def eval_recall5(imgs_enc, caps_enc):
imgs_enc = np.vstack(flatten(imgs_enc))
caps_enc = np.vstack(flatten(caps_enc))
res = avg_recall5(imgs_enc, caps_enc)
return res
def test_flatten(self):
ref = ['foo', 'bar', '123']
result = utils.flatten(ref)
self.assertEquals(ref, result)
result = utils.flatten(['foo', ['bar', '123']])
self.assertEquals(ref, result)
result = utils.flatten([['foo'], ['bar', '123']])
self.assertEquals(ref, result)
def test_flatten(self):
ref = ['foo', 'bar', '123']
result = utils.flatten(ref)
self.assertEquals(ref, result)
result = utils.flatten(['foo', ['bar', '123']])
self.assertEquals(ref, result)
result = utils.flatten([['foo'], ['bar', '123']])
self.assertEquals(ref, result)
def computeEvolutionRoc(temporalListLabels, predictions, classes = None, percentage = 0.001):
"""
Plots the evolution of the auc
Arguments:
temporalListLabels {List of (time, labels)*} -- Ground truth labels
predictions {Dict / List of labels} -- Predicitons (same format than labels in temporalListLabels)
classes {Dict} -- Classes to consider to plot (key: Name to display, Value: label)
percentage {float} -- Evaluate the TPR and TNR at this given value of FNR and FPR
"""
aucs = {}
for time, labels in temporalListLabels:
pred_time, labels_time = selection(predictions, labels, classes)
pred_time, labels_time = flatten(pred_time, labels_time)
fpr, tpr, _ = roc_curve(labels_time, pred_time)
fnr, tnr = (1 - tpr)[::-1], (1 - fpr)[::-1]
auc_time = auc(fpr, tpr)
wilson_tpr = 1.96 * np.sqrt(tpr * (1 - tpr)/len(predictions))
wilson_tnr = 1.96 * np.sqrt(tnr * (1 - tnr)/len(predictions))
aucs[time] = {
"auc": auc_time,
"lower": auc(fpr, tpr - wilson_tpr),
"upper": auc(fpr, tpr + wilson_tpr),
"tpr": np.interp(percentage, fpr, tpr),
"tpr_wilson" : np.interp(percentage, fpr, wilson_tpr),
"tnr": np.interp(percentage, fnr, tnr),
"tnr_wilson" : np.interp(percentage, fnr, wilson_tnr),
}
return pd.DataFrame.from_dict(aucs, orient = "index")
def fcn_G(input_dim, nn, imgsz, channels, requires_grad, depth=2):
def gen_block_params(ni, no):
return {'fc': utils.linear_params(ni, no),}
def gen_group_params(ni, no, count):
return {'block%d' % i: gen_block_params(ni if i == 0 else no, no) for i in range(count)}
flat_params = utils.cast(utils.flatten({
'group0': gen_group_params(input_dim, nn, depth),
'last_proj': utils.linear_params(nn, imgsz*imgsz*channels),
}))
if requires_grad:
utils.set_requires_grad_except_bn_(flat_params)
def block(x, params, base, mode):
return F.relu(F.linear(x, params[base+'.fc.weight'], params[base+'.fc.bias']), inplace=True)
def group(o, params, base, mode):
for i in range(depth):
o = block(o, params, '%s.block%d' % (base,i), mode)
return o
def f(input, params, mode):
o = group(input, params, 'group0', mode)
o = F.linear(o, params['last_proj.weight'], params['last_proj.bias'])
o = torch.tanh(o)
# o = o.view(o.size(0), channels, imgsz, imgsz)
o = o.reshape(o.size(0), channels, imgsz, imgsz)
return o
return f, flat_params
def graph_loss_tols(graph, i, o, filename=None):
"""
Gets all configurations graph pathfinding is loss tolerant to.
Exports output to file, if provided.
"""
print('\n graph_loss_tols \n')
nodes = set(graph.nodes()) - set([i, o])
all_tols = [[]]
loss_tol_nodes = set(nodes)
for r in range(1, len(nodes) + 1):
loss_configs = list(it.combinations(loss_tol_nodes, r))
loss_tol_nodes = set()
while loss_configs:
loss_config = loss_configs.pop()
lost_nodes = \
set(loss_config) | \
set(flatten(map(graph.neighbors, loss_config)))
loss_graph = deepcopy(graph)
loss_graph.remove_nodes_from(lost_nodes)
if i in loss_graph.nodes() and o in loss_graph.nodes() and \
nx.has_path(loss_graph, i, o):
loss_tol_nodes |= set(loss_config)
all_tols.append(list(loss_config))
if filename:
with open(filename, 'w') as fp:
json.dump(all_tols, fp)
return all_tols
def histPlot(predictions, truth, classes = None, label = "Model", newFigure = None, splitPosNeg = False, kde = False):
"""
Computes the histograms of a binary predictions
Arguments:
predictions {Dict / List} -- Label predictions
truth {Dict / List} -- Ground truth
classes {Dict "+":int, "-":int} -- Classes to consider to plot {Default None ie {+":1, "-":0}}
Keyword Arguments:
label {str} -- Legend to plot (default: {"Model"})
newFigure {str} -- Display on a given figure (default: {None} - Create new figure)
splitPosNeg {bool} -- Split between positive and negative (default: {False})
kde {bool} -- Computes the kde of the histogram (default: {False})
"""
predictions, truth = selection(predictions, truth, classes)
predictions, truth = flatten(predictions, truth)
bins = np.linspace(0, 1, 20)
if newFigure is not None:
plt.figure(newFigure)
else:
plt.xlabel('Predicted Probability')
plt.ylabel('Frequency')
plt.title('Histogram Probabilities')
if splitPosNeg:
sns.distplot(predictions[truth == 1], label=label + " Positive", kde = kde, bins = bins)
sns.distplot(predictions[truth == 0], label=label + " Negative", kde = kde, bins = bins)
else:
sns.distplot(predictions, label=label, kde = kde, bins = bins)
def dcganx_D(nn0, imgsz,
channels, # 1: gray-scale, 3: color
norm_type, # 'bn', 'none'
requires_grad,
depth=3, leaky_slope=0.2, nodemul=2, do_bias=True):
ker=5; padding=2
def gen_block_params(ni, no, k):
return {
'conv0': conv2d_params(ni, no, k, do_bias),
'conv1': conv2d_params(no, no, 1, do_bias),
'bn0': utils.bnparams(no) if norm_type == 'bn' else None,
'bn1': utils.bnparams(no) if norm_type == 'bn' else None
}
def gen_group_params(ni, no, count):
return {'block%d' % i: gen_block_params(ni if i == 0 else no, no, ker) for i in range(count)}
count = 1
sz = imgsz // (2**depth)
nn = nn0
p = { 'conv0': conv2d_params(channels, nn0, ker, do_bias) }
for d in range(depth-1):
p['group%d'%d] = gen_group_params(nn, nn*nodemul, count)
nn = nn*nodemul
p['fc'] = utils.linear_params(sz*sz*nn, 1)
flat_params = utils.cast(utils.flatten(p))
if requires_grad:
utils.set_requires_grad_except_bn_(flat_params)
def block(x, params, base, mode, stride):
o = F.conv2d(x, params[base+'.conv0.w'], params.get(base+'conv0.b'), stride=stride, padding=padding)
if norm_type == 'bn':
o = utils.batch_norm(o, params, base + '.bn0', mode)
o = F.leaky_relu(o, negative_slope=leaky_slope, inplace=True)
o = F.conv2d(o, params[base+'.conv1.w'], params.get(base+'conv1.b'), stride=1, padding=0)
if norm_type == 'bn':
o = utils.batch_norm(o, params, base + '.bn1', mode)
o = F.leaky_relu(o, negative_slope=leaky_slope, inplace=True)
return o
def group(o, params, base, mode, stride=2):
n = 1
for i in range(n):
o = block(o, params, '%s.block%d' % (base,i), mode, stride if i == 0 else 1)
return o
def f(input, params, mode):
o = F.conv2d(input, params['conv0.w'], params.get('conv0.b'), stride=2, padding=padding)
o = F.leaky_relu(o, negative_slope=leaky_slope, inplace=True)
for d in range(depth-1):
o = group(o, params, 'group%d'%d, mode)
o = o.view(o.size(0), -1)
o = F.linear(o, params['fc.weight'], params['fc.bias'])
return o
return f, flat_params
def import_loss_tols(in_file, filename=None):
""" Imports and formats loss tols for use. Exports to file, if provided """
with open(in_file, 'r') as fp:
data = json.load(fp)
max_tols = flatten(value for value in data.values())
all_tols = get_all_loss_tols(max_tols)
if filename:
with open(filename, 'w') as fp:
json.dump(all_tols, fp)
return all_tols
def most_common_mnt(avail_pats, qubit_key, measured):
""" Picks measurement that occurs most in the available patterns """
all_mnts = dict(Counter((q, mnt)
for mnt_pat in flatten(avail_pats.values())
for q, mnt in zip(qubit_key, mnt_pat)
if mnt and q not in measured))
max_c = max(c for c in all_mnts.values())
best_mnts = [mnt for mnt, c in all_mnts.items() if c == max_c]
shuffle(best_mnts)
return best_mnts.pop()
def rocPlot(predictions, truth, classes = None, label = "Model", newFigure = None, reverse = False, percentage = None):
"""
Computes the roc with confidence bounds for the given model
Arguments:
predictions {Dict / List} -- Label predictions
truth {Dict / List} -- Ground truth
classes {Dict "+":int, "-":int} -- Classes to consider to plot {Default None ie {+":1, "-":0}}
Keyword Arguments:
label {str} -- Legend to plot (default: {"Model"})
newFigure {str} -- Display on a given figure (default: {None} - Create new figure)
reverse {bool} -- Plot the reverse ROC useful for analyzing TNR (default: {False})
"""
predictions, truth = selection(predictions, truth, classes)
predictions, truth = flatten(predictions, truth)
global_fpr, global_tpr, _ = roc_curve(truth, predictions)
if reverse:
x, y = 1 - global_tpr, 1 - global_fpr # FNR, TNR
x, y = x[::-1], y[::-1]
minx = 1. / np.sum(truth == 1)
if percentage is None:
percentage = minx
str_print = "TNR @{:.2f}% FNR : {:.2f}".format(percentage*100, np.interp(percentage, x, y))
else:
x, y = global_fpr, global_tpr
minx = 1. / np.sum(truth == 0)
if percentage is None:
percentage = minx
str_print = "TPR @{:.2f}% FPR : {:.2f}".format(percentage*100, np.interp(percentage, x, y))
if newFigure is not None:
plt.figure(newFigure)
else:
plt.plot(np.linspace(0, 1, 100), np.linspace(0, 1, 100), 'k--', label="Random")
if reverse:
plt.xlabel('False negative rate')
plt.ylabel('True negative rate')
plt.title('Reverse ROC curve')
else:
plt.xlabel('False positive rate')
plt.ylabel('True positive rate')
plt.title('ROC curve')
newx = np.linspace(minx, 1, 1000)
y = np.interp(newx, x, y)
wilson = 1.96 * np.sqrt(y * (1 - y)/len(predictions))
print(str_print + " +/- {:.2f}".format(np.interp(0.01, newx, wilson)))
upper = np.minimum(y + wilson, 1)
lower = np.maximum(y - wilson, 0)
plRoc = plt.plot(newx, y, label=label + " ({:.2f} +/- {:.2f})".format(aucCompute(predictions, truth, classes), (auc(newx, upper) - auc(newx, lower))/2.), ls = '--' if "train" in label.lower() else '-')
plt.fill_between(newx, lower, upper, color=plRoc[0].get_color(), alpha=.2)
def describe_instances(self, parameters):
"""
Execute the ec2-describe-instances command and returns a summary of the
already running EC2 instances. (Also see documentation for the BaseAgent
class)
Args:
parameters A dictionary containing the 'keyname' parameter
Returns:
A tuple of the form (public_ips, private_ips, instances) where each
member is a list.
"""
keyname = parameters[self.PARAM_KEYNAME]
describe_instances = utils.shell(self.prefix + '-describe-instances 2>&1')
utils.log('describe-instances says {0}'.format(describe_instances))
fqdn_regex = re.compile('\s+({0})\s+({0})\s+running\s+{1}\s'.format(self.FQDN_REGEX, keyname))
instance_regex = re.compile('INSTANCE\s+(i-\w+)')
all_ip_addresses = utils.flatten(fqdn_regex.findall(describe_instances))
instances = utils.flatten(instance_regex.findall(describe_instances))
public_ips, private_ips = self.get_ip_addresses(all_ip_addresses)
return public_ips, private_ips, instances
def get_per_node_loss_tol(all_tols, filename=None):
"""
For each qubit in the state, calculates the number of measurement
patterns that can tolerate it's loss.
"""
tol_counts = Counter(flatten(all_tols))
tol_counts = [[n, count] for n, count in tol_counts.items()]
if filename:
with open(filename, 'wb') as csvfile:
writer = csv.writer(csvfile)
writer.writerow(['node', 'tol_count'])
writer.writerows(tol_counts)
return tol_counts
def format_dataframe(self, data_dictionary):
"""
Method to format the response dictionary from a requested module.
:param data_dictionary: The dictionary data from the requested module.
:type data_dictionary: dict
:return: A formatted dataframe containing the data.
:rtype pd.Dataframe
"""
# Checks to see if there are any dictionaries or lists within the data that need to be flattened.
if isinstance(data_dictionary, list):
module = [flatten(data) for data in data_dictionary]
module = pd.DataFrame(module)
else:
module = flatten(data_dictionary)
module = pd.DataFrame([module])
# Due to the way Yahoo Finance API returns numeric types, the raw integer value is preferred. Therefore, any
# values with the suffix longfmt (long format) or fmt (format) are removed.
module_columns = [
column for column in module.columns
if not ('.fmt' in column or '.longFmt' in column)
]
# Get a new dataframe.
module = module[module_columns]
# Format the headers of the column to match PEP8 standards.
new_columns_dict = {
col: self.reader.pep_pattern.sub('_',
col.split('.')[0]).lower()
for col in module.columns
}
module.rename(columns=new_columns_dict, inplace=True)
return module
def calibrationPlot(predictions,
truth,
classes=None,
label="Model",
newFigure=None,
n_bins=5):
"""
Computes the roc with confidence bounds for the given model
Arguments:
predictions {Dict / List} -- Label predictions
truth {Dict / List} -- Ground truth
classes {Dict "+":int, "-":int} -- Classes to consider to plot {Default None ie {+":1, "-":0}}
Keyword Arguments:
label {str} -- Legend to plot (default: {"Model"})
newFigure {str} -- Display on a given figure (default: {None} - Create new figure)
n_bins {int} -- Numbre of bins for the calibration (default: {5})
"""
predictions, truth = selection(predictions, truth, classes)
predictions, truth = flatten(predictions, truth)
predictions = ((predictions - predictions.min()) /
(predictions.max() - predictions.min())).flatten()
fraction_of_positives, mean_predicted_value = calibration_curve(
truth, predictions, n_bins=n_bins)
bins = np.linspace(0., 1. + 1e-8, n_bins + 1)
binids = np.digitize(predictions, bins) - 1
bin_sums = np.bincount(binids, minlength=len(bins))
bin_sums = bin_sums[bin_sums != 0] * 500 / np.sum(bin_sums)
if newFigure is not None:
plt.figure(newFigure)
else:
plt.xlabel('Mean Predicted Value')
plt.ylabel('Fraction Positive')
plt.title('Calibration')
p = plt.plot(mean_predicted_value,
fraction_of_positives,
alpha=0.5,
ls=':')
plt.scatter(mean_predicted_value,
fraction_of_positives,
s=bin_sums,
label=label +
" ({:.2f})".format(brier_score_loss(truth, predictions)),
color=p[0].get_color(),
alpha=0.5)
def cutnpaste(oracle):
# find the breakpoint for padding
pad_len = 0
for pad in range(32, 100):
oracle_chunks = list(chunks(oracle("A" * pad), 16))
if oracle_chunks[1] == oracle_chunks[2]:
pad_len = pad % 16
break
payload = "A" * (pad_len) + "admin" + "\v" * 11
payload_chunk = list(chunks(oracle(payload)))[1]
cut_payload = "A" * (3 + pad_len)
cut_chunks = list(chunks(oracle(cut_payload)))[:-1]
cut_chunks.append(payload_chunk)
print(decrypt(flatten(cut_chunks)))
def averagePrecisionRecallCompute(predictions, truth, classes=None):
"""
Computes AUC of the given predictions
Arguments:
predictions {Dict / List} -- Label predictions
truth {Dict / List} -- Ground truth
Keyword Arguments:
classes {Dict "+":int, "-":int} -- Classes to consider to plot {Default None ie {+":1, "-":0}}
Returns:
float -- Estimation by pooling of auc
"""
predictions, truth = selection(predictions, truth, classes)
predictions, truth = flatten(predictions, truth)
return average_precision_score(truth, predictions)
def test_measurement_patterns_teleport(self):
""" Finds measurement patterns and tests they teleport the state """
nodes = 8
output = nodes - 1
for i in tqdm(range(100)):
prob_edge = random.uniform(0.2, 0.5) / 2
disablePrint()
psi = RandomGNPGraphChannel(nodes,
prob_edge,
output=output,
use_gpu=True)
psi.update_inputs_and_outputs()
enablePrint()
mnt_patterns, qubit_key = psi.get_mnt_patterns()
mnt_pattern = random.choice(flatten(mnt_patterns.values()))
mnt_pattern = [(qubit, basis)
for qubit, basis in zip(qubit_key, mnt_pattern)
if basis]
random.shuffle(mnt_pattern)
for qubit, basis in mnt_pattern:
try:
psi.pauli_measurement(qubit, basis, forget=False)
except Exception:
print "Measurement failed"
print psi.edges()
print mnt_pattern
sys.exit()
try:
all_nt = psi._test_all_non_trivial_combos_found(
print_stabs=True, join=False, verbose=False)
except Exception:
print "Measurement failed"
print psi.edges()
print mnt_pattern
pprint(psi.gen_combos)
psi._print_stabs()
sys.exit()
stab_combos_correct = psi._test_combo_stabs_correct()
self.assertTrue(all_nt)
self.assertTrue(stab_combos_correct)
self.assertEqual(psi._support(psi.X_op), [output])
self.assertEqual(psi._support(psi.Z_op), [output])
self.assertTrue(anticommute(psi.X_op, psi.Z_op))
def handle_underscores(suffix, text_encoder, prefix=False):
encoder = text_encoder.encoder
if prefix:
tok = "___"
else:
tok = find_underscore_length(suffix)
suffix_parts = [i.strip() for i in suffix.split("{}".format(tok))]
to_flatten = []
for i, part in enumerate(suffix_parts):
if part:
to_flatten.append(text_encoder.encode([part], verbose=False)[0])
if i != len(suffix_parts) - 1 and suffix_parts[i + 1]:
to_flatten.append([encoder["<blank>"]])
else:
to_flatten.append([encoder["<blank>"]])
final_suffix = utils.flatten(to_flatten)
return final_suffix
def get_max_weight_efficiencies(psi, max_weight, filename=None, verbose=False):
"""
Gets loss tolerance of measurement patterns produced with different
absolute maximum weights.
"""
data = []
for w in tqdm(range(1, max_weight + 1)):
mnt_pats, qubit_key = psi.get_mnt_patterns(
max_weight=w, rel_weight=True)
loss_tols = get_loss_tolerance(mnt_pats, qubit_key)
max_tols = flatten(value for value in loss_tols.values())
all_tols = get_all_loss_tols(max_tols)
datum = [w, len(all_tols)]
if verbose:
tqdm.write(str(datum))
data.append(datum)
if filename:
with open(filename, 'wb') as csvfile:
writer = csv.writer(csvfile)
header = ['max_weight', 'loss_tol_configs']
writer.writerow(header)
writer.writerows(data)
def confusionPlot(predictions, truth, classes, percentage = True):
"""
Computes the confusion matrix of the given model
Arguments:
predictions {Dict / List} -- Label predictions
truth {Dict / List} -- Ground truth
classes {Dict "+":int, "-":int} -- Classes to consider to plot
"""
predictions, truth = selection(predictions, truth, classes)
predictions, truth = flatten(predictions, truth)
classes_list = np.array(list(classes.keys()))
confusion = confusion_matrix(truth, predictions, labels=[classes[c] for c in classes_list])
notNull = confusion.sum(axis = 0) != 0
if percentage:
confusion = confusion / confusion.sum(axis = 1, keepdims = True)
sns.heatmap(confusion[:, notNull], xticklabels = classes_list[notNull], yticklabels = classes_list, annot = True, vmin = 0, vmax = 1 if percentage else None)
plt.xlabel("Predicted")
plt.ylabel("Ground truth")
def precisionRecallPlot(predictions,
truth,
classes=None,
label="Model",
newFigure=None,
reverse=False,
percentage=None):
"""
Computes the roc with confidence bounds for the given model
Arguments:
predictions {Dict / List} -- Label predictions
truth {Dict / List} -- Ground truth
classes {Dict "+":int, "-":int} -- Classes to consider to plot {Default None ie {+":1, "-":0}}
Keyword Arguments:
label {str} -- Legend to plot (default: {"Model"})
newFigure {str} -- Display on a given figure (default: {None} - Create new figure)
reverse {bool} -- Plot the reverse ROC useful for analyzing TNR (default: {False})
"""
predictions, truth = selection(predictions, truth, classes)
predictions, truth = flatten(predictions, truth)
precision, recall, _ = precision_recall_curve(truth, predictions)
if newFigure is not None:
plt.figure(newFigure)
else:
plt.xlabel('Precision')
plt.ylabel('Recall')
plt.title('Precision Recall curve')
plt.plot(precision,
recall,
label=label + " ({:.2f})".format(
averagePrecisionRecallCompute(predictions, truth, classes)),
ls='--' if "train" in label.lower() else '-')
def run(self):
if self.params.rng == -1:
seed = random.randrange(2**32 - 1)
else:
seed = int(self.params.rng)
rng = np.random.RandomState(seed)
np.random.seed(seed)
conf_env_dir = "cfgs/env/" + self.params.env_module + "/" + self.params.env_conf_file
env_params = parse_conf(conf_env_dir)
env_params["rng"] = rng
env = get_mod_object("envs",self.params.env_module,"env",(rng,), env_params,mode=1)
pol_train = get_mod_class("pols",self.params.pol_train_module, "pol")
self.params.pol_train_args = flatten(self.params.pol_train_args) if self.params.pol_train_args is not None else []
pol_train_args = parse_conf("cfgs/pol/" + self.params.pol_train_module + "/" + self.params.pol_train_args[0]) if len(self.params.pol_train_args) > 0 and isfile("cfgs/pol/" + self.params.pol_train_module + "/" + self.params.pol_train_args[0]) else parse_conf("cfgs/pol/" + self.params.pol_train_module + "/default")
pol_train_args_2 = erase_dict_from_keyword_list(pol_train_args, self.params.pol_train_args)
pol_train_args = revalidate_dict_from_conf_module(pol_train_args_2, "pol", self.params.pol_train_module)
pol_test = get_mod_class("pols",self.params.pol_test_module, "pol")
self.params.pol_test_args = flatten(self.params.pol_test_args) if self.params.pol_test_args is not None else []
pol_test_args = parse_conf("cfgs/pol/" + self.params.pol_test_module + "/" + self.params.pol_test_args[0]) if len(self.params.pol_test_args) > 0 and isfile("cfgs/pol/" + self.params.pol_test_module + "/" + self.params.pol_test_args[0]) else parse_conf("cfgs/pol/" + self.params.pol_test_module + "/default")
pol_test_args_2 = erase_dict_from_keyword_list(pol_test_args, self.params.pol_test_args)
pol_test_args = revalidate_dict_from_conf_module(pol_test_args_2, "pol", self.params.pol_test_module)
self.params.backend_nnet_conf_file= flatten(self.params.backend_nnet_conf_file) if self.params.backend_nnet_conf_file is not None else []
backend_nnet_params = parse_conf("cfgs/backend_nnet/" + self.params.backend_nnet + "/" + self.params.backend_nnet_conf_file[0]) if len(self.params.backend_nnet_conf_file) > 0 and isfile("cfgs/backend_nnet/" + self.params.backend_nnet + "/" + self.params.backend_nnet_conf_file[0]) else parse_conf("cfgs/backend_nnet/" + self.params.backend_nnet + "/default")
backend_nnet_params_2 = erase_dict_from_keyword_list(backend_nnet_params,self.params.backend_nnet_conf_file)
backend_nnet_params = revalidate_dict_from_conf_module(backend_nnet_params_2, "backend_nnet", self.params.backend_nnet)
neural_net = get_mod_class("neural_nets", self.params.backend_nnet,"neural_net")
self.params.ctrl_neural_nets_conf_file = flatten(self.params.ctrl_neural_nets_conf_file) if self.params.ctrl_neural_nets_conf_file is not None else []
ctrl_neural_nets_params = parse_conf("cfgs/ctrl_nnet/" + self.params.qnetw_module + "/" + self.params.ctrl_neural_nets_conf_file[0]) if len(self.params.ctrl_neural_nets_conf_file) > 0 and isfile("cfgs/ctrl_nnet/" + self.params.qnetw_module + "/" + self.params.ctrl_neural_nets_conf_file[0]) else parse_conf("cfgs/ctrl_nnet/" + self.params.qnetw_module + "/DEFAULT")
ctrl_neural_nets_params_2 = erase_dict_from_keyword_list(ctrl_neural_nets_params,self.params.ctrl_neural_nets_conf_file)
ctrl_neural_nets_params = revalidate_dict_from_conf_module(ctrl_neural_nets_params_2, "ctrl_neural_net", self.params.qnetw_module)
ctrl_neural_nets_params["neural_network"] = neural_net
ctrl_neural_nets_params["neural_network_kwargs"] = backend_nnet_params
ctrl_neural_nets_params["batch_size"] = self.params.batch_size
ctrl_neural_net = get_mod_object("ctrl_neural_nets", self.params.qnetw_module, "ctrl_neural_net", (env,),ctrl_neural_nets_params, mode=0)
agent = NeuralAgent([env], [ctrl_neural_net], replay_memory_size=self.params.replay_memory_size, replay_start_size=None, batch_size=self.params.batch_size, random_state=rng, exp_priority=self.params.exp_priority, train_policy=pol_train,train_policy_kwargs=pol_train_args, test_policy=pol_test, test_policy_kwargs=pol_test_args, only_full_history=self.params.only_full_history)
for tc in self.params.controllers:
len_tc = len(tc)
s = tc[0]
redo_conf = False
if len_tc >= 2:
#Test if sc is a config file or an argument to override
if '=' not in tc[1]:
#This is a config file
conf_ctrl = parse_conf("cfgs/ctrl/" + s + "/" + tc[1])
else:
conf_ctrl = parse_conf("cfgs/ctrl/" + s + "/default")
sc = tc[1].split("=")
if sc[0] in conf_ctrl.keys():
conf_ctrl[sc[0]] = sc[1]
redo_conf = True
else:
print ("Warning : parameter " + str(sc[0]) + " is not included in config specs for the controller " + s)
if len_tc > 2:
remainder = tc[2:]
for a in remainder:
sc = a.split("=")
if len(sc) != 2:
print ("Warning : arg " + a + " for controller parametrization is ill formed. It needs to be in the form key=value.")
else:
redo_conf = True
if sc[0] in conf_ctrl.keys():
conf_ctrl[sc[0]] = sc[1]
else:
print ("Warning : parameter " + str(sc[0]) + " is not included in config specs for the controller " + s)
#Create a temporary config file with the erased parameter and go through parse_conf again
if redo_conf:
write_conf(conf_ctrl, "cfgs/ctrl/" + s + "/temp")
conf_ctrl = parse_conf("cfgs/ctrl/" + s + "/temp")
os.remove("cfgs/ctrl/" + s + "/temp")
else:
conf_ctrl = parse_conf("cfgs/ctrl/" + s + "/default")
controller = get_mod_object("ctrls",s,"ctrl",tuple(),conf_ctrl,mode=0)
agent.attach(controller)
agent.run(self.params.epochs, self.params.max_size_episode)
def run_instances(self, count, parameters, security_configured):
"""
Spawn the specified number of EC2 instances using the parameters
provided. This method relies on the ec2-run-instances command to
spawn the actual VMs in the cloud. This method is blocking in that
it waits until the requested VMs are properly booted up. However
if the requested VMs cannot be procured within 1800 seconds, this
method will treat it as an error and return. (Also see documentation
for the BaseAgent class)
Args:
count No. of VMs to spawned
parameters A dictionary of parameters. This must contain 'keyname',
'group', 'image_id' and 'instance_type' parameters.
security_configured Uses this boolean value as an heuristic to
detect brand new AppScale deployments.
Returns:
A tuple of the form (instances, public_ips, private_ips)
"""
image_id = parameters[self.PARAM_IMAGE_ID]
instance_type = parameters[self.PARAM_INSTANCE_TYPE]
keyname = parameters[self.PARAM_KEYNAME]
group = parameters[self.PARAM_GROUP]
spot = False
utils.log('[{0}] [{1}] [{2}] [{3}] [ec2] [{4}] [{5}]'.format(count,
image_id, instance_type, keyname, group, spot))
start_time = datetime.datetime.now()
active_public_ips = []
active_private_ips = []
active_instances = []
if os.environ.has_key('EC2_URL'):
utils.log('EC2_URL = [{0}]'.format(os.environ['EC2_URL']))
else:
utils.log('Warning: EC2_URL environment not found in the process runtime!')
while True:
active_public_ips, active_private_ips, active_instances =\
self.describe_instances(parameters)
# If security has been configured on this agent just now,
# that's an indication that this is a fresh cloud deployment.
# As such it's not expected to have any running VMs.
if len(active_instances) > 0 or security_configured:
break
args = '-k {0} -n {1} --instance-type {2} --group {3} {4}'.format(keyname,
count, instance_type, group, image_id)
if spot:
price = self.get_optimal_spot_price(instance_type)
command_to_run = '{0}-request-spot-instances -p {1} {2}'.format(self.prefix, price, args)
else:
command_to_run = '{0}-run-instances {1}'.format(self.prefix, args)
while True:
run_instances = utils.shell(command_to_run)
utils.log('Run instances says {0}'.format(run_instances))
status, command_to_run = self.run_instances_response(command_to_run, run_instances)
if status:
break
utils.log('sleepy time')
utils.sleep(5)
instances = []
public_ips = []
private_ips = []
utils.sleep(10)
end_time = datetime.datetime.now() + datetime.timedelta(0, self.MAX_VM_CREATION_TIME)
now = datetime.datetime.now()
while now < end_time:
describe_instances = utils.shell(self.prefix + '-describe-instances 2>&1')
utils.log('[{0}] {1} seconds left...'.format(now, (end_time - now).seconds))
utils.log(describe_instances)
fqdn_regex = re.compile('\s+({0})\s+({0})\s+running\s+{1}\s'.format(self.FQDN_REGEX, keyname))
instance_regex = re.compile('INSTANCE\s+(i-\w+)')
all_ip_addresses = utils.flatten(fqdn_regex.findall(describe_instances))
instances = utils.flatten(instance_regex.findall(describe_instances))
public_ips, private_ips = self.get_ip_addresses(all_ip_addresses)
public_ips = utils.diff(public_ips, active_public_ips)
private_ips = utils.diff(private_ips, active_private_ips)
instances = utils.diff(instances, active_instances)
if count == len(public_ips):
break
time.sleep(self.SLEEP_TIME)
now = datetime.datetime.now()
if not public_ips:
sys.exit('No public IPs were able to be procured within the time limit')
if len(public_ips) != count:
for index in range(0, len(public_ips)):
if public_ips[index] == '0.0.0.0':
instance_to_term = instances[index]
utils.log('Instance {0} failed to get a public IP address and is being terminated'.\
format(instance_to_term))
utils.shell(self.prefix + '-terminate-instances ' + instance_to_term)
pass
end_time = datetime.datetime.now()
total_time = end_time - start_time
if spot:
utils.log('TIMING: It took {0} seconds to spawn {1} spot instances'.format(
total_time.seconds, count))
else:
utils.log('TIMING: It took {0} seconds to spawn {1} regular instances'.format(
total_time.seconds, count))
return instances, public_ips, private_ips
def main():
rates_for_algo = {}
index_comparison = pd.DataFrame(index=config_manager.INDEX_TO_COMPARE)
# Used only for initialization
for func in config_manager.FUNCTION_NAMES:
rates_for_algo[func] = {}
# For each strategy type, for each minute and for each function read data exported
# by the simulation and use them to calculate rates and indexes for comparison
for algo in config_manager.STRATEGIES:
x_func_success_rate = {}
x_func_reject_rate = {}
x_func_reject_num = {}
# Initialize dictionary of rates for all functions
for func in config_manager.FUNCTION_NAMES:
x_func_success_rate[func] = []
x_func_reject_rate[func] = []
x_func_reject_num[func] = []
print("-------------------------- ALGO {} --------------------------".
format(algo))
# Create path for recover tables
base_path = config_manager.SIMULATION_TABLES_OUTPUT_PATH.joinpath(algo)
for minute in range(0, config_manager.SIMULATION_MINUTES):
print("MINUTE {}".format(minute))
print(
">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>"
)
# Complete path for load tables
path = base_path.joinpath("minute_" + str(minute))
# For each minute load invocaion_rate and max_rate table
df_invoc_rate = pd.read_csv(path.joinpath("invoc_rates.csv"),
delimiter='\t',
header=0,
index_col=0)
print("================ INVOCATION RATES ==================")
print(df_invoc_rate)
print("====================================================")
df_max_rate = pd.read_csv(path.joinpath("max_rates.csv"),
delimiter='\t',
header=0,
index_col=0)
print("================ MAX RATES =========================")
print(df_max_rate)
print("====================================================")
# For each minute and foreach function load dataframe
for func in config_manager.FUNCTION_NAMES:
df = pd.read_csv(path.joinpath(func + ".csv"),
delimiter='\t',
header=0,
index_col=0)
print(
"================ FORWARDED REQUESTS for {} ================"
.format(func))
print(df)
print(
"=========================================================="
)
sr, rr, rn = calculate_rates(df, func, df_max_rate[func],
df_invoc_rate[func])
x_func_success_rate[func].append(sr)
x_func_reject_rate[func].append(rr)
x_func_reject_num[func].append(rn)
rates_for_algo[func][algo] = x_func_success_rate[func]
print(
"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
)
print("STATS FOR ALGO {}".format(algo))
# Utility print for success/reject rate and reject nume for func
# TODO: fix it to work with new dictionaties
#
# print(" > Mean success rate for funca: {}".format(np.mean(funca_sr)))
# print(" > Mean reject rate for funca: {}".format(np.mean(funca_rr)))
# print(" > Rejected requests for funca: {}".format(np.sum(funca_reject_num)))
# print(" > Mean success rate for qrcode: {}".format(np.mean(qrcode_sr)))
# print(" > Mean reject rate for qrcode: {}".format(np.mean(qrcode_rr)))
# print(" > Rejected requests for qrcode: {}".format(np.sum(qrcode_reject_num)))
# print(" > Mean success rate for ocr: {}".format(np.mean(ocr_sr)))
# print(" > Mean reject rate for ocr: {}".format(np.mean(ocr_rr)))
# print(" > Rejected requests for ocr: {}".format(np.sum(ocr_reject_num)))
# TEST
#print(x_func_success_rate)
#print(x_func_reject_rate)
#print(x_func_reject_num)
# Metrics prints
##### SUCCESS RATES METRICS #####
# Mean success rate
mean_success_rate = np.mean(
[np.mean(srates)
for k, srates in x_func_success_rate.items()]) * 100
print(" > Mean success rate: {:0.2f}%".format(mean_success_rate))
# Success rate variance
flat_list = [
i * 100 for i in flatten(list(x_func_success_rate.values()))
]
success_rate_variance = np.var(flat_list)
print(" > Success rate variance: {:0.2f}".format(
success_rate_variance))
# Success rate median
flat_list = flatten(list(x_func_success_rate.values()))
success_rate_median = np.median(flat_list) * 100
print(
" > Success rate median: {:0.2f}%".format(success_rate_median))
# Success rate percentile
flat_list = flatten(list(x_func_success_rate.values()))
success_rate_percentile = np.percentile(
flat_list, config_manager.ANALYSIS_PERCENTILE) * 100
print(" > Success rate {}% percentile: {:0.2f}%".format(
config_manager.ANALYSIS_PERCENTILE, success_rate_percentile))
##### SUCCESS RATES (STRESS PERIOD) METRICS #####
# Mean success rate calculated during high traffic period (minutes from 1 to 5)
mean_success_rate_stress_period = np.mean([
np.mean(srates[1:6]) for k, srates in x_func_success_rate.items()
]) * 100
print(
" > Mean success rate during stress period (from minute 1 to 5): {:0.2f}%"
.format(mean_success_rate_stress_period))
# Success rate variance (stress period)
flat_list = [
i * 100 for i in flatten(
[item[1:6] for item in list(x_func_success_rate.values())])
]
success_rate_stress_period_variance = np.var(flat_list)
print(
" > Success rate variance during stress period (from minute 1 to 5): {:0.2f}"
.format(success_rate_stress_period_variance))
# Success rate median (stress period)
flat_list = flatten(
[item[1:6] for item in list(x_func_success_rate.values())])
success_rate_stress_period_median = np.median(flat_list) * 100
print(
" > Success rate median during stress period (from minute 1 to 5): {:0.2f}%"
.format(success_rate_stress_period_median))
# Success rate percentile (stress period)
flat_list = flatten(
[item[1:6] for item in list(x_func_success_rate.values())])
success_rate_stress_period_percentile = np.percentile(
flat_list, config_manager.ANALYSIS_PERCENTILE) * 100
print(
" > Success rate {}% percentile during stress period (from minute 1 to 5): {:0.2f}%"
.format(config_manager.ANALYSIS_PERCENTILE,
success_rate_stress_period_percentile))
##### REJECT RATES METRICS #####
# Total rejected requests num calculated for each algorithm across minutes
total_reject_requests = np.sum(
[np.sum(rejnums) for k, rejnums in x_func_reject_num.items()])
print(" > Total rejected requests: {} req".format(
total_reject_requests))
# Reject number variance
flat_list = flatten(list(x_func_reject_num.values()))
reject_number_variance = np.var(flat_list)
print(" > Reject num variance: {:0.2f}".format(
reject_number_variance))
# Reject number median
flat_list = flatten(list(x_func_reject_num.values()))
reject_number_median = np.median(flat_list)
print(" > Reject num median: {:0.2f}".format(reject_number_median))
# Reject number percentile
flat_list = flatten(list(x_func_reject_num.values()))
reject_number_percentile = np.percentile(
flat_list, config_manager.ANALYSIS_PERCENTILE)
print(" > Reject num {}% percentile: {:0.2f}".format(
config_manager.ANALYSIS_PERCENTILE, reject_number_percentile))
print(
"----------------------------------------------------------------------------"
)
index_comparison[algo] = [
mean_success_rate,
success_rate_variance,
success_rate_median,
success_rate_percentile,
mean_success_rate_stress_period,
success_rate_stress_period_variance,
success_rate_stress_period_median,
success_rate_stress_period_percentile,
total_reject_requests,
reject_number_variance,
reject_number_median,
reject_number_percentile,
]
# Export print for comparison
for func in config_manager.FUNCTION_NAMES:
export_for_minute_rates(func, rates_for_algo[func])
# Export index comparison table
print("> INDEX COMPARISON TABLE")
print(index_comparison.T)
export_index_comparison_table(index_comparison.T)
def dcganx_G(input_dim, n0g, imgsz, channels,
norm_type, # 'bn', 'none'
requires_grad, depth=3,
nodemul=2, do_bias=True):
ker=5; padding=2; output_padding=1
def gen_block_T_params(ni, no, k):
return {
'convT0': conv2dT_params(ni, no, k, do_bias),
'conv1': conv2d_params(no, no, 1, do_bias),
'bn0': utils.bnparams(no) if norm_type == 'bn' else None,
'bn1': utils.bnparams(no) if norm_type == 'bn' else None
}
def gen_group_T_params(ni, no, count):
return {'block%d' % i: gen_block_T_params(ni if i == 0 else no, no, ker) for i in range(count)}
count = 1
nn0 = n0g * (nodemul**(depth-1))
sz = imgsz // (2**depth)
p = { 'proj': utils.linear_params(input_dim, nn0*sz*sz) }
nn = nn0
for d in range(depth-1):
p['group%d'%d] = gen_group_T_params(nn, nn//nodemul, count)
nn = nn//nodemul
p['last_convT'] = conv2dT_params(nn, channels, ker, do_bias)
flat_params = utils.cast(utils.flatten(p))
if requires_grad:
utils.set_requires_grad_except_bn_(flat_params)
def block(x, params, base, mode, stride):
o = F.relu(x, inplace=True)
o = F.conv_transpose2d(o, params[base+'.convT0.w'], params.get(base+'.convT0.b'),
stride=stride, padding=padding, output_padding=output_padding)
if norm_type == 'bn':
o = utils.batch_norm(o, params, base + '.bn0', mode)
o = F.relu(o, inplace=True)
o = F.conv2d(o, params[base+'.conv1.w'], params.get(base+'.conv1.b'),
stride=1, padding=0)
if norm_type == 'bn':
o = utils.batch_norm(o, params, base + '.bn1', mode)
return o
def group(o, params, base, mode, stride=2):
for i in range(count):
o = block(o, params, '%s.block%d' % (base,i), mode, stride if i == 0 else 1)
return o
def f(input, params, mode):
o = F.linear(input, params['proj.weight'], params['proj.bias'])
o = o.view(input.size(0), nn0, sz, sz)
for d in range(depth-1):
o = group(o, params, 'group%d'%d, mode)
o = F.relu(o, inplace=True)
o = F.conv_transpose2d(o, params['last_convT.w'], params.get('last_convT.b'), stride=2,
padding=padding, output_padding=output_padding)
o = torch.tanh(o)
return o
return f, flat_params
def handle(self, *args, **options):
t00 = time()
qid = options['qid']
K = options['K']
alpha = options['alpha']
n_features = options['n_features']
limit = options['limit']
ng = options['ng']
n_samples = options['n_samples']
# Get the docs from the query
docs = Doc.objects.filter(query=qid,content__iregex='\w')
# if we are limiting, probably for testing, then do that
if limit > 0:
docs = docs[:limit]
print('\n###############################\
\n## Doing NMF on query {} with {} documents \
and {} topics\n'.format(qid, docs.count(),K))
# Get the docs into lists
abstracts, docsizes, ids = proc_docs(docs, stoplist)
#############################################
# Use tf-idf features for NMF.
print("Extracting tf-idf features for NMF...")
tfidf_vectorizer = TfidfVectorizer(max_df=0.97, min_df=2,
max_features=n_features,
ngram_range=(ng,ng),
tokenizer=snowball_stemmer(),
stop_words=stoplist)
t0 = time()
tfidf = tfidf_vectorizer.fit_transform(abstracts)
print("done in %0.3fs." % (time() - t0))
del abstracts
gc.collect()
run_id = db.init(n_features)
stat = RunStats.objects.get(run_id=run_id)
stat.query = Query.objects.get(pk=qid)
stat.method = "NM"
stat.alpha = alpha
stat.process_id = os.getpid()
stat.save()
# Get the vocab, add it to db
vocab = tfidf_vectorizer.get_feature_names()
vocab_ids = []
pool = Pool(processes=8)
vocab_ids.append(pool.map(partial(add_features,run_id=run_id),vocab))
pool.terminate()
del vocab
vocab_ids = vocab_ids[0]
## Make some topics
django.db.connections.close_all()
topic_ids = db.add_topics(K, run_id)
gc.collect()
# Fit the NMF model
print("Fitting the NMF model with tf-idf features, "
"n_samples=%d and n_features=%d..."
% (n_samples, n_features))
t0 = time()
nmf = NMF(n_components=K, random_state=1,
alpha=alpha, l1_ratio=.5, verbose=True,
init='nndsvd', max_iter=500).fit(tfidf)
print("done in %0.3fs." % (time() - t0))
## Add topics terms
print("Adding topicterms to db")
t0 = time()
ldalambda = find(csr_matrix(nmf.components_))
topics = range(len(ldalambda[0]))
tts = []
pool = Pool(processes=8)
tts.append(pool.map(partial(db.f_lambda, m=ldalambda,
v_ids=vocab_ids,t_ids=topic_ids,run_id=run_id),topics))
pool.terminate()
tts = flatten(tts)
gc.collect()
sys.stdout.flush()
django.db.connections.close_all()
TopicTerm.objects.bulk_create(tts)
print("done in %0.3fs." % (time() - t0))
## Add topic-docs
gamma = find(csr_matrix(nmf.transform(tfidf)))
glength = len(gamma[0])
chunk_size = 100000
ps = 16
parallel_add = True
all_dts = []
make_t = 0
add_t = 0
### Go through in chunks
for i in range(glength//chunk_size+1):
dts = []
values_list = []
f = i*chunk_size
l = (i+1)*chunk_size
if l > glength:
l = glength
docs = range(f,l)
doc_batches = []
for p in range(ps):
doc_batches.append([x for x in docs if x % ps == p])
pool = Pool(processes=ps)
make_t0 = time()
values_list.append(pool.map(partial(
db.f_gamma_batch, gamma=gamma,
docsizes=docsizes,docUTset=ids,topic_ids=topic_ids,
run_id=run_id
),doc_batches))
#dts.append(pool.map(partial(f_gamma, gamma=gamma,
# docsizes=docsizes,docUTset=ids,topic_ids=topic_ids),doc_batches))
pool.terminate()
make_t += time() - make_t0
django.db.connections.close_all()
add_t0 = time()
values_list = [item for sublist in values_list for item in sublist]
pool = Pool(processes=ps)
pool.map(insert_many,values_list)
pool.terminate()
add_t += time() - add_t0
gc.collect()
sys.stdout.flush()
stat.error = nmf.reconstruction_err_
stat.errortype = "Frobenius"
stat.iterations = nmf.n_iter_
stat.last_update=timezone.now()
stat.save()
management.call_command('update_run',run_id)
totalTime = time() - t00
tm = int(totalTime//60)
ts = int(totalTime-(tm*60))
print("done! total time: " + str(tm) + " minutes and " + str(ts) + " seconds")
print("a maximum of " + str(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1000) + " MB was used")
def run_tm(s_id,
K,
language="german",
verbosity=1,
method='NM',
max_features=0,
max_df=0.95,
min_df=5,
alpha=0.01,
extra_stopwords=set(),
top_chain_var=None,
rng_seed=None,
max_iter=200,
**kwargs):
if method in ['BD', 'BleiDTM'] and top_chain_var is None:
top_chain_var = 0.005
s = Search.objects.get(pk=s_id)
stat = RunStats(psearch=s,
K=K,
min_freq=min_df,
max_df=max_df,
method=method.upper()[0:2],
max_features=max_features,
max_iter=max_iter,
alpha=alpha,
extra_stopwords=list(extra_stopwords),
top_chain_var=top_chain_var,
status=1,
language=language)
stat.save()
django.db.connections.close_all()
if method in ['DT', 'dnmf']:
print("Running dynamic NMF algorithm")
run_dynamic_nmf(stat, **kwargs)
return 0
elif method in ['BD', 'BleiDTM']:
print("Running Blei DTM algorithm")
if rng_seed:
stat.rng_seed = rng_seed
else:
stat.rng_seed = 1
stat.save()
run_blei_dtm(stat, **kwargs)
return 0
print("starting topic model for runstat with settings:")
for field in stat._meta.fields:
field_value = getattr(stat, field.name)
if field_value:
print("{}: {}".format(field.name, field_value))
start_time = time.time()
start_datetime = timezone.now()
stat.status = 1 # 3 = finished
stat.save()
run_id = stat.run_id
if s.search_object_type == 1:
ps = Paragraph.objects.filter(search_matches=s)
docs = ps.filter(text__iregex='\w')
texts, docsizes, ids = process_texts(docs)
elif s.search_object_type == 2:
uts = Utterance.objects.filter(search_matches=s)
texts, docsizes, ids = merge_utterance_paragraphs(uts)
else:
print("search object type invalid")
return 1
if stat.max_features == 0:
n_features = 10000000
else:
n_features = stat.max_features
if stat.language is "german":
stemmer = SnowballStemmer("german")
tokenizer = german_stemmer()
stopword_list = [stemmer.stem(t) for t in stopwords.words("german")]
elif stat.language is "english":
stemmer = SnowballStemmer("english")
stopword_list = [stemmer.stem(t) for t in stopwords.words("english")]
tokenizer = snowball_stemmer()
else:
print("Language not recognized.")
return 1
if stat.extra_stopwords:
stopword_list = list(set(stopword_list) | set(stat.extra_stopwords))
if method in ["NM", "nmf"]:
if verbosity > 0:
print(
"creating term frequency-inverse document frequency matrix ({})"
.format(time.time() - start_time))
# get term frequency-inverse document frequency matrix (using log weighting)
# and min/max document frequency (min_df, max_df)
tfidf_vectorizer = TfidfVectorizer(max_df=stat.max_df,
min_df=stat.min_freq,
max_features=n_features,
ngram_range=(1, stat.ngram),
tokenizer=tokenizer,
stop_words=stopword_list)
tfidf = tfidf_vectorizer.fit_transform(texts)
vectorizer = tfidf_vectorizer
vocab = vectorizer.get_feature_names()
elif method in ["LD", "lda"]:
if verbosity > 0:
print("creating term frequency matrix ({})".format(time.time() -
start_time))
# Use tf (raw term count) features for LDA.
tf_vectorizer = CountVectorizer(max_df=stat.max_df,
min_df=stat.min_freq,
max_features=n_features,
ngram_range=(1, stat.ngram),
tokenizer=tokenizer,
stop_words=stopword_list)
tf = tf_vectorizer.fit_transform(texts)
vectorizer = tf_vectorizer
vocab = vectorizer.get_feature_names()
else:
print("method not implemented")
return 1
if verbosity > 0:
print("save terms to db ({})".format(time.time() - start_time))
paralellized = True
if paralellized:
vocab_ids = []
# multiprocessing: add vocabulary as Term
pool = Pool(processes=8)
vocab_ids.append(
pool.map(partial(db.add_features, run_id=run_id), vocab))
pool.terminate()
del vocab
vocab_ids = vocab_ids[0]
else:
print("without multiprocessing for storing terms")
# without multiprocessing
objects = [Term(title=term_title) for term_title in vocab]
# TODO: if some of the objects already exist, duplicates are created: use uniqueness of field 'title'
Term.objects.bulk_create(objects)
runstats = RunStats.objects.get(run_id=run_id)
runstats.term_set.add(*objects)
runstats.save()
## Make some topics
django.db.connections.close_all()
topic_ids = db.add_topics(K, run_id)
gc.collect()
if verbosity > 1:
v = True
else:
v = False
if method in ["NM", "nmf"]:
if verbosity > 0:
print("running matrix factorization with NMF ({})".format(
time.time() - start_time))
# NMF = non-negative matrix factorization
model = NMF(n_components=K,
random_state=1,
alpha=stat.alpha,
l1_ratio=.1,
verbose=v,
init='nndsvd',
max_iter=stat.max_iter).fit(tfidf)
# initialization with Nonnegative Double Singular Value Decomposition (nndsvd)
print("Reconstruction error of nmf: {}".format(
model.reconstruction_err_))
stat.error = model.reconstruction_err_
stat.errortype = "Frobenius"
# document topic matrix
dtm = csr_matrix(model.transform(tfidf))
elif method in ["LD", "lda"]:
if verbosity > 0:
print(
"running Latent Dirichlet Allocation ({})".format(time.time() -
start_time))
model = LDA(
n_components=K,
doc_topic_prior=stat.
alpha, # this is the concentration parameter of the Dirichlet distribution of topics in documents
topic_word_prior=stat.
beta, # this is the concentration parameter of the Dirichlet distribution of words in topics
# if None, this defaults to 1/n
max_iter=stat.max_iter,
learning_method=
'online', # using 'batch' instead could lead to memory problems
learning_offset=50.
#n_jobs=6
).partial_fit(tf)
stat.error = model.perplexity(tf)
stat.errortype = "Perplexity"
dtm = csr_matrix(model.transform(tf))
else:
print("Method {} not available.".format(method))
return 1
# term topic matrix
ldalambda = find(csr_matrix(model.components_))
# find returns the indices and values of the nonzero elements of a matrix
topics = range(len(ldalambda[0]))
tts = []
# multiprocessing: add TopicTerms and scores
pool = Pool(processes=8)
tts.append(
pool.map(
partial(db.f_lambda,
m=ldalambda,
v_ids=vocab_ids,
t_ids=topic_ids,
run_id=run_id), topics))
pool.terminate()
tts = flatten(tts)
gc.collect()
sys.stdout.flush()
django.db.connections.close_all()
TopicTerm.objects.bulk_create(tts)
if verbosity > 0:
print("saving document topic matrix to db ({})".format(time.time() -
start_time))
#document topic matrix
gamma = find(dtm)
glength = len(gamma[0])
chunk_size = 100000
no_cores = 16
parallel_add = True
all_dts = []
make_t = 0
add_t = 0
### Go through in chunks
for i in range(glength // chunk_size + 1):
values_list = []
f = i * chunk_size
l = (i + 1) * chunk_size
if l > glength:
l = glength
docs = range(f, l)
doc_batches = []
for p in range(no_cores):
doc_batches.append([x for x in docs if x % no_cores == p])
pool = Pool(processes=no_cores)
values_list.append(
pool.map(
partial(db.f_gamma_batch,
gamma=gamma,
docsizes=docsizes,
docUTset=ids,
topic_ids=topic_ids,
run_id=run_id), doc_batches))
pool.terminate()
django.db.connections.close_all()
print(
"... created document topic matrix for saving iteration {}".format(
i))
values_list = [item for sublist in values_list for item in sublist]
pool = Pool(processes=no_cores)
if s.search_object_type == 1:
pool.map(db.insert_many_pars, values_list)
elif s.search_object_type == 2:
pool.map(db.insert_many_utterances, values_list)
pool.terminate()
gc.collect()
sys.stdout.flush()
print("... saved document topic matrix iteration {}".format(i))
stat.iterations = model.n_iter_
stat.status = 3 # 3 = finished
stat.last_update = timezone.now()
stat.runtime = timezone.now() - start_datetime
stat.save()
update_topic_titles(run_id)
update_topic_scores(run_id)
if verbosity > 0:
print("topic model run done ({})".format(time.time() - start_time))
return 0
def run_dynamic_nmf(stat):
"""
Run dynamic NMF model on utterances (speeches) or paragraphs from the parliament data
:param stat: RunStats object with the parameters to run the model with
:return: 0 if successful, 1 otherwise
"""
print("starting topic model for runstat with settings:")
for field in stat._meta.fields:
field_value = getattr(stat, field.name)
if field_value:
print("{}: {}".format(field.name, field_value))
t0 = time()
start_datetime = timezone.now()
s = Search.objects.get(pk=stat.psearch.id)
n_samples = 1000
run_id = stat.run_id
# load time range
if s.search_object_type == 1:
ps = Paragraph.objects.filter(search_matches=s)
wps = ParlPeriod.objects.filter(
document__utterance__paragraph__in=ps).distinct().values('n')
elif s.search_object_type == 2:
uts = Utterance.objects.filter(
search_matches=s).order_by('document__parlperiod__n')
wps = ParlPeriod.objects.filter(
document__utterance__in=uts).distinct().values('n')
else:
print("search object type invalid")
return 1
# language specific settings
if stat.language is "german":
stemmer = SnowballStemmer("german")
tokenizer = german_stemmer()
stopword_list = [stemmer.stem(t) for t in stopwords.words("german")]
elif stat.language is "english":
stemmer = SnowballStemmer("english")
stopword_list = [stemmer.stem(t) for t in stopwords.words("english")]
tokenizer = snowball_stemmer()
else:
print("Language not recognized.")
return 1
if stat.extra_stopwords:
stopword_list = list(set(stopword_list) | set(stat.extra_stopwords))
time_range = sorted([wp['n'] for wp in wps])
for timestep in time_range:
# load text from database
if s.search_object_type == 1:
ps = Paragraph.objects.filter(
search_matches=s, utterance__document__parlperiod__n=timestep)
docs = ps.filter(text__iregex='\w')
texts, docsizes, ids = process_texts(docs)
elif s.search_object_type == 2:
uts = Utterance.objects.filter(search_matches=s,
document__parlperiod__n=timestep)
texts, docsizes, ids = merge_utterance_paragraphs(uts)
else:
print("search object type not known")
return 1
print("\n#######################")
print("in period {}: {} docs".format(timestep, len(texts)))
k = stat.K
# k = predict(text_count)
# print("esimating {} topics...".format(k))
print("Extracting tf-idf features for NMF...")
if stat.max_features == 0:
n_features = 100000000
else:
n_features = stat.max_features
tfidf_vectorizer = TfidfVectorizer(max_df=stat.max_df,
min_df=stat.min_freq,
max_features=n_features,
ngram_range=(1, stat.ngram),
tokenizer=tokenizer,
stop_words=stopword_list)
t1 = time()
tfidf = tfidf_vectorizer.fit_transform(texts)
del texts
gc.collect()
print("done in %0.3fs." % (time() - t1))
print("Save terms to DB")
# Get the vocab, add it to db
vocab = tfidf_vectorizer.get_feature_names()
vocab_ids = []
pool = Pool(processes=8)
vocab_ids.append(
pool.map(partial(db.add_features, run_id=run_id), vocab))
pool.terminate()
del vocab
vocab_ids = vocab_ids[0]
django.db.connections.close_all()
topic_ids = db.add_topics(k, run_id)
for t in topic_ids:
top = Topic.objects.get(pk=t)
top.year = timestep
top.save()
gc.collect()
# Fit the NMF model
print("Fitting the NMF model with tf-idf features, "
"n_samples=%d and max_features=%d..." %
(n_samples, stat.max_features))
t1 = time()
nmf = NMF(n_components=k, random_state=1, alpha=.0001,
l1_ratio=.5).fit(tfidf)
print("done in %0.3fs." % (time() - t1))
print("Adding topicterms to db")
ldalambda = find(csr_matrix(nmf.components_))
topics = range(len(ldalambda[0]))
tts = []
pool = Pool(processes=8)
tts.append(
pool.map(
partial(db.f_lambda,
m=ldalambda,
v_ids=vocab_ids,
t_ids=topic_ids,
run_id=run_id), topics))
pool.terminate()
tts = flatten(tts)
gc.collect()
sys.stdout.flush()
django.db.connections.close_all()
TopicTerm.objects.bulk_create(tts)
print("done in %0.3fs." % (time() - t1))
gamma = find(csr_matrix(nmf.transform(tfidf)))
glength = len(gamma[0])
chunk_size = 100000
no_cores = 16
make_t = 0
add_t = 0
### Go through in chunks
for i in range(glength // chunk_size + 1):
values_list = []
f = i * chunk_size
l = (i + 1) * chunk_size
if l > glength:
l = glength
docs = range(f, l)
doc_batches = []
for p in range(no_cores):
doc_batches.append([x for x in docs if x % no_cores == p])
pool = Pool(processes=no_cores)
make_t0 = time()
values_list.append(
pool.map(
partial(db.f_gamma_batch,
gamma=gamma,
docsizes=docsizes,
docUTset=ids,
topic_ids=topic_ids,
run_id=run_id), doc_batches))
pool.terminate()
make_t += time() - make_t0
django.db.connections.close_all()
add_t0 = time()
values_list = [item for sublist in values_list for item in sublist]
pool = Pool(processes=no_cores)
if s.search_object_type == 1:
pool.map(db.insert_many_pars, values_list)
elif s.search_object_type == 2:
pool.map(db.insert_many_utterances, values_list)
pool.terminate()
add_t += time() - add_t0
gc.collect()
sys.stdout.flush()
stat.error = stat.error + nmf.reconstruction_err_
stat.errortype = "Frobenius"
## After all the years have been run, update the dtops
tops = Topic.objects.filter(run_id=run_id)
highest_id = Term.objects.all().order_by('-id').first().id
B = np.zeros((tops.count(), highest_id))
#print(tops)
wt = 0
for topic in tops:
tts = TopicTerm.objects.filter(topic=topic).order_by('-score')[:50]
for tt in tts:
B[wt, tt.term.id] = tt.score
wt += 1
col_sum = np.sum(B, axis=0)
vocab_ids = np.flatnonzero(col_sum)
# we only want the columns where there are at least some
# topic-term values
B = B[:, vocab_ids]
nmf = NMF(n_components=stat.K, random_state=1, alpha=.1,
l1_ratio=.5).fit(B)
## Add dynamic topics
dtopics = []
for k in range(stat.K):
dtopic = DynamicTopic(run_id=RunStats.objects.get(pk=run_id))
dtopic.save()
dtopics.append(dtopic)
dtopic_ids = list(
DynamicTopic.objects.filter(run_id=run_id).values_list('id',
flat=True))
print(dtopic_ids)
##################
## Add the dtopic*term matrix to the db
print("Adding topicterms to db")
t1 = time()
ldalambda = find(csr_matrix(nmf.components_))
topics = range(len(ldalambda[0]))
tts = []
pool = Pool(processes=8)
tts.append(
pool.map(
partial(db.f_dlambda,
m=ldalambda,
v_ids=vocab_ids,
t_ids=dtopic_ids,
run_id=run_id), topics))
pool.terminate()
tts = flatten(tts)
gc.collect()
sys.stdout.flush()
django.db.connections.close_all()
DynamicTopicTerm.objects.bulk_create(tts)
print("done in %0.3fs." % (time() - t1))
## Add the wtopic*dtopic matrix to the database
gamma = nmf.transform(B)
for topic in range(len(gamma)):
for dtopic in range(len(gamma[topic])):
if gamma[topic][dtopic] > 0:
tdt = TopicDTopic(topic=tops[topic],
dynamictopic_id=dtopic_ids[dtopic],
score=gamma[topic][dtopic])
tdt.save()
## Calculate the primary dtopic for each topic
for t in tops:
try:
t.primary_dtopic.add(
TopicDTopic.objects.filter(
topic=t).order_by('-score').first().dynamictopic)
t.save()
except:
print("saving primary topic not working")
pass
management.call_command('update_run', run_id)
stat.error = stat.error + nmf.reconstruction_err_
stat.errortype = "Frobenius"
stat.last_update = timezone.now()
stat.runtime = timezone.now() - start_datetime
stat.status = 3 # 3 = finished
stat.save()
totalTime = time() - t0
tm = int(totalTime // 60)
ts = int(totalTime - (tm * 60))
print("done! total time: " + str(tm) + " minutes and " + str(ts) +
" seconds")
print("a maximum of " +
str(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1000) +
" MB was used")
return 0
def plot_tsne(r_ind,
tsne_results,
cats,
nocatids,
ax=None,
verbose=False,
hdoc=False,
legend=True,
sc=None,
heat_var=None,
cmapname=None,
topics=None,
min_cluster=100,
psize=1,
t_thresh=0.8,
eps=1,
n_clusters=1,
doc_sets=None,
clabel_size=8,
words_only=False,
fsize=5,
adjust=False,
draw_highlight_points=False,
dot_legend=True,
nocat_colour='#F0F0F026',
nocat_alpha=0.4,
raster=False,
extension="png",
slinewidth=0.1):
cs = []
sizes = []
xs = []
ys = []
if ax == None:
fig, ax = plt.subplots(dpi=188)
t0 = time()
nocatids = np.argwhere(np.isin(r_ind, nocatids))
if hdoc is not False:
hdocs = nocatids[np.isin(nocatids, hdoc)]
ids = nocatids[np.isin(nocatids, hdoc, invert=True)]
ax.scatter(tsne_results[nocatids, 0],
tsne_results[nocatids, 1],
c=nocat_colour,
s=psize,
alpha=nocat_alpha,
linewidth=slinewidth,
edgecolor='#a39c9c66',
rasterized=raster)
# Draw docs to be highlighted separately
if hdoc is not False:
ax.scatter(tsne_results[hdocs, 0],
tsne_results[hdocs, 1],
c='#F0F0F026',
s=psize,
alpha=1,
linewidth=0.5,
edgecolor='black',
rasterized=raster)
# split the data and add layer by layer to prevent top layer overwriting all
splits = 10
for i in range(splits):
for c in cats:
ids = np.array_split(c["dis"], splits)[i]
if hdoc is not False:
hdocs = ids[np.isin(ids, hdoc)]
ids = ids[np.isin(ids, hdoc, invert=True)]
if len(nocatids) > len(r_ind) / 2:
a = 1
else:
a = 0.7
ax.scatter(
tsne_results[ids, 0],
tsne_results[ids, 1],
#zorder = [math.ceil(random.random()*1) for i in range(len(ids))],
c=c['color'],
s=psize,
alpha=a,
linewidth=slinewidth,
edgecolor='#a39c9c66',
rasterized=raster)
if hdoc is not False:
ax.scatter(tsne_results[hdocs, 0],
tsne_results[hdocs, 1],
c=c["color"],
s=psize,
alpha=1,
linewidth=0.5,
edgecolor='black',
rasterized=raster)
ax.grid(linestyle='-')
if verbose:
print("calculating points took %0.3fs." % (time() - t0))
l = ax.get_xlim()[0]
t = ax.get_ylim()[1]
yextent = ax.get_ylim()[1] - ax.get_ylim()[0]
ysp = yextent * 0.04
draw_leg = False
if legend:
for i, c in enumerate(cats):
prop = len(c['docs']) / len(r_ind)
label = "{} {:.1%}".format(c['name'], prop)
if extension == "pdf":
label = label.replace("%", "\%")
if dot_legend:
if prop > 0.001:
draw_leg = True
ax.scatter(
[],
[],
c=c['color'],
label=label,
linewidth=slinewidth,
edgecolor='#a39c9c66',
)
else:
if c['color'] == "#000000":
tcolor = "white"
else:
tcolor = "black"
ax.text(l * 0.95,
t - ysp - i * ysp,
label,
fontsize=fsize,
color=tcolor,
bbox={
'facecolor': c['color'],
'pad': 3
})
if dot_legend and draw_leg:
ax.legend()
if heat_var:
cmap = cm.get_cmap(cmapname)
ys = [
getattr(cs, heat_var) for cs in sc.objects
if getattr(cs, heat_var) is not None
]
X = np.interp(ys, (np.min(ys), np.max(ys)), (0, +1))
f = interpolate.interp1d(ys, X)
for cs in sc.objects:
if getattr(cs, heat_var):
col = cmap(f(getattr(cs, heat_var)).max())
rect = patches.Rectangle((cs.x1, cs.y1),
cs.x2 - cs.x1,
cs.y2 - cs.y1,
linewidth=1,
edgecolor='r',
facecolor=col,
alpha=0.3)
ax.add_patch(rect)
if topics:
texts = []
for t in topics:
if t.run_id.method == "DT":
atdocscores = Doc.objects.filter(
docdynamictopic__topic=t, ).values_list(
'docdynamictopic__score', flat=True)
thresh = np.quantile(atdocscores, t_thresh)
tdocs = Doc.objects.filter(
docdynamictopic__topic=t,
docdynamictopic__score__gt=thresh).order_by(
'-docdynamictopic__score').values_list('id', flat=True)
else:
atdocscores = Doc.objects.filter(
doctopic__topic=t, ).values_list('doctopic__score',
flat=True)
thresh = np.quantile(atdocscores, t_thresh)
tdocs = Doc.objects.filter(
doctopic__topic=t, doctopic__score__gt=thresh).order_by(
'-doctopic__score').values_list('id', flat=True)
highlight_docs = np.argwhere(np.isin(r_ind, tdocs))[:, 0]
if len(highlight_docs) == 0:
continue
points = tsne_results[highlight_docs]
texts.append(
cluster_label_points(t.title, points, ax, eps, min_cluster,
n_clusters, clabel_size, words_only))
if draw_highlight_points:
ax.scatter(points[:, 0],
points[:, 1],
c=c["color"],
s=psize,
alpha=1,
linewidth=0.5,
edgecolor='black',
rasterized=raster)
if adjust:
texts = list(flatten(texts))
adjust_text(texts,
ax=ax,
arrowprops=dict(arrowstyle="->", color='None', lw=0.5))
if doc_sets:
texts = []
for d in doc_sets:
highlight_docs = np.argwhere(np.isin(r_ind, d['docs']))[:, 0]
points = tsne_results[highlight_docs]
texts.append(
cluster_label_points(d['title'], points, ax, eps, min_cluster,
n_clusters, clabel_size, words_only))
if draw_highlight_points:
ax.scatter(points[:, 0],
points[:, 1],
c=c["color"],
s=psize,
alpha=1,
linewidth=0.5,
edgecolor='black',
rasterized=raster)
if adjust:
texts = list(flatten(texts))
adjust_text(texts,
ax=ax,
arrowprops=dict(arrowstyle="->", color='None', lw=0.5))
if topics:
return texts
def resnet4_D(nn, imgsz,
channels, # 1: gray-scale, 3: color
norm_type, # 'bn', 'none'
requires_grad,
do_bias=True):
depth =4
ker = 3
padding = (ker-1)//2
count = 1
def gen_group0_params(no):
ni = channels
return { 'block0' : {
'conv0': conv2d_params(ni, no, ker, do_bias),
'conv1': conv2d_params(no, no, ker, do_bias),
'convdim': utils.conv_params(ni, no, 1),
'bn': utils.bnparams(no) if norm_type == 'bn' else None
}}
def gen_resnet_D_block_params(ni, no, k, norm_type, do_bias):
return {
'conv0': conv2d_params(ni, ni, k, do_bias),
'conv1': conv2d_params(ni, no, k, do_bias),
'convdim': utils.conv_params(ni, no, 1),
'bn': utils.bnparams(no) if norm_type == 'bn' else None
}
def gen_group_params(ni, no):
return {'block%d' % i: gen_resnet_D_block_params(ni if i == 0 else no, no, ker, norm_type, do_bias) for i in range(count)}
sz = imgsz // (2**depth)
flat_params = utils.cast(utils.flatten({
'group0': gen_group0_params(nn),
'group1': gen_group_params(nn, nn*2),
'group2': gen_group_params(nn*2, nn*4),
'group3': gen_group_params(nn*4, nn*8),
'fc': utils.linear_params(sz*sz*nn*8, 1),
}))
if requires_grad:
utils.set_requires_grad_except_bn_(flat_params)
def block(x, params, base, mode, do_downsample, is_first):
o = x
if not is_first:
o = F.relu(o, inplace=True)
o = F.conv2d(x, params[base+'.conv0.w'], params.get(base+'conv0.b'), padding=padding)
o = F.relu(o, inplace=True)
o = F.conv2d(o, params[base+'.conv1.w'], params.get(base+'conv1.b'), padding=padding)
if norm_type == 'bn':
o = utils.batch_norm(o, params, base + '.bn', mode)
if do_downsample:
o = F.avg_pool2d(o,2)
x = F.avg_pool2d(x,2)
if base + '.convdim' in params:
return o + F.conv2d(x, params[base + '.convdim'])
else:
return o + x
def group(o, params, base, mode, do_downsample, is_first=False):
for i in range(count):
o = block(o, params, '%s.block%d' % (base,i), mode,
do_downsample=(do_downsample and i == count-1),
is_first=(is_first and i == 0))
return o
def f(input, params, mode):
o = group(input, params, 'group0', mode, do_downsample=True, is_first=True)
o = group(o, params, 'group1', mode, do_downsample=True)
o = group(o, params, 'group2', mode, do_downsample=True)
o = group(o, params, 'group3', mode, do_downsample=True)
o = F.relu(o, inplace=True)
o = o.view(o.size(0), -1)
o = F.linear(o, params['fc.weight'], params['fc.bias'])
return o
return f, flat_params
def resnet4_G(input_dim, n0g, imgsz, channels,
norm_type, # 'bn', 'none'
requires_grad,
do_bias=True):
depth = 4
ker = 3
padding = (ker-1)//2
count = 1
def gen_resnet_G_block_params(ni, no, k, norm_type, do_bias):
return {
'conv0': conv2d_params(ni, no, k, do_bias),
'conv1': conv2d_params(no, no, k, do_bias),
'convdim': utils.conv_params(ni, no, 1),
'bn': utils.bnparams(no) if norm_type == 'bn' else None
}
def gen_group_params(ni, no):
return {'block%d' % i: gen_resnet_G_block_params(ni if i == 0 else no, no, ker, norm_type, do_bias) for i in range(count)}
nn = n0g * (2**(depth-1)); sz = imgsz // (2**depth)
flat_params = utils.cast(utils.flatten({
'proj': utils.linear_params(input_dim, nn*sz*sz),
'group0': gen_group_params(nn, nn//2),
'group1': gen_group_params(nn//2, nn//4),
'group2': gen_group_params(nn//4, nn//8),
'group3': gen_group_params(nn//8, nn//8),
'last_conv': conv2d_params(nn//8, channels, ker, do_bias),
}))
if requires_grad:
utils.set_requires_grad_except_bn_(flat_params)
def block(x, params, base, mode, do_upsample):
o = F.relu(x, inplace=True)
if do_upsample:
o = F.interpolate(o, scale_factor=2, mode='nearest')
o = F.conv2d(o, params[base+'.conv0.w'], params.get(base+'.conv0.b'), padding=padding)
o = F.relu(o, inplace=True)
o = F.conv2d(o, params[base+'.conv1.w'], params.get(base+'.conv1.b'), padding=padding)
if norm_type == 'bn':
o = utils.batch_norm(o, params, base + '.bn', mode)
xo = F.conv2d(x, params[base + '.convdim'])
if do_upsample:
return o + F.interpolate(xo, scale_factor=2, mode='nearest')
else:
return o + xo
def group(o, params, base, mode, do_upsample):
for i in range(count):
o = block(o, params, '%s.block%d' % (base,i), mode, do_upsample if i == 0 else False)
return o
def show_shape(o, msg=''):
print(o.size(), msg)
def f(input, params, mode):
o = F.linear(input, params['proj.weight'], params['proj.bias'])
o = o.view(input.size(0), nn, sz, sz)
o = group(o, params, 'group0', mode, do_upsample=True)
o = group(o, params, 'group1', mode, do_upsample=True)
o = group(o, params, 'group2', mode, do_upsample=True)
o = group(o, params, 'group3', mode, do_upsample=True)
o = F.relu(o, inplace=True)
o = F.conv2d(o, params['last_conv.w'], params.get('last_conv.b'), padding=padding)
o = torch.tanh(o)
return o
return f, flat_params
def do_nmf(run_id, no_processes=16):
stat = RunStats.objects.get(run_id=run_id)
qid = stat.query.id
K = stat.K
TopicTerm.objects.filter(run_id=run_id).delete()
DocTopic.objects.filter(run_id=run_id).delete()
Topic.objects.filter(run_id=run_id).delete()
stat.term_set.clear()
alpha = stat.alpha
n_features = stat.max_features
if n_features == 0:
n_features = 100000000000
limit = stat.limit
ng = stat.ngram
# if stat.method=="LD" and stat.lda_library!=RunStats.WARP:
# if stat.max_iter == 200:
# stat.max_iter = 10
# if stat.max_iter > 100:
# stat.max_iter = 90
n_samples = stat.max_iter
stat.process_id = os.getpid()
stat.status = 1
stat.save()
if stat.fulltext:
docs = Doc.objects.filter(query=qid, fulltext__iregex='\w')
else:
docs = Doc.objects.filter(query=qid, content__iregex='\w')
# if we are limiting, probably for testing, then do that
if limit > 0:
docs = docs[:limit]
print('\n###############################\
\n## Topic modeling (method: {}, library: {}) on query {} with {} documents \
and {} topics (run_id: {})\n'.format(stat.method, stat.lda_library, qid,
docs.count(), K, run_id))
# Get the docs into lists
abstracts, docsizes, ids, citations = proc_docs(docs, stoplist,
stat.fulltext,
stat.citations)
scaled_citations = 1 + RobustScaler(with_centering=False).fit_transform(
np.array(citations).reshape(-1, 1))
sentences = [get_sentence(x) for x in abstracts]
w2v = gensim.models.Word2Vec(sentences)
validation_measure = WithinTopicMeasure(ModelSimilarity(w2v))
if stat.fancy_tokenization:
######################################
## A fancy tokenizer
from nltk import wordpunct_tokenize
from nltk import WordNetLemmatizer
from nltk import sent_tokenize
from nltk import pos_tag
from nltk.corpus import stopwords as sw
punct = set(string.punctuation)
from nltk.corpus import wordnet as wn
stopwords = set(sw.words('english'))
if stat.extra_stopwords:
stopwords = stopwords | set(stat.extra_stopwords)
def lemmatize(token, tag):
tag = {
'N': wn.NOUN,
'V': wn.VERB,
'R': wn.ADV,
'J': wn.ADJ
}.get(tag[0], wn.NOUN)
return WordNetLemmatizer().lemmatize(token, tag)
kws = Doc.objects.filter(
query=stat.query,
kw__text__iregex='\w+[\-\ ]').values('kw__text').annotate(
n=Count('pk')).filter(n__gt=len(abstracts) //
200).order_by('-n')
kw_text = set([x['kw__text'].replace('-', ' ') for x in kws])
kw_ws = set([x['kw__text'].replace('-', ' ').split()[0]
for x in kws]) - stopwords
def fancy_tokenize(X):
common_words = set([x.lower() for x in X.split()]) & kw_ws
for w in list(common_words):
w = w.replace('(', '').replace(')', '')
wpat = "({}\W*\w*)".format(w)
wn = [
x.lower().replace('-', ' ')
for x in re.findall(wpat, X, re.IGNORECASE)
]
kw_matches = set(wn) & kw_text
if len(kw_matches) > 0:
for m in kw_matches:
insensitive_m = re.compile(m, re.IGNORECASE)
X = insensitive_m.sub(' ', X)
yield m.replace(" ", "-")
for sent in sent_tokenize(X):
for token, tag in pos_tag(wordpunct_tokenize(sent)):
token = token.lower().strip()
if token in stopwords:
continue
if all(char in punct for char in token):
continue
if len(token) < 3:
continue
if all(char in string.digits for char in token):
continue
lemma = lemmatize(token, tag)
yield lemma
tokenizer = fancy_tokenize
else:
tokenizer = snowball_stemmer()
#######################################
#############################################
# Use tf-idf features for NMF.
print("Extracting tf-idf features ...")
tfidf_vectorizer = TfidfVectorizer(max_df=stat.max_df,
min_df=stat.min_freq,
max_features=n_features,
ngram_range=(ng, ng),
tokenizer=tokenizer,
stop_words=stoplist)
count_vectorizer = CountVectorizer(max_df=stat.max_df,
min_df=stat.min_freq,
max_features=n_features,
ngram_range=(ng, ng),
tokenizer=tokenizer,
stop_words=stoplist)
t0 = time()
if stat.method == "NM":
tfidf = tfidf_vectorizer.fit_transform(abstracts)
vectorizer = tfidf_vectorizer
else:
tfidf = count_vectorizer.fit_transform(abstracts)
vectorizer = count_vectorizer
print("done in %0.3fs." % (time() - t0))
stat.tfidf_time = time() - t0
stat.save()
if citations is not False:
tfidf = tfidf.multiply(scaled_citations)
del abstracts
gc.collect()
if stat.db:
vocab = vectorizer.get_feature_names()
vocab_ids = []
pool = Pool(processes=no_processes)
vocab_ids.append(pool.map(partial(add_features, run_id=run_id), vocab))
pool.terminate()
#del vocab
vocab_ids = vocab_ids[0]
## Make some topics
django.db.connections.close_all()
topic_ids = db.add_topics(K, run_id)
gc.collect()
# Fit the NMF model
print("Fitting the model with tf-idf features, "
"n_samples=%d and n_features=%d..." % (n_samples, n_features))
t0 = time()
if stat.method == "NM":
model = NMF(n_components=K,
random_state=1,
alpha=alpha,
l1_ratio=.1,
verbose=True,
init='nndsvd',
max_iter=n_samples).fit(tfidf)
dtm = csr_matrix(model.transform(tfidf))
components = csr_matrix(model.components_)
else:
if stat.lda_library == RunStats.LDA_LIB:
model = lda.LDA(
n_topics=K,
alpha=stat.alpha,
eta=stat.alpha,
n_iter=stat.max_iter * 10,
).fit(tfidf)
dtm = model.doc_topic_
components = csr_matrix(model.components_)
elif stat.lda_library == RunStats.WARP:
# Export warp lda
try:
warp_path = settings.WARP_LDA_PATH
os.chdir(warp_path)
except:
print(
"warplda is not installed, or its path is not defined in settings, exiting...."
)
return
fname = wpu.export_warp_lda(ids, tfidf, vocab, run_id)
# preformat
os.system(f'./format -input {fname} -prefix {run_id} train')
# Run warp lda
runcmd = f'./warplda --prefix {run_id} --k {stat.K}'
if stat.alpha:
runcmd += f' -alpha {stat.alpha}'
if stat.beta:
runcmd += f' -beta {stat.beta}'
else:
stat.beta = 0.01 # default beta value
stat.save()
if stat.max_iter:
runcmd += f' --niter {stat.max_iter}'
runcmd += ' train.model'
print("Running warplda.")
os.system(runcmd)
print("Finished running warplda, importing results.")
warp_vocab = np.loadtxt(f'{run_id}.vocab', dtype=str)
warp_translate = np.argsort(warp_vocab).argsort()
# Import warp lda as matrices
with open(f'{run_id}.model', 'r') as f:
for i, l in enumerate(f):
if i == 0:
M = int(l.split()[0])
N = int(l.split()[1])
components = lil_matrix((N, M))
else:
largs = l.split('\t')[1].strip().split()
for la in largs:
wid = warp_translate[i - 1]
t, n = la.split(':')
components[int(t), wid] = int(n)
components = components.todense()
for k in range(components.shape[0]):
components[k, :] = (components[k, :] + stat.beta) / (
components[k, :].sum() + stat.K * stat.beta)
components = csr_matrix(components)
dtm = lil_matrix((len(ids), N))
with open(f'{run_id}.z.estimate', 'r') as f:
for i, l in enumerate(f):
largs = l.split(' ', maxsplit=1)[1].strip().split()
for la in largs:
w, t = la.split(':')
dtm[i, int(t)] += 1
theta = dtm.todense()
for i in range(dtm.shape[0]):
theta[i, :] = (theta[i, :] + stat.alpha) / (
theta[i, :].sum() + stat.K * stat.alpha)
dtm = csr_matrix(theta)
else:
model = LDA(
n_components=K,
doc_topic_prior=stat.alpha,
topic_word_prior=stat.beta,
learning_method=stat.get_lda_learning_method_display().lower(),
max_iter=stat.max_iter,
n_jobs=2).fit(tfidf)
dtm = csr_matrix(model.transform(tfidf))
components = csr_matrix(model.components_)
print("done in %0.3fs." % (time() - t0))
stat.nmf_time = time() - t0
if stat.db:
## Add topics terms
print("Adding topicterms to db")
t0 = time()
ldalambda = find(components)
topics = range(len(ldalambda[0]))
tts = []
pool = Pool(processes=no_processes)
tts.append(
pool.map(
partial(db.f_lambda,
m=ldalambda,
v_ids=vocab_ids,
t_ids=topic_ids,
run_id=run_id), topics))
pool.terminate()
tts = flatten(tts)
gc.collect()
sys.stdout.flush()
django.db.connections.close_all()
TopicTerm.objects.bulk_create(tts)
print("done in %0.3fs." % (time() - t0))
stat.db_time = stat.db_time + time() - t0
## Add topic-docs
print("Adding DocTopics")
gamma = find(dtm)
glength = len(gamma[0])
chunk_size = 100000
parallel_add = True
all_dts = []
make_t = 0
add_t = 0
t0 = time()
### Go through in chunks
for i in range(glength // chunk_size + 1):
dts = []
values_list = []
f = i * chunk_size
l = (i + 1) * chunk_size
if l > glength:
l = glength
docs = range(f, l)
doc_batches = []
for p in range(no_processes):
doc_batches.append([x for x in docs if x % no_processes == p])
pool = Pool(processes=no_processes)
make_t0 = time()
values_list.append(
pool.map(
partial(db.f_gamma_batch,
gamma=gamma,
docsizes=docsizes,
docUTset=ids,
topic_ids=topic_ids,
run_id=run_id), doc_batches))
#dts.append(pool.map(partial(f_gamma, gamma=gamma,
# docsizes=docsizes,docUTset=ids,topic_ids=topic_ids),doc_batches))
pool.terminate()
make_t += time() - make_t0
print(make_t)
django.db.connections.close_all()
add_t0 = time()
values_list = [item for sublist in values_list for item in sublist]
pool = Pool(processes=no_processes)
pool.map(insert_many, values_list)
pool.terminate()
add_t += time() - add_t0
print(add_t)
gc.collect()
sys.stdout.flush()
stat.db_time = stat.db_time + time() - t0
print("done in %0.3fs." % (time() - t0))
em = 0
for i in range(K):
if dtm[:, i].nnz == 0:
em += 1
stat.empty_topics = em
if stat.method == "NM":
stat.error = model.reconstruction_err_
stat.errortype = "Frobenius"
elif stat.method == "LD":
if stat.lda_library == RunStats.LDA_LIB:
stat.error = model.loglikelihood()
stat.errortype = "Log likelihood"
stat.iterations = model.n_iter
elif stat.lda_library == RunStats.WARP:
pass
else:
stat.error = model.perplexity(tfidf)
stat.errortype = "Perplexity"
stat.iterations = model.n_iter_
stat.last_update = timezone.now()
stat.status = 3
stat.save()
if stat.db:
term_rankings = []
topics = Topic.objects.filter(run_id=run_id)
for topic in topics:
term_ranking = list(
Term.objects.filter(topicterm__topic=topic).order_by(
'-topicterm__score').values_list('title', flat=True)[:50])
term_rankings.append(term_ranking)
stat.coherence = validation_measure.evaluate_rankings(term_rankings)
stat.save()
if stat.db:
management.call_command('update_run', run_id)