def main(expt_dir, repeat=-1):
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment-name"]
if repeat > 0:
experiment_name = repeat_experiment_name(experiment_name, repeat)
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
tasks = parse_tasks_from_jobs(jobs, experiment_name, options, input_space)
for task_name, task in tasks.iteritems():
# print 'Printing results for task %s' % task_name
for i in xrange(len(task.values)):
print 'Iteration %d' % (i + 1)
input_space.paramify_and_print(task.inputs[i], left_indent=0)
print '%s: %s' % (task_name, task.values[i])
print ''
print ''
def main(expt_dir, repeat=-1):
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment_name"]
if repeat > 0:
experiment_name = repeat_experiment_name(experiment_name, repeat)
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
tasks = parse_tasks_from_jobs(jobs, experiment_name, options, input_space)
for job in jobs:
if job['status'] == 'complete':
print 'Job %d' % job['id']
input_space.print_params(job['params'], left_indent=0)
for task, val in job['values'].iteritems():
print '%s: %s' % (task, val)
print ''
def get_optimized_params(tool_name):
# Database connection
db = MongoDB(database_address='localhost')
if not (tool_name == 'macs2' or tool_name == 'cisgenome'
or tool_name == 'swembl' or tool_name == 'sicer'):
dic = {}
print('incorrect tool name')
return dic
jobs = load_jobs(db, tool_name + '_test')
df = pd.DataFrame()
# params names of each tools
macs2_params = ['q', 'm_s', 'm_d']
cisgenome_params = ['b', 'e', 'w']
swembl_params = ['x', 'm', 'f']
sicer_params = ['fs', 'gs', 'w']
if tool_name == 'macs2':
params = macs2_params
elif tool_name == 'cisgenome':
params = cisgenome_params
elif tool_name == 'swembl':
params = swembl_params
elif tool_name == 'sicer':
params = sicer_params
# dict
res = {}
for job in jobs:
df = df.append(
{
params[0]: float(job['params'][params[0]]['values']),
params[1]: float(job['params'][params[1]]['values']),
params[2]: float(job['params'][params[2]]['values']),
'error_rate': float(job['values']['branin'])
},
ignore_index=True)
df = df.sort_values('error_rate').reset_index(drop=True)
# print(df)
#df = df.drop('error_rate', axis=1)
column_list = df.columns
for column in column_list:
res[column] = df[0:1][column][0]
# print(df[0:1][column][0])
# return dictionary of params
return res
def main(expt_dir, n_repeat):
n_repeat = int(n_repeat)
options = parse_config_file(expt_dir, 'config.json')
tasks = options['tasks'].keys()
jobs = dict()
start_times = dict()
for j in xrange(n_repeat):
experiment_name = repeat_experiment_name(options["experiment_name"], j)
db = MongoDB(database_address=options['database']['address'])
jobs[j] = load_jobs(db, experiment_name)
start_times[j] = db.load(experiment_name, 'start-time')['start-time']
time_in_evals = defaultdict(lambda: np.zeros(n_repeat))
time_in_fast_updates = np.zeros(n_repeat)
time_in_slow_updates = np.zeros(n_repeat)
for j in xrange(n_repeat):
last_job_end_time = start_times[j]
for job in jobs[j]:
if job['status'] == 'complete':
time_in_evals[job['tasks'][0]][j] += (job['end time'] -
job['start time']) / 60.0
if job['fast update']:
time_in_fast_updates[j] += (job['start time'] -
last_job_end_time) / 60.0
else:
time_in_slow_updates[j] += (job['start time'] -
last_job_end_time) / 60.0
last_job_end_time = job['end time']
for task in tasks:
print 'Average time on task %s over %d repeats: %f +/- %f minutes (mean +/- std)' % (
task, n_repeat, np.mean(
time_in_evals[task]), np.std(time_in_evals[task]))
total_time_in_evals = sum(time_in_evals.values())
print 'Average time in JOBS over %d repeats: %f +/- %f minutes (mean +/- std)' % (
n_repeat, np.mean(total_time_in_evals), np.std(total_time_in_evals))
print 'Average time in FAST over %d repeats: %f +/- %f minutes (mean +/- std)' % (
n_repeat, np.mean(time_in_fast_updates), np.std(time_in_fast_updates))
print 'Average time in SLOW over %d repeats: %f +/- %f minutes (mean +/- std)' % (
n_repeat, np.mean(time_in_slow_updates), np.std(time_in_slow_updates))
total_optimizer_time = time_in_fast_updates + time_in_slow_updates
print 'Average time in OPTIMIZER over %d repeats: %f +/- %f minutes (mean +/- std)' % (
n_repeat, np.mean(total_optimizer_time), np.std(total_optimizer_time))
print 'Total average time spent: %f' % np.sum([
np.mean(total_time_in_evals),
np.mean(time_in_fast_updates),
np.mean(time_in_slow_updates)
])
def main(expt_dir, n_repeat):
n_repeat = int(n_repeat)
options = parse_config_file(expt_dir, 'config.json')
tasks = options['tasks'].keys()
jobs = dict()
for j in xrange(n_repeat):
experiment_name = repeat_experiment_name(options["experiment_name"], j)
db = MongoDB(database_address=options['database']['address'])
jobs[j] = load_jobs(db, experiment_name)
n_iter_each = map(len, jobs.values())
print 'Found %s iterations' % n_iter_each
n_iter = min(n_iter_each)
cum_evals = defaultdict(lambda: defaultdict(lambda:defaultdict(int)))
for j in xrange(n_repeat):
for i in xrange(n_iter):
for task in tasks:
if task in jobs[j][i]['tasks']:
cum_evals[j][task][i] = cum_evals[j][task][i-1] + 1
else:
cum_evals[j][task][i] = cum_evals[j][task][i-1]
# average over the j repeats
for i in xrange(n_iter):
for task in tasks:
cum_evals["avg"][task][i] = np.mean([cum_evals[j][task][i] for j in xrange(n_repeat)])
cum_evals["err"][task][i] = np.std([cum_evals[j][task][i] for j in xrange(n_repeat)])
plt.figure()
iters = range(n_iter)
for task in tasks:
plt.errorbar(iters, [cum_evals["avg"][task][i] for i in xrange(n_iter)],
yerr=[cum_evals["err"][task][i] for i in xrange(n_iter)], linewidth=2)
plt.legend(tasks, loc='upper left')
plt.xlabel('Iteration number', size=25)
plt.ylabel('Cumulative evaluations',size=25)
# Make the directory for the plots
plots_dir = os.path.join(expt_dir, 'plots')
if not os.path.isdir(plots_dir):
os.mkdir(plots_dir)
figname = os.path.join(plots_dir, 'cumulative_evals.pdf')
print 'Saving figure at %s' % figname
plt.savefig(figname)
def db_to_df(db_address = 'localhost', db_name= "spearmintDB_marfra", experiment_name = 'rnn_3'):
db = MongoDB(database_address=db_address,database_name=db_name)
# Load jobs
jobs = load_jobs(db, experiment_name)
# Remove unfinished jobs
jobs_fin = []
for job in jobs:
if job['status'] == 'complete':
jobs_fin.append(job)
df=pd.DataFrame()
for job in jobs_fin:
# Data from DB to a OrderedDict
tmp=(("job_id",[job["id"]]),)
tmp=tmp + (("exp_values",[np.exp(job["values"]['nlp'])]),)
tmp=tmp + (("values",[job["values"]['nlp']]),)
for par in job["params"]:
tmp= tmp + ((par,[job["params"][par]["values"][0]]),)
tmp=tmp + (("duration_h",[(job["end time"]-job["start time"])/3600.0]),)
try: # for backward compatibility
tmp=tmp + (("manual",[job["manual"]]),)
except:
pass
tmp=tmp + (("start_time",[job["start time"]]),)
tmp=tmp + (("end_time",[job["end time"]]),)
dict_tmp = OrderedDict(tmp)
# From OrderedDict to a pandas dataframe
df_tmp=pd.DataFrame.from_dict(dict_tmp)
# Append dataframe
df=df.append(df_tmp, ignore_index=True)
return df
def returnBest(config_directory):
os.chdir("/home/carrknight/code/oxfish/runs/optimization/spearmint")
options = get_options(config_directory, config_file="config.json")
experiment_name = str(options['experiment-name'])
db = MongoDB()
resources = parse_resources_from_config(options)
resource = resources.itervalues().next()
# load hyper parameters
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(options)
print "chooser", chooser
hypers = db.load(experiment_name, "hypers")
print "loaded hypers", hypers # from GP.to_dict()
jobs = load_jobs(db, experiment_name)
remove_broken_jobs(db, jobs, experiment_name, resources)
task_options = {task: options["tasks"][task] for task in resource.tasks}
task_group = spearmint.main.load_task_group(db, options, resource.tasks)
hypers = spearmint.main.load_hypers(db, experiment_name)
print "loaded hypers", hypers # from GP.to_dict()
hypers = chooser.fit(task_group, hypers, task_options)
print "\nfitted hypers:"
print(hypers)
lp, x = chooser.best()
x = x.flatten()
print "best", lp, x
bestp = task_group.paramify(task_group.from_unit(x))
print "expected best position", bestp
return bestp
def main():
"""
Usage: python make_plots.py PATH_TO_DIRECTORY
TODO: Some aspects of this function are specific to the simple branin example
We should clean this up so that interpretation of plots are more clear and
so that it works in more general cases
(e.g. if objective likelihood is binomial then values should not be
unstandardized)
"""
options, expt_dir = get_options()
print "options:"
print_dict(options)
# reduce the grid size
options["grid_size"] = 400
resources = parse_resources_from_config(options)
# Load up the chooser.
chooser_module = importlib.import_module('spearmint.choosers.' + options['chooser'])
chooser = chooser_module.init(options)
print "chooser", chooser
experiment_name = options.get("experiment-name", 'unnamed-experiment')
# Connect to the database
db_address = options['database']['address']
sys.stderr.write('Using database at %s.\n' % db_address)
db = MongoDB(database_address=db_address)
# testing below here
jobs = load_jobs(db, experiment_name)
remove_broken_jobs(db, jobs, experiment_name, resources)
print "resources:", resources
print_dict(resources)
resource = resources.itervalues().next()
task_options = { task: options["tasks"][task] for task in resource.tasks }
print "task_options:"
print_dict(task_options) # {'main': {'likelihood': u'NOISELESS', 'type': 'OBJECTIVE'}}
task_group = load_task_group(db, options, resource.tasks)
print "task_group", task_group # TaskGroup
print "tasks:"
print_dict(task_group.tasks) # {'main': <spearmint.tasks.task.Task object at 0x10bf63290>}
hypers = load_hypers(db, experiment_name)
print "loaded hypers", hypers # from GP.to_dict()
hypers = chooser.fit(task_group, hypers, task_options)
print "\nfitted hypers:"
print_dict(hypers)
lp, x = chooser.best()
x = x.flatten()
print "best", lp, x
bestp = task_group.paramify(task_group.from_unit(x))
print "expected best position", bestp
# get the grid of points
grid = chooser.grid
# print "chooser objectives:",
# print_dict(chooser.objective)
print "chooser models:", chooser.models
print_dict(chooser.models)
obj_model = chooser.models[chooser.objective['name']]
obj_mean, obj_var = obj_model.function_over_hypers(obj_model.predict, grid)
# un-normalize the function values and variances
obj_task = task_group.tasks['main']
obj_mean = [obj_task.unstandardize_mean(obj_task.unstandardize_variance(v)) for v in obj_mean]
obj_std = [obj_task.unstandardize_variance(np.sqrt(v)) for v in obj_var]
# for xy, m, v in izip(grid, obj_mean, obj_var):
# print xy, m, v
grid = map(task_group.from_unit, grid)
# return
xymv = [(xy[0], xy[1], m, v) for xy, m, v in izip(grid, obj_mean, obj_std)]# if .2 < xy[0] < .25]
x = map(lambda x:x[0], xymv)
y = map(lambda x:x[1], xymv)
m = map(lambda x:x[2], xymv)
sig = map(lambda x:x[3], xymv)
# print y
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111, projection='3d')
ax.plot(x, y, m, marker='.', linestyle="None")
# plot errorbars
for i in np.arange(0, len(x)):
ax.plot([x[i], x[i]], [y[i], y[i]], [m[i]+sig[i], m[i]-sig[i]], marker="_", color='k')
# get the observed points
task = task_group.tasks['main']
idata = task.valid_normalized_data_dict
xy = idata["inputs"]
xy = map(task_group.from_unit, xy)
xy = np.array(xy)
vals = idata["values"]
vals = [obj_task.unstandardize_mean(obj_task.unstandardize_variance(v)) for v in vals]
ax.plot(xy[:,0], xy[:,1], vals, marker='o', color="r", linestyle="None")
plt.show()
def main(dirs,
n_repeat=-1,
n_iter_spec=None,
rec_type="model",
average="mean",
log_scale=False,
violation_value=1.,
constraint_tol=0.,
make_dist_plot=False,
mainfile=None,
stretch_x=False,
task_comp_x=None,
plot_wall_time=False,
bin_size=1.0,
plot_separate=False,
labels=None,
y_axis_label=None,
x_axis_label=None):
# Create the figure that plots utility gap
fig = dict()
ax = dict()
# averaging function
if average == "mean":
avg = np.mean
elif average == "median":
avg = np.median
else:
raise Exception("Unknown average %s" % average)
fig['err'] = plt.figure()
ax['err'] = fig['err'].add_subplot(1, 1, 1)
if plot_wall_time:
ax['err'].set_xlabel("wall time (min)", size=25)
elif x_axis_label:
ax['err'].set_xlabel(x_axis_label, size=25)
else:
ax['err'].set_xlabel('Number of function evaluations', size=25)
ax['err'].tick_params(axis='both', which='major', labelsize=20)
# Create the figure that plots L2 distance from solution
fig['dist'] = plt.figure()
ax['dist'] = fig['dist'].add_subplot(1, 1, 1)
if x_axis_label:
ax['dist'].set_xlabel(x_axis_label, size=25)
else:
ax['dist'].set_xlabel('Number of function evaluations', size=25)
if y_axis_label:
ax['dist'].set_ylabel(y_axis_label, size=25)
elif log_scale:
ax['dist'].set_ylabel('$\log_{10}\, \ell_2$-distance', size=25)
else:
ax['dist'].set_ylabel('$\ell_2$-distance', size=25)
ax['dist'].tick_params(axis='both', which='major', labelsize=20)
db_document_name = 'recommendations'
acq_names = list()
for expt_dir in dirs:
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment_name"]
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
tasks = parse_tasks_from_jobs(jobs, experiment_name, options,
input_space)
if rec_type == "model":
if mainfile is None:
main_file = options['main_file']
else:
main_file = mainfile
sys.path.append(options['main_file_path']
) # TODO: make this nicer with proper importin
if (main_file[-3:] == u'.py') is True:
module = importlib.import_module(main_file[:len(main_file) -
3])
else:
module = importlib.import_module(main_file)
sys.path.remove(options['main_file_path'])
obj, con = get_objectives_and_constraints(options) # get the names
obj = obj[0] # only one objective
print 'Found %d constraints' % len(con)
plot_utility_gap = rec_type == "model" and hasattr(module, 'true_val')
if plot_utility_gap:
print 'PLOTTING UTILITY GAP'
if y_axis_label:
ax['err'].set_ylabel(y_axis_label, size=25)
elif log_scale:
ax['err'].set_ylabel('$\log_{10}$ utility gap', size=25)
else:
ax['err'].set_ylabel('utility gap', size=25)
else:
if y_axis_label:
ax['err'].set_ylabel(y_axis_label, size=25)
elif log_scale:
ax['err'].set_ylabel('$\log_{10}$ objective value', size=25)
else:
ax['err'].set_ylabel('objective value', size=25)
# Make the directory for the plots
plots_dir = os.path.join(expt_dir, 'plots')
if not os.path.isdir(plots_dir):
os.mkdir(plots_dir)
# if the module provides the location of the true solution, plot the distance to this solution vs iterations
if make_dist_plot and not hasattr(module, 'true_sol'):
raise Exception(
"make_dist_plot turned on but cannot find true sol in the main_file"
)
# If repeat >= 0, then we are averaging a number of experiments
# We assume the experiments are stored with the original name plus a hyphen plus the number
n_repeat = int(n_repeat)
if n_repeat < 0:
recs = db.load(experiment_name, db_document_name)
if recs is None:
raise Exception(
"Could not find experiment %s in database at %s" %
(experiment_name, options['database']['address']))
# the x axis represents the number of evals of a particular task given by task_comp_x
# so we only take the data where this number was incrememted, i.e. when this task was evaluated
if task_comp_x:
# only include recommendations when you finish a particular task
new_recs = list()
last_complete = 0
for rec in recs:
cur_complete = rec['num_complete_tasks'][task_comp_x]
if cur_complete > last_complete:
last_complete = cur_complete
new_recs.append(rec)
recs = new_recs
n_iter = len(recs) if n_iter_spec is None else n_iter_spec
iters = range(n_iter)
if plot_wall_time:
if task_comp_x:
raise Exception("Do not use plot wall_time with task_x")
iters = [rec['total_elapsed_time'] / 60.0 for rec in recs]
iters = iters[:n_iter]
iters = np.array(iters, dtype=float)
print 'Found %d iterations' % len(recs)
if rec_type == "model":
values = [
true_func(rec, module, violation_value, constraint_tol,
obj, con) for rec in recs
]
if log_scale:
ax['err'].plot(iters, map(np.log10, values))
else:
ax['err'].plot(iters, values)
else:
if rec_type == "observations":
observations = [x['obj_o'] for x in recs]
elif rec_type == "mixed":
observations = [x['obj_om'] for x in recs]
else:
raise Exception("unknown rec type")
for i in xrange(len(observations)):
if observations[i] is None or np.isnan(observations[i]):
observations[i] = violation_value
# print observations
# print len(observations)
if log_scale:
ax['err'].plot(iters, np.log10(observations))
else:
ax['err'].plot(iters, observations)
if make_dist_plot:
distances = [
params_norm(rec['params'], module.true_sol())
for rec in recs
]
if log_scale:
ax['dist'].plot(iters, np.log10(distances))
else:
ax['dist'].plot(iters, distances)
else:
# MULTIPLE REPEATS
repeat_recs = [
db.load(repeat_experiment_name(experiment_name, j),
db_document_name) for j in xrange(n_repeat)
]
if None in repeat_recs:
for i, repeat_rec in enumerate(repeat_recs):
if repeat_rec is None:
print 'Could not load experiment %s repeat %d' % (
experiment_name, i)
print 'Exiting...'
return
if task_comp_x:
# only include recommendations when you finish a particular task
new_repeat_recs = list()
for recs in repeat_recs:
recs = sorted(recs, key=lambda k: k['id']) # sort by id
new_recs = list()
last_complete = 0
for rec in recs:
cur_complete = rec['num_complete_tasks'][task_comp_x]
if cur_complete == last_complete + 1:
last_complete = cur_complete
new_recs.append(rec)
elif cur_complete == last_complete:
pass
else:
print(
'WARNING: cur complete=%d, last_complete=%d' %
(cur_complete, last_complete))
break
new_repeat_recs.append(new_recs)
repeat_recs = new_repeat_recs
n_iter_each = map(len, repeat_recs)
if plot_wall_time:
""" do everything separately from here if plotting wall time
here is what we do... we can't have a square array because
we don't want to take the minimum number of iterations...
we want to take ALL iterations for each repeat, and this number
may be different for different repeats.
so we store all times/values in a list of arrays
then we chop things up into bins
"""
if rec_type != "model":
values = list()
wall_times = list()
for j in xrange(
n_repeat): # loop over repeated experiments
wall_times.append(
np.array([
repeat_recs[j][i]['total_elapsed_time'] / 60.0
for i in xrange(n_iter_each[j])
]))
if rec_type == "observations":
values.append([
repeat_recs[j][i]['obj_o']
for i in xrange(n_iter_each[j])
])
elif rec_type == "mixed":
values.append([
repeat_recs[j][i]['obj_om']
for i in xrange(n_iter_each[j])
])
else:
raise Exception("unknown rec type")
for i in xrange(n_iter_each[j]):
if values[-1][i] is None or np.isnan(
values[-1][i]):
values[-1][i] = violation_value
values[-1] = np.array(values[-1])
# print values
else: # if plot wall tiem but using model
values = list()
wall_times = list()
for j in xrange(
n_repeat): # loop over repeated experiments
# for this repeat, get all wall times
wall_times.append(
np.array([
repeat_recs[j][i]['total_elapsed_time'] / 60.0
for i in xrange(n_iter_each[j])
]))
values_j = np.zeros(n_iter_each[j])
for i in xrange(
n_iter_each[j]): # loop over iterations
val = true_func(repeat_recs[j][i], module, None,
constraint_tol, obj, con)
if val is None or np.isnan(
val
): #set to violation value here so we can print out this info...
values_j[i] = violation_value
print 'Violation with params %s at repeat %d iter %d' % (
paramify_no_types(
repeat_recs[j][i]['params']), j, i)
else:
values_j[i] = val
values.append(values_j)
# change the data structure to be time bins and include everything in
# those time bins across repeats
end_times = map(max, wall_times)
for j in xrange(n_repeat):
print 'end time for repeat %d: %f' % (j, end_times[j])
iters = np.arange(0.0, np.round(max(end_times)), bin_size)
new_values = list()
for i, timestep in enumerate(iters):
# print 'Creating wall time bin from %f to %f. (%d/%d)' % (i, i+bin_size, i, len(iters))
new_value = list()
for j in xrange(n_repeat):
new_value = np.append(
new_value, values[j][np.logical_and(
wall_times[j] >= timestep, wall_times[j] <
timestep + bin_size)].flatten())
# if a time bin is empty across all repeats:
if len(new_value) == 0:
if i == 0:
new_value = [violation_value]
else:
new_value = new_values[-1]
new_values.append(new_value)
values = new_values
# make the first value equal to the violation value (optional)
iters = np.append(iters, max(iters) + bin_size)
values.insert(0, np.array([violation_value]))
# Average over the repeated experiments
average_values = map(avg, values)
errorbars = bootstrap_errorbars(values, log=log_scale, avg=avg)
# plt.yscale('log', nonposy='clip')
if log_scale:
ax['err'].errorbar(iters,
np.log10(average_values),
yerr=errorbars)
else:
ax['err'].errorbar(iters, average_values, yerr=errorbars)
else:
# NOT WALL TIME
n_iter = reduce(min, n_iter_each, np.inf)
if n_iter_spec is None:
print 'Found %d repeats with at least %d iterations' % (
n_repeat, n_iter)
print {i: n_iter_each[i] for i in xrange(n_repeat)}
elif n_iter < n_iter_spec:
print 'You specified %d iterations but there are only %d available... so plotting %d' % (
n_iter_spec, n_iter, n_iter)
else:
n_iter = n_iter_spec
print 'Plotting %d iterations' % n_iter
iters = range(n_iter)
if rec_type != "model":
values = np.zeros((n_iter, n_repeat))
for j in xrange(
n_repeat): # loop over repeated experiments
for i in iters[j]: # loop over iterations
if rec_type == "observations":
values[i, j] = repeat_recs[j][i]['obj_o']
elif rec_type == "mixed":
values[i, j] = repeat_recs[j][i]['obj_om']
else:
raise Exception("unknown rec type")
if values[i, j] is None or np.isnan(values[i, j]):
values[i, j] = violation_value
print values
else:
values = np.zeros((n_iter, n_repeat))
distances = np.zeros((n_iter, n_repeat))
for j in xrange(
n_repeat): # loop over repeated experiments
for i in iters: # loop over iterations
val = true_func(repeat_recs[j][i], module, None,
constraint_tol, obj, con)
if val is None: #set to violation value here so we can print out this info...
values[i, j] = violation_value
print 'Violation with params %s at repeat %d iter %d' % (
paramify_no_types(
repeat_recs[j][i]['params']), j, i)
else:
values[i, j] = val
if make_dist_plot:
distances[i, j] = params_norm(
repeat_recs[j][i]['params'],
module.true_sol())
if plot_separate:
if log_scale:
ax['err'].plot(iters, np.log10(values))
else:
ax['err'].plot(iters, values)
else:
# Average over the repeated experiments
average_values = map(avg, values)
errorbars = bootstrap_errorbars(values,
log=log_scale,
avg=avg)
# plt.yscale('log', nonposy='clip')
if stretch_x:
fctr = float(n_iter_spec) / float(n_iter)
iters = np.array(iters) * fctr
print 'Stretching x axis by a factor of %f' % fctr
if log_scale:
ax['err'].errorbar(iters,
np.log10(average_values),
yerr=errorbars)
else:
ax['err'].errorbar(iters,
average_values,
yerr=errorbars)
if make_dist_plot:
average_dist = map(avg, distances)
errorbars_dist = bootstrap_errorbars(distances,
log=log_scale,
avg=avg)
if log_scale:
ax['dist'].errorbar(iters,
np.log10(average_dist),
yerr=errorbars_dist)
else:
ax['dist'].errorbar(iters,
average_dist,
yerr=errorbars_dist)
acq_names.append(options["tasks"].values()[0]["acquisition"])
if acq_names[-1] == 'PES':
acq_names[-1] = 'PESC'
if acq_names[-1] == 'ExpectedImprovement':
acq_names[-1] = 'EIC'
if labels:
ax['err'].legend(labels.split(';'), fontsize=16, loc='lower left')
ax['dist'].legend(labels.split(';'), fontsize=20)
elif len(acq_names) > 1:
ax['err'].legend(acq_names, fontsize=20)
ax['dist'].legend(acq_names, fontsize=20)
# save it in the last directory... (if there are multiple directories)
if not plot_wall_time:
if n_repeat >= 0:
print 'Made a plot with %d repeats and %d iterations' % (n_repeat,
n_iter)
else:
print 'Made a plot with %d iterations' % (n_iter)
else:
if n_repeat >= 0:
print 'Made a plot with %d repeats and %f minutes' % (n_repeat,
max(iters))
else:
print 'Made a plot with %f minutes' % (max(iters))
file_prefix = '%s_' % average if n_repeat > 0 else ''
file_postfix = '_wall_time' if plot_wall_time else ''
fig['err'].tight_layout()
figname = os.path.join(plots_dir,
'%serror%s' % (file_prefix, file_postfix))
fig['err'].savefig(figname + '.pdf')
fig['err'].savefig(figname + '.svg')
print 'Saved to %s' % figname
if make_dist_plot:
fig['dist'].tight_layout()
figname_dist = os.path.join(
plots_dir, '%sl2_distance%s.pdf' % (file_prefix, file_postfix))
fig['dist'].savefig(figname_dist)
print 'Saved to %s' % figname_dist
def main(expt_dir):
os.chdir(expt_dir)
sys.path.append(expt_dir)
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment-name"]
# main_file = options['main_file']
main_file = 'wrapper'
if main_file[-3:] == '.py':
main_file = main_file[:-3]
module = __import__(main_file)
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
objective = parse_tasks_from_jobs(jobs, experiment_name, options,
input_space).values()[0]
def create_fun(task):
def fun(params, gradient=False):
if len(params.shape) > 1 and params.shape[1] > 1:
values = np.zeros(params.shape[0])
params_orig = params
for i in range(params_orig.shape[0]):
param = params[i, :]
param = param.flatten()
param = input_space.from_unit(np.array([param])).flatten()
values[i] = module.main(
0, paramify_no_types(input_space.paramify(param)))
else:
return module.main(
0, paramify_no_types(input_space.paramify(params)))
return values
return fun
fun = create_fun(objective)
# We iterate through each recommendation made
i = 0
more_recommendations = True
while more_recommendations:
recommendation = db.load(experiment_name, 'recommendations',
{'id': i + 1})
if recommendation == None:
more_recommendations = False
else:
solution_om = input_space.vectorify(recommendation['params_om'])
M = 1
vsom_acum = 0.0
for j in range(M):
vsom_acum += fun(solution_om, gradient=False)['score']
values_solution_om = -vsom_acum / float(M)
with open('value_solution_om.txt', 'a') as f:
print >> f, "%lf" % (values_solution_om)
with open('params_om.txt', 'a') as f_handle:
np.savetxt(f_handle,
np.array([solution_om]),
delimiter=' ',
newline='\n')
i += 1
def main(filter=None):
"""
Usage: python make_plots.py PATH_TO_DIRECTORY
"""
parser = argparse.ArgumentParser()
parser.add_argument('--clean', action='store_true', help='remove broken jobs')
parser.add_argument('--table', action='store_true', help='print table')
parser.add_argument('--csv', action='store_true', help='save table as csv')
parser.add_argument('--d', type=int, help='sort by distance from dth smallest result')
parser.add_argument('--name', help='experiment name', default=None)
args, unknown = parser.parse_known_args()
options, expt_dir = get_options(unknown)
# print "options:"
# print_dict(options)
# reduce the grid size
options["grid_size"] = 400
resources = parse_resources_from_config(options)
# Load up the chooser.
chooser_module = importlib.import_module('spearmint.choosers.' + options['chooser'])
chooser = chooser_module.init(options)
# print "chooser", chooser
if args.name:
experiment_name = args.name
else:
experiment_name = options.get("experiment-name", 'unnamed-experiment')
# Connect to the database
db_address = options['database']['address']
# sys.stderr.write('Using database at %s.\n' % db_address)
db = MongoDB(database_address=db_address)
# testing below here
jobs = load_jobs(db, experiment_name)
print len(jobs), 'jobs found'
# print jobs
# remove_broken_jobs
if args.clean:
for job in jobs:
if job['status'] == 'pending':
sys.stderr.write('Broken job %s detected.\n' % job['id'])
job['status'] = 'broken'
db.save(job, experiment_name, 'jobs', {'id' : job['id']})
# print "resources:", resources
# print_dict(resources)
resource = resources.itervalues().next()
task_options = {task: options["tasks"][task] for task in resource.tasks}
# print "task_options:"
# print_dict(task_options) # {'main': {'likelihood': u'NOISELESS', 'type': 'OBJECTIVE'}}
task_group = load_task_group(db, options, experiment_name, resource.tasks)
hypers = load_hypers(db, experiment_name)
chooser.fit(task_group, hypers, task_options)
lp, x = chooser.best()
if args.table:
os.chdir(unknown[0])
out_file = open('results.csv', 'w') if args.csv else sys.stdout
# get the observed points
task = task_group.tasks.itervalues().next()
idata = task.valid_normalized_data_dict
inputs = idata["inputs"]
inputs = map(lambda i: [paramify(task_group, task_group.from_unit(i)).values(), i], inputs)
vals = idata["values"]
vals = [task.unstandardize_mean(task.unstandardize_variance(v)) for v in vals]
out_file.write('\n%10s' % 'result')
lengths = [10]
for name, vdict in task.variables_meta.iteritems():
name = '%10s' % name
out_file.write(',' + name)
lengths.append(len(name))
out_file.write('\n')
line_template = '%' + str(lengths[0]) + '.4f,' + ','.join(['%' + str(l) +
('.4f' if 'enum' not in inputs[0][0][i]['type'] else 's') for i, l in enumerate(lengths[1:])])
points = sorted(zip(vals, inputs), key=lambda r: r[0])
if args.d is not None:
target = x
if args.d >= 0:
target = points[args.d][1][1]
points = sorted(points, key=lambda r: np.linalg.norm(r[1][1] - target))
for i, point in enumerate(points):
subs = [point[0]] + [d['values'][0] for d in point[1][0]]
out_file.write(line_template % tuple(subs) + '\n')
out_file.close()
def main(expt_dir):
os.chdir(expt_dir)
sys.path.append(expt_dir)
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment-name"]
options['main_file'] = 'prog_no_noisy'
main_file = options['main_file']
if main_file[-3:] == '.py':
main_file = main_file[:-3]
module = __import__(main_file)
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' + options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
tasks = parse_tasks_from_jobs(jobs, experiment_name, options, input_space)
if len(tasks) < 2:
print 'Not a multi-objective problem!'
return -1
if options['language'] != "PYTHON":
print 'Only python programs supported!'
return -1
for task in tasks:
if tasks[ task ].type != 'objective':
print 'Not a multi-objective problem!'
return -1
def create_fun(task):
def fun(params, gradient = False):
if len(params.shape) > 1 and params.shape[ 1 ] > 1:
params = params.flatten()
params = input_space.from_unit(np.array([ params ])).flatten()
return module.main(0, paramify_no_types(input_space.paramify(params)))[ task ]
return fun
funs = [ create_fun(task) for task in tasks ]
moop = MOOP_basis_functions(funs, input_space.num_dims)
# moop.evolve(1, 8)
grid = sobol_grid.generate(input_space.num_dims, grid_size = 1000 * input_space.num_dims)
moop.solve_using_grid(grid)
# reference = find_reference_point_using_direct(tasks, module, input_space)
# reference = reference + np.abs(reference) * 0.1
reference = np.ones(len(tasks)) * 7
hyper_volume_solution = moop.get_hypervolume(reference.tolist())
result = moop.compute_pareto_front_and_set()
front = result['frontier']
pareto_set = result['pareto_set']
# os.remove('hypervolume_solution.txt')
with open('hypervolume_solution.txt', 'a') as f:
print >> f, "%lf" % (hyper_volume_solution)
# os.remove('hypervolumes.txt')
# We iterate through each recommendation made
i = 0
more_recommendations = True
while more_recommendations:
recommendation = db.load(experiment_name, 'recommendations', {'id' : i + 1})
if recommendation == None:
more_recommendations = False
else:
solution = input_space.to_unit(input_space.vectorify(recommendation[ 'params' ]))
if len(solution.shape) == 1:
solution = solution.reshape((1, len(solution)))
# We compute the objective values associated to this recommendation
values_solution = np.zeros((solution.shape[ 0 ], len(tasks)))
for j in range(values_solution.shape[ 0 ]):
for k in range(values_solution.shape[ 1 ]):
values_solution[ j, k ] = funs[ k ](solution[ j : (j + 1), : ])
moop = MOOP_basis_functions(funs, input_space.num_dims)
moop.set_population(solution)
hyper_volume = moop.get_hypervolume(reference.tolist())
with open('hypervolumes.txt', 'a') as f:
print >> f, "%lf" % (hyper_volume)
with open('mean_min_distance_to_frontier.txt', 'a') as f:
print >> f, "%lf" % (average_min_distance(values_solution, front))
with open('mean_min_distance_from_frontier.txt', 'a') as f:
print >> f, "%lf" % (average_min_distance(front, values_solution))
with open('mean_min_distance_to_pareto_set.txt', 'a') as f:
print >> f, "%lf" % (average_min_distance(input_space.from_unit(solution), \
input_space.from_unit(pareto_set)))
with open('mean_min_distance_from_pareto_set.txt', 'a') as f:
print >> f, "%lf" % (average_min_distance(input_space.from_unit(pareto_set), \
input_space.from_unit(solution)))
with open('evaluations.txt','a') as f_handle:
np.savetxt(f_handle, np.array([recommendation['num_complete_tasks'].values()]), delimiter = ' ', newline = '\n')
i += 1
def main():
"""
Usage: python make_plots.py PATH_TO_DIRECTORY
TODO: Some aspects of this function are specific to the simple branin example
We should clean this up so that interpretation of plots are more clear and
so that it works in more general cases
(e.g. if objective likelihood is binomial then values should not be
unstandardized)
"""
options, expt_dir = get_options()
print("options:")
print_dict(options)
# reduce the grid size
options["grid_size"] = 400
resources = parse_resources_from_config(options)
# Load up the chooser.
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(options)
print("chooser", chooser)
experiment_name = options.get("experiment-name", 'unnamed-experiment')
# Connect to the database
db_address = options['database']['address']
sys.stderr.write('Using database at %s.\n' % db_address)
db = MongoDB(database_address=db_address)
# testing below here
jobs = load_jobs(db, experiment_name)
remove_broken_jobs(db, jobs, experiment_name, resources)
print("resources:", resources)
print_dict(resources)
resource = resources.itervalues().next()
task_options = {task: options["tasks"][task] for task in resource.tasks}
print("task_options:")
print_dict(task_options
) # {'main': {'likelihood': u'NOISELESS', 'type': 'OBJECTIVE'}}
task_group = load_task_group(db, options, resource.tasks)
print("task_group", task_group) # TaskGroup
print("tasks:")
print_dict(task_group.tasks
) # {'main': <spearmint.tasks.task.Task object at 0x10bf63290>}
hypers = load_hypers(db, experiment_name)
print("loaded hypers", hypers) # from GP.to_dict()
hypers = chooser.fit(task_group, hypers, task_options)
print("\nfitted hypers:")
print_dict(hypers)
lp, x = chooser.best()
x = x.flatten()
print("best", lp, x)
bestp = task_group.paramify(task_group.from_unit(x))
print("expected best position", bestp)
# get the grid of points
grid = chooser.grid
# print("chooser objectives:", )
# print_dict(chooser.objective)
print("chooser models:", chooser.models)
print_dict(chooser.models)
obj_model = chooser.models[chooser.objective['name']]
obj_mean, obj_var = obj_model.function_over_hypers(obj_model.predict, grid)
# un-normalize the function values and variances
obj_task = task_group.tasks['main']
obj_mean = [
obj_task.unstandardize_mean(obj_task.unstandardize_variance(v))
for v in obj_mean
]
obj_std = [obj_task.unstandardize_variance(np.sqrt(v)) for v in obj_var]
# for xy, m, v in izip(grid, obj_mean, obj_var):
# print(xy, m, v)
grid = map(task_group.from_unit, grid)
# return
xymv = [(xy[0], xy[1], m, v) for xy, m, v in izip(grid, obj_mean, obj_std)
] # if .2 < xy[0] < .25]
x = map(lambda x: x[0], xymv)
y = map(lambda x: x[1], xymv)
m = map(lambda x: x[2], xymv)
sig = map(lambda x: x[3], xymv)
# print(y)
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111, projection='3d')
ax.plot(x, y, m, marker='.', linestyle="None")
# plot errorbars
for i in np.arange(0, len(x)):
ax.plot([x[i], x[i]], [y[i], y[i]], [m[i] + sig[i], m[i] - sig[i]],
marker="_",
color='k')
# get the observed points
task = task_group.tasks['main']
idata = task.valid_normalized_data_dict
xy = idata["inputs"]
xy = map(task_group.from_unit, xy)
xy = np.array(xy)
vals = idata["values"]
vals = [
obj_task.unstandardize_mean(obj_task.unstandardize_variance(v))
for v in vals
]
ax.plot(xy[:, 0], xy[:, 1], vals, marker='o', color="r", linestyle="None")
plt.show()
def main(expt_dir, repeat=None):
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment-name"]
if repeat is not None:
experiment_name = repeat_experiment_name(experiment_name,repeat)
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' + options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
if input_space.num_dims != 2:
raise Exception("This plotting script is only for 2D optimizations. This problem has %d dimensions." % input_space.num_dims)
tasks = parse_tasks_from_jobs(jobs, experiment_name, options, input_space)
hypers = chooser.fit(tasks, hypers)
print '\nHypers:'
print_hypers(hypers)
recommendation = chooser.best()
current_best_value = recommendation['model_model_value']
current_best_location = recommendation['model_model_input']
plots_dir = os.path.join(expt_dir, 'plots')
if not os.path.isdir(plots_dir):
os.mkdir(plots_dir)
if len(chooser.models) > 1:
for task_name in chooser.models:
plots_subdir = os.path.join(plots_dir, task_name)
if not os.path.isdir(plots_subdir):
os.mkdir(plots_subdir)
print 'Plotting...'
# Plot objective model
# plot_2d_mean_and_var(chooser.objective_model, plots_dir,
# chooser.objective.name,
# input_space, current_best_location)
# plot_hypers(chooser.objective_model, plots_dir, 'objective_function')
for task_name, model in chooser.models.iteritems():
plots_subdir = os.path.join(plots_dir, task_name) if len(chooser.models) > 1 else plots_dir
plot_hypers(model, plots_subdir, task_name)
plot_2d_mean_and_var(model, plots_subdir, task_name, input_space, current_best_location)
if chooser.numConstraints() > 0:
plot_2d_constraints(chooser, plots_dir, input_space, current_best_location)
plot_acquisition_function(chooser, plots_dir, input_space, current_best_location, current_best_value)
print 'Done plotting.'
def runSpearmint(self, name):
options, expt_dir = self.get_options([os.path.abspath(os.path.join(self.scratchPath,name))])
resources = main.parse_resources_from_config(options)
# Load up the chooser.
chooser_module = importlib.import_module('spearmint.choosers.' + options['chooser'])
chooser = chooser_module.init(options)
experiment_name = options.get("experiment-name", 'unnamed-experiment')
# Connect to the database
db_address = options['database']['address']
sys.stderr.write('Using database at %s.\n' % db_address)
db = MongoDB(database_address=db_address)
threshold = 1e-2
look_back = 3
stopping = False
while not stopping:
for resource_name, resource in resources.iteritems():
jobs = main.load_jobs(db, experiment_name)
# resource.printStatus(jobs)
# If the resource is currently accepting more jobs
# TODO: here cost will eventually also be considered: even if the
# resource is not full, we might wait because of cost incurred
# Note: I chose to fill up one resource and them move on to the next
# You could also do it the other way, by changing "while" to "if" here
while resource.acceptingJobs(jobs):
# Load jobs from DB
# (move out of one or both loops?) would need to pass into load_tasks
jobs = main.load_jobs(db, experiment_name)
#pprint.pprint(main.load_hypers(db, experiment_name))
# Remove any broken jobs from pending.
main.remove_broken_jobs(db, jobs, experiment_name, resources)
# Get a suggestion for the next job
suggested_job = main.get_suggestion(chooser, resource.tasks, db, expt_dir, options, resource_name)
# Submit the job to the appropriate resource
process_id = resource.attemptDispatch(experiment_name, suggested_job, db_address, expt_dir)
# Set the status of the job appropriately (successfully submitted or not)
if process_id is None:
suggested_job['status'] = 'broken'
main.save_job(suggested_job, db, experiment_name)
else:
suggested_job['status'] = 'pending'
suggested_job['proc_id'] = process_id
main.save_job(suggested_job, db, experiment_name)
jobs = main.load_jobs(db, experiment_name)
# Print out the status of the resources
# resource.printStatus(jobs)
print_resources_status(resources.values(), jobs)
stalled = []
for task in main.load_task_group(db, options, resource.tasks).tasks.values():
performance = task.valid_normalized_data_dict["values"][::-1]
stalled.append(0)
if len(performance) > look_back:
print performance[0:look_back]
print "Diffs: ",
within_thresh = True
for i,run in enumerate(performance[0:look_back]):
diff = abs(run - performance[i+1])
print str(round(diff,2))+", ",
if diff > threshold:
within_thresh = False
print "...No stall"
break
if within_thresh:
stalled[len(stalled)-1] = 1
if all(stalled):
sys.exit("Stalled!")
# If no resources are accepting jobs, sleep
# (they might be accepting if suggest takes a while and so some jobs already finished by the time this point is reached)
if main.tired(db, experiment_name, resources):
time.sleep(options.get('polling-time', 5))
def main(expt_dir):
os.chdir(expt_dir)
sys.path.append(expt_dir)
options = parse_config_file(expt_dir, 'config.json')
experiment_name = options["experiment-name"]
# main_file = options['main_file']
main_file = 'OSY_no_noisy'
if main_file[-3:] == '.py':
main_file = main_file[:-3]
module = __import__(main_file)
input_space = InputSpace(options["variables"])
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(input_space, options)
db = MongoDB(database_address=options['database']['address'])
jobs = load_jobs(db, experiment_name)
hypers = db.load(experiment_name, 'hypers')
tasks = parse_tasks_from_jobs(jobs, experiment_name, options, input_space)
if len(tasks) < 2:
print 'Not a multi-objective problem!'
return -1
if options['language'] != "PYTHON":
print 'Only python programs supported!'
return -1
objectives = dict()
contraints = dict()
for task in tasks:
if tasks[task].type == 'objective':
objectives[task] = tasks[task]
else:
contraints[task] = tasks[task]
assert len(objectives) >= 2 and len(contraints) >= 1
def create_fun(task):
def fun(params, gradient=False):
if len(params.shape) > 1 and params.shape[1] > 1:
values = np.zeros(params.shape[0])
params_orig = params
for i in range(params_orig.shape[0]):
param = params[i, :]
param = param.flatten()
param = input_space.from_unit(np.array([param])).flatten()
values[i] = module.main(
0,
paramify_no_types(input_space.paramify(param)))[task]
else:
return module.main(
0, paramify_no_types(input_space.paramify(params)))[task]
return values
return fun
funs_o = [create_fun(task) for task in objectives]
funs_c = [create_fun(task) for task in contraints]
moop = MOOP_basis_functions(funs_o,
input_space.num_dims,
constraints=funs_c)
grid = sobol_grid.generate(input_space.num_dims,
grid_size=1000 * input_space.num_dims)
# We only retain the feasible points
moop.solve_using_grid(grid)
reference = np.ones(len(objectives)) * 1e3
hyper_volume_solution = moop.get_hypervolume(reference.tolist())
result = moop.compute_pareto_front_and_set()
front = result['frontier']
pareto_set = result['pareto_set']
with open('hypervolume_solution.txt', 'a') as f:
print >> f, "%lf" % (hyper_volume_solution)
# We iterate through each recommendation made
i = 0
more_recommendations = True
while more_recommendations:
recommendation = db.load(experiment_name, 'recommendations',
{'id': i + 1})
if recommendation == None:
more_recommendations = False
else:
solution = input_space.to_unit(
input_space.vectorify(recommendation['params']))
if len(solution.shape) == 1:
solution = solution.reshape((1, len(solution)))
# We compute the objective values associated to this recommendation
values_solution = np.zeros((solution.shape[0], len(objectives)))
for j in range(values_solution.shape[0]):
for k in range(values_solution.shape[1]):
values_solution[j, k] = funs_o[k](solution[j:(j + 1), :])
moop = MOOP_basis_functions(funs_o, input_space.num_dims)
moop.set_population(solution)
hyper_volume = moop.get_hypervolume(reference.tolist())
# We make sure that there are no infeasible points recommended
# If there are infeasible recommendations we return 0 as the hypervolume
all_feasible = True
for k in range(len(funs_c)):
all_feasible = all_feasible and not np.any(
funs_c[k](solution) < 0)
if not all_feasible:
hyper_volume = 0.0
with open('hypervolumes.txt', 'a') as f:
print >> f, "%lf" % (hyper_volume)
with open('evaluations.txt', 'a') as f_handle:
np.savetxt(
f_handle,
np.array([recommendation['num_complete_tasks'].values()]),
delimiter=' ',
newline='\n')
i += 1
def plot(
config_directory="/home/carrknight/code/oxfish/runs/optimization/spearmint"
):
os.chdir("/home/carrknight/code/oxfish/runs/optimization/spearmint")
options = get_options(config_directory, config_file="config.json")
experiment_name = str(options['experiment-name'])
db = MongoDB()
resources = parse_resources_from_config(options)
resource = resources.itervalues().next()
# load hyper parameters
chooser_module = importlib.import_module('spearmint.choosers.' +
options['chooser'])
chooser = chooser_module.init(options)
print "chooser", chooser
hypers = db.load(experiment_name, "hypers")
print "loaded hypers", hypers # from GP.to_dict()
jobs = load_jobs(db, experiment_name)
remove_broken_jobs(db, jobs, experiment_name, resources)
task_options = {task: options["tasks"][task] for task in resource.tasks}
task_group = spearmint.main.load_task_group(db, options, resource.tasks)
hypers = spearmint.main.load_hypers(db, experiment_name)
print "loaded hypers", hypers # from GP.to_dict()
hypers = chooser.fit(task_group, hypers, task_options)
print "\nfitted hypers:"
print(hypers)
lp, x = chooser.best()
x = x.flatten()
print "best", lp, x
bestp = task_group.paramify(task_group.from_unit(x))
print "expected best position", bestp
print "chooser models:", chooser.models
obj_model = chooser.models[chooser.objective['name']]
grid = chooser.grid
obj_mean, obj_var = obj_model.function_over_hypers(obj_model.predict, grid)
import numpy as np
bounds = dict()
for task_name, task in task_group.tasks.iteritems():
# make a grid, feed it to the predictor:
dimensions = ()
for key in options['variables'].keys():
type = str(options['variables'][key]["type"]).strip().lower()
keyname = key.encode('utf-8')
bounds[keyname] = dict()
bounds[keyname]["type"] = type
if type == "float":
dimension = np.linspace(0, 1, num=SPACING)
dimensions = dimensions + (dimension, )
bounds[keyname]["min"] = options['variables'][key]["min"]
bounds[keyname]["max"] = options['variables'][key]["max"]
elif type == "int":
min = int(options['variables'][key]["min"])
max = int(options['variables'][key]["max"])
dimension = np.linspace(0, 1, num=max - min)
bounds[keyname]["min"] = min
bounds[keyname]["max"] = max
# dimension = np.array([x + min for x in range(max - min + 1)])
dimensions = dimensions + (dimension, )
else:
bounds[keyname]["options"] = options['variables'][key][
"options"]
assert type == "enum"
dimension = tuple([
(0, 1)
for i in range(len(options['variables'][key]["options"]))
])
for t in dimension:
dimensions = dimensions + (t, )
# print(dimension)
data = cartesian(np.array(dimensions))
mean, variance = chooser.models[task_name].predict(data)
mean = [
task.unstandardize_mean(task.unstandardize_variance(v))
for v in mean
]
variance = [task.unstandardize_variance(np.sqrt(v)) for v in variance]
os.chdir(config_directory)
# unzip the data
new_data = zip(*data.transpose().tolist())
datum = zip(new_data, mean, variance)
header = ",".join(options['variables'].keys()) + ",mean,variance"
with open(experiment_name + ".csv", 'w') as fileout:
fileout.write(header + "\n")
for i in range(len(datum)):
fileout.write(
str(datum[i]).replace("(", "").replace(")", "").replace(
",,", ",") + "\n")
with open(experiment_name + "_bounds.yaml", 'w') as outfile:
outfile.write(yaml.dump(bounds, default_flow_style=False))
# grid = cartesian(dimensions)
# mean, variance = obj_model.function_over_hypers(obj_model.predict, grid)
#
# mean = [obj_task.unstandardize_mean(obj_task.unstandardize_variance(v)) for v in mean]
# variance = [obj_task.unstandardize_variance(np.sqrt(v)) for v in variance]
#
# # xymv = [([x for x in xy], m, v) for xy, m, v in izip(new_grid, obj_mean, obj_std)] # if .2 < xy[0] < .25]
# with open(experiment_name + ".csv", 'w') as fileout:
# for i in range(len(mean)):
# fileout.write(str(([x for x in grid[i]], mean[i], variance[i])).replace("(", "").replace(")", "").
# replace("[", "").replace("]", "") + "\n")
xy = np.array(task.inputs)
# function values:
vals = task.values
vals = np.array(vals)
np.savetxt(experiment_name + "_" + task_name + "_runs.csv",
xy,
delimiter=",",
fmt='%.3e')
np.savetxt(experiment_name + "_" + task_name + "_runs_values.csv",
vals,
delimiter=",",
fmt='%.3e')
