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ShowSelectedTracksAction: don't get stuck if there's a loop in the graph #229
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ShowSelectedTracksAction: don't get stuck if there's a loop in the graph
maarzt c2d8ac1
ExampleGraph1, ExampleGraph2: make spots more accessible
maarzt 20cd749
ShowSelectedTrackActions: extract method findSelectedSubtreeRoots
maarzt 617a256
Refactor TreeUtils.findSelectedSubtreeRoots(...)
maarzt 4dde1ad
Add TreeUtils.findRealRoots(...) method
maarzt a8bc77f
Refactor and bug fix in TreeUtils
maarzt ced4b96
TreeUitls: improve javadoc
maarzt cafe95b
TreeUtilsTest: rename test methods
maarzt e49cb67
TreeUtils: change semantics of findRootsOfTheGivenNodes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,149 @@ | ||
| package org.mastodon.util; | ||
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| import java.util.Collection; | ||
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| import org.mastodon.collection.RefCollections; | ||
| import org.mastodon.collection.RefList; | ||
| import org.mastodon.collection.RefSet; | ||
| import org.mastodon.collection.RefStack; | ||
| import org.mastodon.graph.Edge; | ||
| import org.mastodon.graph.Graph; | ||
| import org.mastodon.graph.Vertex; | ||
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| public class TreeUtils | ||
| { | ||
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| private TreeUtils() | ||
| { | ||
| // prevent instantiation of utility class | ||
| } | ||
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| /** | ||
| * This method finds a subset of the given {@code selectedVertices} that | ||
| * contains only the roots of the subtrees that are selected. The order | ||
| * of the returned list follows the order of the {@code roots} list and | ||
| * the order of the outgoing edges of the graphs vertices. | ||
| * <p> | ||
| * Example {@code graph}: | ||
| * <pre> | ||
| * A B | ||
| * / \ / \ | ||
| * a1 a2 b1 b2 | ||
| * | / \ / \ | ||
| * a3 b3 b4 b5 b6 | ||
| * / \ | ||
| * a4 a5 | ||
| * </pre> | ||
| * | ||
| * If {@code selectedVertices} contains: {@code {a2, a4, a5, b1, b3, b4, b6}}, | ||
| * then the returned list will be: {@code [a2, b1, b6]}. | ||
| */ | ||
| public static < V extends Vertex< ? > > RefList< V > findSelectedSubtreeRoots( | ||
| final Graph< V, ? > graph, | ||
| final RefList< V > roots, | ||
| final RefSet< V > selectedVertices ) | ||
| { | ||
| final RefList< V > selectedSubtreeRoots = RefCollections.createRefList( graph.vertices() ); | ||
| final RefSet< V > visitedNodes = RefCollections.createRefSet( graph.vertices() ); | ||
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| for ( final V root : roots ) | ||
| for ( final DepthFirstIteration.Step< V > step : DepthFirstIteration.forRoot( graph, root ) ) | ||
| if ( ensureNoLoop( step, visitedNodes ) && !step.isSecondVisit() ) { | ||
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| final V node = step.node(); | ||
| if ( selectedVertices.contains( node ) ) | ||
| { | ||
| selectedSubtreeRoots.add( node ); | ||
| step.truncate(); // don't visit the child nodes | ||
| } | ||
| } | ||
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| return selectedSubtreeRoots; | ||
| } | ||
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| private static < V extends Vertex< ? > > boolean ensureNoLoop( DepthFirstIteration.Step< V > step, RefSet< V > visitedNodes ) | ||
| { | ||
| if ( !step.isFirstVisit() ) | ||
| return true; | ||
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| boolean isLoop = !visitedNodes.add( step.node() ); // The depth first iteration enters a node for the second time. -> there's a loop. | ||
| if ( isLoop ) | ||
| step.truncate(); // Break the loop by not visiting the child nodes. | ||
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| return !isLoop; | ||
| } | ||
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|
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| /** | ||
| * This method returns the root nodes of the trees containing any of the | ||
| * given {@code nodes}. | ||
| * <p> | ||
| * Example: | ||
| * <pre> | ||
| * A B | ||
| * / \ / \ | ||
| * a1 a2 b1 b2 | ||
| * | / \ / \ | ||
| * a3 b3 b4 b5 b6 | ||
| * / \ | ||
| * a4 a5 | ||
| * </pre> | ||
| * <p> | ||
| * If {@code nodes} contains {@code {a2, a4}} then the method will return | ||
| * {@code {A}}. | ||
| * <p> | ||
| * If {@code nodes} contains {@code {a2, a4, b6}} then the method will | ||
| * return {@code {A, B}}. | ||
| */ | ||
| public static <V extends Vertex<E>, E extends Edge< V > > RefSet< V > findRootsOfTheGivenNodes( Graph< V, E > graph, Collection< V > nodes ) | ||
| { | ||
| return filterRoots( graph, computePredecessors( graph, nodes ) ); | ||
| } | ||
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| /** | ||
| * @return the set of predecessors of the given {@code nodes}. Please note | ||
| * that returned set also contains all the given {@code nodes}. | ||
| */ | ||
| private static < V extends Vertex<E>, E extends Edge< V > > RefSet< V > computePredecessors( Graph< V, E > graph, Collection< V > nodes ) | ||
| { | ||
| // The following code performs an inverse depth first search starting | ||
| // from the given nodes. The set of visited nodes is returned. | ||
| V ref = graph.vertexRef(); | ||
| V ref2 = graph.vertexRef(); | ||
| try | ||
| { | ||
| final RefSet< V > visited = RefCollections.createRefSet( graph.vertices() ); | ||
| visited.addAll( nodes ); | ||
| final RefStack< V > stack = RefCollections.createRefStack( graph.vertices() ); | ||
| stack.addAll( visited ); | ||
| while ( ! stack.isEmpty() ) { | ||
| V node = stack.pop( ref ); | ||
| for ( E edge : node.incomingEdges() ) { | ||
| V previousNode = edge.getSource( ref2 ); | ||
| boolean firstVisit = visited.add( previousNode ); | ||
| if ( firstVisit ) | ||
| stack.add( previousNode ); | ||
| } | ||
| } | ||
| return visited; | ||
| } | ||
| finally | ||
| { | ||
| graph.releaseRef( ref ); | ||
| graph.releaseRef( ref2 ); | ||
| } | ||
| } | ||
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| /** | ||
| * @return a subset of the given {@code nodes} that contains only those | ||
| * nodes that are roots of the {@code graph}. (A note is considered a root | ||
| * if it has no incoming edges.) | ||
| */ | ||
| private static < V extends Vertex<E>, E extends Edge< V > > RefSet< V > filterRoots( Graph< V, E > graph, Collection< V > nodes ) | ||
| { | ||
| final RefSet< V > roots = RefCollections.createRefSet( graph.vertices() ); | ||
| for ( V node : nodes ) | ||
| if ( node.incomingEdges().isEmpty() ) | ||
| roots.add( node ); | ||
| return roots; | ||
| } | ||
| } | ||
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In the
mastodon-graphlib there is RootFinder:https://github.com/mastodon-sc/mastodon-graph/blob/master/src/main/java/org/mastodon/graph/algorithm/RootFinder.java
Maybe we could merge these two?
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I'm not sure what you would like to suggest. Would you like to have a method
TreeUtils.getRoots(graph)that replacesnew RootFinder(graph).get()?There was a problem hiding this comment.
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Yes exactly. Do you think it is a good fit? One fewer class.... that would be nice.
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I think it would make sense organize the utility classes, but maybe not as a part of this PR.
There is already a ticket mastodon-sc/mastodon-tomancak#13, we should have a look at the RootFinder as part of this.