def get_pass():
password_feild.delete(0, END)
if (length_feild.get() == ''):
messagebox.showerror(
"No value Entered", "Please Fill the Entry Feilds"
) # This is to make a default password, this must be changed
else:
try:
tem_len = int(length_feild.get())
tem_spe = int(special_feild.get())
tem_dig = int(digit_feild.get())
except ValueError as e:
messagebox.showerror("Input Error", "Please enter an Number")
else:
data = ((tem_len - (tem_dig + tem_spe), tem_dig, tem_spe)
) # Doing the calculation and porcessing
length_feild.delete(0, END)
digit_feild.delete(0, END)
special_feild.delete(0, END)
generate = Setup(
data
) # This is from the Class Setup which is imported and an instance is created
pass_word = generate.get_password() # Calling the method
password_feild.insert(0, pass_word)
pyperclip.copy(
pass_word
) # This is for copying the password directly into the clipboard
copied_status = Label(
root,
text="The password is copied to the clipboard",
bg="yellow",
fg="black")
copied_status.grid(row=5)
def on_service_state_change(zeroconf, service_type, name, state_change):
logger.info("Service %s of type %s state changed: %s" % (name, service_type, state_change))
logger.info("State change: %s" % state_change)
if state_change is ServiceStateChange.Added:
info = zeroconf.get_service_info(service_type, name)
if info:
logger.info(" Address: %s:%d" % (socket.inet_ntoa(info.address), info.port))
logger.info(" Weight: %d, priority: %d" % (info.weight, info.priority))
logger.info(" Server: %s" % (info.server,))
ip = ("%s:%d" % (socket.inet_ntoa(info.address), info.port))
device = Setup(name, ip)
device.register()
if info.properties:
logger.info(" Properties are:")
for key, value in info.properties.items():
logger.info(" %s: %s" % (key, value))
else:
logger.info(" No properties")
else:
logger.info(" No info")
logger.info('\n')
elif state_change is ServiceStateChange.Removed:
logger.info("Removing %s" % (name))
async def test_file_upload():
NUM_PEERS = 10
conn_matrix = np.zeros((NUM_PEERS, NUM_PEERS))
np.fill_diagonal(conn_matrix[:, 1:], 1)
np.fill_diagonal(conn_matrix[1:, :], 1)
s = Setup(PEERSTER_ROOT, NUM_PEERS, conn_matrix, anti_entropy=2)
s.run_all()
await asyncio.sleep(.5)
# Upload files
files = []
for i, peerster in enumerate(s.peersters):
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "w+") as f:
to_file = "12345678" * 1000 + peerster.name + "12345678" * 1000
files.append(to_file)
f.write(to_file)
peerster.upload_file(f"test{i}.txt")
await asyncio.sleep(.5)
await s.stop_all()
# Assert files are uploaded
for i, peerster in enumerate(s.peersters):
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "rb") as f:
h = Tests._calc_hash(f)
assert h in peerster.uploaded_files
def main():
connect()
Setup.setTable(cur)
Setup.setData(cur)
appNum = input("\nChoose application number below\n\t1. New Vehicle Registration\n\t2. Auto Transaction\n\t3. Driver Licence Registration\n\t4. Violation Record\n\t5. Search Engine\n\n------> ")
status = False
while status==False:
if appNum=='1':
NewVehicle()
break
elif appNum=='2':
Trans()
break
elif appNum=='3':
DLReg()
break
elif appNum=='4':
VioRcd()
break
elif appNum=='5':
Search(cur)
break
else:
print("\n\nInvalid application number!")
appNum = input('Choose application number again\n------> ')
connection.commit()
connection.close()
async def test_public_messages():
NUM_PEERS = 50
conn_matrix = np.zeros((NUM_PEERS, NUM_PEERS))
np.fill_diagonal(conn_matrix[:, 1:], 1)
np.fill_diagonal(conn_matrix[1:, :], 1)
print(conn_matrix)
s = Setup(PEERSTER_ROOT, NUM_PEERS, conn_matrix, anti_entropy=2)
s.run_all()
await asyncio.sleep(1)
for i, peerster in enumerate(s.peersters):
peerster.send_public_message(f"Test{i}")
await asyncio.sleep(10)
await s.stop_all()
for i, peerster in enumerate(s.peersters):
print(peerster.public_messages)
for j, other_peerster in enumerate(s.peersters):
if i == j:
continue
assert peerster.public_messages[f"testPeer{j}"] == {1: f"Test{j}"}
def collect_relevant_files(self):
self.storage = EDF_Store(files_with_categs={},
filenames=[],
categ_names=[])
self.storage.fetch_data()
self.eeg_setup = Setup(params=self.storage.test_user_ids)
self.eeg_setup.run()
def __init__(self, cfg, label):
self.cfg = cfg
self.cfg.check_parametersSet()
self.cfg.log_parametersSet(label)
self.setup = Setup(cfg.parametersSet)
self.trees = self.setup.grow_trees()
self.setup.create_observable()
self.init_selection()
def add_relevant_files_to_database(self):
self.eeg_setup = Setup(params=None)
self.eeg_setup.run()
self.process_files()
self.storage = EDF_Store(self.eeg_setup.files_with_categs,
self.eeg_setup.filenames,
self.eeg_setup.categ_names)
self.storage.record_data()
def main():
if arg.signals_mit:
try:
gs = GetSignals()
gs.mit(mit)
except Exception as e:
print(e)
elif arg.signals_ecgid:
try:
gs = GetSignals()
gs.mit(ecgid)
except Exception as e:
print(e)
elif arg.signals_bmd:
try:
gs = GetSignals()
gs.mit(bmd101)
except Exception as e:
print(e)
elif arg.features_mit:
try:
feats = GetFeatures()
feats.features('mit', mit)
except Exception as e:
print(e)
elif arg.features_ecgid:
try:
feats = GetFeatures()
feats.features('ecgid', mit)
except Exception as e:
print(e)
elif arg.features_bmd:
try:
feats = GetFeatures()
feats.features('bmd', mit)
except Exception as e:
print(e)
elif arg.setup:
try:
su = Setup()
su.load_signals(2500, "cnn", mit[:40], 0)
su.load_signals(2500, "snn", mit[:40], 0)
except Exception as e:
print(e)
elif arg.snn:
try:
snn.main()
except Exception as e:
print(e)
elif arg.cnn:
try:
cnn.main()
except Exception as e:
print(e)
def start():
puzzle = Sudoku()
setup = Setup(puzzle)
setup.runSetup()
print("Setup done, solving...")
puzzleSolver = Solver(puzzle)
solved, iterations = puzzleSolver.solve()
puzzle.print()
print("Solved:", solved, iterations, "iterations")
def main():
Helper.init()
totalTime = 0
duration = args.duration
if args.nosetup:
itopod_setup = True
else:
itopod_setup = False
while True:
if not args.notitans:
if args.verbose:
print('getting available titans')
titans = Adventure.getTitans()
if titans:
# after this needs to reset loadout and diggers and e/m
Adventure.turnIdleOff()
print('calling killTitans with args.snipe {args.snipe}')
Adventure.killTitans(titans,
verbose=args.verbose,
snipe=args.snipe)
itopod_setup = False
if not itopod_setup:
Setup.setup(args.setup)
itopod_setup = True
Navigation.menu('adventure')
if not args.nobeast:
if not Statistics.checkPixelColor(*coords.BEAST_MODE_ON,
coords.BEAST_MODE_COLOR):
Helper.click(*coords.BEAST_MODE)
print('*' * 30)
Itopod.itopodExperimental(duration=duration,
optimal_floor=args.optimal)
totalTime += duration
print(f'total exp: {Itopod.EXP_gained}')
print(f'total ap: {Itopod.AP_gained}')
print(f'kills: {Itopod.kills}')
print(f'total time: {totalTime} minutes')
print('*' * 30)
Navigation.menu('inventory')
if Inventory.getEmptySlots() < 20:
invManagement(boost=0, merge=0)
if not args.noygg:
Yggdrasil.harvestAll()
def __init__(self):
Setup.__init__(self)
self._solution = []
self._value = 0
self._numEval = 0
self._pFileName = ''
self._bestSolution = []
self._bestMinimum = 0
self._avgMinimum = 0
self._sumOfNumEval = 0
self._avgWhen = 0
def __init__(self, uplink, config, session_id, hydra_url):
'''
Constructor
'''
self.uplink = uplink
self.config = config
self.session_id = session_id
self.hydra_url = hydra_url
self.setup = Setup(self)
if self.config.has_option('general', 'fake'):
self.fake = (self.config.get('general', 'fake') == "yes")
else:
self.fake = False
def play(self, reset_gamefile):
self.players = set()
self.hands = set()
self.cards = set()
self.me = None
self.conviction = None
self.gamefile = open('gamefile.txt', 'w+' if reset_gamefile else 'r+', buffering=1)
self.prompt_queue = [x.rstrip("\n") for x in self.gamefile]
setup = Setup()
setup.run(self)
play = Play()
play.run(self)
def __init__(self, label, params={}, **kwargs):
self.label = label
self.setup = Setup()
self.ana = Analytics()
if 'analysis_type' in kwargs:
self.analysis_type = kwargs['analysis_type']
else:
self.analysis_type = 'dynamical'
# set default analysis and circuit parameter
self._set_up_circuit(params, kwargs)
# set parameter derived from analysis and circuit parameter
new_vars = self.setup.get_params_for_analysis(self)
new_vars['label'] = self.label
self._set_class_variables(new_vars)
# set variables which require calculation in analytics class
self._calc_variables()
async def test_file_upload():
NUM_PEERS = 10
s = Setup.create_line_setup(PEERSTER_ROOT, NUM_PEERS)
s.run_all()
await asyncio.sleep(.5)
# Upload files
files = []
for i, peerster in enumerate(s.peersters):
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "w+") as f:
to_file = "12345678" * 1000 + peerster.name + "12345678" * 1000
files.append(to_file)
f.write(to_file)
peerster.upload_file(f"test{i}.txt")
await asyncio.sleep(.5)
await s.stop_all()
# Assert files are uploaded
for i, peerster in enumerate(s.peersters):
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "rb") as f:
h = Tests._calc_hash(f)[0]
assert h in peerster.uploaded_files
async def test_download_searched_files():
NUM_PEERS = 10
DIFF = 2
s = Setup.create_line_setup(PEERSTER_ROOT, NUM_PEERS)
s.run_all()
await asyncio.sleep(.5)
# Send route rumors
for peerster in s.peersters:
peerster.send_public_message(f" ")
hashes = await Tests._setup_searched_files(s, DIFF)
# Download files
for i, peerster in enumerate(s.peersters):
if i - DIFF >= 0 and i + DIFF < len(s.peersters):
peerster.download_searched_file(f"test{i}_left_d.txt", hashes["left"][i][0])
peerster.download_searched_file(f"test{i}_right_d.txt", hashes["right"][i][0])
# Wait for files to be downloaded
await asyncio.sleep(15)
# Stop all peersters
await s.stop_all()
for i, peerster in enumerate(s.peersters):
if i - DIFF >= 0 and i + DIFF < len(s.peersters):
assert f"test{i}_left_d.txt" in peerster.downloaded_files
assert f"test{i}_right_d.txt" in peerster.downloaded_files
async def test_search():
NUM_PEERS = 10
DIFF = 2
BUDGET = None
s = Setup.create_line_setup(PEERSTER_ROOT, NUM_PEERS)
s.run_all()
await asyncio.sleep(.5)
# Send route rumors
for peerster in s.peersters:
peerster.send_public_message(f" ")
hashes = await Tests._setup_searched_files(s, DIFF, budget=BUDGET)
# Stop all peersters
await s.stop_all()
# Assert that searches are correct
for i, peerster in enumerate(s.peersters):
if i - DIFF >= 0 and i + DIFF < len(s.peersters):
assert len(peerster.searches) == 1
results = peerster.searches[0]
assert {"file_name": f"test{i}_left.txt",
"peer": f"testPeer{i-DIFF}",
"meta": hashes["left"][i][0],
"chunks": [f"{i}" for i in range(1, hashes["left"][i][1]+1)]} in results
assert {"file_name": f"test{i}_right.txt",
"peer": f"testPeer{i+DIFF}",
"meta": hashes["right"][i][0],
"chunks": [f"{i}" for i in range(1, hashes["right"][i][1]+1)]} in results
def new_students(self):
"""Checks data for new students."""
print('Checking for new students...')
# Creates list of existing students.
existing_students = []
with open('storage.csv', 'r') as storage:
reader = csv.reader(storage)
for row in reader:
existing_students.append(row[0])
def mask(email):
if email in existing_students:
return False
return True
# Reduces student_data DataFrame to new students only.
new_data = self.student_data[self.student_data['Student Email'].apply(
mask)]
new_students = Data(df=new_data)
if len(new_students.student_data) > 0:
print('New students found.')
print(new_students.student_data)
Setup(new_students)
else:
print('No new students found.')
def __init__(self, test_utility, model, serial_manager, report):
super().__init__()
self.abort_btn = QPushButton("Abort")
self.abort_btn.clicked.connect(self.abort)
self.setButton(QWizard.CustomButton1, self.abort_btn)
self.button(QWizard.FinishButton).clicked.connect(self.finish)
qbtn_layout = [
QWizard.Stretch, QWizard.NextButton, QWizard.FinishButton,
QWizard.CustomButton1
]
self.setButtonLayout(qbtn_layout)
self.button(QWizard.NextButton).setEnabled(False)
# This fixes a bug in the default style which hides the QWizard
# buttons until the window is resized.
self.setWizardStyle(0)
setup_id = self.addPage(
Setup(self, test_utility, serial_manager, model, report))
program_id = self.addPage(
Program(self, test_utility, serial_manager, model, report))
interfaces_id = self.addPage(
Interfaces(self, test_utility, serial_manager, model, report))
final_id = self.addPage(FinalPage(self, test_utility, report))
self.setup_page = self.page(setup_id)
self.program_page = self.page(program_id)
self.interfaces_page = self.page(interfaces_id)
self.final_page = self.page(final_id)
self.tu = test_utility
self.report = report
def run( self, u_info ):
# self, mojo_dir, tmp_dir, /// out_dir, dojoserver
# register two data sources
self.__segmentation = Segmentation( u_info.files_path , u_info.tmpdir, self)
self.__image = Image( u_info.files_path , u_info.tmpdir)
# and the controller
self.__controller = Controller( u_info, self.__segmentation.get_database(), self ) ####
# and the viewer
self.__viewer = Viewer()
# and the controller
if self.__segmentation:
db = self.__segmentation.get_database()
else:
db = None
self.__controller = Controller( u_info, db, self )
# and the setup
self.__setup = Setup(self, u_info.files_path, u_info.tmpdir)
print('path_gfx: ',path_gfx)
# running live
####
asyncio.set_event_loop(u_info.worker_loop)
dojo = tornado.web.Application([
(r'/dojo/gfx/(.*)', tornado.web.StaticFileHandler, {'path': path_gfx}),
(r'/ws', Websockets, dict(controller=self.__controller)),
(r'/(.*)', DojoHandler, dict(logic=self))
],debug=True,autoreload=True) # (r'/dojo/gfx/(.*)', tornado.web.StaticFileHandler, {'path': '/dojo/gfx'})
# dojo.listen(u_info.port, max_buffer_size=1024*1024*150000)
server = tornado.httpserver.HTTPServer(dojo)
server.listen(u_info.port)
print('*'*80)
print('*', 'DOJO RUNNING')
print('*')
print('*', 'open', '[ http://' + u_info.ip + ':' + str(u_info.port) + '/dojo/ ] ')
print('*'*80)
tornado.ioloop.IOLoop.instance().start()
server.stop()
# def sig_handler(signum, frame):
# IOLoop.current().add_callback_from_signal(receiver.shutdown)
print("Tornado web server stops.")
return
def __init__(self, cfg, label):
self.cfg = cfg
self.cfg.check_parametersSet()
self.cfg.log_parametersSet(label)
self.setup = Setup(cfg.parametersSet)
self.trees = self.setup.grow_trees()
self.setup.create_observable()
self.init_selection()
async def test_file_download():
NUM_PEERS = 10
conn_matrix = np.zeros((NUM_PEERS, NUM_PEERS))
np.fill_diagonal(conn_matrix[:, 1:], 1)
np.fill_diagonal(conn_matrix[1:, :], 1)
s = Setup(PEERSTER_ROOT, NUM_PEERS, conn_matrix, anti_entropy=2)
s.run_all()
await asyncio.sleep(.5)
# Send route rumors
for i, peerster in enumerate(s.peersters):
peerster.send_public_message(f" ")
# Upload files
files = []
for i, peerster in enumerate(s.peersters):
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "w+") as f:
to_file = "12345678" * 1000 + peerster.name + "12345678" * 1000
files.append(to_file)
f.write(to_file)
peerster.upload_file(f"test{i}.txt")
await asyncio.sleep(.5)
# Don't calculate hash ourselves, but use peerster hashes: test doesn't fail
# if hashing/chunking is done incorrectly
metas = []
for i, peerster in enumerate(s.peersters):
assert len(peerster.uploaded_files) == 1
hash = next(iter(peerster.uploaded_files))
assert len(hash) == 64
metas.append(hash)
await asyncio.sleep(2)
for i, peerster in enumerate(s.peersters):
other = (i - 7) % len(s.peersters)
peerster.download_file(f"test{other}_d.txt", metas[other], f"testPeer{other}")
await asyncio.sleep(10)
for i, peerster in enumerate(s.peersters):
assert f"test{(i-7)%len(s.peersters)}_d.txt" in peerster.downloaded_files
await s.stop_all()
def __init__(self):
self.settings = Settings()
self.logger = Logger(self.settings.logfile)
self.reporter = Reporter(self.settings)
self.setup = Setup(self.settings, self.logger)
self.grader = Grader(self.settings, self.logger, self.setup)
self.analyser = Analyser(self.settings, self.reporter, self.logger,
self.setup, self.grader)
def move():
# tic = time.time()
data = request.get_json()
#NOTE grid_data[0] = move_grid // grid_data[1] = food_grid
setup_process = Setup()
helper = Helper()
grid_data = setup_process.grid_setup(data)
# Game States
defend = State_Defend()
attack = State_Attack()
grow = State_Grow()
# Assign the global helper methods to each state
defend.helper = helper
attack.helper = helper
grow.helper = helper
max_snake = helper.get_max_snake_length(data)
closest_food_distance = helper.get_closest_food_dist(grid_data[1], data)
board_width = data.get("board").get("width")
if len(data.get("you").get("body")) > max_snake + 1:
# Assign the attack state when we are 2 bigger than any other snake
state = attack
elif closest_food_distance < board_width / 1.5:
# Assign the grow state if a piece of food is within boardlen/1.5
# or if there are more than 5 pieces of food on the board
state = grow
else:
state = defend
#NOTE Get the next move based on the pellet
next_move = state.get_move(grid_data, data)
# toc = time.time()
# print("Move for round: {}".format(data.get("turn")))
# print("Time used: {}ms".format((toc - tic)*1000))
# print("State: {}".format(state.name))
#helper.print_board(grid_data[0])
#NOTE Return the move in the JSON object wrapper
return jsonify(move=next_move)
def setup_files(self):
self.generate_setup_list()
self.setup = Setup(self)
if len(self.setup_list) > 0:
self.setup.status = True
self.setup.sequencer()
else:
print("Nothing to setup proceed to analysis")
self.analysis = Analysis(self, self.setup)
def __init__(self, **kwagrs):
self.setup = Setup(**kwagrs)
self.t0 = dt()
s = self.setup
self.T = self.setup.T
self.v_couple_shape = [(s.na_c, s.nexo_t[t], s.ntheta_coarse)
for t in range(self.T)]
self.v_sf_shape = [(s.na_s, s.n_zf) for t in range(self.T)]
self.v_sm_shape = [(s.na_s, s.n_zm) for t in range(self.T)]
print('setup created, time {}'.format(dt() - self.t0))
self.solve()
def appRun():
s = Setup()
if s.load():
s.showSelf()
else:
s.consInit()
s.save()
frames = JsonFileToFrames(s.inputFile)
print('Frames count = ' + str(len(frames)))
printer = BlenderPrinter(len(frames), s.outputDir, s.FPS)
iter = 0
for frame in frames:
printer.printFrame(frame, iter + 1)
iter += 1
async def test_private_messages():
NUM_PEERS = 50
conn_matrix = np.zeros((NUM_PEERS, NUM_PEERS))
np.fill_diagonal(conn_matrix[:, 1:], 1)
np.fill_diagonal(conn_matrix[1:, :], 1)
s = Setup(PEERSTER_ROOT, NUM_PEERS, conn_matrix, anti_entropy=1)
s.run_all()
await asyncio.sleep(1)
for peerster in s.peersters:
peerster.send_public_message(f" ")
await asyncio.sleep(10)
msg_map = {}
for i, peerster in enumerate(s.peersters):
if i - 7 < 0 and not i + 7 >= len(s.peersters):
other = i + 7
else:
other = i - 7
msg_map[other] = msg_map.get(other, []) + [i]
peerster.send_private_message(f"Test{i}",
f"testPeer{other}")
await asyncio.sleep(30)
await s.stop_all()
for i, peerster in enumerate(s.peersters):
others = msg_map.get(i)
if others is None:
continue
for other in others:
peer = f"testPeer{other}"
assert peer in peerster.private_messages.keys()
assert len(peerster.private_messages[peer]) == 1
assert peerster.private_messages[peer][0] == {"msg": f"Test{other}", "hop-lim": "3"}
def setup():
setup = Setup()
parser = argparse.ArgumentParser(description='Useage: simulator inst.txt data.txt reg.txt config.txt result.txt')
parser.add_argument('inst.txt')
parser.add_argument('data.txt')
parser.add_argument('reg.txt')
parser.add_argument('config.txt')
parser.add_argument('result.txt')
args = parser.parse_args()
if len(vars(args)) != 5:
print "Useage: simulator inst.txt data.txt reg.txt config.txt result.txt"
sys.exit(0)
inst_list, label_list = setup.parse_instructions(vars(args)['inst.txt'])
register = setup.parse_registers(vars(args)['reg.txt'])
memory = setup.parse_memory(vars(args)['data.txt'])
config = setup.parse_config(vars(args)['config.txt'])
priority = setup.return_priority(config)
#print inst_list
#print lable_list
#print register
#print memory
#print config
return inst_list, label_list, register, memory, config, priority
def __init__(self, uplink, config, session_id, hydra_url):
'''
Constructor
'''
self.uplink = uplink
self.config = config
self.session_id = session_id
self.hydra_url = hydra_url
self.setup = Setup(self)
if self.config.has_option('general', 'fake'):
self.fake = (self.config.get('general', 'fake') == "yes")
else:
self.fake = False
def main():
"""Setup and run the backup."""
awsargs = {
'region': 'eu-west-1',
'endpoint': 'http://192.168.99.100:4569',
'key': 'localstack',
'secret': 'localstack'
}
args = _parse_cli_args()
level = logging.DEBUG if args.verbose else logging.INFO
if args.verbose:
for logger in {
'boto3', 'botocore', 'requests',
'botocore.vendored.requests.packages.urllib3.connectionpool'
}:
logging.getLogger(logger).setLevel(level)
LOGGER.error('STARTTINGG')
LOGGER.info('Sleeping for 5 seconds')
time.sleep(5)
LOGGER.info('Woke up')
setup = Setup()
setup.setup()
_execute(args, awsargs)
def __init__(self, ipAddr=None, port=80):
# Init Midi client and display available devices
midiINPort = mido.get_input_names()[0]
midiOUTPort = mido.get_output_names()[0]
self.midiIN = mido.open_input(midiINPort)
self.midiOUT = mido.open_output(midiOUTPort)
self.mcu = MCU()
self.motu = Motu(ipAddr, port)
self.settings = Settings()
self.hwSetup = Setup()
self.mixerUrl = "http://{}:{}".format(ipAddr, port)
print("Will send events to mixer at {}".format(self.mixerUrl))
self.recall()
async def test_confirmed_file():
NUM_PEERS = 8
s = Setup.create_line_setup(PEERSTER_ROOT, NUM_PEERS, hw3ex2=True)
s.run_all()
await asyncio.sleep(.5)
# Send route rumors
for peerster in s.peersters:
peerster.send_public_message(f" ")
await asyncio.sleep(3)
# Upload a file to each node
hashes = []
sizes = []
for i, peerster in enumerate(s.peersters):
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "w+") as f:
to_file = "12345678" * 1000 + peerster.name + "12345678" * 1000
sizes.append(len(to_file))
f.write(to_file)
with open(f"{peerster.root}/_SharedFiles/test{i}.txt", "rb") as f:
hashes.append(Tests._calc_hash(f)[0])
peerster.upload_file(f"test{i}.txt")
await asyncio.sleep(15)
for i, peerster in enumerate(s.peersters):
# check that correct file was rebroadcasted
for re_br in peerster.re_broadcast:
assert len(re_br["witnesses"]) > NUM_PEERS / 2
for j, other in enumerate(s.peersters):
if i == j:
continue
info = {"origin": other.name, "name": f"test{j}.txt", "meta": hashes[j], "id": "3", "size": str(sizes[j])}
assert info in peerster.confirmed
# Now try to upload a duplicate file
for i, peerster in enumerate(s.peersters):
peerster.upload_file(f"test{len(s.peersters)-i-1}.txt")
await asyncio.sleep(3)
await s.stop_all()
# It should not show up in uploaded files!
for i, peerster in enumerate(s.peersters):
assert hashes[-i-1] not in peerster.uploaded_files
def __init__(self, label, params={}, **kwargs):
self.label = label
self.setup = Setup()
self.ana = Analytics()
if 'analysis_type' in kwargs:
self.analysis_type = kwargs['analysis_type']
else:
self.analysis_type = 'dynamical'
# set default analysis and circuit parameter
self._set_up_circuit(params, kwargs)
# set parameter derived from analysis and circuit parameter
new_vars = self.setup.get_params_for_analysis(self)
new_vars['label'] = self.label
self._set_class_variables(new_vars)
# set variables which require calculation in analytics class
self._calc_variables()
def test_setup_load_properties(mock_logIt):
obj = Setup()
assert_equal(obj.installOxAuth, True)
assert_equal(obj.installOxTrust, True)
assert_equal(obj.installLdap, True)
assert_equal(obj.installHttpd, True)
assert_equal(obj.installSaml, False)
assert_equal(obj.installAsimba, False)
assert_equal(obj.installCas, False)
assert_equal(obj.installOxAuthRP, False)
# all false
obj.load_properties('tests/sample1.properties')
assert_equal(obj.installOxAuth, False)
assert_equal(obj.installOxTrust, False)
assert_equal(obj.installLdap, False)
assert_equal(obj.installHttpd, False)
assert_equal(obj.installSaml, False)
assert_equal(obj.installAsimba, False)
assert_equal(obj.installCas, False)
assert_equal(obj.installOxAuthRP, False)
# all true
obj.load_properties('tests/sample2.properties')
assert_equal(obj.installOxAuth, True)
assert_equal(obj.installOxTrust, True)
assert_equal(obj.installLdap, True)
assert_equal(obj.installHttpd, True)
assert_equal(obj.installSaml, True)
assert_equal(obj.installAsimba, True)
assert_equal(obj.installCas, True)
assert_equal(obj.installOxAuthRP, True)
# mix of both true and false
obj.load_properties('tests/sample3.properties')
assert_equal(obj.installOxAuth, False)
assert_equal(obj.installOxTrust, True)
assert_equal(obj.installLdap, False)
assert_equal(obj.installHttpd, True)
assert_equal(obj.installSaml, False)
assert_equal(obj.installAsimba, True)
assert_equal(obj.installCas, False)
assert_equal(obj.installOxAuthRP, True)
def start_game(self):
"""
Hides main menu window and displays the board setup window
"""
# hide the menu window, and the rules window if it is open
self.root.withdraw()
if self.rules_displayed:
self.rules_window.withdraw()
def show_callback():
# after game finishes (by either loss or win), display the windows again
self.root.deiconify()
if self.rules_displayed:
self.rules_window.deiconify()
# create board setup window
self.setup = Setup(self.root, show_callback)
def __init__(self, midas, time):
df = pd.read_csv(midas)
times = np.unique(df.filter(regex='^DA').values.flatten())
if time not in times:
raise ValueError("The time-point %s does not exists in the dataset. Available time-points are: %s" % (time, list(times)))
df.drop(df.columns[0], axis=1, inplace=True)
cond = True
for c in df.filter(regex='^DA').columns:
cond = cond & (df[c] == time)
super(Dataset, self).__init__(df[cond].reset_index(drop=True))
stimuli = map(lambda c: c[3:], filter(lambda c: self.is_stimulus(c), self.columns))
inhibitors = map(lambda c: c[3:-1], filter(lambda c: self.is_inhibitor(c), self.columns))
readouts = map(lambda c: c[3:], filter(lambda c: self.is_readout(c), self.columns))
self.setup = Setup(stimuli, inhibitors, readouts)
class Analyzer():
def __init__(self, cfg, label):
self.cfg = cfg
self.cfg.check_parametersSet()
self.cfg.log_parametersSet(label)
self.setup = Setup(cfg.parametersSet)
self.trees = self.setup.grow_trees()
self.setup.create_observable()
self.init_selection()
def init_selection(self):
selection = Selection()
selection.build_selection(self.setup.configuration)
self.selection = selection.selection
print ''
print 'Applying the following selection:'
print self.selection
print ''
def analyze(self):
self.histograms = {}
for process_name in self.trees:
self.histograms[process_name] = self.setup.make_histogram(process_name)
selection = self.selection
if process_name.find('data')==-1:
weight = str(self.cfg.parametersSet['lumi'])+'*weight'
selection = '('+selection+')*'+weight
self.trees[process_name].Project(self.histograms[process_name].GetName(),
self.setup.observable.plot,
selection)
def format_histograms(self):
self.formatted_histograms = {}
stack = THStack('stack','')
self.legend = TLegend(0.16,0.67,0.4,0.92)
self.legend.SetFillColor(0)
self.legend.SetLineColor(0)
self.legend.SetBorderSize(0)
for process_name in self.setup.order_processes():
try: self.histograms[process_name]
except KeyError: continue
hist = self.histograms[process_name]
# --> events / GeV
for bin in range(1,hist.GetNbinsX()+1):
hist.SetBinContent(bin,hist.GetBinContent(bin)/hist.GetBinWidth(bin))
hist.SetBinError(bin,hist.GetBinError(bin)/hist.GetBinWidth(bin))
# data
if process_name.find('data')>-1:
legendMarker = 'p'
hist.SetMarkerStyle(20)
hist.SetMarkerSize(1.3)
self.formatted_histograms['data'] = hist
# signal
elif process_name.find('signal')>-1:
legendMarker = 'l'
hist.SetLineWidth(2)
hist.SetFillColor(0)
hist.SetLineColor(2)
self.formatted_histograms['signal'] = hist
# MC
else:
legendMarker = 'f'
hist.SetLineColor(processes[process_name]['color'])
hist.SetFillColor(processes[process_name]['color'])
stack.Add(hist)
self.formatted_histograms['background'] = stack
# adding to the legend
self.legend.AddEntry(hist,processes[process_name]['label'],legendMarker)
def draw(self,name):
self.make_canvas(name)
self.formatted_histograms['background'].Draw('fhist')
self.formatted_histograms['background'].GetXaxis().SetTitle(self.setup.observable.labelX)
self.formatted_histograms['background'].GetYaxis().SetTitle(self.setup.observable.labelY)
self.formatted_histograms['background'].GetXaxis().SetNdivisions(505)
self.formatted_histograms['background'].GetYaxis().SetNdivisions(505)
try:
self.formatted_histograms['data'].Draw('ep,same')
self.draw_compare()
except: print 'data not plotted'
try: self.formatted_histograms['signal'].Draw('hist,same')
except: print 'signal not plotted'
self.legend.Draw()
def make_canvas(self,name):
self.canvas = MultiCanvas(name) if self.formatted_histograms.has_key('data') else TCanvas(name,name)
SetOwnership(self.canvas,False)
def __init__(self):
# No communications or arming yet
self.comms = None
self.armed = False
# Do basic Tk initialization
self.root = Tk()
self.root.configure(bg=BACKGROUND_COLOR)
self.root.resizable(False, False)
self.root.title('Hackflight Ground Control Station')
left = (self.root.winfo_screenwidth() - DISPLAY_WIDTH) / 2
top = (self.root.winfo_screenheight() - DISPLAY_HEIGHT) / 2
self.root.geometry('%dx%d+%d+%d' % (DISPLAY_WIDTH, DISPLAY_HEIGHT, left, top))
self.frame = Frame(self.root)
self.root.wm_iconbitmap(bitmap = "@media/icon.xbm")
self.root.tk.call('wm', 'iconphoto', self.root._w, PhotoImage('icon.png'))
self.root.protocol('WM_DELETE_WINDOW', self.quit)
# Create panes for two rows of widgets
self.pane1 = self._add_pane()
self.pane2 = self._add_pane()
# Add a buttons
self.button_connect = self._add_button('Connect', self.pane1, self._connect_callback)
self.button_setup = self._add_button('Setup', self.pane2, self._setup_callback)
self.button_motors = self._add_button('Motors', self.pane2, self._motors_button_callback)
self.button_receiver = self._add_button('Receiver', self.pane2, self._receiver_button_callback)
self.button_messages = self._add_button('Messages', self.pane2, self._messages_button_callback)
#self.button_maps = self._add_button('Maps', self.pane2, self._maps_button_callback, disabled=False)
# Prepare for adding ports as they are detected by our timer task
self.portsvar = StringVar(self.root)
self.portsmenu = None
self.connected = False
self.ports = []
# Finalize Tk stuff
self.frame.pack()
self.canvas = Canvas(self.root, width=DISPLAY_WIDTH, height=DISPLAY_HEIGHT, background='black')
self.canvas.pack()
# Add widgets for motor-testing dialog; hide them immediately
self.motors = Motors(self)
self.motors.stop()
# Create receiver dialog
self.receiver = Receiver(self)
# Create messages dialog
self.messages = Messages(self)
# Create setup dialog
self.setup = Setup(self)
self._schedule_connection_task()
# Create a maps dialog
#self.maps = Maps(self, yoffset=-30)
# Create a splash image
self.splashimage = PhotoImage(file='media/splash.png')
self._show_splash()
# Create a message parser
self.parser = MSP_Parser()
# Set up parser's request strings
self.attitude_request = self.parser.serialize_ATTITUDE_Request()
self.rc_request = self.parser.serialize_RC_Request()
# No messages yet
self.yaw_pitch_roll = 0,0,0
self.rxchannels = 0,0,0,0,0
# A hack to support display in Setup dialog
self.active_axis = 0
class GCS:
def __init__(self):
# No communications or arming yet
self.comms = None
self.armed = False
# Do basic Tk initialization
self.root = Tk()
self.root.configure(bg=BACKGROUND_COLOR)
self.root.resizable(False, False)
self.root.title('Hackflight Ground Control Station')
left = (self.root.winfo_screenwidth() - DISPLAY_WIDTH) / 2
top = (self.root.winfo_screenheight() - DISPLAY_HEIGHT) / 2
self.root.geometry('%dx%d+%d+%d' % (DISPLAY_WIDTH, DISPLAY_HEIGHT, left, top))
self.frame = Frame(self.root)
self.root.wm_iconbitmap(bitmap = "@media/icon.xbm")
self.root.tk.call('wm', 'iconphoto', self.root._w, PhotoImage('icon.png'))
self.root.protocol('WM_DELETE_WINDOW', self.quit)
# Create panes for two rows of widgets
self.pane1 = self._add_pane()
self.pane2 = self._add_pane()
# Add a buttons
self.button_connect = self._add_button('Connect', self.pane1, self._connect_callback)
self.button_setup = self._add_button('Setup', self.pane2, self._setup_callback)
self.button_motors = self._add_button('Motors', self.pane2, self._motors_button_callback)
self.button_receiver = self._add_button('Receiver', self.pane2, self._receiver_button_callback)
self.button_messages = self._add_button('Messages', self.pane2, self._messages_button_callback)
#self.button_maps = self._add_button('Maps', self.pane2, self._maps_button_callback, disabled=False)
# Prepare for adding ports as they are detected by our timer task
self.portsvar = StringVar(self.root)
self.portsmenu = None
self.connected = False
self.ports = []
# Finalize Tk stuff
self.frame.pack()
self.canvas = Canvas(self.root, width=DISPLAY_WIDTH, height=DISPLAY_HEIGHT, background='black')
self.canvas.pack()
# Add widgets for motor-testing dialog; hide them immediately
self.motors = Motors(self)
self.motors.stop()
# Create receiver dialog
self.receiver = Receiver(self)
# Create messages dialog
self.messages = Messages(self)
# Create setup dialog
self.setup = Setup(self)
self._schedule_connection_task()
# Create a maps dialog
#self.maps = Maps(self, yoffset=-30)
# Create a splash image
self.splashimage = PhotoImage(file='media/splash.png')
self._show_splash()
# Create a message parser
self.parser = MSP_Parser()
# Set up parser's request strings
self.attitude_request = self.parser.serialize_ATTITUDE_Request()
self.rc_request = self.parser.serialize_RC_Request()
# No messages yet
self.yaw_pitch_roll = 0,0,0
self.rxchannels = 0,0,0,0,0
# A hack to support display in Setup dialog
self.active_axis = 0
def quit(self):
self.motors.stop()
self.root.destroy()
def hide(self, widget):
widget.place(x=-9999)
def getChannels(self):
return self.rxchannels
def getYawPitchRoll(self):
# configure button to show connected
self._enable_buttons()
self.button_connect['text'] = 'Disconnect'
self._enable_button(self.button_connect)
return self.yaw_pitch_roll
def checkArmed(self):
if self.armed:
self._show_armed(self.root)
self._show_armed(self.pane1)
self._show_armed(self.pane2)
self._disable_button(self.button_motors)
else:
self._show_disarmed(self.root)
self._show_disarmed(self.pane1)
self._show_disarmed(self.pane2)
def scheduleTask(self, delay_msec, task):
self.root.after(delay_msec, task)
def _add_pane(self):
pane = PanedWindow(self.frame, bg=BACKGROUND_COLOR)
pane.pack(fill=BOTH, expand=1)
return pane
def _add_button(self, label, parent, callback, disabled=True):
button = Button(parent, text=label, command=callback)
button.pack(side=LEFT)
button.config(state = 'disabled' if disabled else 'normal')
return button
# Callback for Setup button
def _setup_callback(self):
self._clear()
self.motors.stop()
self.receiver.stop()
self.messages.stop()
#self.maps.stop()
self.parser.set_ATTITUDE_Handler(self._handle_attitude)
self.setup.start()
def _start(self):
self.parser.set_ATTITUDE_Handler(self._handle_attitude)
self._send_attitude_request()
self.setup.start()
self.parser.set_RC_Handler(self._handle_rc)
self._send_rc_request()
# Sends Attitude request to FC
def _send_attitude_request(self):
self.comms.send_request(self.attitude_request)
# Sends RC request to FC
def _send_rc_request(self):
self.comms.send_request(self.rc_request)
# Callback for Motors button
def _motors_button_callback(self):
self._clear()
self.setup.stop()
self.parser.set_ATTITUDE_Handler(self._handle_attitude)
self.receiver.stop()
self.messages.stop()
#self.maps.stop()
self.motors.start()
def _clear(self):
self.canvas.delete(ALL)
# Callback for Receiver button
def _receiver_button_callback(self):
self._clear()
self.setup.stop()
self.motors.stop()
self.messages.stop()
#self.maps.stop()
self.receiver.start()
# Callback for Messages button
def _messages_button_callback(self):
self._clear()
self.setup.stop()
self.motors.stop()
#self.maps.stop()
self.receiver.stop()
self.messages.start()
def _getting_messages(self):
return self.button_connect['text'] == 'Disconnect'
# Callback for Maps button
def _maps_button_callback(self):
self._clear()
if self._getting_messages():
self.receiver.stop()
self.messages.stop()
self.setup.stop()
self.motors.stop()
#self.maps.start()
# Callback for Connect / Disconnect button
def _connect_callback(self):
if self.connected:
self.setup.stop()
#self.maps.stop()
self.motors.stop()
self.messages.stop()
self.receiver.stop()
if not self.comms is None:
self.comms.stop()
self._clear()
self._disable_buttons()
self.button_connect['text'] = 'Connect'
self._show_splash()
else:
#self.maps.stop()
self.comms = Comms(self)
self.comms.start()
self.button_connect['text'] = 'Connecting ...'
self._disable_button(self.button_connect)
self._hide_splash()
self.scheduleTask(CONNECTION_DELAY_MSEC, self._start)
self.connected = not self.connected
# Gets available ports
def _getports(self):
allports = comports()
ports = []
for port in allports:
portname = port[0]
if 'ttyACM' in portname or 'ttyUSB' in portname or 'COM' in portname:
ports.append(portname)
return ports
# Checks for changes in port status (hot-plugging USB cables)
def _connection_task(self):
ports = self._getports()
if ports != self.ports:
if self.portsmenu is None:
self.portsmenu = OptionMenu(self.pane1, self.portsvar, *ports)
else:
for port in ports:
self.portsmenu['menu'].add_command(label=port)
self.portsmenu.pack(side=LEFT)
if ports == []:
self._disable_button(self.button_connect)
self._disable_buttons()
else:
self.portsvar.set(ports[0]) # default value
self._enable_button(self.button_connect)
self.ports = ports
self._schedule_connection_task()
# Mutually recursive with above
def _schedule_connection_task(self):
self.root.after(USB_UPDATE_MSEC, self._connection_task)
def _disable_buttons(self):
self._disable_button(self.button_setup)
self._disable_button(self.button_motors)
self._disable_button(self.button_receiver)
self._disable_button(self.button_messages)
def _enable_buttons(self):
self._enable_button(self.button_setup)
self._enable_button(self.button_motors)
self._enable_button(self.button_receiver)
self._enable_button(self.button_messages)
def _enable_button(self, button):
button['state'] = 'normal'
def _disable_button(self, button):
button['state'] = 'disabled'
def sendMotorMessage(self, index, value):
values = [1000]*4
values[index-1] = value
self.comms.send_message(self.parser.serialize_SET_MOTOR, values)
def _show_splash(self):
self.splash = self.canvas.create_image((400,250), image=self.splashimage)
def _hide_splash(self):
self.canvas.delete(self.splash)
def _show_armed(self, widget):
widget.configure(bg='red')
def _show_disarmed(self, widget):
widget.configure(bg=BACKGROUND_COLOR)
if self._getting_messages():
self._enable_button(self.button_motors)
def _handle_calibrate_response(self):
self.setup.showCalibrated()
def _handle_params_response(self, pitchroll_kp_percent, yaw_kp_percent):
# Only handle parms from firmware on a fresh connection
if self.newconnect:
self.setup.setParams(pitchroll_kp_percent, yaw_kp_percent)
self.newconnect = False
def _handle_attitude(self, x, y, z):
self.yaw_pitch_roll = z, -y/10., x/10.
self.messages.setCurrentMessage('Yaw/Pitch/Roll: %+3.3f %+3.3f %+3.3f' % self.yaw_pitch_roll)
# As soon as we handle the callback from one request, send another request
self._send_attitude_request()
def _handle_rc(self, c1, c2, c3, c4, c5, c6, c7, c8):
self.rxchannels = c1, c2, c3, c4, c5
# As soon as we handle the callback from one request, send another request
self._send_rc_request()
self.messages.setCurrentMessage('Receiver: %04d %04d %04d %04d %04d' % (c1, c2, c3, c4, c5))
def _handle_arm_status(self, armed):
self.armed = armed
self.messages.setCurrentMessage('ArmStatus: %s' % ('ARMED' if armed else 'Disarmed'))
def _handle_battery_status(self, volts, amps):
self.messages.setCurrentMessage('BatteryStatus: %3.3f volts, %3.3f amps' % (volts, amps))
class Circuit(object):
"""Provides functions to calculate the stationary and dynamical
properties of a given circuit.
Arguments:
label: string specifying circuit, options: 'microcircuit'
Keyword Arguments:
params: dictionary specifying parameter of the circuit, default
parameter given in params_circuit.py will be overwritten
analysis_type: string specifying level of analysis that is requested
default: 'dynamical'
options:
- None: only circuit and default analysis parameter
are set
- 'stationary': circuit and default analysis parameter
are set, mean and variance of input to each
populations as well as firing rates are calculated
- 'dynamical': circuit and default analysis parameter
are set, mean and variance of input to each
populations as well as firing rates are calculated,
variables for calculation of spectra are calculated
including the transfer function for all populations
fmin: minimal frequency in Hz, default: 0.1 Hz
fmax: maximal frequency in Hz, default: 150 Hz
df: frequency spacing in Hz, default: 1.0/(2*np.pi) Hz
to_file: boolean specifying whether firing rates and transfer
functions are written to file, default: True
from_file: boolean specifying whether firing rates and transfer
functions are read from file, default: True
if set to True and file is not found firing rates and
transfer function are calculated
"""
def __init__(self, label, params={}, **kwargs):
self.label = label
self.setup = Setup()
self.ana = Analytics()
if 'analysis_type' in kwargs:
self.analysis_type = kwargs['analysis_type']
else:
self.analysis_type = 'dynamical'
# set default analysis and circuit parameter
self._set_up_circuit(params, kwargs)
# set parameter derived from analysis and circuit parameter
new_vars = self.setup.get_params_for_analysis(self)
new_vars['label'] = self.label
self._set_class_variables(new_vars)
# set variables which require calculation in analytics class
self._calc_variables()
# updates variables of Circuit() and Analysis() classes, new variables
# are specified in the dictionary new_vars
def _set_class_variables(self, new_vars):
for key, value in new_vars.items():
setattr(self, key, value)
if 'params' in new_vars:
for key, value in new_vars['params'].items():
setattr(self, key, value)
self.ana.update_variables(new_vars)
# updates class variables of variables of Circuit() and Analysis()
# such that default analysis and circuit parameters are known
def _set_up_circuit(self, params, args):
# set default analysis parameter
new_vars = self.setup.get_default_params(args)
self._set_class_variables(new_vars)
# set circuit parameter
new_vars = self.setup.get_circuit_params(self, params)
self._set_class_variables(new_vars)
# quantities required for stationary analysis are calculated
def _set_up_for_stationary_analysis(self):
new_vars = self.setup.get_working_point(self)
self._set_class_variables(new_vars)
# quantities required for dynamical analysis are calculated
def _set_up_for_dynamical_analysis(self):
new_vars = self.setup.get_params_for_power_spectrum(self)
self._set_class_variables(new_vars)
# calculates quantities needed for analysis specified by analysis_type
def _calc_variables(self):
if self.analysis_type == 'dynamical':
self._set_up_for_stationary_analysis()
self._set_up_for_dynamical_analysis()
elif self.analysis_type == 'stationary':
self._set_up_for_stationary_analysis()
def alter_params(self, params):
"""Parameter specified in dictionary params are changed.
Changeable parameters are default analysis and circuit parameter,
as well as label and analysis_type.
Arguments:
params: dictionary, specifying new parameters
"""
self.params.update(params)
new_vars = self.setup.get_altered_circuit_params(self, self.label)
self._set_class_variables(new_vars)
new_vars = self.setup.get_params_for_analysis(self)
self._set_class_variables(new_vars)
self._calc_variables()
def create_power_spectra(self):
"""Returns frequencies and power spectra.
See: Eq. 9 in Bos et al. (2015)
Shape of output: (len(self.populations), len(self.omegas))
Output:
freqs: vector of frequencies in Hz
power: power spectra for all populations,
dimension len(self.populations) x len(freqs)
"""
power = np.asarray(map(self.ana.spec, self.ana.omegas))
return self.ana.omegas/(2.0*np.pi), np.transpose(power)
def create_power_spectra_approx(self):
"""Returns frequencies and power spectra approximated by
dominant eigenmode.
See: Eq. 15 in Bos et al. (2015)
Shape of output: (len(self.populations), len(self.omegas))
Output:
freqs: vector of frequencies in Hz
power: power spectra for all populations,
dimension len(self.populations) x len(freqs)
"""
power = np.asarray(map(self.ana.spec_approx, self.ana.omegas))
return self.ana.omegas/(2.0*np.pi), np.transpose(power)
def create_eigenvalue_spectra(self, matrix):
"""Returns frequencies and frequency dependence of eigenvalues of
matrix.
Arguments:
matrix: string specifying the matrix, options are the effective
connectivity matrix ('MH'), the propagator ('prop') and
the inverse of the propagator ('prop_inv')
Output:
freqs: vector of frequencies in Hz
eigs: spectra of all eigenvalues,
dimension len(self.populations) x len(freqs)
"""
eigs = [self.ana.eigs_evecs(matrix, w)[0] for w in self.ana.omegas]
eigs = np.transpose(np.asarray(eigs))
return self.ana.omegas/(2.0*np.pi), eigs
def create_eigenvector_spectra(self, matrix, label):
"""Returns frequencies and frequency dependence of
eigenvectors of matrix.
Arguments:
matrix: string specifying the matrix, options are the effective
connectivity matrix ('MH'), the propagator ('prop') and
the inverse of the propagator ('prop_inv')
label: string specifying whether spectra of left or right
eigenvectors are returned, options: 'left', 'right'
Output:
freqs: vector of frequencies in Hz
evecs: spectra of all eigenvectors,
dimension len(self.populations) x len(freqs) x len(self.populations)
"""
# one list entry for every eigenvector, evecs[i][j][k] is the
# ith eigenvectors at the jth frequency for the kth component
evecs = [np.zeros((len(self.ana.omegas), self.ana.dimension),
dtype=complex) for i in range(self.ana.dimension)]
for i, w in enumerate(self.ana.omegas):
eig, vr, vl = self.ana.eigs_evecs(matrix, w)
if label == 'right':
v = vr
elif label == 'left':
v = vl
for j in range(self.ana.dimension):
evecs[j][i] = v[j]
evecs = np.asarray([np.transpose(evecs[i]) for i in range(self.ana.dimension)])
return self.ana.omegas/(2.0*np.pi), evecs
def reduce_connectivity(self, M_red):
"""Connectivity (indegree matrix) is reduced, while the working
point is held constant.
Arguments:
M_red: matrix, with each element specifying how the corresponding
connection is altered, e.g the in-degree from population
j to population i is reduced by 30% with M_red[i][j]=0.7
"""
M_original = self.M_full[:]
M_original_fast = self.M_full_fast[:]
M_original_slow = self.M_full_slow[:]
if M_red.shape != M_original.shape:
raise RuntimeError('Dimension of mask matrix has to be the '
+ 'same as the original indegree matrix.')
self.M = M_original*M_red
self.M_fast = M_original_fast*M_red
self.M_slow = M_original_slow*M_red
self.ana.update_variables({'M': self.M, 'M_fast': self.M_fast,
'M_slow': self.M_slow})
def restore_full_connectivity(self):
'''Restore connectivity to full connectivity.'''
self.M = self.M_full
self.M_fast = self.M_full_fast
self.M_slow = self.M_full_slow
self.ana.update_variables({'M': self.M, 'M_fast': self.M_fast,
'M_slow': self.M_slow})
def get_effective_connectivity(self, freq):
"""Returns effective connectivity matrix.
Arguments:
freq: frequency in Hz
"""
return self.ana.create_MH(2*np.pi*freq)
def get_sensitivity_measure(self, freq, index=None):
"""Returns sensitivity measure.
see: Eq. 21 in Bos et al. (2015)
Arguments:
freq: frequency in Hz
Keyword arguments:
index: specifies index of eigenmode, default: None
if set to None the dominant eigenmode is assumed
"""
MH = self.get_effective_connectivity(freq)
e, U = np.linalg.eig(MH)
U_inv = np.linalg.inv(U)
if index is None:
# find eigenvalue closest to one
index = np.argmin(np.abs(e-1))
T = np.outer(U_inv[index],U[:,index])
T /= np.dot(U_inv[index],U[:,index])
T *= MH
return T
def get_transfer_function(self):
"""Returns dynamical transfer function depending on frequency.
Shape of output: (len(self.populations), len(self.omegas))
Output:
freqs: vector of frequencies in Hz
dyn_trans_func: power spectra for all populations,
dimension len(self.populations) x len(freqs)
"""
dyn_trans_func = np.asarray(map(self.ana.create_H, self.ana.omegas))
return self.ana.omegas/(2.0*np.pi), np.transpose(dyn_trans_func)
class Session(object):
def __init__(self, uplink, config, session_id, hydra_url):
'''
Constructor
'''
self.uplink = uplink
self.config = config
self.session_id = session_id
self.hydra_url = hydra_url
self.setup = Setup(self)
if self.config.has_option('general', 'fake'):
self.fake = (self.config.get('general', 'fake') == "yes")
else:
self.fake = False
def log_format(self, message):
return self.uplink.log_format("[" + self.session_id + "] " + message)
def prepare(self):
logging.info(self.setup.log_format(("preparing setup")))
if not self.fake:
self.setup.load()
self.setup.prepare_base()
def add_node(self, node_id, node_name, ip_address, netmask):
try:
logging.info(self.setup.log_format(("add node " + str(node_id) + " '" + str(node_name) + "'")))
if not self.fake:
self.setup.add_node(node_id, node_name, (ip_address, netmask))
except ValueError:
pass
def remove_node(self, node_id):
logging.info(self.setup.log_format(("remove node " + str(node_id))))
if not self.fake:
self.setup.remove_node(node_id)
def action(self, data):
try:
logging.info(self.setup.log_format(("call action: " + data)))
if not self.fake:
return self.setup.action(data)
except ValueError:
pass
def run(self):
""" run the nodes """
logging.info(self.setup.log_format(("run all the nodes")))
if not self.fake:
self.setup.startup()
def stop(self):
""" stop the nodes """
logging.info(self.setup.log_format(("stop all the nodes")))
if not self.fake:
self.setup.shutdown()
def cleanup(self):
""" cleanup the setup """
logging.info(self.setup.log_format(("cleaning up")))
""" stop all nodes """
if not self.fake:
self.setup.shutdown()
""" delete the setup folder """
if not self.fake:
self.setup.cleanup()
def open_camera(self):
self.setup = Setup(self)
self.setup.base_name = self.base_name
self.setup.camera()
class Source:
def __init__(self, main_window, database, admin):
self.main_window = main_window
self.dbs = database.session
self.admin = admin
self.setup_list = []
self.setup_frames = None
self.analysis_frames = None
self.background = None
self.polygon = None
self.base_name = None
self.media = None
self.video = None
self.out = None
self.location = None
self.path = None
self.analysis = None
self.analysis_dict = None
def open_files(self):
self.setup_files()
def open_camera(self):
self.setup = Setup(self)
self.setup.base_name = self.base_name
self.setup.camera()
def open(self, media):
self.media = media
if media == 'file':
print("Source is a file")
self.setup_list = []
self.files = QtGui.QFileDialog.getOpenFileNames(\
self.main_window, 'Open video file', '', \
'Videos (*.avi *.mp4)')
if self.files:
self.open_files()
if media == 'camera':
print("Source is a camera")
self.window = SourceWindow(self, self.main_window)
def not_exist(self, source_path):
s = self.dbs
result = s.query(Video).filter(Video.path == source_path)
print("result count :", result.count())
if result.count() == 0:
return True
elif result.count() == 1:
print("Source exist", result.first())
else:
print("Multiple source exist!")
return False
def generate_setup_list(self):
for file in self.files:
if self.not_exist(file):
self.setup_list.append(file)
print("Setup list :", self.setup_list)
def setup_files(self):
self.generate_setup_list()
self.setup = Setup(self)
if len(self.setup_list) > 0:
self.setup.status = True
self.setup.sequencer()
else:
print("Nothing to setup proceed to analysis")
self.analysis = Analysis(self, self.setup)
def setup_get_next_frame(self):
ret, read_frame = self.setup_frames.read()
if ret:
self.setup_current_frame = read_frame
else:
self.setup_current_frame = None
def analysis_get_next_frame(self):
ret, read_frame = self.analysis_frames.read()
if ret:
self.analysis_current_frame = read_frame
# save video if source is camera
if self.media == 'camera':
frame = copy(read_frame)
def save_frame():
self.out.write(frame)
thread = Thread(target=save_frame)
thread.start()
else:
self.analysis_current_frame = None
from random import shuffle
from setup import Setup
from Knn import Knn
from OperadoresBuilder import OperadoresBuilder
Setup.setup()
atributos = Setup.atributos
estudiantes = Setup.estudiantes
valoresPosibles = Setup.valoresPosibles
operadores = {}
OperadoresBuilder.multiple(operadores, OperadoresBuilder.hamming, ["school", "sex", "schoolsup", "famsup", "paid",
"activities", "nursery", "higher", "internet",
"romantic", "address", "famsize", "Pstatus",
"Mjob", "Fjob", "reason", "guardian"])
OperadoresBuilder.multiple(operadores, OperadoresBuilder.rango, ["age","Medu","Fedu",
"traveltime","studytime","failures","famrel",
"freetime","goout","Dalc","Walc","health","absences"], valoresPosibles)
knn = Knn(estudiantes, "G3", atributos, operadores)
# Se realizaran multiples pruebas para obtener una estimacion de la efectividad del algoritmo
# para cualquier eleccion de casos de entrenamiento / prueba
CANTIDAD_PRUEBAS = 25
# Separo 1/5 de los casos de prueba
cantEstTest = len(estudiantes)/5
class Dataset(pd.DataFrame):
"""
An experimental phospho-proteomics dataset extending `pandas.DataFrame`_
Parameters
----------
midas : Absolute PATH to a MIDAS file
time : Data acquisition time-point for the early response
Attributes
----------
setup : :class:`caspo.core.setup.Setup`
clampings : :class:`caspo.core.clamping.ClampingList`
readouts : `pandas.DataFrame`_
.. _pandas.DataFrame: http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe
"""
def __init__(self, midas, time):
df = pd.read_csv(midas)
times = np.unique(df.filter(regex='^DA').values.flatten())
if time not in times:
raise ValueError("The time-point %s does not exists in the dataset. Available time-points are: %s" % (time, list(times)))
df.drop(df.columns[0], axis=1, inplace=True)
cond = True
for c in df.filter(regex='^DA').columns:
cond = cond & (df[c] == time)
super(Dataset, self).__init__(df[cond].reset_index(drop=True))
stimuli = map(lambda c: c[3:], filter(lambda c: self.is_stimulus(c), self.columns))
inhibitors = map(lambda c: c[3:-1], filter(lambda c: self.is_inhibitor(c), self.columns))
readouts = map(lambda c: c[3:], filter(lambda c: self.is_readout(c), self.columns))
self.setup = Setup(stimuli, inhibitors, readouts)
@property
def clampings(self):
clampings = []
for i, row in self.filter(regex='^TR').iterrows():
literals = []
for v,s in row.iteritems():
if self.is_stimulus(v):
literals.append(Literal(v[3:], 1 if s == 1 else -1))
else:
if s == 1:
literals.append(Literal(v[3:-1], -1))
clampings.append(Clamping(literals))
return ClampingList(clampings)
@property
def readouts(self):
return self.filter(regex='^DV').rename(columns=lambda c: c[3:]).astype(float)
def is_stimulus(self, name):
"""
Returns if the given species name is a stimulus or not
Parameters
----------
name : str
Returns
-------
boolean
True if the given name is a stimulus, False otherwise.
"""
return name.startswith('TR') and not name.endswith('i')
def is_inhibitor(self, name):
"""
Returns if the given species name is a inhibitor or not
Parameters
----------
name : str
Returns
-------
boolean
True if the given name is a inhibitor, False otherwise.
"""
return name.startswith('TR') and name.endswith('i')
def is_readout(self, name):
"""
Returns if the given species name is a readout or not
Parameters
----------
name : str
Returns
-------
boolean
True if the given name is a readout, False otherwise.
"""
return name.startswith('DV')
def to_funset(self, discrete):
"""
Converts the dataset to a set of `gringo.Fun`_ instances
Parameters
----------
discrete : callable
A discretization function
Returns
-------
set
Representation of the dataset as a set of `gringo.Fun`_ instances
.. _gringo.Fun: http://potassco.sourceforge.net/gringo.html#Fun
"""
fs = self.clampings.to_funset("exp")
fs = fs.union(self.setup.to_funset())
for i,row in self.readouts.iterrows():
for var,val in row.iteritems():
if not np.isnan(val):
fs.add(gringo.Fun('obs',[i,var,discrete(val)]))
return fs
def main():
try:
opts, extra_params = getopt.getopt(sys.argv[1:], "hgl:e:w:p:", ["help", "generate", "language=", "export=", "workspace=", "project="])
except getopt.GetoptError:
usage()
sys.exit(2)
language = None
export = None
generate = False
dir = None
for opt, arg in opts:
if opt in ['-h', '--help']:
usage()
sys.exit()
else:
if opt in ['-g', '--generate']:
generate = True
if opt in ['-l', '--language']:
language = arg
if opt in ['-e', '--export']:
export = arg
if opt in ['-w', '--workspace', '-p', '--project']:
dir = arg
if language is None:
usage()
sys.exit()
# if len(extra_params) > 1:
# usage()
# sys.exit()
# else:
# project_name = extra_params[0]
if dir != None:
if opt == '-p':
project_name = os.path.abspath(dir)
print ''
print project_name
# Set the variables
print ''
print 'Setting up...'
setup = Setup(language, project_name)
# Set the project type (C or Java)
project = setup.getProject()
print 'Done.'
print ''
print '==================================='
# Create the work directory (pl_stats directory)
print ''
print 'Creating directories...'
project.createDirectories()
print 'Done.'
print ''
print '==================================='
# Copy files from project to work directory
print ''
print 'Copying source files to work directory...'
project.copyFiles()
print 'Done.'
print ''
print '==================================='
# Create XML files from project source code
print ''
print 'Converting source files...'
project.createXMLFiles()
# Remove source files from work directory
project.moveXMLFiles()
print 'Done.'
print ''
print '==================================='
# Create the object to manipulate project statistics
print ''
print 'Generating statistics...'
stats = project.getStats()
# Get project statistics
dict_methods, dict_features, dict_cbr, dict_vsoc, dict_decl_coupling, dict_assign_coupling = stats.getStatistics()
print 'Done.'
print ''
print '==================================='
# Export directives results do XLS file
# print ''
# print 'Creating directives sheet...'
# stats.exportDirectivesToXLS(dict_methods, dict_features)
# print 'Done.'
# print ''
# print '==================================='
#
# # Export dependencies results do XLS file
# print ''
# print 'Creating dependencies sheet...'
# stats.exportDependenciesToXLS(dict_decl_coupling, dict_assign_coupling)
# print 'Done.'
# print ''
# print '==================================='
# Export directives data to CSV file
print ''
print 'Creating directives_data csv file...'
stats.exportDirectivesDataToCSV(dict_methods, dict_features)
print 'Done.'
print ''
print '==================================='
# Export directives results do CSV file
print ''
print 'Creating directives_results csv file...'
stats.exportDirectivesResultsToCSV(dict_methods, dict_features)
print 'Done.'
print ''
print '==================================='
# Export dependencies results do CSV file
print ''
print 'Creating dependencies csv file...'
stats.exportDependenciesToCSV(dict_decl_coupling, dict_assign_coupling)
print 'Done.'
print ''
print '==================================='
else:
for project_dir in os.listdir(os.path.abspath(dir)):
project_name = os.path.abspath(dir+project_dir)
print ''
print project_name
# Set the variables
print ''
print 'Setting up...'
setup = Setup(language, project_name)
# Set the project type (C or Java)
project = setup.getProject()
print 'Done.'
print ''
print '==================================='
# Create the work directory (pl_stats directory)
print ''
print 'Creating directories...'
project.createDirectories()
print 'Done.'
print ''
print '==================================='
# Copy files from project to work directory
print ''
print 'Copying source files to work directory...'
project.copyFiles()
print 'Done.'
print ''
print '==================================='
# Create XML files from project source code
print ''
print 'Converting source files...'
project.createXMLFiles()
# Remove source files from work directory
project.moveXMLFiles()
print 'Done.'
print ''
print '==================================='
# Create the object to manipulate project statistics
print ''
print 'Generating statistics...'
stats = project.getStats()
# Get project statistics
dict_methods, dict_features, dict_cbr, dict_vsoc, dict_decl_coupling, dict_assign_coupling = stats.getStatistics()
print 'Done.'
print ''
print '==================================='
# Export directives results do XLS file
# print ''
# print 'Creating directives sheet...'
# stats.exportDirectivesToXLS(dict_methods, dict_features)
# print 'Done.'
# print ''
# print '==================================='
#
# # Export dependencies results do XLS file
# print ''
# print 'Creating dependencies sheet...'
# stats.exportDependenciesToXLS(dict_decl_coupling, dict_assign_coupling)
# print 'Done.'
# print ''
# print '==================================='
# Export directives data to CSV file
print ''
print 'Creating directives_data csv file...'
stats.exportDirectivesDataToCSV(dict_methods, dict_features)
print 'Done.'
print ''
print '==================================='
# Export directives results do CSV file
print ''
print 'Creating directives_results csv file...'
stats.exportDirectivesResultsToCSV(dict_methods, dict_features)
print 'Done.'
print ''
print '==================================='
# Export dependencies results do CSV file
print ''
print 'Creating dependencies csv file...'
stats.exportDependenciesToCSV(dict_decl_coupling, dict_assign_coupling)
print 'Done.'
print ''
print '==================================='
print '==================================='
print '######### PL-Stats - v. 0.5 #########'
print '-----------------------------------'
print '# Project: ' + project_name.__str__()
print '-----------------------------------'
print '# Total of project methods: ' + len(dict_methods).__str__()
print '==================================='