def test_closure_small():
""" closure on small graph. """
A = np.asarray([[0.0, 0.1, 0.0, 0.2], [0.0, 0.0, 0.3, 0.0],
[0.0, 0.0, 0.0, 0.0], [0.0, 0.3, 0.0, 0.0]])
# ultrametric
source = 0
proxs, paths = clo.closuress(A, source)
proxs2, paths2 = clo.cclosuress(A, source, retpaths=1)
assert np.allclose(proxs, proxs2)
for p1, p2 in zip(paths, paths2):
assert np.all(p1 == p2)
# metric
proxs, paths = clo.closuress(A, source, kind='metric')
proxs2, paths2 = clo.cclosuress(A, source, retpaths=1, kind='metric')
assert np.allclose(proxs, proxs2)
for p1, p2 in zip(paths, paths2):
assert np.all(p1 == p2)
def test_closure_big():
""" closure on large graph + speed test. """
np.random.seed(100)
N = 500
thresh = 0.1
A = sp.rand(N, N, thresh, 'csr')
A = np.asarray(A.todense())
source = 0
tic = time()
proxs, _ = clo.closuress(A, source)
toc = time()
py_time = toc - tic
tic = time()
proxs2, _ = clo.cclosuress(A, source)
toc = time()
cy_time = toc - tic
assert np.allclose(proxs, proxs2)
assert py_time > cy_time, \
'python: {:.2g} s, cython: {:.2g} s.'.format(py_time, cy_time)
def test_closureap():
""" Correctedness of all-pairs parallel closure. """
np.random.seed(100)
dt = DirTree('test', (2, 5, 10), root='test_parallel')
N = 100
thresh = 0.1
A = sp.rand(N, N, thresh, 'csr')
nnz = A.getnnz()
sparsity = float(nnz) / N**2
print 'Number of nnz = {}, sparsity = {:g}'.format(nnz, sparsity)
A = np.asarray(A.todense())
clo.closureap(A, dt)
coords = np.asarray(fromdirtree(dt, N), dtype=coo_dtype)
coo = (coords['weight'], (coords['row'], coords['col']))
B = np.asarray(sp.coo_matrix(coo, shape=(N, N)).todense())
rows = []
for row in xrange(N):
r, _ = clo.cclosuress(A, row)
rows.append(r)
C = np.asarray(rows)
assert np.allclose(B, C)
# cleanup
for logpath in glob('closure-*.log'):
os.remove(logpath)