def plot_probe_results(filename, outdir):
log("Loading probe results from %s" % filename)
with open(filename, "r") as f:
results = pickle.load(f)
results = [((probe, n_models, analysis_count_from_file_name(fname)), val)
for ((fname, n_models, probe), val) in results.iteritems()]
plot_results(results, outdir=outdir)
def snapshot():
log('vacuuming')
bdb.sql_execute('vacuum')
cur_infix = '-%dm-%di' % (num_models, cur_iter_ct)
save_file_name = out_file_name('satellites', cur_infix + '.bdb')
meta_file_name = out_file_name('satellites', cur_infix + '-meta.txt')
log('recording snapshot ' + save_file_name)
os.system("cp %s %s" % (bdb_file, save_file_name))
report(save_file_name, meta_file_name)
def snapshot():
log('vacuuming')
bdb.sql_execute('vacuum')
cur_infix = '-%dm-%di' % (num_models, cur_iter_ct)
save_file_name = out_file_name('satellites', cur_infix + '.bdb')
meta_file_name = out_file_name('satellites', cur_infix + '-meta.txt')
log('recording snapshot ' + save_file_name)
os.system("cp %s %s" % (bdb_file, save_file_name))
report(save_file_name, meta_file_name)
def final_report():
# create a diagnostics plot
plot_file_name = out_file_name('satellites', '-logscores.pdf')
log('writing diagnostic plot to %s' % plot_file_name)
_fig = bdbcontrib.plot_crosscat_chain_diagnostics(bdb, 'logscore',
'satellites_cc')
plt.savefig(plot_file_name)
final_metadata_file = out_file_name('satellites', '-meta.txt')
report(bdb_file, final_metadata_file,
echo=True, plot_file_name=plot_file_name)
def final_report():
# create a diagnostics plot
plot_file_name = out_file_name('satellites', '-logscores.pdf')
log('writing diagnostic plot to %s' % plot_file_name)
_fig = bdbcontrib.crosscat_utils.plot_crosscat_chain_diagnostics(
bdb, 'logscore', 'satellites_cc')
plt.savefig(plot_file_name)
final_metadata_file = out_file_name('satellites', '-meta.txt')
report(bdb_file,
final_metadata_file,
echo=True,
plot_file_name=plot_file_name)
def doit(files, outfile, model_schedule, n_replications):
out_dir = os.path.dirname(outfile)
if out_dir and not os.path.isdir(out_dir):
os.makedirs(out_dir)
results = probe_fileset(
files, "satellites_cc",
[country_purpose_probes,
unlikely_periods_probes,
orbit_type_imputation_probes],
model_schedule = model_schedule,
n_replications = n_replications)
with open(outfile, "w") as f:
pickle.dump(results, f)
log("Saved probe results to %s" % outfile)
def doit(files, outfile, model_schedule, n_replications):
out_dir = os.path.dirname(outfile)
if out_dir and not os.path.isdir(out_dir):
os.makedirs(out_dir)
results = probe_fileset(
files,
"satellites_cc",
[country_purpose_probes, unlikely_periods_probes, orbit_type_imputation_probes],
model_schedule=model_schedule,
n_replications=n_replications,
)
with open(outfile, "w") as f:
pickle.dump(results, f)
log("Saved probe results to %s" % outfile)
def plot_results(results, outdir="figures", ext=".png"):
"""Plot the aggregate results of probing.
`results` is a list of pairs giving probe conditions and
aggregated probe results.
`outdir` is the name of a directory to which to write the visualizations.
Default: "figures".
`ext` is the file extension for visualizations, which determines
the image format used. Default ".png".
Each probe condition is expected to be a 3-tuple: probe name,
model count, analysis iteration count. Each result is expected to
be a tagged aggregate (see aggregation.py).
Each numerical probe produces one plot, named after the probe.
The plot facets over the model count, displays the iteration count
on the x-axis, and a violin plot of the results on the y axis.
All boolean probes are aggregated into one plot named
"boolean-probes", whose y axis is the frequency of a "True"
result. Each probe is a line giving the relationship of the
frequency to the number of analysis iterations.
"""
if not os.path.exists(outdir):
os.makedirs(outdir)
replications = num_replications(results)
probes = sorted(
set((pname, ptype) for ((pname, _, _), (ptype, _)) in results))
for probe, ptype in probes:
if not ptype == 'num': continue
grid = plot_results_numerical(results, probe)
grid.fig.suptitle(probe + ", %d replications" % replications)
# XXX Actually shell quote the probe name
figname = string.replace(probe, " ", "-").replace("/", "") + ext
savepath = os.path.join(outdir, figname)
grid.savefig(savepath)
plt.close(grid.fig)
log("Probe '%s' results saved to %s" % (probe, savepath))
grid = plot_results_boolean(results)
grid.fig.suptitle("Boolean probes, %d replications" % replications)
figname = "boolean-probes" + ext
savepath = os.path.join(outdir, figname)
grid.savefig(savepath)
plt.close(grid.fig)
log("Boolean probe results saved to %s" % (savepath, ))
def plot_results(results, outdir="figures", ext=".png"):
"""Plot the aggregate results of probing.
`results` is a list of pairs giving probe conditions and
aggregated probe results.
`outdir` is the name of a directory to which to write the visualizations.
Default: "figures".
`ext` is the file extension for visualizations, which determines
the image format used. Default ".png".
Each probe condition is expected to be a 3-tuple: probe name,
model count, analysis iteration count. Each result is expected to
be a tagged aggregate (see aggregation.py).
Each numerical probe produces one plot, named after the probe.
The plot facets over the model count, displays the iteration count
on the x-axis, and a violin plot of the results on the y axis.
All boolean probes are aggregated into one plot named
"boolean-probes", whose y axis is the frequency of a "True"
result. Each probe is a line giving the relationship of the
frequency to the number of analysis iterations.
"""
if not os.path.exists(outdir):
os.makedirs(outdir)
replications = num_replications(results)
probes = sorted(set((pname, ptype)
for ((pname, _, _), (ptype, _)) in results))
for probe, ptype in probes:
if not ptype == 'num': continue
grid = plot_results_numerical(results, probe)
grid.fig.suptitle(probe + ", %d replications" % replications)
# XXX Actually shell quote the probe name
figname = string.replace(probe, " ", "-").replace("/", "") + ext
savepath = os.path.join(outdir, figname)
grid.savefig(savepath)
plt.close(grid.fig)
log("Probe '%s' results saved to %s" % (probe, savepath))
grid = plot_results_boolean(results)
grid.fig.suptitle("Boolean probes, %d replications" % replications)
figname = "boolean-probes" + ext
savepath = os.path.join(outdir, figname)
grid.savefig(savepath)
plt.close(grid.fig)
log("Boolean probe results saved to %s" % (savepath,))
def execute(bql):
log("executing %s" % bql)
bdb.execute(bql)
def doit(out_dir, num_models, num_iters, checkpoint_freq, seed):
then = time.time()
timestamp = datetime.datetime.fromtimestamp(then).strftime('%Y-%m-%d')
user = subprocess.check_output(["whoami"]).strip()
host = subprocess.check_output(["hostname"]).strip()
filestamp = '-' + timestamp + '-' + user
def out_file_name(base, ext):
return out_dir + '/' + base + filestamp + ext
csv_file = os.path.join(os.path.dirname(__file__), 'satellites.csv')
bdb_file = out_file_name('satellites', '.bdb')
# so we can build bdb models
os.environ['BAYESDB_WIZARD_MODE'] = '1'
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
if os.path.exists(bdb_file):
print 'Error: File', bdb_file, 'already exists. Please remove it.'
sys.exit(1)
# create database mapped to filesystem
log('opening bdb on disk: %s' % bdb_file)
bdb = bayeslite.bayesdb_open(pathname=bdb_file, builtin_metamodels=False)
def execute(bql):
log("executing %s" % bql)
bdb.execute(bql)
# read csv into table
log('reading data from %s' % csv_file)
bayeslite.bayesdb_read_csv_file(bdb,
'satellites',
csv_file,
header=True,
create=True,
ifnotexists=True)
# Add a "not applicable" orbit sub-type
log('adding "not applicable" orbit sub-type')
bdb.sql_execute('''UPDATE satellites
SET type_of_orbit = 'N/A'
WHERE (class_of_orbit = 'GEO' OR class_of_orbit = 'MEO')
AND type_of_orbit = 'NaN'
''')
# nullify "NaN"
log('nullifying NaN')
bdbcontrib.bql_utils.nullify(bdb, 'satellites', 'NaN')
# register crosscat metamodel
cc = ccme.MultiprocessingEngine(seed=seed)
ccmm = bayeslite.metamodels.crosscat.CrosscatMetamodel(cc)
bayeslite.bayesdb_register_metamodel(bdb, ccmm)
# create the crosscat generator using
execute('''
CREATE GENERATOR satellites_cc FOR satellites USING crosscat (
GUESS(*),
name IGNORE,
Country_of_Operator CATEGORICAL,
Operator_Owner CATEGORICAL,
Users CATEGORICAL,
Purpose CATEGORICAL,
Class_of_Orbit CATEGORICAL,
Type_of_Orbit CATEGORICAL,
Perigee_km NUMERICAL,
Apogee_km NUMERICAL,
Eccentricity NUMERICAL,
Period_minutes NUMERICAL,
Launch_Mass_kg NUMERICAL,
Dry_Mass_kg NUMERICAL,
Power_watts NUMERICAL,
Date_of_Launch NUMERICAL,
Anticipated_Lifetime NUMERICAL,
Contractor CATEGORICAL,
Country_of_Contractor CATEGORICAL,
Launch_Site CATEGORICAL,
Launch_Vehicle CATEGORICAL,
Source_Used_for_Orbital_Data CATEGORICAL,
longitude_radians_of_geo NUMERICAL,
Inclination_radians NUMERICAL
)
''')
execute('INITIALIZE %d MODELS FOR satellites_cc' % (num_models, ))
cur_iter_ct = 0
def snapshot():
log('vacuuming')
bdb.sql_execute('vacuum')
cur_infix = '-%dm-%di' % (num_models, cur_iter_ct)
save_file_name = out_file_name('satellites', cur_infix + '.bdb')
meta_file_name = out_file_name('satellites', cur_infix + '-meta.txt')
log('recording snapshot ' + save_file_name)
os.system("cp %s %s" % (bdb_file, save_file_name))
report(save_file_name, meta_file_name)
def record_metadata(f,
saved_file_name,
sha_sum,
total_time,
plot_file_name=None):
f.write("DB file " + saved_file_name + "\n")
f.write(sha_sum)
f.write("built from " + csv_file + "\n")
f.write("by %s@%s\n" % (user, host))
f.write("at seed %s\n" % seed)
f.write("in %3.2f seconds\n" % total_time)
f.write("with %s models analyzed for %s iterations\n" %
(num_models, num_iters))
f.write("by bayeslite %s, with crosscat %s and bdbcontrib %s\n" %
(bayeslite.__version__, crosscat.__version__,
bdbcontrib.__version__))
if plot_file_name is not None:
f.write("diagnostics recorded to %s\n" % plot_file_name)
f.flush()
def report(saved_file_name,
metadata_file,
echo=False,
plot_file_name=None):
sha256 = hashlib.sha256()
with open(saved_file_name, 'rb') as fd:
for chunk in iter(lambda: fd.read(65536), ''):
sha256.update(chunk)
sha_sum = sha256.hexdigest() + '\n'
total_time = time.time() - then
with open(metadata_file, 'w') as fd:
record_metadata(fd, saved_file_name, sha_sum, total_time,
plot_file_name)
fd.write('using script ')
fd.write('-' * 57)
fd.write('\n')
fd.flush()
os.system("cat %s >> %s" % (__file__, metadata_file))
if echo:
record_metadata(sys.stdout, saved_file_name, sha_sum, total_time,
plot_file_name)
def final_report():
# create a diagnostics plot
plot_file_name = out_file_name('satellites', '-logscores.pdf')
log('writing diagnostic plot to %s' % plot_file_name)
_fig = bdbcontrib.crosscat_utils.plot_crosscat_chain_diagnostics(
bdb, 'logscore', 'satellites_cc')
plt.savefig(plot_file_name)
final_metadata_file = out_file_name('satellites', '-meta.txt')
report(bdb_file,
final_metadata_file,
echo=True,
plot_file_name=plot_file_name)
snapshot()
while cur_iter_ct < num_iters:
execute('ANALYZE satellites_cc FOR %d ITERATIONS WAIT' %
checkpoint_freq)
cur_iter_ct += checkpoint_freq
snapshot()
final_report()
log('closing bdb %s' % bdb_file)
bdb.close()
os.system("cd %s && ln -s satellites%s.bdb satellites.bdb" %
(out_dir, filestamp))
def execute(bql):
log("executing %s" % bql)
bdb.execute(bql)
def doit(out_dir, num_models, num_iters, checkpoint_freq, seed):
then = time.time()
timestamp = datetime.datetime.fromtimestamp(then).strftime('%Y-%m-%d')
user = subprocess.check_output(["whoami"]).strip()
host = subprocess.check_output(["hostname"]).strip()
filestamp = '-' + timestamp + '-' + user
def out_file_name(base, ext):
return out_dir + '/' + base + filestamp + ext
csv_file = os.path.join(os.path.dirname(__file__), 'satellites.csv')
bdb_file = out_file_name('satellites', '.bdb')
# so we can build bdb models
os.environ['BAYESDB_WIZARD_MODE']='1'
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
if os.path.exists(bdb_file):
print 'Error: File', bdb_file, 'already exists. Please remove it.'
sys.exit(1)
# create database mapped to filesystem
log('opening bdb on disk: %s' % bdb_file)
bdb = bayeslite.bayesdb_open(pathname=bdb_file, builtin_metamodels=False)
def execute(bql):
log("executing %s" % bql)
bdb.execute(bql)
# read csv into table
log('reading data from %s' % csv_file)
bayeslite.bayesdb_read_csv_file(bdb, 'satellites', csv_file,
header=True, create=True, ifnotexists=True)
# Add a "not applicable" orbit sub-type
log('adding "not applicable" orbit sub-type')
bdb.sql_execute('''UPDATE satellites
SET type_of_orbit = 'N/A'
WHERE (class_of_orbit = 'GEO' OR class_of_orbit = 'MEO')
AND type_of_orbit = 'NaN'
''')
# nullify "NaN"
log('nullifying NaN')
bdbcontrib.nullify(bdb, 'satellites', 'NaN')
# register crosscat metamodel
cc = ccme.MultiprocessingEngine(seed=seed)
ccmm = bayeslite.metamodels.crosscat.CrosscatMetamodel(cc)
bayeslite.bayesdb_register_metamodel(bdb, ccmm)
# create the crosscat generator using
execute('''
CREATE GENERATOR satellites_cc FOR satellites USING crosscat (
GUESS(*),
name IGNORE,
Country_of_Operator CATEGORICAL,
Operator_Owner CATEGORICAL,
Users CATEGORICAL,
Purpose CATEGORICAL,
Class_of_Orbit CATEGORICAL,
Type_of_Orbit CATEGORICAL,
Perigee_km NUMERICAL,
Apogee_km NUMERICAL,
Eccentricity NUMERICAL,
Period_minutes NUMERICAL,
Launch_Mass_kg NUMERICAL,
Dry_Mass_kg NUMERICAL,
Power_watts NUMERICAL,
Date_of_Launch NUMERICAL,
Anticipated_Lifetime NUMERICAL,
Contractor CATEGORICAL,
Country_of_Contractor CATEGORICAL,
Launch_Site CATEGORICAL,
Launch_Vehicle CATEGORICAL,
Source_Used_for_Orbital_Data CATEGORICAL,
longitude_radians_of_geo NUMERICAL,
Inclination_radians NUMERICAL
)
''')
execute('INITIALIZE %d MODELS FOR satellites_cc' % (num_models,))
cur_iter_ct = 0
def snapshot():
log('vacuuming')
bdb.sql_execute('vacuum')
cur_infix = '-%dm-%di' % (num_models, cur_iter_ct)
save_file_name = out_file_name('satellites', cur_infix + '.bdb')
meta_file_name = out_file_name('satellites', cur_infix + '-meta.txt')
log('recording snapshot ' + save_file_name)
os.system("cp %s %s" % (bdb_file, save_file_name))
report(save_file_name, meta_file_name)
def record_metadata(f, saved_file_name, sha_sum, total_time,
plot_file_name=None):
f.write("DB file " + saved_file_name + "\n")
f.write(sha_sum)
f.write("built from " + csv_file + "\n")
f.write("by %s@%s\n" % (user, host))
f.write("at seed %s\n" % seed)
f.write("in %3.2f seconds\n" % total_time)
f.write("with %s models analyzed for %s iterations\n"
% (num_models, num_iters))
f.write("by bayeslite %s, with crosscat %s and bdbcontrib %s\n"
% (bayeslite.__version__, crosscat.__version__, bdbcontrib.__version__))
if plot_file_name is not None:
f.write("diagnostics recorded to %s\n" % plot_file_name)
f.flush()
def report(saved_file_name, metadata_file, echo=False, plot_file_name=None):
sha256 = hashlib.sha256()
with open(saved_file_name, 'rb') as fd:
for chunk in iter(lambda: fd.read(65536), ''):
sha256.update(chunk)
sha_sum = sha256.hexdigest() + '\n'
total_time = time.time() - then
with open(metadata_file, 'w') as fd:
record_metadata(fd, saved_file_name,
sha_sum, total_time, plot_file_name)
fd.write('using script ')
fd.write('-' * 57)
fd.write('\n')
fd.flush()
os.system("cat %s >> %s" % (__file__, metadata_file))
if echo:
record_metadata(sys.stdout, saved_file_name,
sha_sum, total_time, plot_file_name)
def final_report():
# create a diagnostics plot
plot_file_name = out_file_name('satellites', '-logscores.pdf')
log('writing diagnostic plot to %s' % plot_file_name)
_fig = bdbcontrib.plot_crosscat_chain_diagnostics(bdb, 'logscore',
'satellites_cc')
plt.savefig(plot_file_name)
final_metadata_file = out_file_name('satellites', '-meta.txt')
report(bdb_file, final_metadata_file,
echo=True, plot_file_name=plot_file_name)
snapshot()
while cur_iter_ct < num_iters:
execute('ANALYZE satellites_cc FOR %d ITERATIONS WAIT' % checkpoint_freq)
cur_iter_ct += checkpoint_freq
snapshot()
final_report()
log('closing bdb %s' % bdb_file)
bdb.close()
os.system("cd %s && ln -s satellites%s.bdb satellites.bdb" % (out_dir, filestamp))
