def calcBackProject(image, tags, histograms):
probability = {}
cl.kmeans(image)
for tag in tags:
print tag
result = cv2.calcBackProject([image], [0, 1, 2], histograms[tag], [0, 180, 0, 256, 0, 256], 1)
probabilityValue = cv2.countNonZero(result)/float(image.shape[0] * image.shape[1])
probability[tag] = probabilityValue
return probability
def k (tags, data, K, tries=5):
#first get the clustering info
idxs=kmeans(str(data), K, tries)
idxs=eval(idxs)
print len(idxs)==len(tags)
#for the clusters, get the numbers for eac``
return idxs
def onlytransfer(n_clusters, fb_kmeans=True):
X = np.load('data/chan/8chan_pol/VGG16/fc1/featuresx.npy')
X = X.astype('float32')
pathfile = open('data/chan/8chan_pol/VGG16/fc1/paths.txt', "r")
pathlist = pathfile.readlines()
pathlist = [path[:-1] for path in pathlist]
pathfile.close()
if fb_kmeans:
#features = torch.from_numpy(features)
images_lists, loss = kmeans(X,
nmb_clusters=n_clusters,
preprocess=False)
Y_pred = arrange_clustering(images_lists)
else:
km = KMeans(n_clusters=n_clusters, n_init=20)
Y_pred = km.fit_predict(X)
for y_pred, path in zip(Y_pred, pathlist):
savedir = '/home/elahe/NortfaceProject/codes/DEC-keras/results/clusters/8chan_pol/%s/%s/%s' % (
'transfer', 'fc1', y_pred)
if not os.path.exists(savedir):
os.makedirs(savedir)
shutil.copy(path, savedir)
def main():
# check command-line arguments
if len(sys.argv) not in [3, 4]:
print "Error, incorrect number of arguments"
usage()
sys.exit(1)
k = check_k(sys.argv[1])
check_argv(sys.argv[2])
if len(sys.argv) == 4: # optional, file containing annotations
check_argv(sys.argv[3])
# initialize gene matrix using annotations
geneMatrix = construct_geneMatrix(sys.argv[2], sys.argv[3])
else:
# index instances by line number in original file
geneMatrix = construct_geneMatrix(sys.argv[2], None)
#normalize matrix
geneMatrix = normalize_matrix(geneMatrix)
# call kmeans clustering on input files
sse, aic, silhouette = kmeans(geneMatrix, k)
# print results
print "K-means with k = %d\n" % k
print "%-15s %.2f\n%-15s %.2f\n%-15s %.2f\n" % ('SSE:', sse, 'AIC:', aic,
'Silhouette:', silhouette)
def run_k_means(self):
print("RUNNING KMEANS")
print("Points")
print(self.points)
print("Starting Centers: {}".format([self.points[0], self.points[1]]))
centers, clusters = clustering.kmeans(self.points, [self.points[0], self.points[1]] )
# whichever center is lower is the blue center
blue_center = centers[0]
if centers[1][1] < centers[0][1]:
blue_center = centers[1]
# draw the centers and points
self.click_canvas.delete("all")
for center_i, center in enumerate(centers):
color = None
if center is blue_center:
color='blue'
else:
color='red'
print("Cluster {} with center {}".format(color, center))
print("Cluster Points:")
print(clusters[center_i])
self.draw_center(center, color=color)
for cluster_coord in clusters[center_i]:
self.draw_dot(cluster_coord, color=color)
def quantize_single_sample(points, k):
"""
Applies quantization to a single sample with accelerometer observations.
"""
X = np.asarray(points, dtype=np.float)
centroids, _ = kmeans(X, n_clusters=k)
feature_vector = centroids.flatten()
return feature_vector
def __init__(self):
super(ClustersWidget, self).__init__()
layout = QtGui.QVBoxLayout()
clusters = kmeans()
for cluster in clusters:
if len(cluster.palettes) == 0: continue
cw = ClusterWidget(cluster)
layout.addWidget(cw)
self.setLayout(layout)
def test_ffh_10(self):
finalObj = []
for rep in range(10):
np.random.seed(1234 + rep)
mu0 = clustering.initialize_clusters(self.X, 10, 'ffh')
(mu, z, obj) = clustering.kmeans(self.X, mu0, doPlot=False)
finalObj.append(obj[-1])
targetObj = 0.44031610993896342
self.assertTrue(abs(np.mean(finalObj) - targetObj) <= 1e4)
def test_km_plus_plus_10(self):
finalObj = []
for rep in range(20):
np.random.seed(1234 + rep)
mu0 = clustering.initialize_clusters(self.X, 10, 'km++')
(mu, z, obj) = clustering.kmeans(self.X, mu0, doPlot=False)
finalObj.append(obj[-1])
targetObj = 0.4392510535744174
self.assertTrue(abs(np.mean(finalObj) - targetObj) <= 1e4)
def cluster(algorithm, similarity, encoding, outlier, rep, chart_id, key=None):
"""Returns the cluster each time series was placed in.
Args:
algorithm: The algorithm used for clustering. Must be "K-means"
or "DBSCAN".
similarity: The similarity measure used for scaling the data
before clustering. Must be "Proximity" or "Correlation".
encoding: The method used for encoding the labels. Must
be "None" or "One-Hot".
outlier: Whether outliers are identified, must be "on" or "off".
rep: Whether the data is represented as "lines" or "bands".
chart_id: The id of the file containing the data that k-means
clustering is run on.
key: The key for the time series labels that are saved. If None,
then all label values may be kept, otherwise only label
values with that key are kept.
Returns:
A json with a list containing the label of the cluster each
time series was grouped in, and the min_max of each cluster and
the corresponding dates for each value if rep == "bands",
otheriwse and dates are empty lists.
"""
data = load_data(chart_id)
if "timeSeries" not in data:
return data
(time_series_data, label_dict, ts_to_labels, dates,
old_range) = clustering.time_series_array(data, key)
ts_data_updated = clustering.preprocess(time_series_data, encoding,
similarity, ts_to_labels,
algorithm)
if algorithm == "k-means":
labels = clustering.kmeans(ts_data_updated, outlier).tolist()
elif algorithm == "k-means-constrained" or algorithm == "k-medians":
labels = clustering.kmeans_kmedians(ts_data_updated, label_dict,
ts_to_labels, algorithm,
outlier).tolist()
elif algorithm == "zone":
labels = clustering.cluster_zone(label_dict, ts_to_labels)
else:
labels = clustering.dbscan(ts_data_updated, similarity, encoding,
outlier).tolist()
min_max, ordered_dates, outlier_indexes = [], [], []
if rep == "bands":
min_max, ordered_dates, outlier_indexes = clustering.clusters_min_max(
time_series_data, labels, dates, old_range, outlier)
return jsonify({
"cluster_labels": labels,
"min_max": min_max,
"dates": ordered_dates,
"outlier_indexes": outlier_indexes
})
def test_kmeans(self):
# Run k-means clustering on the test set using 4 clusters and check if the cluster centres
# (centroids) lie close to the expected centroids based on a fixed seed
centroids, assignments, numIts = clustering.kmeans(self.data,
self.numClusters,
maxNumIts=10)
expectedCentroids = np.float32([[2.80, -2.73], [-3.38, -2.94],
[2.62, 3.10], [-2.46, 2.78]])
# np.testing.assert_almost_equal(centroids, expectedCentroids, 2)
if self.plotResults:
self.plotData_kMeans(self.data, centroids, assignments, 1)
def step2_cal():
"""第二步计算，判断其他类是否需要分裂，若需要，则对其他类进行文本聚类，并做聚类评价
"""
# 聚类评价时选取TOPK_FREQ_WORD的高频词
TOPK_FREQ_WORD = 50
# 聚类评价时最小簇的大小
LEAST_SIZE = 8
# 判断其他类是否需要分裂
ifsplit = event.check_ifsplit(initializing)
print '[%s] ' % ts2datetime(int(time.time())), 'event ', eventid, ' split ', ifsplit, ' %s start step2' % ts2datetime(timestamp)
if ifsplit:
inputs, kmeans_cluster_num, reserve_num = event.getOtherSubEventInfos(initializing)
print eventid, ' after classify before split: ', len(inputs), kmeans_cluster_num, reserve_num
if len(inputs) > 2:
items = []
for r in inputs:
r["title"] = r["title"].encode("utf-8")
r["content"] = r["content168"].encode("utf-8")
items.append(r)
# kmeans聚类
kmeans_results = kmeans(items, k=kmeans_cluster_num)
# 聚类评价
if initializing or now_hour == 0:
min_tfidf = event.get_min_tfidf()
final_cluster_results, tfidf_dict = cluster_evaluation(kmeans_results, top_num=reserve_num, topk_freq=TOPK_FREQ_WORD, least_size=LEAST_SIZE, min_tfidf=min_tfidf)
else:
# 每小时聚类时，不用和已有簇的最小tfidf作比
final_cluster_results, tfidf_dict = cluster_evaluation(kmeans_results, top_num=reserve_num, topk_freq=TOPK_FREQ_WORD, least_size=LEAST_SIZE)
# 更新新闻簇标签，更新子事件表
for label, items in final_cluster_results.iteritems():
if label == "other":
label = event.getOtherSubEventID()
event.save_subevent(label, timestamp)
if label != event.getOtherSubEventID():
# 更新每类的tfidf
event.update_subevent_tfidf(label, tfidf_dict[label])
for r in items:
news = News(r["_id"], event.id)
news.update_news_subeventid(label)
else:
print 'inputs less than 2, kmeans aborted'
print '[%s] ' % ts2datetime(int(time.time())), 'event ', eventid, ' %s end step2' % ts2datetime(timestamp)
def kmeans(model_file=None, nclusters=None, output_file=None):
word_vectors = KeyedVectors.load_word2vec_format(model_file, binary=False)
clusters = clustering.kmeans(word_vectors, nclusters)[0]
if output_file:
out = open(output_file, 'w')
else:
out = sys.stdout
for k in clusters:
out.write("%s\n" % " ".join([fn for fn in clusters[k]]))
if output_file:
out.close()
def getOptimalWordCluster(self, target_words, bomb_words):
''' Creates clusters of words by cosine similarity, with increasing
centriod count until a cluster is created containing only target_words
params:
target_words (iterable, str):
words to maximize in clusters
bomb_words (iterable, str):
words to be avoided in clusters
returns:
potential_groups (tuple)
A tuple containing the best cluster of words
format -> (group center word embedding, list of words in group)
'''
if len(target_words) < 1:
raise ValueError("Empty target word list provided")
if len(target_words) == 1:
return target_words[0]
full_word_set = np.array(target_words + bomb_words)
embeddings = self.getWordEmbeddings(full_word_set)
potential_groups = []
num_groups = max(int(len(target_words) / 2), 1)
# keep clustering until found a group of similar words without bomb_words
# increase number of clusters after each failed iteration
while not potential_groups:
grouper = clustering.kmeans(k=num_groups, measure='cosine')
grouper.fit(embeddings)
cluster_labels = np.array(grouper.train_labels)
#verify if any potential clusters were created
for cluster in np.unique(cluster_labels):
cluster_indices = cluster_labels == cluster
current_cluster_words = full_word_set[cluster_indices]
if len(current_cluster_words)>0 and \
not any([word in bomb_words for word in current_cluster_words]):
potential_groups.append(
[grouper.centroids[cluster], current_cluster_words])
num_groups += 1
# sort potential_groups by number of group members
potential_groups = sorted(potential_groups,
key=lambda x: len(x[1]),
reverse=True)
return potential_groups[0]
def main():
np.random.seed(1)
data_path = join(dirname(__file__), 'datasets', 'blobs.csv')
X, _ = read_csv(data_path)
figure, axes = plt.subplots(2, 2, figsize=(12, 12))
axes = axes.flatten()
font_path = join(dirname(__file__), 'fonts', 'RobotoSlab-Regular.ttf')
font = font_manager.FontProperties(fname=font_path)
font.set_size(16)
gray = '#3c3c3c'
for i, n_clusters in enumerate((2, 3, 4, 5)):
print('Running K-means with k=%d' % n_clusters)
centroids, score = kmeans(X, n_clusters)
print('Best inertia score: %.2f' % score)
letter = string.ascii_letters[i]
title = '(%s) k=%d, inertia=%2.2f' % (letter, n_clusters, score)
labels = assign_labels(X, centroids)
get_color = palette()
colors = [get_color(l) for l in labels]
axes[i].scatter(X[:, 0], X[:, 1], c=colors, s=50, alpha=0.6)
axes[i].set_title(title, fontproperties=font, color=gray)
axes[i].set_xticks([])
axes[i].set_yticks([])
for spine in ('top', 'right', 'bottom', 'left'):
axes[i].spines[spine].set_color(gray)
for (x, y) in centroids:
axes[i].plot(x,
y,
color='white',
markeredgewidth=1,
markeredgecolor=gray,
markersize=10,
marker='d')
figure.tight_layout()
figure.savefig('clusters.png', transparent=False)
def frequency(similarity, algorithm, label_encoding, chart_id):
"""Runs kmeans and gets the frequencies of labels per time series
and labels per cluster.
Args:
similarity: The similarity measure used for scaling the data
before clustering. Must be "proximity" or "correlation".
label_encoding: The method used for encoding the labels. Must
be "none" or "one-hot".
chart_id: The id of the file containing the data that k-means
clustering is run on.
Returns:
A json with a list of cluster labels generated by running
kmeans, an array of labels per time series and an array of
labels per cluster.
"""
data = load_data(chart_id)
if "timeSeries" not in data:
return data
(time_series_data, label_dict, ts_to_labels, _,
_) = clustering.time_series_array(data, None)
time_series_data = clustering.preprocess(time_series_data, label_encoding,
similarity, ts_to_labels,
"k-means")
if algorithm == "k-means":
labels = clustering.kmeans(time_series_data, "off")
elif algorithm == "k-means-constrained":
labels = clustering.kmeans_kmedians(time_series_data, label_dict,
ts_to_labels, algorithm, "off")
cluster_labels = clustering.cluster_to_labels(labels, ts_to_labels)
ordered_labels, ordered_clusters, ordered_ts = clustering.sort_labels(
label_dict, cluster_labels, ts_to_labels)
return jsonify({
"labels": ordered_labels,
"ts_labels": ordered_ts.tolist(),
"cluster_labels": ordered_clusters.tolist()
})
def get_evaluation_scores(X,
ground_truth_labels,
clusters,
filepath,
ignored_indices=(),
result_file=None,
files=None):
if result_file is not None:
X = read_distance_matrix_from_file(result_file, (),
len(ground_truth_labels))
n_clusters_, predicted_labels = kmeans(X, clusters)
ari_k = metrics.adjusted_rand_score(ground_truth_labels, predicted_labels)
n_clusters_, predicted_labels = spectral_clustering(X, clusters)
ari_s = metrics.adjusted_rand_score(ground_truth_labels, predicted_labels)
filepath.write("Silhouttee, K-mean ARI, Spectral-ARI\n")
filepath.write("%s,%s,%s\n" %
(silhouette_score(X, ground_truth_labels), ari_k, ari_s))
def train_kmeans_layer(X, in_shape, K, ksize, n_patches_per_image, prep_type=None, pad_h=0, pad_w=0, repeat=1, **kwargs):
train_data = get_random_patches(X, in_shape, ksize, n_patches_per_image, pad_h=pad_h, pad_w=pad_w)
if prep_type is not None:
prep = pp.choose_preprocessor_by_name(prep_type)
prep.train(train_data)
train_data = prep.process(train_data)
else:
prep = None
C_best = None
loss_best = None
for i_repeat in xrange(repeat):
print '*** repeat #%d ***' % (i_repeat + 1)
gnp.free_reuse_cache()
C, _, loss = clust.kmeans(train_data, K, **kwargs)
if loss_best is None or loss < loss_best:
loss_best = loss
C_best = C
print '>>> best loss: %.2f' % loss_best
return KMeansModel(C_best, kwargs.get('dist', 'euclidean'), in_shape.c, ksize, prep)
def train_kmeans_layer(X,
in_shape,
K,
ksize,
n_patches_per_image,
prep_type=None,
pad_h=0,
pad_w=0,
repeat=1,
**kwargs):
train_data = get_random_patches(X,
in_shape,
ksize,
n_patches_per_image,
pad_h=pad_h,
pad_w=pad_w)
if prep_type is not None:
prep = pp.choose_preprocessor_by_name(prep_type)
prep.train(train_data)
train_data = prep.process(train_data)
else:
prep = None
C_best = None
loss_best = None
for i_repeat in xrange(repeat):
print '*** repeat #%d ***' % (i_repeat + 1)
gnp.free_reuse_cache()
C, _, loss = clust.kmeans(train_data, K, **kwargs)
if loss_best is None or loss < loss_best:
loss_best = loss
C_best = C
print '>>> best loss: %.2f' % loss_best
return KMeansModel(C_best, kwargs.get('dist', 'euclidean'), in_shape.c,
ksize, prep)
def recolor_left_half(rgb_lh_arr,
number_of_colors,
useElbowMethod=False,
low=2,
high=10,
num_of_iters=1000):
rgb_lh_arr_flat_shape = (rgb_lh_arr.shape[0] * rgb_lh_arr.shape[1], 3)
rgb_lh_arr_flat = rgb_lh_arr.reshape(
rgb_lh_arr_flat_shape
) # matrix flattened into a vector of data points (r,g,b)
if not useElbowMethod: # if elbow method is False
number_of_clusters = number_of_colors # k = given number of colors
else:
elbow_data = cl.elbow(
rgb_lh_arr_flat, low, high,
num_of_iters) # compute sse for k = low to k = high
df = pd.DataFrame(elbow_data, columns=['k', 'cost'])
cl.plot_elbow_data(df)
number_of_clusters = int(
input('Enter value of k at elbow point in the plot'))
# number_of_clusters = number_of_colors
centroids_arr, assigned_clusters_arr_flat = cl.kmeans(
rgb_lh_arr_flat, number_of_clusters, 1000) # execute k-means algorithm
assigned_clusters_arr = assigned_clusters_arr_flat.reshape(
(rgb_lh_arr.shape[0], rgb_lh_arr.shape[1])) # reshape into a matrix
recolored_lh_arr = np.zeros(
(rgb_lh_arr.shape)) # array of zeros to recolor left-half of an image
for index, centroid in enumerate(centroids_arr):
bool_indices = (assigned_clusters_arr == index) # boolean array
recolored_lh_arr[bool_indices] = centroid # vectorized assignment
recolored_lh_arr = np.asarray(
recolored_lh_arr,
dtype='uint8') # convert all float numbers into 8-bit integers (0-255)
centroids_arr = centroids_arr.astype(
dtype='uint8') # convert all float numbers into 8-bit integers (0-255)
return centroids_arr, assigned_clusters_arr, recolored_lh_arr, number_of_clusters
def add_filter(filters_list, column_index, column):
from clustering import kmeans
filters_list.append((column_index, kmeans(column)))
return filters_list
from clustering import svdpca,kmeans import os, sys, string, numpy ss=[[1,2],[4,2],[300,200]] ll=svdpca(str(ss), 3, 2); print ll; ss=[[300,200],[1,2],[4,2]] ll=kmeans(str(ss), 2, 2); print ll; #exchange #sss = [[1,2],[4,2],[3,1]] #ll=svdpca(str(ss), 3,2); #print ll; #ll=svdpca(str(sss), 3,2); #print ll;
def _select_centers(self, X):
# random_args = np.random.choice(len(X), self.n_neurons)
# centers = X[random_args]
centers, _, sigmas = kmeans(X, self.n_neurons, 'kmeanspp', 100)
return centers, sigmas
def sensors_keywords_detection(task_detail):
task_name = task_detail[0]
social_sensors = task_detail[1]
keywords_list = task_detail[2]
sensitive_words = task_detail[3]
stop_time = task_detail[4]
forward_warning_status = task_detail[5]
ts = task_detail[7]
forward_result = get_forward_numerical_info(task_name, ts, keywords_list)
# 1. 聚合前12个小时内传感人物发布的所有与关键词相关的原创微博
forward_origin_weibo_list = query_mid_list(ts-time_interval, keywords_list, forward_time_range, 1, social_sensors)
# 2. 聚合当前阶段内的原创微博
current_mid_list = query_mid_list(ts, keywords_list, time_interval, 1, social_sensors)
all_mid_list = []
all_mid_list.extend(current_mid_list)
all_mid_list.extend(forward_origin_weibo_list)
all_mid_list = list(set(all_mid_list))
print len(all_mid_list)
# 3. 查询当前的原创微博和之前12个小时的原创微博在当前时间内的转发和评论数, 聚合按照message_type
statistics_count = query_related_weibo(ts, all_mid_list, time_interval, keywords_list, 1, social_sensors)
current_total_count = statistics_count['total_count']
# 当前阶段内所有微博总数
print "current all weibo: ", statistics_count
current_origin_count = statistics_count['origin']
current_retweeted_count = statistics_count['retweeted']
current_comment_count = statistics_count['comment']
# 4. 聚合当前时间内积极、中性、悲伤、愤怒情绪分布
sentiment_count = {"0": 0, "1": 0, "2": 0, "3": 0}
datetime = ts2datetime(ts)
datetime_1 = ts2datetime(ts-time_interval)
if datetime == datetime_1:
index_name = flow_text_index_name_pre + datetime
else:
index_name = flow_text_index_name_pre + datetime_1
exist_es = es_text.indices.exists(index_name)
if exist_es:
search_results = aggregation_sentiment_related_weibo(ts, all_mid_list, time_interval, keywords_list, 1)
sentiment_count = search_results
print "sentiment_count: ", sentiment_count
negetive_count = sentiment_count['2'] + sentiment_count['3']
# 5. 那些社会传感器参与事件讨论
query_body = {
"query":{
"filtered":{
"filter":{
"bool":{
"must":[
{"range":{
"timestamp":{
"gte": ts - time_interval,
"lt": ts
}
}},
{"terms":{"uid": social_sensors}}
],
"should":[
{"terms": {"root_mid": all_mid_list}},
{"terms": {"mid": all_mid_list}}
]
}
}
}
},
"size": 10000
}
datetime = ts2datetime(ts)
datetime_1 = ts2datetime(ts - time_interval)
if datetime == datetime_1:
index_name = flow_text_index_name_pre + datetime
else:
index_name = flow_text_index_name_pre + datetime_1
search_results = es_text.search(index=index_name, doc_type=flow_text_index_type, body=query_body)['hits']['hits']
attend_users = []
if search_results:
for item in search_results:
attend_users.append(item['_source']['uid'])
important_users = list(set(attend_users))
print "important users", important_users
# 6. 敏感词识别，如果传感器的微博中出现这么一个敏感词，那么就会预警------PS.敏感词是一个危险的设置
sensitive_origin_weibo_number = 0
sensitive_retweeted_weibo_number = 0
sensitive_comment_weibo_number = 0
sensitive_total_weibo_number = 0
if sensitive_words:
query_sensitive_body = {
"query":{
"filtered":{
"filter":{
"bool":{
"must":[
{"range":{
"timestamp":{
"gte": ts - time_interval,
"lt": ts
}}
},
{"terms": {"keywords_string": sensitive_words}},
{"terms": {"uid": social_sensors}}
]
}
}
}
},
"aggs":{
"all_list":{
"terms":{"field": "message_type"}
}
}
}
sensitive_results = es_text.search(index=index_name, doc_type=flow_text_index_type, body=query_sensitive_body)['aggregations']['all_list']["buckets"]
if sensitive_results:
for item in sensitive_results:
if int(item["key"]) == 1:
sensitive_origin_weibo_number = item['doc_count']
elif int(item["key"]) == 2:
sensitive_comment_weibo_number = item['doc_count']
elif int(item["key"]) == 3:
sensitive_retweeted_weibo_number = item["doc_count"]
else:
pass
sensitive_total_weibo_number = sensitive_origin_weibo_number + sensitive_comment_weibo_number + sensitive_retweeted_weibo_number
burst_reason = signal_nothing_variation
warning_status = signal_nothing
finish = unfinish_signal # "0"
if sensitive_total_weibo_number: # 敏感微博的数量异常
print "======================"
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason = signal_sensitive_variation
if forward_result[0]:
# 根据移动平均判断是否有时间发生
mean_count = forward_result[1]
std_count = forward_result[2]
mean_sentiment = forward_result[3]
std_sentiment = forward_result[4]
if current_total_count > mean_count+1.96*std_count: # 异常点发生
print "====================================================="
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason += signal_count_varition # 数量异常
if negetive_count > mean_sentiment+1.96*std_sentiment:
warning_status = signal_brust
burst_reason += signal_sentiment_varition # 负面情感异常, "12"表示两者均异常
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
if int(stop_time) <= ts: # 检查任务是否已经完成
finish = finish_signal
tmp_burst_reason = burst_reason
topic_list = []
# 7. 感知到的事, all_mid_list
if burst_reason: # 有事情发生
text_list = []
mid_set = set()
if signal_sensitive_variation in burst_reason:
query_sensitive_body = {
"query":{
"filtered":{
"filter":{
"bool":{
"must":[
{"range":{
"timestamp":{
"gte": ts - time_interval,
"lt": ts
}}
},
{"terms": {"keywords_string": sensitive_words}}
]
}
}
}
},
"size": 10000
}
if social_sensors:
query_sensitive_body['query']['filtered']['filter']['bool']['must'].append({"terms":{"uid": social_sensors}})
sensitive_results = es_text.search(index=index_name, doc_type=flow_text_index_type, body=query_sensitive_body)['hits']["hits"]
if sensitive_results:
for item in sensitive_results:
iter_mid = item['_source']['mid']
iter_text = item['_source']['text']
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
if iter_mid not in mid_set:
text_list.append(temp_dict) # 整理后的文本，mid，text
mid_set.add(iter_mid)
burst_reason.replace(signal_sensitive_variation, "")
if burst_reason and all_mid_list:
sensing_text = es_text.mget(index=index_name, doc_type=flow_text_index_type, body={"ids": all_mid_list}, fields=["mid", "text"])["docs"]
if sensing_text:
for item in sensing_text:
if item['found']:
iter_mid = item["fields"]["mid"][0]
iter_text = item["fields"]["text"][0]
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
if iter_mid not in mid_set:
text_list.append(temp_dict)
mid_set.add(iter_mid)
if len(text_list) == 1:
top_word = freq_word(text_list[0])
topic_list = top_word.keys()
elif len(text_list) == 0:
topic_list = []
tmp_burst_reason = "" #没有相关微博，归零
print "***********************************"
else:
feature_words, input_word_dict = tfidf(text_list) #生成特征词和输入数据
word_label, evaluation_results = kmeans(feature_words, text_list) #聚类
inputs = text_classify(text_list, word_label, feature_words)
clustering_topic = cluster_evaluation(inputs)
sorted_dict = sorted(clustering_topic.items(), key=lambda x:x[1], reverse=True)[0:5]
topic_list = []
if sorted_dict:
for item in sorted_dict:
topic_list.append(word_label[item[0]])
print "topic_list:", topic_list
if not topic_list:
tmp_burst_reason = signal_nothing_variation
warning_status = signal_nothing
results = dict()
results['sensitive_origin_weibo_number'] = sensitive_origin_weibo_number
results['sensitive_retweeted_weibo_number'] = sensitive_retweeted_weibo_number
results['sensitive_comment_weibo_number'] = sensitive_comment_weibo_number
results['sensitive_weibo_total_number'] = sensitive_total_weibo_number
results['origin_weibo_number'] = current_origin_count
results['retweeted_weibo_number'] = current_retweeted_count
results['comment_weibo_number'] = current_comment_count
results['weibo_total_number'] = current_total_count
results['sentiment_distribution'] = json.dumps(sentiment_count)
results['important_users'] = json.dumps(important_users)
results['burst_reason'] = tmp_burst_reason
results['timestamp'] = ts
if tmp_burst_reason:
results["clustering_topic"] = json.dumps(topic_list)
# es存储当前时段的信息
doctype = task_name
es_user_portrait.index(index=index_sensing_task, doc_type=doctype, id=ts, body=results)
# 更新manage social sensing的es信息
temporal_result = es_user_portrait.get(index=index_manage_social_task, doc_type=task_doc_type, id=task_name)['_source']
temporal_result['warning_status'] = warning_status
temporal_result['burst_reason'] = tmp_burst_reason
temporal_result['finish'] = finish
history_status = json.loads(temporal_result['history_status'])
history_status.append([ts, ' '.join(keywords_list), warning_status])
temporal_result['history_status'] = json.dumps(history_status)
es_user_portrait.index(index=index_manage_social_task, doc_type=task_doc_type, id=task_name, body=temporal_result)
return "1"
def rbf_train(x,
y,
gamma=1,
x_validation=None,
y_validation=None,
num_hidden_nodes=10,
output="regression",
num_epochs=100,
alpha=1,
mini_batch_size=1,
compute_loss=True):
# Preprocess the input and output data
x_matrix = x
y = y.copy()
if len(y.shape) == 1:
y = y[:, None]
if y_validation is not None:
y_validation = y_validation.copy()
if len(y_validation.shape) == 1:
y_validation = y_validation[:, None]
# Select the hidden and output activation functions
activation_function = activation_functions.rbf
out_activation_function, out_grad_activation_function, loss = select_output_type(
output, y)
# Initialize the weights
w_hidden = clustering.kmeans(x_matrix,
num_hidden_nodes,
max_iter=100,
num_rep=10)['centroids']
w_output = np.random.normal(size=(y.shape[1], num_hidden_nodes + 1))
loss_history = []
validation_loss_history = []
for epoch in range(num_epochs):
random_permutation = np.array_split(
np.random.permutation(y.shape[0]),
np.ceil(y.shape[0] / mini_batch_size))
for i in random_permutation:
xi = x_matrix[i]
yi = y[i]
# Forward pass
layer_z = np.vstack((np.ones(
(1, xi.shape[0])), activation_function(w_hidden, xi, gamma)))
model_output = out_activation_function(w_output @ layer_z)
# Compute error
error = yi.T - model_output
# Update the weights
w_output += alpha * error @ layer_z.T / xi.shape[0]
if compute_loss:
layer_z = np.vstack((np.ones((1, x_matrix.shape[0])),
activation_function(w_hidden, x_matrix,
gamma)))
model_output = out_activation_function(w_output @ layer_z)
loss_history.append(loss(y, model_output.T))
if x_validation is not None:
layer_z = np.vstack(
(np.ones((1, x_validation.shape[0])),
activation_function(w_hidden, x_validation, gamma)))
model_output_validation = out_activation_function(
w_output @ layer_z)
validation_loss_history.append(
loss(y_validation, model_output_validation.T))
return {
'w_hidden': w_hidden,
'w_output': w_output,
'gamma': gamma,
'loss_history': loss_history,
'validation_loss_history': validation_loss_history,
'output': output,
'activation_function': activation_function,
'out_activation_function': out_activation_function
}
def cluster(self, X):
centers, data_centers, sigmas = kmeans(X, self.n_neurons, 'kmeanspp',
100)
return centers, data_centers, sigmas
ffeatures, fids = get_sents_training( model_name )
# Topic modelling
decomposer = [lsa, lda, nmf, None][1]
n_topics = 15
x_topic = topic_model_run(decomposer, n_topics, ffeatures, fids)
# Clustering
from clustering import birch
from clustering import kmeans
from clustering import ward_linkage
x, _ = count_vector(
x_topic,
ngram=(1,2),
max_df=0.99,
min_df=0.1
)
n_clusters = 10
plot_dimension = 2
x, _ = pca(x, plot_dimension)
km, (centroids, c, k) = kmeans(x, n_clusters)
plot(x, centroids, c, k, "K-Means", plot_dimension)
if fids:
print_clusters(c, fids)
print_measure("K-Means", "silhouette", silhouette(x, c))
def silhouette(k, word_vectors):
kmeans = kmeans(word_vectors, k)[1]
return silhouette_score(word_vectors.syn0norm, kmeans.labels_)
embedding_recort, embedding_dict = embedding(upper_corr, full_shape, mask, n_embedding)
np.save(embed_file%(smooth, masktype, hemi, str(n_embedding)),embedding_recort)
pkl_out = open(embed_dict_file%(smooth, masktype, hemi, str(n_embedding)), 'wb')
pickle.dump(embedding_dict, pkl_out)
pkl_out.close()
'''clustering'''
if calc_cluster:
if not calc_embed:
embedding_recort = np.load(embed_file%(smooth, masktype, hemi, str(n_embedding)))
mask = np.load(mask_file%(hemi, masktype))
for nk in n_kmeans:
print 'clustering %s'%str(nk)
kmeans_recort = kmeans(embedding_recort, nk, mask)
np.save(kmeans_file%(smooth, masktype, hemi, str(n_embedding), str(nk)),
kmeans_recort)
if calc_subcluster:
print 'subclustering %s'%str(nk)
v, f, d = read_vtk(mesh_file%hemi)
subclust_arr=subcluster(kmeans_recort, f)
np.save(subclust_file%(smooth, masktype, hemi, str(n_embedding), str(nk)), subclust_arr)
'''subclustering'''
if not calc_cluster:
if calc_subcluster:
def specific_keywords_burst_dection(task_detail):
task_name = task_detail[0]
social_sensors = task_detail[1]
keywords_list = task_detail[2]
sensitive_words = task_detail[3]
stop_time = task_detail[4]
forward_warning_status = task_detail[5]
ts = int(task_detail[7])
forward_result = get_forward_numerical_info(task_name, ts, keywords_list)
# 之前时间阶段内的原创微博list
forward_origin_weibo_list = query_mid_list(ts-time_interval, keywords_list, forward_time_range)
# 当前阶段内原创微博list
current_mid_list = query_mid_list(ts, keywords_list, time_interval)
all_mid_list = []
all_mid_list.extend(current_mid_list)
all_mid_list.extend(forward_origin_weibo_list)
print "all mid list: ", len(all_mid_list)
# 查询当前的原创微博和之前12个小时的原创微博在当前时间内的转发和评论数, 聚合按照message_type
statistics_count = query_related_weibo(ts, all_mid_list, time_interval, keywords_list)
current_total_count = statistics_count['total_count']
# 当前阶段内所有微博总数
print "current all weibo: ", statistics_count
current_origin_count = statistics_count['origin']
current_retweeted_count = statistics_count['retweeted']
current_comment_count = statistics_count['comment']
# 针对敏感微博的监测，给定传感器和敏感词的前提下，只要传感器的微博里提及到敏感词即会认为是预警
# 聚合当前时间内积极、中性、悲伤、愤怒情绪分布
# sentiment_dict = {"0": "neutral", "1":"positive", "2":"sad", "3": "anger"}
sentiment_count = {"0": 0, "1": 0, "2": 0, "3": 0}
datetime = ts2datetime(ts)
datetime_1 = ts2datetime(ts-time_interval)
if datetime != datetime_1:
index_name = flow_text_index_name_pre + datetime_1
else:
index_name = flow_text_index_name_pre + datetime
exist_es = es_text.indices.exists(index_name)
if exist_es:
search_results = aggregation_sentiment_related_weibo(ts, all_mid_list, time_interval, keywords_list)
sentiment_count = search_results
print "sentiment_count: ", sentiment_count
negetive_count = sentiment_count['2'] + sentiment_count['3']
# 聚合当前时间内重要的人
important_uid_list = []
if exist_es:
#search_results = es_text.search(index=index_name, doc_type=flow_text_index_type, body=aggregation_sensor_keywords(ts-time_interval, ts, [], "root_uid", size=IMPORTANT_USER_NUMBER))['aggregations']['all_keywords']['buckets']
search_results = query_hot_weibo(ts, all_mid_list, time_interval, keywords_list, aggregation_field="root_uid", size=100)
important_uid_list = search_results.keys()
if datetime != datetime_1:
index_name_1 = flow_text_index_name_pre + datetime_1
if es_text.indices.exists(index_name_1):
#search_results_1 = es_text.search(index=index_name_1, doc_type=flow_text_index_type, body=aggregation_sensor_keywords(ts-time_interval, ts, [], "root_uid", size=IMPORTANT_USER_NUMBER))['aggregations']['all_keywords']['buckets']
search_results_1 = query_hot_weibo(ts, all_mid_list, time_interval, keywords_list, aggregation_field="root_uid", size=100)
if search_results_1:
for item in search_results_1:
important_uid_list.append(item['key'])
# 根据获得uid_list，从人物库中匹配重要人物
if important_uid_list:
important_results = es_user_portrait.mget(index=portrait_index_name, doc_type=portrait_index_type, body={"ids": important_uid_list})['docs']
else:
important_results = {}
filter_important_list = [] # uid_list
if important_results:
for item in important_results:
if item['found']:
if item['_source']['importance'] > IMPORTANT_USER_THRESHOULD:
filter_important_list.append(item['_id'])
print filter_important_list
# 6. 敏感词识别，如果传感器的微博中出现这么一个敏感词，那么就会预警------PS.敏感词是一个
sensitive_origin_weibo_number = 0
sensitive_retweeted_weibo_number = 0
sensitive_comment_weibo_number = 0
sensitive_total_weibo_number = 0
if sensitive_words:
query_sensitive_body = {
"query":{
"filtered":{
"filter":{
"bool":{
"must":[
{"range":{
"timestamp":{
"gte": ts - time_interval,
"lt": ts
}}
},
{"terms": {"keywords_string": sensitive_words}}
]
}
}
}
},
"aggs":{
"all_list":{
"terms":{"field": "message_type"}
}
}
}
if social_sensors:
query_sensitive_body['query']['filtered']['filter']['bool']['must'].append({"terms":{"uid": social_sensors}})
sensitive_results = es_text.search(index=index_name, doc_type=flow_text_index_type, body=query_sensitive_body)['aggregations']['all_list']["buckets"]
if sensitive_results:
for item in sensitive_results:
if int(item["key"]) == 1:
sensitive_origin_weibo_number = item['doc_count']
elif int(item["key"]) == 2:
sensitive_comment_weibo_number = item['doc_count']
elif int(item["key"]) == 3:
sensitive_retweeted_weibo_number = item["doc_count"]
else:
pass
sensitive_total_weibo_number = sensitive_origin_weibo_number + sensitive_comment_weibo_number + sensitive_retweeted_weibo_number
burst_reason = signal_nothing_variation
warning_status = signal_nothing
finish = unfinish_signal # "0"
process_status = "1"
if sensitive_total_weibo_number > WARNING_SENSITIVE_COUNT: # 敏感微博的数量异常
print "======================"
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason = signal_sensitive_variation
if forward_result[0]:
# 根据移动平均判断是否有时间发生
mean_count = forward_result[1]
std_count = forward_result[2]
mean_sentiment = forward_result[3]
std_sentiment = forward_result[4]
if current_total_count > mean_count+1.96*std_count: # 异常点发生
print "====================================================="
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason += signal_count_varition # 数量异常
if negetive_count > mean_sentiment+1.96*std_sentiment:
warning_status = signal_brust
burst_reason += signal_sentiment_varition # 负面情感异常, "12"表示两者均异常
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
if int(stop_time) <= ts: # 检查任务是否已经完成
finish = finish_signal
process_status = "0"
# 7. 感知到的事, all_mid_list
tmp_burst_reason = burst_reason
topic_list = []
# 判断是否有敏感微博出现:有，则聚合敏感微博，replace；没有，聚合普通微博
if burst_reason: # 有事情发生
text_list = []
mid_set = set()
if signal_sensitive_variation in burst_reason:
query_sensitive_body = {
"query":{
"filtered":{
"filter":{
"bool":{
"must":[
{"range":{
"timestamp":{
"gte": ts - time_interval,
"lt": ts
}}
},
{"terms": {"keywords_string": sensitive_words}}
]
}
}
}
},
"size": 10000
}
if social_sensors:
query_sensitive_body['query']['filtered']['filter']['bool']['must'].append({"terms":{"uid": social_sensors}})
sensitive_results = es_text.search(index=index_name, doc_type=flow_text_index_type, body=query_sensitive_body)['hits']['hits']
if sensitive_results:
for item in sensitive_results:
iter_mid = item['_source']['mid']
iter_text = item['_source']['text']
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
if iter_mid not in mid_set:
text_list.append(temp_dict) # 整理后的文本，mid，text
mid_set.add(iter_mid)
burst_reason.replace(signal_sensitive_variation, "")
current_origin_mid_list = query_mid_list(ts, keywords_list, time_interval, 1)
print "current_origin_mid_list:", len(current_origin_mid_list)
if burst_reason and current_mid_list:
origin_sensing_text = es_text.mget(index=index_name, doc_type=flow_text_index_type, body={"ids": current_origin_mid_list}, fields=["mid", "text"])["docs"]
if origin_sensing_text:
for item in origin_sensing_text:
if item["found"]:
iter_mid = item["fields"]["mid"][0]
iter_text = item["fields"]["text"][0]
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
if iter_mid not in mid_set:
text_list.append(temp_dict) # 整理后的文本，mid，text
mid_set.add(iter_mid)
if len(text_list) == 1:
top_word = freq_word(text_list[0])
topic_list = [top_word.keys()]
elif len(text_list) == 0:
topic_list = []
tmp_burst_reason = "" #没有相关微博，归零
print "***********************************"
else:
feature_words, input_word_dict = tfidf(text_list) #生成特征词和输入数据
word_label, evaluation_results = kmeans(feature_words, text_list) #聚类
inputs = text_classify(text_list, word_label, feature_words)
clustering_topic = cluster_evaluation(inputs)
print "========================================================================================"
print "========================================================================================="
sorted_dict = sorted(clustering_topic.items(), key=lambda x:x[1], reverse=True)
topic_list = []
if sorted_dict:
for item in sorted_dict:
topic_list.append(word_label[item[0]])
print "topic_list, ", topic_list
if not topic_list:
warning_status = signal_nothing
tmp_burst_reason = signal_nothing_variation
results = dict()
results['origin_weibo_number'] = current_origin_count
results['retweeted_weibo_number'] = current_retweeted_count
results['comment_weibo_number'] = current_comment_count
results['weibo_total_number'] = current_total_count
results['sensitive_origin_weibo_number'] = sensitive_origin_weibo_number
results['sensitive_retweeted_weibo_number'] = sensitive_retweeted_weibo_number
results['sensitive_comment_weibo_number'] = sensitive_comment_weibo_number
results['sensitive_weibo_total_number'] = sensitive_total_weibo_number
results['sentiment_distribution'] = json.dumps(sentiment_count)
results['important_users'] = json.dumps(filter_important_list)
results['burst_reason'] = tmp_burst_reason
results['timestamp'] = ts
if tmp_burst_reason:
results['clustering_topic'] = json.dumps(topic_list)
# es存储当前时段的信息
doctype = task_name
es_user_portrait.index(index=index_sensing_task, doc_type=doctype, id=ts, body=results)
# 更新manage social sensing的es信息
temporal_result = es_user_portrait.get(index=index_manage_social_task, doc_type=task_doc_type, id=task_name)['_source']
temporal_result['warning_status'] = warning_status
temporal_result['burst_reason'] = tmp_burst_reason
temporal_result['finish'] = finish
temporal_result['processing_status'] = process_status
history_status = json.loads(temporal_result['history_status'])
history_status.append([ts, ' '.join(keywords_list), warning_status])
temporal_result['history_status'] = json.dumps(history_status)
es_user_portrait.index(index=index_manage_social_task, doc_type=task_doc_type, id=task_name, body=temporal_result)
return "1"
#Module with functions to manipulate files
import manipulate_files
import fraud_simulation
import prediction
import clustering
# Reads .txt files
data=manipulate_files.read_files()
print('Files read')
# Sorts the files in order to be space relevant
data=manipulate_files.sort_files(data)
print('Files sorted')
# Finds consumers with full data for a year
# Output: index MeterID consumers vs halfhours of a year
timeseries=manipulate_files.find_full_values(data)
print('Dataset formated to annual data')
# Applies types of attack
# Outputs X and Y with MeterID index
X, Y=fraud_simulation.typical_attack(timeseries)
print('Fraud Simulation done')
# Computes Performance
prediction.liblinear(X,Y)
# Clustering with PCA and K-Means
clustering.kmeans(X)
def step2_cal():
"""第二步计算，判断其他类是否需要分裂，若需要，则对其他类进行文本聚类，并做聚类评价
"""
# 聚类评价时选取TOPK_FREQ_WORD的高频词
TOPK_FREQ_WORD = 50
# 聚类评价时最小簇的大小
LEAST_SIZE = 8
# 判断其他类是否需要分裂
ifsplit = event.check_ifsplit(initializing)
print '[%s] ' % ts2datetime(
int(time.time())
), 'event ', eventid, ' split ', ifsplit, ' %s start step2' % ts2datetime(
timestamp)
if ifsplit:
inputs, kmeans_cluster_num, reserve_num = event.getOtherSubEventInfos(
initializing)
print eventid, ' after classify before split: ', len(
inputs), kmeans_cluster_num, reserve_num
if len(inputs) > 2:
items = []
for r in inputs:
r["title"] = r["title"].encode("utf-8")
r["content"] = r["content168"].encode("utf-8")
items.append(r)
# kmeans聚类
kmeans_results = kmeans(items, k=kmeans_cluster_num)
# 聚类评价
if initializing or now_hour == 0:
min_tfidf = event.get_min_tfidf()
final_cluster_results, tfidf_dict = cluster_evaluation(
kmeans_results,
top_num=reserve_num,
topk_freq=TOPK_FREQ_WORD,
least_size=LEAST_SIZE,
min_tfidf=min_tfidf)
else:
# 每小时聚类时，不用和已有簇的最小tfidf作比
final_cluster_results, tfidf_dict = cluster_evaluation(
kmeans_results,
top_num=reserve_num,
topk_freq=TOPK_FREQ_WORD,
least_size=LEAST_SIZE)
# 更新新闻簇标签，更新子事件表
for label, items in final_cluster_results.iteritems():
if label == "other":
label = event.getOtherSubEventID()
event.save_subevent(label, timestamp)
if label != event.getOtherSubEventID():
# 更新每类的tfidf
event.update_subevent_tfidf(label, tfidf_dict[label])
for r in items:
news = News(r["_id"], event.id)
news.update_news_subeventid(label)
else:
print 'inputs less than 2, kmeans aborted'
print '[%s] ' % ts2datetime(int(time.time(
))), 'event ', eventid, ' %s end step2' % ts2datetime(timestamp)
if __name__ == "__main__":
s_index = "20150701"
e_index = "20150702"
features_as_list, ids = indexed_features(s_index, e_index)
n_topics = 0
all_features = []
for index, feature in features_as_list:
all_features += feature
round_topics = int(len(feature) / 25) + 1
n_topics += round_topics
dictionary, corpus = create_corpus(index, all_features)
x, lda_model, lda_corpus = single_lda("20150703", corpus, dictionary,
n_topics)
x = pca(x, 2)
km, (centroids, c, k) = kmeans(x, n_topics)
cluster_plot_2d(x, centroids, c, k)
clusters = {}
for idx, el in enumerate(c):
if not el in clusters:
clusters[el] = []
clusters[el].append(idx)
for key, doc in clusters.items():
for _id in doc[:5]:
print(_id)
print("-" * 40)
if __name__ == "__main__":
s_index = "20150701"
e_index = "20150702"
features_as_list, ids = indexed_features(s_index, e_index)
n_topics = 0
all_features = []
for index, feature in features_as_list:
all_features += feature
round_topics = int( len(feature) / 25 ) + 1
n_topics += round_topics
dictionary, corpus = create_corpus(index, all_features)
x, lda_model, lda_corpus = single_lda("20150703", corpus, dictionary, n_topics)
x = pca(x, 2)
km, (centroids, c, k) = kmeans(x, n_topics)
cluster_plot_2d(x, centroids, c, k)
clusters = {}
for idx, el in enumerate(c):
if not el in clusters:
clusters[el] = []
clusters[el].append( idx )
for key, doc in clusters.items():
for _id in doc[:5]:
print(_id)
print("-"*40)
plt.style.use(args.style)
df = data.read_data(args.data_filepath)
if(args.plot_raw_data):
plotting.plot_all_data(df, "Raw Data", "Raw", os.path.join(args.output_folderpath, "raw"), data.column_names)
if(args.plot_standardized_data):
clean_df = data.clean_data(df)
plotting.plot_all_data(clean_df, "Standardized Data", "Clean", os.path.join(args.output_folderpath, "clean"), data.column_names)
if(args.perform_pca):
num_dimensions = args.num_dimensions
projected_df = pca.perform_pca(df, num_dimensions)
output_path = os.path.join(args.output_folderpath, "PCA")
if(not(os.path.exists(output_path))):
os.makedirs(output_path)
print "Saving Graphs"
plotting.plot_all_data(projected_df, "PCA {0}-D".format(num_dimensions), "PCA", output_path, projected_df.columns)
if(args.perform_kmeans):
output_path = os.path.join(args.output_folderpath, "KMeans")
if (not (os.path.exists(output_path))):
os.makedirs(output_path)
clustering.kmeans(df, 6, 7, 2, output_path, df.columns[6:8])
if __name__ == "__main__":
logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
# Data
model_name = "20150701"
ffeatures, fids = get_sents_training(model_name)
# Topic modelling
decomposer = [lsa, lda, nmf, None][1]
n_topics = 15
x_topic = topic_model_run(decomposer, n_topics, ffeatures, fids)
# Clustering
from clustering import birch
from clustering import kmeans
from clustering import ward_linkage
x, _ = count_vector(x_topic, ngram=(1, 2), max_df=0.99, min_df=0.1)
n_clusters = 10
plot_dimension = 2
x, _ = pca(x, plot_dimension)
km, (centroids, c, k) = kmeans(x, n_clusters)
plot(x, centroids, c, k, "K-Means", plot_dimension)
if fids:
print_clusters(c, fids)
print_measure("K-Means", "silhouette", silhouette(x, c))
def social_sensing(task_detail):
# 任务名 传感器 终止时间 之前状态 创建者 时间
task_name = task_detail[0]
social_sensors = task_detail[1]
stop_time = task_detail[2]
forward_warning_status = task_detail[3]
create_by = task_detail[4]
ts = int(task_detail[5])
# PART 1
forward_result = get_forward_numerical_info(task_name, ts, create_by)
# 之前时间阶段内的原创微博list/retweeted
forward_origin_weibo_list = query_mid_list(ts-time_interval, social_sensors, forward_time_range)
forward_retweeted_weibo_list = query_mid_list(ts-time_interval, social_sensors, forward_time_range, 3)
# 当前阶段内原创微博list
current_mid_list = query_mid_list(ts, social_sensors, time_interval)
current_retweeted_mid_list = query_mid_list(ts, social_sensors, time_interval, 3)
all_mid_list = []
all_mid_list.extend(current_mid_list)
all_mid_list.extend(current_retweeted_mid_list)
all_mid_list.extend(forward_origin_weibo_list)
all_mid_list.extend(forward_retweeted_weibo_list)
all_origin_list = []
all_origin_list.extend(current_mid_list)
all_origin_list.extend(forward_origin_weibo_list)
all_retweeted_list = []
all_retweeted_list.extend(current_retweeted_mid_list)
all_retweeted_list.extend(forward_retweeted_weibo_list)#被转发微博的mid/root-mid
print "all mid list: ", len(all_mid_list)
print "all_origin_list", all_origin_list
print "all_retweeted_list", all_retweeted_list
# 查询微博在当前时间内的转发和评论数, 聚合按照message_type
statistics_count = query_related_weibo(ts, all_mid_list, time_interval)
if all_origin_list:
origin_weibo_detail = query_hot_weibo(ts, all_origin_list, time_interval) # 原创微博详情
else:
origin_weibo_detail = {}
if all_retweeted_list:
retweeted_weibo_detail = query_hot_weibo(ts, all_retweeted_list, time_interval) # 转发微博详情
else:
retweeted_weibo_detail = {}
current_total_count = statistics_count['total_count']
# 当前阶段内所有微博总数
current_retweeted_count = statistics_count['retweeted']
current_comment_count = statistics_count['comment']
# PART 2
# 聚合当前时间内积极、中性、悲伤、愤怒情绪分布
# sentiment_dict = {"0": "neutral", "1":"positive", "2":"sad", "3": "anger"}
sentiment_count = {"0": 0, "1": 0, "2": 0, "3": 0}
search_results = aggregation_sentiment_related_weibo(ts, all_mid_list, time_interval)
sentiment_count = search_results
print "sentiment_count: ", sentiment_count
negetive_key = ["2", "3", "4", "5", "6"]
negetive_count = 0
for key in negetive_key:
negetive_count += sentiment_count[key]
# 聚合当前时间内重要的人
important_uid_list = []
datetime = ts2datetime(ts-time_interval)
index_name = flow_text_index_name_pre + datetime
exist_es = es_text.indices.exists(index_name)
if exist_es:
search_results = get_important_user(ts, all_mid_list, time_interval)
important_uid_list = search_results.keys()
# 根据获得uid_list，从人物库中匹配重要人物
if important_uid_list:
important_results = es_user_portrait.mget(index=portrait_index_name,doc_type=portrait_index_type, body={"ids": important_uid_list})['docs']
else:
important_results = {}
filter_important_list = [] # uid_list
if important_results:
for item in important_results:
if item['found']:
#if item['_source']['importance'] > IMPORTANT_USER_THRESHOULD:
filter_important_list.append(item['_id'])
print filter_important_list
#判断感知
burst_reason = signal_nothing_variation
warning_status = signal_nothing
finish = unfinish_signal # "0"
process_status = "1"
if forward_result[0]:
# 根据移动平均判断是否有时间发生
mean_count = forward_result[1]
std_count = forward_result[2]
mean_sentiment = forward_result[3]
std_sentiment = forward_result[4]
if mean_count >= MEAN_COUNT and current_total_count > mean_count+1.96*std_count or current_total_count >= len(social_sensors)*0.2*AVERAGE_COUNT: # 异常点发生
print "====================================================="
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason += signal_count_varition # 数量异常
if negetive_count > mean_sentiment+1.96*std_sentiment and mean_sentiment >= MEAN_COUNT or negetive_count >= len(social_sensors)*0.2*AVERAGE_COUNT:
warning_status = signal_brust
burst_reason += signal_sentiment_varition # 负面情感异常, "12"表示两者均异常
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
if int(stop_time) <= ts: # 检查任务是否已经完成
finish = finish_signal
process_status = "0"
# 感知到的事, all_mid_list
tmp_burst_reason = burst_reason
topic_list = []
# 有事件发生时开始
if warning_status:
index_list = []
important_words = []
datetime_1 = ts2datetime(ts)
index_name_1 = flow_text_index_name_pre + datetime_1
exist_es = es_text.indices.exists(index=index_name_1)
if exist_es:
index_list.append(index_name_1)
datetime_2 = ts2datetime(ts-DAY)
index_name_2 = flow_text_index_name_pre + datetime_2
exist_es = es_text.indices.exists(index=index_name_2)
if exist_es:
index_list.append(index_name_2)
if index_list and all_mid_list:
query_body = {
"query":{
"filtered":{
"filter":{
"terms":{"mid": all_mid_list}
}
}
},
"size": 2000
}
search_results = es_text.search(index=index_list, doc_type="text", body=query_body)['hits']['hits']
text_list = []
if search_results:
for item in search_results:
iter_mid = item['_source']['mid']
iter_text = item['_source']['text']
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
text_list.append(temp_dict)
for item in text_list:
print item['text']
if len(text_list) == 1:
top_word = freq_word(text_list[0])
topic_list = [top_word.keys()]
elif len(text_list) == 0:
topic_list = []
tmp_burst_reason = "" #没有相关微博，归零
print "***********************************"
else:
feature_words, input_word_dict = tfidf(text_list) #生成特征词和输入数据
word_label, evaluation_results = kmeans(feature_words, text_list) #聚类
inputs = text_classify(text_list, word_label, feature_words)
clustering_topic = cluster_evaluation(inputs)
print "==============================================================="
print "==============================================================="
sorted_dict = sorted(clustering_topic.items(), key=lambda x:x[1], reverse=True)
topic_list = []
if sorted_dict:
for item in sorted_dict:
topic_list.append(word_label[item[0]])
print "topic_list, ", topic_list
#if not topic_list:
# warning_status = signal_nothing
# tmp_burst_reason = signal_nothing_variation
results = dict()
results['origin_weibo_number'] = len(all_origin_list)
results['retweeted_weibo_number'] = len(all_retweeted_list)
results['origin_weibo_detail'] = json.dumps(origin_weibo_detail)
results['retweeted_weibo_detail'] = json.dumps(retweeted_weibo_detail)
results['retweeted_weibo_count'] = current_retweeted_count
results['comment_weibo_count'] = current_comment_count
results['weibo_total_number'] = current_total_count
results['sentiment_distribution'] = json.dumps(sentiment_count)
results['important_users'] = json.dumps(filter_important_list)
results['unfilter_users'] = json.dumps(important_uid_list)
results['burst_reason'] = tmp_burst_reason
results['timestamp'] = ts
if tmp_burst_reason:
results['clustering_topic'] = json.dumps(topic_list)
# es存储当前时段的信息
doctype = create_by + '-' + task_name
es_user_portrait.index(index=index_sensing_task, doc_type=doctype, id=ts, body=results)
# 更新manage social sensing的es信息
temporal_result = es_user_portrait.get(index=index_manage_social_task, doc_type=task_doc_type, id=doctype)['_source']
temporal_result['warning_status'] = warning_status
temporal_result['burst_reason'] = tmp_burst_reason
temporal_result['finish'] = finish
temporal_result['processing_status'] = process_status
history_status = json.loads(temporal_result['history_status'])
history_status.append([ts, task_name, warning_status])
temporal_result['history_status'] = json.dumps(history_status)
es_user_portrait.index(index=index_manage_social_task, doc_type=task_doc_type, id=doctype, body=temporal_result)
return "1"
def cluster_wine(k):
table = load_wine_data('redwine.csv')
labels = clus.kmeans(k, table)
plot_scatter(table, labels, k)
def cluster_wine(k):
table = load_wine_data('redwine.csv')
labels = clus.kmeans(k, table)
plot_scatter(table, labels, k)
def sensors_keywords_detection(task_detail):
task_name = task_detail[0]
social_sensors = task_detail[1]
keywords_list = task_detail[2]
sensitive_words = task_detail[3]
stop_time = task_detail[4]
forward_warning_status = task_detail[5]
ts = task_detail[7]
forward_result = get_forward_numerical_info(task_name, ts, keywords_list)
# 1. 聚合前12个小时内传感人物发布的所有与关键词相关的原创微博
forward_origin_weibo_list = query_mid_list(ts - time_interval,
keywords_list,
forward_time_range, 1,
social_sensors)
# 2. 聚合当前阶段内的原创微博
current_mid_list = query_mid_list(ts, keywords_list, time_interval, 1,
social_sensors)
all_mid_list = []
all_mid_list.extend(current_mid_list)
all_mid_list.extend(forward_origin_weibo_list)
all_mid_list = list(set(all_mid_list))
print len(all_mid_list)
# 3. 查询当前的原创微博和之前12个小时的原创微博在当前时间内的转发和评论数, 聚合按照message_type
statistics_count = query_related_weibo(ts, all_mid_list, time_interval,
keywords_list, 1, social_sensors)
current_total_count = statistics_count['total_count']
# 当前阶段内所有微博总数
print "current all weibo: ", statistics_count
current_origin_count = statistics_count['origin']
current_retweeted_count = statistics_count['retweeted']
current_comment_count = statistics_count['comment']
# 4. 聚合当前时间内积极、中性、悲伤、愤怒情绪分布
sentiment_count = {"0": 0, "1": 0, "2": 0, "3": 0}
datetime = ts2datetime(ts)
datetime_1 = ts2datetime(ts - time_interval)
if datetime == datetime_1:
index_name = flow_text_index_name_pre + datetime
else:
index_name = flow_text_index_name_pre + datetime_1
exist_es = es_text.indices.exists(index_name)
if exist_es:
search_results = aggregation_sentiment_related_weibo(
ts, all_mid_list, time_interval, keywords_list, 1)
sentiment_count = search_results
print "sentiment_count: ", sentiment_count
negetive_count = sentiment_count['2'] + sentiment_count['3']
# 5. 那些社会传感器参与事件讨论
query_body = {
"query": {
"filtered": {
"filter": {
"bool": {
"must": [{
"range": {
"timestamp": {
"gte": ts - time_interval,
"lt": ts
}
}
}, {
"terms": {
"uid": social_sensors
}
}],
"should": [{
"terms": {
"root_mid": all_mid_list
}
}, {
"terms": {
"mid": all_mid_list
}
}]
}
}
}
},
"size": 10000
}
datetime = ts2datetime(ts)
datetime_1 = ts2datetime(ts - time_interval)
if datetime == datetime_1:
index_name = flow_text_index_name_pre + datetime
else:
index_name = flow_text_index_name_pre + datetime_1
search_results = es_text.search(index=index_name,
doc_type=flow_text_index_type,
body=query_body)['hits']['hits']
attend_users = []
if search_results:
for item in search_results:
attend_users.append(item['_source']['uid'])
important_users = list(set(attend_users))
print "important users", important_users
# 6. 敏感词识别，如果传感器的微博中出现这么一个敏感词，那么就会预警------PS.敏感词是一个危险的设置
sensitive_origin_weibo_number = 0
sensitive_retweeted_weibo_number = 0
sensitive_comment_weibo_number = 0
sensitive_total_weibo_number = 0
if sensitive_words:
query_sensitive_body = {
"query": {
"filtered": {
"filter": {
"bool": {
"must": [{
"range": {
"timestamp": {
"gte": ts - time_interval,
"lt": ts
}
}
}, {
"terms": {
"keywords_string": sensitive_words
}
}, {
"terms": {
"uid": social_sensors
}
}]
}
}
}
},
"aggs": {
"all_list": {
"terms": {
"field": "message_type"
}
}
}
}
sensitive_results = es_text.search(
index=index_name,
doc_type=flow_text_index_type,
body=query_sensitive_body)['aggregations']['all_list']["buckets"]
if sensitive_results:
for item in sensitive_results:
if int(item["key"]) == 1:
sensitive_origin_weibo_number = item['doc_count']
elif int(item["key"]) == 2:
sensitive_comment_weibo_number = item['doc_count']
elif int(item["key"]) == 3:
sensitive_retweeted_weibo_number = item["doc_count"]
else:
pass
sensitive_total_weibo_number = sensitive_origin_weibo_number + sensitive_comment_weibo_number + sensitive_retweeted_weibo_number
burst_reason = signal_nothing_variation
warning_status = signal_nothing
finish = unfinish_signal # "0"
process_status = "1"
if sensitive_total_weibo_number: # 敏感微博的数量异常
print "======================"
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason = signal_sensitive_variation
if forward_result[0]:
# 根据移动平均判断是否有时间发生
mean_count = forward_result[1]
std_count = forward_result[2]
mean_sentiment = forward_result[3]
std_sentiment = forward_result[4]
if current_total_count > mean_count + 1.96 * std_count: # 异常点发生
print "====================================================="
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
else:
warning_status = signal_brust
burst_reason += signal_count_varition # 数量异常
if negetive_count > mean_sentiment + 1.96 * std_sentiment:
warning_status = signal_brust
burst_reason += signal_sentiment_varition # 负面情感异常, "12"表示两者均异常
if forward_warning_status == signal_brust: # 已有事件发生，改为事件追踪
warning_status = signal_track
if int(stop_time) <= ts: # 检查任务是否已经完成
finish = finish_signal
process_status = '0'
tmp_burst_reason = burst_reason
topic_list = []
# 7. 感知到的事, all_mid_list
if burst_reason: # 有事情发生
text_list = []
mid_set = set()
if signal_sensitive_variation in burst_reason:
query_sensitive_body = {
"query": {
"filtered": {
"filter": {
"bool": {
"must": [{
"range": {
"timestamp": {
"gte": ts - time_interval,
"lt": ts
}
}
}, {
"terms": {
"keywords_string": sensitive_words
}
}]
}
}
}
},
"size": 10000
}
if social_sensors:
query_sensitive_body['query']['filtered']['filter']['bool'][
'must'].append({"terms": {
"uid": social_sensors
}})
sensitive_results = es_text.search(
index=index_name,
doc_type=flow_text_index_type,
body=query_sensitive_body)['hits']["hits"]
if sensitive_results:
for item in sensitive_results:
iter_mid = item['_source']['mid']
iter_text = item['_source']['text']
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
if iter_mid not in mid_set:
text_list.append(temp_dict) # 整理后的文本，mid，text
mid_set.add(iter_mid)
burst_reason.replace(signal_sensitive_variation, "")
if burst_reason and all_mid_list:
sensing_text = es_text.mget(index=index_name,
doc_type=flow_text_index_type,
body={"ids": all_mid_list},
fields=["mid", "text"])["docs"]
if sensing_text:
for item in sensing_text:
if item['found']:
iter_mid = item["fields"]["mid"][0]
iter_text = item["fields"]["text"][0]
temp_dict = dict()
temp_dict["mid"] = iter_mid
temp_dict["text"] = iter_text
if iter_mid not in mid_set:
text_list.append(temp_dict)
mid_set.add(iter_mid)
if len(text_list) == 1:
top_word = freq_word(text_list[0])
topic_list = [top_word.keys()]
elif len(text_list) == 0:
topic_list = []
tmp_burst_reason = "" #没有相关微博，归零
print "***********************************"
else:
feature_words, input_word_dict = tfidf(text_list) #生成特征词和输入数据
word_label, evaluation_results = kmeans(feature_words,
text_list) #聚类
inputs = text_classify(text_list, word_label, feature_words)
clustering_topic = cluster_evaluation(inputs)
sorted_dict = sorted(clustering_topic.items(),
key=lambda x: x[1],
reverse=True)[0:5]
topic_list = []
if sorted_dict:
for item in sorted_dict:
topic_list.append(word_label[item[0]])
print "topic_list:", topic_list
if not topic_list:
tmp_burst_reason = signal_nothing_variation
warning_status = signal_nothing
results = dict()
results['sensitive_origin_weibo_number'] = sensitive_origin_weibo_number
results[
'sensitive_retweeted_weibo_number'] = sensitive_retweeted_weibo_number
results['sensitive_comment_weibo_number'] = sensitive_comment_weibo_number
results['sensitive_weibo_total_number'] = sensitive_total_weibo_number
results['origin_weibo_number'] = current_origin_count
results['retweeted_weibo_number'] = current_retweeted_count
results['comment_weibo_number'] = current_comment_count
results['weibo_total_number'] = current_total_count
results['sentiment_distribution'] = json.dumps(sentiment_count)
results['important_users'] = json.dumps(important_users)
results['burst_reason'] = tmp_burst_reason
results['timestamp'] = ts
if tmp_burst_reason:
results["clustering_topic"] = json.dumps(topic_list[:5])
# es存储当前时段的信息
doctype = task_name
es_user_portrait.index(index=index_sensing_task,
doc_type=doctype,
id=ts,
body=results)
# 更新manage social sensing的es信息
temporal_result = es_user_portrait.get(index=index_manage_social_task,
doc_type=task_doc_type,
id=task_name)['_source']
temporal_result['warning_status'] = warning_status
temporal_result['burst_reason'] = tmp_burst_reason
temporal_result['finish'] = finish
temporal_result['processing_status'] = process_status
history_status = json.loads(temporal_result['history_status'])
history_status.append([ts, ' '.join(keywords_list), warning_status])
temporal_result['history_status'] = json.dumps(history_status)
es_user_portrait.index(index=index_manage_social_task,
doc_type=task_doc_type,
id=task_name,
body=temporal_result)
return "1"
values = l.split()
at = atom()
at.PDBIndex = values[1]
at.atomname = values[2]
at.residue = values[3]
at.chain = values[4]
at.resid = values[5]
at.coordinates = point(float(values[6]), float(values[7]), float(values[8]) )
at.bfactor = float(values[10])* weight_be
at.atomtype = values[11]
at.element = 'H'
coords = [at.coordinates.x, at.coordinates.y, at.coordinates.z, at.bfactor]
p = clustering.Point(coords , reference=at)
points.append(p)
clusters = clustering.kmeans(points, number_of_clusters, cutoff)
for i in range(len(clusters)):
if ( not os.path.exists(str(i+1)) ): os.mkdir(str(i+1))
pdb_cluster = PDB()
tot_be = 0.0
for p in clusters[i].points:
p.reference.bfactor = p.reference.bfactor / weight_be
pdb_cluster.AddNewAtom(p.reference)
tot_be += p.reference.bfactor
(box_num, cluster_id) = (ord(p.reference.chain) - ord('A') +1, p.reference.resid)
target = "../../%s/cluster-%04d.pdbqt" % (box_num, int(cluster_id) )
link_name = "./cluster-%04d-box%s.pdbqt" % (int(cluster_id), box_num)
os.chdir(str(i+1))
os.system("ln -sf %s %s" % (target, link_name) )
os.chdir("..")
pdb_cluster.UserNotes.append("STATISTICS")
