def segmentation(self, points, useSnake = True):
## make ellipse
if len(points)==0:
print "the input points size is ZERO!"
return None
Initial_ellipsePoints = ImageProcessing.FindEllipse(points)
self._convex_xy = Initial_ellipsePoints # back up the data
outPoints = []
if self._state == False:
for i in range(self._volume_data.shape[2]): # iterating through the vertical stacks
print "uncropped: " + str(i)
slice_snake = np.empty([Initial_ellipsePoints.shape[0],3]) # Make N by 3 points
if useSnake == True:
snake = ImageProcessing.ActiveEllipse(self._volume_data[:,:,i], Initial_ellipsePoints)
else:
snake = Initial_ellipsePoints
slice_snake[:,0] = snake[:,0] # create 3d points
slice_snake[:,1] = snake[:,1]
slice_snake[:,2] = i
outPoints.append(slice_snake)
elif self._state == True:
for i in range(self._start, self._end+1): # iterating through the vertical stacks
print "cropped: " + str(i)
slice_snake = np.empty([Initial_ellipsePoints.shape[0],3]) # Make N by 3 points
if useSnake == True:
snake = ImageProcessing.ActiveEllipse(self._volume_data[:,:,i], Initial_ellipsePoints)
else:
snake = Initial_ellipsePoints
slice_snake[:,0] = snake[:,0] # create 3d points
slice_snake[:,1] = snake[:,1]
slice_snake[:,2] = i
outPoints.append(slice_snake)
for i in range(len(outPoints)): # reshape the list
if i == 0: fb = outPoints[i]
else: fb = np.concatenate((fb,outPoints[i]),axis=0)
self._periPoint = fb
