def mala_clustering(graph, edge_features, edge_sizes, threshold):
n_nodes = graph.numberOfNodes
policy = nagglo.malaClusterPolicy(graph=graph,
edgeIndicators=edge_features,
nodeSizes=np.zeros(n_nodes, dtype='float'),
edgeSizes=edge_sizes,
threshold=threshold)
clustering = nagglo.agglomerativeClustering(policy)
clustering.run()
return clustering.result()
def cluster(threshold):
policy = nagglo.malaClusterPolicy(graph=graph,
edgeIndicators=probs,
edgeSizes=edge_sizes,
nodeSizes=node_sizes,
threshold=threshold)
clustering = nifty.graph.agglo.agglomerativeClustering(policy)
clustering.run()
node_labels = clustering.result()
return (node_labels[lifted_uvs[:, 0]] !=
node_labels[lifted_uvs[:, 1]]).astype('float32')
def mala_clustering(graph, edge_features, edge_sizes, threshold):
""" Compute segmentation with mala-style clustering.
Arguments:
graph [nifty.graph] - graph to cluster
edge_features [np.ndarray] - features used for clustering
edge_sizes [np.ndarray] - sizes of edges
threshold [float] - threshold to stop clustering
"""
n_nodes = graph.numberOfNodes
policy = nagglo.malaClusterPolicy(graph=graph,
edgeIndicators=edge_features,
nodeSizes=np.zeros(n_nodes,
dtype='float'),
edgeSizes=edge_sizes,
threshold=threshold)
clustering = nagglo.agglomerativeClustering(policy)
clustering.run()
return clustering.result()
def mala_clustering(graph, edge_features, edge_sizes, threshold):
""" Compute segmentation with mala-style clustering.
In "Large Scale Image Segmentation with Structured Loss based Deep Learning for Connectome Reconstruction":
https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8364622
Arguments:
graph [nifty.graph] - graph to cluster
edge_features [np.ndarray] - features used for clustering
edge_sizes [np.ndarray] - sizes of edges
threshold [float] - threshold to stop clustering
"""
n_nodes = graph.numberOfNodes
policy = nagglo.malaClusterPolicy(graph=graph,
edgeIndicators=edge_features,
nodeSizes=np.zeros(n_nodes,
dtype='float'),
edgeSizes=edge_sizes,
threshold=threshold)
clustering = nagglo.agglomerativeClustering(policy)
clustering.run()
return clustering.result()
def _cluster_policy(self, graph, edge_features, node_sizes, edge_sizes):
return nagglo.malaClusterPolicy(graph=graph,
edgeIndicators=edge_features,
nodeSizes=node_sizes,
edgeSizes=edge_sizes,
threshold=self.threshold)