def test_GiftiMesh_create_loadAll():
testdir = op.join(op.dirname(__file__), 'testdata')
testfile = op.join(testdir, 'example.surf.gii')
with tempdir() as td:
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)
mesh = gifti.GiftiMesh(vertSets[0], loadAll=True)
assert mesh.selectedVertices() == vertSets[0]
mesh.vertices = vertSets[1]
assert mesh.selectedVertices() == vertSets[1]
mesh.vertices = vertSets[2]
assert mesh.selectedVertices() == vertSets[2]
def test_GiftiMesh_loadVertexData():
testdir = op.join(op.dirname(__file__), 'testdata')
surffile = op.join(testdir, 'example.surf.gii')
shapefile = op.join(testdir, 'example.shape.gii')
txtfile = op.join(testdir, 'test_mesh_data.txt')
memdata = np.random.randint(1, 10, 642)
# load from .gii file
surf = gifti.GiftiMesh(surffile)
assert surf.loadVertexData(shapefile).shape == (642, 1)
# load from .txt file
assert surf.loadVertexData(txtfile).shape == (642, 1)
# add from memory
assert np.all(
np.isclose(surf.addVertexData('inmemdata', memdata),
memdata.reshape(-1, 1)))
# check cached
assert surf.getVertexData(shapefile).shape == (642, 1)
assert surf.getVertexData(txtfile).shape == (642, 1)
assert surf.getVertexData('inmemdata').shape == (642, 1)
def Mesh(filename):
"""
Reads in a mesh from either a GIFTI (.surf.gii) or a VTK (.vtk) file
:param filename: filename provided by the user
:return: GIFTI or VTK sub-class of fsl.data.mesh.Mesh
"""
try:
full_filename = path.addExt(filename, ['.surf.gii', '.vtk'])
except path.PathError as e:
raise argparse.ArgumentTypeError(*e.args)
if path.hasExt(full_filename, '.surf.gii'):
return gifti.GiftiMesh(full_filename)
else:
return vtk.VTKMesh(full_filename)
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))
def test_loadVertices():
testdir = op.join(op.dirname(__file__), 'testdata')
testfile = op.join(testdir, 'example.surf.gii')
with tempdir():
mesh = gifti.GiftiMesh(testfile)
shutil.copy(testfile, 'example2.surf.gii')
verts = mesh.vertices
verts2 = verts * 2
np.savetxt('verts.txt', verts2)
assert np.all(np.isclose(mesh.loadVertices('example2.surf.gii'),
verts))
assert np.all(np.isclose(mesh.loadVertices('verts.txt'), verts2))
def test_GiftiMesh_create():
testdir = op.join(op.dirname(__file__), 'testdata')
testfile = op.join(testdir, 'example.surf.gii')
surf = gifti.GiftiMesh(testfile)
minbounds = np.array([59.50759888, 88.43039703, 72.10890198])
maxbounds = np.array([77.72619629, 128.40600586, 94.82050323])
minb, maxb = surf.bounds
assert surf.name == 'example'
assert surf.dataSource == testfile
assert tuple(surf.vertices.shape) == (642, 3)
assert tuple(surf.indices.shape) == (1280, 3)
assert isinstance(surf.getMeta(testfile), nib.gifti.GiftiImage)
assert np.all(np.isclose(minbounds, minb))
assert np.all(np.isclose(maxbounds, maxb))
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')
verts3 = nib.gifti.GiftiDataArray(TEST_VERTS * 10,
intent='NIFTI_INTENT_POINTSET')
gimg = nib.gifti.GiftiImage(darrays=[verts1, verts2, tris])
gimg2 = nib.gifti.GiftiImage(darrays=[verts3, tris])
with tempdir():
fname = op.abspath('test.gii')
fname2 = op.abspath('test2.gii')
gimg.to_filename(fname)
gimg2.to_filename(fname2)
surf = gifti.GiftiMesh(fname)
expvsets = [fname, '{}_1'.format(fname)]
expbounds1 = np.min(verts1.data, axis=0), np.max(verts1.data, axis=0)
expbounds2 = np.min(verts2.data, axis=0), np.max(verts2.data, axis=0)
expbounds3 = np.min(verts3.data, axis=0), np.max(verts3.data, axis=0)
assert np.all(surf.vertices == TEST_VERTS)
assert np.all(surf.indices == TEST_IDXS)
assert surf.vertexSets() == expvsets
assert np.all(np.isclose(surf.bounds, expbounds1))
surf.vertices = expvsets[1]
assert np.all(surf.vertices == TEST_VERTS * 5)
assert np.all(np.isclose(surf.bounds, expbounds2))
surf.loadVertices(fname2, select=True)
assert np.all(surf.vertices == TEST_VERTS * 10)
assert np.all(np.isclose(surf.bounds, expbounds3))