Merge branch 'bf/gifti_readonly' into 'master'

Bf/gifti readonly

See merge request fsl/fslpy!98

CHANGELOG.rst

@@ -27,6 +27,13 @@ Changed
   vertex data.
 
 
+Fixed
+^^^^^
+
+* Fixed an issue in the :class:`.GiftiMesh` class, where
+  ``numpy``/``nibabel`` was returning read-only index arrays.
+
+
 Removed
 ^^^^^^^
 

fsl/data/gifti.py

@@ -211,8 +211,8 @@ def loadGiftiMesh(filename):
         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
+    vertices = [np.array(ps.data) for ps in pointsets]
+    indices  = np.array(triangles[0].data)
 
     if len(vdata) == 0: vdata = None
     else:               vdata = prepareGiftiVertexData(vdata, filename)

tests/test_gifti.py

@@ -299,3 +299,23 @@ def test_GiftiMesh_multiple_vertices():
         surf.vertices = expvsets[1]
 
         assert np.all(surf.vertices == TEST_VERTS * 5)
+
+
+def test_GiftiMesh_needsFixing():
+    from . import test_mesh
+
+    verts      = test_mesh.CUBE_VERTICES
+    idxs       = test_mesh.CUBE_TRIANGLES_CW
+    idxs_fixed = test_mesh.CUBE_TRIANGLES_CCW
+
+    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)
+
+        surf = gifti.GiftiMesh(fname, fixWinding=True)
+
+        assert np.all(np.isclose(surf.indices, idxs_fixed))

tests/test_mesh.py

@@ -248,9 +248,11 @@ def test_needsFixing():
     fnormals = np.array(CUBE_CCW_VERTEX_NORMALS)
     blo      = verts.min(axis=0)
     bhi      = verts.max(axis=0)
+    mesh     = fslmesh.Mesh(tris_cw, vertices=verts, fixWinding=True)
 
     assert not fslmesh.needsFixing(verts, tris_ccw, fnormals, blo, bhi)
     assert     fslmesh.needsFixing(verts, tris_cw, -fnormals, blo, bhi)
+    assert     np.all(np.isclose(mesh.indices, tris_ccw))
 
 
 def test_trimesh_no_trimesh():