def centerline(self):
""" determine the center line of the tail """
mask, offset = self.mask
dist_map = cv2.distanceTransform(mask, cv2.DIST_L2, 5)
# setup active contour algorithm
ac = ActiveContour(
blur_radius=self.centerline_blur_radius,
closed_loop=False,
alpha=0, #< line length is constraint by beta
beta=self.centerline_bending_stiffness,
gamma=self.centerline_adaptation_rate)
ac.max_iterations = self.centerline_max_iterations
ac.set_potential(dist_map)
# find centerline starting from the ventral_side
points = curves.translate_points(self.ventral_side, -offset[0],
-offset[1])
spacing = self.centerline_spacing
points = curves.make_curve_equidistant(points, spacing=spacing)
# use the active contour algorithm
points = ac.find_contour(points)
points = curves.make_curve_equidistant(points, spacing=spacing)
# translate points back into global coordinate system
points = curves.translate_points(points, offset[0], offset[1])
# orient the centerline such that it starts at the posterior end
dist1 = curves.point_distance(points[0], self.endpoints[0])
dist2 = curves.point_distance(points[-1], self.endpoints[0])
if dist1 > dist2:
points = points[::-1]
return points
def centerline(self):
""" determine the center line of the tail """
mask, offset = self.mask
dist_map = cv2.distanceTransform(mask, cv2.DIST_L2, 5)
# setup active contour algorithm
ac = ActiveContour(blur_radius=self.centerline_blur_radius,
closed_loop=False,
alpha=0, #< line length is constraint by beta
beta=self.centerline_bending_stiffness,
gamma=self.centerline_adaptation_rate)
ac.max_iterations = self.centerline_max_iterations
ac.set_potential(dist_map)
# find centerline starting from the ventral_side
points = curves.translate_points(self.ventral_side,
-offset[0], -offset[1])
spacing = self.centerline_spacing
points = curves.make_curve_equidistant(points, spacing=spacing)
# use the active contour algorithm
points = ac.find_contour(points)
points = curves.make_curve_equidistant(points, spacing=spacing)
# translate points back into global coordinate system
points = curves.translate_points(points, offset[0], offset[1])
# orient the centerline such that it starts at the posterior end
dist1 = curves.point_distance(points[0], self.endpoints[0])
dist2 = curves.point_distance(points[-1], self.endpoints[0])
if dist1 > dist2:
points = points[::-1]
return points
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 extend_mouse_trail(self):
""" extends the mouse trail using the current mouse position """
ground_line = self.ground.linestring
# remove points which are in front of the mouse
if self.mouse_trail:
spacing = self.params['mouse/model_radius']
trail = np.array(self.mouse_trail)
# get distance between the current point and the previous ones
dist = np.hypot(trail[:, 0] - self.mouse_pos[0],
trail[:, 1] - self.mouse_pos[1])
points_close = (dist < spacing)
# delete obsolete points
if np.any(points_close):
i = np.nonzero(points_close)[0][0]
del self.mouse_trail[i:]
# check the two ends of the mouse trail
if self.mouse_trail:
# move first point to ground
ground_point = curves.get_projection_point(ground_line,
self.mouse_trail[0])
self.mouse_trail[0] = ground_point
# check whether a separate point needs to be inserted
p1, p2 = self.mouse_trail[-1], self.mouse_pos
if curves.point_distance(p1, p2) > spacing:
mid_point = (0.5 * (p1[0] + p2[0]), 0.5 * (p1[1] + p2[1]))
self.mouse_trail.append(mid_point)
# append the current point
self.mouse_trail.append(self.mouse_pos)
ground_dist = curves.curve_length(self.mouse_trail)
else:
# create a mouse trail if it is not too far from the ground
# the latter can happen, when the mouse suddenly appears underground
ground_point = curves.get_projection_point(ground_line,
self.mouse_pos)
ground_dist = curves.point_distance(ground_point, self.mouse_pos)
if ground_dist < self.params['mouse/speed_max']:
self.mouse_trail = [ground_point, self.mouse_pos]
return ground_dist
def extend_mouse_trail(self):
""" extends the mouse trail using the current mouse position """
ground_line = self.ground.linestring
# remove points which are in front of the mouse
if self.mouse_trail:
spacing = self.params['mouse/model_radius']
trail = np.array(self.mouse_trail)
# get distance between the current point and the previous ones
dist = np.hypot(trail[:, 0] - self.mouse_pos[0],
trail[:, 1] - self.mouse_pos[1])
points_close = (dist < spacing)
# delete obsolete points
if np.any(points_close):
i = np.nonzero(points_close)[0][0]
del self.mouse_trail[i:]
# check the two ends of the mouse trail
if self.mouse_trail:
# move first point to ground
ground_point = curves.get_projection_point(ground_line,
self.mouse_trail[0])
self.mouse_trail[0] = ground_point
# check whether a separate point needs to be inserted
p1, p2 = self.mouse_trail[-1], self.mouse_pos
if curves.point_distance(p1, p2) > spacing:
mid_point = (0.5*(p1[0] + p2[0]), 0.5*(p1[1] + p2[1]))
self.mouse_trail.append(mid_point)
# append the current point
self.mouse_trail.append(self.mouse_pos)
ground_dist = curves.curve_length(self.mouse_trail)
else:
# create a mouse trail if it is not too far from the ground
# the latter can happen, when the mouse suddenly appears underground
ground_point = curves.get_projection_point(ground_line, self.mouse_pos)
ground_dist = curves.point_distance(ground_point, self.mouse_pos)
if ground_dist < self.params['mouse/speed_max']:
self.mouse_trail = [ground_point, self.mouse_pos]
return ground_dist
def determine_endpoint_indices(self, tail_prev=None):
""" locate the end points as contour points with maximal distance
The posterior point is returned first.
If `tail_prev` is given, the end points are oriented in the same way as
in the previous tail, otherwise they are assigned automatically.
"""
# get the points which are farthest away from each other
dist = distance.squareform(distance.pdist(self.contour))
indices = np.unravel_index(np.argmax(dist), dist.shape)
if tail_prev is None:
# determine the mass of tissue to determine posterior end
mass = []
for k in indices:
radius = self.endpoint_mass_radius
endzone = geometry.Point(self.contour[k]).buffer(radius)
poly = self.polygon.buffer(0) #< clean the polygon
mass.append(poly.intersection(endzone).area)
# determine posterior end point by measuring the surrounding
if mass[1] < mass[0]:
indices = indices[::-1]
else:
# sort end points according to previous frame
prev_p, prev_a = tail_prev.endpoints
this_1 = self.contour[indices[0]]
this_2 = self.contour[indices[1]]
dist1 = curves.point_distance(this_1, prev_p) + \
curves.point_distance(this_2, prev_a)
dist2 = curves.point_distance(this_1, prev_a) + \
curves.point_distance(this_2, prev_p)
if dist2 < dist1:
indices = indices[::-1]
# save indices in cache
self.persistence_data['endpoint_indices'] = indices
return indices
def determine_endpoint_indices(self, tail_prev=None):
""" locate the end points as contour points with maximal distance
The posterior point is returned first.
If `tail_prev` is given, the end points are oriented in the same way as
in the previous tail, otherwise they are assigned automatically.
"""
# get the points which are farthest away from each other
dist = distance.squareform(distance.pdist(self.contour))
indices = np.unravel_index(np.argmax(dist), dist.shape)
if tail_prev is None:
# determine the mass of tissue to determine posterior end
mass = []
for k in indices:
radius = self.endpoint_mass_radius
endzone = geometry.Point(self.contour[k]).buffer(radius)
poly = self.polygon.buffer(0) #< clean the polygon
mass.append(poly.intersection(endzone).area)
# determine posterior end point by measuring the surrounding
if mass[1] < mass[0]:
indices = indices[::-1]
else:
# sort end points according to previous frame
prev_p, prev_a = tail_prev.endpoints
this_1 = self.contour[indices[0]]
this_2 = self.contour[indices[1]]
dist1 = curves.point_distance(this_1, prev_p) + \
curves.point_distance(this_2, prev_a)
dist2 = curves.point_distance(this_1, prev_a) + \
curves.point_distance(this_2, prev_p)
if dist2 < dist1:
indices = indices[::-1]
# save indices in cache
self.persistence_data['endpoint_indices'] = indices
return indices
def get_track_graph(self, tracks, threshold, highlight_nodes=None):
""" builds a weighted, directed graph representing the possible trajectories """
if highlight_nodes:
highlight_nodes = set(highlight_nodes)
else:
highlight_nodes = set()
graph = nx.DiGraph()
# find all possible connections
time_scale = self.params['tracking/time_scale']
tolerated_overlap = self.params['tracking/tolerated_overlap']
look_back_count = int(tolerated_overlap) + 5
for a_idx, a in enumerate(tracks):
# compare to other nodes (look back into past, too)
for b in tracks[max(a_idx - look_back_count, 0):]:
if a is b or graph.has_edge(a, b):
continue # don't add self-loops or multiple loops
gap_length = b.start - a.end #< time gap between the two chunks
if gap_length > -tolerated_overlap:
# calculate the cost of this gap
# lower is better; all terms should be normalized to one
distance = curves.point_distance(a.last.pos, b.first.pos)
cost = (
#+ (2 - a.mouse_score - b.mouse_score) # is it a mouse?
+ distance/self.params['mouse/speed_max'] # how close are the positions
+ abs(gap_length)/time_scale # is it a long gap?
)
# add the edge if the cost is not too high
if cost < threshold:
graph.add_edge(a, b, cost=cost)
# highlight node if necessary
if a in graph:
graph.node[a]['highlight'] = (a_idx in highlight_nodes)
return graph
def _get_burrow_exit_length(self, burrow):
""" calculates the length of all exists of the given burrow """
# identify all points that are close to the ground line
dist_max = burrow.parameters['ground_point_distance']
g_line = self.ground_line.linestring
points = burrow.contour
exitpoints = [g_line.distance(geometry.Point(point)) < dist_max
for point in points]
# find the indices of contiguous true regions
indices = math.contiguous_true_regions(exitpoints)
# find the total length of all exits
exit_length = 0
for a, b in indices:
exit_length += curves.curve_length(points[a : b+1])
# handle the first and last point if they both belong to an exit
if exitpoints[0] and exitpoints[-1]:
exit_length += curves.point_distance(points[0], points[-1])
return exit_length
def add_tracks_to_trajectory(self, tracks, trajectory):
""" iterates through all tracks and adds them to the trajectory, using
linear interpolation where necessary and appropriate """
time_last, obj_last = None, None
for track in tracks:
# check the connection between the previous point and the current one
if obj_last is not None:
time_now, obj_now = track.start, track.first
time_gap = time_now - time_last
small_gap = (time_gap < self.params['tracking/maximal_gap'])
obj_dist = curves.point_distance(obj_last.pos, obj_now.pos)
small_jump = (obj_dist < self.params['tracking/maximal_jump'])
# check whether we should interpolate
if small_gap and small_jump:
frames = np.arange(time_last + 1, time_now)
ratio = np.linspace(0, 1, len(frames) + 2)[1:-1]
x1, x2 = obj_last.pos[0], obj_now.pos[0]
trajectory[frames, 0] = x1 + (x2 - x1)*ratio
y1, y2 = obj_last.pos[1], obj_now.pos[1]
trajectory[frames, 1] = y1 + (y2 - y1)*ratio
# check whether the tracking went wrong
if time_gap <= 1 and not small_jump:
# make sure that there is a gap indicated by nan between
# the two chunks
trajectory[time_now - 1:time_last + 1, :] = np.nan
# add the data of this track directly
for time, obj in track:
if np.all(np.isfinite(trajectory[time, :])):
# average overlapping tracks
trajectory[time, :] = (trajectory[time, :] + obj.pos)/2
else:
trajectory[time, :] = obj.pos
time_last, obj_last = time, obj
def _get_burrow_exit_length(self, burrow):
""" calculates the length of all exists of the given burrow """
# identify all points that are close to the ground line
dist_max = burrow.parameters['ground_point_distance']
g_line = self.ground_line.linestring
points = burrow.contour
exitpoints = [
g_line.distance(geometry.Point(point)) < dist_max
for point in points
]
# find the indices of contiguous true regions
indices = math.contiguous_true_regions(exitpoints)
# find the total length of all exits
exit_length = 0
for a, b in indices:
exit_length += curves.curve_length(points[a:b + 1])
# handle the first and last point if they both belong to an exit
if exitpoints[0] and exitpoints[-1]:
exit_length += curves.point_distance(points[0], points[-1])
return exit_length
def adapt_tail_contours(self, tails):
""" adapt tail contour to _frame, assuming that they are already close """
# get the tails that we want to adapt
if self.params['detection/every_frame']:
tails_estimate = self.locate_tails_roughly(tails)
else:
tails_estimate = tails[:] #< copy list
if len(tails_estimate) != len(tails):
raise RuntimeError('Found %d instead of %d tails in this frame.' %
(len(tails), len(tails_estimate)))
# setup active contour algorithm
ac = ActiveContour(blur_radius=self.params['contour/blur_radius'],
closed_loop=True,
alpha=self.params['contour/line_tension'],
beta=self.params['contour/bending_stiffness'],
gamma=self.params['contour/adaptation_rate'])
ac.max_iterations = self.params['contour/max_iterations']
#potential_approx = self.threshold_gradient_strength(gradient_mag)
ac.set_potential(self.contour_potential)
# debug.show_shape(*[t.contour for t in tails],
# background=self.contour_potential)
# get rectangle describing the interior of the _frame
height, width = self._frame.shape
region_center = shapes.Rectangle(0, 0, width, height)
region_center.buffer(-self.params['contour/border_anchor_distance'])
# iterate through all previous tails
for k, tail_prev in enumerate(tails):
# find the tail that is closest
center = tail_prev.centroid
idx = np.argmin([curves.point_distance(center, t.centroid)
for t in tails_estimate])
# adapt this contour to the potential
tail_estimate = tails_estimate.pop(idx)
# determine the points close to the boundary that will be anchored
# at their position, because there are no features to track at the
# boundary
anchor_idx = ~region_center.points_inside(tail_estimate.contour)
# disable anchoring for points at the posterior end of the tail
ps = tail_estimate.contour[anchor_idx]
dists = spatial.distance.cdist(ps, [tail_estimate.endpoints[0]])
dist_threshold = self.params['contour/typical_width']
anchor_idx[anchor_idx] = (dists.flat > dist_threshold)
# use an active contour algorithm to adapt the contour points
contour = ac.find_contour(tail_estimate.contour, anchor_idx,
anchor_idx)
logging.debug('Active contour took %d iterations.',
ac.info['iteration_count'])
# update the old tail to keep the identity of sides
tails[k] = Tail.create_similar(contour, tail_prev)
return tails
def classify_mouse_track(self):
""" classifies the mouse at all times """
self.log_event('Pass 2 - Start classifying the mouse.')
# load the mouse, the ground, and the burrows
mouse_track = self.data['pass2/mouse_trajectory']
ground_profile = self.data['pass2/ground_profile']
burrow_tracks = self.data['pass1/burrows/tracks']
# load some variables
mouse_radius = self.params['mouse/model_radius']
trail_spacing = self.params['burrows/centerline_segment_length']
burrow_next_change = 0
mouse_trail = None
for frame_id, mouse_pos in enumerate(mouse_track.pos):
if not np.all(np.isfinite(mouse_pos)):
# the mouse position is invalid
continue
# initialize variables
state = {}
# check the mouse position
ground = ground_profile.get_ground_profile(frame_id)
if ground is not None:
if ground.above_ground(mouse_pos):
state['underground'] = False
if mouse_pos[1] + mouse_radius < ground.get_y(mouse_pos[0]):
state['location'] = 'air'
elif mouse_pos[1] < ground.midline:
state['location'] = 'hill'
else:
state['location'] = 'valley'
mouse_trail = None
# get index of the ground line
dist = np.linalg.norm(ground.points - mouse_pos[None, :], axis=1)
ground_idx = np.argmin(dist)
# get distance from ground line
ground_dist = ground.linestring.distance(geometry.Point(mouse_pos))
else:
state['underground'] = True
# check the burrow structure
if frame_id >= burrow_next_change:
burrows, burrow_next_change = \
burrow_tracks.find_burrows(frame_id, ret_next_change=True)
# check whether the mouse is inside a burrow
mouse_point = geometry.Point(mouse_pos)
for burrow in burrows:
if burrow.polygon.contains(mouse_point):
state['location'] = 'burrow'
break
# keep the ground index from last time
ground_idx = mouse_track.ground_idx[frame_id - 1]
# handle mouse trail
if mouse_trail is None:
# start a new mouse trail and initialize it with the
# ground point closest to the mouse
mouse_prev = mouse_track.pos[frame_id - 1]
ground_point = curves.get_projection_point(ground.linestring, mouse_prev)
mouse_trail = [ground_point, mouse_pos]
else:
# work with an existing mouse trail
p_trail = mouse_trail[-2]
if curves.point_distance(p_trail, mouse_pos) < trail_spacing:
# old trail should be modified
if len(mouse_trail) > 2:
# check whether the trail has to be shortened
p_trail = mouse_trail[-3]
if curves.point_distance(p_trail, mouse_pos) < trail_spacing:
del mouse_trail[-1] #< shorten trail
mouse_trail[-1] = mouse_pos
else:
# old trail must be extended
mouse_trail.append(mouse_pos)
# get distance the mouse is under ground
ground_dist = -curves.curve_length(mouse_trail)
# set the mouse state
mouse_track.set_state(frame_id, state, ground_idx, ground_dist)
self.log_event('Pass 2 - Finished classifying the mouse.')
def classify_mouse_state(self, mouse_track):
""" classifies the mouse in the current _frame """
if (not np.all(np.isfinite(self.mouse_pos)) or
self.ground is None):
# Not enough information to do anything
self.mouse_trail = None
return
# initialize variables
state = {}
margin = self.params['mouse/model_radius']/2
mouse_radius = self.params['mouse/model_radius']
# check the horizontal position
if self.mouse_pos[0] > self.background.shape[1]//2:
state['position_horizontal'] = 'right'
else:
state['position_horizontal'] = 'left'
# compare y value of mouse and ground (y-axis points down)
if self.mouse_pos[1] > self.ground.get_y(self.mouse_pos[0]) + margin:
# handle mouse trail
ground_dist = self.extend_mouse_trail()
# store the ground distance as a negative number
ground_dist *= -1
# score the burrow based on its entry point
if self.ground_idx is None:
# only necessary if mouse starts inside burrow
dist = np.linalg.norm(self.ground.points - self.mouse_pos[None, :], axis=1)
self.ground_idx = np.argmin(dist)
entry_point = self.ground.points[self.ground_idx]
if entry_point[1] > self.ground.midline:
state['location'] = 'burrow'
else:
state['location'] = 'dimple'
# check whether we are at the end of the burrow
for burrow in self.burrows:
dist = curves.point_distance(burrow.end_point, self.mouse_pos)
if dist < mouse_radius:
state['location_detail'] = 'end point'
break
else:
state['location_detail'] = 'general'
else:
if self.mouse_pos[1] + 2*mouse_radius < self.ground.get_y(self.mouse_pos[0]):
state['location'] = 'air'
elif self.mouse_pos[1] < self.ground.midline:
state['location'] = 'hill'
else:
state['location'] = 'valley'
state['location_detail'] = 'general'
# get index of the ground line
dist = np.linalg.norm(self.ground.points - self.mouse_pos[None, :], axis=1)
self.ground_idx = np.argmin(dist)
# get distance from ground line
mouse_point = geometry.Point(self.mouse_pos)
ground_dist = self.ground.linestring.distance(mouse_point)
# report the distance as negative, if the mouse is under the ground line
if self.mouse_pos[1] > self.ground.get_y(self.mouse_pos[0]):
ground_dist *= -1
# reset the mouse trail since the mouse is over the ground
self.mouse_trail = None
# determine whether the mouse is moving or not
velocity = self.data['pass2/mouse_trajectory'].velocity[self.frame_id, :]
speed = np.hypot(velocity[0], velocity[1])
if speed > self.params['mouse/moving_threshold_pixel_frame']:
state['dynamics'] = 'moving'
else:
state['dynamics'] = 'stationary'
# set the mouse state
mouse_track.set_state(self.frame_id, state, self.ground_idx, ground_dist)
def classify_mouse_state(self, mouse_track):
""" classifies the mouse in the current _frame """
if (not np.all(np.isfinite(self.mouse_pos)) or self.ground is None):
# Not enough information to do anything
self.mouse_trail = None
return
# initialize variables
state = {}
margin = self.params['mouse/model_radius'] / 2
mouse_radius = self.params['mouse/model_radius']
# check the horizontal position
if self.mouse_pos[0] > self.background.shape[1] // 2:
state['position_horizontal'] = 'right'
else:
state['position_horizontal'] = 'left'
# compare y value of mouse and ground (y-axis points down)
if self.mouse_pos[1] > self.ground.get_y(self.mouse_pos[0]) + margin:
# handle mouse trail
ground_dist = self.extend_mouse_trail()
# store the ground distance as a negative number
ground_dist *= -1
# score the burrow based on its entry point
if self.ground_idx is None:
# only necessary if mouse starts inside burrow
dist = np.linalg.norm(self.ground.points -
self.mouse_pos[None, :],
axis=1)
self.ground_idx = np.argmin(dist)
entry_point = self.ground.points[self.ground_idx]
if entry_point[1] > self.ground.midline:
state['location'] = 'burrow'
else:
state['location'] = 'dimple'
# check whether we are at the end of the burrow
for burrow in self.burrows:
dist = curves.point_distance(burrow.end_point, self.mouse_pos)
if dist < mouse_radius:
state['location_detail'] = 'end point'
break
else:
state['location_detail'] = 'general'
else:
if self.mouse_pos[1] + 2 * mouse_radius < self.ground.get_y(
self.mouse_pos[0]):
state['location'] = 'air'
elif self.mouse_pos[1] < self.ground.midline:
state['location'] = 'hill'
else:
state['location'] = 'valley'
state['location_detail'] = 'general'
# get index of the ground line
dist = np.linalg.norm(self.ground.points - self.mouse_pos[None, :],
axis=1)
self.ground_idx = np.argmin(dist)
# get distance from ground line
mouse_point = geometry.Point(self.mouse_pos)
ground_dist = self.ground.linestring.distance(mouse_point)
# report the distance as negative, if the mouse is under the ground line
if self.mouse_pos[1] > self.ground.get_y(self.mouse_pos[0]):
ground_dist *= -1
# reset the mouse trail since the mouse is over the ground
self.mouse_trail = None
# determine whether the mouse is moving or not
velocity = self.data['pass2/mouse_trajectory'].velocity[
self.frame_id, :]
speed = np.hypot(velocity[0], velocity[1])
if speed > self.params['mouse/moving_threshold_pixel_frame']:
state['dynamics'] = 'moving'
else:
state['dynamics'] = 'stationary'
# set the mouse state
mouse_track.set_state(self.frame_id, state, self.ground_idx,
ground_dist)