def channelPulseOn(self, device,channelNo):
# make sure the channelNo is valid
if channelNo < 0 or channelNo > len(BIOPAC_CHANNELS):
raise ValueError('Invalid channel number passed to the LabJackBIC channelOff method: $i' %(channelNo))
# based on which device is being used, determine the channel number to pass to the driver
channel = None
if device == BIOPAC_DEVICE_ID:
channel = BIOPAC_CHANNELS[channelNo]
elif device == EYETRACKER_DEVICE_ID:
channel = EYETRACKER_CHANNELS[channelNo]
elif device == DIGITIMER_DEVICE_ID:
channel = DIGITIMER_CHANNELS[channelNo]
else:
raise ValueError('Invalid Device ID passed to the LabJackBIC channelOff method: %i' %(device))
# set the given channel to the On state
self.sendMsg(u6.BitStateWrite(IONumber=channel, State=ON_STATE))
time.sleep(0.5)
self.sendMsg(u6.BitStateWrite(IONumber=channel, State=OFF_STATE))
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 pulse_led_task(self):
"""LED Should be off before this is called."""
if ( (self.pulse_led) & (self.backLED) ):
LJ.getFeedback(u6.BitStateWrite(3,1))
self.inject.send_command("led 1")
time.sleep(LED_PULSE_TIME)
LJ.getFeedback(u6.BitStateWrite(3,0))
self.inject.send_command("led 0")
def cmd_backLED(self, the_command):
'''Command to control IR LED backfeed.'''
commands = str.split(the_command)
if len(commands) != 2: return 'ERROR'
if commands[1] == 'on':
LJ.getFeedback(u6.BitStateWrite(3,1))
self.backLED=True
return 'backLED on'
elif commands[1] == 'off':
LJ.getFeedback(u6.BitStateWrite(3,0))
self.backLED=False
return 'backLED off'
else: return 'ERROR'
def clearChannels(self, device):
# based on which device is being used, determine the channel number to pass to the driver
channels = None
if device == BIOPAC_DEVICE_ID:
channels = BIOPAC_CHANNELS
elif device == EYETRACKER_DEVICE_ID:
channels = EYETRACKER_CHANNELS
elif device == DIGITIMER_DEVICE_ID:
channels = DIGITIMER_CHANNELS
else:
raise ValueError('Invalid Device ID passed to the LabJackBIC clearChannels method: %i' %(device))
# set the given channel to the On state
for channel in channels:
#self.jack.getFeedback(u6.BitStateWrite(IONumber=channel, State=OFF_STATE))
self.sendMsg(u6.BitStateWrite(IONumber=channel, State=OFF_STATE))
def writeBitState(self, pinNum, state):
"""
Name: EI1050.writeBitState(pinNum, state)
Desc: Device independent way to write bit state
"""
if self.deviceType == EI1050.U3: self.device.getFeedback(u3.BitStateWrite(pinNum,state))
elif self.deviceType == EI1050.U6: self.device.getFeedback(u6.BitStateWrite(pinNum,state))
elif self.deviceType == EI1050.UE9: self.device.singleIO(1, pinNum, Dir=1, State=state)
def ToggleOn(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), 1))
self.LJ.getFeedback(u6.BitStateWrite(int(IONumber), 0))
relay['status'] = 'On'
dummy=indi.set_and_send_text("SX CCD SXVR-H694","CCD_COOLER","COOLER_OFF","Off")
# Default binning is 1x1. Not need to set this as it is a CCD default.
# dummy=indi.set_and_send_float("SX CCD SXVR-H694","CCD_BINNING","VER_BIN",2)
if not os.path.exists('./images/'):
dummy=subprocess.call('mkdir ./images', shell=True)
dummy=indi.set_and_send_text("SX CCD SXVR-H694","UPLOAD_SETTINGS","UPLOAD_DIR","images")
dummy=indi.set_and_send_text("SX CCD SXVR-H694","UPLOAD_SETTINGS","UPLOAD_PREFIX","TEMPIMAGE")
try:
LJ=u6.U6()
#Need to set up fancy DAC here for the temperature control
#LJ.configIO(NumberOfTimersEnabled = 2, EnableCounter0 = 1, TimerCounterPinOffset=8)
#LJ.getFeedback(u3.Timer0Config(8), u3.Timer1Config(8)) #Sets up the dome tracking wheel
#Start off with no current:
LJ.getFeedback(u6.BitStateWrite(1,0)) #H-Bridge bit 1
LJ.getFeedback(u6.BitStateWrite(2,0)) #H-Bridge bit 2
LJ.getFeedback(u6.BitStateWrite(3,0)) #Back-LED Off
except Exception:
print 'Unable to connect to the labjack.'
class Subaru():
"""As this server class controls several pieces of hardware at once, d
defaults for this class are in blocks, in the order below...
SX CAMERA
Labjack
IPPower
Micro Maestro
break
continueRoutine = False # will revert to True if at least one component still running
for thisComponent in IntroductionComponents:
if hasattr(thisComponent, "status") and thisComponent.status != FINISHED:
continueRoutine = True
break # at least one component has not yet finished
# check for quit (the [Esc] key)
if event.getKeys(["escape"]):
core.quit()
# refresh the screen
if continueRoutine: # don't flip if this routine is over or we'll get a blank screen
win.flip()
d.getFeedback(u6.BitStateWrite( 0, 1 ) ) # FI00 (0), i.e. START RECORD Trigger
core.wait(introDuration, hogCPUperiod=0) # need hogCPUperiod < wait time
# from: https://groups.google.com/forum/#!topic/psychopy-dev/GcObydzJgyw
#-------Ending Routine "Introduction"-------
for thisComponent in IntroductionComponents:
if hasattr(thisComponent, "setAutoDraw"):
thisComponent.setAutoDraw(False)
# START THE BLOCK
CycleLoop = data.TrialHandler(nReps=noOfBlockLoops, method=u'sequential',
extraInfo=expInfo, originPath=None,
trialList=[None],
seed=None, name='CycleLoop')
def set_dio_state(self,channel, state): """sets DIO state. 1=High, 0=Low""" channel = self._check_dio_channel_input(channel) cmd = u6.BitStateWrite(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)