def clean_by_radius(points, radius=15.0):
"""
Bins points by radius and returns only one per radius, removing duplicates.
:param points: Input points
:param radius: Radius
:return: Filtered points
>>> clean_by_radius(np.array([[1.0, 1.0],
... [1.1, 1.1],
... [9.0, 9.0]]), radius=1.5)
array([[1., 1.],
[9., 9.]])
"""
if len(points) == 0:
return points
tree = KDTree(points)
mapping = tree.query_ball_tree(tree, radius)
unique_indices = np.unique(list(l[0] for l in sorted(mapping)))
return points[unique_indices]
class NodeFrame(object):
"""
Node frame is a representation of an image stack frame on the graph/node level, it populates its values from
a PixelFrame passed.
"""
def __init__(self, pf):
"""
Initializes the NodeFrame
:param pf: PixelFrame the NodeFrame corresponds to
"""
# initializing vars
self.timepoint = None
self.calibration = None
self.junction_shift = None
self.endpoint_shift = None
self.data = None
self.endpoint_tree = None
self.junction_tree = None
self.endpoint_tree_data = None
self.junction_tree_data = None
self.adjacency = None
self.every_endpoint = None
self.every_junction = None
self.predecessors = None
self.shortest_paths = None
self.shortest_paths_num = None
self.connected_components_count = None
self.connected_components = None
self._cycles = None
self.self_to_successor = None
self.successor_to_self = None
self.self_to_successor_alternatives = None
# /initializing vars
self.timepoint = pf.timepoint # copy this information, so we can set pf to None for serialization
self.calibration = pf.calibration
self.prepare_graph(pf)
def prepare_graph(self, pf):
"""
Prepares the graph from the data stored in the PixelFrame pf.
:param pf: PixelFrame
:return:
"""
endpoint_tree_data = clean_by_radius(pf.endpoints, NodeEndpointMergeRadius.value / self.calibration)
junction_tree_data = clean_by_radius(pf.junctions, NodeJunctionMergeRadius.value / self.calibration)
e_length = len(endpoint_tree_data)
j_length = len(junction_tree_data)
total_length = e_length + j_length
data = np.r_[endpoint_tree_data, junction_tree_data]
endpoint_tree_data = data[:e_length]
junction_tree_data = data[e_length:]
if e_length > 0:
endpoint_tree = KDTree(endpoint_tree_data)
else:
endpoint_tree = None
if j_length > 0:
junction_tree = KDTree(junction_tree_data)
else:
junction_tree = None
junction_shift = e_length
endpoint_shift = 0
# while ends and junctions need to remain different,
# they are put in the same graph / adjacency matrix
# so, first come end nodes, then junction nodes
# => shifts
adjacency = lil_matrix((total_length, total_length), dtype=float)
# little bit of nomenclature:
# a pathlet (pixel graph so to say) is a path of on the image
# its begin is the 'left' l_ side, its end is the 'right' r_ side
# (not using begin / end not to confuse end with endpoint ...)
distance_threshold = NodeLookupRadius.value / self.calibration
cutoff_radius = NodeLookupCutoffRadius.value / self.calibration
for pathlet in pf.pathlets:
pathlet_length = calculate_length(pathlet)
l_side = pathlet[0]
r_side = pathlet[-1]
# experiment
l_test_distance, l_test_index = endpoint_tree.query(l_side, k=1)
if l_test_distance < distance_threshold:
l_is_end = True
else:
# original code
l_is_end = pf.endpoints_map[l_side[0], l_side[1]]
# experiment
r_test_distance, r_test_index = endpoint_tree.query(r_side, k=1)
if r_test_distance < distance_threshold:
r_is_end = True
else:
# original code
r_is_end = pf.endpoints_map[r_side[0], r_side[1]]
l_index_shift = endpoint_shift if l_is_end else junction_shift
r_index_shift = endpoint_shift if r_is_end else junction_shift
l_tree = endpoint_tree if l_is_end else junction_tree
r_tree = endpoint_tree if r_is_end else junction_tree
# first tuple value would be distance, but we don't care
try:
l_distance, l_index = l_tree.query(l_side, k=1)
r_distance, r_index = r_tree.query(r_side, k=1)
except AttributeError:
continue
if l_distance > cutoff_radius or r_distance > cutoff_radius:
# probably does not happen
continue
adjacency_left_index = l_index + l_index_shift
adjacency_right_index = r_index + r_index_shift
adjacency[adjacency_left_index, adjacency_right_index] = pathlet_length
adjacency[adjacency_right_index, adjacency_left_index] = pathlet_length
self.junction_shift = junction_shift
self.endpoint_shift = endpoint_shift
self.data = data
self.endpoint_tree = endpoint_tree
self.junction_tree = junction_tree
self.endpoint_tree_data = endpoint_tree_data
self.junction_tree_data = junction_tree_data
self.adjacency = adjacency
self.every_endpoint = range(self.endpoint_shift, self.junction_shift)
self.every_junction = range(self.junction_shift, self.junction_shift + len(self.junction_tree_data))
cleanup_graph_after_creation = True
if cleanup_graph_after_creation:
self.cleanup_adjacency()
self.adjacency = self.adjacency.tocsr()
self.generate_derived_data()
def cleanup_adjacency(self):
"""
Cleans up the adjacency matrix after alterations on the node level have been performed.
:return:
"""
non_empty_mask = (self.adjacency.getnnz(axis=0) + self.adjacency.getnnz(axis=1)) > 0
# noinspection PyTypeChecker
empty_indices, = np.where(~non_empty_mask)
# if this ever becomes multi threaded, we should lock the trees now
# endpoint_tree, junction_tree = None, None
e_length = non_empty_mask[:self.junction_shift].sum()
j_length = non_empty_mask[self.junction_shift:].sum()
total_length = e_length + j_length
self.junction_shift = e_length
self.endpoint_shift = 0
self.data = self.data[non_empty_mask]
self.endpoint_tree_data = self.data[:e_length]
self.junction_tree_data = self.data[e_length:]
if e_length > 0:
self.endpoint_tree = KDTree(self.endpoint_tree_data)
else:
self.endpoint_tree = None
if j_length > 0:
self.junction_tree = KDTree(self.junction_tree_data)
else:
self.junction_tree = None
new_adjacency = lil_matrix((total_length, total_length), dtype=self.adjacency.dtype)
coo = self.adjacency.tocoo()
for n, m, value in zip(coo.row, coo.col, coo.data):
npos, = np.where(n >= empty_indices)
mpos, = np.where(m >= empty_indices)
npos = 0 if len(npos) == 0 else npos[-1] + 1
mpos = 0 if len(mpos) == 0 else mpos[-1] + 1
new_adjacency[n-npos, m-mpos] = value
self.adjacency = new_adjacency
self.every_endpoint = range(self.endpoint_shift, self.junction_shift)
self.every_junction = range(self.junction_shift, self.junction_shift + len(self.junction_tree_data))
def generate_derived_data(self):
"""
Generates derived data from the current adjacency matrix.
Derived data are shortest paths, as well as connected components.
:return:
"""
self.shortest_paths, self.predecessors = shortest_path(self.adjacency, return_predecessors=True)
self.shortest_paths_num = shortest_path(self.adjacency, unweighted=True)
self.connected_components_count, self.connected_components = connected_components(self.adjacency)
@property
def cycles(self):
"""
Detects whether a cycle exists in the graph.
:return:
"""
if self._cycles is None:
g = self.get_networkx_graph()
try:
find_cycle(g)
self._cycles = True
except NetworkXNoCycle:
self._cycles = False
return self._cycles
def get_path(self, start_node, end_node):
"""
Walks from start_node to end_node in the graph and returns the list of nodes (including both).
:param start_node:
:param end_node:
:return:
"""
predecessor = end_node
path = [predecessor]
while predecessor != start_node:
predecessor = self.predecessors[start_node, predecessor]
path.append(predecessor)
return path[::-1]
def is_endpoint(self, i):
"""
Returns whether node i is an endpoint.
:param i:
:return:
"""
return i in self.every_endpoint
def is_junction(self, i):
"""
Returns whether node i is a junction.
:param i:
:return:
"""
return i in self.every_junction
def get_connected_nodes(self, some_node):
"""
Get all nodes which are (somehow) connected to node some_node.
:param some_node:
:return:
"""
label = self.connected_components[some_node]
return np.where(self.connected_components[self.connected_components == label])[0]
def track(self, successor):
"""
Tracks nodes on this frame to nodes on a successor frame.
:param successor:
:return:
"""
delta_t = (successor.timepoint - self.timepoint) / (60.0*60.0)
junction_shift_radius = (NodeTrackingJunctionShiftRadius.value / self.calibration) * delta_t
endpoint_shift_radius = (NodeTrackingEndpointShiftRadius.value / self.calibration) * delta_t
##
self_len = len(self.data)
successor_len = len(successor.data)
self_to_successor = np.zeros(self_len, dtype=int)
successor_to_self = np.zeros(successor_len, dtype=int)
self_to_successor[:] = -1
successor_to_self[:] = -1
self_to_successor_alternatives = [[]] * self_len
if self.junction_tree is not None and successor.junction_tree is not None:
junction_mapping = self.junction_tree.query_ball_tree(successor.junction_tree, junction_shift_radius)
else:
junction_mapping = []
if self.endpoint_tree is not None and successor.endpoint_tree is not None:
endpoint_mapping = self.endpoint_tree.query_ball_tree(successor.endpoint_tree, endpoint_shift_radius)
else:
endpoint_mapping = []
# print(self.timepoint, get_or_else(lambda: self.endpoint_tree.data), endpoint_mapping)
for self_hit, n in enumerate(chain(endpoint_mapping, junction_mapping)):
if len(n) == 0:
n = -1
ordered_n = []
else:
search_point = self.data[self_hit]
hit_points = np.array([successor.data[h] for h in n])
distances = np.sqrt(((hit_points - search_point) ** 2).sum(axis=1))
indexed = np.c_[distances, n]
ordered_n = [int(nn[1]) for nn in sorted(indexed, key=lambda t: t[0])]
min_distance = np.argmin(distances)
n = n[min_distance]
if self_hit > self.junction_shift:
n += successor.junction_shift
self_to_successor_alternatives[self_hit] = ordered_n
self_to_successor[self_hit] = n
successor_to_self[n] = self_hit
self.self_to_successor = self_to_successor # this is mainly used
self.successor_to_self = successor_to_self
self.self_to_successor_alternatives = self_to_successor_alternatives
def get_networkx_graph(self, with_z=0, return_positions=False):
"""
Convert the adjacency matrix based internal graph representation to a networkx graph representation.
Positions are additionally set based upon the pixel coordinate based positions of the nodes.
:param with_z: Whether z values should be set based upon the timepoint the nodes appear on
:param return_positions: Whether positions should be returned jointly with the graph
:return:
"""
g = from_scipy_sparse_matrix(self.adjacency)
positions = {}
for n, pos in enumerate(self.data):
positions[n] = (float(pos[1]), float(pos[0]))
g.nodes[n]['x'] = float(pos[1])
g.nodes[n]['y'] = float(pos[0])
if with_z > 0:
g.nodes[n]['z'] = float(self.timepoint * with_z)
positions[n] = (float(pos[1]), float(pos[0]), float(self.timepoint * with_z))
if not return_positions:
return g
else:
return g, positions
