def _node_centrality_by_synapse(tree, nodes: Dict, totalOutputs: int,
totalInputs: int) -> None:
""" tree: a DiGraph
nodes: a dictionary of treenode ID vs Counts instance
totalOutputs: the total number of output synapses of the tree
totalInputs: the total number of input synapses of the tree
Returns nothing, the results are an update to the Counts instance of each treenode entry in nodes, namely the nPossibleIOPaths. """
# 1. Ensure the root is an end by checking that it has only one child; otherwise reroot at the first end node found
if 0 == totalOutputs:
# Not computable
for counts in nodes.values():
counts.synapse_centrality = -1
return
if len(list(tree.successors(find_root(tree)))) > 1:
# Reroot at the first end node found
tree = tree.copy()
endNode = next(nodeID for nodeID in nodes.keys()
if not list(tree.successors(nodeID)))
reroot(tree, endNode)
# 2. Partition into sequences, sorted from small to large
sequences = sorted(partition(tree), key=len)
# 3. Traverse all partitions counting synapses seen
for seq in sequences:
# Each seq runs from an end node towards the root or a branch node
seenI = 0
seenO = 0
for nodeID in seq:
counts = nodes[nodeID]
seenI += counts.inputs + counts.seenInputs
seenO += counts.outputs + counts.seenOutputs
counts.seenInputs = seenI
counts.seenOutputs = seenO
counts.nPossibleIOPaths = counts.seenInputs * (
totalOutputs - counts.seenOutputs) + counts.seenOutputs * (
totalInputs - counts.seenInputs)
counts.synapse_centrality = counts.nPossibleIOPaths / float(
totalOutputs)
def _node_centrality_by_synapse(tree, nodes, totalOutputs, totalInputs):
""" tree: a DiGraph
nodes: a dictionary of treenode ID vs Counts instance
totalOutputs: the total number of output synapses of the tree
totalInputs: the total number of input synapses of the tree
Returns nothing, the results are an update to the Counts instance of each treenode entry in nodes, namely the nPossibleIOPaths. """
# 1. Ensure the root is an end by checking that it has only one child; otherwise reroot at the first end node found
if 0 == totalOutputs:
# Not computable
for counts in nodes.values():
counts.synapse_centrality = -1
return
if len(tree.successors(find_root(tree))) > 1:
# Reroot at the first end node found
tree = tree.copy()
endNode = next(nodeID for nodeID in nodes.keys() if not tree.successors(nodeID))
reroot(tree, endNode)
# 2. Partition into sequences, sorted from small to large
sequences = sorted(partition(tree), key=len)
# 3. Traverse all partitions counting synapses seen
for seq in sequences:
# Each seq runs from an end node towards the root or a branch node
seenI = 0
seenO = 0
for nodeID in seq:
counts = nodes[nodeID]
seenI += counts.inputs + counts.seenInputs
seenO += counts.outputs + counts.seenOutputs
counts.seenInputs = seenI
counts.seenOutputs = seenO
counts.nPossibleIOPaths = counts.seenInputs * (totalOutputs - counts.seenOutputs) + counts.seenOutputs * (totalInputs - counts.seenInputs)
counts.synapse_centrality = counts.nPossibleIOPaths / float(totalOutputs)
def last_openleaf(request, project_id=None, skeleton_id=None):
""" Return the ID of the nearest node (or itself), and its location string;
or two nulls if none found. """
tnid = int(request.POST['tnid'])
cursor = connection.cursor()
cursor.execute("SELECT id FROM relation WHERE project_id=%s AND relation_name='labeled_as'" % int(project_id))
labeled_as = cursor.fetchone()[0]
# Select all nodes and their tags
cursor.execute('''
SELECT t.id, t.parent_id, t.location_x, t.location_y, t.location_z, ci.name
FROM treenode t LEFT OUTER JOIN (treenode_class_instance tci INNER JOIN class_instance ci ON tci.class_instance_id = ci.id AND tci.relation_id = %s) ON t.id = tci.treenode_id
WHERE t.skeleton_id = %s
''' % (labeled_as, int(skeleton_id)))
# Some entries repeated, when a node has more than one tag
# Create a graph with edges from parent to child, and accumulate parents
tree = nx.DiGraph()
for row in cursor.fetchall():
nodeID = row[0]
if row[1]:
# It is ok to add edges that already exist: DiGraph doesn't keep duplicates
tree.add_edge(row[1], nodeID)
else:
tree.add_node(nodeID)
tree.node[nodeID]['loc'] = (row[2], row[3], row[4])
if row[5]:
props = tree.node[nodeID]
tags = props.get('tags')
if tags:
tags.append(row[5])
else:
props['tags'] = [row[5]]
if tnid not in tree:
raise Exception("Could not find %s in skeleton %s" % (tnid, int(skeleton_id)))
reroot(tree, tnid)
distances = edge_count_to_root(tree, root_node=tnid)
# Iterate end nodes, find closest
nearest = None
distance = tree.number_of_nodes() + 1
loc = None
other_tags = set(('uncertain continuation', 'not a branch', 'soma'))
for nodeID, out_degree in tree.out_degree_iter():
if 0 == out_degree:
# Found an end node
props = tree.node[nodeID]
# Check if not tagged with a tag containing 'end'
if not 'tags' in props and not [s for s in props if 'end' in s or s in other_tags]:
# Found an open end
d = distances[nodeID]
if d < distance:
nearest = nodeID
distance = d
loc = props['loc']
return HttpResponse(json.dumps((nearest, loc)))