def test_all_coarse_grains_for_blackbox():
blackbox = macro.Blackbox(((0, 1), ), (0, 1))
assert list(macro.all_coarse_grains_for_blackbox(blackbox)) == [
macro.CoarseGrain(((0, 1), ), (((0, 1), (2, )), )),
macro.CoarseGrain(((0, 1), ), (((0, 2), (1, )), )),
macro.CoarseGrain(((0, 1), ), (((0, ), (1, 2)), )),
]
def test_coarse_grain_indices():
partition = ((1, 2), ) # Node 0 not in system
grouping = (((0, ), (1, 2)), )
cg = macro.CoarseGrain(partition, grouping)
assert cg.micro_indices == (1, 2)
assert cg.macro_indices == (0, )
assert cg.reindex() == macro.CoarseGrain(((0, 1), ), grouping)
def test_validate_blackbox_and_coarsegrain():
blackbox = None
coarse_grain = macro.CoarseGrain(((0, 1), (2, )), ((0, 1), (2, )))
validate.blackbox_and_coarse_grain(blackbox, coarse_grain)
blackbox = macro.Blackbox(((0, 1), (2, )), (0, 2))
coarse_grain = None
validate.blackbox_and_coarse_grain(blackbox, coarse_grain)
blackbox = macro.Blackbox(((0, 1), (2, )), (0, 1, 2))
coarse_grain = macro.CoarseGrain(((0, 1), (2, )), ((0, 1), (2, )))
validate.blackbox_and_coarse_grain(blackbox, coarse_grain)
# Blackboxing with multiple outputs must be coarse-grained
blackbox = macro.Blackbox(((0, 1), (2, )), (0, 1, 2))
coarse_grain = None
with pytest.raises(ValueError):
validate.blackbox_and_coarse_grain(blackbox, coarse_grain)
# Coarse-graining does not group multiple outputs of a box into the same
# macro element
blackbox = macro.Blackbox(((0, 1), (2, )), (0, 1, 2))
coarse_grain = macro.CoarseGrain(((0, ), (1, 2)), ((0, 1), (2, )))
with pytest.raises(ValueError):
validate.blackbox_and_coarse_grain(blackbox, coarse_grain)
def test_macro2micro(s):
# Only blackboxing
blackbox = macro.Blackbox(((0, 2), (1, )), (1, 2))
subsys = macro.MacroSubsystem(s.network,
s.state,
s.node_indices,
blackbox=blackbox)
assert subsys.macro2micro((0, )) == (0, 2)
assert subsys.macro2micro((1, )) == (1, )
assert subsys.macro2micro((1, 0)) == (0, 1, 2)
assert subsys.macro2blackbox_outputs((0, )) == (2, )
assert subsys.macro2blackbox_outputs((1, )) == (1, )
assert subsys.macro2blackbox_outputs((1, 0)) == (1, 2)
# Only coarse-graining
coarse_grain = macro.CoarseGrain(((0, ), (1, 2)),
(((0, ), (1, )), ((0, ), (1, 2))))
subsys = macro.MacroSubsystem(s.network,
s.state,
s.node_indices,
coarse_grain=coarse_grain)
assert subsys.macro2micro((0, )) == (0, )
assert subsys.macro2micro((1, )) == (1, 2)
assert subsys.macro2micro((0, 1)) == (0, 1, 2)
with pytest.raises(ValueError):
subsys.macro2blackbox_outputs((0, ))
# Blackboxing and coarse-graining
blackbox = macro.Blackbox(((0, 2), (1, )), (1, 2))
coarse_grain = macro.CoarseGrain(((1, 2), ), (((0, ), (1, 2)), ))
subsys = macro.MacroSubsystem(s.network,
s.state,
s.node_indices,
blackbox=blackbox,
coarse_grain=coarse_grain)
assert subsys.macro2micro((0, )) == (0, 1, 2)
assert subsys.macro2blackbox_outputs((0, )) == (1, 2)
# Pure micro
subsys = macro.MacroSubsystem(s.network, s.state, s.node_indices)
assert subsys.macro2micro((1, )) == (1, )
assert subsys.macro2micro((0, 1)) == (0, 1)
with pytest.raises(ValueError):
subsys.macro2blackbox_outputs((1, ))
def test_coarse_grain_state():
partition = ((0, 1), )
grouping = (((0, ), (1, 2)), )
cg = macro.CoarseGrain(partition, grouping)
with pytest.raises(AssertionError):
assert cg.macro_state((1, 1, 0)) == (1, )
assert cg.macro_state((0, 0)) == (0, )
assert cg.macro_state((0, 1)) == (1, )
assert cg.macro_state((1, 1)) == (1, )
partition = ((1, ), (2, ))
grouping = (((0, ), (1, )), ((1, ), (0, )))
cg = macro.CoarseGrain(partition, grouping)
assert cg.macro_state((0, 1)) == (0, 0)
assert cg.macro_state((1, 1)) == (1, 0)
def test_macro_tpm_sbs():
# fmt: off
micro_tpm = np.array([
[1, 0.0, 0.0, 0, 0, 0, 0, 0],
[0, 0.5, 0.5, 0, 0, 0, 0, 0],
[0, 0.5, 0.5, 0, 0, 0, 0, 0],
[0, 0.0, 0.0, 1, 0, 0, 0, 0],
[1, 0.0, 0.0, 0, 0, 0, 0, 0],
[0, 0.5, 0.5, 0, 0, 0, 0, 0],
[0, 0.5, 0.5, 0, 0, 0, 0, 0],
[0, 0.0, 0.0, 1, 0, 0, 0, 0],
])
answer_tpm = np.array([
[1, 0, 0, 0],
[0, 1 / 2, 1 / 2, 0],
[1 / 3, 1 / 3, 1 / 3, 0],
[0, 1 / 6, 1 / 6, 2 / 3],
])
# fmt: on
partition = ((0, ), (1, 2))
grouping = (((0, ), (1, )), ((0, ), (
1,
2,
)))
coarse_grain = macro.CoarseGrain(partition, grouping)
macro_tpm = coarse_grain.macro_tpm_sbs(micro_tpm)
assert np.array_equal(answer_tpm, macro_tpm)
def test_blackbox_and_coarse_grain_external():
# Larger, with external nodes, blackboxed and coarse-grained
tpm = np.zeros((2**6, 6))
network = pyphi.Network(tpm)
state = (0, 0, 0, 0, 0, 0)
blackbox = macro.Blackbox((
(1, 4),
(2, ),
(3, ),
(5, ),
), (1, 2, 3, 5))
partition = ((1, ), (2, ), (3, 5))
grouping = (((0, ), (1, )), ((1, ), (0, )), ((0, ), (1, 2)))
coarse_grain = macro.CoarseGrain(partition, grouping)
ms = macro.MacroSubsystem(network,
state, (1, 2, 3, 4, 5),
blackbox=blackbox,
coarse_grain=coarse_grain)
answer_tpm = np.array([[[[0, 1, 0], [0, 1, 0]], [[0, 1, 0], [0, 1, 0]]],
[[[0, 1, 0], [0, 1, 0]], [[0, 1, 0], [0, 1, 0]]]])
assert np.array_equal(ms.tpm, answer_tpm)
assert np.array_equal(ms.cm, np.ones((3, 3)))
assert ms.node_indices == (0, 1, 2)
assert ms.size == 3
assert ms.state == (0, 1, 0)
def macro_subsystem():
tpm = np.zeros((16, 4)) + 0.3
tpm[12:, 0:2] = 1
tpm[3, 2:4] = 1
tpm[7, 2:4] = 1
tpm[11, 2:4] = 1
tpm[15, 2:4] = 1
# fmt: off
cm = np.array([
[0, 0, 1, 1],
[0, 0, 1, 1],
[1, 1, 0, 0],
[1, 1, 0, 0],
])
# fmt: on
state = (0, 0, 0, 0)
network = pyphi.Network(tpm, cm=cm, node_labels="ABCD")
partition = ((0, 1), (2, 3))
grouping = (((0, 1), (2, )), ((0, 1), (2, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
return macro.MacroSubsystem(network,
state,
network.node_indices,
coarse_grain=coarse_grain)
def test_validate_coarse_grain():
# Good:
cg = macro.CoarseGrain(((2, ), (3, )), (((0, ), (1, )), (((0, ), (1, )))))
validate.coarse_grain(cg)
# Mismatched output and state lengths
cg = macro.CoarseGrain(((2, ), ), (((0, ), (1, )), (((0, ), (1, )))))
with pytest.raises(ValueError):
validate.coarse_grain(cg)
# Missing 1-node-on specification in second state grouping
cg = macro.CoarseGrain(((2, ), (3, )), (((0, ), (1, )), (((0, ), ()))))
with pytest.raises(ValueError):
validate.coarse_grain(cg)
# Two partitions contain same element
cg = macro.CoarseGrain(((5, ), (5, )), (((0, ), (1, )), (((0, ), (1, )))))
with pytest.raises(ValueError):
validate.coarse_grain(cg)
def test_blackbox_and_coarse_grain(s):
blackbox = macro.Blackbox(((0, 1, 2),), (0, 2))
coarse_grain = macro.CoarseGrain(partition=((0, 2),),
grouping=((((0, 1), (2,)),)))
ms = macro.MacroSubsystem(s.network, s.state, s.node_indices,
blackbox=blackbox, coarse_grain=coarse_grain)
assert np.array_equal(ms.tpm, np.array([[0], [1]]))
assert np.array_equal(ms.cm, [[1]])
assert ms.node_indices == (0,)
assert ms.size == 1
assert ms.state == (0,)
def test_make_macro_tpm_conditional_independence_check():
micro_tpm = np.array([
[1, 0.0, 0.0, 0],
[0, 0.5, 0.5, 0],
[0, 0.5, 0.5, 0],
[0, 0.0, 0.0, 1],
])
partition = ((0, ), (1, ))
grouping = (((0, ), (1, )), ((0, ), (1, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
with pytest.raises(ConditionallyDependentError):
macro_tpm = coarse_grain.macro_tpm(micro_tpm, check_independence=True)
def test_make_mapping():
partition = ((0, 1), (2, 3))
grouping = (((0, 1), (2, )), ((0, 1), (2, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
mapping = coarse_grain.make_mapping()
assert np.array_equal(
mapping,
np.array(
(0., 0., 0., 1., 0., 0., 0., 1., 0., 0., 0., 1., 2., 2., 2., 3.)))
partition = ((0, 1), (2, ))
grouping = (((0, 2), (1, )), ((0, ), (1, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
mapping = coarse_grain.make_mapping()
assert np.array_equal(mapping, np.array((0., 1., 1., 0., 2., 3., 3., 2.)))
partition = ((0, 1, 2), )
grouping = (((0, 3), (1, 2)), )
coarse_grain = macro.CoarseGrain(partition, grouping)
mapping = coarse_grain.make_mapping()
assert np.array_equal(mapping, np.array((0., 1., 1., 1., 1., 1., 1., 0.)))
def test_coarse_grain(s):
coarse_grain = macro.CoarseGrain(partition=((0, 1), (2, )),
grouping=((((0, 1), (2, )), ((0, ),
(1, )))))
ms = macro.MacroSubsystem(s.network,
s.state,
s.node_indices,
coarse_grain=coarse_grain)
answer_tpm = np.array([[[0, 0.66666667], [1, 0.66666667]], [[0, 0], [1,
0]]])
assert np.allclose(ms.tpm, answer_tpm)
assert np.array_equal(ms.cm, np.ones((2, 2)))
assert ms.node_indices == (0, 1)
assert ms.state == (0, 0)
def test_make_mapping():
partition = ((0, 1), (2, 3))
grouping = (((0, 1), (2, )), ((0, 1), (2, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
mapping = coarse_grain.make_mapping()
answer = np.array([
0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 2.0, 2.0,
2.0, 3.0
])
assert np.array_equal(mapping, answer)
partition = ((0, 1), (2, ))
grouping = (((0, 2), (1, )), ((0, ), (1, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
mapping = coarse_grain.make_mapping()
assert np.array_equal(mapping,
np.array([0.0, 1.0, 1.0, 0.0, 2.0, 3.0, 3.0, 2.0]))
partition = ((0, 1, 2), )
grouping = (((0, 3), (1, 2)), )
coarse_grain = macro.CoarseGrain(partition, grouping)
mapping = coarse_grain.make_mapping()
assert np.array_equal(mapping,
np.array([0.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.0]))
def test_subsystem_equality(s):
macro_subsys = macro.MacroSubsystem(s.network, s.state, s.node_indices)
assert s != macro_subsys
assert hash(s) != hash(macro_subsys)
blackbox = macro.Blackbox(((0, 1, 2),), (2,))
macro_subsys_bb = macro.MacroSubsystem(
s.network, s.state, s.node_indices, blackbox=blackbox, time_scale=2)
assert macro_subsys != macro_subsys_bb
assert hash(macro_subsys) != hash(macro_subsys_bb)
coarse_grain = macro.CoarseGrain(
((0, 1), (2,)), (((0, 1), (2,)), ((0,), (1,))))
macro_subsys_cg = macro.MacroSubsystem(
s.network, s.state, s.node_indices, coarse_grain=coarse_grain)
assert macro_subsys != macro_subsys_cg
assert hash(macro_subsys) != hash(macro_subsys_cg)
def test_coarsegrain_spatial_degenerate():
# TODO: move to docs?
# macro-micro examples from Hoel2016
# Example 2 - Spatial Degenerate
# The micro system has a full complex, and big_phi = 0.19
# The optimal coarse-graining groups AB, CD and EF, each with state
# mapping ((0, 1), (2))
nodes = 6
tpm = np.zeros((2**nodes, nodes))
for psi, ps in enumerate(utils.all_states(nodes)):
cs = [0 for i in range(nodes)]
if ps[0] == 1 and ps[1] == 1:
cs[2] = 1
cs[3] = 1
if ps[2] == 1 and ps[3] == 1:
cs[4] = 1
cs[5] = 1
if ps[4] == 1 and ps[5] == 1:
cs[0] = 1
cs[1] = 1
tpm[psi, :] = cs
cm = np.array([[0, 0, 1, 1, 0, 0], [0, 0, 1, 1, 0, 0], [0, 0, 0, 0, 1, 1],
[0, 0, 0, 0, 1, 1], [1, 1, 0, 0, 0, 0], [1, 1, 0, 0, 0, 0]])
state = (0, 0, 0, 0, 0, 0)
net = Network(tpm, cm)
mc = compute.major_complex(net, state)
assert mc.phi == 0.194445
partition = ((0, 1), (2, 3), (4, 5))
grouping = (((0, 1), (2, )), ((0, 1), (2, )), ((0, 1), (2, )))
coarse = macro.CoarseGrain(partition, grouping)
sub = macro.MacroSubsystem(net,
state,
range(net.size),
coarse_grain=coarse)
sia = compute.sia(sub)
assert sia.phi == 0.834183
def test_make_macro_tpm():
answer_tpm = convert.state_by_state2state_by_node(
np.array([
[0.375, 0.375, 0.125, 0.125],
[0.375, 0.375, 0.125, 0.125],
[0.375, 0.375, 0.125, 0.125],
[0.375, 0.375, 0.125, 0.125],
]))
partition = ((0, ), (1, 2))
grouping = (((0, ), (1, )), ((0, 1), (2, )))
coarse_grain = macro.CoarseGrain(partition, grouping)
assert np.array_equal(coarse_grain.make_mapping(),
[0, 1, 0, 1, 0, 1, 2, 3])
micro_tpm = np.zeros((8, 3)) + 0.5
macro_tpm = coarse_grain.macro_tpm(micro_tpm)
assert np.array_equal(answer_tpm, macro_tpm)
micro_tpm = np.zeros((8, 8)) + 0.125
macro_tpm = coarse_grain.macro_tpm(micro_tpm)
assert np.array_equal(answer_tpm, macro_tpm)
def test_all_coarse_grains():
assert tuple(macro.all_coarse_grains(
(1, ))) == (macro.CoarseGrain(partition=((1, ), ),
grouping=(((0, ), (1, )), )), )
def test_coarse_grain_len():
partition = ((1, 2), )
grouping = (((0, ), (1, 2)), )
cg = macro.CoarseGrain(partition, grouping)
assert len(cg) == 1
