def operator_difference_and_compound_experiment():
"""Take the 6 permutation operators in pairs, and for each calculate
the GINI/stddev/etc of the compound operator, and also the
difference between the pair.
"""
opss = ("two_opt", "twoh_opt", "three_opt", "three_opt_broad", "swap_two", "swap_adj")
for n in range(6, 11):
diff = np.zeros((len(opss), len(opss)))
Gini = np.zeros((len(opss), len(opss)))
SD = np.zeros((len(opss), len(opss)))
CV = np.zeros((len(opss), len(opss)))
for i, opi in enumerate(opss):
for j, opj in enumerate(opss):
basedir = sys.argv[1] + "/tsp_length_%d_" % n
ops = [opi, opj]
ps = [np.genfromtxt(basedir + op + "/TP_row0.dat") for op in ops]
names = "+".join(ops)
delta = random_walks.operator_difference_RMSE(*ps)
print "delta", names, delta
diff[i][j] = delta
wts = [1.0 / len(ops) for _ in ops]
compound_tp = random_walks.compound_operator(wts, ps)
gini = random_walks.gini_coeff(compound_tp)
sd = np.std(compound_tp)
cv = np.std(compound_tp) / np.mean(compound_tp)
print "compound gini", names, gini
Gini[i][j] = gini
print "compound stddev", names, sd
SD[i][j] = sd
print "compound coefvar", names, cv
CV[i][j] = cv
basedir = sys.argv[1] + "/permutation_size_%d_compound_diff/" % n
filename = os.path.join(basedir + "diff")
np.savetxt(filename+".dat", diff)
plot_grid(filename, ("Operator difference %d" % n), opss, diff)
filename = os.path.join(basedir + "diff_mds")
op_diff_mds(filename, ("Operator difference %d" % n), opss, diff)
filename = os.path.join(basedir + "compound_gini")
np.savetxt(filename+".dat", Gini)
plot_grid(filename, ("Compound operator Gini %d" % n), opss, Gini)
filename = os.path.join(basedir + "compound_sd")
np.savetxt(filename+".dat", SD)
plot_grid(filename, ("Compound operator SD %d" % n), opss, SD)
filename = os.path.join(basedir + "compound_cv")
np.savetxt(filename+".dat", CV)
plot_grid(filename, ("Compound operator CV %d" % n), opss, CV)
def operator_difference_and_compound_experiment():
"""Take the 6 operators in pairs, and for each calculate the
GINI/stddev of the compound operator, and also the difference
between the pair.
"""
opss = ("two_opt", "twoh_opt", "three_opt", "three_opt_broad", "swap", "swap_adj")
for n in range(6, 11):
diff_result = np.zeros((len(opss), len(opss)))
comp_result = np.zeros((len(opss), len(opss)))
comp_result_stddev = np.zeros((len(opss), len(opss)))
for i, opi in enumerate(opss):
for j, opj in enumerate(opss):
basedir = "/Users/jmmcd/Dropbox/GPDistance/results/tsp_length_%d_" % n
ops = [opi, opj]
ps = [np.genfromtxt(basedir + op + "/TP_row0.dat") for op in ops]
names = "+".join(ops)
delta = random_walks.operator_difference_RMSE(*ps)
print "delta", names, delta
diff_result[i][j] = delta
wts = [1.0 / len(ops) for _ in ops]
compound_tp = random_walks.compound_operator(wts, ps)
gini = random_walks.gini_coeff(compound_tp)
stddev = np.std(compound_tp)
print "compound gini", names, gini
comp_result[i][j] = gini
print "compound stddev", names, stddev
comp_result_stddev[i][j] = stddev
op_diff_filename = "/Users/jmmcd/Dropbox/GPDistance/results/EURO2015/tsp_length_%d_op_diff" % n
np.savetxt(op_diff_filename+".dat", diff_result)
plot_grid(op_diff_filename, ("Operator difference %d" % n), opss, diff_result)
comp_op_filename = "/Users/jmmcd/Dropbox/GPDistance/results/EURO2015/tsp_length_%d_comp_op" % n
np.savetxt(comp_op_filename+".dat", comp_result)
plot_grid(comp_op_filename, ("Compound operator Gini %d" % n), opss, comp_result)
comp_op_stddev_filename = "/Users/jmmcd/Dropbox/GPDistance/results/EURO2015/tsp_length_%d_comp_op_stddev" % n
np.savetxt(comp_op_stddev_filename+".dat", comp_result_stddev)
plot_grid(comp_op_stddev_filename, ("Compound operator stddev %d" % n), opss, comp_result_stddev)
mds_filename = "/Users/jmmcd/Dropbox/GPDistance/results/EURO2015/tsp_length_%d_mds" % n
op_diff_mds(mds_filename, ("Operator difference %d" % n), opss, diff_result)
def basic_stats_and_plots():
"""For several TSP operators, read in their first rows and calculate
the basic stats (Gini and stddev) and nneighbours, and make the basic
plots of these."""
basename = sys.argv[1]
ops = ("two_opt", "twoh_opt", "three_opt", "three_opt_broad", "swap", "swap_adj")
opfs = {
"two_opt": tsp.two_opt,
"twoh_opt": tsp.twoh_opt,
"three_opt": tsp.three_opt,
"three_opt_broad": tsp.three_opt_broad,
"swap": tsp.swap_two,
"swap_adj": tsp.swap_adj
}
lengths = range(6, 11)
for length in lengths:
stddev = []
gini = []
nneighbours = []
prop_unique = []
for op in ops:
filename = os.path.join(basename,
"tsp_length_%d_%s" % (length, op),
"TP_row0.dat")
print op, length
x = np.genfromtxt(filename)
# stats to get:
stddev.append(np.std(x))
gini.append(random_walks.gini_coeff(x))
nneighbours.append(np.sum(x > 0))
mu, sigma = rw_experiment_with_op(length, opfs[op])
prop_unique.append((mu, sigma))
gini_barchart(length, gini, ops)
stddev_barchart(length, stddev, ops)
plot_gini_v_nneighbours(length, gini, nneighbours, ops)
plot_stddev_v_nneighbours(length, stddev, nneighbours, ops)
plot_gini_v_prop_unique(length, gini, prop_unique, ops)
plot_stddev_v_prop_unique(length, stddev, prop_unique, ops)
def basic_stats_and_plots(space, do_rw_experiment=False):
"""For several operators, read in their first rows and calculate the
basic stats (SD, CV, logN SD, sqrtN SD, cuberootN SD, Gini) and nneighbours, and
make the basic plots of these.
"""
basename = sys.argv[1]
if space == "permutation":
ops = ("two_opt", "twoh_opt", "three_opt", "three_opt_broad", "swap_two", "swap_adj")
opfs = {
"two_opt": tsp.two_opt,
"twoh_opt": tsp.twoh_opt,
"three_opt": tsp.three_opt,
"three_opt_broad": tsp.three_opt_broad,
"swap_two": tsp.swap_two,
"swap_adj": tsp.swap_adj
}
sizes = (9, 10, 11)
elif space == "bitstring":
ops = ("per_gene_0.0001", "per_gene_0.0003",
"per_gene_0.0010", "per_gene_0.0033",
"per_gene_0.0100", "per_gene_0.0333",
"per_gene_0.1000", "per_gene_0.3333",
"per_ind")
opfs = {
"per_ind": bitstring.bitstring_per_ind_mutation,
"per_gene_0.0001": bitstring.make_bitstring_per_gene_mutation(0.0001),
"per_gene_0.0003": bitstring.make_bitstring_per_gene_mutation(0.0003),
"per_gene_0.0010": bitstring.make_bitstring_per_gene_mutation(0.0010),
"per_gene_0.0033": bitstring.make_bitstring_per_gene_mutation(0.0033),
"per_gene_0.0100": bitstring.make_bitstring_per_gene_mutation(0.0100),
"per_gene_0.0333": bitstring.make_bitstring_per_gene_mutation(0.0333),
"per_gene_0.1000": bitstring.make_bitstring_per_gene_mutation(0.1000),
"per_gene_0.3333": bitstring.make_bitstring_per_gene_mutation(0.3333),
}
sizes = (10, 12, 14)
elif space == "tree" and do_rw_experiment:
basic_stats_and_plots_tree()
return
for size in sizes:
prop_unique_v_expl = []
stddev = []
coefvar = []
logN_sd_vals = []
sqrtN_sd_vals = []
cbrtN_sd_vals = []
gini = []
nneighbours = []
prop_unique = []
for op in ops:
filename = os.path.join(basename,
"space_%s/size_%d_op_%s" % (space, size, op),
"TP_row0.dat")
print op, size
x = np.genfromtxt(filename)
N = len(x)
# stats to get:
sd = np.std(x)
stddev.append(sd)
cv = np.std(x) * N
coefvar.append(cv)
logN_sd = np.std(x) * np.log(N)
logN_sd_vals.append(logN_sd)
sqrtN_sd = np.std(x) * (N**0.5)
sqrtN_sd_vals.append(sqrtN_sd)
cbrtN_sd = np.std(x) * (N**(1.0/3))
cbrtN_sd_vals.append(cbrtN_sd)
g = random_walks.gini_coeff(x)
gini.append(g)
nneighbours.append(np.sum(x > 0))
if do_rw_experiment:
try:
# load the results from a previous rw run
results = np.genfromtxt(basename + "/space_%s/rw_results_size_%d_op_%s.dat" % (space, size, op))
except:
# but if there *was* no previous run, do it now and save
results = rw_experiment_with_op(basename, space, size, opfs[op])
np.savetxt(basename + "/space_%s/rw_results_size_%d_op_%s.dat" % (space, size, op), results)
mu, sigma = np.mean(results), np.std(results)
prop_unique.append((mu, sigma))
prop_unique_v_expl.append("%s %d %s %f %f %f %f %f %f %f %f" % (
space, size, op, sd, cv, logN_sd, sqrtN_sd, cbrtN_sd, g, mu, sigma))
basename = sys.argv[1]
# barcharts
barchart(basename, space, size, "Gini", gini, ops)
barchart(basename, space, size, "SD", stddev, ops)
barchart(basename, space, size, "CV", coefvar, ops)
barchart(basename, space, size, "log(N) SD", logN_sd_vals, ops)
barchart(basename, space, size, "sqrt(N) SD", sqrtN_sd_vals, ops)
barchart(basename, space, size, "cbrt(N) SD", cbrtN_sd_vals, ops)
# scatterplots v nneighbours
scatterplot(basename, space, size, "Gini", "# Neighbours", gini, nneighbours, ops)
scatterplot(basename, space, size, "SD", "# Neighbours", stddev, nneighbours, ops)
scatterplot(basename, space, size, "CV", "# Neighbours", coefvar, nneighbours, ops)
scatterplot(basename, space, size, "log(N) SD", "# Neighbours", logN_sd_vals, nneighbours, ops)
scatterplot(basename, space, size, "sqrt(N) SD", "# Neighbours", sqrtN_sd_vals, nneighbours, ops)
scatterplot(basename, space, size, "cbrt(N) SD", "# Neighbours", cbrtN_sd_vals, nneighbours, ops)
if do_rw_experiment:
# scatterplots v prop unique
prop_unique = np.array(prop_unique)
prop_unique[:,0] = 1.0 - prop_unique[:,0]
scatterplot(basename, space, size, "Gini", "1 - prop. unique", gini, prop_unique, ops)
scatterplot(basename, space, size, "SD", "1 - prop. unique", stddev, prop_unique, ops)
scatterplot(basename, space, size, "CV", "1 - prop. unique", coefvar, prop_unique, ops)
scatterplot(basename, space, size, "log(N) SD", "1 - prop. unique", logN_sd_vals, prop_unique, ops)
scatterplot(basename, space, size, "sqrt(N) SD", "1 - prop. unique", sqrtN_sd_vals, prop_unique, ops)
scatterplot(basename, space, size, "cbrt(N) SD", "1 - prop. unique", cbrtN_sd_vals, prop_unique, ops)
filename = os.path.join(basename, "space_%s/size_%d_prop_unique_v_expl.dat" % (space, size))
open(filename, "w").write("\n".join(prop_unique_v_expl))