def processing(self):
if self.abafile and self.syncfile and self.segfile and self.poifile:
self.ppdata = pre_processing(self.abafile, self.syncfile,
self.segfile, self.poifile, None)
self.savefileButton.setVisible(True)
self.pprocessButton.setVisible(False)
self.abaEdit.setText("ABA file")
self.syncEdit.setText("SYNC file")
self.segEdit.setText("SEG file")
self.poiEdit.setText("POI file")
else:
msg = QMessageBox()
msg.setIcon(QMessageBox.Critical)
msg.setText("File Error")
msg.setInformativeText('Please load all the required files...')
msg.setWindowTitle("File missing!")
msg.exec_()
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import data_processing
import tensorflow as tf
import tensorflow.contrib.slim as slim
import tensorflow.contrib.slim.nets as nets
import csv as csv
CHECK_POINT_PATH = 'check_point/train_model.ckpt-2'
NUM_KAGGLE_TEST = 12500
BATCH_SIZE = 50
batch_test_set = data_processing.pre_processing(data_set='test',
batch_size=BATCH_SIZE)
prediction_file = open('kaggle_result_file.csv', 'wb')
prediction_file_object = csv.writer(prediction_file)
prediction_file_object.writerow(['id', 'label'])
with tf.Graph().as_default():
images = tf.placeholder(tf.float32, [BATCH_SIZE, 224, 224, 3])
keep_prob = tf.placeholder(tf.float32)
logits, _ = nets.vgg.vgg_19(inputs=images,
num_classes=2,
dropout_keep_prob=keep_prob,
is_training=False)
variables_to_restore = slim.get_variables_to_restore()
restorer = tf.train.Saver(variables_to_restore)
pros = tf.nn.softmax(logits)
from data_processing import pre_processing, _window_logs, get_session_attributes
from parsing import parse_log_file
from detection_rules import (
has_robots_txt_request,
has_bot_name_in_user_agent,
has_high_number_requests,
has_low_request_interrarival_time,
)
import numpy as np
import datetime as dt
# Processing the input
print("Starting app...")
parsed_logs = parse_log_file("./access.log", from_date=dt.date(2014, 2, 20))
requests = pre_processing(parsed_logs)
# Generating features
hourly_windowed_logs = _window_logs(requests, window_time_frame="hour")
daily_windowed_logs = _window_logs(requests, window_time_frame="day")
hour_sessions = get_session_attributes(requests, aggregation_level="hour")
day_sessions = get_session_attributes(requests, aggregation_level="day")
# Examine generated features to flag potential bots
robots_txt = has_robots_txt_request(requests)
bot_names = has_bot_name_in_user_agent(requests)
low_inter_request_time_hour = has_low_request_interrarival_time(
hour_sessions, threshold_number_requests_no_referrer=100)
low_inter_request_time_day = has_low_request_interrarival_time(
day_sessions, threshold_number_requests_no_referrer=1000)
high_number_requests_hour = has_high_number_requests(hour_sessions,
import os
import os.path
import time
TRAIN_LOG_DIR = os.path.join('Log/train/', time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(time.time())))
TRAIN_CHECK_POINT = 'check_point/train_model.ckpt'
VALIDATION_LOG_DIR = 'Log/validation/'
VGG_19_MODEL_DIR = 'check_point/vgg_19.ckpt'
BATCH_SIZE = 32
EPOCH = 3
if not tf.gfile.Exists(TRAIN_LOG_DIR):
tf.gfile.MakeDirs(TRAIN_LOG_DIR)
if not tf.gfile.Exists(VALIDATION_LOG_DIR):
tf.gfile.MakeDirs(VALIDATION_LOG_DIR)
batch_train_set, batch_validation_set, images_num = data_processing.pre_processing(data_set='train', batch_size=BATCH_SIZE)
def get_accuracy(logits, labels):
correct_prediction = tf.equal(tf.argmax(logits, 1), tf.argmax(labels, 1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
return accuracy
with tf.Graph().as_default():
images = tf.placeholder(tf.float32, [BATCH_SIZE, 224, 224, 3])
labels = tf.placeholder(tf.float32, [BATCH_SIZE, len(data_processing.IMG_CLASSES)])
keep_prob = tf.placeholder(tf.float32)
with slim.arg_scope(nets.vgg.vgg_arg_scope()):
logits, _ = nets.vgg.vgg_19(inputs=images, num_classes=2, dropout_keep_prob=keep_prob, is_training=True)
variables_to_restore = slim.get_variables_to_restore(exclude=['vgg_19/fc8'])
restorer = tf.train.Saver(variables_to_restore)
def anomaly_detection(self, pprocessed_file, seg_file, features='RMS', sliding_window=1000, sub_sampling=128, impurity=0.05, num_trees=100):
self.processed_file = pprocessed_file
# In case pre-processed file is not available
if not os.path.isfile(self.processed_file):
pre_processing(self.data_file, self.sync_file, self.seg_file, self.poi_file, self.processed_file)
else:
geo_list = []
with open(self.poi_file) as csv_file:
csv_reader = csv.reader(csv_file)
line_count = 0
for row in csv_reader:
tempStr = ''.join(row)
if tempStr.startswith('#') or len(tempStr) == 0:
continue
elif tempStr.startswith('CNT'):
print(f'Column names are {", ".join(row)}')
line_count += 1
else:
line_count += 1
tlist = tempStr.split(";")
ttlist = [float(x) for x in tlist if len(x) > 0]
geo_list.append(ttlist)
print(f'Processed {line_count} lines in POI file.')
geo_list = np.array(geo_list)
lat = geo_list[:, 1]
lon = geo_list[:, 2]
# Interpolation external and geo-coordinates
get_lat = interp1d(geo_list[:, 0], lat, fill_value='extrapolate')
get_long = interp1d(geo_list[:, 0], lon, fill_value='extrapolate')
# read pre-processed data in dataframe
processed_data = pd.read_hdf(self.processed_file, 'processed', mode='r')
# CHC1 = np.array(processed_data.CHC1)
# CHC3 = np.array(processed_data.CHC3)
# CHD1 = np.array(processed_data.CHD1)
# CHD3 = np.array(processed_data.CHD3)
EDIR = np.array(processed_data.ERS_DIR)
CHA1 = np.array(processed_data.CHA1)
CHA3 = np.array(processed_data.CHA3)
CHB1 = np.array(processed_data.CHB1)
CHB3 = np.array(processed_data.CHB3)
# read internal and external counters
int_count = np.array(processed_data.INTCNT)
ext_count = np.array(processed_data.EXTCNT)
# date_time = syncdat.DateTime
# Pushing & Pulling ABA data for one side (left or right)
pull_data_cha1 = CHA1[(EDIR == 1)]
push_data_cha1 = CHA1[(EDIR == -1)]
pull_data_cha3 = CHA3[(EDIR == 1)]
push_data_cha3 = CHA3[(EDIR == -1)]
pull_int_count = int_count[(EDIR == 1)]
push_int_count = int_count[(EDIR == -1)]
pull_ext_count = ext_count[(EDIR == 1)]
push_ext_count = ext_count[(EDIR == -1)]
if len(push_ext_count) == 0:
push_ext_count = pull_ext_count
# transformed data from X and Z axes
pull_data = np.power((np.power(pull_data_cha1, 2) + np.power(pull_data_cha3, 2)), 1 / 2)
push_data = np.power((np.power(push_data_cha1, 2) + np.power(push_data_cha3, 2)), 1 / 2)
cha_data = np.power((np.power(CHA1, 2) + np.power(CHA3, 2)), 1 / 2)
# Pulling and pushing data for other side of the rail
pull_data_chb1 = CHB1[(EDIR == 1)]
push_data_chb1 = CHB1[(EDIR == -1)]
pull_data_chb3 = CHB3[(EDIR == 1)]
push_data_chb3 = CHB3[(EDIR == -1)]
# transformed data from X and Z axes
pull_data2 = np.power((np.power(pull_data_chb1, 2) + np.power(pull_data_chb3, 2)), 1 / 2)
push_data2 = np.power((np.power(push_data_chb1, 2) + np.power(push_data_chb3, 2)), 1 / 2)
########################################
rail_data = []
rail_counters = []
rail_xcounters = []
data_list = []
counters_list = []
xcounters_list = []
data_list.append(pull_data)
# check if data exist for push mode
if len(push_data) != 0:
data_list.append(push_data)
counters_list.append(pull_int_count)
counters_list.append(push_int_count)
xcounters_list.append(pull_ext_count)
if len(push_ext_count) != 0:
xcounters_list.append(push_ext_count)
########################################
data_list2 = []
data_list2.append(pull_data2)
# check if data exist for push mode
if len(push_data2) != 0:
data_list2.append(push_data2)
rail_data.append(data_list)
rail_data.append(data_list2)
rail_counters.append(counters_list)
rail_counters.append(counters_list)
rail_xcounters.append(xcounters_list)
rail_xcounters.append(xcounters_list)
# interpolating internal and external counters
get_xcount = interp1d(int_count, ext_count, fill_value='extrapolate')
get_icount = interp1d(ext_count, int_count, fill_value='extrapolate')
# ///////////// Feature Extraction //////////////
aba_data_side = []
all_xcount_mode = []
anom_xcount_mode = []
anom_score_mode = []
for i in range(2):
aba_data_mode = []
int_count_mode = []
anom_xcount_list = []
anom_score_list = []
input_data = rail_data[i]
for j in range(len(data_list)):
in_data = input_data[j]
if len(in_data) == 0:
continue
counters = counters_list[j]
# inputs are ABA data, counters and the sliding window size
list_of_features = extract_features(in_data, counters, sliding_window)
rms = np.array(list_of_features[:, 0])
kurtosis = np.array(list_of_features[:, 2])
skewness = np.array(list_of_features[:, 3])
peak_to_peak = np.array(list_of_features[:, 4])
crest_factor = np.array(list_of_features[:, 5])
impulse_factor = np.array(list_of_features[:, 6])
rmsf = np.array(list_of_features[:, 12])
int_count = np.array(list_of_features[:, 13])
# features comparison
# plt.figure(2)
# plt.subplot(211)
# plt.ylabel('ABA')
# plt.plot(list(range(0, 401000)), in_data[:401000])
# plt.subplot(212)
# plt.ylabel('RMS')
# plt.plot(list(range(1000, 401000, 2000)), rms[:200], '*')
# plt.subplot(413)
# plt.ylabel('Kurtosis')
# plt.plot(list(range(1000, 401000, 2000)), kurtosis[:200], '*')
# plt.subplot(212)
# plt.ylabel('Peak to peak')
# plt.xlabel('Data Samples')
# plt.plot(list(range(1000, 401000, 2000)), peak_to_peak[:200], '*')
# plt.show()
# plt.figure(2)
# plt.subplot(211)
# plt.ylabel('ABA')
# plt.plot(list(range(390000, 400000)), in_data[390000:400000])
# plt.subplot(212)
# plt.ylabel('RMS')
# plt.xlabel('Samples')
# plt.plot(list(range(391000, 401000, 2000)), rms[195:200], 'r*')
# plt.xlim(390000, 400000)
# plt.show()
if features == 'RMS':
mylist = np.stack((rms, rms), axis=-1)
if features == 'Kurtosis':
mylist = np.stack((kurtosis, kurtosis), axis=-1)
if features == 'Crest factor':
mylist = np.stack((crest_factor, crest_factor), axis=-1)
if features == 'Impulse factor':
mylist = np.stack((impulse_factor, impulse_factor), axis=-1)
if features == 'Skewness':
mylist = np.stack((skewness, skewness), axis=-1)
if features == 'Peak-to-peak':
mylist = np.stack((peak_to_peak, peak_to_peak), axis=-1)
if features == 'All':
mylist = np.stack((rms, kurtosis, peak_to_peak, crest_factor, impulse_factor, skewness), axis=-1)
else:
mylist = np.stack((kurtosis, peak_to_peak),
axis=-1)
norm_train, anom_train, norm_test, anom_test, anom_icount, anom_icount_train, anom_score = isolation_forest(
mylist, int_count, sub_sampling, impurity, num_trees)
print("Return from Anomaly detection")
all_xcount_mode.append(get_xcount(int_count))
anom_xcount_test = get_xcount(anom_icount)
anom_xcount_train = get_xcount(anom_icount_train)
anom_xcount = np.concatenate((anom_xcount_train, anom_xcount_test), axis=0)
anom_score = anom_score
anom_xcount_list.append(anom_xcount)
anom_score_list.append(anom_score)
# validation of anomalies
latitude = get_lat(anom_xcount)
longitude = get_long(anom_xcount)
dist = [0]
for z in range(len(latitude) - 1):
point_one = (latitude[z], longitude[z])
point_two = (latitude[z + 1], longitude[z + 1])
# distance = geodesic(point_one, point_two).km
# dist.append(1000 * distance)
dist.append(longitude[z])
anom_xcount = [str(x) for x in anom_xcount]
latitude = [str(x) for x in latitude]
longitude = [str(x) for x in longitude]
dist = [str(x) for x in dist]
write_data = zip(anom_xcount, latitude, longitude, dist)
track_side = 'chb' if i else 'cha'
train_mode = 'pushing' if j else 'pulling'
with open(self.counters_path + '\Prorail17112805si12_' + track_side + '_' + train_mode + '.csv', 'w',
newline='') as file:
try:
writer = csv.writer(file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
writer.writerow(['counters', 'latitude', 'longitude', 'distance'])
for cnt, lat, lon, dist in write_data:
writer.writerow([cnt, lat, lon, dist])
finally:
file.close()
#######################################################
lat_list = get_lat(anom_xcount).tolist()
long_list = get_long(anom_xcount).tolist()
lat_list_train = get_lat(anom_xcount_train).tolist()
long_list_train = get_long(anom_xcount_train).tolist()
# gmap_plot(lat_list_train + lat_list, long_list_train + long_list)
aba_data_side.append(aba_data_mode)
anom_xcount_mode.append(anom_xcount_list)
anom_score_mode.append(anom_score_list)
# function call: compare anomalies in ABA on both channels i.e. CHA and CHB and return anomaly_positions
anomaly_positions = match_anomaly(rail_data, rail_xcounters, anom_xcount_mode, seg_file)
# ///////////////////////////////////////////
if len(anomaly_positions) > 2:
anom_pos_cha = np.round(anomaly_positions[0] + anomaly_positions[2], 2)
anom_xcount_cha = np.round(np.concatenate((anom_xcount_mode[0][0], anom_xcount_mode[0][1]), axis=0), 2)
anom_score_cha = np.round(np.concatenate((anom_score_mode[0][0], anom_score_mode[0][1]), axis=0), 3)
else:
anom_pos_cha = np.round(anomaly_positions[0], 2)
anom_xcount_cha = np.round(anom_xcount_mode[0][0], 2)
anom_score_cha = np.round(anom_score_mode[0][0], 3)
anom_pos_xcount = np.stack((anom_pos_cha, anom_xcount_cha, anom_score_cha), axis=-1)
anom_pos_xcount_sorted = anom_pos_xcount[anom_pos_xcount[:, 0].argsort()]
anom_pos_cha = list(anom_pos_xcount_sorted[:, 0])
anom_xcount_cha = list(anom_pos_xcount_sorted[:, 1])
anom_score_cha = list(anom_pos_xcount_sorted[:, 2])
# Severity analysis (head-checks vs ABA anomaly severity)
# dict = {'position': anom_pos_cha, 'counters': anom_xcount_cha, 'score': anom_score_cha}
# df_anom_pos_score = pd.DataFrame(data=dict)
# ectpath = r'D:\strukton_project\WP_180306\ECT\EC_data_2018_FC_FO_LR.csv'
# headchecks = DefectSeverity(df_anom_pos_score, ectpath).get_trend()
#
# plotlist = []
# depth = normalize(headchecks['depth'].tolist())
# score = headchecks['score'].tolist()
# plotlist.append(depth)
# plotlist.append(score)
# pltlist = [[plotlist[j][i] for j in range(len(plotlist))] for i in range(len(plotlist[0]))]
# pltarr = np.array(pltlist)
# sorted = pltarr[pltarr[:, 0].argsort()]
# cracksize = sorted[:, 0]
# anomscore = sorted[:, 1]
#
# write_data = zip(cracksize, anomscore)
# track_side = 'cha_crack_anom'
#
# with open(self.counters_path + '\Prorail18030614si12_' + track_side + '.csv', 'w',
# newline='') as file:
# try:
# writer = csv.writer(file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
# writer.writerow(['crack_depth', 'anom_severity'])
# for crack, sev in write_data:
# writer.writerow([crack, sev])
# finally:
# file.close()
#
# ##################################
write_data = zip(anom_pos_cha, anom_xcount_cha, anom_score_cha)
return anom_pos_xcount_sorted