):
if key is None:
key = infile
- surfimg, vertices, _ = loadGiftiMesh(infile)
+ surfimg, _, vertices, _ = loadGiftiMesh(infile)
vertices = self.addVertices(vertices, key, *args, **kwargs)
@@ -157,9 +165,10 @@ def loadGiftiMesh(filename):
The image is expected to contain the following``<DataArray>`` elements:
- - one comprising ``NIFTI_INTENT_POINTSET`` data (the surface vertices)
- one comprising ``NIFTI_INTENT_TRIANGLE`` data (vertex indices
defining the triangles).
+ - one or more comprising ``NIFTI_INTENT_POINTSET`` data (the surface
+ vertices)
A ``ValueError`` will be raised if this is not the case.
@@ -169,42 +178,65 @@ def loadGiftiMesh(filename):
- The loaded ``nibabel.gifti.GiftiImage`` instance
- - A ``(N, 3)`` array containing ``N`` vertices.
-
- - A ``(M, 3))`` array containing the vertex indices for
+ - A ``(M, 3)`` array containing the vertex indices for
``M`` triangles.
- """
- gimg = nib.load(filename)
+ - A list of at least one ``(N, 3)`` arrays containing ``N``
+ vertices.
- pointsetCode = constants.NIFTI_INTENT_POINTSET
- triangleCode = constants.NIFTI_INTENT_TRIANGLE
+ - A ``(M, N)`` numpy array containing ``N`` data points for
+ ``M`` vertices, or ``None`` if the file does not contain
+ any vertex data.
+ """
- pointsets = [d for d in gimg.darrays if d.intent == pointsetCode]
- triangles = [d for d in gimg.darrays if d.intent == triangleCode]
+ gimg = nib.load(filename)
- if len(gimg.darrays) != 2:
- raise ValueError('{}: GIFTI surface files must contain '
- 'exactly one pointset array and one '
- 'triangle array'.format(filename))
+ pscode = constants.NIFTI_INTENT_POINTSET
+ tricode = constants.NIFTI_INTENT_TRIANGLE
- if len(pointsets) != 1:
- raise ValueError('{}: GIFTI surface files must contain '
- 'exactly one pointset array'.format(filename))
+ pointsets = [d for d in gimg.darrays if d.intent == pscode]
+ triangles = [d for d in gimg.darrays if d.intent == tricode]
+ 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))
- vertices = pointsets[0].data
+ if len(pointsets) == 0:
+ raise ValueError('{}: GIFTI surface files must contain '
+ 'at least one pointset array'.format(filename))
+
+ vertices = [ps.data for ps in pointsets]
indices = triangles[0].data
- return gimg, vertices, indices
+ if len(vdata) == 0: vdata = None
+ else: vdata = prepareGiftiVertexData(vdata, filename)
+
+ return gimg, indices, vertices, vdata
def loadGiftiVertexData(filename):
"""Loads vertex data from the given GIFTI file.
+ See :func:`prepareGiftiVertexData`.
+
+ Returns a tuple containing:
+
+ - The loaded ``nibabel.gifti.GiftiImage`` object
+
+ - A ``(M, N)`` numpy array containing ``N`` data points for ``M``
+ vertices
+ """
+ gimg = nib.load(filename)
+ return gimg, prepareGiftiVertexData(gimg.darrays, filename)
+
+
+def prepareGiftiVertexData(darrays, filename=None):
+ """Prepares vertex data from the given list of GIFTI data arrays.
+
+ All of the data arrays are concatenated into one ``(M, N)`` array,
+ containing ``N`` data points for ``M`` vertices.
+
It is assumed that the given file does not contain any
``NIFTI_INTENT_POINTSET`` or ``NIFTI_INTENT_TRIANGLE`` data arrays, and
which contains either:
@@ -215,17 +247,11 @@ def loadGiftiVertexData(filename):
- One or more ``(M, 1)`` data arrays each containing a single data point
for ``M`` vertices, and all with the same intent code
- Returns a tuple containing:
-
- - The loaded ``nibabel.gifti.GiftiImage`` object
-
- - A ``(M, N)`` numpy array containing ``N`` data points for ``M``
- vertices
+ Returns a ``(M, N)`` numpy array containing ``N`` data points for ``M``
+ vertices.
"""
- gimg = nib.load(filename)
-
- intents = set([d.intent for d in gimg.darrays])
+ intents = set([d.intent for d in darrays])
if len(intents) != 1:
raise ValueError('{} contains multiple (or no) intents'
@@ -235,20 +261,19 @@ def loadGiftiVertexData(filename):
if intent in (constants.NIFTI_INTENT_POINTSET,
constants.NIFTI_INTENT_TRIANGLE):
-
raise ValueError('{} contains surface data'.format(filename))
# Just a single array - return it as-is.
# n.b. Storing (M, N) data in a single
# DataArray goes against the GIFTI spec,
# but hey, it happens.
- if len(gimg.darrays) == 1:
- vdata = gimg.darrays[0].data
- return gimg, vdata.reshape(vdata.shape[0], -1)
+ if len(darrays) == 1:
+ vdata = darrays[0].data
+ return vdata.reshape(vdata.shape[0], -1)
# Otherwise extract and concatenate
# multiple 1-dimensional arrays
- vdata = [d.data for d in gimg.darrays]
+ 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 '
@@ -257,7 +282,7 @@ def loadGiftiVertexData(filename):
vdata = np.vstack(vdata).T
vdata = vdata.reshape(vdata.shape[0], -1)
- return gimg, vdata
+ return vdata
def relatedFiles(fname, ftypes=None):
diff --git a/tests/test_gifti.py b/tests/test_gifti.py
index b01635d1f85fc768dab8f6808c429a150d430f63..e39e05b6e54532ed36e4d93086335c0726468b31 100644
--- a/tests/test_gifti.py
+++ b/tests/test_gifti.py
@@ -70,11 +70,12 @@ def test_loadGiftiMesh():
testdir = op.join(op.dirname(__file__), 'testdata')
testfile = op.join(testdir, 'example.surf.gii')
- gimg, verts, idxs = gifti.loadGiftiMesh(testfile)
+ gimg, idxs, verts, _ = gifti.loadGiftiMesh(testfile)
assert isinstance(gimg, nib.gifti.GiftiImage)
- assert tuple(verts.shape) == (642, 3)
- assert tuple(idxs.shape) == (1280, 3)
+ assert len(verts) == 1
+ assert tuple(verts[0].shape) == (642, 3)
+ assert tuple(idxs.shape) == (1280, 3)
badfiles = glob.glob(op.join(testdir, 'example_bad*surf.gii'))
@@ -234,3 +235,67 @@ def test_relatedFiles():
for s in rsurfaces:
result = gifti.relatedFiles(s)
assert sorted(rrelated) == sorted(result)
+
+TEST_VERTS = np.array([
+ [0, 0, 0],
+ [1, 0, 0],
+ [0, 1, 0],
+ [0, 0, 1]])
+TEST_IDXS = np.array([
+ [0, 1, 2],
+ [0, 3, 1],
+ [0, 2, 3],
+ [1, 3, 2]])
+
+TEST_VERT_ARRAY = nib.gifti.GiftiDataArray(
+ TEST_VERTS, intent='NIFTI_INTENT_POINTSET')
+TEST_IDX_ARRAY = nib.gifti.GiftiDataArray(
+ TEST_IDXS, intent='NIFTI_INTENT_TRIANGLE')
+
+def test_GiftiMesh_surface_and_data():
+
+ data1 = np.random.randint(0, 10, len(TEST_VERTS))
+ data2 = np.random.randint(0, 10, len(TEST_VERTS))
+ expdata = np.vstack([data1, data2]).T
+ verts = TEST_VERT_ARRAY
+ tris = TEST_IDX_ARRAY
+ data1 = nib.gifti.GiftiDataArray(data1, intent='NIFTI_INTENT_SHAPE')
+ data2 = nib.gifti.GiftiDataArray(data2, intent='NIFTI_INTENT_SHAPE')
+ gimg = nib.gifti.GiftiImage(darrays=[verts, tris, data1, data2])
+
+ with tempdir():
+ fname = op.abspath('test.gii')
+ gimg.to_filename(fname)
+ surf = gifti.GiftiMesh(fname)
+
+ assert np.all(surf.vertices == TEST_VERTS)
+ assert np.all(surf.indices == TEST_IDXS)
+ assert surf.vertexDataSets() == [fname]
+ assert np.all(surf.getVertexData(fname) == expdata)
+
+
+
+def test_GiftiMesh_multiple_vertices():
+
+ tris = TEST_IDX_ARRAY
+ verts1 = TEST_VERT_ARRAY
+ verts2 = nib.gifti.GiftiDataArray(
+ TEST_VERTS * 5, intent='NIFTI_INTENT_POINTSET')
+
+ gimg = nib.gifti.GiftiImage(darrays=[verts1, verts2, tris])
+
+ with tempdir():
+ fname = op.abspath('test.gii')
+ gimg.to_filename(fname)
+ surf = gifti.GiftiMesh(fname)
+
+ expvsets = [fname,
+ '{} [{}]'.format(fname, 1)]
+
+ assert np.all(surf.vertices == TEST_VERTS)
+ assert np.all(surf.indices == TEST_IDXS)
+ assert surf.vertexSets() == expvsets
+
+ surf.vertices = expvsets[1]
+
+ assert np.all(surf.vertices == TEST_VERTS * 5)