def system_initialize():
ham_int, reader_int, reader_int, shaker, *_ = sys_state.instruments
if mid_run:
print('CONTINUING A PREVIOUSLY INITIALIZED AND PAUSED RUN. WILL SKIP CLEANING. OK? 5 SECONDS TO CANCEL...')
time.sleep(5)
local_log_dir = os.path.join(method_local_dir, 'log')
if not os.path.exists(local_log_dir):
os.mkdir(local_log_dir)
main_logfile = os.path.join(local_log_dir, 'main.log')
logging.basicConfig(filename=main_logfile, level=logging.DEBUG, format='[%(asctime)s] %(name)s %(levelname)s %(message)s')
add_robot_level_log()
add_stderr_logging()
for banner_line in log_banner('Begin execution of ' + __file__):
logging.info(banner_line)
if sys_state.disable_pumps or simulation_on:
pump_int.disable()
if simulation_on:
reader_int.disable()
shaker.disable()
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
if mid_run:
prime_and_clean = None
else:
prime_and_clean = run_async(lambda: (#pump_int.prime(), # important that the shaker is
shaker.start(shake_speed), pump_int.bleach_clean(),
shaker.stop())) # started and stopped at least once
initialize(ham_int)
hepa_on(ham_int, simulate=int(simulation_on))
method_start_time = time.time()
if not sys_state.disable_pumps:
wash_empty_refill(ham_int, refillAfterEmpty=2, chamber2WashLiquid=0) # 2=chamber 1 only; 0=Liquid 1 (bleach)
if prime_and_clean:
prime_and_clean.join()
shaker.start(shake_speed) # TODO: For asynchrony
def new_tips(num=num_phage_dilutions, ttype='agar'):
ham_int, *_ = sys_state.instruments
while True:
try:
if ttype == 'agar':
tip_batch = [next(agar_tips_gen) for _ in range(num)]
elif ttype == 'culture':
tip_batch = [next(culture_tips_gen) for _ in range(num)]
else:
raise ValueError()
tip_pick_up(ham_int, tip_batch)
break
except pyhamilton.NoTipError:
initialize(ham_int) # eject tips if present
continue
return tip_batch
def system_initialize(ham_int, reader_int):
ham_int, *_ = sys_state.instruments
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
initialize(ham_int)
hepa_on(ham_int, 30, simulate=int(simulation_on))
def system_initialize():
ham_int, *_ = sys_state.instruments
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
initialize(ham_int)
wash_vols = [wash_vol for _ in media_poss]
bleach_poss = [(bleach_site, j) for j in array_idxs]
aspirate(ham_int, bleach_poss, wash_vols, **liq_move_param)
dispense(ham_int, bleach_poss, wash_vols, **liq_move_param)
water_poss = [(water_site, j) for j in array_idxs]
aspirate(ham_int, water_poss, wash_vols, **liq_move_param)
dispense(ham_int, water_poss, wash_vols, **liq_move_param)
tip_eject(ham_int, tip_poss)
remember.replace_vols = None # make sure these transfers are only executed once
with HamiltonInterface(
simulate=simulation_on) as ham_int, ClarioStar() as reader_int:
if no_reader or simulation_on:
reader_int.disable()
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
initialize(ham_int)
hepa_on(ham_int, 30, simulate=int(simulation_on))
std_class = 'StandardVolumeFilter_Water_DispenseSurface_Part_no_transport_vol'
remember = SimpleNamespace()
remember.od_readings = None
def measure_plate(plate,
reader_protocols,
simultaneously_execute=lambda: None):
reader_protocols = [
proto_name + '_fast' for proto_name in reader_protocols
] # use the speed optimized versions
ham_int, reader_int, *_ = sys_state.instruments
platedatas = read_plate(ham_int,
reader_int,
reader_tray,