def read_data():
data = ser.readline().decode()
while data.isspace(): # if faulty reading (whitespace), keep trying
data = ser.readline().decode()
millis = str(round(time.time() * 1000))
datafile.write(data + ',' + millis)
return list(map(int, data.split(",")))
def update():
global sample_plot, samples, sample_count, start_time_ms
line = raw.readline().strip()
if (chr(line[0]) == "#"):
print(line)
return
line_list = line.decode('ascii').split(' ')
samples.extend(list(map(int, line_list)))
sample_count = sample_count + len(line_list)
if (len(samples) > samples_to_show):
del samples[0:4]
if (sample_count % (samples_to_show / 2) == 0):
delta_time_s = (time.time() - start_time_s)
print("Sample rate = " + str(sample_count/delta_time_s))
np_samples = np.array(samples, dtype='uint32')
sample_plot.setData(np_samples)
app.processEvents()
def update():
global curve, data
line = ser.readline()
try:
# 188uV per bit is ADS1115 16-bit ADC scaling (5V)
# 3.223mV per bit is Arduino Yun Mini 10-bit ADS scaling (3.3V)
data.append(float(line) * 3.223) # Scaling factor
t.append(time.time() - start_time)
curve.setData(t, data)
# data_filtered = f.butter_lowpass_filter(rate=100, data=data, freqHighCutoff=45, order=5)
# curve.setData(t, data_filtered)
p.setXRange(t[-1] - 5, t[-1] + 1)
app.processEvents()
# print('time taken = ' + str((t[-1]-t[-2])*1000) + 'ms')
# print('bits waiting=' + str(ser.in_waiting), 'mseconds=' + str((t[-1] - t[-2])*1000), 'data=' + str(data[-1]))
if len(data) > 5000:
del data[0:-2]
del t[0:-2]
if ser.in_waiting > 100:
print('queue buffer is incresing', ser.in_waiting)
except ValueError:
print('!!! VALUE ERROR', line)
def update():
global curve, data
bytesR_H = raw.read()
bytesR_L = raw.read()
valueR = (ord(bytesR_H) << 5) + ord(bytesR_L)
# raw.flushInput()
# raw.flushOutput()
global i
elapsedtime = time.time() - start_time
datax.append(elapsedtime)
datay.append(valueR)
xdata = datax
ydata = datay
# filtering
i += 1
data_filter.append(
sum([x * y for x, y in zip(filter_coef, ydata[i:i + 18])]))
# print(data_filter[i])
# display filtered data
if (i % 2) == 0:
curve1.setData(xdata, ydata)
# app.processEvents()
p1.setXRange(elapsedtime - 3, elapsedtime)
curve2.setData(xdata, data_filter)
# app.processEvents()
p2.setXRange(elapsedtime - 3, elapsedtime)
#record data
now = datetime.now()
current_time = now.strftime("%y%m%d_%H%M%S")
print(current_time, ',', valueR, file=record)
def update():
global curve, data
line = ser.readline()
try:
data = float(line)
angle.append(180 - (data - arm_straight) /
(arm_bent - arm_straight) * 135)
t.append(time.time() - start_time)
# curve.setData(t, angle)
angle_filtered = f.butter_lowpass_filter(rate=100,
data=angle,
freqHighCutoff=45,
order=5)
curve.setData(t, angle_filtered)
p.setXRange(t[-1] - 5, t[-1] + 1)
app.processEvents()
# print('time taken = ' + str((t[-1]-t[-2])*1000) + 'ms')
# print('bits waiting=' + str(ser.in_waiting), 'mseconds=' + str((t[-1] - t[-2])*1000), 'data=' + str(data[-1]))
if ser.in_waiting > 100:
print('queue buffer is incresing', ser.in_waiting)
except ValueError:
print('!!! VALUE ERROR', line)
from pyqtgraph.Qt import QtGui, QtCore
import numpy as np
import pyqtgraph as pg
from pyqtgraph.ptime import time
import serial
import time
import software.signal_filters as f
app = QtGui.QApplication([])
start_time = time.time()
p = pg.plot()
p.setWindowTitle('live plot from serial')
p.setLabels(left=('millivolts', 'mV'))
curve = p.plot()
data = [0]
ser = serial.Serial("COM6", 9600, timeout=0.5)
t = [0]
def update():
global curve, data
line = ser.readline()
try:
# 188uV per bit is ADS1115 16-bit ADC scaling (5V)
# 3.223mV per bit is Arduino Yun Mini 10-bit ADS scaling (3.3V)
data.append(float(line) * 3.223) # Scaling factor
t.append(time.time() - start_time)
curve.setData(t, data)
return
line_list = line.decode('ascii').split(' ')
samples.extend(list(map(int, line_list)))
sample_count = sample_count + len(line_list)
if (len(samples) > samples_to_show):
del samples[0:4]
if (sample_count % (samples_to_show / 2) == 0):
delta_time_s = (time.time() - start_time_s)
print("Sample rate = " + str(sample_count/delta_time_s))
np_samples = np.array(samples, dtype='uint32')
sample_plot.setData(np_samples)
app.processEvents()
if __name__ == '__main__':
plt = pg.plot()
plt.setWindowTitle("ADPD4000Z-PPG Eval Board Data Plot")
sample_plot = plt.plot(pen='r')
samples = []
raw = serial.Serial(com_port, 115200)
timer = QtCore.QTimer()
timer.timeout.connect(update)
timer.start(0)
start_time_s = time.time()
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
p.addLegend()
#p.showGrid(True, True, 0.1)
curve = p.plot(name='my black curve')
pen = pg.mkPen(color='k')
curve.setPen(pen)
another_curve = p.plot(name='my red curve')
another_curve.setPen(pg.mkPen(color='r'))
print p.listDataItems()
x = np.arange(10**5)
y = np.random.random(10**5)
itr = 0
import time
t = time.time()
app.processEvents() ## force complete redraw for every plot
while True:
itr += 1
curve.clear()
another_curve.clear()
curve.setData(x[0:itr], y[0:itr])
another_curve.setData(x[0:itr], 5 + y[0:itr])
app.processEvents() ## force complete redraw for every plot
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
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)
from pyqtgraph.Qt import QtGui, QtCore
import numpy as np
import pyqtgraph as pg
from pyqtgraph.ptime import time
import serial
import time
import software.signal_filters as f
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()