def _connect_burrow_to_structure(self, contour, structure):
""" extends the burrow contour such that it connects to the ground line
or to other burrows """
outline = geometry.Polygon(contour)
# determine burrow points close to the structure
dist = structure.distance(outline)
conn_points = []
while len(conn_points) == 0:
dist += self.params['burrows/width']/2
conn_points = [point for point in contour
if structure.distance(geometry.Point(point)) < dist]
conn_points = np.array(conn_points)
# cluster the points to detect multiple connections
# this is important when a burrow has multiple exits to the ground
if len(conn_points) >= 2:
dist_max = self.params['burrows/width']
data = cluster.hierarchy.fclusterdata(conn_points, dist_max,
method='single',
criterion='distance')
else:
data = np.ones(1, np.int)
burrow_width_min = self.params['burrows/width_min']
for cluster_id in np.unique(data):
p_exit = conn_points[data == cluster_id].mean(axis=0)
p_ground = curves.get_projection_point(structure, p_exit)
line = geometry.LineString((p_exit, p_ground))
tunnel = line.buffer(distance=burrow_width_min/2,
cap_style=geometry.CAP_STYLE.flat)
# add this to the burrow outline
outline = outline.union(tunnel.buffer(0.1))
# get the contour points
outline = regions.get_enclosing_outline(outline)
outline = regions.regularize_linear_ring(outline)
contour = np.array(outline.coords)
# fill the burrow mask, such that this extension does not have to be
# done next time again
cv2.fillPoly(self.burrow_mask, [np.asarray(contour, np.int32)], 1)
return contour
def connect_burrow_chunks(self, burrow_chunks):
""" takes a list of burrow chunks and connects them such that in the
end all burrow chunks are connected to the ground line. """
if len(burrow_chunks) == 0:
return []
dist_max = self.params['burrows/chunk_dist_max']
# build the contour profiles of the burrow chunks
linear_rings = [geometry.LinearRing(c) for c in burrow_chunks]
# handle all burrows close to the ground
connected, disconnected = [], []
for k, ring in enumerate(linear_rings):
ground_dist = self.ground.linestring.distance(ring)
if ground_dist < dist_max:
# burrow is close to ground
if 1 < ground_dist:
burrow_chunks[k] = \
self._connect_burrow_to_structure(burrow_chunks[k],
self.ground.linestring)
connected.append(k)
else:
disconnected.append(k)
assert (set(connected) | set(disconnected)) == set(range(len(burrow_chunks)))
# calculate distances to other burrows
burrow_dist = np.empty([len(burrow_chunks)]*2)
np.fill_diagonal(burrow_dist, np.inf)
for x, contour1 in enumerate(linear_rings):
for y, contour2 in enumerate(linear_rings[x+1:], x+1):
dist = contour1.distance(contour2)
burrow_dist[x, y] = dist
burrow_dist[y, x] = dist
# handle all remaining chunks, which need to be connected to other chunks
while connected and disconnected:
# find chunks which is closest to all the others
dist = burrow_dist[disconnected, :][:, connected]
k1, k2 = np.unravel_index(dist.argmin(), dist.shape)
if dist[k1, k2] > dist_max:
# don't connect structures that are too far from each other
break
c1, c2 = disconnected[k1], connected[k2]
# k1 is chunk to connect, k2 is closest chunk to connect it to
# connect the current chunk to the other structure
structure = geometry.LinearRing(burrow_chunks[c2])
enlarged_chunk = self._connect_burrow_to_structure(burrow_chunks[c1], structure)
# merge the two structures
poly1 = geometry.Polygon(enlarged_chunk)
poly2 = regions.regularize_polygon(geometry.Polygon(structure))
poly = poly1.union(poly2).buffer(0.1)
# find and regularize the common contour
contour = regions.get_enclosing_outline(poly)
contour = regions.regularize_linear_ring(contour)
contour = contour.coords
# replace the current chunk by the merged one
burrow_chunks[c1] = contour
# replace all other burrow chunks with the same id
id_c2 = id(burrow_chunks[c2])
for k, bc in enumerate(burrow_chunks):
if id(bc) == id_c2:
burrow_chunks[k] = contour
# mark the cluster as connected
del disconnected[k1]
connected.append(c1)
# return the unique burrow structures
burrows = []
connected_chunks = (burrow_chunks[k] for k in connected)
for contour in unique_based_on_id(connected_chunks):
contour = regions.regularize_contour_points(contour)
try:
burrow = Burrow(contour)
except ValueError:
continue
else:
if burrow.area >= self.params['burrows/area_min']:
burrows.append(burrow)
return burrows
