def __init__(self, args):
# create logger
self.logger = logging.getLogger(__name__)
self.logger.setLevel(logging.DEBUG)
# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
# add ch to logger
self.logger.addHandler(ch)
self.logger.debug("Starting Collector process in %s" % os.getcwd())
self.logger.debug("Gevent Version %s" % gevent.__version__)
#TODO: move output file name to config
#fname = "./NetFlow.%s.bin"%str(time.time()*100000)
#WARN: might want to remove this after testing
#self.out = open(fname,"wb")
#create tool instances
self.interface = Interface()
self.parse = Parse()
self.describe = Describe()
self.standardize = Standardize()
self.transform = Transform()
self.partition = Partition()
self.q = Queue()
self.inWindow = False
self.score = Score()
#TODO: move csv name to config
self.csv = CSV("output.csv")
return super(Collector, self).__init__(args)
def main():
sd = SynthData()
ca = coordinateAscent()
cal = CoordinateAscentLasso()
st = Standardize()
beta0Seperate = True
lam = 0.1
X, y, b = sd.generateData(noise=False,
w=np.array([1, 1, 1, 1, 1, 0, 0, 0, 0,
0])[np.newaxis].T)
#if beta0Seperate:
# beta = np.array([1, 1, 1, 1, 0, 0, 0, 0])[np.newaxis].T
#else:
# beta = np.array([1, 1, 1, 1, 1, 0, 0, 0, 0])[np.newaxis].T
#if beta0Seperate:
# y = 1 + np.dot(X, beta)
#else:
# X = np.append(np.ones((X.shape[0], 1)), X, 1)
# y = np.dot(X, beta)
print('Fitting the model with Lasso:')
print('Lambda = ' + str(lam))
print('beta0, array of betas:')
t0 = time()
print(cal.coordinateAscentLasso(y, X, lam, [], False, beta0Seperate))
dt = time() - t0
print('done in %.4fs.' % dt)
print()
print('Fitting the model with plain \'ol Coordinate Ascent')
print('beta0, array of betas:')
t0 = time()
print(ca.coordinateAscent(y, X, [], False))
dt = time() - t0
print('done in %.4fs.' % dt)
print()
#print('Dictionary Learning')
#dl = decomposition.DictionaryLearning(fit_algorithm='cd')
#print(dl.fit(X))
#print(np.shape(dl.components_))
#print(dl.components_)
print('Fitting the model with LARS (from the scikit library)')
clf = linear_model.LassoLars(alpha=0.01)
t0 = time()
print(clf.fit(X, y))
dt = time() - t0
print('done in %.4fs.' % dt)
print('array of betas:')
print(clf.coef_)
return 1
def __init__(self,args):
# create logger
self.logger = logging.getLogger(__name__)
self.logger.setLevel(logging.DEBUG)
# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
# add ch to logger
self.logger.addHandler(ch)
self.logger.debug( "Starting Collector process in %s"%os.getcwd())
#self.logger.debug( "Gevent Version %s"%gevent.__version__)
#TODO: move output file name to config
fname = "./NetFlow.%d.bin"%int(time.time())
#WARN: might want to remove this after testing
self.out = open(fname,"wb")
#create tool instances
self.interface = Interface()
self.parse = Parse()
self.context = Context()
self.describe = Describe()
self.standardize = Standardize()
self.transform = Transform()
self.partition = Partition()
self.q = Queue()
self.inWindow = settings.SETTINGS.get("collector","inWindow")
self.score = Score()
#TODO: move csv name to config
#self.csv = CSV("output.csv")
self.output = Output()
return super(Collector,self).__init__(args)
def main():
np.set_printoptions(suppress=True)
# loads the spambase data
f = open("data/spambase.data")
spam_data = np.array(np.loadtxt(f, delimiter=','))
k_fold_nr = 10
nr_samples = len(spam_data)
# chooses which stochastic gradients to use on the run-through
# takes defaults or you can provide command line arguments such as:
# python3 cross_validation.py batch linear
# python3 cross_validation.py batch linear stochastic linear batch logistic stochastic logistic
gradient_descent_methods = get_command_line_args()
k_fold_indices = createKFoldIndices(nr_samples, k_fold_nr)
st = Standardize()
# The last column, our complete y_true, which we will always take a subset from
# based on our current k-fold group
email_is_spam = spam_data[:, -1]
# take all the features apart from the last one, since that is our y_true
# containing all the information if an email actually is a spa,
spam_data = spam_data[:, 0:-1]
# normalising the spam_data
spam_data_normalized = st.standardize(spam_data)
# the spam data split into k_fold groups
k_fold_spam_data = []
for indices in k_fold_indices:
k_fold_spam_data.append(spam_data_normalized[indices, :])
lambdas = [1, 0.1, 0.01]
num_iters = 100
for gradient_descent_method in gradient_descent_methods:
train_err_history, predictions, y_test_sets = run_cross_validation(
gradient_descent_method, k_fold_nr, lambdas, num_iters, k_fold_spam_data, email_is_spam, k_fold_indices)
train_err_history = np.array(train_err_history)
# print(train_err_history)
# print(train_err_history.shape)
collapsed_train_err_history = [[], [], []]
for lam_i in range(len(lambdas)):
lam_err_history = train_err_history[lam_i]
# print(lam_err_history)
# print(np.mean(lam_err_history.tolist(), axis=0))
collapsed_train_err_history[lam_i].extend(np.mean(lam_err_history, axis=0))
# print(collapsed_train_err_history)
#
# print(len(collapsed_train_err_history))
# print(len(collapsed_train_err_history[0]))
# print(len(collapsed_train_err_history[1]))
# print(len(collapsed_train_err_history[2]))
iterations0 = [i for i in range(len(collapsed_train_err_history[0]))]
iterations1 = [i for i in range(len(collapsed_train_err_history[1]))]
iterations2 = [i for i in range(len(collapsed_train_err_history[2]))]
# print(collapsed_train_err_history)
# best lambda based on test errors (should have 3 test errors, where-as each is the
# mean of the 10 k-fold runs)
# take the best lambda from the 3-d predictions array for the ROC curve
# y_test as well, that is dependent on the k-group I chose
print('plotting now')
plt.figure(1)
plt.plot(iterations0, collapsed_train_err_history[0], 'g-', iterations1,
collapsed_train_err_history[1], 'b-', iterations2, collapsed_train_err_history[2], 'r-')
plt.legend(['lambda=1.0', 'lambda=0.1', 'lambda=0.01'])
# plt.plot(iterations, collapsed_train_err_history[1], 'b-', iterations, collapsed_train_err_history[2], 'r-')
# plt.legend(['lambda=0.1', 'lambda=0.01'])
plt.xlabel('iteration')
plt.ylabel('cost')
plt.show()
step_size = 0.01
nr_steps = (1 / step_size) + 1
false_positive_rates = []
true_positive_rates = []
for spam_threshold in np.linspace(0, 1, nr_steps):
spam_indices = [i for i, x in zip(range(len(y_test_sets)), y_test_sets) if x == 1]
nr_spam = len(spam_indices)
no_spam_indices = [i for i, x in zip(range(len(y_test_sets)), y_test_sets) if x == 0]
nr_no_spam = len(no_spam_indices)
nr_spam_predictions = len([element for element in predictions[spam_indices] if element > spam_threshold])
nr_no_spam_predictions = len([element for element in predictions[no_spam_indices]
if element > spam_threshold])
# print('Nr of spam total', nr_spam)
# print('Nr of spam classified', nr_spam_predictions)
# x-coordinate = false_positive_rate
false_positive_rates.append(nr_no_spam_predictions / nr_no_spam)
# y-coordinate = true_positve_rate
true_positive_rates.append(nr_spam_predictions / nr_spam)
# find all the ones in the y_test and what percentage are they in the predictions
# taken from y_test is true_positive
# 30 true positives 70 false positive
# true positive rate is e.g. 30 (classified above given threshold out of the 70) /70 (number of 1s)
# false positive rate is e.g. 20 (classified above given threshold out of the 30) / 30 (number of 0s)
# then plot as a point y = true positive rate, x = false positive rate
# connected up = ROC curve
# 1 ROC curve for all the 10 k-folds
# false positives, what are 0s in y_test but are above the threshold in the predictions
# sort the x and y coordinates so the AUC can be calculated properly
false_positive_rates.sort()
true_positive_rates.sort()
auc_sum = 0
for i in range(1, len(false_positive_rates)):
x_subtracted = false_positive_rates[i] - false_positive_rates[i - 1]
y_added = true_positive_rates[i] + true_positive_rates[i - 1]
auc_sum += x_subtracted * y_added
auc = (1/2) * auc_sum
print('The AUC of my classifier is ' + str(auc))
plt.figure(2)
plt.plot(false_positive_rates, true_positive_rates)
plt.legend(['ROC-Curve with AUC ' + str(auc)])
plt.show()
class Collector(DatagramServer):
x = 0
def __init__(self,args):
# create logger
self.logger = logging.getLogger(__name__)
self.logger.setLevel(logging.DEBUG)
# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
# add ch to logger
self.logger.addHandler(ch)
self.logger.debug( "Starting Collector process in %s"%os.getcwd())
#self.logger.debug( "Gevent Version %s"%gevent.__version__)
#TODO: move output file name to config
fname = "./NetFlow.%d.bin"%int(time.time())
#WARN: might want to remove this after testing
self.out = open(fname,"wb")
#create tool instances
self.interface = Interface()
self.parse = Parse()
self.context = Context()
self.describe = Describe()
self.standardize = Standardize()
self.transform = Transform()
self.partition = Partition()
self.q = Queue()
self.inWindow = settings.SETTINGS.get("collector","inWindow")
self.score = Score()
#TODO: move csv name to config
#self.csv = CSV("output.csv")
self.output = Output()
return super(Collector,self).__init__(args)
def done(self):
#pass
self.out.close()
#really important to call del on the csv obj to ensure it closes correctly
#del self.csv
def handle(self, rawData, address):
Collector.x += 1
#print '%s %s: got %r' % (Collector.x, address[0], rawData)
self.out.write(rawData)
interfacedData = self.interface.run(rawData)
#self.logger.debug("Interface: %s"%(repr(interfacedData)))
#once the rawData is "interfaced" we are passing it around by reference
# interfaced data must be iterable
try:
for record in interfacedData:
self.parse.run(record)
#self.logger.debug("Parse: %s"%(repr(record)))
self.context.run(record)
#self.logger.debug("Context: %s"%(repr(record)))
self.describe.run(record)
#self.logger.debug("Describe: %s"%(repr(record)))
#push the record onto the queue until window
if not (self.inWindow):
self.q.put(record)
#self.logger.debug("adding record to queue %s"%(repr(record)))
if (self.q.qsize() == int(settings.SETTINGS.get("collector","describeWindow"))):
#self.logger.debug("Describe Window of %s records met, Begin Processing queue"%settings.SETTINGS.get("collector","describeWindow"))
self.inWindow = True
while not self.q.empty():
item = self.q.get()
#self.logger.debug("processing record from queue %s"%(repr(item)))
self.standardize.run(item)
self.transform.run(item)
self.partition.run(item)
#self.csv.writeRow(self.csv.format(item))
self.output.run(item)
self.q.task_done()
else:
self.standardize.run(record)
#self.logger.debug("Standardize: %s"%(repr(record)))
self.transform.run(record)
#self.logger.debug("Transform: %s"%(repr(record)))
self.partition.run(record)
#self.logger.debug("Partition: %s"%(repr(record)))
#self.csv.writeRow(self.csv.format(record))
self.output.run(record)
#self.score.run(record)
except Exception as e:
self.logger.error("Interfaced data is not iterable %s"%(str(e)))
class Collector(DatagramServer):
x = 0
def __init__(self, args):
# create logger
self.logger = logging.getLogger(__name__)
self.logger.setLevel(logging.DEBUG)
# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
# add ch to logger
self.logger.addHandler(ch)
self.logger.debug("Starting Collector process in %s" % os.getcwd())
self.logger.debug("Gevent Version %s" % gevent.__version__)
#TODO: move output file name to config
#fname = "./NetFlow.%s.bin"%str(time.time()*100000)
#WARN: might want to remove this after testing
#self.out = open(fname,"wb")
#create tool instances
self.interface = Interface()
self.parse = Parse()
self.describe = Describe()
self.standardize = Standardize()
self.transform = Transform()
self.partition = Partition()
self.q = Queue()
self.inWindow = False
self.score = Score()
#TODO: move csv name to config
self.csv = CSV("output.csv")
return super(Collector, self).__init__(args)
def done(self):
#self.out.close()
#really important to call del on the csv obj to ensure it closes correctly
del self.csv
def handle(self, rawData, address):
Collector.x += 1
#print '%s %s: got %r' % (Collector.x, address[0], data)
#self.out.write(rawData)
interfacedData = self.interface.run(rawData)
#once the rawData is "interfaced" we are passing it around by reference
# interfaced data must be iterable
try:
for record in interfacedData:
self.parse.run(record)
self.describe.run(record)
#push the record onto the queue until window
if not (self.inWindow):
self.q.put(record)
#self.logger.debug("adding record to queue %s"%(repr(record)))
if (self.q.qsize() == int(
settings.SETTINGS.get("collector",
"describeWindow"))):
self.logger.debug(
"Describe Window of %s records met, Begin Processing queue"
% settings.SETTINGS.get("collector",
"describeWindow"))
self.inWindow = True
while not self.q.empty():
item = self.q.get()
#self.logger.debug("processing record from queue %s"%(repr(item)))
self.standardize.run(item)
self.transform.run(item)
self.partition.run(item)
self.csv.writeRow(self.csv.format(item))
self.q.task_done()
else:
self.standardize.run(record)
self.transform.run(record)
self.partition.run(record)
self.csv.writeRow(self.csv.format(record))
self.score.run(record)
except Exception as e:
self.logger.error("Interfaced data is not iterable %s" % (str(e)))