def get_input_fields(resource, referrer=None):
"""New list of input fields
"""
if referrer is None:
referrer = {}
input_fields_ids = resource.get('input_fields', [])
if referrer:
referrer_input_fields = [[]]
# compare fields by name
resource_fields = Fields({
'resource': resource['resource'],
'object': resource
})
referrer_fields = Fields({
'resource': referrer['resource'],
'object': referrer
})
input_fields = [
resource_fields.field_name(field_id)
for field_id in input_fields_ids
]
input_fields = sorted(input_fields)
referrer_type = get_resource_type(referrer)
if referrer_type == 'dataset':
referrer_fields = Fields(referrer_fields.preferred_fields())
referrer_fields_names = sorted( \
[field['name'] for _, field in referrer_fields.fields.items()])
else:
referrer_fields_names = sorted( \
referrer_fields.fields_by_name.keys())
# check referrer input fields to see if they are equal
referrer_input_fields.append(referrer_fields_names)
# check whether the resource has an objective field not included in
# the input fields list
resource_type = get_resource_type(resource)
if resource_type == 'model':
objective_id = resource.get('objective_field')
try:
objective_id = objective_id.get('id')
except AttributeError:
pass
referrer_objective = resource_fields.field_name(objective_id)
referrer_input_fields.append([
name for name in referrer_fields_names
if name != referrer_objective
])
if input_fields in referrer_input_fields:
return []
return referrer_fields.fields.keys()
def get_input_fields(resource, referrer=None):
"""New list of input fields
"""
if referrer is None:
referrer = {}
input_fields_ids = resource.get('input_fields', [])
if referrer:
referrer_input_fields = [[]]
# compare fields by name
resource_fields = Fields(
{'resource': resource['resource'], 'object': resource})
referrer_fields = Fields(
{'resource': referrer['resource'], 'object': referrer})
input_fields = [resource_fields.field_name(field_id) for field_id in
input_fields_ids]
input_fields = sorted(input_fields)
referrer_type = get_resource_type(referrer)
if referrer_type == 'dataset':
referrer_fields = Fields(referrer_fields.preferred_fields())
referrer_fields_names = sorted( \
[field['name'] for _, field in referrer_fields.fields.items()])
else:
referrer_fields_names = sorted( \
referrer_fields.fields_by_name.keys())
# check referrer input fields to see if they are equal
referrer_input_fields.append(referrer_fields_names)
# check whether the resource has an objective field not included in
# the input fields list
resource_type = get_resource_type(resource)
if resource_type == 'model':
objective_id = resource.get('objective_field')
try:
objective_id = objective_id.get('id')
except AttributeError:
pass
referrer_objective = resource_fields.field_name(
objective_id)
referrer_input_fields.append([name for name in
referrer_fields_names
if name != referrer_objective])
if input_fields in referrer_input_fields:
return []
return referrer_fields.fields.keys()
def reify_dataset(self, resource_id):
"""Extracts the REST API arguments from the dataset JSON structure
"""
child = self.get_resource(resource_id)
origin, parent_id = u.get_origin_info(child)
parent = self.get_resource(parent_id)
opts = {"create": {}, "update": {}, "get": {}}
# as two-steps result from a cluster or batch prediction, centroid
# or anomaly score
grandparent = parent
if origin in ['origin_batch_resource', 'cluster']:
if origin == "cluster":
opts['create'].update({"centroid": child['centroid']})
grandparents = u.get_origin_info(parent)
# batch resources have two parents, choose the dataset
if origin == "origin_batch_resource" and \
isinstance(grandparents, list):
for gp_origin, grandparent in grandparents:
if gp_origin == "dataset":
break
else:
_, grandparent = grandparents
grandparent = self.get_resource(grandparent)
# options common to all model types
call = "update" if origin == "origin_batch_resource" else "create"
u.common_dataset_opts(child, grandparent, opts, call=call)
# update options
dataset_defaults = DEFAULTS["dataset"].get("update", {})
for attribute, default_value in dataset_defaults.items():
opts["update"].update(
u.default_setting(child, attribute, *default_value))
# name, exclude automatic naming alternatives
autonames = [u'']
u.non_automatic_name(child, opts, autonames=autonames)
# objective field
resource_fields = Fields({
'resource': child['resource'],
'object': child
})
objective_id = child['objective_field']['id']
preferred_fields = resource_fields.preferred_fields()
# if there's no preferred fields, use the fields structure
if len(preferred_fields.keys()) == 0:
preferred_fields = resource_fields.fields
max_column = sorted([
field['column_number'] for _, field in preferred_fields.items()
if field['optype'] != "text"
],
reverse=True)[0]
objective_column = resource_fields.fields[objective_id][ \
'column_number']
if objective_column != max_column:
opts['create'].update({"objective_field": {"id": objective_id}})
if origin != "origin_batch_resource":
# resize
if (child['size'] != grandparent['size']
and get_resource_type(parent) == 'source'):
opts['create'].update({"size": child['size']})
# generated fields
if child.get('new_fields', None):
new_fields = child['new_fields']
for new_field in new_fields:
new_field['field'] = new_field['generator']
del new_field['generator']
opts['create'].update({"new_fields": new_fields})
u.range_opts(child, grandparent, opts)
# for batch_predictions, batch_clusters, batch_anomalies generated
# datasets, attributes cannot be set at creation time, so we
# must update the resource instead
suffix = None
if origin == "origin_batch_resource":
opts["update"].update(opts["create"])
opts["create"] = {}
suffix = "['object']['output_dataset_resource']"
calls = u.build_calls(resource_id, [parent_id], opts, suffix=suffix)
self.add(resource_id, calls)
dataset = json.loads(dataset_handler.read())
except IOError:
dataset = api.check_resource(dataset_id,
query_string=ALL_FIELDS_QS)
# initial feature set
fields = Fields(dataset)
excluded_features = ([] if args.exclude_features is None else
args.exclude_features.split(
args.args_separator))
try:
excluded_ids = [fields.field_id(feature) for
feature in excluded_features]
objective_id = fields.field_id(objective_name)
except ValueError, exc:
sys.exit(exc)
field_ids = [field_id for field_id in fields.preferred_fields()
if field_id != objective_id and
not field_id in excluded_ids]
# headers are extended with a column per field
fields_names = [fields.field_name(field_id) for field_id in field_ids]
features_header.extend(fields_names)
features_writer.writerow(features_header)
initial_state = [False for field_id in field_ids]
open_list = [(initial_state, - float('inf'), -float('inf'), 0)]
closed_list = []
best_state, best_score, best_metric_value, best_counter = open_list[0]
best_unchanged_count = 0
metric = args.optimize
while best_unchanged_count < staleness and open_list:
loop_counter += 1
features_set = find_max_state(open_list)
dataset = json.loads(dataset_handler.read())
except IOError:
dataset = api.check_resource(dataset_id, query_string=ALL_FIELDS_QS)
# initial feature set
fields = Fields(dataset)
excluded_features = ([] if args.exclude_features is None else
args.exclude_features.split(args.args_separator))
try:
excluded_ids = [
fields.field_id(feature) for feature in excluded_features
]
objective_id = fields.field_id(objective_name)
except ValueError, exc:
sys.exit(exc)
field_ids = [
field_id for field_id in fields.preferred_fields()
if field_id != objective_id and not field_id in excluded_ids
]
field_ids.sort()
# headers are extended with a column per field
fields_names = [fields.field_name(field_id) for field_id in field_ids]
features_header.extend(fields_names)
features_writer.writerow(features_header)
initial_state = [False for field_id in field_ids]
open_list = [(initial_state, -float('inf'), -float('inf'), 0)]
closed_list = []
best_state, best_score, best_metric_value, best_counter = open_list[0]
best_unchanged_count = 0
metric = args.optimize
while best_unchanged_count < staleness and open_list:
loop_counter += 1
def reify_dataset(self, resource_id):
"""Extracts the REST API arguments from the dataset JSON structure
"""
child = self.get_resource(resource_id)
origin, parent_id = u.get_origin_info(child)
parent = self.get_resource(parent_id)
opts = {"create": {}, "update": {}, "get": {}}
# as two-steps result from a cluster or batch prediction, centroid
# or anomaly score
grandparent = parent
if origin in ['origin_batch_resource', 'cluster']:
if origin == "cluster":
opts['create'].update({"centroid": child['centroid']})
grandparents = u.get_origin_info(parent)
# batch resources have two parents, choose the dataset
if origin == "origin_batch_resource" and \
isinstance(grandparents, list):
for gp_origin, grandparent in grandparents:
if gp_origin == "dataset":
break
else:
_, grandparent = grandparents
grandparent = self.get_resource(grandparent)
# options common to all model types
call = "update" if origin == "origin_batch_resource" else "create"
u.common_dataset_opts(child, grandparent, opts, call=call)
# update options
dataset_defaults = DEFAULTS["dataset"].get("update", {})
for attribute, default_value in dataset_defaults.items():
opts["update"].update(
u.default_setting(child, attribute, *default_value))
# name, exclude automatic naming alternatives
autonames = [u'']
u.non_automatic_name(child, opts, autonames=autonames)
# objective field
resource_fields = Fields(
{'resource': child['resource'], 'object': child})
objective_id = child['objective_field']['id']
preferred_fields = resource_fields.preferred_fields()
# if there's no preferred fields, use the fields structure
if len(preferred_fields.keys()) == 0:
preferred_fields = resource_fields.fields
max_column = sorted([field['column_number']
for _, field in preferred_fields.items()
if field['optype'] != "text"],
reverse=True)[0]
objective_column = resource_fields.fields[objective_id][ \
'column_number']
if objective_column != max_column:
opts['create'].update({"objective_field": {"id": objective_id}})
if origin != "origin_batch_resource":
# resize
if (child['size'] != grandparent['size'] and
get_resource_type(parent) == 'source'):
opts['create'].update({"size": child['size']})
# generated fields
if child.get('new_fields', None):
new_fields = child['new_fields']
for new_field in new_fields:
new_field['field'] = new_field['generator']
del new_field['generator']
opts['create'].update({"new_fields": new_fields})
u.range_opts(child, grandparent, opts)
# for batch_predictions, batch_clusters, batch_anomalies generated
# datasets, attributes cannot be set at creation time, so we
# must update the resource instead
suffix = None
if origin == "origin_batch_resource":
opts["update"].update(opts["create"])
opts["create"] = {}
suffix = "['object']['output_dataset_resource']"
calls = u.build_calls(resource_id, [parent_id], opts, suffix=suffix)
self.add(resource_id, calls)
def reify_dataset(self, resource_id):
"""Extracts the REST API arguments from the dataset JSON structure
"""
child = self.get_resource(resource_id)
origin, parent_id = u.get_origin_info(child)
parent = self.get_resource(parent_id)
opts = {"create": {}, "update": {}}
# as two-steps result from a cluster or batch prediction, centroid
# or anomaly score
if origin in ["origin_batch_resource", "cluster"]:
if origin == "cluster":
opts["create"].update({"centroid": child["centroid"]})
_, grandparent = u.get_origin_info(parent)
grandparent = self.get_resource(grandparent)
else:
grandparent = parent
# options common to all model types
u.common_dataset_opts(child, grandparent, opts)
# update options
dataset_defaults = DEFAULTS["dataset"].get("update", {})
dataset_defaults.update(COMMON_DEFAULTS.get("update", {}))
for attribute, default_value in dataset_defaults.items():
opts["update"].update(u.default_setting(child, attribute, *default_value))
# name, exclude automatic naming alternatives
autonames = [u""]
suffixes = [
u"filtered",
u"sampled",
u"dataset",
u"extended",
u"- batchprediction",
u"- batchanomalyscore",
u"- batchcentroid",
u"- merged",
]
autonames.extend([u"%s %s" % (grandparent.get("name", ""), suffix) for suffix in suffixes])
autonames.append(u"%s's dataset" % ".".join(parent["name"].split(".")[0:-1]))
autonames.append(u"%s' dataset" % ".".join(parent["name"].split(".")[0:-1]))
autonames.append(u"Cluster %s - %s" % (int(child.get("centroid", "0"), base=16), parent["name"]))
autonames.append(u"Dataset from %s model - segment" % parent["name"])
u.non_automatic_name(child, opts, autonames=autonames)
# objective field
resource_fields = Fields({"resource": child["resource"], "object": child})
objective_id = child["objective_field"]["id"]
preferred_fields = resource_fields.preferred_fields()
max_column = sorted([field["column_number"] for _, field in preferred_fields.items()], reverse=True)[0]
objective_column = resource_fields.fields[objective_id]["column_number"]
if objective_column != max_column:
opts["create"].update({"objective_field": {"id": objective_id}})
# resize
if child["size"] != grandparent["size"] and get_resource_type(parent) == "source":
opts["create"].update({"size": child["size"]})
# generated fields
if child.get("new_fields", None):
new_fields = child["new_fields"]
for new_field in new_fields:
new_field["field"] = new_field["generator"]
del new_field["generator"]
opts["create"].update({"new_fields": new_fields})
u.range_opts(child, grandparent, opts)
calls = u.build_calls(resource_id, [parent_id], opts)
self.add(resource_id, calls)
def reify_dataset(self, resource_id):
"""Extracts the REST API arguments from the dataset JSON structure
"""
child = self.get_resource(resource_id)
origin, parent_id = u.get_origin_info(child)
parent = self.get_resource(parent_id)
opts = {"create": {}, "update": {}}
# as two-steps result from a cluster or batch prediction, centroid
# or anomaly score
if origin in ['origin_batch_resource', 'cluster']:
if origin == "cluster":
opts['create'].update({"centroid": child['centroid']})
_, grandparent = u.get_origin_info(parent)
grandparent = self.get_resource(grandparent)
else:
grandparent = parent
# options common to all model types
u.common_dataset_opts(child, grandparent, opts)
# update options
dataset_defaults = DEFAULTS["dataset"].get("update", {})
dataset_defaults.update(COMMON_DEFAULTS.get("update", {}))
for attribute, default_value in dataset_defaults.items():
opts["update"].update(
u.default_setting(child, attribute, *default_value))
# name, exclude automatic naming alternatives
autonames = [u'']
suffixes = [
u"filtered", u"sampled", u"dataset", u"extended",
u"- batchprediction", u"- batchanomalyscore", u"- batchcentroid",
u"- merged"
]
autonames.extend([
u'%s %s' % (grandparent.get('name', ''), suffix)
for suffix in suffixes
])
autonames.append(u"%s's dataset" %
'.'.join(parent['name'].split('.')[0:-1]))
autonames.append(u"%s' dataset" %
'.'.join(parent['name'].split('.')[0:-1]))
autonames.append(
u"Cluster %s - %s" %
(int(child.get('centroid', "0"), base=16), parent['name']))
autonames.append(u"Dataset from %s model - segment" % parent['name'])
u.non_automatic_name(child, opts, autonames=autonames)
# objective field
resource_fields = Fields({
'resource': child['resource'],
'object': child
})
objective_id = child['objective_field']['id']
preferred_fields = resource_fields.preferred_fields()
max_column = sorted(
[field['column_number'] for _, field in preferred_fields.items()],
reverse=True)[0]
objective_column = resource_fields.fields[objective_id][ \
'column_number']
if objective_column != max_column:
opts['create'].update({"objective_field": {"id": objective_id}})
# resize
if (child['size'] != grandparent['size']
and get_resource_type(parent) == 'source'):
opts['create'].update({"size": child['size']})
# generated fields
if child.get('new_fields', None):
new_fields = child['new_fields']
for new_field in new_fields:
new_field['field'] = new_field['generator']
del new_field['generator']
opts['create'].update({"new_fields": new_fields})
u.range_opts(child, grandparent, opts)
calls = u.build_calls(resource_id, [parent_id], opts)
self.add(resource_id, calls)
def best_first_search(datasets_file, api, args, common_options,
staleness=None, penalty=None, objective_name=None,
resume=False):
"""Selecting the fields to be used in the model construction
"""
counter = 0
loop_counter = 0
features_file = os.path.normpath(os.path.join(args.output_dir,
FEATURES_LOG))
with open(features_file, 'w', 0) as features_handler:
features_writer = csv.writer(features_handler, lineterminator="\n")
features_writer.writerow([
"step", "state", "score", "metric_value", "best_score"])
features_handler.flush()
if staleness is None:
staleness = DEFAULT_STALENESS
if penalty is None:
penalty = DEFAULT_PENALTY
# retrieving the first dataset in the file
try:
with open(datasets_file) as datasets_handler:
dataset_id = datasets_handler.readline().strip()
except IOError, exc:
sys.exit("Could not read the generated datasets file: %s" %
str(exc))
dataset = api.check_resource(dataset_id, api.get_dataset)
# initial feature set
fields = Fields(dataset)
excluded_features = ([] if args.exclude_features is None else
args.exclude_features.split(
args.args_separator))
excluded_ids = [fields.field_id(feature) for
feature in excluded_features]
objective_id = fields.field_id(objective_name)
field_ids = [field_id for field_id in fields.preferred_fields()
if field_id != objective_id and
not field_id in excluded_ids]
initial_state = [False for field_id in field_ids]
open_list = [(initial_state, - float('inf'), -float('inf'))]
closed_list = []
best_state, best_score, best_metric_value = open_list[0]
best_unchanged_count = 0
metric = args.maximize
while best_unchanged_count < staleness and open_list:
loop_counter += 1
features_set = find_max_state(open_list)
state, score, metric_value = features_set
features_writer.writerow([
loop_counter, [int(in_set) for in_set in state],
score, metric_value, best_score])
features_handler.flush()
state_fields = [fields.field_name(field_ids[index])
for (index, in_set) in enumerate(state) if in_set]
closed_list.append(features_set)
open_list.remove(features_set)
if (score - EPSILON) > best_score:
best_state, best_score, best_metric_value = features_set
best_unchanged_count = 0
if state_fields:
message = 'New best state: %s\n' % (state_fields)
u.log_message(message, log_file=session_file,
console=args.verbosity)
if metric in PERCENT_EVAL_METRICS:
message = '%s = %0.2f%% (score = %s)\n' % (
metric.capitalize(), metric_value * 100, score)
else:
message = '%s = %f (score = %s)\n' % (
metric.capitalize(),metric_value, score)
u.log_message(message, log_file=session_file,
console=args.verbosity)
else:
best_unchanged_count += 1
children = expand_state(state)
for child in children:
if (child not in [state for state, _, _ in open_list] and
child not in [state for state, _, _ in closed_list]):
input_fields = [fields.field_name(field_id)
for (i, field_id)
in enumerate(field_ids) if child[i]]
# create models and evaluation with input_fields
args.model_fields = args.args_separator.join(input_fields)
counter += 1
(score,
metric_value,
metric,
resume) = kfold_evaluate(datasets_file,
args, counter, common_options,
penalty=penalty, resume=resume,
metric=metric)
open_list.append((child, score, metric_value))
best_features = [fields.field_name(field_ids[i]) for (i, score)
in enumerate(best_state) if score]
message = (u'The best feature subset is: %s \n'
% u", ".join(best_features))
u.log_message(message, log_file=session_file, console=1)
if metric in PERCENT_EVAL_METRICS:
message = (u'%s = %0.2f%%\n' % (metric.capitalize(),
(best_metric_value * 100)))
else:
message = (u'%s = %f\n' % (metric.capitalize(), best_metric_value))
u.log_message(message, log_file=session_file, console=1)
message = (u'Evaluated %d/%d feature subsets\n' %
((len(open_list) + len(closed_list)), 2 ** len(field_ids)))
u.log_message(message, log_file=session_file, console=1)
