def write_request_to_log(self, dev):
'''Records the subvolume requested of this sample in a log'''
if self.log is not None:
log_line1 = self.sec_name
log_line2 = "subvolume: [{},{},{}] requested".format(dev[0],dev[1],dev[2])
utils.write_to_log(self.log, log_line1)
utils.write_to_log(self.log, log_line2)
def do_point_query(points, raster, csv_pth, num, log_out):
try:
u.verify_dir(csv_pth)
dataset = raster.split('\\')[-2].replace(' ', '_')
raster_name_to_csv = os.path.basename(raster).replace('.tif', '.csv')
csv_name = '__'.join([dataset, raster_name_to_csv])
csv_out = os.path.join(csv_pth, csv_name)
start = timer()
u.write_to_log(' {}) Raster: {}'.format(num, os.path.basename(raster)), log_out)
stats = point_query(points, raster, interpolate='nearest', geojson_out=True)
print(' point_query... ({} sec.)'.format(round(timer()-start, 2)))
start = timer()
attributes = []
for item in stats:
#print ('{}'.format(item['properties']))
attributes.append(item['properties'])
print(' append dicts... ({} sec.)'.format(round(timer()-start, 2)))
start = timer()
with open(csv_out, 'w', newline='') as outfile:
fp = csv.DictWriter(outfile, attributes[0].keys())
fp.writeheader()
fp.writerows(attributes)
print(' write to csv... ({} sec.)'.format(round(timer()-start, 2)))
u.write_to_log(' CSV file: {}'.format(csv_out), log_out)
u.write_to_log(' Log file: {}'.format(log_out), log_out)
except Exception as e:
u.write_to_log(str(e), log_out)
u.write_to_log('FINISH POINTS: {}'.format(time.strftime("%Y-%m-%d %H:%M:%S")), log_out)
def get_initial_company_info():
"""Gets the initial information for each company"""
company_dict = utils.open_json(MONITOR)
for company in company_dict:
# Gets symbol for company
if company_dict[company]["Symbol"] == "unknown":
try:
with urllib.request.urlopen(
f'https://finance.yahoo.com/_finance_doubledown/'
f'api/resource/searchassist;searchTerm={company}'
) as response:
html = response.read().decode()
d = json.loads(html)
company_dict[company]["Symbol"] = d['items'][0][
'symbol']
except urllib.error.HTTPError as error:
utils.write_to_log(f'Error opening URL: {error}')
# Gets initial share price
if company_dict[company]["Initial-share-price"] == 1:
yahoo = Share(company_dict[company]["Symbol"])
share = yahoo.get_price()
company_dict[company]["Initial-share-price"] = float(share)
company_dict[company]["Current-share-price"] = float(share)
utils.write_to_json(MONITOR, company_dict)
def write_request_to_log(self, dev):
'''Records the subvolume requested of this sample in a log'''
if self.log is not None:
log_line1 = self.sec_name
log_line2 = "subvolume: [{},{},{}] requested".format(
dev[0], dev[1], dev[2])
utils.write_to_log(self.log, log_line1)
utils.write_to_log(self.log, log_line2)
def check_mentions(self):
"""Checks mentions for sign up's via email or twitter
via "Sign up / Sign up [email]"""
try:
mentions = self.api.mentions_timeline(count=3)
for mention in mentions:
if "stop" in mention.text.lower():
# Unsubscribe for email
if len(mention.text.split()) == 3:
email = mention.text.split()[2]
email_list = utils.open_file(EMAILS).split()
if email in email_list:
email_list.remove(email)
utils.write_to_file(EMAILS, ' '.join(email_list))
# Unsubscribe for Twitter handle
else:
twitter_name = mention.user.screen_name
twitter_name_list = utils.open_file(
TWITTER_NAMES).split()
if twitter_name in twitter_name_list:
twitter_name_list.remove(twitter_name)
utils.write_to_file(TWITTER_NAMES,
' '.join(twitter_name_list))
elif "sign up" in mention.text.lower():
# Email sign up
if len(mention.text.split()) > 3:
email = mention.text.split()[3]
email_list = utils.open_file(EMAILS).split()
if email not in email_list:
email_list.append(email)
utils.append_to_file(EMAILS, email)
# Twitter handle sign up
else:
twitter_name = mention.user.screen_name
twitter_name_list = utils.open_file(
TWITTER_NAMES).split()
if twitter_name not in twitter_name_list:
twitter_name_list.append(twitter_name)
utils.append_to_file(TWITTER_NAMES, twitter_name)
except tweepy.TweepError as error:
utils.write_to_log(f'Error checking mentions: {error}')
def track_directories(directories, session, bucket_name):
global aws_session, bucket
aws_session = session
bucket = bucket_name
observer = Observer()
# Create event handler and set the function to call when event occurs.
event_handler = FileSystemEventHandler()
event_handler.on_created = upload_file_to_S3
# Schedule the observer to monitor every directory in the config file.
for directory in directories:
observer.schedule(event_handler, directory, recursive=True)
write_to_log('Scheduled observer for ' + directory)
# Start the observer.
observer.start()
try:
write_to_log('Beginning to wait for events.')
# Constantly wait for events.
while True:
time.sleep(1)
# Stop when user presses Ctrl + C.
except KeyboardInterrupt:
write_to_log('Stopping observers...')
observer.stop()
observer.join()
write_to_log('Stopped observers.')
def upload_file_to_S3(event):
global observer_paused, aws_session, bucket
# Don't respond to events if paused flag is true.
# Make sure to only upload files and ignore directories.
if observer_paused or not os.path.isfile(event.src_path):
return
# Unify folder names. (username replaced with placeholder)
s3_key = event.src_path.replace(getpass.getuser(), core.user_placeholder).replace('\\', '/')
s3_client = aws_session.resource('s3')
s3_client.meta.client.upload_file(event.src_path, bucket, s3_key)
write_to_log('Uploaded file ' + s3_key)
def main_code(raster_dir, pts, csv_path, log, raster_regex,):
# Main stuff
start_all = timer()
u.write_to_log('\nSTART POINTS: {}'.format(time.strftime("%Y-%m-%d %H:%M:%S")), log)
raster_list = []
for filename in glob.iglob(raster_dir+raster_regex, recursive=True):
raster_list.append(filename)
count = 0
for tif in raster_list:
count+=1
try:
do_point_query(pts, tif, csv_path, count, log)
except Exception as e:
print(e)
u.write_to_log('FINISH POINTS: {}\nELAPSED TIME: ({} sec.)'.format(time.strftime("%Y-%m-%d %H:%M:%S"), round(timer()-start_all, 2)), log)
def test_write_to_log_func():
"""Test write_to_log function from utils"""
email = '*****@*****.**'
event = 'TEST'
today = datetime.date.today().strftime('%d-%m-%Y')
record = email + ', ' + event
log_str = '[' + today + '] -- ' + record + '\n'
write_to_log(email, event)
with open(LOG_FILE) as log_file:
assert log_str in log_file.read()
# clean log from test records
with open(LOG_FILE, 'r') as log_file:
lines = log_file.readlines()
with open(LOG_FILE, 'w') as log_file:
for line in lines:
if line != log_str:
log_file.write(line)
def email(self):
"""Emails a list of people"""
company_output = ', '.join(self.matches)
try:
email_list = utils.open_file(EMAILS).split()
server = smtplib.SMTP('smtp.gmail.com', 587)
server.starttls()
server.login(EMAIL, PASSWORD)
server.sendmail(
EMAIL, email_list,
f'Trump just tweeted about {company_output}. '
f'Might be time to check your shares...')
server.quit()
except smtplib.SMTPResponseException as error:
utils.write_to_log(f'Email error: {error}')
def share_output():
"""Calls difference_in_shares from the Companies class,
Outputs the data to twitter."""
share_difference_dict = Companies().difference_in_shares()
for company in share_difference_dict:
try:
# If you're following one person, this can be changed to look better
# Remove "[Mentioned by: {company["Handle"]}" in the first line.
Twitter().api.update_status(
f'{company} [Mentioned by: {company["Handle"]} - '
f'Initial Share Price: {company["Initial"]} '
f'Current Share Price: {company["Current"]}'
f'Change: {company["Change"]}'
f'Max Change: {company["Max-change"]} ')
except tweepy.TweepError as error:
utils.write_to_log(f'Twitter output Error: {error}')
def tweet(self):
"""Tweets and DMs the company that has been mentioned"""
try:
for company in self.matches:
self.twitter.api.update_status(
f'Yelp, looks like a good time to take a look at your shares in {company.upper()}! '
f'{self.handle} just mentioned them!')
twitter_users = utils.open_file(TWITTER_NAMES).split()
for user in twitter_users:
time.sleep(2)
self.twitter.api.send_direct_message(
screen_name=user,
text=f'{self.handle} just tweeted about {company.upper()}! '
f'Might be time to check your shares!')
except tweepy.TweepError as error:
utils.write_to_log(f'Error tweeting: {error}')
def check_tweets(self):
"""Checks the twitter handle for new tweets.
If there has been a new tweet, checks it in the Companies
class to see if a company is contained in it"""
try:
new_tweet = self.api.user_timeline(screen_name=self.handle,
count=1)
for tweet in new_tweet: # Need to find a fix for this loop
old_tweet = utils.open_file(
f'{GENERIC}{self.handle}.txt').strip()
if old_tweet != tweet.text.encode('utf8'):
utils.write_to_file(f'{GENERIC}{self.handle}.txt',
tweet.text)
return tweet.text.encode('utf8')
except tweepy.TweepError as error:
utils.write_to_log(f'Error checking for new tweets: {error}')
def okta():
""" View for user creation in Okta """
result = list()
data = request.get_data()
users = users_list_gen(data)
if not users:
return 'No users to create!'
for user in users:
okta_user = {
"profile": {
"firstName": user["firstName"],
"lastName": user["lastName"],
"email": user["email"],
"login": user["email"]
},
"credentials": {
"password": {
"value": settings.OKTA_USER_PASS
}
},
}
if settings.OKTA_USER_GROUP:
okta_user.update({"groupIds": [
settings.OKTA_USER_GROUP,
]})
okta_req = post(settings.OKTA_API_URL,
headers=settings.OKTA_HEADERS,
data=json.dumps(okta_user))
if okta_req.status_code != 200:
result.append('%s: %s' %
(user['email'],
okta_req.json()['errorCauses'][0]['errorSummary']))
else:
result.append('%s: user succefully created.' % user['email'])
write_to_log(user['email'], 'OKTA')
return '\n'.join(result)
def write_request_to_log(self, dev, rft):
'''Records the subvolume requested of this sample in a log'''
if self.log is not None:
rft_string = utils.rft_to_string(rft)
log_line1 = self.sec_name
log_line2 = "subvolume: [{},{},{}] requested".format(dev[0],dev[1],dev[2])
log_line3 = "transformation: {}".format(rft_string)
utils.write_to_log(self.log, log_line1)
utils.write_to_log(self.log, log_line2)
utils.write_to_log(self.log, log_line3)
def write_request_to_log(self, dev, rft):
'''Records the subvolume requested of this sample in a log'''
if self.log is not None:
rft_string = utils.rft_to_string(rft)
log_line1 = self.sec_name
log_line2 = "subvolume: [{},{},{}] requested".format(
dev[0], dev[1], dev[2])
log_line3 = "transformation: {}".format(rft_string)
utils.write_to_log(self.log, log_line1)
utils.write_to_log(self.log, log_line2)
utils.write_to_log(self.log, log_line3)
def active_directory():
"""
View for user creation in Active Directory
Useful info about python ldap lib
http://marcitland.blogspot.com/2011/02/python-active-directory-linux.html
"""
result = list()
data = request.get_data()
users = users_list_gen(data)
if not users:
return 'No users to create!'
ldap.set_option(ldap.OPT_X_TLS_REQUIRE_CERT, ldap.OPT_X_TLS_NEVER)
ad_srv = ldap.initialize(settings.AD_SERVER)
ad_srv.set_option(ldap.OPT_REFERRALS, 0)
ad_srv.set_option(ldap.OPT_PROTOCOL_VERSION, 3)
ad_srv.set_option(ldap.OPT_X_TLS, ldap.OPT_X_TLS_DEMAND)
ad_srv.set_option(ldap.OPT_X_TLS_DEMAND, True)
ad_srv.set_option(ldap.OPT_DEBUG_LEVEL, 255)
try:
ad_srv.start_tls_s()
except ldap.LDAPError as err:
msg = get_err_msg(err)
result.append('Failed to connect to LDAP server! Error message: %s.' %
msg)
return '\n'.join(result)
ad_srv.simple_bind_s(settings.AD_BIND_DN, settings.AD_ADMIN_PASS)
for user in users:
user_dn = 'CN=' + user['fullName'] + ',' + settings.AD_USER_DN
user_attrs = {}
user_attrs['objectClass'] = [
b'top', b'person', b'organizationalPerson', b'user'
]
user_attrs['cn'] = str.encode(user['fullName'])
user_attrs['userPrincipalName'] = str.encode(user['adName'] + '@' +
settings.AD_DOMAIN)
user_attrs['sAMAccountName'] = str.encode(user['adName'])
user_attrs['givenName'] = str.encode(user['firstName'])
user_attrs['sn'] = str.encode(user['lastName'])
user_attrs['displayName'] = str.encode(user['fullName'])
user_attrs['description'] = str.encode(user['jobtitle'])
user_attrs['userAccountControl'] = b'514' # user is disabled
# add user
user_ldif = modlist.addModlist(user_attrs)
try:
ad_srv.add_s(user_dn, user_ldif)
result.append('%s: User succefully created.' % user['adName'])
write_to_log(user['email'], 'AD')
except ldap.LDAPError as err:
msg = get_err_msg(err)
result.append('%s: Failed to create user! Error message: %s' %
(user['adName'], msg))
return '\n'.join(result)
# change pass
unicode_pass = '******' + settings.AD_USER_PASS + '\"'
password_value = unicode_pass.encode('utf-16-le')
add_pass = [(ldap.MOD_REPLACE, 'unicodePwd', [password_value])]
try:
ad_srv.modify_s(user_dn, add_pass)
result.append('%s: Password has changed succefully.' %
user['adName'])
except ldap.LDAPError as err:
msg = get_err_msg(err)
result.append('%s: Failed to change password! Error message: %s.' %
(user['adName'], msg))
return '\n'.join(result)
# enable user
mod_acct = [(ldap.MOD_REPLACE, 'userAccountControl', b'512')]
try:
ad_srv.modify_s(user_dn, mod_acct)
result.append('%s: user enabled succefully' % user['adName'])
except ldap.LDAPError as err:
msg = get_err_msg(err)
result.append('%s: Failed to enable user! Error message: %s.' %
(user['adName'], msg))
return '\n'.join(result)
if settings.AD_GROUP_NAME:
# add to group
add_member = [(ldap.MOD_ADD, 'member', str.encode(user_dn))]
try:
ad_srv.modify_s(settings.AD_GROUP_DN, add_member)
result.append('%s: User succefully added to group %s.' %
(user['adName'], settings.AD_GROUP_NAME))
except ldap.LDAPError as err:
msg = get_err_msg(err)
result.append(
'%s: Failed to add user to group %s! Error message: %s.' %
(user['adName'], settings.AD_GROUP_NAME, msg))
# Disconnect from AD server
ad_srv.unbind_s()
return '\n'.join(result)
def main_code(buff_dir, pt_dir, combine_dir, log):
u.verify_dir(combine_dir)
start_all = timer()
u.write_to_log(
'\nSTART COMBINE: {}'.format(time.strftime("%Y-%m-%d %H:%M:%S")), log)
buff_list = []
for filename in glob.iglob(buff_dir + '/*.csv'):
buff_list.append(filename)
pt_list = []
for filename in glob.iglob(pt_dir + '/*.csv'):
pt_list.append(filename)
match_count = 0
for buff_csv in buff_list:
buff_name = os.path.basename(buff_csv)
process_buff = buff_csv
for pt_csv in pt_list:
pt_name = os.path.basename(pt_csv)
if buff_name == pt_name:
process_pt = pt_csv
match_count += 1
u.write_to_log(
' {}) buffers: {} points: {}'.format(
match_count, buff_name, pt_name), log)
#csv_name = os.path.basename(os.path.basename(buff_csv).replace('.csv', '_pandas.csv'))
out_csv = os.path.join(combine_dir, buff_name)
buff_df = pd.read_csv(buff_csv, dtype='object')
pt_df = pd.read_csv(pt_csv, dtype='object')
print(' buff shape: {}'.format(buff_df.shape))
print(' pt shape: {}'.format(pt_df.shape))
merged = pd.merge(left=buff_df, right=pt_df, on='DHSID')
print(' merge shape: {}'.format(merged.shape))
for col in list(merged):
if col.endswith("_y"):
merged = merged.drop(str(col), 1)
# These select columns by name and merge point values into them if
# the buffer analysis resulted in a blank value.
try:
merged.loc[merged['mean'].isnull(),
'mean'] = merged['value']
except:
print(' no MEAN column')
try:
merged.loc[merged['sum'].isnull(), 'sum'] = merged['value']
except:
print(' no SUM column')
try:
merged.loc[merged['majority'].isnull(),
'majority'] = merged['value']
except:
print(' no MAJORITY column')
try:
merged = merged.drop('nodata', 1)
except:
print(' no NODATA column')
merged = merged.drop('value', 1)
merged.to_csv(out_csv, sep=',')
u.write_to_log(
'FINISH COMBINE: {}\nELAPSED TIME: {} sec.'.format(
time.strftime("%Y-%m-%d %H:%M:%S"), round(timer() - start_all,
3)), log)
import dirtracker
import syncmonitor
import utils
import threading
user_placeholder = 'USER'
#---------------------------------------------------------
# Run order
#---------------------------------------------------------
if __name__ == '__main__':
config = utils.get_config()
credentials = utils.get_credentials(config)
aws_session = utils.get_session(credentials, config)
# Start the sync monitor in a separate daemon thread.
sync = threading.Thread(target=syncmonitor.sync_monitor, args=(aws_session, config), daemon=True)
sync.start()
utils.write_to_log('Started sync monitor.')
# Start monitoring for new files in directories using main thread.
utils.write_to_log('Started directory trackers.')
dirtracker.track_directories(config['folders'], aws_session, config['bucket'])
def main( conf_file='config.cfg', logfile=None ):
#%% parameters
print "reading config parameters..."
config, pars = zconfig.parser( conf_file )
if pars.has_key('logging') and pars['logging']:
print "recording configuration file..."
zlog.record_config_file( pars )
logfile = zlog.make_logfile_name( pars )
#%% create and initialize the network
if pars['train_load_net'] and os.path.exists(pars['train_load_net']):
print "loading network..."
net = znetio.load_network( pars )
# load existing learning curve
lc = zstatistics.CLearnCurve( pars['train_load_net'] )
# the last iteration we want to continue training
iter_last = lc.get_last_it()
else:
if pars['train_seed_net'] and os.path.exists(pars['train_seed_net']):
print "seeding network..."
net = znetio.load_network( pars, is_seed=True )
else:
print "initializing network..."
net = znetio.init_network( pars )
# initalize a learning curve
lc = zstatistics.CLearnCurve()
iter_last = lc.get_last_it()
# show field of view
print "field of view: ", net.get_fov()
# total voxel number of output volumes
vn = utils.get_total_num(net.get_outputs_setsz())
# set some parameters
print 'setting up the network...'
eta = pars['eta']
net.set_eta( pars['eta'] )
net.set_momentum( pars['momentum'] )
net.set_weight_decay( pars['weight_decay'] )
# initialize samples
outsz = pars['train_outsz']
print "\n\ncreate train samples..."
smp_trn = zsample.CSamples(config, pars, pars['train_range'], net, outsz, logfile)
print "\n\ncreate test samples..."
smp_tst = zsample.CSamples(config, pars, pars['test_range'], net, outsz, logfile)
# initialization
elapsed = 0
err = 0.0 # cost energy
cls = 0.0 # pixel classification error
re = 0.0 # rand error
# number of voxels which accumulate error
# (if a mask exists)
num_mask_voxels = 0
if pars['is_malis']:
malis_cls = 0.0
print "start training..."
start = time.time()
total_time = 0.0
print "start from ", iter_last+1
#Saving initialized network
if iter_last+1 == 1:
znetio.save_network(net, pars['train_save_net'], num_iters=0)
lc.save( pars, 0.0 )
for i in xrange(iter_last+1, pars['Max_iter']+1):
# get random sub volume from sample
vol_ins, lbl_outs, msks, wmsks = smp_trn.get_random_sample()
# forward pass
# apply the transformations in memory rather than array view
vol_ins = utils.make_continuous(vol_ins, dtype=pars['dtype'])
props = net.forward( vol_ins )
# cost function and accumulate errors
props, cerr, grdts = pars['cost_fn']( props, lbl_outs, msks )
err += cerr
cls += cost_fn.get_cls(props, lbl_outs)
num_mask_voxels += utils.sum_over_dict(msks)
# gradient reweighting
grdts = utils.dict_mul( grdts, msks )
grdts = utils.dict_mul( grdts, wmsks )
if pars['is_malis'] :
malis_weights, rand_errors = cost_fn.malis_weight(pars, props, lbl_outs)
grdts = utils.dict_mul(grdts, malis_weights)
# accumulate the rand error
re += rand_errors.values()[0]
malis_cls_dict = utils.get_malis_cls( props, lbl_outs, malis_weights )
malis_cls += malis_cls_dict.values()[0]
total_time += time.time() - start
start = time.time()
# test the net
if i%pars['Num_iter_per_test']==0:
lc = test.znn_test(net, pars, smp_tst, vn, i, lc)
if i%pars['Num_iter_per_show']==0:
# normalize
if utils.dict_mask_empty(msks):
err = err / vn / pars['Num_iter_per_show']
cls = cls / vn / pars['Num_iter_per_show']
else:
err = err / num_mask_voxels / pars['Num_iter_per_show']
cls = cls / num_mask_voxels / pars['Num_iter_per_show']
lc.append_train(i, err, cls)
# time
elapsed = total_time / pars['Num_iter_per_show']
if pars['is_malis']:
re = re / pars['Num_iter_per_show']
lc.append_train_rand_error( re )
malis_cls = malis_cls / pars['Num_iter_per_show']
lc.append_train_malis_cls( malis_cls )
show_string = "iteration %d, err: %.3f, cls: %.3f, re: %.6f, mc: %.3f, elapsed: %.1f s/iter, learning rate: %.6f"\
%(i, err, cls, re, malis_cls, elapsed, eta )
else:
show_string = "iteration %d, err: %.3f, cls: %.3f, elapsed: %.1f s/iter, learning rate: %.6f"\
%(i, err, cls, elapsed, eta )
if pars.has_key('logging') and pars['logging']:
utils.write_to_log(logfile, show_string)
print show_string
# reset err and cls
err = 0
cls = 0
re = 0
num_mask_voxels = 0
if pars['is_malis']:
malis_cls = 0
# reset time
total_time = 0
start = time.time()
if i%pars['Num_iter_per_annealing']==0:
# anneal factor
eta = eta * pars['anneal_factor']
net.set_eta(eta)
if i%pars['Num_iter_per_save']==0:
# save network
znetio.save_network(net, pars['train_save_net'], num_iters=i)
lc.save( pars, elapsed )
if pars['is_malis']:
utils.save_malis(malis_weights, pars['train_save_net'], num_iters=i)
# run backward pass
grdts = utils.make_continuous(grdts, dtype=pars['dtype'])
net.backward( grdts )
def main(args):
config, pars, logfile = parse_args(args)
#%% create and initialize the network
net, lc = znetio.create_net(pars)
# total voxel number of output volumes
vn = utils.get_total_num(net.get_outputs_setsz())
# initialize samples
outsz = pars['train_outsz']
print "\n\ncreate train samples..."
smp_trn = zsample.CSamples(config, pars, pars['train_range'], net, outsz,
logfile)
print "\n\ncreate test samples..."
smp_tst = zsample.CSamples(config, pars, pars['test_range'], net, outsz,
logfile)
if pars['is_check']:
import zcheck
zcheck.check_patch(pars, smp_trn)
# gradient check is not working now.
# zcheck.check_gradient(pars, net, smp_trn)
# initialization
eta = pars['eta']
elapsed = 0
err = 0.0 # cost energy
cls = 0.0 # pixel classification error
re = 0.0 # rand error
# number of voxels which accumulate error
# (if a mask exists)
num_mask_voxels = 0
if pars['is_malis']:
malis_cls = 0.0
malis_eng = 0.0
else:
malis_weights = None
# the last iteration we want to continue training
iter_last = lc.get_last_it()
print "start training..."
start = time.time()
total_time = 0.0
print "start from ", iter_last + 1
#Saving initial/seeded network
# get file name
fname, fname_current = znetio.get_net_fname(pars['train_net_prefix'],
iter_last,
suffix="init")
znetio.save_network(net, fname, pars['is_stdio'])
lc.save(pars, fname, elapsed=0.0, suffix="init_iter{}".format(iter_last))
# no nan detected
nonan = True
for i in xrange(iter_last + 1, pars['Max_iter'] + 1):
# time cumulation
total_time += time.time() - start
start = time.time()
# get random sub volume from sample
vol_ins, lbl_outs, msks, wmsks = smp_trn.get_random_sample()
# forward pass
# apply the transformations in memory rather than array view
vol_ins = utils.make_continuous(vol_ins)
props = net.forward(vol_ins)
# cost function and accumulate errors
props, cerr, grdts = pars['cost_fn'](props, lbl_outs, msks)
err += cerr
cls += cost_fn.get_cls(props, lbl_outs)
# compute rand error
if pars['is_debug']:
assert not np.all(lbl_outs.values()[0] == 0)
re += pyznn.get_rand_error(props.values()[0], lbl_outs.values()[0])
num_mask_voxels += utils.sum_over_dict(msks)
# check whether there is a NaN here!
if pars['is_debug']:
nonan = nonan and utils.check_dict_nan(vol_ins)
nonan = nonan and utils.check_dict_nan(lbl_outs)
nonan = nonan and utils.check_dict_nan(msks)
nonan = nonan and utils.check_dict_nan(wmsks)
nonan = nonan and utils.check_dict_nan(props)
nonan = nonan and utils.check_dict_nan(grdts)
if not nonan:
utils.inter_save(pars, net, lc, vol_ins, props, lbl_outs, \
grdts, malis_weights, wmsks, elapsed, i)
# stop training
return
# gradient reweighting
grdts = utils.dict_mul(grdts, msks)
if pars['rebalance_mode']:
grdts = utils.dict_mul(grdts, wmsks)
if pars['is_malis']:
malis_weights, rand_errors, num_non_bdr = cost_fn.malis_weight(
pars, props, lbl_outs)
if num_non_bdr <= 1:
# skip this iteration
continue
grdts = utils.dict_mul(grdts, malis_weights)
dmc, dme = utils.get_malis_cost(props, lbl_outs, malis_weights)
malis_cls += dmc.values()[0]
malis_eng += dme.values()[0]
# run backward pass
grdts = utils.make_continuous(grdts)
net.backward(grdts)
total_time += time.time() - start
start = time.time()
if i % pars['Num_iter_per_show'] == 0:
# time
elapsed = total_time / pars['Num_iter_per_show']
# normalize
if utils.dict_mask_empty(msks):
err = err / vn / pars['Num_iter_per_show']
cls = cls / vn / pars['Num_iter_per_show']
else:
err = err / num_mask_voxels / pars['Num_iter_per_show']
cls = cls / num_mask_voxels / pars['Num_iter_per_show']
re = re / pars['Num_iter_per_show']
lc.append_train(i, err, cls, re)
if pars['is_malis']:
malis_cls = malis_cls / pars['Num_iter_per_show']
malis_eng = malis_eng / pars['Num_iter_per_show']
lc.append_train_malis_cls(malis_cls)
lc.append_train_malis_eng(malis_eng)
show_string = "update %d, cost: %.3f, pixel error: %.3f, rand error: %.3f, me: %.3f, mc: %.3f, elapsed: %.1f s/iter, learning rate: %.5f"\
%(i, err, cls, re, malis_eng, malis_cls, elapsed, eta )
else:
show_string = "update %d, cost: %.3f, pixel error: %.3f, rand error: %.3f, elapsed: %.1f s/iter, learning rate: %.5f"\
%(i, err, cls, re, elapsed, eta )
if pars.has_key('logging') and pars['logging']:
utils.write_to_log(logfile, show_string)
print show_string
# reset err and cls
err = 0
cls = 0
re = 0
num_mask_voxels = 0
if pars['is_malis']:
malis_cls = 0
# reset time
total_time = 0
start = time.time()
# test the net
if i % pars['Num_iter_per_test'] == 0:
# time accumulation should skip the test
total_time += time.time() - start
lc = test.znn_test(net, pars, smp_tst, vn, i, lc)
start = time.time()
if i % pars['Num_iter_per_save'] == 0:
utils.inter_save(pars, net, lc, vol_ins, props, lbl_outs, \
grdts, malis_weights, wmsks, elapsed, i)
if i % pars['Num_iter_per_annealing'] == 0:
# anneal factor
eta = eta * pars['anneal_factor']
net.set_eta(eta)
# stop the iteration at checking mode
if pars['is_check']:
print "only need one iteration for checking, stop program..."
break
def gmail():
""" View for user creation in Gmail """
result = list()
data = request.get_data()
users = users_list_gen(data)
if not users:
return 'No users to create!'
scopes = [
'https://www.googleapis.com/auth/admin.directory.user',
'https://www.googleapis.com/auth/admin.directory.group'
]
creds = None
if os.path.exists('token.pickle'):
with open('token.pickle', 'rb') as token:
creds = pickle.load(token)
if not creds or not creds.valid:
if creds and creds.expired and creds.refresh_token:
creds.refresh(Request())
else:
flow = InstalledAppFlow.from_client_secrets_file(
settings.GMAIL_CREDENTIALS, scopes)
creds = flow.run_local_server(port=0)
with open('token.pickle', 'wb') as token:
pickle.dump(creds, token)
service = build('admin', 'directory_v1', credentials=creds)
for user in users:
gmail_user = {
'primaryEmail': user['email'],
'name': {
'givenName': user['firstName'],
'familyName': user['lastName']
},
'orgUnitPath': settings.GMAIL_ORG_UNIT_PATH,
'password': settings.GMAIL_USER_PASS
}
member = {'email': user['email']}
# add user
try:
service.users().insert(body=gmail_user).execute()
result.append('%s: user succefully created.' % user['email'])
write_to_log(user['email'], 'GMAIL')
except HttpError as err:
msg = json.loads(err.content.decode())['error']['message']
result.append('%s: Failed to create user. Error message: %s' %
(user['email'], msg))
return '\n'.join(result)
# add user to group
if settings.GMAIL_GROUP:
try:
service.members().insert(groupKey=settings.GMAIL_GROUP,
body=member).execute()
result.append('%s: User succefully added to group %s.' %
(user['email'], settings.GMAIL_GROUP))
except HttpError as err:
msg = json.loads(err.content.decode())['error']['message']
result.append(
'%s: Failed to add user to group %s. Error message: %s.' %
(user['email'], settings.GMAIL_GROUP, msg))
return '\n'.join(result)
def main( conf_file='config.cfg', logfile=None ):
#%% parameters
print "reading config parameters..."
config, pars = front_end.parser( conf_file )
if pars.has_key('logging') and pars['logging']:
print "recording configuration file..."
front_end.record_config_file( pars )
logfile = front_end.make_logfile_name( pars )
#%% create and initialize the network
if pars['train_load_net'] and os.path.exists(pars['train_load_net']):
print "loading network..."
net = netio.load_network( pars )
# load existing learning curve
lc = zstatistics.CLearnCurve( pars['train_load_net'] )
else:
if pars['train_seed_net'] and os.path.exists(pars['train_seed_net']):
print "seeding network..."
net = netio.load_network( pars, is_seed=True )
else:
print "initializing network..."
net = netio.init_network( pars )
# initalize a learning curve
lc = zstatistics.CLearnCurve()
# show field of view
print "field of view: ", net.get_fov()
print "output volume info: ", net.get_outputs_setsz()
# set some parameters
print 'setting up the network...'
vn = utils.get_total_num(net.get_outputs_setsz())
eta = pars['eta'] #/ vn
net.set_eta( eta )
net.set_momentum( pars['momentum'] )
net.set_weight_decay( pars['weight_decay'] )
# initialize samples
outsz = pars['train_outsz']
print "\n\ncreate train samples..."
smp_trn = front_end.CSamples(config, pars, pars['train_range'], net, outsz, logfile)
print "\n\ncreate test samples..."
smp_tst = front_end.CSamples(config, pars, pars['test_range'], net, outsz, logfile)
# initialization
elapsed = 0
err = 0
cls = 0
# interactive visualization
plt.ion()
plt.show()
# the last iteration we want to continue training
iter_last = lc.get_last_it()
print "start training..."
start = time.time()
print "start from ", iter_last+1
for i in xrange(iter_last+1, pars['Max_iter']+1):
vol_ins, lbl_outs, msks = smp_trn.get_random_sample()
# forward pass
vol_ins = utils.make_continuous(vol_ins, dtype=pars['dtype'])
props = net.forward( vol_ins )
# cost function and accumulate errors
props, cerr, grdts = pars['cost_fn']( props, lbl_outs )
err = err + cerr
cls = cls + cost_fn.get_cls(props, lbl_outs)
# mask process the gradient
grdts = utils.dict_mul(grdts, msks)
# run backward pass
grdts = utils.make_continuous(grdts, dtype=pars['dtype'])
net.backward( grdts )
if pars['is_malis'] :
malis_weights = cost_fn.malis_weight(props, lbl_outs)
grdts = utils.dict_mul(grdts, malis_weights)
if i%pars['Num_iter_per_test']==0:
# test the net
lc = test.znn_test(net, pars, smp_tst, vn, i, lc)
if i%pars['Num_iter_per_show']==0:
# anneal factor
eta = eta * pars['anneal_factor']
net.set_eta(eta)
# normalize
err = err / vn / pars['Num_iter_per_show']
cls = cls / vn / pars['Num_iter_per_show']
lc.append_train(i, err, cls)
# time
elapsed = time.time() - start
elapsed = elapsed / pars['Num_iter_per_show']
show_string = "iteration %d, err: %.3f, cls: %.3f, elapsed: %.1f s/iter, learning rate: %.6f"\
%(i, err, cls, elapsed, eta )
if pars.has_key('logging') and pars['logging']:
utils.write_to_log(logfile, show_string)
print show_string
if pars['is_visual']:
# show results To-do: run in a separate thread
front_end.inter_show(start, lc, eta, vol_ins, props, lbl_outs, grdts, pars)
if pars['is_rebalance'] and 'aff' not in pars['out_type']:
plt.subplot(247)
plt.imshow(msks.values()[0][0,0,:,:], interpolation='nearest', cmap='gray')
plt.xlabel('rebalance weight')
if pars['is_malis']:
plt.subplot(248)
plt.imshow(malis_weights.values()[0][0,0,:,:], interpolation='nearest', cmap='gray')
plt.xlabel('malis weight (log)')
plt.pause(2)
plt.show()
# reset err and cls
err = 0
cls = 0
# reset time
start = time.time()
if i%pars['Num_iter_per_save']==0:
# save network
netio.save_network(net, pars['train_save_net'], num_iters=i)
lc.save( pars, elapsed )
def main(conf_file='config.cfg', logfile=None):
#%% parameters
print "reading config parameters..."
config, pars = front_end.parser(conf_file)
if pars.has_key('logging') and pars['logging']:
print "recording configuration file..."
front_end.record_config_file(pars)
logfile = front_end.make_logfile_name(pars)
#%% create and initialize the network
if pars['train_load_net'] and os.path.exists(pars['train_load_net']):
print "loading network..."
net = netio.load_network(pars)
# load existing learning curve
lc = zstatistics.CLearnCurve(pars['train_load_net'])
else:
if pars['train_seed_net'] and os.path.exists(pars['train_seed_net']):
print "seeding network..."
net = netio.seed_network(pars, is_seed=True)
else:
print "initializing network..."
net = netio.init_network(pars)
# initalize a learning curve
lc = zstatistics.CLearnCurve()
# show field of view
print "field of view: ", net.get_fov()
print "output volume info: ", net.get_outputs_setsz()
# set some parameters
print 'setting up the network...'
vn = utils.get_total_num(net.get_outputs_setsz())
eta = pars['eta'] #/ vn
net.set_eta(eta)
net.set_momentum(pars['momentum'])
net.set_weight_decay(pars['weight_decay'])
# initialize samples
outsz = pars['train_outsz']
print "\n\ncreate train samples..."
smp_trn = front_end.CSamples(config, pars, pars['train_range'], net, outsz,
logfile)
print "\n\ncreate test samples..."
smp_tst = front_end.CSamples(config, pars, pars['test_range'], net, outsz,
logfile)
# initialization
elapsed = 0
err = 0
cls = 0
# interactive visualization
plt.ion()
plt.show()
# the last iteration we want to continue training
iter_last = lc.get_last_it()
print "start training..."
start = time.time()
print "start from ", iter_last + 1
for i in xrange(iter_last + 1, pars['Max_iter'] + 1):
vol_ins, lbl_outs, msks = smp_trn.get_random_sample()
# forward pass
vol_ins = utils.make_continuous(vol_ins, dtype=pars['dtype'])
props = net.forward(vol_ins)
# cost function and accumulate errors
props, cerr, grdts = pars['cost_fn'](props, lbl_outs)
err = err + cerr
cls = cls + cost_fn.get_cls(props, lbl_outs)
# mask process the gradient
grdts = utils.dict_mul(grdts, msks)
# run backward pass
grdts = utils.make_continuous(grdts, dtype=pars['dtype'])
net.backward(grdts)
if pars['is_malis']:
malis_weights = cost_fn.malis_weight(props, lbl_outs)
grdts = utils.dict_mul(grdts, malis_weights)
if i % pars['Num_iter_per_test'] == 0:
# test the net
lc = test.znn_test(net, pars, smp_tst, vn, i, lc)
if i % pars['Num_iter_per_show'] == 0:
# anneal factor
eta = eta * pars['anneal_factor']
net.set_eta(eta)
# normalize
err = err / vn / pars['Num_iter_per_show']
cls = cls / vn / pars['Num_iter_per_show']
lc.append_train(i, err, cls)
# time
elapsed = time.time() - start
elapsed = elapsed / pars['Num_iter_per_show']
show_string = "iteration %d, err: %.3f, cls: %.3f, elapsed: %.1f s/iter, learning rate: %.6f"\
%(i, err, cls, elapsed, eta )
if pars.has_key('logging') and pars['logging']:
utils.write_to_log(logfile, show_string)
print show_string
if pars['is_visual']:
# show results To-do: run in a separate thread
front_end.inter_show(start, lc, eta, vol_ins, props, lbl_outs,
grdts, pars)
if pars['is_rebalance'] and 'aff' not in pars['out_type']:
plt.subplot(247)
plt.imshow(msks.values()[0][0, 0, :, :],
interpolation='nearest',
cmap='gray')
plt.xlabel('rebalance weight')
if pars['is_malis']:
plt.subplot(248)
plt.imshow(malis_weights.values()[0][0, 0, :, :],
interpolation='nearest',
cmap='gray')
plt.xlabel('malis weight (log)')
plt.pause(2)
plt.show()
# reset err and cls
err = 0
cls = 0
# reset time
start = time.time()
if i % pars['Num_iter_per_save'] == 0:
# save network
netio.save_network(net, pars['train_save_net'], num_iters=i)
lc.save(pars, elapsed)
