diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 6e1d981ce2f7ea6176dffd2e29a9dc70b7d0495a..ae4a1b6fe971ff6aa14b7a7edfa57440d5b328a3 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -31,6 +31,13 @@ Deprecated
library on [PyPI](https://pypi.org/project/file-tree/).
+Fixed
+^^^^^
+
+* Fixed an edge-case in the :mod:`.gifti` module, where a surface with a
+ single triangle was being loaded incorrectly.
+
+
3.5.3 (Tuesday 9th February 2021)
---------------------------------
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index d75c73a79a1f66d2fb8617848d48d4e11f7e9a36..077b7c4e14eea3c84064b45d9d69f9253a5ed742 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -229,7 +229,7 @@ def loadGiftiMesh(filename):
'at least one pointset array'.format(filename))
vertices = [ps.data for ps in pointsets]
- indices = triangles[0].data
+ indices = np.atleast_2d(triangles[0].data)
if len(vdata) == 0: vdata = None
else: vdata = prepareGiftiVertexData(vdata, filename)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index b03a628e2eec368f592a1d84a913b1302d9e2d00..41aee35425b16753f1a3e078b20d78d5c958894a 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -573,7 +573,7 @@ class Mesh(notifier.Notifier, meta.Meta):
# sort by ray. I'm Not sure if this is
# needed - does trimesh do it for us?
- rayIdxs = np.asarray(np.argsort(rays), np.int)
+ rayIdxs = np.asarray(np.argsort(rays))
locs = locs[rayIdxs]
tris = tris[rayIdxs]
@@ -687,7 +687,7 @@ def calcFaceNormals(vertices, indices):
fnormals = np.cross((v1 - v0), (v2 - v0))
fnormals = affine.normalise(fnormals)
- return fnormals
+ return np.atleast_2d(fnormals)
def calcVertexNormals(vertices, indices, fnormals):
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index 74788a3dc0ebf8b2bcd98a053837858975b027f9..7a9b8e786bdf35a6cfb7d1eeca15d554477a1842 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -280,7 +280,7 @@ class DeformationField(NonLinearTransform):
# Mask out the coordinates
# that are out of bounds of
# the deformation field
- voxels = np.round(voxels).astype(np.int)
+ voxels = np.round(voxels).astype(np.int32)
voxmask = (voxels >= [0, 0, 0]) & (voxels < self.shape[:3])
voxmask = voxmask.all(axis=1)
voxels = voxels[voxmask]
@@ -508,9 +508,9 @@ class CoefficientField(NonLinearTransform):
u = np.remainder(i, 1)
v = np.remainder(j, 1)
w = np.remainder(k, 1)
- i = np.floor(i).astype(np.int)
- j = np.floor(j).astype(np.int)
- k = np.floor(k).astype(np.int)
+ i = np.floor(i).astype(np.int32)
+ j = np.floor(j).astype(np.int32)
+ k = np.floor(k).astype(np.int32)
disps = np.zeros(coords.shape)
diff --git a/tests/test_atlases_query.py b/tests/test_atlases_query.py
index fedb0a00d9fa30405c50d2a1a880d78288e20f4e..c90a122e7e3a5b4f12e51e0e5df36428f89f2cb4 100644
--- a/tests/test_atlases_query.py
+++ b/tests/test_atlases_query.py
@@ -85,7 +85,7 @@ def _get_zero_mask(aimg):
elif isinstance(aimg, fslatlases.ProbabilisticAtlas):
# Keep memory usage down
- zmask = np.ones(aimg.shape[:3], dtype=np.bool)
+ zmask = np.ones(aimg.shape[:3], dtype=bool)
for vol in range(aimg.shape[-1]):
zmask = np.logical_and(zmask, aimg[..., vol] == 0)
diff --git a/tests/test_gifti.py b/tests/test_gifti.py
index 6d23e665e105f24e4756148ec896ea6c86436ff4..9266e86d98ee3804cdbaf3f7e3da0229270bad4f 100644
--- a/tests/test_gifti.py
+++ b/tests/test_gifti.py
@@ -381,3 +381,21 @@ def test_GiftiMesh_needsFixing():
surf = gifti.GiftiMesh(fname, fixWinding=True)
assert np.all(np.isclose(surf.indices, idxs_fixed))
+
+
+def test_loadGiftiMesh_onetriangle():
+ verts = np.array([[0, 0, 0], [1, 1, 1], [0, 1, 0]])
+ idxs = np.array([[0, 1, 2]])
+ verts = nib.gifti.GiftiDataArray(verts, intent='NIFTI_INTENT_POINTSET')
+ idxs = nib.gifti.GiftiDataArray(idxs, intent='NIFTI_INTENT_TRIANGLE')
+ gimg = nib.gifti.GiftiImage(darrays=[verts, idxs])
+
+ with tempdir():
+ fname = op.abspath('test.gii')
+ gimg.to_filename(fname)
+
+ gimg, tris, verts, _ = gifti.loadGiftiMesh('test.gii')
+ verts = verts[0]
+
+ assert verts.shape == (3, 3)
+ assert tris.shape == (1, 3)
diff --git a/tests/test_image_resample.py b/tests/test_image_resample.py
index 6961e7aa71c63a09d21f93ca5e128d8622b678a9..ccc0b8935780c2793b060a5065133e792fb823b1 100644
--- a/tests/test_image_resample.py
+++ b/tests/test_image_resample.py
@@ -75,7 +75,7 @@ def test_resample(seed):
(np.isclose(np.modf(origtestcoords)[0], 0.5)))
out = np.any(out, axis=1) | (resvals == 0)
- origtestcoords = np.array(origtestcoords.round(), dtype=np.int)
+ origtestcoords = np.array(origtestcoords.round(), dtype=int)
origtestcoords = origtestcoords[~out, :]
restestcoords = restestcoords[ ~out, :]
@@ -166,8 +166,8 @@ def test_resampleToPixdims():
img = fslimage.Image(make_random_image(dims=(10, 10, 10)))
imglo, imghi = affine.axisBounds(img.shape, img.voxToWorldMat)
- oldpix = np.array(img.pixdim, dtype=np.float)
- oldshape = np.array(img.shape, dtype=np.float)
+ oldpix = np.array(img.pixdim, dtype=float)
+ oldshape = np.array(img.shape, dtype=float)
for i, origin in it.product(range(25), ('centre', 'corner')):
@@ -215,16 +215,16 @@ def test_resampleToReference2():
# More specific test - output
# data gets transformed correctly
# into reference space
- img = np.zeros((5, 5, 5), dtype=np.float)
+ img = np.zeros((5, 5, 5), dtype=float)
img[1, 1, 1] = 1
img = fslimage.Image(img)
refv2w = affine.scaleOffsetXform([1, 1, 1], [-1, -1, -1])
- ref = np.zeros((5, 5, 5), dtype=np.float)
+ ref = np.zeros((5, 5, 5), dtype=float)
ref = fslimage.Image(ref, xform=refv2w)
res = resample.resampleToReference(img, ref, order=0)
- exp = np.zeros((5, 5, 5), dtype=np.float)
+ exp = np.zeros((5, 5, 5), dtype=float)
exp[2, 2, 2] = 1
assert np.all(np.isclose(res[0], exp))
diff --git a/tests/test_imagewrapper.py b/tests/test_imagewrapper.py
index 868245fefd24738197b47c2eab4e3214ffc28837..9de727fc98040f2ab7dcb21c17ff198bb65faf0a 100644
--- a/tests/test_imagewrapper.py
+++ b/tests/test_imagewrapper.py
@@ -1195,7 +1195,7 @@ def test_3D_indexing(shape=None, img=None):
assert type(img[0, 0, 0]) == np.float64
- mask1 = np.zeros(shape, dtype=np.bool)
+ mask1 = np.zeros(shape, dtype=bool)
mask1[0, 0, 0] = True
mask1[1, 0, 0] = True
@@ -1252,7 +1252,7 @@ def test_3D_4D_indexing():
assert type(img[0, 0, 0, 0]) == np.float64
assert type(img[0, 0, 0, :]) == np.float64
- mask = np.zeros(padShape, dtype=np.bool)
+ mask = np.zeros(padShape, dtype=bool)
mask[0, 0, 0, 0] = True
assert type(img[mask]) == np.ndarray
@@ -1282,13 +1282,13 @@ def test_3D_len_one_indexing(shape=None, img=None):
assert type(img[0, 0]) == np.ndarray
assert type(img[0, 0, 0]) == np.float64
- mask = np.zeros(shape[:2], dtype=np.bool)
+ mask = np.zeros(shape[:2], dtype=bool)
mask[0, 0] = True
assert type(img[mask]) == np.ndarray
assert img[mask].shape == (1, )
- mask = np.zeros(shape, dtype=np.bool)
+ mask = np.zeros(shape, dtype=bool)
mask[0, 0, 0] = True
assert type(img[mask]) == np.ndarray
@@ -1352,7 +1352,7 @@ def test_4D_indexing(shape=None, img=None):
assert type(img[0, 0, 0, 0]) == np.float64
- mask1 = np.zeros(shape, dtype=np.bool)
+ mask1 = np.zeros(shape, dtype=bool)
mask1[0, 0, 0, 0] = True
mask1[1, 0, 0, 0] = True
diff --git a/tests/test_mesh.py b/tests/test_mesh.py
index f5ae5ead39be0dc3621a847c2083636cbf23e6a7..3a3ff94b87dd8ea5ad55423290050f2b304d5f08 100644
--- a/tests/test_mesh.py
+++ b/tests/test_mesh.py
@@ -234,6 +234,13 @@ def test_normals():
-fnormals, fslmesh.calcFaceNormals(verts, triangles_cw)))
assert np.all(np.isclose(
fnormals, fslmesh.calcFaceNormals(verts, triangles_ccw)))
+
+ # Make sure result is (1, 3) for input of (1, 3)
+ onetri = np.atleast_2d(triangles_ccw[0, :])
+ result = fslmesh.calcFaceNormals(verts, onetri)
+ assert result.shape == (1, 3)
+ assert np.all(np.isclose(fnormals[0, :], result))
+
assert np.all(np.isclose(
-vnormals, fslmesh.calcVertexNormals(verts, triangles_cw, -fnormals)))
assert np.all(np.isclose(
diff --git a/tests/test_transform/test_affine.py b/tests/test_transform/test_affine.py
index 469c6c13d98950e379a9a042467b0a4f4d517dcb..f1dceb61312c7f05f97c9d871dc8a4a0ae95f492 100644
--- a/tests/test_transform/test_affine.py
+++ b/tests/test_transform/test_affine.py
@@ -395,7 +395,7 @@ def test_transform():
mask = np.array([[1, 0, 0, 1],
[0, 1, 0, 1],
[0, 0, 1, 1],
- [0, 0, 0, 1]], dtype=np.bool)
+ [0, 0, 0, 1]], dtype=bool)
return np.all((xform != 0) == mask)
diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index 8bfb0c3aba0d7d0746cf48d56b19631dfc1c2536..1cb8cf8f7df8e2fea674961d00b898f72b1858f7 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -161,7 +161,7 @@ def test_convertDeformationSpace():
refcoords = [np.random.randint(0, basefield.shape[0], 5),
np.random.randint(0, basefield.shape[1], 5),
np.random.randint(0, basefield.shape[2], 5)]
- refcoords = np.array(refcoords, dtype=np.int).T
+ refcoords = np.array(refcoords, dtype=int).T
refcoords = affine.transform(refcoords, ref.voxToScaledVoxMat)
srccoords = basefield.transform(refcoords)