def stop_rfpower(self):
print('stop rf pwoer ')
self.flag_rfpower = False
time.sleep(1)
stop_thread(self.sub_rfpower_thread)
self.timer_rfpower.stop()
def stop_gassupply(self):
print('stop gas supply ')
self.flag_gassupply = False
time.sleep(1)
stop_thread(self.sub_gassupply_thread)
self.timer_gassupply.stop()
def stop_water(self):
print('stop water')
self.flag_water = False
time.sleep(1)
stop_thread(self.sub_water_thread)
self.timer_water.stop()
def stop_pgpower(self):
print('stop pgpower ')
self.flag_pgpower = False
time.sleep(1)
stop_thread(self.sub_pgpower_thread)
self.timer_pgpower.stop()
def stop_egpower(self):
print('stop egpower ')
self.flag_egpowerhs1_2 = False
self.flag_egpowerhs2_3_4 = False
self.flag_egpowerhs3_5 = False
time.sleep(1)
stop_thread(self.sub_egpowerhs1_2_thread)
stop_thread(self.sub_egpowerhs2_3_4_thread)
stop_thread(self.sub_egpowerhs3_5_thread)
self.timer_egpower.stop()
def stop_total(self):
print('stop gas supply ')
self.flag_total = False
time.sleep(1)
stop_thread(self.sub_gassupply_thread)
stop_thread(self.sub_rfpower_thread)
stop_thread(self.sub_pgpower_thread)
stop_thread(self.sub_egpowerhs1_1_2_thread)
stop_thread(self.sub_egpowerhs3_6)
self.timer_total.stop()
def runEpoch(mmc,device,rep):
import time
global epoch_seq #epochs items as list (name,exp,led,odor,duration,noRec)
global meta_index # list: epoch name, start frame, end frame
namep=window.path.text()
print "create hdf5"
hdfpath = createHdf5andClose(namep,savepath)
n_epoch=len(epoch_seq)
total =0
epoch_times =[]
eps = 0.005 #delay... error in time passed
lj_delay = 0#0.012
count = 1 #epoch 0 effectuated before loop
m=0 #tiff saving index
namep=window.path.text()
print "namep..."+str(namep)
window.progressBar.setMinimum(0)
window.progressBar.setMaximum(n_epoch+(rep-1)*n_epoch)
print str(n_epoch)
for i in range(n_epoch):
total += epoch_seq[i][4]
epoch_times.append(total)
print str(n_epoch)+" epochs"
print "should take "+str(total)+"s and repeated "+str(rep)+" time(s)"
mmc.prepareSequenceAcquisition('Zyla')
#print "preparing sequence acquisition took", time.clock()-start, "seconds"
# cv2.namedWindow('Video')
text_file_globalTime = open(savepath+"/globalTime"+namep+".txt", 'w')
#text_file_globalTime.write(str(time.clock()-start)+", "+ser.readline()+"\n")
for i in range(rep): #LOOP FOR TRIALS
print "trial "+str(i+1)
text_file = open(savepath+"/respi"+namep+"_trial_"+str(i+1)+".txt", 'w')
text_file_globalTime.write( str(time.time())+", "+str(i+1)+"\n")
frame_i=0
#mmc.setProperty(DEVICE[0], 'Exposure', epoch_seq[0][1])
setLed(device,epoch_seq[0][2])
setOdor(device,epoch_seq[0][3])
mmc.initializeCircularBuffer()
mmc.startContinuousSequenceAcquisition(10)
start=time.clock()
while time.clock()-start < total:
if mmc.getRemainingImageCount()>0 :
im = mmc.popNextImage()
#im = mmc.getLastImage()
#cv2.imshow('Video', im)
#raw_input("pause")
frames.append(im)
timestamps.append(time.clock()-start) #0.6s from start !!!
meta.append( (epoch_seq[count-1], i))
if (count < n_epoch) and (time.clock()-start+eps > epoch_times[count-1]) :
print "count "+str(count)
print epoch_seq[count-1][0]
print frame_i
print len(frames)-1
#mmc.setProperty(DEVICE[0], 'Exposure', epoch_seq[count][1])
setLed(device,epoch_seq[count][2])
setOdor(device,epoch_seq[count][3])
window.progressBar.setValue(count+i*n_epoch)
# #saving index of previous epoch (name,start frame, end frame)
# frame_f=len(frames)-1
# meta_index.append((epoch_seq[count-1][0],frame_i,frame_f))
# frame_i=len(frames)
if epoch_seq[count-1][5] == 0 :
frame_f=len(frames)-1
meta_index.append((epoch_seq[count-1][0],frame_i,frame_f))
frame_i=len(frames)
# nrec = 0
# mmc.stopSequenceAcquisition()
# mmc.clearCircularBuffer()
if (epoch_seq[count][5] == 1):
print "stop recording "+str(epoch_seq[count][4])+ "sec"
time.sleep(epoch_seq[count][4])
mmc.clearCircularBuffer()
#meta_index.pop()
# if epoch_seq[count-1][5] == 1:
# mmc.initializeCircularBuffer()
# mmc.startContinuousSequenceAcquisition(10)
# nrec=1
count += 1
if ser.inWaiting() :
text_file.write(str(time.clock()-start)+", "+ser.readline()+"\n")
# if cv2.waitKey(1) >= 0:
# break
frame_f=len(frames)-1
meta_index.append((epoch_seq[count-1][0],frame_i,frame_f))
frame_i=len(frames)
m_i_trial.append(meta_index)
meta_index=[]
window.progressBar.setValue(n_epoch+i*n_epoch)
#reset
device.setFIOState(green_lj, 0)
device.setFIOState(red_lj, 1)
#device.setFIOState(v1_lj, 0)
#device.setFIOState(v2_lj, 0)
DAC0_VALUE = device.voltageToDACBits(0, dacNumber = 0, is16Bits = False)
device.getFeedback(u3.DAC0_8(DAC0_VALUE))
DAC1_VALUE = device.voltageToDACBits(0, dacNumber = 1, is16Bits = False)
device.getFeedback(u3.DAC1_8(DAC1_VALUE))
print str(total)+"s acquisition took", time.clock()-start, "seconds"
mmc.stopSequenceAcquisition()
mmc.clearCircularBuffer()
if i < rep: #end of an epoch
#time spent savong files
savingTime=time.time()
#print "saving tiff.."+str(len(frames))+" frames"
#namep=window.path.text()
framesnp = np.asarray(frames)
#display avg green
print "save green"+str(i)+" in "+savepath
scipy.misc.imsave(savepath+'/green'+str(i)+'.jpg', np.mean(framesnp[0:20],axis=0))
#plt.imshow(np.mean(framesnp[0:20],axis=0))
#saveAsMultipageTif(framesnp,savepath,namep,meta,k=512)#
#m = saveAsMultipageTif_inter(framesnp,savepath,namep,m)
#print "number of tiff files :"+str(m)
print "save trial hdf5"
print m_i_trial[-1]
print i+1
hdfs=saveTrialHdf5andClose(hdfpath,framesnp,m_i_trial[-1],i+1,epoch_seq) #modified added epoch
print "closing hdfs"
hdfs.close()
print "closed"
#print "save respiratory signal"
# text_file = open("respi"+".txt", 'w')
print "empty frames list.."
frames[:]=[]
text_file.close()
timeSpentSaving=time.time()-savingTime
newDelay=window.dur_2.value()-timeSpentSaving
print "in total wating for "+str(window.dur_2.value())+" s"
print "after time spent saving wating for "+str(newDelay)+" s"
if (newDelay>0):
time.sleep(newDelay)
count =1
#cv2.destroyAllWindows()
#print "nOfFrames :"+str(len(frames))
print "exposure was", mmc.getProperty('Zyla','Exposure')
print "Framerate was", mmc.getProperty('Zyla','FrameRate')
print "saving metadata, timestamps and comments"
if not os.path.exists(savepath+"/"+namep):
os.makedirs(savepath+"/"+namep)
with open(savepath+"/"+namep+"/epoch.p", "wb") as fp: #Pickling
pickle.dump(epoch_seq, fp)
with open(savepath+"/"+namep+"/comment.p", "wb") as fpp: #Pickling
pickle.dump(window.comment.toPlainText(), fpp)
with open(savepath+"/"+namep+"/timestamps.p", "wb") as fppp: #Pickling
pickle.dump(timestamps, fppp)
with open(savepath+"/"+namep+"/meta.p", "wb") as fppp: #Pickling
pickle.dump(meta, fppp)
with open(savepath+"/"+namep+"/m_i_trial.p", "wb") as fppp: #Pickling
pickle.dump(m_i_trial, fppp)
print "restart kernel to be safe"
text_file_globalTime.close()
print "global time txt closed"
window.progressBar.setValue(0)
import sys
data = [0]
ser = serial.Serial("COM4", 9600, timeout=0.5)
t = [0]
start_time = time.time()
time2 = []
while time.time() - start_time < 3:
line = ser.readline()
print('data: ', float(line))
# Calibration
print('Beginning calibration')
print('Please make your arm straight for 3 seconds...')
time.sleep(3)
ser.reset_input_buffer()
ser.reset_output_buffer()
arm_straight = float(ser.readline()) # Voltage for ~180 degrees
print('Done')
print('Please bend your arm for 3 seconds...')
time.sleep(3)
ser.reset_input_buffer()
ser.reset_output_buffer()
arm_bent = float(ser.readline()) # Voltage for 45 degrees
print('Done')
print(arm_straight, arm_bent)
ser.reset_input_buffer()