def measure_single_tail(self, frame, tail):
""" do line scans along the measurement segments of the tails """
l = self.params['measurement/line_scan_width']
w = self.params['measurement/line_scan_step'] #< width of each individual line scan
result = []
for line in self.get_measurement_lines(tail):
ps = curves.make_curve_equidistant(line, spacing=2*w)
profile = []
for pp, p, pn in itertools.izip(ps[:-2], ps[1:-1], ps[2:]):
# slope
dx, dy = pn - pp
dlen = math.hypot(dx, dy)
dx /= dlen; dy /= dlen
# get end points of line scan
p1 = (p[0] + l*dy, p[1] - l*dx)
p2 = (p[0] - l*dy, p[1] + l*dx)
lscan = image.line_scan(frame, p1, p2, half_width=w)
profile.append(lscan.mean())
self.output.add_points([p1, p2], 1, 'w')
result.append(profile)
return result
def _get_cage_boundary(self, ground_point, frame, direction='left'):
""" determines the cage boundary starting from a ground_point
going in the given direction """
# check whether we have to calculate anything
if not self.params['cage/determine_boundaries']:
if direction == 'left':
return (0, ground_point[1])
elif direction == 'right':
return (frame.shape[1] - 1, ground_point[1])
else:
raise ValueError('Unknown direction `%s`' % direction)
# extend the ground line toward the left edge of the cage
if direction == 'left':
border_point = (0, ground_point[1])
elif direction == 'right':
image_width = frame.shape[1] - 1
border_point = (image_width, ground_point[1])
else:
raise ValueError('Unknown direction `%s`' % direction)
# do the line scan
profile = image.line_scan(frame, border_point, ground_point,
self.params['cage/linescan_width'])
# smooth the profile slightly
profile = ndimage.filters.gaussian_filter1d(profile,
self.params['cage/linescan_smooth'])
# add extra points to make determining the extrema reliable
profile = np.r_[0, profile, 255]
# determine first maximum and first minimum after that
maxima = signal.argrelextrema(profile, comparator=np.greater_equal)
pos_max = maxima[0][0]
minima = signal.argrelextrema(profile[pos_max:],
comparator=np.less_equal)
pos_min = minima[0][0] + pos_max
# we have to use argrelextrema instead of argrelmax and argrelmin,
# because the latter don't capture wide maxima like [0, 1, 1, 0]
if pos_min - pos_max >= 2:
# get steepest point in this interval
pos_edge = np.argmin(np.diff(profile[pos_max:pos_min + 1])) + pos_max
else:
# get steepest point in complete profile
pos_edge = np.argmin(np.diff(profile))
if direction == 'right':
pos_edge = image_width - pos_edge
return (pos_edge, ground_point[1])
def refine_ground(self, frame):
""" adapts a points profile given as points to a given frame.
Here, we fit a ridge profile in the vicinity of every point of the curve.
The only fitting parameter is the distance by which a single points moves
in the direction perpendicular to the curve. """
# make sure the curve has equidistant points
spacing = int(self.params['ground/point_spacing'])
self.ground.make_equidistant(spacing=spacing)
# consider all points that are far away from the borders
frame_margin = int(self.params['ground/frame_margin'])
x_max = frame.shape[1] - frame_margin
points = [point for point in self.ground.points
if frame_margin < point[0] < x_max]
points = np.array(np.round(points), np.int32)
# iterate over all but the boundary points
curvature_energy_factor = self.params['ground/curvature_energy_factor']
if 'ground/energy_factor_last' in self._cache:
# load the energy factor for the next iteration
snake_energy_max = self.params['ground/snake_energy_max']
energy_factor_last = self._cache['energy_factor_last']
else:
# initialize values such that the energy factor is calculated
# for the next iteration
snake_energy_max = np.inf
energy_factor_last = 1
# parameters of the line scan
ray_len = int(self.params['ground/linescan_length']/2)
profile_width = self.params['ground/point_spacing']/2
ridge_width = self.params['ground/ridge_width']
len_ratio = ray_len/ridge_width
model_std = math.sqrt(1 - math.tanh(len_ratio)/len_ratio)
assert 0.5 < model_std < 1
# iterate through all points in random order and correct profile
energies_image = []
num_points = len(points) - 2 #< disregard the boundary points
candidate_points = [None]*num_points
for k in np.random.permutation(num_points):
# get local points and slopes
p_p, p, p_n = points[k], points[k+1], points[k+2]
dx, dy = p_n - p_p
dist = math.hypot(dx, dy)
if dist == 0: #< something went wrong
continue #< skip this point
dx /= dist; dy /= dist
# do the line scan perpendicular to the ground line
p_a = (p[0] - ray_len*dy, p[1] + ray_len*dx)
p_b = (p[0] + ray_len*dy, p[1] - ray_len*dx)
profile = image.line_scan(frame, p_a, p_b, half_width=profile_width)
# scale profile to -1, 1
profile -= profile.mean()
try:
profile /= profile.std()
except RuntimeWarning:
# this can happen in strange cases where the profile is flat
continue
plen = len(profile)
xs = np.linspace(-plen/2 + 0.5, plen/2 - 0.5, plen)
def energy_image((pos, model_mean, model_std)):
""" part of the energy related to the line scan """
# get image part
model = np.tanh(-(xs - pos)/ridge_width)
img_diff = profile - model_std*model - model_mean
squared_diff = np.sum(img_diff**2)
return energy_factor_last*squared_diff
# energy_image has units of color^2
def energy_curvature(pos):
""" part of the energy related to the curvature of the ground line """
# get curvature part: http://en.wikipedia.org/wiki/Menger_curvature
p_c = (p[0] + pos*dy, p[1] - pos*dx)
a = curves.point_distance(p_p, p_c)
b = curves.point_distance(p_c, p_n)
c = curves.point_distance(p_n, p_p)
# determine curvature of circle through the three points
A = regions.triangle_area(a, b, c)
curvature = 4*A/(a*b*c)*spacing
# We don't scale by with the arc length a + b, because this
# would increase the curvature weight in situations where
# fitting is complicated (close to burrow entries)
return curvature_energy_factor*curvature
def energy_snake(data):
""" energy function of this part of the ground line """
return energy_image(data) + energy_curvature(data[0])
# fit the simple model to the line scan profile
fit_bounds = ((-spacing, spacing), (None, None), (None, None))
try:
#res = optimize.fmin_powell(energy_snake, [0, 0, model_std], disp=False)
res, snake_energy, _ = \
optimize.fmin_l_bfgs_b(energy_snake, approx_grad=True,
x0=np.array([0, 0, model_std]),
bounds=fit_bounds)
except RuntimeError:
continue #< skip this point
# use this point, if it is good enough
if snake_energy < snake_energy_max:
# save final energy for determining the energy scale later
energies_image.append(energy_image(res))
pos, _, model_std = res
p_x, p_y = p[0] + pos*dy, p[1] - pos*dx
candidate_points[k] = (int(p_x), int(p_y))
# filter points, where the fit did not work
# FIXME: fix overhanging ridge detection (changed sign of comparison Oct. 27)
points = []
for candidate in candidate_points:
if candidate is None:
continue
# check for overhanging ridge
if len(points) == 0 or candidate[0] > points[-1][0]:
points.append(candidate)
# there is an overhanging part, since candidate[0] <= points[-1][0]:
elif candidate[1] < points[-1][1]:
# current point is above previous point
# => replace the previous candidate point
points[-1] = candidate
else:
# current point is below previous point
# => do not add the current candidate point
pass
# save the energy factor for the next iteration
energy_factor_last /= np.mean(energies_image)
self._cache['ground/energy_factor_last'] = energy_factor_last
if len(points) < 0.5*num_points:
# refinement failed for too many points => return original ground
self.logger.debug('%d: Ground profile shortened too much.',
self.frame_id)
return self.ground
# extend the ground line toward the left edge of the cage
edge_point = self._get_cage_boundary(points[0], frame, 'left')
if edge_point is not None:
points.insert(0, edge_point)
# extend the ground line toward the right edge of the cage
edge_point = self._get_cage_boundary(points[-1], frame, 'right')
if edge_point is not None:
points.append(edge_point)
self.ground = GroundProfile(points)
return self.ground