def __init__(self, name, pumpname, max, isSerial, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.name = name
self.max = max
self.isPaused = False
self.pumpname = pumpname
self.resultsvector = []
self.changevector = []
self.isSerial = isSerial
self.kwargs = kwargs
self.signals = WorkerSignals()
self.running = True
if (self.isSerial == True):
try:
self.pumpPort = serial.Serial(port=self.pumpname,
baudrate=4800,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
timeout=1)
except:
self.pumpPort.close()
self.pumpPort = serial.Serial(port=self.pumpname,
baudrate=4800,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
timeout=1)
self.scalePort = MettlerToledoDevice(port=self.name)
class ScaleThread(QThread):
def __init__(self, portName):
QThread.__init__(self)
self.portName = portName
self.txq = queue.queue()
self.running = True
def ser_out(self, s):
self.txq.put(s)
def ser_in(self, s):
display(s)
def run(self):
try:
self.scalePort = MettlerToledoDevice(port=self.portName)
except:
self.scalePort = None
if not self.scalePort:
print("Serial Port troubs")
self.running = False
while (self.running):
s = self.scalePort.get_weight()
if s:
num = s[0]
numstr = int.Parse(num)
self.ser_in(numstr)
if not self.txq.empty():
txd = str(self.txq.get())
self.ser_out(txd)
if self.scalePort:
self.scalePort.close()
self.scalePort = None
def __init__(self, name, max, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.name = name
self.max = max
self.kwargs = kwargs
self.signals = WorkerSignals()
self.running = True
self.isPaused = False
self.scalePort = MettlerToledoDevice(port=self.name)
def run(self):
try:
self.scalePort = MettlerToledoDevice(port=self.portName)
except:
self.scalePort = None
if not self.scalePort:
print("Serial Port troubs")
self.running = False
while (self.running):
s = self.scalePort.get_weight()
if s:
num = s[0]
numstr = int.Parse(num)
self.ser_in(numstr)
if not self.txq.empty():
txd = str(self.txq.get())
self.ser_out(txd)
if self.scalePort:
self.scalePort.close()
self.scalePort = None
def __init__(self, name, pumpname, max, isSerial, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.name = name
self.max = max
self.pumpname = pumpname
self.isSerial = isSerial
self.kwargs = kwargs
self.signals = WorkerSignals()
self.running = True
self.txq = queue.Queue()
self.scalePort = MettlerToledoDevice(port=self.name)
if (self.isSerial == True):
try:
self.pumpPort = MasterflexSerial(self.pumpname, self.pumpPort)
except:
self.pumpPort.close()
def __init__(self,
config_file_path,
calibration_file_path,
*args,**kwargs):
if 'debug' in kwargs:
self._debug = kwargs['debug']
else:
kwargs.update({'debug': DEBUG})
self._debug = DEBUG
with open(config_file_path,'r') as config_stream:
self._config = yaml.load(config_stream)
with open(calibration_file_path,'r') as calibration_stream:
self._calibration = yaml.load(calibration_stream)
self._valves = self._config['head']
self._valves.update(self._config['manifold'])
ports = find_serial_device_ports(debug=self._debug)
self._debug_print('Found serial devices on ports ' + str(ports))
self._debug_print('Identifying connected devices (may take some time)...')
self._balance = MettlerToledoDevice()
ports.remove(self._balance.get_port())
# try:
# self._bsc = BioshakeDevice()
# except RuntimeError:
# # try one more time
# self._bsc = BioshakeDevice()
# self._debug_print('Found bioshake device on port ' + str(self._bsc.get_port()))
# ports.remove(self._bsc.get_port())
# self._SHAKE_SPEED_MIN = self._bsc.get_shake_speed_min()
# self._SHAKE_SPEED_MAX = self._bsc.get_shake_speed_max()
# self._SHAKE_DURATION_MIN = 10
# self._SHAKE_ATTEMPTS = 2
# self._POST_SHAKE_OFF_DURATION = 5
modular_devices = ModularDevices(try_ports=ports)
try:
msc_dict = modular_devices['mixed_signal_controller']
except KeyError:
raise HybridizerError('Could not find mixed_signal_controller. Check connections and permissions.')
if len(msc_dict) > 1:
raise HybridizerError('More than one mixed_signal_controller found. Only one should be connected.')
self._msc = msc_dict[msc_dict.keys()[0]]
self._debug_print('Found mixed_signal_controller on port ' + str(self._msc.get_port()))
# self._adc_values_min = None
# self._adc_values_max = None
self._adc_sample_count = 21
self._fill_duration_all_cylinders = 250
self._fill_duration_one_cylinder = 100
self._volume_crossover = 6
self._volume_threshold_initial = 1.0
class Connection:
def __init__(self, address, device_id):
self.address = address
self.device_id = device_id
self.dev = MettlerToledoDevice(port=self.address)
def get_weight(self):
weight = self.dev.get_weight()
return {
'value': weight[0],
'unit': weight[1],
'stable': True if weight[2] is 'S' else False
}
def get_info(self):
data = self.dev.get_balance_data()
sn = self.dev.get_serial_number()
sw = self.dev.get_software_version()
if len(data) > 3:
info = {
'model': data[0],
'model-type': data[1],
'sn': sn,
'sw-version': sw[0],
'sw-type': sw[1],
'capacity': data[1],
'unit': data[2]
}
else:
info = {
'model': data[0],
'sn': sn,
'sw-version': sw[0],
'sw-type': sw[1],
'capacity': data[1],
'unit': data[2]
}
return info
def get_address(self):
return self.dev.get_port()
def close(self):
self.dev.close()
class Worker(QObject):
'''
Worker thread
Inherits from QRunnable to handler worker thread setup, signals and wrap-up.
:param callback: The function callback to run on this worker thread. Supplied args and
kwargs will be passed through to the runner.
:type callback: function
:param args: Arguments to pass to the callback function
:param kwargs: Keywords to pass to the callback function
'''
def __init__(self, name, max, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.name = name
self.max = max
self.kwargs = kwargs
self.signals = WorkerSignals()
self.running = True
self.isPaused = False
self.scalePort = MettlerToledoDevice(port=self.name)
# Add the callback to our kwargs
def stop(self):
self.event
@Slot()
def pause(self):
self.isPaused = True
@Slot()
def resume(self):
self.isPaused = False
def cancel(self):
self.scalePort.close()
self.running = False
def factor_conversion(self):
if 0 < self.maxed < 5001:
factor = 0.9
elif 5001 <= self.max < 20001:
factor = 0.99
elif 20001 <= self.max:
factor = 0.999
return factor
@Slot()
def run(self):
resultcounter = 0
resultarray = npy.array([])
deltaarray = npy.array([])
changecounter = 0
while (self.running):
while self.isPaused() == True:
time.wait(0)
try:
s = self.scalePort.get_weight()
if s:
resultcounter += 1
num = s[0]
inum = int(num)
result = str(num)
if resultcounter >= 5:
resultarray.append(result)
resultcounter = 0
changecounter += 1
p
if changecounter >= 5:
deltaarray.append(resultarray[len(resultarray) -
1] - resultarray[-1])
changecounter = 0
if deltaarray[len(deltaarray) -
1] - deltaarray[-1] <= 50:
self.cancel()
if len(resultarray) > 10:
if len(resultarray) < 25:
if sum(resultarray) / len(resultarray) <= 100:
self.cancel()
self.signals.result.emit(result)
self.signals.progress.emit(
100 * inum / int(0.9 * self.factor_conversion()))
if (inum > int(self.factor_conversion())):
self.cancel()
break
if self.scalePort is None:
self.cancel()
break
except:
self.cancel()
break
# Return the result of the processin
# Done
if (self.running == False):
self.signals.finished.emit()
end='')
sys.stdout.flush()
time.sleep(drop_wait_s)
print('done')
robot.moveXY(pump_xy_approach[-1])
#zvial_travel = robot.z2_to_worksurface - 2 * vial_grip_height - 3
# (to simplify things for now)
zvial_travel = 0
robot.moveZ2(zvial_travel)
for xy in pump_xy_approach[:-1][::-1]:
robot.moveXY(xy)
if weigh_aliquots:
from mettler_toledo_device import MettlerToledoDevice
scale = MettlerToledoDevice(port='/dev/ttyUSB2')
# TODO some scale command to automate this? setting to make it not
# sleep?
print('Tap the scale to wake it up, if it is not already.')
#
zeroed = False
# TODO this doesn't seem to work if we can't wake the scale...
print('Waiting for stable weight to zero... ', end='')
sys.stdout.flush()
while not zeroed:
zeroed = scale.zero_stable()
print('done')
scale_xy = (632, 2)
# 23 would stick sometimes
class Worker(QRunnable):
'''
Worker thread
Inherits from QRunnable to handler worker thread setup, signals and wrap-up.
:param callback: The function callback to run on this worker thread. Supplied args and
kwargs will be passed through to the runner.
:type callback: function
:param args: Arguments to pass to the callback function
:param kwargs: Keywords to pass to the callback function
'''
def __init__(self, name, pumpname, max, isSerial, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.name = name
self.max = max
self.isPaused = False
self.pumpname = pumpname
self.resultsvector = []
self.changevector = []
self.isSerial = isSerial
self.kwargs = kwargs
self.signals = WorkerSignals()
self.running = True
if (self.isSerial == True):
try:
self.pumpPort = serial.Serial(port=self.pumpname,
baudrate=4800,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
timeout=1)
except:
self.pumpPort.close()
self.pumpPort = serial.Serial(port=self.pumpname,
baudrate=4800,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
timeout=1)
self.scalePort = MettlerToledoDevice(port=self.name)
# Add the callback to our kwargs
def stop(self):
self.event
def pause(self):
self.isPaused = True
def resume(self):
self.isPaused = False
def cancel(self):
if (self.isSerial == True):
try:
self.scalePort.close()
self.running = False
self.resultsvector = []
self.changevector = []
self.pumpPort.close()
except:
self.scalePort = None
self.pumpPort = None
else:
#self.signals.pumpStop.emit()
self.scalePort.close()
self.running = False
def factor_conversion(self):
if 0 < self.max < 5001:
factor = 0.9
elif 5001 <= self.max < 20001:
factor = 0.99
elif 20001 <= self.max:
factor = 0.999
return factor
def convertToVoltage(self, rpm):
volt = self.rpm * 0.016
@Slot()
def run(self):
if (self.isSerial == True):
if (self.pumpPort):
self.pumpPort.close()
while (self.running):
while self.isPaused:
time.sleep(0)
try:
s = self.scalePort.get_weight()
if s:
num = s[0]
inum = int(num)
result = str(num)
changes = []
self.resultsvector.append(int(inum))
self.signals.result.emit(result)
self.signals.progress.emit(100 * inum /
int(0.97 * self.max))
if (len(self.resultsvector) > 5):
if (self.resultsvector[-1] != self.resultsvector[-2]):
change = float(self.resultsvector[-1]) - float(
self.resultsvector[-2])
self.changevector.append(float(change))
if (len(self.changevector) > 5):
avg = sum(self.changevector) / len(
self.changevector)
if ((self.changevector[-1]) / avg < 0.1):
self.signals.result.emit(
"Air in the line or still clamped")
self.signals.error.emit((str(
self.changevector[-1]
), "Rate of change has fallen to low, check line"
))
self.cancel()
break
if (inum > int(0.999 * self.max)):
self.cancel()
break
if self.scalePort is None:
self.cancel()
break
except:
self.cancel()
break
# Return the result of the processin
# Done
if (self.running == False):
self.signals.finished.emit()
def __init__(self, address, device_id):
self.address = address
self.device_id = device_id
self.dev = MettlerToledoDevice(port=self.address)
import io
import random
import picamera
import datetime as dt
from time import gmtime, strftime
import csv
from mettler_toledo_device import MettlerToledoDevice
dev = MettlerToledoDevice() # Might automatically find device if one available
# if it is not found automatically, specify port directly
dev = MettlerToledoDevice(port='/dev/ttyACM0') # Linux specific port
filename = dt.datetime.now().strftime('%Y-%m-%d hr%H_min%M_s%S')
filename += '.csv'
saveFile = open(filename, 'w')
#saveFile = open('timedata.csv', 'aw')
writer = csv.writer(saveFile)
# Main #
# get current weight
print('program started')
weight, units, stability = dev.get_weight()
currWeight = weight
# start picamera
camera = picamera.PiCamera()
stream = picamera.PiCameraCircularIO(camera, seconds=10)
camera.start_recording(stream, format='h264')
try:
while True:
print('waiting')
# # Annotate camera
class Worker(QRunnable):
'''
Worker thread
Inherits from QRunnable to handler worker thread setup, signals and wrap-up.
:param callback: The function callback to run on this worker thread. Supplied args and
kwargs will be passed through to the runner.
:type callback: function
:param args: Arguments to pass to the callback function
:param kwargs: Keywords to pass to the callback function
'''
def __init__(self, name, pumpname, max, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.name = name
self.max = max
self.pumpname = pumpname
self.kwargs = kwargs
self.signals = WorkerSignals()
self.running = True
self.resultsvector = []
self.changevector = []
self.txq = queue.Queue()
self.scalePort = MettlerToledoDevice(port=self.name)
try:
self.pumpPort = serial.Serial(port=self.pumpname,
baudrate=4800,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
timeout=1)
except:
self.pumpPort.close()
self.pumpPort = serial.Serial(port=self.pumpname,
baudrate=4800,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
timeout=1)
# Add the callba ck to our kwargs
def stop(self):
self.event
def cancel(self):
try:
self.scalePort.close()
self.running = False
self.pumpPort.close()
self.resultsvector = []
self.changevector = []
except:
self.scalePort = None
self.pumpPort = None
@Slot()
def run(self):
if (self.pumpPort):
self.pumpPort.close()
while (self.running):
try:
s = self.scalePort.get_weight()
if s:
num = s[0]
inum = int(num)
result = str(num)
changes = []
self.resultsvector.append(int(inum))
self.signals.result.emit(result)
self.signals.progress.emit(100 * inum /
int(0.97 * self.max))
if (len(self.resultsvector) > 2):
if (self.resultsvector[-1] != self.resultsvector[-2]):
change = float(self.resultsvector[-1]) - float(
self.resultsvector[-2])
self.changevector.append(float(change))
if (len(self.changevector) > 5):
avg = sum(self.changevector) / len(self.changevector)
if (avg > 0 and (self.changevector[-1]) / avg < 0.1):
self.signals.result.emit(
"Air in the line or still clamped")
self.signals.error.emit(
(str(self.changevector[-1]),
"Rate of change has fallen to low, check line"
))
self.cancel()
break
elif (avg == 0 and len(self.changevector) < 2):
self.signals.result.emit(
"Air in the line or still clamped")
self.signals.error.emit(
(str(self.changevector[-1]),
"Rate of change has fallen to low, check line"
))
self.cancel()
break
if (inum > int(0.99 * self.max)):
self.cancel()
break
if self.scalePort is None:
self.cancel()
break
except:
traceback.print_exc()
exctype, value = sys.exc_info()[:2]
self.signals.error.emit(
(exctype, value, traceback.format_exc()))
self.cancel()
break
# Return the result of the processin
# Done
if (self.running == False):
self.signals.finished.emit()
from mettler_toledo_device import MettlerToledoDevice dev = MettlerToledoDevice() # Might automatically find device if one available # if it is not found automatically, specify port directly dev = MettlerToledoDevice(port='/dev/ttyACM0') # Linux specific port #dev = MettlerToledoDevice(port='/dev/tty.usbmodem262471') # Mac OS X specific port #dev = MettlerToledoDevice(port='COM3') # Windows specific port dev.get_serial_number() #1126493049 dev.get_balance_data() #['XS204', 'Excellence', '220.0090', 'g'] dev.get_weight_stable() #[-0.0082, 'g'] #if weight is stable #None #if weight is dynamic dev.get_weight() #[-0.6800, 'g', 'S'] #if weight is stable #[-0.6800, 'g', 'D'] #if weight is dynamic dev.zero_stable() #True #zeros if weight is stable #False #does not zero if weight is not stable dev.zero() #'S' #zeros if weight is stable #'D' #zeros if weight is dynamic
class Hybridizer(object):
'''
This Python package (hybridizer) creates a class named Hybridizer to
communcate with and control the Janelia Hybridizer. The hybridizer
uses two hardware control devices, the mixed_signal_controller
modular_device, and the bioshake_device. The
mixed_signal_controller both switches the valves and reads the
analog signals from the cylinder hall effect sensors. The
bioshake_device controls the heater/shaker.
Example Usage:
hyb = Hybridizer('example_config.yaml')
hyb.run_protocol()
'''
# def __init__(self,
# config_file_path,
# *args,**kwargs):
def __init__(self,
config_file_path,
calibration_file_path,
*args,**kwargs):
if 'debug' in kwargs:
self._debug = kwargs['debug']
else:
kwargs.update({'debug': DEBUG})
self._debug = DEBUG
with open(config_file_path,'r') as config_stream:
self._config = yaml.load(config_stream)
with open(calibration_file_path,'r') as calibration_stream:
self._calibration = yaml.load(calibration_stream)
self._valves = self._config['head']
self._valves.update(self._config['manifold'])
ports = find_serial_device_ports(debug=self._debug)
self._debug_print('Found serial devices on ports ' + str(ports))
self._debug_print('Identifying connected devices (may take some time)...')
self._balance = MettlerToledoDevice()
ports.remove(self._balance.get_port())
# try:
# self._bsc = BioshakeDevice()
# except RuntimeError:
# # try one more time
# self._bsc = BioshakeDevice()
# self._debug_print('Found bioshake device on port ' + str(self._bsc.get_port()))
# ports.remove(self._bsc.get_port())
# self._SHAKE_SPEED_MIN = self._bsc.get_shake_speed_min()
# self._SHAKE_SPEED_MAX = self._bsc.get_shake_speed_max()
# self._SHAKE_DURATION_MIN = 10
# self._SHAKE_ATTEMPTS = 2
# self._POST_SHAKE_OFF_DURATION = 5
modular_devices = ModularDevices(try_ports=ports)
try:
msc_dict = modular_devices['mixed_signal_controller']
except KeyError:
raise HybridizerError('Could not find mixed_signal_controller. Check connections and permissions.')
if len(msc_dict) > 1:
raise HybridizerError('More than one mixed_signal_controller found. Only one should be connected.')
self._msc = msc_dict[msc_dict.keys()[0]]
self._debug_print('Found mixed_signal_controller on port ' + str(self._msc.get_port()))
# self._adc_values_min = None
# self._adc_values_max = None
self._adc_sample_count = 21
self._fill_duration_all_cylinders = 250
self._fill_duration_one_cylinder = 100
self._volume_crossover = 6
self._volume_threshold_initial = 1.0
def prime_system(self):
self._setup()
self._debug_print('priming system...')
manifold = self._config['manifold']
chemicals = manifold.keys()
try:
chemicals.remove('aspirate')
except ValueError:
pass
try:
chemicals.remove('separate')
except ValueError:
pass
self._set_valves_on(['separate','aspirate'])
for chemical in chemicals:
self._prime_chemical(chemical,self._config['system_prime_count'])
self._set_all_valves_off()
self._debug_print('priming finished!')
def run_protocol(self):
self._setup()
self.protocol_start_time = time.time()
self._debug_print('running protocol...')
self._set_valves_on(['separate','aspirate'])
for chemical_info in self._config['protocol']:
chemical = chemical_info['chemical']
try:
prime_count = chemical_info['prime_count']
except KeyError:
prime_count = 1
try:
dispense_count = chemical_info['dispense_count']
except KeyError:
dispense_count = 1
try:
shake_speed = chemical_info['shake_speed']
except KeyError:
shake_speed = None
try:
shake_duration = chemical_info['shake_duration']
except KeyError:
shake_duration = None
try:
post_shake_duration = chemical_info['post_shake_duration']
except KeyError:
post_shake_duration = 0
try:
separate = chemical_info['separate']
except KeyError:
separate = False
try:
aspirate = chemical_info['aspirate']
except KeyError:
aspirate = True
try:
temperature = chemical_info['temperature']
except KeyError:
temperature = None
try:
repeat = chemical_info['repeat']
except KeyError:
repeat = 0
self._run_chemical(chemical,
prime_count,
dispense_count,
shake_speed,
shake_duration,
post_shake_duration,
separate,
aspirate,
temperature,
repeat)
self._set_all_valves_off()
self.protocol_end_time = time.time()
protocol_run_time = self.protocol_end_time - self.protocol_start_time
self._debug_print('protocol finished! it took ' + str(round(protocol_run_time/60)) + ' mins to run.')
def _setup(self):
# self._bsc.reset_device()
self._msc.remove_all_set_fors()
self._set_all_valves_off()
self._set_valves_on(['primer','quad1','quad2','quad3','quad4','quad5','quad6'])
self._debug_print('setting up for ' + str(self._config['setup_duration']) + 's...')
time.sleep(self._config['setup_duration'])
self._set_all_valves_off()
self._debug_print('setup finished!')
def _prime_chemical(self,chemical,prime_count):
if prime_count > 0:
self._set_valve_on(chemical)
for i in range(prime_count):
self._set_valves_on(['primer','system'])
self._debug_print('priming ' + chemical + ' for ' + str(self._config['prime_duration']) + 's ' + str(i+1) + '/' + str(prime_count) + '...')
time.sleep(self._config['prime_duration'])
self._set_valves_off(['system'])
self._debug_print('emptying ' + chemical + ' for ' + str(self._config['prime_aspirate_duration']) + 's ' + str(i+1) + '/' + str(prime_count) + '...')
time.sleep(self._config['prime_aspirate_duration'])
self._set_valve_off('primer')
if prime_count > 0:
self._set_valve_off(chemical)
def _run_chemical(self,
chemical,
prime_count=1,
dispense_count=1,
shake_speed=None,
shake_duration=None,
post_shake_duration=0,
separate=False,
aspirate=True,
temp_target=None,
repeat=0):
if (chemical not in self._valves):
raise HybridizerError(chemical + ' is not listed as part of the manifold in the config file!')
if repeat < 0:
repeat = 0
run_count = repeat + 1
if temp_target is not None:
self._debug_print('turning on temperature control for ' + chemical + '...')
self._bsc.temp_on(temp_target)
temp_actual = self._bsc.get_temp_actual()
self._debug_print('actual temperature: ' + str(temp_actual) + ',target temperature: ' + str(temp_target))
while abs(temp_target - temp_actual) > 0.5:
time.sleep(1)
temp_actual = self._bsc.get_temp_actual()
self._debug_print('actual temperature: ' + str(temp_actual) + ',target temperature: ' + str(temp_target))
self._debug_print()
self._prime_chemical(chemical,prime_count)
for run in range(run_count):
self._debug_print('running ' + chemical + ' ' + str(run+1) + '/' + str(run_count) + '...')
self._set_valve_on(chemical)
self._set_valves_on(['quad1','quad2','quad3','quad4','quad5','quad6','aspirate'])
for i in range(dispense_count):
if i > 0:
dispense_shake_duration = self._config['inter_dispense_shake_duration']
if dispense_shake_duration < self._SHAKE_DURATION_MIN:
dispense_shake_duration = self._SHAKE_DURATION_MIN
dispense_shake_speed = self._shake_on(self._config['inter_dispense_shake_speed'])
self._debug_print('shaking at ' + str(dispense_shake_speed) + 'rpm for ' + str(dispense_shake_duration) + 's...')
time.sleep(dispense_shake_duration)
self._shake_off(dispense_shake_speed)
self._set_valve_on('system')
self._debug_print('loading ' + chemical + ' into syringes for ' + str(self._config['load_duration']) + 's ' + str(i+1) + '/' + str(dispense_count) + '...')
time.sleep(self._config['load_duration'])
self._set_valve_off('system')
self._debug_print('dispensing ' + chemical + ' into microplate for ' + str(self._config['dispense_duration']) + 's ' + str(i+1) + '/' + str(dispense_count) + '...')
time.sleep(self._config['dispense_duration'])
self._set_valves_off(['quad1','quad2','quad3','quad4','quad5','quad6'])
if not ((shake_duration is None) or (shake_duration <= 0)):
actual_shake_duration = shake_duration
if shake_duration < self._SHAKE_DURATION_MIN:
actual_shake_duration = self._SHAKE_DURATION_MIN
actual_shake_speed = self._shake_on(shake_speed)
self._debug_print('shaking at ' + str(actual_shake_speed) + 'rpm for ' + str(actual_shake_duration) + 's...')
time.sleep(actual_shake_duration)
self._shake_off(actual_shake_speed)
if (post_shake_duration > 0):
self._debug_print('waiting post shake for ' + str(post_shake_duration) + 's...')
time.sleep(post_shake_duration)
if separate:
separate_shake_speed = self._shake_on(self._config['separate_shake_speed'])
self._set_valve_off('separate')
self._debug_print('separating ' + chemical + ' for ' + str(self._config['chemical_separate_duration']) + 's...')
time.sleep(self._config['chemical_separate_duration'])
self._set_valve_on('separate')
self._shake_off(separate_shake_speed)
if aspirate:
aspirate_shake_speed = self._shake_on(self._config['aspirate_shake_speed'])
self._set_valve_off('aspirate')
self._debug_print('aspirating ' + chemical + ' from microplate for ' + str(self._config['chemical_aspirate_duration']) + 's...')
time.sleep(self._config['chemical_aspirate_duration'])
self._set_valve_on('aspirate')
self._shake_off(aspirate_shake_speed)
self._set_valve_off(chemical)
self._debug_print(chemical + ' finished!')
self._debug_print()
if temp_target is not None:
self._debug_print('turning off temperature control for ' + chemical + '...')
try:
self._bsc.temp_off()
except BioshakeError:
pass
self._debug_print()
def _shake_on(self,shake_speed):
if (shake_speed is None) or (shake_speed < self._SHAKE_SPEED_MIN):
shake_speed = 0
elif shake_speed > self._SHAKE_SPEED_MAX:
shake_speed = self._SHAKE_SPEED_MAX
if shake_speed != 0:
shook = False
shake_try = 0
while (not shook) and (shake_try < self._SHAKE_ATTEMPTS):
shake_try += 1
try:
self._bsc.shake_on(shake_speed)
shook = True
except BioshakeError:
self._debug_print('bioshake_device.get_error_list(): ' + str(self._bsc.get_error_list()))
self._debug_print('BioshakeError! Resetting for ' + str(self._config['setup_duration']) + 's and trying again...')
self._bsc.reset_device()
time.sleep(self._config['setup_duration'])
return shake_speed
def _shake_off(self,shake_speed):
if shake_speed != 0:
shook = False
shake_try = 0
while (not shook) and (shake_try < self._SHAKE_ATTEMPTS):
shake_try += 1
try:
self._bsc.shake_off()
shook = True
except BioshakeError:
self._debug_print('bioshake_device.get_error_list(): ' + str(self._bsc.get_error_list()))
self._debug_print('BioshakeError! Resetting for ' + str(self._config['setup_duration']) + 's and trying again...')
self._bsc.reset_device()
time.sleep(self._config['setup_duration'])
time.sleep(self._POST_SHAKE_OFF_DURATION)
def _debug_print(self,*args):
if self._debug:
print(*args)
def _set_valve_on(self,valve_key):
try:
valve = self._valves[valve_key]
channels = [valve['channel']]
self._msc.set_channels_on(channels)
except KeyError:
raise HybridizerError('Unknown valve: ' + str(valve_key) + '. Check yaml config file for errors.')
def _set_valves_on(self,valve_keys):
try:
channels = [self._valves[valve_key]['channel'] for valve_key in valve_keys]
self._msc.set_channels_on(channels)
except KeyError:
raise HybridizerError('Unknown valve: ' + str(valve_key) + '. Check yaml config file for errors.')
def _set_valve_off(self,valve_key):
try:
valve = self._valves[valve_key]
channels = [valve['channel']]
self._msc.set_channels_off(channels)
except KeyError:
raise HybridizerError('Unknown valve: ' + str(valve_key) + '. Check yaml config file for errors.')
def _set_valves_off(self,valve_keys):
try:
channels = [self._valves[valve_key]['channel'] for valve_key in valve_keys]
self._msc.set_channels_off(channels)
except KeyError:
raise HybridizerError('Unknown valve: ' + str(valve_key) + '. Check yaml config file for errors.')
def _set_all_valves_off(self):
valve_keys = self._get_valves()
self._set_valves_off(valve_keys)
def _get_valves(self):
valve_keys = self._valves.keys()
valve_keys.sort()
return valve_keys
def _get_adc_values_filtered(self):
adc_values = None
for sample_n in range(self._adc_sample_count):
sample_values = self._msc.get_analog_inputs_filtered()
if adc_values is None:
adc_values = numpy.array([sample_values],int)
else:
adc_values = numpy.append(adc_values,[sample_values],axis=0)
time.sleep(0.1)
adc_values_filtered = numpy.median(adc_values,axis=0)
adc_values_filtered = adc_values_filtered.astype(int)
return adc_values_filtered
# def _store_adc_values_min(self):
# self._adc_values_min = {}
# adc_values_filtered = self._get_adc_values_filtered()
# head_valves = self._config['head']
# for head_valve in head_valves:
# try:
# ain = self._config['head'][head_valve]['analog_inputs']['low']
# adc_value = adc_values_filtered[ain]
# self._adc_values_min[head_valve] = adc_value
# except KeyError:
# continue
# self._debug_print(self._adc_values_min)
# def _set_valves_on_until(self,valve_keys,volume):
# for valve_key in valve_keys:
# valve = self._valves[valve_key]
# channels = [valve['channel']]
# adc_value_goal,ain = self._volume_to_adc_and_ain(valve_key,volume)
# set_until_index = self._msc.set_channels_on_until(channels,ain,adc_value_goal)
# while not self._msc.are_all_set_untils_complete():
# self._debug_print('Waiting...')
# time.sleep(1)
# self._msc.remove_all_set_untils()
# for valve_key in valve_keys:
# valve = self._valves[valve_key]
# adc_value_goal,ain = self._volume_to_adc_and_ain(valve_key,volume)
# adc_value = self._msc.get_analog_input(ain)
# volume = self._adc_to_volume_low(valve_key,adc_value)
def _set_valves_on_until(self,valve_keys,volume):
channels = []
adc_value_goals = []
ains = []
jumps = {}
valve_keys_copy = copy.copy(valve_keys)
for valve_key in valve_keys:
valve = self._valves[valve_key]
channels.append(valve['channel'])
adc_value_goal,ain = self._volume_to_adc_and_ain(valve_key,volume)
adc_value_goals.append(adc_value_goal)
ains.append(ain)
jumps[valve_key] = 0
volume_goal_initial = volume - self._volume_threshold_initial
fill_duration_initial_max = 0
fill_durations_initial = []
if volume_goal_initial >= self._volume_threshold_initial/2:
for valve_key in valve_keys:
fill_duration_initial = self._volume_to_fill_duration(valve_key,volume_goal_initial)
fill_durations_initial.append(fill_duration_initial)
fill_duration_initial_min = min(fill_durations_initial)
self._msc.set_channels_on_for(channels,fill_duration_initial_min)
while not self._msc.are_all_set_fors_complete():
self._debug_print('Waiting...')
time.sleep(0.5 + fill_duration_initial_min/1000)
self._msc.remove_all_set_fors()
fill_duration_base = self._fill_duration_one_cylinder
fill_duration_per_cylinder = (self._fill_duration_all_cylinders - self._fill_duration_one_cylinder)//(len(channels)-1)
while len(channels) > 0:
fill_duration = fill_duration_base + fill_duration_per_cylinder*(len(channels)-1)
self._debug_print("Setting {0} valves on for {1}ms".format(valve_keys_copy,fill_duration))
self._msc.set_channels_on_for(channels,fill_duration)
while not self._msc.are_all_set_fors_complete():
self._debug_print('Waiting...')
time.sleep(fill_duration/1000)
self._msc.remove_all_set_fors()
adc_values_filtered = self._get_adc_values_filtered()
ains_copy = copy.copy(ains)
for ain in ains_copy:
index = ains.index(ain)
valve_key_copy = valve_keys_copy[index]
jumps[valve_key_copy] += 1
if adc_values_filtered[ain] >= adc_value_goals[index]:
channels.pop(index)
adc_value_goals.pop(index)
ains.pop(index)
valve_keys_copy.pop(index)
adc_values_filtered = self._get_adc_values_filtered()
final_adc_values = []
jumps_list = []
for valve_key in valve_keys:
adc_value_goal,ain = self._volume_to_adc_and_ain(valve_key,volume)
adc_value = adc_values_filtered[ain]
final_adc_values.append(adc_value)
jumps_list.append(jumps[valve_key])
# volume = self._adc_to_volume_low(valve_key,adc_value)
return final_adc_values,jumps_list
# def _volume_to_adc_and_ain(self,valve_key,volume):
# valve = self._valves[valve_key]
# if volume <= self._config['volume_crossover']:
# ain = valve['analog_inputs']['low']
# else:
# ain = valve['analog_inputs']['low']
# if volume > self._config['volume_max']:
# raise HybridizerError('Asking for volume greater than the max volume of {0}!'.format(self._config['volume_max']))
# if volume <= self._config['volume_crossover']:
# poly = Polynomial(self._config['poly_coefficients']['volume_to_adc_low'])
# adc_value = int(round(poly(volume)))
# adc_value += self._adc_values_min[valve_key]
# self._debug_print("valve: {0}, adc_value: {1}, ain: {2}".format(valve_key,adc_value,ain))
# return adc_value,ain
# else:
# return 400,ain
def _volume_to_adc_and_ain(self,valve_key,volume):
valve = self._valves[valve_key]
if volume <= self._volume_crossover:
ain = valve['analog_inputs']['low']
else:
ain = valve['analog_inputs']['high']
if volume > self._config['volume_max']:
raise HybridizerError('Asking for volume greater than the max volume of {0}!'.format(self._config['volume_max']))
if volume <= self._volume_crossover:
poly = Polynomial(self._calibration[valve_key]['volume_to_adc_low'])
adc_value = int(round(poly(volume)))
self._debug_print("valve: {0}, adc_value: {1}, ain: {2}".format(valve_key,adc_value,ain))
return adc_value,ain
else:
poly = Polynomial(self._calibration[valve_key]['volume_to_adc_high'])
adc_value = int(round(poly(volume)))
self._debug_print("valve: {0}, adc_value: {1}, ain: {2}".format(valve_key,adc_value,ain))
return adc_value,ain
def _volume_to_fill_duration(self,valve_key,volume):
poly = Polynomial(self._calibration[valve_key]['volume_to_fill_duration'])
fill_duration = int(round(poly(volume)))
return fill_duration
# def _adc_to_volume_low(self,valve_key,adc_value):
# valve = self._valves[valve_key]
# adc_value -= self._adc_values_min[valve_key]
# poly = Polynomial(self._config['poly_coefficients']['adc_to_volume_low'])
# volume = poly(adc_value)
# self._debug_print("valve: {0}, adc_value: {1}, volume: {2}".format(valve_key,adc_value,volume))
# return volume
def run_dispense_tests(self):
self._debug_print('pre setup sequence...')
valves = ['quad1','quad2','quad3','quad4','quad5','quad6']
self._set_valve_on('aspirate')
self._set_valve_on('system')
self._set_valves_on(valves)
time.sleep(10)
self._set_valve_off('system')
time.sleep(10)
self._set_valve_off('aspirate')
time.sleep(20)
self._setup()
self._set_valve_on('aspirate')
time.sleep(10)
# self._debug_print('zeroing hall effect sensors...')
# self._store_adc_values_min()
self._debug_print('zeroing balance...')
self._balance.zero()
self._debug_print('running dispense tests...')
timestr = time.strftime("%Y%m%d-%H%M%S")
data_file = open(timestr+'.csv','w')
data_writer = csv.writer(data_file)
header = ['dispense_goal','initial_weight']
valve_adc = [valve+'_adc' for valve in valves]
header.extend(valve_adc)
valve_jumps = [valve+'_jumps' for valve in valves]
header.extend(valve_jumps)
header.extend(valves)
data_writer.writerow(header)
# dispense_goals = [5,4,3,2,1]
# dispense_goals = [1,0.75,0.5,0.25]
dispense_goals = [5,1,0.5]
# dispense_goals = [2,1]
# run_count = 10
run_count = 1
# dispense_goals = [1]
# run_count = 2
for dispense_goal in dispense_goals:
for run in range(run_count):
self._set_valve_on('aspirate')
time.sleep(2)
self._debug_print('dispense_goal: {0}, run: {1} out of {2}'.format(dispense_goal,run+1,run_count))
row_data = []
row_data.append(dispense_goal)
initial_weight = self._balance.get_weight()[0]
self._debug_print('initial_weight: {0}'.format(initial_weight))
row_data.append(initial_weight)
self._set_valve_on('system')
time.sleep(2)
final_adc_values,jumps = self._set_valves_on_until(valves,dispense_goal)
row_data.extend(final_adc_values)
row_data.extend(jumps)
self._set_valve_off('system')
time.sleep(4)
weight_prev = initial_weight
for valve in valves:
self._debug_print('Dispensing {0}'.format(valve))
self._set_valve_on(valve)
time.sleep(4)
self._set_valve_off(valve)
time.sleep(2)
weight_total = self._balance.get_weight()[0]
weight = weight_total - weight_prev
self._debug_print('{0} measured {1}'.format(valve,weight))
row_data.append(weight)
weight_prev = weight_total
self._set_valve_off('aspirate')
self._debug_print('aspirating...')
time.sleep(20)
self._set_all_valves_off()
data_writer.writerow(row_data)
data_file.close()
def run_calibration(self):
self._debug_print('pre setup sequence...')
valves = ['quad1','quad2','quad3','quad4','quad5','quad6']
self._set_valve_on('aspirate')
self._set_valve_on('system')
self._set_valves_on(valves)
time.sleep(10)
self._set_valve_off('system')
time.sleep(10)
self._set_valve_off('aspirate')
time.sleep(20)
self._setup()
self._set_valve_on('aspirate')
time.sleep(10)
# self._debug_print('zeroing hall effect sensors...')
# self._store_adc_values_min()
self._debug_print('zeroing balance...')
self._balance.zero()
self._debug_print('running calibration...')
timestr = time.strftime("%Y%m%d-%H%M%S")
data_file = open(timestr+'.csv','w')
data_writer = csv.writer(data_file)
header = ['fill_duration','initial_weight']
valve_adc_low = [valve+'_adc_low' for valve in valves]
header.extend(valve_adc_low)
valve_adc_high = [valve+'_adc_high' for valve in valves]
header.extend(valve_adc_high)
header.extend(valves)
data_writer.writerow(header)
duration_inc = 250
duration_max = 10000
fill_durations = range(duration_inc,duration_max+duration_inc,duration_inc)
run_count = 3
for run in range(run_count):
for fill_duration in fill_durations:
self._set_valve_on('aspirate')
time.sleep(2)
self._debug_print('fill_duration: {0}, run: {1} out of {2}'.format(fill_duration,run+1,run_count))
row_data = []
row_data.append(fill_duration)
initial_weight = self._balance.get_weight()[0]
self._debug_print('initial_weight: {0}'.format(initial_weight))
row_data.append(initial_weight)
self._set_valve_on('system')
time.sleep(2)
channels = []
adc_low_ain = []
adc_high_ain = []
for valve_key in valves:
valve = self._valves[valve_key]
channels.append(valve['channel'])
adc_low_ain.append(valve['analog_inputs']['low'])
adc_high_ain.append(valve['analog_inputs']['high'])
self._msc.set_channels_on_for(channels,fill_duration)
while not self._msc.are_all_set_fors_complete():
self._debug_print('Waiting...')
time.sleep(fill_duration/1000)
self._msc.remove_all_set_fors()
adc_values_filtered = self._get_adc_values_filtered()
adc_low_values = [adc_values_filtered[ain] for ain in adc_low_ain]
adc_high_values = [adc_values_filtered[ain] for ain in adc_high_ain]
row_data.extend(adc_low_values)
row_data.extend(adc_high_values)
self._set_valve_off('system')
time.sleep(4)
weight_prev = initial_weight
for valve in valves:
self._debug_print('Dispensing {0}'.format(valve))
self._set_valve_on(valve)
time.sleep(4)
self._set_valve_off(valve)
time.sleep(2)
weight_total = self._balance.get_weight()[0]
weight = weight_total - weight_prev
self._debug_print('{0} measured {1}'.format(valve,weight))
row_data.append(weight)
weight_prev = weight_total
self._set_valve_off('aspirate')
self._debug_print('aspirating...')
time.sleep(20)
self._set_all_valves_off()
data_writer.writerow(row_data)
data_file.close()
from mettler_toledo_device import MettlerToledoDevice
dev = MettlerToledoDevice() # Might automatically find device if one available
# if it is not found automatically, specify port directly
#dev = MettlerToledoDevice(port='/dev/ttyUSB0') # Linux specific port
dev = MettlerToledoDevice(
port='/dev/ttyACM0') # Linux specific port for abstract control model
dev = MettlerToledoDevice(
port='/dev/tty.usbmodem262471') # Mac OS X specific port
#dev = MettlerToledoDevice(port='COM3') # Windows specific port
dev.get_serial_number()
#1126493049
dev.get_balance_data()
#['XS204', 'Excellence', '220.0090', 'g']
dev.get_weight_stable()
#[-0.0082, 'g'] #if weight is stable
#None #if weight is dynamic
dev.get_weight()
#[-0.6800, 'g', 'S'] #if weight is stable
#[-0.6800, 'g', 'D'] #if weight is dynamic
dev.zero_stable()
#True #zeros if weight is stable
#False #does not zero if weight is not stable
dev.zero()
#'S' #zeros if weight is stable
#'D' #zeros if weight is dynamic
import serial
from time import gmtime, strftime
import picamera
import datetime as dt
import csv
from mettler_toledo_device import MettlerToledoDevice
dev = MettlerToledoDevice() # Might automatically find device if one available
# if it is not found automatically, specify port directly
dev = MettlerToledoDevice(port='/dev/ttyACM0') # Linux specific port
#ser = serial.Serial('/dev/ttyACM0',9600)
#weightdata = ser.readline()
weightdata = dev.get_weight()
timedata = strftime("%Y-%m-%d %H:%M:%S", gmtime())
file = open('timedata.csv','aw')
writer = csv.writer(file)
# with picamera.PiCamera() as camera:
# camera.resolution = (640, 480)
#weightdata = ser.readline()
weightdata = dev.get_weight()
timedata = strftime("%Y-%m-%d %H:%M:%S", gmtime())
print(weightdata,timedata)
camera = picamera.PiCamera(resolution=(1280, 720), framerate=24)
camera.start_preview()
camera.annotate_background = picamera.Color('black')
from mettler_toledo_device import MettlerToledoDevice dev = MettlerToledoDevice() # Might automatically find device if one available # if it is not found automatically, specify port directly #dev = MettlerToledoDevice(port='/dev/ttyUSB0') # Linux specific port dev = MettlerToledoDevice(port='/dev/ttyACM0') # Linux specific port for abstract control model dev = MettlerToledoDevice(port='/dev/tty.usbmodem262471') # Mac OS X specific port #dev = MettlerToledoDevice(port='COM3') # Windows specific port dev.get_serial_number() #1126493049 dev.get_balance_data() #['XS204', 'Excellence', '220.0090', 'g'] dev.get_weight_stable() #[-0.0082, 'g'] #if weight is stable #None #if weight is dynamic dev.get_weight() #[-0.6800, 'g', 'S'] #if weight is stable #[-0.6800, 'g', 'D'] #if weight is dynamic dev.zero_stable() #True #zeros if weight is stable #False #does not zero if weight is not stable dev.zero() #'S' #zeros if weight is stable #'D' #zeros if weight is dynamic
import io
import random
import picamera
import datetime as dt
from time import gmtime, strftime
import csv
from mettler_toledo_device import MettlerToledoDevice
dev = MettlerToledoDevice() # Might automatically find device if one available
# if it is not found automatically, specify port directly
dev = MettlerToledoDevice(port='/dev/ttyACM0') # Linux specific port
filename = dt.datetime.now().strftime('%Y-%m-%d hr%H_min%M_s%S')
filename += '.csv'
saveFile = open(filename, 'w')
#saveFile = open('timedata.csv', 'aw')
writer = csv.writer(saveFile)
# Main #
# get current weight
print('program started')
weight, units, stability = dev.get_weight()
currWeight = weight
# start picamera
camera = picamera.PiCamera()
stream = picamera.PiCameraCircularIO(camera, seconds=10)
camera.start_recording(stream, format='h264')
try:
while True:
print('waiting')
# # Annotate camera
timestamp = dt.datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')
