def main(pixThreshold, frameRate, videoStream):
expDuration = 600000 # duration of experiment, in seconds; only relevant for live feed
saveFreq = 4500 # how often to save data, in frames
i, m = imageTools.loadImageAndMask()
m, w = imageTools.convertMaskToWeights(m)
videoType, displayDiffs = imageTools.getVideoType(videoStream)
cap = cv2.VideoCapture(videoStream)
print 'Camera resolution is %s x %s' % (str(m.shape[1]), str(m.shape[0]))
cap.set(3, m.shape[1])
cap.set(4, m.shape[0])
ret, frame = cap.read()
storedFrame = imageTools.grayBlur(frame)
pixThreshold = int(np.floor(pixThreshold * storedFrame.shape[0]))
print('PixelThreshold is %i') % pixThreshold
pixData = np.zeros([saveFreq, len(np.unique(w)) + 1])
i = 0 # a counter for saving chunks of data
totalFrames = 0
startTime = datetime.now()
oldTime = startTime
elapsed = 0
print('Analyzing motion data...')
moviedeq = []
while (cap.isOpened()):
ret, frame = cap.read()
if ret == False:
print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
moviedeq.append(currentFrame)
diff = imageTools.diffImage(storedFrame, currentFrame, pixThreshold,
displayDiffs)
timeDiff = 1. / frameRate
elapsed = elapsed + timeDiff
counts = np.bincount(w, weights=diff.ravel())
pixData[i, :] = np.hstack((elapsed, counts))
totalFrames += 1
storedFrame = currentFrame # comment out if nothing is in first frame
i += 1
pixData = pixData[:i, :]
pixData = pixData[:, 2:] # get rid of timing column and background column
file = open(videoStream + ".motion2", 'w')
file.write("12/8/2015" + '\015')
for x in range(0, 285):
#print "x", x
for y in range(0, 96):
file.write(str(int(pixData[x, :][y])) + '\n')
cap.release()
cv2.destroyAllWindows()
vidInfo = {}
return vidInfo
def imageMode(movielist, modename):
moviedeq = []
i2 = 0
#print (movielist)
#movielist = ["hsmovieTue, Nov 8, 2016_1.avi", "hsmovieTue, Nov 8, 2016_2.avi", "hsmovieTue, Nov 8, 2016_3.avi", "hsmovieTue, Nov 8, 2016_4.avi", "hsmovieTue, Nov 8, 2016_5.avi", "hsmovieTue, Nov 8, 2016_6.avi"]
#modename = ''.join(map(str,movielist))
for filenumber in movielist:
#for file in glob.glob(movielist):
#for file in glob.glob("*avi"):
#if i2 == 100:
# break
# print (filenumber)
#file = "*_" + str(filenumber) + ".avi"
#file2 = glob.glob("*_" + str(filenumber) + ".avi"[0])
#print (file2)
cap = cv2.VideoCapture(glob.glob("*_" + str(filenumber) + ".avi")[0])
#cap = cv2.VideoCapture(file2)
#cap = cv2.VideoCapture(videoStream.split('-')[x])
ret,frame = cap.read()
storedFrame = imageTools.grayBlur(frame)
totalFrames = 0
while(cap.isOpened()):
ret,frame = cap.read()
if ret == False:
#print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
if totalFrames < 50:
if totalFrames % 3 == 0:
#print "adding frames: ", totalFrames
moviedeq.append(currentFrame)
totalFrames += 1
storedFrame = currentFrame # comment out if nothing is in first frame
i2 += 1
testing = calc_mode(moviedeq, np.zeros([660,1088]))
#print "saving mode.png"
cv2.imwrite("mode_" + modename + ".png", testing)
#cv2.imwrite("mode_"+ movielist[0] + "_to_" + movielist[len(movielist)] + ".png", testing)
cap.release()
cv2.destroyAllWindows()
def main(pixThreshold, frameRate, videoStream):
row = {0: 0, 1: 12, 2: 24, 3: 36, 4: 48, 5: 60, 6: 72, 7: 84}
saveFreq = 4500 # how often to save data, in frames, just making sure this is really big, so I don't have any issues, would be important for memory considerations if I was doing a long movie
#i,m = imageTools.loadImageAndMask()
filenumber = videoStream.split('.')[0].split('_')[
len(videoStream.split('.')[0].split('_')) - 1]
#print "testing: ", filenumber
# if 1 <= int(filenumber) <= 20:
# movielist = list(range(1,21))
# if 21 <= int(filenumber) <= 40:
# movielist = list(range(21,41))
# if 41 <= int(filenumber) <= 60:
# movielist = list(range(41,61))
# if 61 <= int(filenumber) <= 70:
# movielist = list(range(51,71))
# if 71 <= int(filenumber) <= 80:
# movielist = list(range(71,91))
# if 81 <= int(filenumber) <= 478:
# movielist = list(range(int(filenumber)-10,int(filenumber)+10))
# if 479 <= filenumber <= 488:
# movielist = list(range(468,488))
# if 489 <= int(filenumber) <= 498:
# movielist = list(range(489,509))
# if 499 <= int(filenumber) <= 598:
# movielist = list(range(int(filenumber)-10,int(filenumber)+10))
# if 599 <= int(filenumber) <= 608:
# movielist = list(range(599,609))
# if 609 <= int(filenumber) <= 631:
# movielist = list(range(609,632))
# if 632 <= int(filenumber) <= 661:
# movielist = list(range(632,662))
# if 662 <= int(filenumber) <= 691:
# movielist = list(range(662,692))
# if 692 <= int(filenumber) <= 721:
# movielist = list(range(692,722))
# if 722 <= int(filenumber) <= 741:
# movielist = list(range(722,742))
# if 742 <= int(filenumber) <= 781:
# movielist = list(range(742,782))
# if 782 <= int(filenumber) <= 821:
# movielist = list(range(782,822))
# if 822 <= int(filenumber) <= 862:
# movielist = list(range(822,862))
# if 862 <= int(filenumber) <= 901:
# movielist = list(range(862,901))
if 1 <= int(filenumber) <= 20:
movielist = list(range(1, 21))
if 21 <= int(filenumber) <= 40:
movielist = list(range(21, 41))
if 41 <= int(filenumber) <= 60:
movielist = list(range(41, 61))
if 61 <= int(filenumber) <= 70:
movielist = list(range(61, 71))
# if 1 <= int(filenumber) <= 70:
# movielist = list(range(71,111))
if 71 <= int(filenumber) <= 100:
movielist = list(range(71, 111))
if 101 <= int(filenumber) <= 448:
movielist = list(range(int(filenumber) - 20, int(filenumber) + 20))
if 449 <= int(filenumber) <= 488:
movielist = list(range(448, 488))
if 489 <= int(filenumber) <= 528:
movielist = list(range(489, 529))
if 529 <= int(filenumber) <= 568:
movielist = list(range(529, 569))
#movielist = list(range(int(filenumber)-20,int(filenumber)+20))
if 569 <= int(filenumber) <= 608:
movielist = list(range(569, 609))
if 609 <= int(filenumber) <= 631:
movielist = list(range(609, 632))
if 632 <= int(filenumber) <= 661:
movielist = list(range(632, 662))
if 662 <= int(filenumber) <= 691:
movielist = list(range(662, 692))
if 692 <= int(filenumber) <= 721:
movielist = list(range(692, 722))
if 722 <= int(filenumber) <= 741:
movielist = list(range(722, 742))
#if 632 <= int(filenumber) <= 741:
# movielist = list(range(609,632))
if 742 <= int(filenumber) <= 781:
movielist = list(range(742, 782))
if 782 <= int(filenumber) <= 821:
movielist = list(range(782, 822))
if 822 <= int(filenumber) <= 862:
movielist = list(range(822, 862))
if 862 <= int(filenumber) <= 901:
movielist = list(range(862, 901))
modename = str(movielist[0]) + "to" + str(movielist[len(movielist) - 1])
#modename = ''.join(map(str,movielist))
imageMode(movielist, modename)
modefilename = "mode_" + modename + ".png"
#print movielist
try:
mpimg.imread(modefilename)
#print "mode file already generated"
except:
imageMode(movielist, modename)
e = imageTools.loadmodeImage(modefilename)
#e = imageTools.loadModeImage()
roimask = np.zeros((660, 1088))
(maxxysnp, minxysnp) = max_min()
maxxs = []
minxs = []
maxys = []
minys = []
for j in range(0, numberofwells * 2, 2):
if maxxysnp[j] == -100:
# if nothing ever moved in this well and there is no max or min value (could happen with a totally empty well)
maxxs.append(np.nan)
maxys.append(np.nan)
minxs.append(np.nan)
minys.append(np.nan)
else:
maxxs.append(maxxysnp[j])
maxys.append(maxxysnp[j + 1])
minxs.append(minxysnp[j])
minys.append(minxysnp[j + 1])
npmaxxs = np.asarray(maxxs)
npmaxys = np.asarray(maxys)
npminxs = np.asarray(minxs)
npminys = np.asarray(minys)
npmaxxs = np.reshape(npmaxxs, (numberofcols, numberofrows))
npmaxys = np.reshape(npmaxys, (numberofcols, numberofrows)) #12,8
npminxs = np.reshape(npminxs, (numberofcols, numberofrows))
npminys = np.reshape(npminys, (numberofcols, numberofrows))
#print npmaxxs
#print npmaxys
#print npminxs
#print npminys
cmaxxs = []
cminxs = []
cmaxys = []
cminys = []
for j2 in range(0, numberofwells):
maxx = maxxs[well_conversion[j2]]
maxy = maxys[well_conversion[j2]]
miny = minys[well_conversion[j2]]
minx = minxs[well_conversion[j2]]
#print "j2: ", j2, well_conversion[j2], maxx, maxy, minx, miny
#print "wcj2/8: ", well_conversion[j2]/8
#print npmaxxs[well_conversion[j2]/8,:]
#print npminxs[well_conversion[j2]/8,:]
#print np.nanmean(npmaxxs[well_conversion[j2]/8,:])
#print np.nanmean(npminxs[well_conversion[j2]/8,:])
#print "j2/12: ", j2/12
#print npmaxys[:,j2/12]
#print npminys[:,j2/12]
#print np.nanmean(npmaxys[:,j2/12])
#print np.nanmean(npminys[:,j2/12])
if minx == maxx:
maxx = maxx + 2
if miny == maxy:
maxy = maxy + 2
if math.isnan(
float(maxx)
): # could also add a condition if min and max are equal to each other
#print "very first if statement"
maxx = np.nanmean(npmaxxs[well_conversion[j2] / numberofrows, :])
minx = np.nanmean(npminxs[well_conversion[j2] / numberofrows, :])
maxy = np.nanmean(npmaxys[:, j2 / numberofcols])
miny = np.nanmean(npminys[:, j2 / numberofcols])
#print "new means: ", maxx, minx, maxy, miny
# In the case that the entire row never gets any values in any wells and the mean is still NaN
# not 100% sure that this is going to work, will get a runtime warning, so then can check it out??
# mostly not sure about the well_conversions for the Xs
if math.isnan(float(maxx)) and math.isnan(float(minx)):
# print "first if statement"
if well_conversion[j2] < 8:
#print "2nd if statement"
minx = well_conversion[j2]
maxx = well_conversion[j2] + 85
else:
# print "2nd else statement"
minx = cminxs[well_conversion[j2] - 8] + 85
maxx = cmaxxs[well_conversion[j2] - 8] + 85
###if j2 <= 11:
# print "3rd if statement"
### miny = j2
### maxy = j2+60
### minx = j2
if math.isnan(float(maxy)) and math.isnan(float(miny)):
#print "4th if statement"
if j2 < 12:
# print "5th if statement"
miny = j2
maxy = j2 + 85
else:
# print "5th else statement"
miny = cminys[j2 - 12] + 85
maxy = cmaxys[j2 - 12] + 85
# End of untested section
cmaxxs.append(maxx)
cmaxys.append(maxy)
cminxs.append(minx)
cminys.append(miny)
#print miny, maxy, minx, maxx, j2, j2+1
roimask[miny:maxy, minx:maxx] = j2 + 1
np.set_printoptions(threshold=np.nan) # printing entire array
cmaxxs.sort()
cmaxys.sort()
cminxs.sort()
cminys.sort()
rm, roimaskweights = imageTools.convertMaskToWeights(roimask)
# start camera or open video
videoType, displayDiffs = imageTools.getVideoType(videoStream)
cap = cv2.VideoCapture(videoStream)
# adjust video resolution if necessary (sized to mask)
print 'Camera resolution is %s x %s' % (str(
roimask.shape[1]), str(roimask.shape[0]))
cap.set(3, roimask.shape[1])
cap.set(4, roimask.shape[0])
# Set Pixel Threshold
ret, frame = cap.read()
storedImage = np.array(e * 255, dtype=np.uint8)
# have to convert the float32 to uint8
storedMode = imageTools.Blur(storedImage)
storedFrame = imageTools.grayBlur(frame)
#pixThreshold = int(np.floor( pixThreshold * storedFrame.shape[0] ))
print('PixelThreshold is %i') % pixThreshold
#cenData = np.zeros([ saveFreq, len(np.unique(roimaskweights))*2])
cenData = np.zeros([saveFreq, len(np.unique(roimaskweights)) * 2 - 2])
#print "cenData shape: ", np.shape(cenData)
pixData = np.zeros([saveFreq, len(np.unique(roimaskweights))])
#pixData = np.zeros([ saveFreq, len(np.unique(roimaskweights))])
i = 0 # a counter for saving chunks of data
totalFrames = 0
startTime = datetime.now()
print('Analyzing motion data...')
frame_roi = []
while (cap.isOpened()):
ret, frame = cap.read()
if ret == False:
print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
currentFrame2 = imageTools.grayBlur(frame)
diffpix = imageTools.diffImage(storedFrame, currentFrame2,
pixThreshold, displayDiffs)
diff = imageTools.trackdiffImage(storedMode, currentFrame,
pixThreshold, displayDiffs)
#cv2.imwrite(videoStream + '_diffimage_' + str(i) + ".png", diff)
diff.dtype = np.uint8
_, contours, hierarchy = cv2.findContours(diff, cv2.RETR_TREE,
cv2.CHAIN_APPROX_NONE)
MIN_THRESH = 20.0
MIN_THRESH_P = 20.0
roi_dict = {}
for r in range(0, numberofwells):
roi_dict[r + 1] = []
for cs in range(0, len(contours)):
#print "area and lenght: ", cv2.contourArea(contours[cs]), cv2.arcLength(contours[cs], True)
if cv2.contourArea(contours[cs]) < 1.0:
continue
if cv2.arcLength(contours[cs], True) < 1.0:
continue
if cv2.contourArea(contours[cs]) > MIN_THRESH or cv2.arcLength(
contours[cs], True) > MIN_THRESH_P:
M = cv2.moments(contours[cs])
#print M
cX = int(M["m10"] / M["m00"])
cY = int(M["m01"] / M["m00"])
#print "cX, cY :", cX, cY
r = 1
c = 1
for x in range(0, len(cmaxxs)):
#print "cmaxxs: ", cmaxxs[x]
if cX > cmaxxs[x]:
r = x + 1
#print "r: ", r
#print "r: ", r
for y in range(0, len(cmaxys)):
#print "cmaxys: ", cmaxys[x]
if cY > cmaxys[y]:
c = y + 1
# print "c: ", c
if c == numberofwells:
c = c - 1
if r == numberofwells:
r = r - 1
area = cv2.contourArea(contours[cs])
perim = cv2.arcLength(contours[cs], True)
#print c, numberofcols, c/numberofcols
if not roi_dict[r / numberofrows + 1 + row[c / numberofcols]]:
roi_dict[r / numberofrows + 1 +
row[c / numberofcols]].append(
(area * perim, cX, cY))
else:
if roi_dict[r / numberofrows + 1 +
row[c / numberofcols]] < area * perim:
roi_dict[r / numberofrows + 1 +
row[c / numberofcols]][0] = (area * perim, cX,
cY)
frame_roi.append(roi_dict)
pixcounts = []
pixcounts = np.bincount(roimaskweights, weights=diffpix.ravel())
pixData[i, :] = np.hstack((pixcounts))
counts = []
keys = roi_dict.keys()
keys.sort()
for k in keys:
#print "k: ", k
x = -10000
y = -10000
if roi_dict[k]:
x = roi_dict[k][0][1]
y = roi_dict[k][0][2]
counts.append(x)
counts.append(y)
cv2.line(storedImage, (x, y), (x, y), (255, 255, 255), 2)
if i == 284:
cv2.imwrite(
videoStream + '_trackedimagewithlines_' + str(i) + ".png",
storedImage)
cenData[i, :] = np.asarray(counts)
totalFrames += 1
storedFrame = currentFrame
i += 1
file = open(videoStream + ".centroid2", 'w')
for x in range(0, 285):
for y in range(0, 192):
file.write(str(int(cenData[x, :][y])) + '\n')
pixData = pixData[:i, :]
pixData = pixData[:, 1:] # get rid of background column
file = open(videoStream + ".motion2", 'w')
#file.write("12/8/2015" + '\015')
for x in range(0, 285):
for y in range(0, numberofwells):
file.write(str(int(pixData[x, :][y])) + '\n')
# vidInfo = {}
# release camera
cap.release()
cv2.destroyAllWindows()
def main(pixThreshold, frameRate, videoStream):
expDuration = 600000 # duration of experiment, in seconds; only relevant for live feed
saveFreq = 4500 # how often to save data, in frames
i, m = imageTools.loadImageAndMask()
# convert mask to integer values for bincount weights
m, w = imageTools.convertMaskToWeights(m)
#print m,w
# start camera or open video
videoType, displayDiffs = imageTools.getVideoType(videoStream)
cap = cv2.VideoCapture(videoStream)
# adjust video resolution if necessary (sized to mask)
print 'Camera resolution is %s x %s' % (str(m.shape[1]), str(m.shape[0]))
cap.set(3, m.shape[1])
cap.set(4, m.shape[0])
# Set Pixel Threshold
ret, frame = cap.read()
storedFrame = imageTools.grayBlur(frame)
pixThreshold = int(np.floor(pixThreshold * storedFrame.shape[0]))
print('PixelThreshold is %i') % pixThreshold
# Acquire data
if saveFreq / frameRate > expDuration: # do shorter of expDuration vs. saveFreq
saveFreq = expDuration * frameRate
pixData = np.zeros([saveFreq, len(np.unique(w)) + 1])
i = 0 # a counter for saving chunks of data
totalFrames = 0
startTime = datetime.now()
oldTime = startTime
elapsed = 0
print('Analyzing motion data...')
moviedeq = []
while (cap.isOpened()):
ret, frame = cap.read()
if ret == False:
print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
moviedeq.append(currentFrame)
# check if i bigger than saveFreq. If yes, save and reset values
## if i >= saveFreq:
# save data
## timeStamp = datetime.now()
# make a directory to save stuff in? %m%d%y%H%M
## fname = 'data' + videoStream + timeStamp.strftime('%m%d%y%H%M%S') + '.npy'
#fname = 'data' + timeStamp.strftime('%m%d%y%H%M%S') + '.npy'
## np.save(fname,pixData)
# reset pixData and i
## pixData = np.zeros([ saveFreq, len(np.unique(w)) + 1])
## i = 0
# stop experiment if user presses 'q' or if experiment duration is up
if (cv2.waitKey(1) & 0xFF == ord('q') or len(sys.argv) == 1 and
datetime.now() > startTime + timedelta(seconds=expDuration)):
break
# record pixel differences in all of the ROIs
diff = imageTools.diffImage(storedFrame, currentFrame, pixThreshold,
displayDiffs)
timeDiff = 1. / frameRate
elapsed = elapsed + timeDiff
#print elapsed
# calculate and record pixel differences
counts = np.bincount(w, weights=diff.ravel())
#print counts # output
pixData[i, :] = np.hstack((elapsed, counts))
totalFrames += 1
storedFrame = currentFrame # comment out if nothing is in first frame
#oldTime = newTime
i += 1
# done recording. Remove empty rows (those bigger than i) from PixData
pixData = pixData[:i, :]
#print np.shape(pixData)
#print pixData
#testing = calc_mode(moviedeq, np.zeros([660,1088]))
#cv2.imwrite('test_img.jpg', testing)
# Write data to file with timestamp:
# np.save(movieName[:-4] + '.npy', pixData)
##timeStamp = datetime.now()
##fname = 'data' + videoStream + timeStamp.strftime('%m%d%y%H%M%S') + '.npy'
#fname = 'data' + timeStamp.strftime('%m%d%y%H%M%S') + '.npy'
##np.save(fname,pixData)
pixData = pixData[:, 2:] # get rid of timing column and background column
#print np.shape(pixData)
#print pixData
#pixData = deltaPix[:,1:] # get rid of background column
file = open(videoStream + ".motion2", 'w')
file.write("12/8/2015" + '\015')
for x in range(0, 285):
#print "x", x
for y in range(0, 96):
#print "y", y
#print str(int(pixData[x,:][y]))
file.write(str(int(pixData[x, :][y])) + '\n')
# Save info (elapsed time and framerate) for later use
vidInfo = {}
#analysisTime = timeStamp - startTime
#vidInfo['analysisTime'] = float(str(analysisTime.seconds) + '.' + str(analysisTime.microseconds))
vidInfo['TotalFrames'] = totalFrames
#vidInfo['fps'] = int(totalFrames/vidInfo['analysisTime'])
vidInfo['pixThreshold'] = pixThreshold
vidInfo['CameraResolution'] = '%s x %s' % (str(m.shape[1]), str(
m.shape[0]))
vidInfo['NamePrefix'] = videoStream
#vidInfo['NamePrefix'] = videoStream.split('.')[0]
#print ('Analyzed %i frames in %f seconds') % (vidInfo['TotalFrames'],vidInfo['analysisTime'])
#print('FrameRate is about %i fps') % vidInfo['fps']
print 'Motion threshold is %i pixels' % int(pixThreshold)
print 'Camera resolution is %s' % vidInfo['CameraResolution']
# release camera
cap.release()
cv2.destroyAllWindows()
return vidInfo
def main(pixThreshold,frameRate,videoStream):
#elate_loc={(1,1):1, (1,2):2, (1,3):3, (1,4):4, (1:5):5, (1,6):6, (1,7):7, (1,8):8, (1,9):9,(1,10):10,(1,11):11,(1,12):12,(2,1):13,(2,2):14,(2,3):15,(2,4):16,(2:5):17,(2,6):18,(2,7):19,(2,8):20,(2,9):21,(2,10):22,(2,11):23,(2,12):24,(3,1):25,(3,2):26,(3,3):27,(3,4):28,(3,5):29,(3,6):30,(3,7)}
rowold={1:0,2:12,3:24,4:36,5:48,6:60,7:72,8:84}
row={0:0,1:12,2:24,3:36,4:48,5:60,6:72,7:84}
expDuration = 600000 # duration of experiment, in seconds; only relevant for live feed
saveFreq = 4500 # how often to save data, in frames
i,m = imageTools.loadImageAndMask()
e = imageTools.loadModeImage()
roimask = np.zeros((660,1088))
(maxxysnp, minxysnp) = max_min()
print "maxxysnp: ", maxxysnp
print "minxysnp: ", minxysnp
maxxs = []
minxs = []
maxys = []
minys = []
for j in range (0, numberofwells*2,2):
maxx = maxxysnp[j]
maxxs.append(maxxysnp[j])
maxy = maxxysnp[j+1]
maxys.append(maxxysnp[j+1])
minx = minxysnp[j]
minxs.append(minxysnp[j])
miny = minxysnp[j+1]
minys.append(minxysnp[j+1])
roimask[miny:maxy,minx:maxx] = j+1
maxxs.sort()
maxys.sort()
minxs.sort()
minys.sort()
#smaxxs = []
#sminxs = []
#smaxys = []
#sminys = []
#rx = 8
#cy = 12
#realmaxx = 0
#realmaxxs = []
#for z in range(0, len(maxxs)):
# if z == cy - 1:
# realmaxxs.append(realmaxx)
# realmaxx = 0
# if maxxs[z] > realmaxx:
# realmaxx = maxxs[z]
np.set_printoptions(threshold=np.nan) # printing entire array
print roimask
# print maxx,maxy,minx,miny
#print e
#cv2.imwrite('testinge.jpg', e)
#cv2.imwrite('testingm.jpg', m)
#cv2.imwrite('testingi.jpg', i)
# convert mask to integer values for bincount weights
#print "mask1: ", np.shape(m), m
m,w = imageTools.convertMaskToWeights(m)
rm,roimaskweights = imageTools.convertMaskToWeights(roimask)
#print "mask2: ", np.shape(m), m
#print "weights: ", np.shape(w), w
unique = np.unique(m)
print "unique: ", unique
unique2 = np.unique(rm)
print "unique2: ", unique2
#print np.shape(m)
rminr = set()
rminc = set()
rmaxr = set()
rmaxc = set()
for x in unique2:
#print "x: ", x
#if x == 0:
# continue
#print np.shape(np.where(m==x))
#print np.where(m==x)
rmaxdimc = np.amax(np.where(rm==x)[0])
rmaxc.add(rmaxdimc)
#print "max dimc: ", np.amax(np.where(m==x)[0])
rmaxdimr = np.amax(np.where(rm==x)[1])
rmaxr.add(rmaxdimr)
#print "max dimr: ", np.amax(np.where(m==x)[1])
rmindimc = np.amin(np.where(rm==x)[0])
rminc.add(rmindimc)
#print "min dimc: ", np.amin(np.where(m==x)[0])
rmindimr = np.amin(np.where(rm==x)[1])
rminr.add(rmindimr)
#print "min dimr: ", np.amin(np.where(m==x)[1])
rlminx = list(rminr)
rlminx.sort()
rlmaxx = list(rmaxr)
rlmaxx.sort()
rlminy = list(rminc)
rlminy.sort()
rlmaxy = list(rmaxc)
rlmaxy.sort()
print rlminx, rlmaxx, rlminy, rlmaxy
minr = set()
minc = set()
maxr = set()
maxc = set()
for x in unique:
#print "x: ", x
if x == 0:
continue
#print np.shape(np.where(m==x))
#print np.where(m==x)
maxdimc = np.amax(np.where(m==x)[0])
maxc.add(maxdimc)
#print "max dimc: ", np.amax(np.where(m==x)[0])
maxdimr = np.amax(np.where(m==x)[1])
maxr.add(maxdimr)
#print "max dimr: ", np.amax(np.where(m==x)[1])
mindimc = np.amin(np.where(m==x)[0])
minc.add(mindimc)
#print "min dimc: ", np.amin(np.where(m==x)[0])
mindimr = np.amin(np.where(m==x)[1])
minr.add(mindimr)
#print "min dimr: ", np.amin(np.where(m==x)[1])
#print minr, maxr, minc, maxc
lminx = list(minr)
lminx.sort()
lmaxx = list(maxr)
lmaxx.sort()
lminy = list(minc)
lminy.sort()
lmaxy = list(maxc)
lmaxy.sort()
print "real mask: ", lminx, lmaxx, lminy, lmaxy
#print lminr, lmaxr, lminc, lmaxc
#print np.where(m==75)
#for x in len(m):
#print m[x]
#print "mask2: ", np.shape(m), m
#print "mask: ", np.nonzero(m)
#print m,w
# start camera or open video
videoType, displayDiffs = imageTools.getVideoType(videoStream)
cap = cv2.VideoCapture(videoStream)
# adjust video resolution if necessary (sized to mask)
print 'Camera resolution is %s x %s' % (str(m.shape[1]),str(m.shape[0]))
cap.set(3,m.shape[1])
cap.set(4,m.shape[0])
# Set Pixel Threshold
ret,frame = cap.read()
storedImage = np.array(e * 255, dtype = np.uint8)
# have to convert the float32 to uint8
storedMode = imageTools.Blur(storedImage)
storedFrame = imageTools.grayBlur(frame)
pixThreshold = int(np.floor( pixThreshold * storedFrame.shape[0] ))
print('PixelThreshold is %i') % pixThreshold
cenData = np.zeros([ saveFreq, len(np.unique(w))*2 -2])
pixData = np.zeros([ saveFreq, len(np.unique(w)) + 1])
i = 0 # a counter for saving chunks of data
totalFrames = 0
startTime = datetime.now()
oldTime = startTime
elapsed = 0
print('Analyzing motion data...')
frame_roi = []
while(cap.isOpened()):
#print "frames", totalFrames
ret,frame = cap.read()
if ret == False:
print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
currentFrame2 = imageTools.grayBlur(frame)
diffpix = imageTools.diffImage(storedFrame,currentFrame2,pixThreshold,displayDiffs)
#print np.shape(diffpix)
#print diffpix # This is 660x1088
diff = imageTools.trackdiffImage(storedMode,currentFrame,pixThreshold,displayDiffs)
diff.dtype = np.uint8
_,contours,hierarchy = cv2.findContours(diff, cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
MIN_THRESH = 20.0
MIN_THRESH_P = 20.0
#if cv2.contourArea(contours[0]) > MIN_THRESH:
# M = cv2.moments(contours[0])
# cX = int(M["m10"] / M["m00"])
# cY = int(M["m01"] / M["m00"])
# print cX,cY
roi_dict = {}
for r in range(0,numberofwells):
roi_dict[r+1] = []
for cs in range(0,len(contours)):
if cv2.contourArea(contours[cs]) > MIN_THRESH or cv2.arcLength(contours[cs],True) > MIN_THRESH_P:
#if cv2.contourArea(contours[cs]) > MIN_THRESH and cv2.arcLength(contours[cs],True) > MIN_THRESH_P:
M = cv2.moments(contours[cs])
cX = int(M["m10"] / M["m00"])
cY = int(M["m01"] / M["m00"])
print i, " cX and cY:", cX, cY
#print lmaxx
#print lmaxy
r=1
c=1
for x in range(0,len(lmaxx)):
if cX > lmaxx[x]:
r=x+2
print "Lx,cX,lmaxx[x],lmin[x] ",x, cX, lmaxx[x], lminx[x]
for y in range(0, len(lmaxy)):
if cY > lmaxy[y]:
c=y+2
print "Ly,cY,maxy[y],lmin[x],r,c ",y, cY, lmaxy[y], lminy[y],r,c
area = cv2.contourArea(contours[cs])
perim = cv2.arcLength(contours[cs],True)
perim = cv2.arcLength(contours[cs],True)
print "L r + c + row[c]: ", r, c, rowold[c]," final well: ", r + rowold[c]
if not roi_dict[r+rowold[c]]:
# roi_dict[r+row[c]].append((area*perim))
roi_dict[r+rowold[c]].append((area*perim,cX,cY))
#roi_dict[r+rowold[c]].append((area*perim,contours[cs]))
else:
if roi_dict[r+rowold[c]] < area*perim:
roi_dict[r+rowold[c]][0] = (area*perim,cX,cY)
print len(maxxs), maxxs, maxys, minxs, minys
for x in range(0,len(maxxs)):
if cX > maxxs[x]:
r=x+1 # maybe DONT ADD TWO?
#r=x+2 # maybe DONT ADD TWO?
print "x,cX,maxx[x],minx[x],r,c: ",x, cX, maxxs[x], minxs[x],r,c
for y in range(0, len(maxys)):
if cY > maxys[y]:
c=y+1
#c=y+2
print "y,cY,maxy[y].miny[y],r,c", y, cY, maxys[y], minys[y],r,c
area = cv2.contourArea(contours[cs])
perim = cv2.arcLength(contours[cs],True)
print "r + c + r/8+1 + c/12: ", r, c, r/8+1, c/12, " row[c/12]: ", row[c/12], " final well: ", r/8 + 1 + row[c/12]
if not roi_dict[r/8+1+row[c/12]]:
# roi_dict[r+row[c]].append((area*perim))
roi_dict[r/8+1+row[c/12]].append((area*perim,cX,cY))
#roi_dict[r+row[c]].append((area*perim,contours[cs]))
else:
if roi_dict[r/8+1+row[c/12]] < area*perim:
roi_dict[r/8+1+row[c/12]][0] = (area*perim,cX,cY)
frame_roi.append(roi_dict)
timeDiff = 1. / frameRate
elapsed = elapsed + timeDiff
pixcounts = []
pixcounts = np.bincount(w, weights=diffpix.ravel())
pixData[i,:] = np.hstack((elapsed,pixcounts))
counts = []
keys = roi_dict.keys()
keys.sort()
for k in keys:
x = -10000
y = -10000
if roi_dict[k]:
x = roi_dict[k][0][1]
y = roi_dict[k][0][2]
counts.append(x)
counts.append(y)
cv2.line(storedImage,(x,y),(x,y),(255,255,255),2)
if i == 284:
cv2.imwrite('trackedimagewithlines_' + str(i) + ".png", storedImage)
cenData[i,:] = np.asarray(counts)
totalFrames += 1
storedFrame = currentFrame
i += 1
file = open(videoStream + ".centroid2",'w')
for x in range(0,285):
for y in range(0,192):
file.write(str(int(cenData[x,:][y])) + '\n')
pixData = pixData[:i,:]
pixData = pixData[:,2:] # get rid of timing column and background column
file = open(videoStream + ".motion2",'w')
file.write("12/8/2015" + '\015')
for x in range(0,285):
#print "x", x
for y in range(0,numberofwells):
file.write(str(int(pixData[x,:][y])) + '\n')
vidInfo = {}
# release camera
cap.release()
cv2.destroyAllWindows()
return vidInfo
def main(pixThreshold, frameRate, videoStream):
#elate_loc={(1,1):1, (1,2):2, (1,3):3, (1,4):4, (1:5):5, (1,6):6, (1,7):7, (1,8):8, (1,9):9,(1,10):10,(1,11):11,(1,12):12,(2,1):13,(2,2):14,(2,3):15,(2,4):16,(2:5):17,(2,6):18,(2,7):19,(2,8):20,(2,9):21,(2,10):22,(2,11):23,(2,12):24,(3,1):25,(3,2):26,(3,3):27,(3,4):28,(3,5):29,(3,6):30,(3,7)}
col = {1: 0, 2: 12, 3: 24, 4: 36, 5: 48, 6: 60, 7: 72, 8: 84}
expDuration = 600000 # duration of experiment, in seconds; only relevant for live feed
saveFreq = 4500 # how often to save data, in frames
i, m = imageTools.loadImageAndMask()
e = imageTools.loadModeImage()
#print e
#cv2.imwrite('testinge.jpg', e)
#cv2.imwrite('testingm.jpg', m)
#cv2.imwrite('testingi.jpg', i)
# convert mask to integer values for bincount weights
np.set_printoptions(threshold=np.nan) # printing entire array
#print "mask1: ", np.shape(m), m
m, w = imageTools.convertMaskToWeights(m)
#print "mask2: ", np.shape(m), m
unique = np.unique(m)
#print np.shape(m)
minr = set()
minc = set()
maxr = set()
maxc = set()
for x in unique:
#print "x: ", x
if x == 0:
continue
#print np.shape(np.where(m==x))
#print np.where(m==x)
maxdimc = np.amax(np.where(m == x)[0])
maxc.add(maxdimc)
#print "max dimc: ", np.amax(np.where(m==x)[0])
maxdimr = np.amax(np.where(m == x)[1])
maxr.add(maxdimr)
#print "max dimr: ", np.amax(np.where(m==x)[1])
mindimc = np.amin(np.where(m == x)[0])
minc.add(mindimc)
#print "min dimc: ", np.amin(np.where(m==x)[0])
mindimr = np.amin(np.where(m == x)[1])
minr.add(mindimr)
#print "min dimr: ", np.amin(np.where(m==x)[1])
#print minr, maxr, minc, maxc
lminx = list(minr)
lminx.sort()
lmaxx = list(maxr)
lmaxx.sort()
lminy = list(minc)
lminy.sort()
lmaxy = list(maxc)
lmaxy.sort()
#print lminr, lmaxr, lminc, lmaxc
#print np.where(m==75)
#for x in len(m):
#print m[x]
#print "mask2: ", np.shape(m), m
#print "mask: ", np.nonzero(m)
#print m,w
# start camera or open video
videoType, displayDiffs = imageTools.getVideoType(videoStream)
cap = cv2.VideoCapture(videoStream)
# adjust video resolution if necessary (sized to mask)
print 'Camera resolution is %s x %s' % (str(m.shape[1]), str(m.shape[0]))
cap.set(3, m.shape[1])
cap.set(4, m.shape[0])
# Set Pixel Threshold
ret, frame = cap.read()
storedImage = np.array(e * 255, dtype=np.uint8)
# have to convert the float32 to uint8, hopefully this is doing it correctly (found online)
storedFrame = imageTools.Blur(storedImage)
#storedFrame = imageTools.grayBlur(frame)
pixThreshold = int(np.floor(pixThreshold * storedFrame.shape[0]))
print('PixelThreshold is %i') % pixThreshold
# Acquire data
if saveFreq / frameRate > expDuration: # do shorter of expDuration vs. saveFreq
saveFreq = expDuration * frameRate
pixData = np.zeros([saveFreq, len(np.unique(w)) * 2 - 2])
i = 0 # a counter for saving chunks of data
totalFrames = 0
startTime = datetime.now()
oldTime = startTime
elapsed = 0
print('Analyzing motion data...')
moviedeq = []
frame_roi = []
while (cap.isOpened()):
ret, frame = cap.read()
if ret == False:
print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
moviedeq.append(currentFrame)
# stop experiment if user presses 'q' or if experiment duration is up
if (cv2.waitKey(1) & 0xFF == ord('q') or len(sys.argv) == 1 and
datetime.now() > startTime + timedelta(seconds=expDuration)):
break
diff = imageTools.trackdiffImage(storedFrame, currentFrame,
pixThreshold, displayDiffs)
diff.dtype = np.uint8
_, contours, hierarchy = cv2.findContours(diff, cv2.RETR_TREE,
cv2.CHAIN_APPROX_NONE)
MIN_THRESH = 20.0
MIN_THRESH_P = 20.0
#if cv2.contourArea(contours[0]) > MIN_THRESH:
# M = cv2.moments(contours[0])
# cX = int(M["m10"] / M["m00"])
# cY = int(M["m01"] / M["m00"])
# print cX,cY
roi_dict = {}
for r in range(0, 96):
roi_dict[r + 1] = []
for cs in range(0, len(contours)):
if cv2.contourArea(contours[cs]) > MIN_THRESH or cv2.arcLength(
contours[cs], True) > MIN_THRESH_P:
#if cv2.contourArea(contours[cs]) > MIN_THRESH and cv2.arcLength(contours[cs],True) > MIN_THRESH_P:
M = cv2.moments(contours[cs])
cX = int(M["m10"] / M["m00"])
cY = int(M["m01"] / M["m00"])
#print i, " cX and cY:", cX, cY
#print lmaxx
#print lmaxy
r = 1
c = 1
for x in range(0, len(lmaxx)):
if cX > lmaxx[x]:
r = x + 2
# print x, cX, lmaxx[x], lminx[x]
for y in range(0, len(lmaxy)):
if cY > lmaxy[y]:
c = y + 2
# print y, cY, lmaxy[y], lminy[y]
area = cv2.contourArea(contours[cs])
perim = cv2.arcLength(contours[cs], True)
if not roi_dict[r + col[c]]:
# roi_dict[r+col[c]].append((area*perim))
roi_dict[r + col[c]].append((area * perim, cX, cY))
#roi_dict[r+col[c]].append((area*perim,contours[cs]))
else:
if roi_dict[r + col[c]] < area * perim:
roi_dict[r + col[c]][0] = (area * perim, cX, cY)
frame_roi.append(roi_dict)
timeDiff = 1. / frameRate
elapsed = elapsed + timeDiff
counts = []
keys = roi_dict.keys()
keys.sort()
for k in keys:
x = -10000
y = -10000
if roi_dict[k]:
x = roi_dict[k][0][1]
y = roi_dict[k][0][2]
counts.append(x)
counts.append(y)
cv2.line(storedImage, (x, y), (x, y), (255, 255, 255), 2)
cv2.imwrite('withlines' + str(i) + ".png", storedImage)
pixData[i, :] = np.asarray(counts)
totalFrames += 1
file = open(videoStream + ".centroid2", 'w')
for x in range(0, 285):
for y in range(0, 192):
file.write(str(int(pixData[x, :][y])) + '\n')
# Save info (elapsed time and framerate) for later use
vidInfo = {}
analysisTime = timeStamp - startTime
vidInfo['analysisTime'] = float(
str(analysisTime.seconds) + '.' + str(analysisTime.microseconds))
vidInfo['TotalFrames'] = totalFrames
vidInfo['fps'] = int(totalFrames / vidInfo['analysisTime'])
vidInfo['pixThreshold'] = pixThreshold
vidInfo['CameraResolution'] = '%s x %s' % (str(m.shape[1]), str(
m.shape[0]))
vidInfo['NamePrefix'] = videoStream
#vidInfo['NamePrefix'] = videoStream.split('.')[0]
print('Analyzed %i frames in %f seconds') % (vidInfo['TotalFrames'],
vidInfo['analysisTime'])
print('FrameRate is about %i fps') % vidInfo['fps']
print 'Motion threshold is %i pixels' % int(pixThreshold)
print 'Camera resolution is %s' % vidInfo['CameraResolution']
# release camera
cap.release()
cv2.destroyAllWindows()
return vidInfo
def main(pixThreshold,frameRate,videoStream):
row={0:0,1:12,2:24,3:36,4:48,5:60,6:72,7:84}
saveFreq = 4500 # how often to save data, in frames, just making sure this is really big, so I don't have any issues, would be important for memory considerations if I was doing a long movie
#print (videoStream)
filenumber = videoStream.split('.')[0].split('_')[len(videoStream.split('.')[0].split('_'))-1]
# print (filenumber)
# if 1 <= int(filenumber) <= 20:
# movielist = list(range(1,21))
# if 21 <= int(filenumber) <= 40:
# movielist = list(range(21,41))
# if 41 <= int(filenumber) <= 60:
# movielist = list(range(41,61))
# if 61 <= int(filenumber) <= 70:
# movielist = list(range(51,71))
# if 71 <= int(filenumber) <= 80:
# movielist = list(range(71,91))
# if 81 <= int(filenumber) <= 478:
# movielist = list(range(int(filenumber)-10,int(filenumber)+10))
# if 479 <= filenumber <= 488:
# movielist = list(range(468,488))
# if 489 <= int(filenumber) <= 498:
# movielist = list(range(489,509))
# if 499 <= int(filenumber) <= 598:
# movielist = list(range(int(filenumber)-10,int(filenumber)+10))
# if 599 <= int(filenumber) <= 608:
# movielist = list(range(599,609))
# if 609 <= int(filenumber) <= 631:
# movielist = list(range(609,632))
# if 632 <= int(filenumber) <= 661:
# movielist = list(range(632,662))
# if 662 <= int(filenumber) <= 691:
# movielist = list(range(662,692))
# if 692 <= int(filenumber) <= 721:
# movielist = list(range(692,722))
# if 722 <= int(filenumber) <= 741:
# movielist = list(range(722,742))
# if 742 <= int(filenumber) <= 781:
# movielist = list(range(742,782))
# if 782 <= int(filenumber) <= 821:
# movielist = list(range(782,822))
# if 822 <= int(filenumber) <= 862:
# movielist = list(range(822,862))
# if 862 <= int(filenumber) <= 901:
# movielist = list(range(862,901))
# if 241 <= int(filenumber) <= 270:
# movielist = list(range(241,271))
# if 271 <= int(filenumber) <= 275:
# movielist = list(range(271,276))
# if 276 <= int(filenumber) <= 292:
# movielist = list(range(276,293))
# if 306 <= int(filenumber) <= 335:
# movielist = list(range(306,336))
# if 336 <= int(filenumber) <= 365:
# movielist = list(range(336,366))
# if 366 <= int(filenumber) <= 395:
# movielist = list(range(366,396))
# if 396 <= int(filenumber) <= 425:
# movielist = list(range(396,426))
# if 426 <= int(filenumber) <= 455:
# movielist = list(range(426,456))
# if 456 <= int(filenumber) <= 485:
# movielist = list(range(456,486))
# if 486 <= int(filenumber) <= 503:
# movielist = list(range(486,504))
# f = open(eventsfile, 'r')
# lines = f.readlines()
# numcounter = 0
# counter = 0
# fullcounter = 0
#1:06:24\tPM\t0\t2\n'
# movielist = []
# movielists =[]
# timestamp_list = []
# filteredlist = []
# startdate = "2020-02-26"
# for line in lines:
# TAPES = line.split('\t')
#print(TAPES)
# if int(TAPES[2]) == 1 or int(TAPES[2]) == 2:
# filteredlist.append(line)
# for newline in filteredlist:
# print(line)
# TAPES = newline.split('\t')
# print(line)
# something = TAPES[2]
# fullcounter +=1
#print "early", TAPES[2], TAPES[3]
# need to be splitting on tab for the new format of the input file with the spaces in last column
#TAPES = line.split('')
# if int(TAPES[2]) == 2:
# timestamp_list.append(0)
# continue
# startdate2 = startdate.split("-")[1] + "/" + startdate.split("-")[2] + "/" + startdate.split("-")[0]
# dateplustime = startdate2 + TAPES[0][0:len(TAPES[0])]
# thistime = faststrptime(dateplustime)
# unixtimestamp = dt.timestamp(thistime)
# timestamp_list.append(int(unixtimestamp))
# i = 0
# for element in timestamp_list:
# if i < (len(timestamp_list)-1) and timestamp_list[i+(counter - i)]-timestamp_list[i] >= 3600:
# counter += 1
# i = counter
# movielist.append(counter)
#
# if len(movielist) <= 15:
# numcounter = 0
# j = 0
# for step in movielist:
# movielists[len(movielists)-1].append(movielist[j])
# j += 1
# movielist = []
# continue
# else:
# movielists.append(movielist)
# movielist = []
# numcounter = 0
# continue
# if i < (len(timestamp_list)-1) and timestamp_list[i+1]-timestamp_list[i] >= 3600:
# counter += 1
# i = counter
# movielist.append(counter)
# if len(movielist) <= 15:
# numcounter = 0
# j = 0
# for step in movielist:
# movielists[len(movielists)-1].append(movielist[j])
# j += 1
# movielist = []
# continue
# else:
# movielists.append(movielist)
# movielist = []
# numcounter = 0
# continue
# counter += 1
# numcounter += 1
# if element != 0:
# movielist.append(counter)
# i += 1
# if numcounter == 30:
# numcounter = 0
# movielists.append(movielist)
# movielist = []
# if i > (len(timestamp_list)-1):
# movielists.append(movielist)
# movielist = []
# numcounter = 0
# print(movielists)
# numendlists = counter - fullcounter
# first = len(movielists)-numendlists
# last = len(movielists)
# del movielists[first:last]
# for x in movielists:
# for y in x:
# if int(filenumber) == y:
# movielist = x
# print(movielists)
movielist = [1,2]
modename = str(movielist[0]) + "to" + str(movielist[len(movielist)-1])
#imageMode(movielist, modename)
modefilename = "mode_" + modename + ".png"
#print (movielist)
try:
# mpimg.imread(modefilename)
imageTools.loadmodeImage(modefilename)
#cv2.imread(modefilename)
except:
imageMode(movielist, modename)
e = imageTools.loadmodeImage(modefilename)
#e = imageTools.loadModeImage()
roimask = np.zeros((660,1088))
(maxxysnp, minxysnp) = max_min()
maxxs = []
minxs = []
maxys = []
minys = []
for j in range (0, numberofwells*2,2):
if maxxysnp[j] == -100:
# if nothing ever moved in this well and there is no max or min value (could happen with a totally empty well)
maxxs.append(np.nan)
maxys.append(np.nan)
minxs.append(np.nan)
minys.append(np.nan)
else:
maxxs.append(maxxysnp[j])
maxys.append(maxxysnp[j+1])
minxs.append(minxysnp[j])
minys.append(minxysnp[j+1])
npmaxxs = np.asarray(maxxs)
npmaxys = np.asarray(maxys)
npminxs = np.asarray(minxs)
npminys = np.asarray(minys)
npmaxxs = np.reshape(npmaxxs, (numberofcols,numberofrows))
npmaxys = np.reshape(npmaxys, (numberofcols,numberofrows)) #12,8
npminxs = np.reshape(npminxs, (numberofcols,numberofrows))
npminys = np.reshape(npminys, (numberofcols,numberofrows))
#print npmaxxs
#print npmaxys
#print npminxs
#print npminys
cmaxxs = []
cminxs = []
cmaxys = []
cminys = []
for j2 in range (0, numberofwells):
maxx = maxxs[well_conversion[j2]]
maxy = maxys[well_conversion[j2]]
miny = minys[well_conversion[j2]]
minx = minxs[well_conversion[j2]]
#print "j2: ", j2, well_conversion[j2], maxx, maxy, minx, miny
#print "wcj2/8: ", well_conversion[j2]/8
#print npmaxxs[well_conversion[j2]/8,:]
#print npminxs[well_conversion[j2]/8,:]
#print np.nanmean(npmaxxs[well_conversion[j2]/8,:])
#print np.nanmean(npminxs[well_conversion[j2]/8,:])
#print "j2/12: ", j2/12
#print npmaxys[:,j2/12]
#print npminys[:,j2/12]
#print np.nanmean(npmaxys[:,j2/12])
#print np.nanmean(npminys[:,j2/12])
if minx == maxx:
maxx = maxx + 2
if miny == maxy:
maxy = maxy + 2
if math.isnan(float(maxx)): # could also add a condition if min and max are equal to each other
#print "very first if statement"
maxx = np.nanmean(npmaxxs[int(well_conversion[j2]/numberofrows),:])
minx = np.nanmean(npminxs[int(well_conversion[j2]/numberofrows),:])
maxy = np.nanmean(npmaxys[:,int(j2/numberofcols)])
miny = np.nanmean(npminys[:,int(j2/numberofcols)])
#print "new means: ", maxx, minx, maxy, miny
# In the case that the entire row never gets any values in any wells and the mean is still NaN
# not 100% sure that this is going to work, will get a runtime warning, so then can check it out??
# mostly not sure about the well_conversions for the Xs
if math.isnan(float(maxx)) and math.isnan(float(minx)):
# print "first if statement"
if well_conversion[j2] < 8:
#print "2nd if statement"
minx = well_conversion[j2]
maxx = well_conversion[j2]+85
else:
# print "2nd else statement"
minx = cminxs[well_conversion[j2]-8] + 85
maxx = cmaxxs[well_conversion[j2]-8] + 85
###if j2 <= 11:
# print "3rd if statement"
### miny = j2
### maxy = j2+60
### minx = j2
if math.isnan(float(maxy)) and math.isnan(float(miny)):
#print "4th if statement"
if j2 < 12:
# print "5th if statement"
miny = j2
maxy = j2+85
else:
# print "5th else statement"
miny = cminys[j2-12] + 85
maxy = cmaxys[j2-12] + 85
# End of untested section
# hack, 06/11/18
if miny == maxy:
maxy = maxy+1
if minx == maxx:
maxx = maxx+1
# end of hack
cmaxxs.append(maxx)
cmaxys.append(maxy)
cminxs.append(minx)
cminys.append(miny)
#print (miny, maxy, minx, maxx, j2, j2+1)
roimask[int(miny):int(maxy),int(minx):int(maxx)] = j2+1
#np.set_printoptions(threshold=np.nan) # printing entire array
cmaxxs.sort()
cmaxys.sort()
cminxs.sort()
cminys.sort()
rm,roimaskweights = imageTools.convertMaskToWeights(roimask)
# start camera or open video
videoType, displayDiffs = imageTools.getVideoType(videoStream)
cap = cv2.VideoCapture(videoStream)
# adjust video resolution if necessary (sized to mask)
#print 'Camera resolution is %s x %s' % (str(roimask.shape[1]),str(roimask.shape[0]))
cap.set(3,roimask.shape[1])
cap.set(4,roimask.shape[0])
# Set Pixel Threshold
ret,frame = cap.read()
storedImage = np.array(e * 255, dtype = np.uint8)
# have to convert the float32 to uint8
storedMode = imageTools.Blur(storedImage)
storedFrame = imageTools.grayBlur(frame)
#pixThreshold = int(np.floor( pixThreshold * storedFrame.shape[0] ))
#print('PixelThreshold is %i') % pixThreshold
#cenData = np.zeros([ saveFreq, len(np.unique(roimaskweights))*2])
# print "roimaskweights: "
# print np.shape(roimaskweights)
# print roimaskweights
# print "Unique: "
# print np.unique(roimaskweights)
# print (len(np.unique(roimaskweights))*2 - 2)
# print np.shape(roimaskweights)
cenData = np.zeros([ saveFreq, len(np.unique(roimaskweights))*2 -2])
# print "cenData shape: ", np.shape(cenData)
#print "testing hack below!"
#cenData = np.zeros([4500, 192])
pixData = np.zeros([ saveFreq, len(np.unique(roimaskweights))])
#print "testing hack below!"
#pixData = np.zeros([4500, 95])
#pixData = np.zeros([ saveFreq, len(np.unique(roimaskweights))])
i = 0 # a counter for saving chunks of data
totalFrames = 0
# startTime = datetime.now()
#print('Analyzing motion data...')
frame_roi = []
# storedImage = cv2.cvtColor(e*255, cv2.COLOR_GRAY2BGR)
completed_t = []
f_t = []
while(cap.isOpened()):
ret,frame = cap.read()
if ret == False:
#print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
currentFrame2 = imageTools.grayBlur(frame)
diffpix = imageTools.diffImage(storedFrame,currentFrame2,pixThreshold,displayDiffs)
diff = imageTools.trackdiffImage(storedMode,currentFrame,pixThreshold,displayDiffs)
#cv2.imwrite(videoStream + '_diffimage_' + str(i) + ".png", diff)
diff.dtype = np.uint8
contours,hierarchy = cv2.findContours(diff, cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
area = 20
fishfilter_top = []
for t in contours:
if area <= cv2.contourArea(t) < 200:
(x,y), r = cv2.minEnclosingCircle(t)
center = (int(x),int(y))
fishfilter_top.append(center)
# fishfiltertop = [cv2.minEnclosingCircle(t)[0] for t in contours if area <= cv2.contourArea(t) < 50]
if i == 0:
f_t = [Fish(i, fish) for fish in fishfilter_top]
# print([pr.location for pr in p_t])
number_of_colors = len(f_t)
else:
for n in f_t:
n.nearby(fishfilter_top)
newfish_t = [Fish(i, cord) for cord in fishfilter_top]
#if i == 1:
# print([pr.location for pr in newfish_t])
# print(len(newfish_t))
f_t = f_t + newfish_t
xy_complete = list(filter(lambda x: x.completed, f_t))
completed_t = completed_t + xy_complete
f_t = list(filter(lambda x: not x.completed, f_t))
# if i == 100:
# cv2.imwrite(videoStream + '_frame_' + str(i) + ".png", frame)
# if i == 284:
# cv2.imwrite(videoStream + '_frame_' + str(i) + ".png", frame)
# if i == 1:
# cv2.imwrite(videoStream + '_frame_' + str(i) + ".png", frame)
# img = cv2.drawContours(frame, contours, -1, (0, 255, 0), 2)
# cv2.imwrite(videoStream + '_contourimage_' + str(i) + ".png", img)
MIN_THRESH = 20.0
MIN_THRESH_P = 20.0
roi_dict = {}
for r in range(0,numberofwells):
roi_dict[r+1] = []
for cs in range(0,len(contours)):
#print "area and lenght: ", cv2.contourArea(contours[cs]), cv2.arcLength(contours[cs], True)
if cv2.contourArea(contours[cs]) < 1.0:
continue
if cv2.arcLength(contours[cs],True) < 1.0:
continue
if cv2.contourArea(contours[cs]) > MIN_THRESH or cv2.arcLength(contours[cs],True) > MIN_THRESH_P:
M = cv2.moments(contours[cs])
#print M
cX = int(M["m10"] / M["m00"])
cY = int(M["m01"] / M["m00"])
#print "cX, cY :", cX, cY
r=1
c=1
for x in range(0,len(cmaxxs)):
#print "cmaxxs: ", cmaxxs[x]
if cX > cmaxxs[x]:
r=x+1
#print "r: ", r
#print "r: ", r
for y in range(0, len(cmaxys)):
#print "cmaxys: ", cmaxys[x]
if cY > cmaxys[y]:
c=y+1
# print "c: ", c
if c == numberofwells:
c = c-1
if r == numberofwells:
r = r-1
area = cv2.contourArea(contours[cs])
perim = cv2.arcLength(contours[cs],True)
#print (c, numberofcols, c/numberofcols, r, numberofrows, r/numberofrows)
#print ("TEST: ", roi_dict[int(r/numberofrows)+1+row[int(c/numberofcols)]], area*perim)
# if not roi_dict[int(r/numberofrows)+1+row[int(c/numberofcols)]]:
# roi_dict[int(r/numberofrows)+1+row[int(c/numberofcols)]].append((area*perim,cX,cY))
# else:
#print ("TEST2")
# if roi_dict[int(r/numberofrows)+1+row[int(c/numberofcols)]][0][0] < area*perim:
# roi_dict[int(r/numberofrows)+1+row[int(c/numberofcols)]][0] = (area*perim,cX,cY)
frame_roi.append(roi_dict)
pixcounts = []
pixcounts = np.bincount(roimaskweights, weights=diffpix.ravel())
pixData[i,:] = np.hstack((pixcounts))
counts = []
keys = roi_dict.keys()
keys = sorted(keys)
for k in keys:
#print "k: ", k
x = -10000
y = -10000
if roi_dict[k]:
x = roi_dict[k][0][1]
y = roi_dict[k][0][2]
counts.append(x)
counts.append(y)
cv2.line(storedImage,(x,y),(x,y),(255,255,255),2)
# cv2.line(storedImage,(x,y),(x,y),(233,178,101),2)
if i == 749:
cv2.imwrite(videoStream + '_trackedimagewithlines_' + str(i) + ".png", storedImage)
#print len(counts)
cenData[i,:] = np.asarray(counts)
totalFrames += 1
storedFrame = currentFrame
i += 1
# print(len(p_t))
all_xy = []
all_xy = completed_t + f_t
all_xy = sorted(all_xy, key=lambda x: len(x.location))
all_xy.reverse()
for n in all_xy:
n.calcdistance()
# print(n.totaldistance)
print(n.displacement)
all_xy = [fish for fish in all_xy if fish.timestamp + len(fish.location) > 745 and int(fish.displacement) > 10]
myFrameNumber = 749
cap = cv2.VideoCapture(videoStream)
totalFrames = cap.get(cv2.CAP_PROP_FRAME_COUNT)
if myFrameNumber >= 0 & myFrameNumber <= totalFrames:
cap.set(cv2.CAP_PROP_POS_FRAMES,myFrameNumber)
ret, frame = cap.read()
# cv2.imwrite("lastframe.png", frame)
image = plt.imread('lastframefilter.png')
# implot = plt.imshow(image)
# colours = []
# for i in range(number_of_colors):
# r = random.randint(0,255)
# g = random.randint(0,255)
# b = random.randint(0,255)
# rgb = tuple([r,g,b])
# colours.append(rgb)
plt.figure(figsize=(20,20))
implot = plt.imshow(image)
# fig,ax = plt.subplots(1)
# ax.set_aspect('equal')
# ax.axis('off')
for i,fish in enumerate(all_xy):
# print(fish.location)
xylist = [list(num) for num in fish.location]
newlist = []
newlist.append(xylist[0])
for j in range(0,len(xylist)-1):
distance = math.sqrt((xylist[j+1][0]-xylist[j][0])*(xylist[j+1][0]-xylist[j][0]) + (xylist[j+1][1]-xylist[j][1])*(xylist[j+1][1]-xylist[j][1]))
if distance > -1:
newlist.append(xylist[j+1])
xlist = [x[0] for x in newlist]
ylist = [y[1] for y in newlist]
r = float(random.randint(0,255)/255)
g = float(random.randint(0,255)/255)
b = float(random.randint(0,255)/255)
num = round(random.uniform(0, 3), 2)
palette = sns.cubehelix_palette(n_colors=6, start=num, rot=0, gamma=0.3, hue=0.8, light=1, dark=0, reverse=False, as_cmap=True)
# palette = sns.light_palette((r, g, b), n_colors=1, reverse=False, as_cmap=True)
plt.scatter(xlist,ylist, s=6, c=list(range(0,len(newlist))), cmap=palette)
# for j,num in fish.location:
# print(type(j))
# coord = list(num)
# plt.scatter(coord[0],coord[1], s=1, cmap=palette
# cv2.line(image,num,num,cmap[j],2)
# if i == number_of_colors:
# r = random.randint(0,255)
# g = random.randint(0,255)
# b = random.randint(0,255)
# rgb = tuple([r,g,b])
# colours.append(rgb)
# number_of_colors += 1
# cv2.imwrite("newimage.png", image)
plt.savefig("omrlighttodark_forward.png")
# print(len(all_xy))
file = open(videoStream + ".centroid2",'w')
for x in range(0,750):
for y in range(0,1):
file.write(str(int(cenData[x,:][y])) + '\n')
pixData = pixData[:i,:]
pixData = pixData[:,1:] # get rid of background column
file = open(videoStream + ".motion2",'w')
#file.write("12/8/2015" + '\015')
for x in range(0,750):
for y in range(0,numberofwells):
file.write(str(int(pixData[x,:][y])) + '\n')
# vidInfo = {}
# release camera
cap.release()
cv2.destroyAllWindows()
def main(pixThreshold, frameRate, videoStream):
expDuration = 600000 # duration of experiment, in seconds; only relevant for live feed
saveFreq = 4500 # how often to save data, in frames
i, m = imageTools.loadImageAndMask()
# convert mask to integer values for bincount weights
m, w = imageTools.convertMaskToWeights(m)
#print m,w
moviedeq = []
i2 = 0
for file in glob.glob("*_4*avi"):
if i2 == 15:
break
#for x in range(0,5):
# start camera or open video
videoType, displayDiffs = imageTools.getVideoType(videoStream)
# print "testing: ", file
#print "testing: ", videoStream.split('-')[x]
cap = cv2.VideoCapture(file)
#cap = cv2.VideoCapture(videoStream.split('-')[x])
# adjust video resolution if necessary (sized to mask)
# print 'Camera resolution is %s x %s' % (str(m.shape[1]),str(m.shape[0]))
# cap.set(3,m.shape[1])
# cap.set(4,m.shape[0])
# Set Pixel Threshold
ret, frame = cap.read()
storedFrame = imageTools.grayBlur(frame)
#pixThreshold = int(np.floor( pixThreshold * storedFrame.shape[0] ))
#print('PixelThreshold is %i') % pixThreshold
# Acquire data
if saveFreq / frameRate > expDuration: # do shorter of expDuration vs. saveFreq
saveFreq = expDuration * frameRate
pixData = np.zeros([saveFreq, len(np.unique(w)) + 1])
#i = 0 # a counter for saving chunks of data
totalFrames = 0
startTime = datetime.now()
oldTime = startTime
elapsed = 0
print('Analyzing motion data...')
#moviedeq = []
while (cap.isOpened()):
ret, frame = cap.read()
if ret == False:
print 'End of Video'
break
currentFrame = imageTools.grayBlur(frame)
moviedeq.append(currentFrame)
# stop experiment if user presses 'q' or if experiment duration is up
if (cv2.waitKey(1) & 0xFF == ord('q')
or len(sys.argv) == 1 and datetime.now() >
startTime + timedelta(seconds=expDuration)):
break
# record pixel differences in all of the ROIs
#diff = imageTools.diffImage(storedFrame,currentFrame,pixThreshold,0)
timeDiff = 1. / frameRate
elapsed = elapsed + timeDiff
# print elapsed
# calculate and record pixel differences
#counts = np.bincount(w, weights=diff.ravel())
# print counts # output
#pixData[i,:] = np.hstack((elapsed,counts))
totalFrames += 1
storedFrame = currentFrame # comment out if nothing is in first frame
#oldTime = newTime
i2 += 1
# done recording. Remove empty rows (those bigger than i) from PixData
#pixData = pixData[:i,:]
#print pixData
testing = calc_mode(moviedeq, np.zeros([660, 1088]))
print "saving mode.png"
cv2.imwrite('mode.png', testing)
# Save info (elapsed time and framerate) for later use
vidInfo = {}
# analysisTime = timeStamp - startTime
# vidInfo['analysisTime'] = float(str(analysisTime.seconds) + '.' + str(analysisTime.microseconds))
# vidInfo['TotalFrames'] = totalFrames
# vidInfo['fps'] = int(totalFrames/vidInfo['analysisTime'])
# #vidInfo['pixThreshold']=pixThreshold
# vidInfo['CameraResolution']='%s x %s' % (str(m.shape[1]),str(m.shape[0]))
#vidInfo['NamePrefix'] = videoStream.split('-')[x]
#vidInfo['NamePrefix'] = videoStream.split('.')[0]
# print ('Analyzed %i frames in %f seconds') % (vidInfo['TotalFrames'],vidInfo['analysisTime'])
# print('FrameRate is about %i fps') % vidInfo['fps']
# print 'Motion threshold is %i pixels' % int(pixThreshold)
# print 'Camera resolution is %s' % vidInfo['CameraResolution']
# release camera
cap.release()
cv2.destroyAllWindows()
return vidInfo