def testThreePointSoma(self):
mtree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'threepoint_soma.swc'))
for n, idx in zip(mtree, [1,4,5]):
assert n.index == idx
idxs = [1,2,3,4,5]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_surface = 2. * np.pi * 5. * 5. + \
2. * np.pi * 5. * 5.
s_radius = np.sqrt(s_surface / (4.*np.pi))
assert mtree[1].R == s_radius
def testMultiCylinderSoma(self):
mtree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'multicylinder_soma.swc'))
for n, idx in zip(mtree, [1,7,8,9,10]):
assert n.index == idx
idxs = [1,2,3,7,8,9,10]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_radius = np.sqrt(2.*np.pi*10. * 5. / (4.*np.pi))
assert mtree[1].R == s_radius
assert np.allclose(mtree[1].xyz, np.array([0.,2.5,0.]))
def testThreePointSoma(self):
mtree = MorphTree('test_morphologies/threepoint_soma.swc')
for n, idx in zip(mtree, [1,4,5]):
assert n.index == idx
idxs = [1,2,3,4,5]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_surface = 2. * np.pi * 5. * 5. + \
2. * np.pi * 5. * 5.
s_radius = np.sqrt(s_surface / (4.*np.pi))
assert mtree[1].R == s_radius