def StartExposure(self):
self.nReadOut = 0
self._n_frames_leftover = 0
self._frameRate = self.getCamPropValue('INTERNAL FRAME RATE')
# From parent
HamamatsuDCAM.StartExposure(self)
# Allocate buffers (2 seconds of buffers)
self.bs = int(max(int(2.0 * self._frameRate), 1))
self.checkStatus(
dcam.dcambuf_alloc(self.handle, ctypes.c_int32(self.bs)),
"dcambuf_alloc")
self._image_frame_bytes = int(self.getCamPropValue('IMAGE FRAMEBYTES'))
if self._mode == self.MODE_SOFTWARE_TRIGGER:
self.setCamPropValue('TRIGGER SOURCE',
DCAMPROP_TRIGGERSOURCE_SOFTWARE)
else:
#continuous mode, internal trigger
self.setCamPropValue('TRIGGER SOURCE',
DCAMPROP_TRIGGERSOURCE_INTERNAL)
eventLog.logEvent('StartAq', '')
# Start the capture
#print str(self.getCamPropValue('SENSOR MODE'))
#TODO - this is probably where we would need to deal with continuous vs single shot modes.
self.checkStatus(
dcam.dcamcap_start(self.handle, DCAMCAP_START_SEQUENCE),
"dcamcap_start")
self._aq_active = True
return 0
def OnFrame(self, frameNum):
if frameNum > self.startFrame:
fn = int(
floor((frameNum - self.startFrame) / self.dwellTime) %
len(self.zPoss))
if not fn == self.pos:
self.pos = fn
#self.piezo.MoveTo(self.piezoChan, self.zPoss[self.pos])
scope.state.setItem(self.piezoName,
self.zPoss[self.pos],
stopCamera=self.require_camera_restart)
eventLog.logEvent(
'ProtocolFocus',
'%d, %3.3f' % (frameNum, self.zPoss[self.pos]))
TaskListProtocol.OnFrame(self, frameNum)
if frameNum == -1:
# Make move to initial position **after** all other -1 setup tasks have been performed (in super-class
# OnFrame() call above).
# This is currently required as a work-around on the HTSMS system which needs to unlock the focus
# lock before changing focus (issue 766).
scope.state.setItem(self.piezoName,
self.zPoss[self.pos],
stopCamera=self.require_camera_restart)
eventLog.logEvent('ProtocolFocus',
'%d, %3.3f' % (-1, self.zPoss[self.pos]))
def StartExposure(self):
eventLog.logEvent('StartAq', '')
self.compT.StartExp()
#self.compTOld = self.compTCur
#self.compTCur = compThread(self.XVals, self.YVals, (self.zPiezo.GetPos() - self.zOffset)*1e3,self.fluors, self.noiseMaker, laserPowers=self.laserPowers, intTime=self.intTime*1e-3)
#self.compTCur.start()
return 0
def StartExposure(self):
eventLog.logEvent('StartAq', '')
self.compT.StartExp()
#self.compTOld = self.compTCur
#self.compTCur = compThread(self.XVals, self.YVals, (self.zPiezo.GetPos() - self.zOffset)*1e3,self.fluors, self.noiseMaker, laserPowers=self.laserPowers, intTime=self.intTime*1e-3)
#self.compTCur.start()
return 0
def start(self):
self.running = True
#pixels = np.array(pixels)
# if np.isscalar(self.pixels):
# #constant - use as number of pixels
# #center on current piezo position
# self.xp = self.pixelsize*np.arange(-self.pixels/2, self.pixels/2 +1) + self.xpiezo[0].GetPos(self.xpiezo[1])
# self.yp = self.pixelsize*np.arange(-self.pixels/2, self.pixels/2 +1) + self.ypiezo[0].GetPos(self.ypiezo[1])
# elif np.isscalar(self.pixels[0]):
# #a 1D array - numbers in either direction centered on piezo pos
# self.xp = self.pixelsize*np.arange(-self.pixels[0]/2, self.pixels[0]/2 +1) + self.xpiezo[0].GetPos(self.xpiezo[1])
# self.yp = self.pixelsize*np.arange(-self.pixels[1]/2, self.pixels[1]/2 +1) + self.ypiezo[0].GetPos(self.ypiezo[1])
# else:
# #actual pixel positions
# self.xp = self.pixels[0]
# self.yp = self.pixels[1]
#
# self.nx = len(self.xp)
# self.ny = len(self.yp)
#
# self.imsize = self.nx*self.ny
self.genCoords()
self.callNum = 0
if self.avg:
self.image = np.zeros((self.nx, self.ny))
#self.ds = scope.frameWrangler.currentFrame
self.view = View3D(self.image)
#self.xpiezo[0].MoveTo(self.xpiezo[1], self.xp[0])
#self.ypiezo[0].MoveTo(self.ypiezo[1], self.yp[0])
#self.scope.SetPos(x=self.xp[0], y = self.yp[0])
self.scope.frameWrangler.stop()
self.scope.state.setItems({'Positioning.x' : self.xp[0], 'Positioning.y' : self.yp[0]}, stopCamera = True)
if self.trigger:
self.scope.cam.SetAcquisitionMode(self.scope.cam.MODE_SOFTWARE_TRIGGER)
self.scope.frameWrangler.start()
#if self.sync:
# while not self.xpiezo[0].IsOnTarget(): #wait for stage to move
# time.sleep(.05)
if self.evtLog:
eventLog.logEvent('ScannerXPos', '%3.6f' % self.xp[0])
eventLog.logEvent('ScannerYPos', '%3.6f' % self.yp[0])
#self.scope.frameWrangler.WantFrameNotification.append(self.tick)
self.scope.frameWrangler.onFrame.connect(self.tick, dispatch_uid=self._uuid)
if self.trigger:
self.scope.cam.FireSoftwareTrigger()
def OnFinish(self):
while not self.listPos >= len(self.taskList):
t = self.taskList[self.listPos]
self.listPos += 1
t.what(*t.params)
eventLog.logEvent(
'ProtocolTask', '%s, ' % (t.what.__name__, ) +
', '.join(['%s' % p for p in t.params]))
def _Loop(self):
while self.loopActive:
self.lock.acquire()
try:
# check position
time.sleep(self._update_rate)
self.position[0] = float(gcs.qPOS(self.id, b'A')[0])+ self.osen
self.errCode = int(gcs.qERR(self.id))
if not self.errCode == 0:
logging.info(('Stage Error: %d' % self.errCode))
# print self.targetPosition, self.stopMove
if not np.all(self.targetPosition == self.lastTargetPosition):
# update our target position
pos = np.clip(self.targetPosition, 0, self.max_travel)
gcs.MOV(self.id, b'A', pos[:1])
self.lastTargetPosition = pos.copy()
# print('p')
# logging.debug('Moving piezo to target: %f' % (pos[0],))
if np.allclose(self.position, self.targetPosition, atol=self._target_tol):
if not self.onTarget:
logEvent('PiezoOnTarget', '%.3f' % self.position[0], time.time())
self.onTarget = True
# check to see if we're on target
#self.ser_port.write('ONT? A\n')
#self.ser_port.flushOutput()
#time.sleep(0.005)
#res1 = self.ser_port.readline()
#if res1 == '':
# time.sleep(.5)
# res1 = self.ser_port.readline()
#try:
# self.onTarget = int(res1) == 1
#except ValueError:
# self.onTarget = False
# logging.exception('Value error on response from ONT')
# time.sleep(.1)
except IndexError:
print('IndexException')
finally:
self.stopMove = False
self.lock.release()
# close port on loop exit
gcs.CloseConnection(self.id)
logging.info("Piezo USB connection closed")
def OnFrame(self, frameNum):
if frameNum > self.startFrame:
fn = floor((frameNum - self.startFrame)/self.dwellTime) % len(self.zPoss)
if not fn == self.pos:
self.pos = fn
self.piezo.MoveTo(self.piezoChan, self.zPoss[self.pos])
eventLog.logEvent('ProtocolFocus', '%d, %3.3f' % (frameNum, self.zPoss[self.pos]))
TaskListProtocol.OnFrame(self, frameNum)
def OnFrame(self, frameNum):
while not self.listPos >= len(
self.taskList) and frameNum >= self.taskList[
self.listPos].when:
t = self.taskList[self.listPos]
t.what(*t.params)
eventLog.logEvent(
'ProtocolTask', '%d, %s, ' % (frameNum, t.what.__name__) +
', '.join(['%s' % p for p in t.params]))
self.listPos += 1
def StartExposure(self):
self.__selectCamera()
self._GetCCDTemp()
self._GetAcqTimings()
self._GetBufferSize()
eventLog.logEvent('StartAq', '')
ret = ac.StartAcquisition()
if not ret == ac.DRV_SUCCESS:
raise RuntimeError('Error starting acquisition: %s' % ac.errorCodes[ret])
return 0
def StartExposure(self):
#make sure no acquisiton is running
self.StopAq()
self._temp = self.SensorTemperature.getValue()
self._frameRate = self.FrameRate.getValue()
eventLog.logEvent('StartAq', '')
self._flush()
self.InitBuffers()
self.AcquisitionStart()
return 0
def StartExposure(self):
#make sure no acquisiton is running
self.StopAq()
self._temp = self.SensorTemperature.getValue()
self._frameRate = self.FrameRate.getValue()
eventLog.logEvent('StartAq', '')
self._flush()
self.InitBuffers()
self.AcquisitionStart()
return 0
def OnFrame(self, frameNum):
if frameNum > self.startFrame:
fn = floor((frameNum - self.startFrame) / self.dwellTime) % len(
self.zPoss)
if not fn == self.pos:
self.pos = fn
self.piezo.MoveTo(self.piezoChan, self.zPoss[self.pos])
eventLog.logEvent(
'ProtocolFocus',
'%d, %3.3f' % (frameNum, self.zPoss[self.pos]))
TaskListProtocol.OnFrame(self, frameNum)
def StartExposure(self):
self._get_temps()
if self._recording == False:
self._init_buffers()
eventLog.logEvent('StartAq', '')
self._recording = True
if (self._mode == self.MODE_SINGLE_SHOT) or (self._mode == self.MODE_SOFTWARE_TRIGGER):
self.TriggerAq()
return 0
def MoveTo(self, iChannel, fPos, bTimeOut=True):
stepPos = round(fPos/self.stepsize)
print(stepPos)
if (stepPos >= self.hardMin):
if (fPos < self.max_travel):
nik.ZDrive.Position = int(stepPos)
else:
nik.ZDrive.Position = int(round(self.max_travel/self.stepsize))
else:
nik.ZDrive.Position = self.hardMin
eventLog.logEvent('Focus Change', 'New z-pos = %f' % stepPos)
def StartExposure(self):
self.__selectCamera()
self._GetCCDTemp()
self._GetAcqTimings()
self._GetBufferSize()
eventLog.logEvent('StartAq', '')
ret = ac.StartAcquisition()
if not ret == ac.DRV_SUCCESS:
raise RuntimeError('Error starting acquisition: %s' %
ac.errorCodes[ret])
return 0
def StartExposure(self):
if self.doPoll:
print('StartAq')
self.StopAq()
self.InitBuffers()
eventLog.logEvent('StartAq', '')
ret = uc480.CALL('CaptureVideo', self.boardHandle, uc480.IS_DONT_WAIT)
if not ret == 0:
raise RuntimeError('Error starting exposure: %d: %s' %
GetError(self.boardHandle))
return 0
def MoveTo(self, iChannel, fPos, bTimeOut=True):
stepPos = round(fPos / self.stepsize)
print(stepPos)
if (stepPos >= self.hardMin):
if (fPos < self.max_travel):
nik.ZDrive.Position = int(stepPos)
else:
nik.ZDrive.Position = int(
round(self.max_travel / self.stepsize))
else:
nik.ZDrive.Position = self.hardMin
eventLog.logEvent('Focus Change', 'New z-pos = %f' % stepPos)
def _poll_loop(self, sleep_interval=.01):
"""
This loop runs in a background thread to continuously poll the camera and deal with frames as they arrive.
Parameters
----------
sleep_interval : float
length of time to sleep within the polling thread
Returns
-------
"""
while (self._poll_camera):
if (not self.cam.CamReady()): # and self.piezoReady())):
# Stop the aquisition if there is a hardware error
wx.CallAfter(self.stop)
else:
#is there a picture waiting for us?
#if so do the relevant processing
#otherwise do nothing ...
#nFrames = 0 #number of frames grabbed this pass
#bufferOverflowed = False
while (self.cam.ExpReady()
): #changed to deal with multiple frames being ready
if 'GetNumImsBuffered' in dir(self.cam):
bufferOverflowing = self.cam.GetNumImsBuffered() >= (
self.cam.GetBufferSize() - 2)
else:
bufferOverflowing = False
if bufferOverflowing:
self.bufferOverflowed = True
print(
'Warning: Camera buffer overflowing - purging buffer'
)
eventLog.logEvent('Camera Buffer Overflow')
#stop the aquisition - we're going to restart after we're read out to purge the buffer
#doing it this way _should_ stop the black frames which I guess are being caused by the reading the frame which is
#currently being written to
wx.CallAfter(self.cam.StopAq)
#self.needExposureStart = True
self.onExpReady()
self.n_frames_in_group += 1
time.sleep(sleep_interval)
def StartExposure(self):
logger.debug('StartAq')
if self._poll:
# stop, we'll allocate buffers and restart
self.StopAq()
# allocate at least 2 seconds of buffers
buffer_size = int(max(2 * self.GetFPS(), 50))
self.InitBuffers(buffer_size, buffer_size)
event_log.logEvent('StartAq', '')
if self._cont_mode:
self.check_success(ueye.is_CaptureVideo(self.h, ueye.IS_DONT_WAIT))
else:
self.check_success(ueye.is_FreezeVideo(self.h, ueye.IS_DONT_WAIT))
return 0
def OnFrame(self, frameNum):
if frameNum > self.startFrame:
fn = int(
floor((frameNum - self.startFrame) / self.dwellTime) %
len(self.zPoss))
if not fn == self.pos:
self.pos = fn
#self.piezo.MoveTo(self.piezoChan, self.zPoss[self.pos])
scope.state.setItem(self.piezoName,
self.zPoss[self.pos],
stopCamera=self.require_camera_restart)
eventLog.logEvent(
'ProtocolFocus',
'%d, %3.3f' % (frameNum, self.zPoss[self.pos]))
TaskListProtocol.OnFrame(self, frameNum)
def _thread_target(self):
fast_pz, fast_chan, mult = self.scope.positioning[self.fast_axis]
mult = abs(mult)
old_vel = fast_pz.GetVelocity(fast_chan) #remember the old velocity
fast_pz.SetVelocity(
fast_chan,
self.vel / abs(mult)) #set velocity to give desired pixel sampling
slow_pz, slow_chan, smult = self.scope.positioning[self.slow_axis]
smult = abs(smult)
#do stripes, alternating direction
for i, slow_v in enumerate(self.slow_steps):
if (i % 2):
fs, fe = self.fast_max, self.fast_min
else:
fe, fs = self.fast_max, self.fast_min
#self.scope.pa.stop()
print('Moving to %f, %f' % (fs, slow_v))
fast_pz.MoveTo(fast_chan, fs / mult)
slow_pz.MoveTo(slow_chan, slow_v / smult)
# wait for the slow axis to get there
print('waiting for stage [slow move]')
while not slow_pz.onTarget:
time.sleep(0.1)
if self.log_events:
#TODO - fixme for axis selection
eventLog.logEvent('ScannerXPos', '%3.6f' % slow_v)
eventLog.logEvent('ScannerYPos', '%3.6f' % fs)
#self.scope.pa.start()
print('Slow move done, making fast move')
#start the move with acquisition running
fast_pz.MoveTo(fast_chan, fe / mult)
print('waiting for stage [fast move]')
while not fast_pz.onTarget:
#wait for the fast axis to get there
time.sleep(.1)
fast_pz.SetVelocity(fast_chan, old_vel) #restore old velocity
print('Scan complete')
def StartExposure(self):
# self.StopAq()
self.n_read = 0
d = self.cam.sdk.get_delay_exposure_time()
self._cycle_time = d['exposure']*timebase[d['exposure timebase']] \
+ d['delay']*timebase[d['delay timebase']]
if self._mode == self.MODE_SINGLE_SHOT:
self.cam.record(number_of_images=1, mode='sequence')
elif self._mode == self.MODE_CONTINUOUS:
# Allocate buffer (2 seconds of buffer)
self.buffer_size = int(max(int(2.0 * self.GetFPS()), 1))
self.cam.record(number_of_images=self.buffer_size,
mode='ring buffer')
self.recording = True
eventLog.logEvent('StartAq', '')
return 0
def StartExposure(self):
#make sure no acquisiton is running
self.StopAq()
self._temp = self.SensorTemperature.getValue()
self._frameRate = self.FrameRate.getValue()
self.tKin = 1.0 / self._frameRate
self._frame_wait_time = ctypes.c_uint(int(max(2*1000*self.tKin, 100)))
self.hardware_overflowed = False
self._n_timeouts = 0
#logger.debug('StartAq')
eventLog.logEvent('StartAq', '')
self._flush()
self.InitBuffers()
self.AcquisitionStart()
return 0
def StartExposure(self):
if self.doPoll:
print('StartAq')
self.StopAq()
# allocate at least 2 seconds of buffers
buffer_size = int(max(2 * self.GetFPS(), 50))
self.InitBuffers(buffer_size, buffer_size)
eventLog.logEvent('StartAq', '')
if self._cont_mode:
ret = uc480.CALL('CaptureVideo', self.boardHandle, uc480.IS_DONT_WAIT)
else:
ret = uc480.CALL('FreezeVideo', self.boardHandle, uc480.IS_DONT_WAIT)
if not ret == 0:
raise RuntimeError('Error starting exposure: %d: %s' % GetError(self.boardHandle))
return 0
def _poll_loop(self):
"""
This loop runs in a background thread to continuously poll the camera
and deal with frames as they arrive. `FrameWrangler._polling_interval`
is used to set the delay between loops.
"""
while (self._poll_camera):
if (not self.cam.CamReady()):# and self.piezoReady())):
# Stop the aquisition if there is a hardware error
self._event_loop.call_in_main_thread(self.stop)
else:
#is there a picture waiting for us?
#if so do the relevant processing
#otherwise do nothing ...
#nFrames = 0 #number of frames grabbed this pass
#bufferOverflowed = False
while (self.cam.ExpReady()): #changed to deal with multiple frames being ready
if 'GetNumImsBuffered' in dir(self.cam):
bufferOverflowing = self.cam.GetNumImsBuffered() >= (self.cam.GetBufferSize() - 2)
else:
bufferOverflowing = False
if bufferOverflowing:
with self._notify_lock:
#acquire lock before flagging the buffer as overflowed so that we can be sure that StopAq
# gets called before StartAq in Notify()
self.bufferOverflowed = True
logger.warning('Camera buffer overflowing - purging buffer')
eventLog.logEvent('Camera Buffer Overflow')
#stop the aquisition - we're going to restart after we're read out to purge the buffer
#doing it this way _should_ stop the black frames which I guess are being caused by the reading the frame which is
#currently being written to
self._event_loop.call_in_main_thread(self.cam.StopAq)
#self.needExposureStart = True
self.onExpReady()
self.n_frames_in_group += 1
time.sleep(self._polling_interval)
def Init(self, spooler):
self.zPoss = np.arange(
scope.stackSettings.GetStartPos(),
scope.stackSettings.GetEndPos() +
.95 * scope.stackSettings.GetStepSize(),
scope.stackSettings.GetStepSize() *
scope.stackSettings.GetDirection())
if self.slice_order != 'saw':
if self.slice_order == 'random':
self.zPoss = self.zPoss[np.argsort(
np.random.rand(len(self.zPoss)))]
elif self.slice_order == 'triangle':
if len(self.zPoss) % 2:
# odd
self.zPoss = np.concatenate(
[self.zPoss[1::2], self.zPoss[::-2]])
else:
# even
self.zPoss = np.concatenate(
[self.zPoss[::2], self.zPoss[-1::-2]])
self.piezoName = 'Positioning.%s' % scope.stackSettings.GetScanChannel(
)
self.startPos = scope.state[
self.piezoName +
'_target'] #FIXME - _target positions shouldn't be part of scope state
self.pos = 0
spooler.md.setEntry('Protocol.PiezoStartPos', self.startPos)
spooler.md.setEntry('Protocol.ZStack', True)
scope.state.setItem(self.piezoName,
self.zPoss[self.pos],
stopCamera=self.require_camera_restart)
eventLog.logEvent('ProtocolFocus',
'%d, %3.3f' % (0, self.zPoss[self.pos]))
TaskListProtocol.Init(self, spooler)
def tick(self, frameData, **kwargs):
with self._rlock:
if not self.running:
return
try:
cam_trigger = self.scope.cam.GetAcquisitionMode() == self.scope.cam.MODE_SOFTWARE_TRIGGER
except AttributeError:
cam_trigger = False
#logger.debug('Cam_trigger: %s' % repr(cam_trigger))
#print self.callNum
if (self.callNum % self.dwellTime) == 0:
#record pixel in overview
callN = int(self.callNum/self.dwellTime)
if self.avg:
self.image[callN % self.nx, int((callN % (self.image.size))/self.nx)] = self.scope.currentFrame.mean() - self.background
self.view.Refresh()
if self.callNum >= self.dwellTime * self.imsize - 1:
# we've acquired the last frame
if self._stop_on_complete:
self._stop()
return
if ((self.callNum +1) % self.dwellTime) == 0:
#move piezo
callN = int((self.callNum+1)/self.dwellTime)
new_x, new_y = self._position_for_index(callN)
self.scope.state.setItems({'Positioning.x' : new_x,
'Positioning.y' : new_y
}, stopCamera = not cam_trigger)
#print 'SetP'
if self.evtLog:
#eventLog.logEvent('ScannerXPos', '%3.6f' % self.xp[callN % self.nx])
#eventLog.logEvent('ScannerYPos', '%3.6f' % self.yp[(callN % (self.imsize))/self.nx])
eventLog.logEvent('ScannerXPos', '%3.6f' % self.scope.state['Positioning.x'])
eventLog.logEvent('ScannerYPos', '%3.6f' % self.scope.state['Positioning.y'])
if cam_trigger:
#logger.debug('Firing camera trigger')
self.scope.cam.FireSoftwareTrigger()
if self.evtLog:
eventLog.logEvent('StartAq',"")
#
#
#if self.sync:
# while not self.xpiezo[0].IsOnTarget(): #wait for stage to move
# time.sleep(.05)
self.callNum += 1
def start(self):
#pixels = np.array(pixels)
# if np.isscalar(self.pixels):
# #constant - use as number of pixels
# #center on current piezo position
# self.xp = self.pixelsize*np.arange(-self.pixels/2, self.pixels/2 +1) + self.xpiezo[0].GetPos(self.xpiezo[1])
# self.yp = self.pixelsize*np.arange(-self.pixels/2, self.pixels/2 +1) + self.ypiezo[0].GetPos(self.ypiezo[1])
# elif np.isscalar(self.pixels[0]):
# #a 1D array - numbers in either direction centered on piezo pos
# self.xp = self.pixelsize*np.arange(-self.pixels[0]/2, self.pixels[0]/2 +1) + self.xpiezo[0].GetPos(self.xpiezo[1])
# self.yp = self.pixelsize*np.arange(-self.pixels[1]/2, self.pixels[1]/2 +1) + self.ypiezo[0].GetPos(self.ypiezo[1])
# else:
# #actual pixel positions
# self.xp = self.pixels[0]
# self.yp = self.pixels[1]
#
# self.nx = len(self.xp)
# self.ny = len(self.yp)
#
# self.imsize = self.nx*self.ny
self.genCoords()
self.callNum = -1
if self.avg:
self.image = np.zeros((self.nx, self.ny, self.nz))
self.ds = self.scope.frameWrangler.currentFrame
self.view = View3D(self.image)
self.xpiezo[0].MoveTo(self.xpiezo[1], self.xp[0])
self.ypiezo[0].MoveTo(self.ypiezo[1], self.yp[0])
self.zpiezo[0].MoveTo(self.zpiezo[1], self.zp[0])
self.ix_o = 0
self.iy_o = 0
#if self.sync:
# while not self.xpiezo[0].IsOnTarget(): #wait for stage to move
# time.sleep(.05)
if self.evtLog:
eventLog.logEvent('ScannerXPos', '%3.6f' % self.xp[0])
eventLog.logEvent('ScannerYPos', '%3.6f' % self.yp[0])
eventLog.logEvent('ScannerZPos', '%3.6f' % self.zp[0])
self.scope.frameWrangler.WantFrameNotification.append(self.tick)
if self.sync:
self.scope.frameWrangler.HardwareChecks.append(self.onTarget)
def tick(self, caller=None):
#print self.callNum
if self.callNum > 0 and (self.callNum % self.dwellTime) == 0:
#record pixel in overview
callN = int(self.callNum/self.dwellTime)
#vary z fastest
iz = callN % self.nz
ix = (callN/self.nz) % self.nx
iy = (callN/(self.nz*self.nx)) % self.ny
if self.avg:
self.image[ix, iy, iz] = self.ds.mean() - self.background
self.view.Refresh()
if ((self.callNum +1) % self.dwellTime) == 0:
#move piezo
callN = int((self.callNum+1)/self.dwellTime)
#vary z fastest
iz = callN % self.nz
ix = (callN/self.nz) % self.nx
iy = (callN/(self.nz*self.nx)) % self.ny
self.zpiezo[0].MoveTo(self.zpiezo[1], self.zp[iz])
if self.evtLog:
eventLog.logEvent('ScannerZPos', '%3.6f' % self.zp[iz])
if not ix == self.ix_o:
self.xpiezo[0].MoveTo(self.xpiezo[1], self.xp[ix])
self.ix_o = ix
if self.evtLog:
eventLog.logEvent('ScannerXPos', '%3.6f' % self.xp[ix])
if not iy == self.iy_o:
self.ypiezo[0].MoveTo(self.ypiezo[1], self.yp[iy])
self.iy_o = iy
if self.evtLog:
eventLog.logEvent('ScannerYPos', '%3.6f' % self.yp[iy])
# if self.sync:
# while not self.xpiezo[0].IsOnTarget(): #wait for stage to move
# time.sleep(.05)
self.callNum += 1
def _Loop(self):
while self.loopActive:
self.lock.acquire()
try:
# check position
time.sleep(self._update_rate)
self.position[0] = float(gcs.qPOS(self.id, b'A')[0])+ self.osen
self.errCode = int(gcs.qERR(self.id))
if not self.errCode == 0: # I have yet to see this work
logging.info(('Stage Error: %d' % self.errCode))
# print self.targetPosition, self.stopMove
if not np.all(self.targetPosition == self.lastTargetPosition):
# update our target position
pos = np.clip(self.targetPosition, 0, self.max_travel)
gcs.MOV(self.id, b'A', pos[:1])
self.lastTargetPosition = pos.copy()
# print('p')
# logging.debug('Moving piezo to target: %f' % (pos[0],))
if np.allclose(self.position, self.targetPosition, atol=self._target_tol):
if not self.onTarget:
logEvent('PiezoOnTarget', '%.3f' % self.position[0], time.time())
self.onTarget = True
# check to see if we're on target
#self.ser_port.write('ONT? A\n')
#self.ser_port.flushOutput()
#time.sleep(0.005)
#res1 = self.ser_port.readline()
#if res1 == '':
# time.sleep(.5)
# res1 = self.ser_port.readline()
#try:
# self.onTarget = int(res1) == 1
#except ValueError:
# self.onTarget = False
# logging.exception('Value error on response from ONT')
# time.sleep(.1)
except RuntimeError as e:
# gcs.fcnWrap.HandleError throws Runtimes for everything
logger.error(str(e))
try:
self.errCode = int(gcs.qERR(self.id))
logger.error('error code: %s' % str(self.errCode))
except:
logger.error('no error code retrieved')
if '-1' in str(e):
logger.debug('reinitializing GCS connection, 10 s pause')
gcs.CloseConnection(self.id)
time.sleep(10.0) # this takes at least more than 1 s
try:
self.id = gcs.ConnectUSB(self._identifier)
logger.debug('restablished connection to piezo')
except RuntimeError as e:
logger.error('trying to get new device ID')
devices = get_connected_devices()
self._identifier = devices[0]
logger.debug('new device ID acquired')
self.id = gcs.ConnectUSB(self._identifier)
time.sleep(1.0)
logger.debug('turning on servo')
gcs.SVO(self.id, b'A', [1])
time.sleep(1.0)
finally:
self.lock.release()
# close port on loop exit
gcs.CloseConnection(self.id)
logging.info("Piezo USB connection closed")
def Notify(self, event=None):
"""Callback which is called regularly by a system timer to poll the
camera"""
#check to see if we are already running
if self.inNotify:
print('Already in notify, skip for now')
return
try:
self.inNotify = True
"Should be called on each timer tick"
self.te = time.clock()
#print self.te - self.tl
self.tl = self.te
#print "Notify"
#self.loopnuf = self.loopnuf + 1
if (True): #check that we are aquiring
if (not (self.cam.CamReady() and self.piezoReady())):
# Stop the aquisition if there is a hardware error
self.stop()
return
#is there a picture waiting for us?
#if so do the relevant processing
#otherwise do nothing ...
nFrames = 0 #number of frames grabbed this pass
bufferOverflowed = False
while (self.cam.ExpReady()
): #changed to deal with multiple frames being ready
if 'GetNumImsBuffered' in dir(self.cam):
bufferOverflowing = self.cam.GetNumImsBuffered() >= (
self.cam.GetBufferSize() - 1)
else:
bufferOverflowing = False
if bufferOverflowing:
bufferOverflowed = True
print(
'Warning: Camera buffer overflowing - purging buffer'
)
eventLog.logEvent('Camera Buffer Overflow')
#stop the aquisition - we're going to restart after we're read out to purge the buffer
#doing it this way _should_ stop the black frames which I guess are being caused by the reading the frame which is
#currently being written to
self.cam.StopAq()
self.onExpReady()
nFrames += 1
#te= time.clock()
#If we can't deal with the data fast enough (e.g. due to file i/o limitations) this can turn into an infinite loop -
#avoid this by bailing out with a warning if nFrames exceeds a certain value. This will probably lead to buffer overflows
#and loss of data, but is arguably better than an unresponsive app.
#This value is (currently) chosen fairly arbitrarily, taking the following facts into account:
#the buffer has enough storage for ~3s when running flat out,
#we're polling at ~5hz, and we should be able to get more frames than would be expected during the polling intervall to
#allow us to catch up following glitches of one form or another, although not too many more.
if ('GetNumImsBuffered' in dir(self.cam)) and (
nFrames > self.cam.GetBufferSize() / 2):
print((
'Warning: not keeping up with camera, giving up with %d frames still in buffer'
% self.cam.GetNumImsBuffered()))
break
if bufferOverflowed:
print('nse')
self.needExposureStart = True
if self.needExposureStart and self.checkHardware():
self.needExposureStart = False
self.cam.StartExposure(
) #restart aquisition - this should purge buffer
#if 'nQueued' in dir(self.cam):
# print '\n', nFrames, self.cam.nQueued, self.cam.nFull , self.cam.doPoll
if nFrames > 0:
self.n_Frames += nFrames
self.tLastFrame = self.tThisFrame
self.nFrames = nFrames
self.tThisFrame = time.clock()
self.onFrameGroup.send_robust(self)
else:
self._stop()
except:
traceback.print_exc()
finally:
self.inNotify = False
#self.timer.StartOnce(self.tiint)
self.timer.Start(self.tiint, wx.TIMER_ONE_SHOT)
def OnFrame(self, frameNum):
while not self.listPos >= len(self.taskList) and frameNum >= self.taskList[self.listPos].when:
t = self.taskList[self.listPos]
t.what(*t.params)
eventLog.logEvent('ProtocolTask', '%d, %s, ' % (frameNum, t.what.__name__) + ', '.join(['%s' % p for p in t.params]))
self.listPos += 1
def OnFinish(self):
while not self.listPos >= len(self.taskList):
t = self.taskList[self.listPos]
t.what(*t.params)
eventLog.logEvent('ProtocolTask', '%s, ' % ( t.what.__name__,) + ', '.join(['%s' % p for p in t.params]))
self.listPos += 1
def Notify(self):
#check to see if we are already running
if self.inNotify:
print('Already in notify, skip for now')
return
try:
self.inNotify = True
"Should be called on each timer tick"
self.te = time.clock()
#print self.te - self.tl
self.tl = self.te
#print "Notify"
#self.loopnuf = self.loopnuf + 1
if (True): #check that we are aquiring
if(not (self.cam.CamReady() and self.piezoReady())):
# Stop the aquisition if there is a hardware error
self.stop()
return
#is there a picture waiting for us?
#if so do the relevant processing
#otherwise do nothing ...
nFrames = 0 #number of frames grabbed this pass
bufferOverflowed = False
while(self.cam.ExpReady()): #changed to deal with multiple frames being ready
if 'GetNumImsBuffered' in dir(self.cam):
bufferOverflowing = self.cam.GetNumImsBuffered() >= (self.cam.GetBufferSize() - 1)
else:
bufferOverflowing = False
if bufferOverflowing:
bufferOverflowed = True
print('Warning: Camera buffer overflowing - purging buffer')
eventLog.logEvent('Camera Buffer Overflow')
#stop the aquisition - we're going to restart after we're read out to purge the buffer
#doing it this way _should_ stop the black frames which I guess are being caused by the reading the frame which is
#currently being written to
self.cam.StopAq()
self.onExpReady()
nFrames += 1
#te= time.clock()
#If we can't deal with the data fast enough (e.g. due to file i/o limitations) this can turn into an infinite loop -
#avoid this by bailing out with a warning if nFrames exceeds a certain value. This will probably lead to buffer overflows
#and loss of data, but is arguably better than an unresponsive app.
#This value is (currently) chosen fairly arbitrarily, taking the following facts into account:
#the buffer has enough storage for ~3s when running flat out,
#we're polling at ~5hz, and we should be able to get more frames than would be expected during the polling intervall to
#allow us to catch up following glitches of one form or another, although not too many more.
if ('GetNumImsBuffered' in dir(self.cam)) and (nFrames > self.cam.GetBufferSize()/2):
print(('Warning: not keeping up with camera, giving up with %d frames still in buffer' % self.cam.GetNumImsBuffered()))
break
if bufferOverflowed:
print('nse')
self.needExposureStart = True
if self.needExposureStart and self.checkHardware():
self.needExposureStart = False
self.cam.StartExposure() #restart aquisition - this should purge buffer
#if 'nQueued' in dir(self.cam):
# print '\n', nFrames, self.cam.nQueued, self.cam.nFull , self.cam.doPoll
if nFrames > 0:
self.n_Frames += nFrames
self.tLastFrame = self.tThisFrame
self.nFrames = nFrames
self.tThisFrame = time.clock()
for a in self.WantFrameGroupNotification:
a(self)
else:
self._stop()
except:
traceback.print_exc()
finally:
self.inNotify = False
def tick(self, **kwargs):
targetZ = self.piezo.GetTargetPos(0)
if not 'mask' in dir(
self
) or not self.scope.frameWrangler.currentFrame.shape[:
2] == self.mask.shape[:
2]:
self.initialise()
#called on a new frame becoming available
if self.calibState == 0:
#print "cal init"
#redefine our positions for the calibration
self.homePos = self.piezo.GetPos(0)
self.calPositions = self.homePos + self.deltaZ * np.arange(
-float(self.stackHalfSize), float(self.stackHalfSize + 1))
self.NCalibStates = len(self.calPositions)
self.refImages = np.zeros(self.mask.shape[:2] +
(self.NCalibStates, ))
self.calImages = np.zeros(self.mask.shape[:2] +
(self.NCalibStates, ))
self.calFTs = np.zeros(self.mask.shape[:2] + (self.NCalibStates, ),
dtype='complex64')
self.piezo.MoveTo(0, self.calPositions[0])
#self.piezo.SetOffset(0)
self.calibState += .5
elif self.calibState < self.NCalibStates:
# print "cal proceed"
if (self.calibState % 1) == 0:
#full step - record current image and move on to next position
self.setRefN(int(self.calibState - 1))
self.piezo.MoveTo(0, self.calPositions[int(self.calibState)])
#increment our calibration state
self.calibState += 0.5
elif (self.calibState == self.NCalibStates):
# print "cal finishing"
self.setRefN(int(self.calibState - 1))
#perform final bit of calibration - calcuate gradient between steps
#self.dz = (self.refC - self.refB).ravel()
#self.dzn = 2./np.dot(self.dz, self.dz)
self.dz = np.gradient(self.calImages)[2].reshape(
-1, self.NCalibStates)
self.dzn = np.hstack([
1. / np.dot(self.dz[:, i], self.dz[:, i])
for i in range(self.NCalibStates)
])
self.piezo.MoveTo(0, self.homePos)
#reset our history log
self.history = []
self.historyCorrections = []
self.calibState += 1
elif (self.calibState > self.NCalibStates) and np.allclose(
self._last_target_z, targetZ):
# print "fully calibrated"
dx, dy, dz, cCoeff, dzcorr, nomPos, posInd, calPos, posDelta = self.compare(
)
self.corrRef = max(self.corrRef, cCoeff)
#print dx, dy, dz
#FIXME: logging shouldn't call piezo.GetOffset() etc ... for performance reasons
self.history.append((time.time(), dx, dy, dz, cCoeff, self.corrRef,
self.piezo.GetOffset(), self.piezo.GetPos(0)))
eventLog.logEvent('PYME2ShiftMeasure',
'%3.4f, %3.4f, %3.4f' % (dx, dy, dz))
self.lockActive = self.lockFocus and (cCoeff > .5 * self.corrRef)
if self.lockActive:
if abs(self.piezo.GetOffset()) > 20.0:
self.lockFocus = False
logger.info("focus lock released")
if abs(
dz
) > self.focusTolerance and self.lastAdjustment >= self.minDelay:
zcorr = self.piezo.GetOffset() - dz
if zcorr < -self.maxfac * self.focusTolerance:
zcorr = -self.maxfac * self.focusTolerance
if zcorr > self.maxfac * self.focusTolerance:
zcorr = self.maxfac * self.focusTolerance
self.piezo.SetOffset(zcorr)
#FIXME: this shouldn't be needed as it is logged during LogShifts anyway
self.piezo.LogFocusCorrection(
zcorr) #inject offset changing into 'Events'
eventLog.logEvent('PYME2UpdateOffset', '%3.4f' % (zcorr))
self.historyCorrections.append((time.time(), dz))
self.lastAdjustment = 0
else:
self.lastAdjustment += 1
if self.logShifts:
self.piezo.LogShifts(dx, dy, dz, self.lockActive)
self._last_target_z = targetZ
