def run_homology_selftest(output=sys.stdout):
ok = True
# second, try known cases and inspect results
for (g, n, ok) in [ (0,3, [1,0,0]),
(0,4, [1,2,0,0,0,0]),
(0,5, [1,5,6,0,0,0,0,0,0]),
(1,1, [1,0,0]),
(1,2, [1,0,0,0,0,0]),
(2,1, [1,0,1,0,0,0,0,0,0]),
]:
output.write(" Computation of M_{%d,%d} homology: " % (g,n))
# compute homology of M_{g,n}
timing.start("homology M%d,%d" % (g,n))
hs = compute_homology(g,n)
timing.stop("homology M%d,%d" % (g,n))
# check result
if hs == ok:
output.write("OK (elapsed: %0.3fs)\n"
% timing.get("homology M%d,%d" % (g,n)))
else:
logging.error("Computation of M_{%d,%d} homology: FAILED, got %s expected %s"
% (g,n,hs,ok))
output.write("FAILED, got %s expected %s\n" % (hs,ok))
ok = False
return ok
def compute_boundary_operators(self):
#: Matrix form of boundary operators; the `i`-th differential
#: `D[i]` is `dim C[i-1]` rows (range) by `dim C[i]` columns
#: (domain).
m = self.module # micro-optimization
D = DifferentialComplex()
D.append(NullMatrix, 0, len(m[0]))
for i in xrange(1, len(self)):
timing.start("D[%d]" % i)
p = len(m[i - 1]) # == dim C[i-1]
q = len(m[i]) # == dim C[i]
try:
checkpoint = os.path.join(runtime.options.checkpoint_dir,
('M%d,%d-D%d.sms' %
(runtime.g, runtime.n, i)))
except AttributeError:
checkpoint = None
# maybe load `D[i]` from persistent storage
if checkpoint and p > 0 and q > 0 and runtime.options.restart:
d = SimpleMatrix(p, q)
if d.load(checkpoint):
D.append(d, p, q)
logging.info(" Loaded %dx%d matrix D[%d] from file '%s'",
p, q, i, checkpoint)
continue # with next `i`
# compute `D[i]`
d = SimpleMatrix(p, q)
j0 = 0
for pool1 in m[i].iterblocks():
k0 = 0
for pool2 in m[i - 1].iterblocks():
for edgeno in xrange(pool1.graph.num_edges):
if pool1.graph.is_loop(edgeno):
continue # with next `edgeno`
for (j, k, s) in NumberedFatgraphPool.facets(
pool1, edgeno, pool2):
assert k < len(pool2)
assert j < len(pool1)
assert k + k0 < p
assert j + j0 < q
d.addToEntry(k + k0, j + j0, s)
k0 += len(pool2)
# # `pool2` will never be used again, so clear it from the cache.
# # XXX: using implementation detail!
# pool2.graph._cache_isomorphisms.clear()
j0 += len(pool1)
# `pool1` will never be used again, so clear it from the cache.
# XXX: using implementation detail!
pool1.graph._cache_isomorphisms.clear()
timing.stop("D[%d]" % i)
if checkpoint:
d.save(checkpoint)
D.append(d, p, q)
logging.info(" Computed %dx%d matrix D[%d] (elapsed: %.3fs)", p,
q, i, timing.get("D[%d]" % i))
return D
def compute_boundary_operators(self):
#: Matrix form of boundary operators; the `i`-th differential
#: `D[i]` is `dim C[i-1]` rows (range) by `dim C[i]` columns
#: (domain).
m = self.module # micro-optimization
D = DifferentialComplex()
D.append(NullMatrix, 0, len(m[0]))
for i in xrange(1, len(self)):
timing.start("D[%d]" % i)
p = len(m[i-1]) # == dim C[i-1]
q = len(m[i]) # == dim C[i]
try:
checkpoint = os.path.join(runtime.options.checkpoint_dir,
('M%d,%d-D%d.sms' % (runtime.g, runtime.n, i)))
except AttributeError:
checkpoint = None
# maybe load `D[i]` from persistent storage
if checkpoint and p>0 and q>0 and runtime.options.restart:
d = SimpleMatrix(p, q)
if d.load(checkpoint):
D.append(d, p, q)
logging.info(" Loaded %dx%d matrix D[%d] from file '%s'",
p, q, i, checkpoint)
continue # with next `i`
# compute `D[i]`
d = SimpleMatrix(p, q)
j0 = 0
for pool1 in m[i].iterblocks():
k0 = 0
for pool2 in m[i-1].iterblocks():
for edgeno in xrange(pool1.graph.num_edges):
if pool1.graph.is_loop(edgeno):
continue # with next `edgeno`
for (j, k, s) in NumberedFatgraphPool.facets(pool1, edgeno, pool2):
assert k < len(pool2)
assert j < len(pool1)
assert k+k0 < p
assert j+j0 < q
d.addToEntry(k+k0, j+j0, s)
k0 += len(pool2)
# # `pool2` will never be used again, so clear it from the cache.
# # XXX: using implementation detail!
# pool2.graph._cache_isomorphisms.clear()
j0 += len(pool1)
# `pool1` will never be used again, so clear it from the cache.
# XXX: using implementation detail!
pool1.graph._cache_isomorphisms.clear()
timing.stop("D[%d]" % i)
if checkpoint:
d.save(checkpoint)
D.append(d, p, q)
logging.info(" Computed %dx%d matrix D[%d] (elapsed: %.3fs)",
p, q, i, timing.get("D[%d]" % i))
return D
def compute_homology_ranks(self):
"""Compute and return (list of) homology group ranks.
Returns a list of integers: item at index `n` is the rank of
the `n`-th homology group of this differential complex. Since
the differential complex has finite length, homology group
indices can only run from 0 to the length of the complex (all
other groups being, trivially, null).
"""
# check that the differentials form a complex
# if __debug__:
# for i in xrange(1, len(self)-1):
# assert is_null_product(self[i-1][0], self[i][0]), \
# "DifferentialComplex.compute_homology_ranks:" \
# " Product of boundary operator matrices D[%d] and D[%d]" \
# " is not null!" \
# % (i-1, i)
#: ranks of `D[n]` matrices, for 0 <= n < len(self); the differential
#: `D[0]` is the null map.
ranks = list()
# only compute those ranks that were not saved
for (i, (A, ddim, cdim)) in enumerate(self):
try:
checkpoint = (os.path.join(
runtime.options.checkpoint_dir,
"M%d,%d-rkD%d.txt" % (runtime.g, runtime.n, i)))
except AttributeError:
# running tests, so no `runtime.options`
checkpoint = None
# XXX: LinBox segfaults if asked to compute the rank of a 0xL matrix
if A.num_rows > 0 and A.num_columns > 0:
rs = None
if checkpoint is not None and runtime.options.restart:
rs = load(checkpoint)
if rs:
r = rs[0]
logging.info(" rank D[%d]=%d (loaded from file '%s')",
i, r, checkpoint)
if rs is None: # `rs` was not loaded from checkpoint file
timing.start("rank D[%d]" % i)
r = A.rank()
timing.stop("rank D[%d]" % i)
# checkpoint the computation so far
if checkpoint is not None:
save([r], checkpoint)
logging.info(" rank D[%d]=%d (computed in %.3fs)", i, r,
timing.get("rank D[%d]" % i))
else: # A is a 0xL matrix
r = 0
logging.info(" rank D[%d]=%d (immediate)", i, r)
ranks.append(r)
## compute homology group ranks from rank and nullity
## of boundary operators.
##
## By the rank-nullity theorem, if A:V-->W is a linear map,
## then null(A) = dim(V) - rk(A), hence:
## dim(Z_i) = null(D_i) = dim(C_i) - rk(D_i)
## dim(B_i) = rk(D_{i+1})
## Therefore:
## h_i = dim(H_i) = dim(Z_i / B_i) = dim(Z_i) - dim(B_i)
## = (dim(C_i) - rk(D_i)) - rk(D_{i+1})
## = dim(C_i) - (rk(D_i) + rk(D_{i+1}))
## where D_i:C_i-->C_{i+1}
##
domain_dim = [ddim for (A, ddim, cdim) in self]
domain_dim.append(self[-1][2]) # add dimension of last vector space
ranks.append(0) # augment complex with the null map.
# note: `domain_dim` indices are offset by 1 w.r.t. to `ranks` indices
return [(domain_dim[i + 1] - ranks[i] - ranks[i + 1])
for i in xrange(len(self))]
def compute_homology_ranks(self):
"""Compute and return (list of) homology group ranks.
Returns a list of integers: item at index `n` is the rank of
the `n`-th homology group of this differential complex. Since
the differential complex has finite length, homology group
indices can only run from 0 to the length of the complex (all
other groups being, trivially, null).
"""
# check that the differentials form a complex
# if __debug__:
# for i in xrange(1, len(self)-1):
# assert is_null_product(self[i-1][0], self[i][0]), \
# "DifferentialComplex.compute_homology_ranks:" \
# " Product of boundary operator matrices D[%d] and D[%d]" \
# " is not null!" \
# % (i-1, i)
#: ranks of `D[n]` matrices, for 0 <= n < len(self); the differential
#: `D[0]` is the null map.
ranks = list()
# only compute those ranks that were not saved
for (i, (A, ddim, cdim)) in enumerate(self):
try:
checkpoint = (os.path.join(runtime.options.checkpoint_dir,
"M%d,%d-rkD%d.txt" % (runtime.g, runtime.n, i)))
except AttributeError:
# running tests, so no `runtime.options`
checkpoint = None
# XXX: LinBox segfaults if asked to compute the rank of a 0xL matrix
if A.num_rows > 0 and A.num_columns > 0:
rs = None
if checkpoint is not None and runtime.options.restart:
rs = load(checkpoint)
if rs:
r = rs[0]
logging.info(" rank D[%d]=%d (loaded from file '%s')",
i, r, checkpoint)
if rs is None: # `rs` was not loaded from checkpoint file
timing.start("rank D[%d]" % i)
r = A.rank()
timing.stop("rank D[%d]" % i)
# checkpoint the computation so far
if checkpoint is not None:
save([r], checkpoint)
logging.info(" rank D[%d]=%d (computed in %.3fs)",
i, r, timing.get("rank D[%d]" % i))
else: # A is a 0xL matrix
r = 0
logging.info(" rank D[%d]=%d (immediate)", i, r)
ranks.append(r)
## compute homology group ranks from rank and nullity
## of boundary operators.
##
## By the rank-nullity theorem, if A:V-->W is a linear map,
## then null(A) = dim(V) - rk(A), hence:
## dim(Z_i) = null(D_i) = dim(C_i) - rk(D_i)
## dim(B_i) = rk(D_{i+1})
## Therefore:
## h_i = dim(H_i) = dim(Z_i / B_i) = dim(Z_i) - dim(B_i)
## = (dim(C_i) - rk(D_i)) - rk(D_{i+1})
## = dim(C_i) - (rk(D_i) + rk(D_{i+1}))
## where D_i:C_i-->C_{i+1}
##
domain_dim = [ ddim for (A, ddim, cdim) in self ]
domain_dim.append(self[-1][2]) # add dimension of last vector space
ranks.append(0) # augment complex with the null map.
# note: `domain_dim` indices are offset by 1 w.r.t. to `ranks` indices
return [ (domain_dim[i+1] - ranks[i] - ranks[i+1])
for i in xrange(len(self)) ]
# valences -- show vertex valences for given g,n
elif 'valences' == cmdline.action:
logging.debug("Computing vertex valences occurring in g=%d,n=%d fatgraphs ...", g, n)
vvs = compute_valences(g,n)
for vv in vvs:
outfile.write("%s\n" % str(vv))
# graphs -- create graphs from given g,n but do not compute homology
elif "graphs" == cmdline.action:
logging.info("Will save graph list files into directory '%s'.",
runtime.options.checkpoint_dir)
graphs, D = compute_graphs(g,n)
logging.info("Graph family computation took %.3fs.",
timing.get("compute_graphs(%d,%d)" % (g,n)))
# homology -- compute homology ranks
elif 'homology' == cmdline.action:
# compute graph complex and its homology ranks
hs = compute_homology(g, n)
logging.info("Homology computation took %.3fs.",
timing.get("compute_homology(%d,%d)" % (g,n)))
# print results
for (i, h) in enumerate(hs):
outfile.write("h_%d(M_{%d,%d}) = %d\n" % (i, g, n, h))
if cmdline.outfile is not None:
logging.info("Results written to file '%s'" % cmdline.outfile)
