def loadTiffStack(self):
self.stack = TiffStack(self.file)
class OpenCV():
prev_points = None
points = None
features = None
prev_features = None
file = None
grey = None
prev_grey = None
image = None
prev_image = None
win_name = None
grey_arr = None
arr = None
tmp = None
def __init__(self, name="opencv"):
self.win_name = name
def load(self, file):
self.file = file
def loadTiffStack(self):
self.stack = TiffStack(self.file)
def getTiff(self, ix):
return self.stack.__getitem__(ix)
def setCurrIm(self, im):
self.image = im
def expandCurrIm(self):
self.image, self.tmp = expand(self.image)
self.arr = cv2array(self.image)
def setGrey(self):
self.grey = CreateImage(GetSize(self.image), 8, 1)
Copy(self.image, self.grey)
self.grey_arr = cv2array(self.grey)
self.image = CreateImage(GetSize(self.image), 8, 3)
CvtColor(self.grey, self.image, CV_GRAY2BGR)
def setFeatures(self, num_features = 100):
self.setGrey()
self.features = getFeatures(self.grey, num_features)
def save(self, count):
SaveImage("images/frame%d.png"%count, self.image)
def setQuickFeatures(self):
self.setGrey()
self.features = getQuickFeatures(self.grey_arr)
def drawFeatures(self, features=None):
if not features: features = self.features
self.image = drawFeatures(self.image, features)
def drawPoints(self):
self.image = drawPoints(self.tmp, self.points)
def show(self, wait=None):
cv.NamedWindow(self.win_name)
cv.ShowImage(self.win_name, self.image)
if not wait:
cv.WaitKey()
else:
cv.WaitKey(wait)
def step(self):
self.prev_features = self.features
self.prev_points = self.points
self.prev_grey = self.grey
self.prev_image = self.image
def thresh(self, min=110, max=255):
self.image = thresh(self.image, min, max)
def removeOverlaps(self):
seen = []
for i in self.points:
already_seen = False
for j in seen:
if already_seen or dist((j.x, j.y), i) < i.radius:
already_seen = True
if not already_seen:
seen.append(i)
self.points = seen
def correctPoints(self, features):
to_remove = []
im = self.image
t = mahotas.thresholding.otsu(self.grey_arr)
for i in self.points:
bright = []
mindist = i.radius*2
mind = dist(features[0], i)
mini = features[0]
for j in features:
if dist(j, i) < mind:
mind = dist(j,i)
mini = j
if mind < mindist:
i.x = mini[0]
i.y = mini[1]
i.x = int(max(min(i.x, im.width),0))
i.y = int(max(min(i.y, im.height),0))
x_0 = int(max(min(i.x-i.radius, im.width),0))
x_1 = int(max(min(i.x+i.radius, im.width),0))
y_0 = int(max(min(i.y-i.radius, im.height),0))
y_1 = int(max(min(i.y+i.radius, im.height),0))
brightness = []
for x in xrange(x_0,x_1):
for y in xrange(y_0,y_1):
pixel = self.grey_arr[x][y]
brightness.append(pixel)
bright = np.sum(brightness)
# if np.max(brightness) > t:
i.brightness = bright
# else: to_remove.append(i)
for i in to_remove:
self.points.remove(i)
self.removeOverlaps()
def getPoints(self):
global r
self.points = []
prev_seen = []
if not self.prev_points:
self.prev_points = [Point(i[0], i[1]) for i in self.prev_features]
for i in self.features:
min = dist(i, self.prev_points[0])
mini = self.prev_points[0]
for j in self.prev_points:
if dist(i,j) < min:
min = dist(i,j)
mini = j
if min < r * 4 and not mini.next:
prev_seen.append(mini)
point = Point(i[0], i[1])
point.prev = mini
point.color = mini.color
mini.next = point
self.points.append(point)
def opticalFlow(self):
self.features = calcOptimalFlow(self.prev_grey, self.grey, self.prev_features)
self.points = []
def plotPoints(self,total_count):
plots = []
pylab.clf()
for i in self.points:
plot = []
origin = i
while origin.prev:
origin = origin.prev
count = 1
while origin:
plot.append(origin.brightness)
origin = origin.next
count = count+1
#print plot
pylab.plot(plot)
plots.append(plot)
pylab.savefig("graphs/graph%d.png"%total_count)
np.save("plots/plot%d.dat"%total_count, plots)