def frameSaving(mmc, tiffWriterList, nbImages, maxFrames, window, app, exit):
"In charge of saving frames and actualize the GUI"
imageCount = 0
mmc.startContinuousSequenceAcquisition(1)
while (imageCount < (nbImages) and not exit.is_set()):
if mmc.getRemainingImageCount(
) > 0: #Returns number of image in circular buffer, stop when seq acq finished #Enter this loop BETWEEN acquisition
#trigImage(labjack) #Generate a pulse, which allows to flag the entry in this code statement with the oscilloscope
img = mmc.popNextImage(
) #Gets and removes the next image from the circular buffer
##read input from labjack
saveFrame(img, tiffWriterList, (imageCount),
maxFrames) # saving frame of previous acquisition
imageCount += 1
##UPDATE of the GUI
window.progressBar.setValue(
imageCount) #Update the gui of evolution of the acquisition
# if (imageCount % 10) == 0: ##Process events in the Queue each 10 frames
# app.processEvents() #Keep the GUI responsive even while this fct is executing
# print 'processEvents im num : ',imageCount
#Close tiff file open
tiffWritersClose(tiffWriterList)
#Stop camera acquisition
mmc.stopSequenceAcquisition()
mmc.clearCircularBuffer()
return imageCount
def _circularBufferCleaning(self, imageCount):
"""
Get the last images in the circular buffer if the acquisition was aborted.
This step ensure that there is the same amount of metadata than frames saved.
"""
if (not self.acqRunning) or (
not self.loopRunning
): #Check if sequence acquisition was aborted or loop was paused.
print('cycleTime :', self.cycleTime)
sleep(self.cycleTime)
print('remaining images in the circular buffer :',
self.mmc.getRemainingImageCount())
while (self.mmc.getRemainingImageCount() > 0):
print 'getting last image, num : ', imageCount
img = self.mmc.popNextImage(
) #Gets and removes the next image from the circular buffer
saveFrame(
img, self.tiffWriterList, (imageCount),
self.maxFrames) # saving frame of previous acquisition
imageCount += 1
sleep(self.cycleTime)
#Close tiff file open
tiffWritersClose(self.tiffWriterList)
if ((self.nbFrames / self.maxFrames) >=
1): #check that multiples .tif were initialized
# --> CHECK WICH .tif are empty and suppress it
if self.stimName:
emptyTiffDel(self.stimName, self.savePath, imageCount,
self.maxFrames, self.tiffWriterList)
else:
emptyTiffDel(self.experimentName, self.savePath,
imageCount, self.maxFrames,
self.tiffWriterList)
def _frameSaving(self):
"""
In charge of saving frames
"""
self.mmc.clearCircularBuffer()
imageCount = 0
self.mmc.startContinuousSequenceAcquisition(1)
while (imageCount < (self.nbFrames) and self.acqRunning
and self.loopRunning):
if self.mmc.getRemainingImageCount(
) > 0: #Returns number of image in circular buffer, stop when seq acq finished #Enter this loop BETWEEN acquisition
#trigImage(labjack) #Generate a pulse, which allows to flag the entry in this code statement with the oscilloscope
img = self.mmc.popNextImage(
) #Gets and removes the next image from the circular buffer
saveFrame(
img, self.tiffWriterList, (imageCount),
self.maxFrames) # saving frame of previous acquisition
imageCount += 1
self.progressSig.emit(imageCount)
#Stop camera acquisition #Ensure that no more frames are taken
self.mmc.stopSequenceAcquisition()
#### IF ABORTED acquisition #####
self._circularBufferCleaning(imageCount)
#Close tiff file open
tiffWritersClose(self.tiffWriterList)
print 'end of the _frameSavingThread'
return imageCount
def sequenceAcqCamTrig(mmc, nbImages, maxFrames, intervalMs, deviceLabel,
ledList, tiffWriterList, textFile, labjack, window, app,
exit):
"Prepare and start the sequence acquisition. Write frame in an tiff file during acquisition. LED triggered by camera output"
readOutFrame = 10 #ms ##Minimal time between 2 frames (cf page 45 zyla hardware guide)
#Get the time ##TO FIX : is it the right place to put it on ?
timeStamps = []
#timeStamps.append(time()) #Useless to have a timestamp here
#exp = mmc.getProperty(deviceLabel,'Exposure')
print "Interval between images : ", (intervalMs + readOutFrame), "ms"
print "Nb of frames : ", nbImages
imageCount = 0
#mmc.prepareSequenceAcquisition(deviceLabel)
#mmc.startSequenceAcquisition(nbImages, intervalMs, False) #numImages Number of images requested from the camera
#intervalMs The interval between images, currently only supported by Andor cameras
#stopOnOverflow whether or not the camera stops acquiring when the circular buffer is full
mmc.startContinuousSequenceAcquisition(intervalMs + readOutFrame)
timeStamps.append(time())
while (
imageCount < (nbImages) and not exit.is_set()
): #Loop stops if we have the number of frames wanted OR if abort button is press (see abortFunc)
#sleep(0.001*(intervalMs-10)) #Delay in seconds, can be closed to intervalMs to limit loops for nothing
#Launching acquisition
if mmc.getRemainingImageCount(
) > 0: #Returns number of image in circular buffer, stop when seq acq finished #Enter this loop BETWEEN acquisition
#trigImage(labjack)
imageCount += 1
img = mmc.popNextImage(
) #Gets and removes the next image from the circular buffer
timeStamps.append(time())
saveFrame(img, tiffWriterList, (imageCount - 1),
maxFrames) # saving frame of previous acquisition
window.progressBar.setValue(
imageCount) #Update the gui of evolution of the acquisition
app.processEvents(
) #Allows the GUI to be responsive even while this fct is executing /!\ check time affection of this skills
#Print the real interval between images ## Can be done in post-processing with timeStamps
for i in range(0, len(timeStamps) - 1):
print "delta time between t", i + 1, " and t", i, " : ", (
timeStamps[i + 1] - timeStamps[i])
#Close tiff file open
tiffWritersClose(tiffWriterList)
#Stop camera acquisition
mmc.stopSequenceAcquisition()
mmc.clearCircularBuffer()
return imageCount
def run(self):
self.isStarted.emit()
#Launching the frame acquisition
# if self.acquMode == "Labjack":
# print'sequ acq about to start'
# self.imageCount = self._sequenceAcqu()
# print'run fct done'
if self.acquMode == "Run":
#self.arduinoSync()
self.imageCount = self._seqAcqCyclops()
elif self.acquMode == "Loop":
interruptAIN = 1
stopSignalState = False
waitToCheckSignal = 0.5
#Instanciate a SignalInterrupt object to listen to the labjack and the moment when SYNC signal goes low
self.stopInterrupt = SignalInterrupt(self.labjack, interruptAIN,
waitToCheckSignal,
stopSignalState)
self.stopInterrupt.stateReachedInterrupt.connect(self.pauseLoop)
self.stopInterrupt.start()
stimNumber = 1
self.startAcquisitionTime = time()
print 'start acquisition time :', self.startAcquisitionTime
while (self.acqRunning):
print 'Stimulation nb ', stimNumber
self._loopPreparation(stimNumber)
#Wait for the raise of the SYNC signal
#if waitForSignal(self.labjack, channel=1): #waitForSignal(device, signalType="TTL", channelType="AIN", channel=1)
while (not risingEdge(self.labjack,
interruptAIN)) and self.acqRunning:
continue
if self.acqRunning:
self.loopRunning = True
self.imageCount = self._seqAcqCyclops()
print self.imageCount
stimNumber += 1
else:
#Close tiff file open
tiffWritersClose(self.tiffWriterList)
#close the metadata .txt file
self.textFile.close()
saveFcts.acqFilesDel(self.stimName, self.savePath)
print 'abort loop'
self.stopInterrupt.abort(
) #Stop the listenning action of the Interrupt
else:
print 'Please select a valid mode of triggering the LED'
print 'end of the thread'
self.isFinished.emit()
def saveImageSeqThreads(self):
name = window.name.text() ## get Name from text area
duration = self.dur.value()*1000 ## get duration from spinbox and converted it in ms
ledRatio = [self.rRatio.value(),self.gRatio.value(),self.bRatio.value()] # [r,g,b]## get LED ratio
maxFrames = int(self.framesPerFileLabel.text())
expRatio =self.expRatio.value()
#intervalMs = 0 ## TO remove from every code file
#If abort button was hit, enable execution again, and exit.is_set() will return False (cf sequAcq fct)
exit.clear()
#Initialise sequence acqu
(ledList, nbFrames) = sequenceInit(duration, ledRatio, int(float(mmc.getProperty(DEVICE[0], 'Exposure'))))
#Initialize progressBar
window.progressBar.setMaximum(nbFrames)
#Initialize tiffWriter object
(tiffWriterList, textFile,savePath) = filesInit(name, nbFrames, maxFrames)
pool = ThreadPool(processes=2)
async_result1 = pool.apply_async(sequenceAcqLabjackTrig, (mmc, nbFrames, maxFrames, expRatio, DEVICE[0], ledList, tiffWriterList, textFile, labjack, window, app, exit,))
async_result2 = pool.apply_async(guiUpdating, (self.dur.value(), app, exit,))
# do some other stuff in the main process
imageCount = async_result1.get() # get the return value from your function.
print imageCount
#close the pool and wait for the work to finish
pool.close()
pool.join()
print 'execution done'
#print 'Labjack trig cam fct'
#imageCount = sequenceAcqLabjackTrig(mmc, nbFrames, maxFrames, expRatio, DEVICE[0], ledList, tiffWriterList, textFile, labjack, window, app, exit)
##### IF ABORTED acquisition --> CHECK WICH .tif are empty and suppress it #####
if exit.is_set() and ((nbFrames/maxFrames)>=1): #check if abort fct was called and that multiples .tif were initialized
tiffWriterDel(name, savePath, imageCount, maxFrames, tiffWriterList)
#Closing all files opened
textFile.close()
tiffWritersClose(tiffWriterList)
print 'Acquisition done'
window.progressBar.setValue(0)
def saveImageSeq(self):
name = self.name.text() ## get Name from text area
duration = self.dur.value()*1000 ## get duration from spinbox and converted it in ms
ledRatio = [self.rRatio.value(),self.gRatio.value(),self.bRatio.value()] # [r,g,b]## get LED ratio
maxFrames = int(self.framesPerFileLabel.text())
expRatio =self.expRatio.value()
intervalMs = 0 ## TO remove from every code file
#If abort button was hit, enable execution again, and exit.is_set() will return False (cf sequAcq fct)
exit.clear()
#Initialise sequence acqu
(ledList, nbFrames) = sequenceInit(duration, ledRatio, int(float(mmc.getProperty(DEVICE[0], 'Exposure'))))
#Initialize progressBar
window.progressBar.setMaximum(nbFrames)
#Initialize tiffWriter object
(tiffWriterList, textFile,savePath) = filesInit(name, nbFrames, maxFrames)
if self.ledTrigBox.currentText() == 'Software' :
#Launch seq acq : carries the images acquisition AND saving
imageCount = sequenceAcqSoftTrig(mmc, nbFrames, maxFrames, intervalMs, DEVICE[0], ledList, tiffWriterList, textFile,labjack,window, app, exit)
elif self.ledTrigBox.currentText() == 'Camera' :
print 'LED camera trigger function'
imageCount = sequenceAcqCamTrig(mmc, nbFrames, maxFrames, intervalMs, DEVICE[0], ledList, tiffWriterList, textFile,labjack,window, app, exit)
elif self.ledTrigBox.currentText() == 'Labjack - Cyclops mode':
print 'Labjack trig cam fct'
imageCount = sequenceAcqLabjackTrig(mmc, nbFrames, maxFrames, expRatio, DEVICE[0], ledList, tiffWriterList, textFile, labjack, window, app, exit)
else:
print 'Labjack trig custom fct'
imageCount = sequenceAcqLabjackTrig2(mmc, nbFrames, maxFrames, expRatio, DEVICE[0], ledList, tiffWriterList, textFile, labjack, window, app, exit)
##### IF ABORTED acquisition --> CHECK WICH .tif are empty and suppress it #####
if exit.is_set() and ((nbFrames/maxFrames)>=1): #check if abort fct was called and that multiples .tif were initialized
tiffWriterDel(name, savePath, imageCount, maxFrames, tiffWriterList)
#Closing all files opened
textFile.close()
tiffWritersClose(tiffWriterList)
print 'Acquisition done'
window.progressBar.setValue(0)
def sequenceAcqSoftTrig(mmc, nbImages, maxFrames, intervalMs, deviceLabel,
ledList, tiffWriterList, textFile, labjack, window,
app, exit):
"Prepare and start the sequence acquisition. Write frame in an tiff file during acquisition."
readOutFrame = 10 #ms ##Minimal time between 2 frames (cf page 45 zyla hardware guide)
#Get the time ##TO FIX : is it the right place to put it on ?
timeStamps = []
#timeStamps.append(time()) #Useless to have a timestamp here
#exp = mmc.getProperty(deviceLabel,'Exposure')
print "Interval between images : ", (intervalMs + readOutFrame), "ms"
print "Nb of frames : ", nbImages
imageCount = 0
#Initialize the good LED for first image
if ledList[imageCount] == 'r':
#print "Blue off"
greenOff(labjack)
redOn(labjack)
elif ledList[imageCount] == 'g':
redOff(labjack)
greenOn(labjack)
else:
redOff(labjack)
greenOff(labjack)
#mmc.prepareSequenceAcquisition(deviceLabel)
#mmc.startSequenceAcquisition(nbImages, intervalMs, False) #numImages Number of images requested from the camera
#intervalMs The interval between images, currently only supported by Andor cameras
#stopOnOverflow whether or not the camera stops acquiring when the circular buffer is full
mmc.startContinuousSequenceAcquisition(intervalMs + readOutFrame)
timeStamps.append(time())
while (
imageCount < (nbImages) and not exit.is_set()
): #Loop stops if we have the number of frames wanted OR if abort button is press (see abortFunc)
#Launching acquisition
if mmc.getRemainingImageCount(
) > 0: #Returns number of image in circular buffer, stop when seq acq finished #Enter this loop BETWEEN acquisition
#trigImage(labjack) #Generate a pulse, which allows to flag the entry in this code statement with the oscilloscope
imageCount += 1
#Lighting good LED for next acquisition
if ledList[imageCount] == 'r':
#print "Blue off"
greenOff(labjack)
redOn(labjack)
elif ledList[imageCount] == 'g':
redOff(labjack)
greenOn(labjack)
else:
redOff(labjack)
greenOff(labjack)
#sleep(0.005) #Wait 5ms to ensure LEDS are on
img = mmc.popNextImage(
) #Gets and removes the next image from the circular buffer
t = time()
timeStamps.append(t)
##read input from labjack
saveMetadata(textFile, str(t), ledList[(imageCount - 1)],
str(imageCount - 1))
saveFrame(img, tiffWriterList, (imageCount - 1),
maxFrames) # saving frame of previous acquisition
window.progressBar.setValue(
imageCount) #Update the gui with evolution of the acquisition
app.processEvents(
) #Keep the GUI responsive even while this fct is executing
#Turning off all LEDS
greenOff(labjack)
redOff(labjack)
#Print the real interval between images ## Can be done in post-processing with timeStamps
for i in range(0, len(timeStamps) - 1):
print "delta time between t", i + 1, " and t", i, " : ", (
timeStamps[i + 1] - timeStamps[i])
#Close tiff file open
tiffWritersClose(tiffWriterList)
#Stop camera acquisition
mmc.stopSequenceAcquisition()
mmc.clearCircularBuffer()
return imageCount