def connect(self):
iscompleted = False
nbattempts = 0
while not(iscompleted) and nbattempts<1000:#while iscompleted is false and nb<1000 will be doing this constantly
try:
nbattempts = nbattempts +1
#print ('Attempt nb ' + str(nbattempts))
self.jack = u6.U6()
iscompleted = True
except:
print('Pb with labjack initialisation nb '+ str(nbattempts))
time.sleep(0.01)
if not(iscompleted): #if iscompleted equals false which would give true he
raise IOError('Labjack could not connect')
# the FIO0-FIO7 inputs are flexible, meaning they can be analog or digital, so ensure
# they are all digital by sending a zero for the FIO Analog parameter
# self.jack.configIO(FIOAnalog = 0)
# now set all the channels to output, since each digital IO channel supports input and output
for channel in BIOPAC_CHANNELS:
#self.jack.getFeedback(u6.BitDirWrite(channel,DIGITAL_CHANNEL_DIRECTION_OUTPUT))
self.sendMsg(u6.BitDirWrite(channel,DIGITAL_CHANNEL_DIRECTION_OUTPUT))
for channel in EYETRACKER_CHANNELS:
#self.jack.getFeedback(u6.BitDirWrite(channel,DIGITAL_CHANNEL_DIRECTION_OUTPUT))
self.sendMsg(u6.BitDirWrite(channel,DIGITAL_CHANNEL_DIRECTION_OUTPUT))
for channel in DIGITIMER_CHANNELS:
#self.jack.getFeedback(u6.BitDirWrite(channel, DIGITAL_CHANNEL_DIRECTION_OUTPUT))
self.sendMsg(u6.BitDirWrite(channel, DIGITAL_CHANNEL_DIRECTION_OUTPUT))
def acquireStack(cam, nFrames, downscaleTuple, animal, outdir):
""" Get an image stack from the camera.
Args:
cam: (TIS_CAM) initialized camera object
nFrames: (int) number of frames to acquire
sendCounter (bool) whether or not to send strobe signal
downscaleTuple: (tuple) downscale factor in (z, x, y), e.g. (1, 2, 2) for 2x downscale
animal: (str) animal ID, used for output naming
outdir: (str) path to output directory
Returns:
stack: (np.ndarray) image stack in (z, x, y)
"""
# setup the labjack
dioPortNum = 0 # FIO0
u6Obj = u6.U6()
u6Obj.configU6()
u6Obj.configIO()
u6Obj.setDOState(dioPortNum, state=0)
stack = []
cam.StartLive(1)
# Not using 191001: strobe code below.
# if sendCounter:
# _set_and_check(cam.SetPropertyValue, 'GPIO', 'GP Out', 1)
# _set_and_check(cam.PropertyOnePush, 'GPIO', 'Write')
t_start = time.time()
for iF in np.arange(nFrames):
pulseLengthTicks = int(1000/64)
u6Obj.getFeedback(u6.BitDirWrite(dioPortNum, 1),
u6.BitStateWrite(dioPortNum, State=1),
u6.WaitShort(pulseLengthTicks),
u6.BitStateWrite(dioPortNum, State=0))
cam.SnapImage()
im = cam.GetImage() # appears to have three identical(?) frames
im = np.mean(im, axis=2).astype('int16')
stack.append(im) # averaging to one frame
# Not using 191001: strobe code below.
# if sendCounter:
# _set_and_check(cam.SetPropertyValue, 'GPIO', 'GP Out', 0)
# _set_and_check(cam.PropertyOnePush, 'GPIO', 'Write')
cam.StopLive()
print('Done. Downsizing and saving.')
stack = np.r_[stack]
stack = transform.downscale_local_mean(stack, downscaleTuple)
stack = stack.astype('int16')
timeStr = time.strftime("_%y%m%d_%H-%M-%S", time.localtime(t_start))
outfile = os.path.join(outdir, '{}{}.tif'.format(animal, timeStr))
tfl.imsave(outfile, stack)
nFrames = stack.shape[0]
print('Saved {} frames to {}'.format(nFrames, outfile))
return stack
def ToggleOff(self, relay, name):
if relay['key'].startswith('E'):
IONumber = int(relay['key'][3:])+8
elif relay['key'].startswith('C'):
IONumber = int(relay['key'][3:])+16
else:
IONumber = int(relay['key'][3:])
if not self.DevFlag:
self.LJ.getFeedback(u6.BitDirWrite(int(IONumber), 0))
relay['status'] = 'Off'
def __init__(self, device, autoUpdate=True, enablePinNum=-1, dataPinNum = -1, clockPinNum = -1, shtOptions = 0xc0):
self.device = device
self.autoUpdate = autoUpdate
self.dataPinNum = dataPinNum
self.clockPinNum = clockPinNum
self.shtOptions = shtOptions
self.enablePinNum = enablePinNum
self.curState = { 'StatusReg' : None, 'StatusCRC' : None, 'Temperature' : None, 'TemperatureCRC' : None, 'Humidity' : None, 'HumidityCRC' : None }
# Determine device type
if self.device.__class__.__name__ == EI1050.U3_STRING: self.deviceType = EI1050.U3
elif self.device.__class__.__name__ == EI1050.U6_STRING: self.deviceType = EI1050.U6
elif self.device.__class__.__name__ == EI1050.UE9_STRING: self.deviceType = EI1050.UE9
else:
raise TypeError('Invalid device passed. Can not get default values.')
# If not specified otherwise, use class default for the data pin number
if self.enablePinNum == -1:
if self.deviceType == EI1050.U3: self.enablePinNum = EI1050.U3_DEFAULT_ENABLE_PIN_NUM
elif self.deviceType == EI1050.U6: self.enablePinNum = EI1050.U6_DEFAULT_ENABLE_PIN_NUM
elif self.deviceType == EI1050.UE9: self.enablePinNum = EI1050.UE9_DEFAULT_ENABLE_PIN_NUM
else:
raise TypeError('Invalid device passed. Can not get default values.')
# If not specified otherwise, use class default for the data pin number
if self.dataPinNum == -1:
if self.deviceType == EI1050.U3: self.dataPinNum = EI1050.U3_DEFAULT_DATA_PIN_NUM
elif self.deviceType == EI1050.U6: self.dataPinNum = EI1050.U6_DEFAULT_DATA_PIN_NUM
elif self.deviceType == EI1050.UE9: self.dataPinNum = EI1050.UE9_DEFAULT_DATA_PIN_NUM
else:
raise TypeError('Invalid device passed. Can not get default values.')
# If not specified otherwise, use class default for the clock pin number
if self.clockPinNum == -1:
if self.deviceType == EI1050.U3: self.clockPinNum = EI1050.U3_DEFAULT_CLOCK_PIN_NUM
elif self.deviceType == EI1050.U6: self.clockPinNum = EI1050.U6_DEFAULT_CLOCK_PIN_NUM
elif self.deviceType == EI1050.UE9: self.clockPinNum = EI1050.UE9_DEFAULT_CLOCK_PIN_NUM
else:
raise TypeError('Invalid device passed. Can not get default values.')
# Set U3 pins
if self.deviceType == EI1050.U3:
self.device.configIO(FIOAnalog = EI1050.FIO_PIN_STATE)
# Set to write out
if self.deviceType == EI1050.U3: self.device.getFeedback(u3.BitDirWrite(self.enablePinNum,1))
elif self.deviceType == EI1050.U6: self.device.getFeedback(u6.BitDirWrite(self.enablePinNum,1))
def __init__(self):
super().__init__()
self.grid_rowconfigure(0, w=1)
self.grid_columnconfigure(0, w=1)
self.grid_columnconfigure(1, w=1)
self.Dict = {
'AIN0' : 'Failure',
'AIN1' : 'Low Speed',
'AIN2' : 'Frequency',
'AIN3' : 'Supply Current',
'AIN4' : 'Driving Frequency',
'FIO3' : 'Error Reset',
'FIO4' : 'On/Off',
'FIO5' : 'Low Speed Activate',
'FIO6' : 'Enable Override',
'DAC0' : 'Direction',
'FIO0' : 'Frequency Driver',
'FIO1' : 'Timer Stop',
'AIN5' : 'Inner Limit Switch',
'AIN6' : 'Outer Limit Switch',
}
s = ttk.Style()
s.configure('.', font=('Times', 18))
s.configure('Header.TLabel', font=('Times', 24))
self.DevFlag = False
try:
self.LJ = u6.U6()
self.LJ.getCalibrationData()
for i in range(20):
self.LJ.getFeedback(u6.BitDirWrite(i, 0)) # output
self.LJ.configTimerClock(TimerClockBase=3, TimerClockDivisor=2)
self.LJ.configIO(NumberTimersEnabled=2)
except:
self.DevFlag = True
print('Dev')
self.turbo = TurboController(self)
self.turbo.grid(row=0, column=0, sticky='news')
self.stepper = StepperController(self)
self.stepper.grid(row=0, column=1, sticky='news')
def set_dio_dir(self, channel, state): """sets DIO direction. 0=Input, 1=Output""" channel = self._check_dio_channel_input(channel) cmd = u6.BitDirWrite(channel, state) self.d.getFeedback(cmd)
#! /usr/bin/python import u6 import time import numpy d = u6.U6() # open LabJack U6 d.getCalibrationData() # get calibration info for U6 runtime=[] for i in range(0,2): d.getFeedback(u6.BitDirWrite(0,1)) d.getFeedback(u6.BitDirWrite(1,0)) t1 = time.time() d.getFeedback(u6.BitStateWrite(0,1)) #ain = d.getAIN(0) d.getFeedback(u6.BitStateRead(1)) runtime.append(time.time()-t1) print numpy.mean(runtime)
