class Assay:
# Initialize the pumps
def __init__(self, fname, nrepeat=10, ard_port="/dev/ttyACM0", pump_port="/dev/ttyUSB0"):
self.__observers = [] # define an observer
self.step = -1 # before execution
self.conf_label = "R" + "CUCI" * nrepeat
print(self.conf_label)
self.n_session = 1 + nrepeat * 4
self.sessions = len(self.conf_label) # the number of steps
self.__construct__()
self.time_flag = pd.Series(np.zeros(self.n_session), index=list(self.conf_label))
ard_reset(ard_port)
self.ard = Arduino(ard_port)
self.ard.output([pin_LED, pin_Servo])
self.ard.setLow(pin_LED) # Initial
self.fname = fname
self.pump_init(pump_port)
def blink_start(self, nblink=5):
# give a blinking start, the LED blinks at 1 Hz
for ii in range(nblink):
self.ard.setHigh(pin_LED)
time.sleep(0.50)
self.ard.setLow(pin_LED)
time.sleep(0.50)
print(ii + 1)
millis = int(round(time.time() * 1000))
self.onset = millis
def pump_init(self, pump_port):
self.pser = serial.Serial(pump_port, 19200, timeout=0.1)
print("connected to", self.pser.name)
pumps = new_era.find_pumps(self.pser)
self.pump = pumps[0]
self.infuse = False
new_era.set_diameter(self.pser, self.pump, dia_1ml)
new_era.set_direct(self.pser, self.pump, 1)
new_era.set_rate(self.pser, self.pump, flowrate)
def register_observer(self, observer):
self.__observers.append(observer)
def notify_observers(self, *args, **kwargs):
for observer in self.__observers:
observer.notify(self, *args, **kwargs)
def __construct__(self):
# construct the configuration array
self.CS_config = np.zeros([self.n_session, 4])
ii = 0
for ch in self.conf_label:
if ch == "R":
self.CS_config[ii] = CONFIG_REST
elif ch == "C":
self.CS_config[ii] = CONFIG_CS
elif ch == "U":
self.CS_config[ii] = CONFIG_US
else:
self.CS_config[ii] = CONFIG_INTER
ii += 1
# then, we need to update duration of intersessions
inter_pos = self.CS_config[:, 0] < 0 # take out the positions of intersessions, a boolean array
inter_dur = self.CS_config[inter_pos, 0]
self.CS_config[inter_pos, 0] = np.random.randint(40, 70, size=len(inter_dur))
print(self.CS_config)
self.duration = self.CS_config[:, 0].sum() / 60.0
print("Total experimental time: %4.1f min" % self.duration)
def blink(self, duration, freq=2):
# blink the LED
# duration: the duration of blinking
nblink = int(duration * freq)
thp = 1 / (freq * 2.0) # half-period
for ii in range(nblink):
self.ard.setHigh(pin_LED)
time.sleep(thp)
self.ard.setLow(pin_LED)
time.sleep(thp)
def run_step(self, sblink=False):
millis = int(round(time.time() * 1000))
self.step += 1
self.time_flag[self.step] = millis
self.notify_observers(self.step)
config_list = self.CS_config[self.step]
print(config_list[0])
# take the row
# turn on or off all the stimuli
# turn on or off the delivery
if config_list[2] == 0:
if self.infuse == True:
new_era.stop_pump(self.pser, self.pump)
self.infuse = False
elif config_list[2] == 1:
if self.infuse == False:
new_era.set_rate(self.pser, self.pump, flowrate)
new_era.run_all(self.pser)
self.infuse = True
if config_list[1] == 0:
self.ard.setLow(pin_LED) # keep the LED off
time.sleep(config_list[0])
elif config_list[1] == 1:
if sblink:
self.blink(config_list[0])
else:
self.ard.setHigh(pin_LED)
time.sleep(config_list[0])
# insert or retract the feeding tube
# if config_list[3] == 0:
# self.ard.analogWrite(pin_Servo, 0)
# elif config_list[3] == 0:
# self.ard.analogWrite(pin_Servo, 80)
# time.sleep(config_list[0])
# self.terminate_step()
def terminate_step(self):
# terminate a step
self.ard.setLow(pin_LED)
self.ard.analogWrite(pin_Servo, 0)
new_era.stop_pump(self.pser, self.pump)
def run_through(self, sblink=False):
self.blink_start()
self.step = -1
ii = 0
for ii in range(self.n_session):
self.run_step(sblink)
print("The" + str(ii) + "th session.")
# def shuffle_steps(self):
# # shuffle the steps of
# CS_total = np.inner(self.CS_config[:,0], self.CS_config[:,1]) # inner product of the first two columns, total duration of CS
# US_total = np.inner(self.CS_config[:,0], self.CS_config[:,2]) # total duration of US
# time_total = self.CS_config[:,0].sum() # The total amount of time should be equal
#
# # use 10 seconds as a unit of the
# NC_chunk = np.round(CS_total/10.).astype('int')
# NU_chunk = np.round(US_total/10.).astype('int')
# Total_chunk = np.round(time_total/10.).astype('int')
#
# shuff_LED = random_split(NC_chunk)
#
def close(self):
# destruct the class
self.ard.setLow(pin_LED)
self.ard.close()
np.save("../Data/" + self.fname, self.time_flag)
pd.Series.to_csv(self.time_flag, "../Data/" + self.fname + ".csv")
print("Arduino port closed. ")
class Assay():
# Initialize the pumps
def __init__(self,
fname,
nrepeat=10,
ard_port='/dev/ttyACM0',
pump_port='/dev/ttyUSB0'):
self.__observers = [] # define an observer
self.step = -1 # before execution
self.conf_label = 'R' + 'CUCI' * nrepeat
print(self.conf_label)
self.n_session = 1 + nrepeat * 4
self.sessions = len(self.conf_label) # the number of steps
self.__construct__()
self.time_flag = pd.Series(np.zeros(self.n_session),
index=list(self.conf_label))
ard_reset(ard_port)
self.ard = Arduino(ard_port)
self.ard.output([pin_LED, pin_Servo])
self.ard.setLow(pin_LED) # Initial
self.fname = fname
self.pump_init(pump_port)
def blink_start(self, nblink=5):
# give a blinking start, the LED blinks at 1 Hz
for ii in range(nblink):
self.ard.setHigh(pin_LED)
time.sleep(0.50)
self.ard.setLow(pin_LED)
time.sleep(0.50)
print(ii + 1)
millis = int(round(time.time() * 1000))
self.onset = millis
def pump_init(self, pump_port):
self.pser = serial.Serial(pump_port, 19200, timeout=.1)
print('connected to', self.pser.name)
pumps = new_era.find_pumps(self.pser)
self.pump = pumps[0]
self.infuse = False
new_era.set_diameter(self.pser, self.pump, dia_1ml)
new_era.set_direct(self.pser, self.pump, 1)
new_era.set_rate(self.pser, self.pump, flowrate)
def register_observer(self, observer):
self.__observers.append(observer)
def notify_observers(self, *args, **kwargs):
for observer in self.__observers:
observer.notify(self, *args, **kwargs)
def __construct__(self):
# construct the configuration array
self.CS_config = np.zeros([self.n_session, 4])
ii = 0
for ch in self.conf_label:
if (ch == 'R'):
self.CS_config[ii] = CONFIG_REST
elif (ch == 'C'):
self.CS_config[ii] = CONFIG_CS
elif (ch == 'U'):
self.CS_config[ii] = CONFIG_US
else:
self.CS_config[ii] = CONFIG_INTER
ii += 1
# then, we need to update duration of intersessions
inter_pos = self.CS_config[:,
0] < 0 # take out the positions of intersessions, a boolean array
inter_dur = self.CS_config[inter_pos, 0]
self.CS_config[inter_pos, 0] = np.random.randint(40,
70,
size=len(inter_dur))
print(self.CS_config)
self.duration = self.CS_config[:, 0].sum() / 60.0
print('Total experimental time: %4.1f min' % self.duration)
def blink(self, duration, freq=2):
# blink the LED
# duration: the duration of blinking
nblink = int(duration * freq)
thp = 1 / (freq * 2.0) # half-period
for ii in range(nblink):
self.ard.setHigh(pin_LED)
time.sleep(thp)
self.ard.setLow(pin_LED)
time.sleep(thp)
def run_step(self, sblink=False):
millis = int(round(time.time() * 1000))
self.step += 1
self.time_flag[self.step] = millis
self.notify_observers(self.step)
config_list = self.CS_config[self.step]
print(config_list[0])
# take the row
# turn on or off all the stimuli
# turn on or off the delivery
if config_list[2] == 0:
if (self.infuse == True):
new_era.stop_pump(self.pser, self.pump)
self.infuse = False
elif config_list[2] == 1:
if (self.infuse == False):
new_era.set_rate(self.pser, self.pump, flowrate)
new_era.run_all(self.pser)
self.infuse = True
if config_list[1] == 0:
self.ard.setLow(pin_LED) # keep the LED off
time.sleep(config_list[0])
elif config_list[1] == 1:
if sblink:
self.blink(config_list[0])
else:
self.ard.setHigh(pin_LED)
time.sleep(config_list[0])
# insert or retract the feeding tube
# if config_list[3] == 0:
# self.ard.analogWrite(pin_Servo, 0)
# elif config_list[3] == 0:
# self.ard.analogWrite(pin_Servo, 80)
# time.sleep(config_list[0])
# self.terminate_step()
def terminate_step(self):
# terminate a step
self.ard.setLow(pin_LED)
self.ard.analogWrite(pin_Servo, 0)
new_era.stop_pump(self.pser, self.pump)
def run_through(self, sblink=False):
self.blink_start()
self.step = -1
ii = 0
for ii in range(self.n_session):
self.run_step(sblink)
print('The' + str(ii) + 'th session.')
# def shuffle_steps(self):
# # shuffle the steps of
# CS_total = np.inner(self.CS_config[:,0], self.CS_config[:,1]) # inner product of the first two columns, total duration of CS
# US_total = np.inner(self.CS_config[:,0], self.CS_config[:,2]) # total duration of US
# time_total = self.CS_config[:,0].sum() # The total amount of time should be equal
#
# # use 10 seconds as a unit of the
# NC_chunk = np.round(CS_total/10.).astype('int')
# NU_chunk = np.round(US_total/10.).astype('int')
# Total_chunk = np.round(time_total/10.).astype('int')
#
# shuff_LED = random_split(NC_chunk)
#
def close(self):
# destruct the class
self.ard.setLow(pin_LED)
self.ard.close()
np.save('../Data/' + self.fname, self.time_flag)
pd.Series.to_csv(self.time_flag, '../Data/' + self.fname + '.csv')
print("Arduino port closed. ")
from arduino import Arduino
import time
b = Arduino('/dev/ttyUSB0')
pin = 9
#declare output pins as a list/tuple
b.output([pin])
brightness = 0
fadeAmount = 3
b.output([pin])
while (True):
b.analogWrite(pin, brightness)
time.sleep(0.05)
print b.analogRead(pin)
brightness = brightness + fadeAmount
if (brightness == 0 or brightness == 255):
fadeAmount = -fadeAmount
from arduino import Arduino
from arduino import mode
bot = Arduino("COM5")
bot.pinMode(6, mode.OUT)
bot.pinMode(7, mode.OUT)
_in = ''
while _in != 'q':
_in = input()
if _in == 'w':
bot.analogWrite(6, 50)
bot.digitalWrite(7, 0)
if _in == 'd':
bot.analogWrite(6, 50)
bot.digitalWrite(7, 1)
if _in == 's':
bot.analogWrite(6, 0)
bot.digitalWrite(7, 0)
if _in == 'u':
print(bot.sonicRead(10, 8))
print(bot.sonicRead(10, 8))
print(bot.sonicRead(10, 8))
from arduino import Arduino
import time
b = Arduino('/dev/ttyUSB0')
pin = 9
#declare output pins as a list/tuple
b.output([pin])
brightness = 0
fadeAmount = 3
b.output([pin])
while (True):
b.analogWrite(pin, brightness)
time.sleep(0.05)
print b.analogRead(pin)
brightness = brightness + fadeAmount
if (brightness == 0 or brightness == 255):
fadeAmount = -fadeAmount
ard.analogWrite(5, A[i])
if aller == 0: V.append(ard.analogRead(1) * m / 1023)
msleep(delay)
stop()
ard.digitalWrite(5, ard.LOW)
ard.end()
plt.plot(X, V, "o")
plt.show()
'''
print(ard.analogRead(1))
ard.end()
'''
for i in range(15):
alpha = sin()
alpha = 0.5
ard.analogWrite(5, floor(alpha * 255))
freq = 2
T = 1./freq
for i in range(5):
right()
msleep((T / 2) * 1000)
left()
msleep((T / 3) * 1000)
