def inject(direction, volume, **params):
WaitTime = 0.0055 #wait between steps to make 1mL/min spead
if "speed" in params:
coeff = float(params['speed']) #speed in mL/min
WaitTime = WaitTime / coeff
sul10 = 10.71 / 0.976698 / 1.038 #number of steps in 1 uL
steps = int(float(volume) * sul10)
print("Starting {} ({}ul, {} steps)".format(direction, volume, steps))
gpio.setmode(gpio.BCM)
gpio.setup(PIN_STEP, gpio.OUT)
gpio.setup(PIN_DIR, gpio.OUT)
if direction == 'out':
homeinc = -1 #increment coefficient to modify home positions
gpio.output(PIN_DIR, True)
elif direction == 'in':
homeinc = 1
gpio.output(PIN_DIR, False)
else:
print("Attention: wrong direction")
StepCounter = 0
while StepCounter < steps:
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
bufferSteps = StepCounter
time.sleep(WaitTime)
gpio.cleanup()
#temp() ##measuring temperature in the end of a cycle
lastvalue = int(config.readvalue('antibody'))
newvalue = lastvalue + homeinc * StepCounter
config.writevalue('antibody', str(newvalue))
def home(**params):
WaitTime = 0.0055 / 5 #wait between steps to make 5mL/min spead
if "speed" in params:
coeff = float(params['speed']) #speed in mL/min
WaitTime = WaitTime / coeff
steps = int(config.readvalue('antibody'))
print("Started homing antibody syringe ({} steps)".format(steps))
config.writevalue('antibody', '0')
gpio.setmode(gpio.BCM)
gpio.setup(PIN_STEP, gpio.OUT)
gpio.setup(PIN_DIR, gpio.OUT)
gpio.output(PIN_DIR, True) #always out syringe press
StepCounter = 0
if steps <= 0:
steps *= -1 #if negative, do in
gpio.output(PIN_DIR, False)
else:
gpio.output(PIN_DIR, True)
while StepCounter < steps:
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
bufferSteps = StepCounter
time.sleep(WaitTime)
gpio.cleanup()
def move(direction):
if not (direction == 'up' or direction == 'down'):
print("ATTENTION: wrong parameter for needle movement (only 'up' and 'down' are allowed; your input: "+direction)
input()
WaitTime = 0.0005
steps = 200*30 #1mm = 200 steps; 40 mm overall
current_position = config.readvalue('needle')
if direction == current_position:
inp = ""
while not (inp == "OK"):
print ("ATTENTION: needle seems to be already in {} position (Ctrl+C to stop execution)".format (direction))
inp = input()
print("Needle move ({})".format(direction.capitalize()))
gpio.setmode(gpio.BCM)
gpio.setup(PIN_STEP, gpio.OUT) #steps
gpio.setup(PIN_DIR, gpio.OUT) #direction
config.writevalue('needle',direction)
if direction == 'down':
gpio.output(PIN_DIR, False)
elif direction == 'up':
gpio.output(PIN_DIR, True)
StepCounter = 0
while StepCounter < steps:
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
time.sleep(WaitTime)
gpio.cleanup()
def prime (direction, volume, **params): #same as inject, but without stirring
WaitTime = 0.0055 #wait between steps to make 1mL/min spead
if "speed" in params:
coeff = float(params['speed']) #speed in mL/min
WaitTime = WaitTime/coeff
sul10 = 182.14/1.495*0.985 #number of steps in 1 uL
steps = int(float(volume)*sul10)
gpio.setmode(gpio.BCM)
gpio.setup(PIN_DIR, gpio.OUT)
gpio.setup(PIN_STEP, gpio.OUT)
if direction == 'out':
gpio.output(PIN_DIR, True)
homeinc = -1
elif direction == 'in':
gpio.output(PIN_DIR, False)
homeinc = 1
StepCounter = 0
print("Starting reagent {} prime ({}uL, {} steps)".format(direction,int(volume),steps))
while StepCounter < steps:
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
time.sleep(WaitTime)
lastvalue = int(config.readvalue('reagent')) #reading last position in steps
newvalue = lastvalue + homeinc*StepCounter
config.writevalue('reagent',str(newvalue))
gpio.cleanup()
def home(**params):
WaitTime = 0.00324/5 #wait between steps to make 5mL/min speed
if "speed" in params:
coeff = float(params['speed']) #speed in mL/min
WaitTime = WaitTime/coeff
steps = int(config.readvalue('reagent'))
print("Started homing reagent syringe ({} steps)".format(steps))
config.writevalue('reagent','0')
gpio.setmode(gpio.BCM)
gpio.setup(PIN_DIR, gpio.OUT)
gpio.setup(PIN_STEP, gpio.OUT)
if steps >= 0:
gpio.output(PIN_DIR, True) ##in direction
else:
steps = steps * (-1)
gpio.output(PIN_DIR, False) ##out direction
StepCounter = 0
while StepCounter < steps:
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
bufferSteps = StepCounter
time.sleep(WaitTime)
# print("Ended homing reagent syringe")
gpio.cleanup()
def main(win):
global dir
global speed
WaitTime = 0.0055 / speed #wait between steps to make 1mL/min spead
sul10 = 10.71 / 0.976698 / 1.038 #number of steps in 1 uL
maxsteps = 12000 * sul10 ##max volume of 15 mL
gpio.setmode(gpio.BCM)
gpio.setup(PIN_DIR, gpio.OUT)
gpio.setup(PIN_STEP, gpio.OUT)
if dir == "in" or dir == "IN":
gpio.output(PIN_DIR, False)
homeinc = 1 #for config (direction of steps)
elif dir == "out" or dir == "OUT":
gpio.output(PIN_DIR, True)
homeinc = -1
else:
print(
"Wrong direction provided (should be IN or OUT). Starting IN direction."
)
dir = "IN"
gpio.output(PIN_DIR, False)
homeinc = 1
win.nodelay(True)
key = ""
win.clear()
outmessage = "Measuring reactor volume (press C to measure or E to stop). Direction: {}.\n".format(
dir)
win.addstr(outmessage)
StepCounter = 0
while StepCounter < maxsteps:
try:
key = win.getkey()
win.clear()
win.addstr(outmessage)
if key == "c" or key == "C":
win.clear()
outmessage += "[{}] Current volume: {}uL\n".format(
datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
str(int(StepCounter / sul10)))
win.addstr(outmessage)
if key == "e" or key == "E":
outmessage += "[{}] Final volume: {}uL".format(
datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
str(int(StepCounter / sul10)))
break
except Exception as e:
pass
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
time.sleep(WaitTime)
gpio.cleanup()
lastvalue = int(
config.readvalue('antibody')) #reading last position in steps
newvalue = lastvalue + homeinc * StepCounter
config.writevalue('antibody', str(newvalue))
return outmessage
def inject (direction, volume, **params):
WaitTime = 0.00324 #wait between steps to make 100uL/min speed
if "speed" in params:
coeff = float(params['speed']) #speed in 0.1mL/min
WaitTime = WaitTime/coeff
sul10 = 182.14/1.495*0.985 #number of steps in 1 uL
steps = int(float(volume)*sul10)
print("Mixing started")
print("Starting reagent {} injection ({}uL, {} steps)".format(direction,round(volume,1),steps))
gpio.setmode(gpio.BCM)
gpio.setup(PIN_DIR, gpio.OUT)
gpio.setup(PIN_STEP, gpio.OUT)
##routine of mixing + stopping all other motors
gpio.setup(14,gpio.OUT)
gpio.output(14, False)
gpio.setup(16,gpio.OUT)
gpio.output(16, False)
#strating agitation
gpio.setup(PIN_MIX, gpio.OUT)
if direction == 'out':
gpio.output(PIN_DIR, True)
homeinc = -1
elif direction == 'in':
homeinc = 1
gpio.output(PIN_DIR, False)
StepCounter = 0
while StepCounter < steps:
gpio.output(PIN_STEP, True)
gpio.output(PIN_STEP, False)
StepCounter += 1
time.sleep(WaitTime)
lastvalue = int(config.readvalue('reagent')) #reading last position in steps
newvalue = lastvalue + homeinc*StepCounter
config.writevalue('reagent',str(newvalue))
time.sleep(post_inj_mix)
print("Mixing ended")
gpio.cleanup()