nifty.graph¶
Functions¶
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nifty.graph.components()¶
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nifty.graph.connectedComponentsFromNodeLabels()¶ compute connected component labels of a node labeling
All nodes which have zero as nodeLabel will keep a zeroArguments:
- graph : the input graph
nodeLabels (numpy.ndarray): node labeling dense (bool): should the returned labeling be dense (default {True})
ignoreBackground (bool): if true, all input zeros are mapped to zeros (default {False})
Returns: connected components labels Return type: numpy.ndarray compute connected component labels of a node labeling
All nodes which have zero as nodeLabel will keep a zeroArguments:
- graph : the input graph
nodeLabels (numpy.ndarray): node labeling dense (bool): should the returned labeling be dense (default {True})
ignoreBackground (bool): if true, all input zeros are mapped to zeros (default {False})
Returns: connected components labels Return type: numpy.ndarray compute connected component labels of a node labeling
All nodes which have zero as nodeLabel will keep a zeroArguments:
- graph : the input graph
nodeLabels (numpy.ndarray): node labeling dense (bool): should the returned labeling be dense (default {True})
ignoreBackground (bool): if true, all input zeros are mapped to zeros (default {False})
Returns: connected components labels Return type: numpy.ndarray
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nifty.graph.drawGraph(graph, method='spring')¶
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nifty.graph.edgeContractionGraph(g, callback)¶
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nifty.graph.edgeWeightedWatershedsSegmentation()¶ Edge weighted watershed on a graph
Parameters: graph – the input graph seeds (numpy.ndarray): the seeds edgeWeights (numpy.ndarray): the edge weights Returns: the segmentation Return type: numpy.ndarray Edge weighted watershed on a graph
Parameters: graph – the input graph seeds (numpy.ndarray): the seeds edgeWeights (numpy.ndarray): the edge weights Returns: the segmentation Return type: numpy.ndarray Edge weighted watershed on a graph
Parameters: graph – the input graph seeds (numpy.ndarray): the seeds edgeWeights (numpy.ndarray): the edge weights Returns: the segmentation Return type: numpy.ndarray
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nifty.graph.gridGraph(shape, simpleNh=True)¶
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nifty.graph.longRangeGridGraph(shape, offsets)¶
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nifty.graph.longRangeGridGraph3D()¶
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nifty.graph.nodeWeightedWatershedsSegmentation()¶ Node weighted watershed on a graph
Parameters: graph – the input graph seeds (numpy.ndarray): the seeds nodeWeights (numpy.ndarray): the node weights Returns: the segmentation Return type: numpy.ndarray Node weighted watershed on a graph
Parameters: graph – the input graph seeds (numpy.ndarray): the seeds nodeWeights (numpy.ndarray): the node weights Returns: the segmentation Return type: numpy.ndarray Node weighted watershed on a graph
Parameters: graph – the input graph seeds (numpy.ndarray): the seeds nodeWeights (numpy.ndarray): the node weights Returns: the segmentation Return type: numpy.ndarray
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nifty.graph.randomGraph(numberOfNodes, numberOfEdges)¶
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nifty.graph.shortestPathMultiTargetParallel()¶
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nifty.graph.shortestPathSingleTargetParallel()¶
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nifty.graph.undirectedGraph(numberOfNodes)¶
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nifty.graph.undirectedGridGraph(shape, simpleNh=True)¶
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nifty.graph.undirectedLongRangeGridGraph(shape, offsets)¶
Classes¶
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class
nifty.graph.ComponentsUndirectedGraph¶ -
build()¶
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buildFromEdgeLabels()¶
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buildFromNodeLabels()¶
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componentLabels()¶
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class
nifty.graph.ComponentsUndirectedGridGraph2DSimpleNh¶ -
build()¶
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buildFromEdgeLabels()¶
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buildFromNodeLabels()¶
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componentLabels()¶
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class
nifty.graph.ComponentsUndirectedGridGraph3DSimpleNh¶ -
build()¶
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buildFromEdgeLabels()¶
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buildFromNodeLabels()¶
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componentLabels()¶
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class
nifty.graph.EdgeContractionGraphCallback¶
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class
nifty.graph.EdgeContractionGraphCallbackImpl¶ -
contractEdgeCallback¶
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contractEdgeDoneCallback¶
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mergeEdgesCallback¶
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mergeNodesCallback¶
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class
nifty.graph.EdgeContractionGraphUndirectedGraph¶ -
MincutObjective¶ alias of
MincutObjectiveEdgeContractionGraphUndirectedGraph
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MulticutObjective¶ alias of
MulticutObjectiveEdgeContractionGraphUndirectedGraph
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baseGraph¶
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bfsEdges()¶
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contractEdge()¶
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edgeIdUpperBound¶
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edges()¶ Get an edge iterator
Get an edge iterator to iterate over all edges
Returns: edge iterator
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findEdge()¶ Find an edge in the graph
Parameters: uv (tuple) – a pair of nodes Returns: edge index if edge is in graph, -1 otherwise. Return type: int Find an edge in the graph
Parameters: - u (int) – first node
- v (int) – second node
Returns: edge index if edge is in graph, -1 otherwise.
Return type: int
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findEdges()¶ Find multiple edges in the graph simultaneous
Parameters: uv (numpy.ndarray) – array with pairs of nodes (Ex2) Returns: array filed with edge indexes for all pairs of nodes which are in the graph and -1 otherwise. Return type: numpy.ndarray
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findRepresentativeEdge()¶
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findRepresentativeNode()¶
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nodeAdjacency()¶
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nodeIdUpperBound¶
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nodeOfDeadEdge()¶
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nodeUfd¶
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nodes()¶ Get an node iterator
Get an node iterator to iterate over all nodes
Returns: node iterator
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numberOfEdges¶
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numberOfNodes¶
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reset()¶
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u()¶ Get first endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the first endpoint of the edge. Return type: int
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uv()¶ Get both endpoints of an edge
Parameters: edge (int) – edge index Returns: pair of node indexes / enpoints of the edge. Return type: tuple
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uvIds()¶ Get the two endpoints of all edges simultaneous.
Returns: uv-ids as array with shape [numberOfEdges,2] Return type: numpy.ndarray
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v()¶ Get second endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the second endpoint of the edge. Return type: int
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class
nifty.graph.EdgeContractionGraphUndirectedGraphAdjacencyIter¶
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class
nifty.graph.EdgeContractionGraphUndirectedGraphEdgeIter¶
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class
nifty.graph.EdgeContractionGraphUndirectedGraphEdgeMapFloat64¶
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class
nifty.graph.EdgeContractionGraphUndirectedGraphNodeIter¶
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class
nifty.graph.EdgeContractionGraphUndirectedGraphNodeMapFloat64¶
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class
nifty.graph.ShortestPathDijkstra¶ -
runSingleSourceMultiTarget()¶
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runSingleSourceSingleTarget()¶
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class
nifty.graph.UndirectedGraph¶ -
EdgeContractionGraph¶ alias of
EdgeContractionGraphUndirectedGraph
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LiftedMulticutObjective¶ alias of
LiftedMulticutObjectiveUndirectedGraph
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MincutObjective¶ alias of
MincutObjectiveUndirectedGraph
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MulticutObjective¶ alias of
MulticutObjectiveUndirectedGraph
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bfsEdges()¶
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deserialize()¶
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edgeIdUpperBound¶
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edges()¶ Get an edge iterator
Get an edge iterator to iterate over all edges
Returns: edge iterator
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extractSubgraphFromNodes()¶
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findEdge()¶ Find an edge in the graph
Parameters: uv (tuple) – a pair of nodes Returns: edge index if edge is in graph, -1 otherwise. Return type: int Find an edge in the graph
Parameters: - u (int) – first node
- v (int) – second node
Returns: edge index if edge is in graph, -1 otherwise.
Return type: int
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findEdges()¶ Find multiple edges in the graph simultaneous
Parameters: uv (numpy.ndarray) – array with pairs of nodes (Ex2) Returns: array filed with edge indexes for all pairs of nodes which are in the graph and -1 otherwise. Return type: numpy.ndarray
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insertEdge()¶
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insertEdges()¶
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nodeAdjacency()¶
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nodeIdUpperBound¶
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nodes()¶ Get an node iterator
Get an node iterator to iterate over all nodes
Returns: node iterator
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numberOfEdges¶
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numberOfNodes¶
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serialize()¶
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shrinkToFit()¶
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u()¶ Get first endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the first endpoint of the edge. Return type: int
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uv()¶ Get both endpoints of an edge
Parameters: edge (int) – edge index Returns: pair of node indexes / enpoints of the edge. Return type: tuple
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uvIds()¶ Get the two endpoints of all edges simultaneous.
Returns: uv-ids as array with shape [numberOfEdges,2] Return type: numpy.ndarray
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v()¶ Get second endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the second endpoint of the edge. Return type: int
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class
nifty.graph.UndirectedGraphAdjacencyIter¶
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class
nifty.graph.UndirectedGraphEdgeIter¶
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class
nifty.graph.UndirectedGraphEdgeMapFloat64¶
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class
nifty.graph.UndirectedGraphNodeIter¶
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class
nifty.graph.UndirectedGraphNodeMapFloat64¶
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class
nifty.graph.UndirectedGridGraph2DSimpleNh¶ 2Dimensional Grid Graph
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bfsEdges()¶
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coordianteToNode()¶
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edgeIdUpperBound¶
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edges()¶ Get an edge iterator
Get an edge iterator to iterate over all edges
Returns: edge iterator
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findEdge()¶ Find an edge in the graph
Parameters: uv (tuple) – a pair of nodes Returns: edge index if edge is in graph, -1 otherwise. Return type: int Find an edge in the graph
Parameters: - u (int) – first node
- v (int) – second node
Returns: edge index if edge is in graph, -1 otherwise.
Return type: int
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findEdges()¶ Find multiple edges in the graph simultaneous
Parameters: uv (numpy.ndarray) – array with pairs of nodes (Ex2) Returns: array filed with edge indexes for all pairs of nodes which are in the graph and -1 otherwise. Return type: numpy.ndarray
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imageToEdgeMap()¶ convert an image to an edge map
Parameters: image (numpy.ndarray) – the image mode str: mode can be:
- ’min’: Minimum of the two image values at edges endpoints of coordinates.
- ’max’: Maximum of the two image values at edges endpoints of coordinates.
- ’sum’: Sum of the two image values at edges endpoints of coordinates.
- ’prod’: Product of the two image values at edges endpoints of coordinates.
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nodeAdjacency()¶
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nodeIdUpperBound¶
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nodeToCoordinate()¶
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nodes()¶ Get an node iterator
Get an node iterator to iterate over all nodes
Returns: node iterator
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numberOfEdges¶
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numberOfNodes¶
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u()¶ Get first endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the first endpoint of the edge. Return type: int
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uv()¶ Get both endpoints of an edge
Parameters: edge (int) – edge index Returns: pair of node indexes / enpoints of the edge. Return type: tuple
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uvIds()¶ Get the two endpoints of all edges simultaneous.
Returns: uv-ids as array with shape [numberOfEdges,2] Return type: numpy.ndarray
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v()¶ Get second endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the second endpoint of the edge. Return type: int
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class
nifty.graph.UndirectedGridGraph2DSimpleNhAdjacencyIter¶
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class
nifty.graph.UndirectedGridGraph2DSimpleNhEdgeIter¶
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class
nifty.graph.UndirectedGridGraph2DSimpleNhEdgeMapFloat64¶
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class
nifty.graph.UndirectedGridGraph2DSimpleNhNodeIter¶
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class
nifty.graph.UndirectedGridGraph2DSimpleNhNodeMapFloat64¶
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class
nifty.graph.UndirectedGridGraph3DSimpleNh¶ 3Dimensional Grid Graph
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bfsEdges()¶
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coordianteToNode()¶
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edgeIdUpperBound¶
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edges()¶ Get an edge iterator
Get an edge iterator to iterate over all edges
Returns: edge iterator
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findEdge()¶ Find an edge in the graph
Parameters: uv (tuple) – a pair of nodes Returns: edge index if edge is in graph, -1 otherwise. Return type: int Find an edge in the graph
Parameters: - u (int) – first node
- v (int) – second node
Returns: edge index if edge is in graph, -1 otherwise.
Return type: int
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findEdges()¶ Find multiple edges in the graph simultaneous
Parameters: uv (numpy.ndarray) – array with pairs of nodes (Ex2) Returns: array filed with edge indexes for all pairs of nodes which are in the graph and -1 otherwise. Return type: numpy.ndarray
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imageToEdgeMap()¶ convert an image to an edge map
Parameters: image (numpy.ndarray) – the image mode str: mode can be:
- ’min’: Minimum of the two image values at edges endpoints of coordinates.
- ’max’: Maximum of the two image values at edges endpoints of coordinates.
- ’sum’: Sum of the two image values at edges endpoints of coordinates.
- ’prod’: Product of the two image values at edges endpoints of coordinates.
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nodeAdjacency()¶
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nodeIdUpperBound¶
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nodeToCoordinate()¶
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nodes()¶ Get an node iterator
Get an node iterator to iterate over all nodes
Returns: node iterator
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numberOfEdges¶
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numberOfNodes¶
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u()¶ Get first endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the first endpoint of the edge. Return type: int
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uv()¶ Get both endpoints of an edge
Parameters: edge (int) – edge index Returns: pair of node indexes / enpoints of the edge. Return type: tuple
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uvIds()¶ Get the two endpoints of all edges simultaneous.
Returns: uv-ids as array with shape [numberOfEdges,2] Return type: numpy.ndarray
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v()¶ Get second endpoint of an edge
Parameters: edge (int) – edge index Returns: node index of the second endpoint of the edge. Return type: int
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class
nifty.graph.UndirectedGridGraph3DSimpleNhAdjacencyIter¶
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class
nifty.graph.UndirectedGridGraph3DSimpleNhEdgeIter¶
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class
nifty.graph.UndirectedGridGraph3DSimpleNhEdgeMapFloat64¶
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class
nifty.graph.UndirectedGridGraph3DSimpleNhNodeIter¶
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class
nifty.graph.UndirectedGridGraph3DSimpleNhNodeMapFloat64¶