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 _search_predug_in_region(self, region, reflect=False):
""" searches the predug using a template """
slice_x, slice_y = region.slices
# determine the image in the region, only considering under ground
img = self.image[slice_y, slice_x].astype(np.uint8)
# load the file that describes the template data
filename = self.params['predug/template_file']
path = os.path.join(os.path.dirname(__file__), '..', 'assets', filename)
if not os.path.isfile(path):
logging.warn('Predug template file `%s` was not found', path)
return None
with open(path, 'r') as infile:
yaml_content = yaml.load(infile)
if not yaml_content:
logging.warn('Predug template file `%s` is empty', path)
return None
# load the template image
img_file = yaml_content['image']
coords = np.array(yaml_content['coordinates'], np.double)
path = os.path.join(os.path.dirname(__file__), '..', 'assets', img_file)
# read the image from the file as grey scale
template = cv2.imread(path)[:, :, 0]
if self.params['predug/scale_predug']:
# get the scaled size of the template image
target_size = (int(self.params['predug/template_width']),
int(self.params['predug/template_height']))
# scale the predug coordinates to match the template size
coords[:, 0] *= target_size[0] / template.shape[1] #< x-coordinates
coords[:, 1] *= target_size[1] / template.shape[0] #< y-coordinates
# scale the template image itself
template = cv2.resize(template, target_size)
if reflect:
# reflect the image on the vertical center line
template = cv2.flip(template, 1)
template_width = template.shape[1]
coords[:, 0] = template_width - coords[:, 0] - 1
# do the template matching
# res = cv2.matchTemplate(img, template, cv2.TM_SQDIFF_NORMED)
# val_best, _, loc_best, _ = cv2.minMaxLoc(res)
res = cv2.matchTemplate(img, template, cv2.TM_CCOEFF_NORMED)
_, val_best, _, loc_best = cv2.minMaxLoc(res)
# determine the rough outline of the predug in the region
coords = curves.translate_points(coords, *loc_best)
# determine the outline of the predug in the video
coords = curves.translate_points(coords, region.x, region.y)
return val_best, shapes.Polygon(coords)
def _refine_predug(self, candidate):
""" uses the color information directly to specify the predug """
# determine a bounding rectangle
region = candidate.bounds
size = max(region.width, region.height)
region.buffer(0.5 * size) # < increase by 50% in each direction
# extract the region from the image
slice_x, slice_y = region.slices
img = self.image[slice_y, slice_x].astype(np.uint8, copy=True)
# build the estimate polygon
poly_p = affinity.translate(candidate.polygon, -region.x, -region.y)
poly_s = affinity.translate(self.ground.get_sky_polygon(), -region.x, -region.y)
def fill_mask(color, margin=0):
""" fills the mask with the buffered regions """
for poly in (poly_p, poly_s):
pts = np.array(poly.buffer(margin).boundary.coords, np.int32)
cv2.fillPoly(mask, [pts], color)
# prepare the mask for the grabCut algorithm
burrow_width = self.params["burrows/width"]
mask = np.full_like(img, cv2.GC_BGD, dtype=np.uint8) # < sure background
fill_mask(cv2.GC_PR_BGD, 0.25 * burrow_width) # < possible background
fill_mask(cv2.GC_PR_FGD, 0) # < possible foreground
fill_mask(cv2.GC_FGD, -0.25 * burrow_width) # < sure foreground
# run GrabCut algorithm
img = cv2.cvtColor(img, cv2.COLOR_GRAY2RGB)
bgdmodel = np.zeros((1, 65), np.float64)
fgdmodel = np.zeros((1, 65), np.float64)
try:
cv2.grabCut(img, mask, (0, 0, 1, 1), bgdmodel, fgdmodel, 2, cv2.GC_INIT_WITH_MASK)
except:
# any error in the GrabCut algorithm makes the whole function useless
logging.warn("GrabCut algorithm failed for predug")
return candidate
# turn the sky into background
pts = np.array(poly_s.boundary.coords, np.int32)
cv2.fillPoly(mask, [pts], cv2.GC_BGD)
# extract a binary mask determining the predug
predug_mask = (mask == cv2.GC_FGD) | (mask == cv2.GC_PR_FGD)
predug_mask = predug_mask.astype(np.uint8)
# simplify the mask using binary operations
w = int(0.5 * burrow_width)
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (w, w))
predug_mask = cv2.morphologyEx(predug_mask, cv2.MORPH_OPEN, kernel)
# extract the outline of the predug
contour = regions.get_contour_from_largest_region(predug_mask)
# translate curves back into global coordinate system
contour = curves.translate_points(contour, region.x, region.y)
return shapes.Polygon(contour)
def calculate_burrow_centerline(self, burrow, point_start=None):
""" determine the centerline of a burrow with one exit """
if point_start is None:
point_start = burrow.centerline[0]
# get a binary image of the burrow
mask, shift = burrow.get_mask(margin=2,
dtype=np.int32,
ret_offset=True)
# move starting point onto ground line
ground_line = self.ground.linestring
point_start = curves.get_projection_point(ground_line, point_start)
point_start = (int(point_start[0]) - shift[0],
int(point_start[1]) - shift[1])
mask[point_start[1], point_start[0]] = 1
# calculate the distance from the start point
regions.make_distance_map(mask, [point_start])
# find the second point by locating the farthest point
_, _, _, p_end = cv2.minMaxLoc(mask)
# find an estimate for the centerline from the shortest distance from
# the end point to the burrow exit
points = regions.shortest_path_in_distance_map(mask, p_end)
# translate the points back to global coordinates
centerline = curves.translate_points(points, shift[0], shift[1])
# save centerline such that burrow exit is first point
centerline = centerline[::-1]
# add points that might be outside of the burrow contour
ground_start = curves.get_projection_point(ground_line, centerline[0])
centerline.insert(0, ground_start)
# simplify the curve
centerline = cv2.approxPolyDP(np.array(centerline, np.int),
epsilon=1,
closed=False)
# save the centerline in the burrow structure
burrow.centerline = centerline[:, 0, :]
def calculate_burrow_centerline(self, burrow, point_start=None):
""" determine the centerline of a burrow with one exit """
if point_start is None:
point_start = burrow.centerline[0]
# get a binary image of the burrow
mask, shift = burrow.get_mask(margin=2, dtype=np.int32, ret_offset=True)
# move starting point onto ground line
ground_line = self.ground.linestring
point_start = curves.get_projection_point(ground_line, point_start)
point_start = (int(point_start[0]) - shift[0],
int(point_start[1]) - shift[1])
mask[point_start[1], point_start[0]] = 1
# calculate the distance from the start point
regions.make_distance_map(mask, [point_start])
# find the second point by locating the farthest point
_, _, _, p_end = cv2.minMaxLoc(mask)
# find an estimate for the centerline from the shortest distance from
# the end point to the burrow exit
points = regions.shortest_path_in_distance_map(mask, p_end)
# translate the points back to global coordinates
centerline = curves.translate_points(points, shift[0], shift[1])
# save centerline such that burrow exit is first point
centerline = centerline[::-1]
# add points that might be outside of the burrow contour
ground_start = curves.get_projection_point(ground_line, centerline[0])
if isinstance(centerline, np.ndarray):
centerline = np.insert(centerline, 0, ground_start).reshape(-1, 2)
else:
centerline.insert(0, ground_start)
# simplify the curve
centerline = cv2.approxPolyDP(np.array(centerline, np.int),
epsilon=1, closed=False)
# save the centerline in the burrow structure
burrow.centerline = centerline[:, 0, :]
def _get_burrow_centerline(self, burrow, points_start, points_end=None):
""" determine the centerline of a burrow with one exit """
ground_line = self.ground.linestring
# get a binary image of the burrow
mask, shift = burrow.get_mask(margin=2, dtype=np.int32, ret_offset=True)
# mark the start points according to their distance to the ground line
# dists_g = [ground_line.distance(geometry.Point(p))
# for p in points_start]
points_start = curves.translate_points(points_start, -shift[0], -shift[1])
for p in points_start:
mask[p[1], p[0]] = 1
if points_end is None:
# end point is not given and will thus be determined automatically
# calculate the distance from the start point
regions.make_distance_map(mask.T, points_start)
# find the second point by locating the farthest point
_, _, _, p_end = cv2.minMaxLoc(mask)
else:
# prepare the end point if present
# translate that point to the mask _frame
points_end = curves.translate_points(points_end, -shift[0], -shift[1])
for p in points_end:
mask[p[1], p[0]] = 1
# calculate the distance from the start point
regions.make_distance_map(mask.T, points_start, points_end)
# get the distance between the start and the end point
dists = [mask[p[1], p[0]] for p in points_end]
best_endpoint = np.argmin(dists)
p_end = points_end[best_endpoint]
# find an estimate for the centerline from the shortest distance from
# the end point to the burrow exit
points = regions.shortest_path_in_distance_map(mask, p_end)
# debug.show_shape(geometry.MultiPoint(points_start),
# geometry.Point(p_end),
# background=mask)
# exit()
# translate the points back to global coordinates
centerline = curves.translate_points(points, shift[0], shift[1])
# save centerline such that burrow exit is first point
centerline = centerline[::-1]
# add points that might be outside of the burrow contour
ground_start = curves.get_projection_point(ground_line, centerline[0])
centerline.insert(0, ground_start)
if points_end is not None:
ground_end = curves.get_projection_point(ground_line, centerline[-1])
centerline.append(ground_end)
# simplify the curve
centerline = cv2.approxPolyDP(np.array(centerline, np.int),
epsilon=1, closed=False)
# save the centerline in the burrow structure
burrow.centerline = centerline[:, 0, :]
def calculate_burrow_properties(self, burrow, ground_line=None):
""" calculates additional properties of the burrow """
# load some parameters
burrow_width = self.params['burrow/width_typical']
min_length = self.params['burrow/branch_length_min']
# determine the burrow end points
endpoints = burrow.get_endpoints(ground_line)
# get distance map from centerline
distance_map, offset = burrow.get_mask(margin=2, dtype=np.uint16,
ret_offset=True)
cline = burrow.centerline
start_points = curves.translate_points(cline, -offset[0], -offset[1])
regions.make_distance_map(distance_map, start_points)
# determine endpoints, which are not already part of the centerline
end_coords = np.array([ep.coords for ep in endpoints])
dists = spatial.distance.cdist(end_coords, cline)
extra_ends = end_coords[dists.min(axis=1) > burrow_width, :].tolist()
extra_ends = curves.translate_points(extra_ends, -offset[0], -offset[1])
# get additional points that are far away from the centerline
map_max = ndimage.filters.maximum_filter(distance_map, burrow_width)
map_maxima = (distance_map == map_max) & (distance_map > min_length)
maxima = np.array(np.nonzero(map_maxima)).T
# determine the object from which we measure the distance to the sky
if ground_line is not None:
outside = ground_line.linestring
else:
outside = geometry.MultiPoint(end_coords)
# define a helper function for checking the connection to the ground
burrow_poly = burrow.polygon.buffer(2)
def _direct_conn_to_ground(point, has_offset=False):
""" helper function checking the connection to the ground """
if has_offset:
point = (point[0] + offset[0], point[1] + offset[1])
p_ground = curves.get_projection_point(outside, point)
conn_line = geometry.LineString([point, p_ground])
return conn_line.length < 1 or conn_line.within(burrow_poly)
branch_points = []
branch_point_separation = self.params['burrow/branch_point_separation']
if maxima.size > 0:
if len(maxima) == 1:
clusters = [0]
else:
# cluster maxima to reduce them to single end points
# this is important when a burrow has multiple exits to the ground
clusters = cluster.hierarchy.fclusterdata(
maxima, branch_point_separation,
method='single', criterion='distance'
)
cluster_ids = np.unique(clusters)
logging.debug('Found %d possible branch point(s)' % len(cluster_ids))
# find the additional point from the clusters
for cluster_id in cluster_ids:
candidates = maxima[clusters == cluster_id, :]
# get point with maximal distance from center line
dists = [distance_map[x, y] for x, y in candidates]
y, x = candidates[np.argmax(dists)]
# check whether this point is close to an endpoint
point = geometry.Point(x + offset[0], y + offset[1])
branch_depth = point.distance(outside)
if (branch_depth > min_length or
not _direct_conn_to_ground((x, y), has_offset=True)):
branch_points.append((x, y))
# save some output for debugging
self._debug['possible_branches'] = \
curves.translate_points(branch_points, offset[0], offset[1])
# find the burrow branches
burrow.branches = []
if extra_ends or branch_points:
num_branches = len(extra_ends) + len(branch_points)
logging.info('Found %d possible branch(es)' % num_branches)
# create generator for iterating over all additional points
gen = ((p_class, p_coords)
for p_class, points in enumerate([extra_ends, branch_points])
for p_coords in points)
# connect all additional points to the centerline -> branches
for ep_id, ep in gen:
line = regions.shortest_path_in_distance_map(distance_map, ep)
line = curves.translate_points(line, offset[0], offset[1])
# estimate the depth of the branch
depth = max(geometry.Point(p).distance(outside)
for p in (line[0], line[-1]))
# check whether the line corresponds to an open branch
# open branches are branches where all connection lines between
# the branch and ground line are fully contained in the burrow
# polygon
if ep_id == 1 and depth < min_length:
num_direct = sum(1 for p_branch in line
if _direct_conn_to_ground(p_branch))
ratio_direct = num_direct / len(line)
if ratio_direct > 0.75:
# the ground is directly reachable from most points
line = None
if line:
burrow.branches.append(line)
if ground_line:
self._add_burrow_angle_statistics(burrow, ground_line)
return
# filter branches to make sure that they are not all connected to ground
# determine the morphological graph
graph = burrow.get_morphological_graph()
# combine multiple branches at exits and remove short branches that are
# not exits
exit_nodes = []
for points_exit in burrow.get_exit_regions(ground_line):
exit_line = geometry.LineString(points_exit)
# find the graph nodes that are close to the exit
graph_nodes = []
for node, data in graph.nodes(data=True):
node_point = geometry.Point(data['coords'])
if exit_line.distance(node_point) < 3:
graph_nodes.append((node, node_point))
# find the graph node that is closest to the exit point
exit_point = exit_line.interpolate(0.5, normalized=True)
dists = [exit_point.distance(node_point)
for _, node_point in graph_nodes]
exit_id = np.argmin(dists)
for node_id, (node, _) in enumerate(graph_nodes):
if node_id == exit_id:
# save the exit node for later use
exit_nodes.append(node)
else:
# remove additional graph nodes
graph.remove_node(node)
# remove short branches that are not exit nodes
length_min = self.params['burrow/branch_length_min']
graph.remove_short_edges(length_min=length_min,
exclude_nodes=exit_nodes)
# remove nodes of degree two
graph.simplify()
burrow.morphological_graph = graph