Examples with Clusters edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.Clusters used on opensource projects

Example 6 with Clusters

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.Clusters in project clusterMaker2 by RBVI.

the class RunAP method run.

public List<NodeCluster> run(CyNetwork network, TaskMonitor monitor) {
    double numClusters;
    monitor.setProgress(0.01);
    for (int i = 0; i < number_iterations; i++) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Exchanging messages: iteration " + i);
        iterate_message_exchange(monitor, i);
        if (canceled) {
            monitor.showMessage(TaskMonitor.Level.INFO, "canceled");
            return null;
        }
        monitor.setProgress((double) i / (double) number_iterations);
    }
    if (debug) {
        for (int i = 0; i < s_matrix.rows(); i++) {
            monitor.showMessage(TaskMonitor.Level.INFO, "Node " + nodes.get(i) + " has exemplar " + get_exemplar(i));
        }
    }
    monitor.showMessage(TaskMonitor.Level.INFO, "Assigning nodes to clusters");
    Map<Integer, NodeCluster> clusterMap = getClusterMap();
    // Update node attributes in network to include clusters. Create cygroups from clustered nodes
    monitor.showMessage(TaskMonitor.Level.INFO, "Created " + clusterMap.size() + " clusters");
    if (clusterCount == 0) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Created 0 clusters!!!!");
        return null;
    }
    int clusterNumber = 1;
    Map<NodeCluster, NodeCluster> cMap = new HashMap<NodeCluster, NodeCluster>();
    for (NodeCluster cluster : NodeCluster.sortMap(clusterMap)) {
        if (cMap.containsKey(cluster))
            continue;
        if (debug) {
            monitor.showMessage(TaskMonitor.Level.INFO, "Cluster " + clusterNumber);
            String s = "";
            for (CyNode node : cluster) {
                s += node.toString() + "\t";
            }
            monitor.showMessage(TaskMonitor.Level.INFO, s);
        }
        cMap.put(cluster, cluster);
        cluster.setClusterNumber(clusterNumber);
        clusterNumber++;
    }
    Set<NodeCluster> clusters = cMap.keySet();
    return new ArrayList<NodeCluster>(clusters);
}

Example 7 with Clusters

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.Clusters in project clusterMaker2 by RBVI.

the class RunAP method getClusterMap.

private Map<Integer, NodeCluster> getClusterMap() {
    HashMap<Integer, NodeCluster> clusterMap = new HashMap<Integer, NodeCluster>();
    for (int i = 0; i < s_matrix.rows(); i++) {
        int exemplar = get_exemplar(i);
        if (clusterMap.containsKey(exemplar)) {
            if (i == exemplar)
                continue;
            // Already seen exemplar
            NodeCluster exemplarCluster = clusterMap.get(exemplar);
            if (clusterMap.containsKey(i)) {
                // We've already seen i also -- join them
                NodeCluster iCluster = clusterMap.get(i);
                if (iCluster != exemplarCluster) {
                    exemplarCluster.addAll(iCluster);
                    // System.out.println("Combining "+i+"["+iCluster+"] and "+exemplar+" ["+exemplarCluster+"]");
                    clusterCount--;
                    clusterMap.remove(i);
                }
            } else {
                exemplarCluster.add(nodes, i);
            // System.out.println("Adding "+i+" to ["+exemplarCluster+"]");
            }
            // Update Clusters
            updateClusters(exemplarCluster, clusterMap);
        } else {
            NodeCluster iCluster;
            // First time we've seen this "exemplar" -- have we already seen "i"?
            if (clusterMap.containsKey(i)) {
                if (i == exemplar)
                    continue;
                // Yes, just add exemplar to i's cluster
                iCluster = clusterMap.get(i);
                iCluster.add(nodes, exemplar);
            // System.out.println("Adding "+exemplar+" to ["+iCluster+"]");
            } else {
                // No create new cluster from scratch
                iCluster = new NodeCluster();
                iCluster.add(nodes, i);
                if (exemplar != i)
                    iCluster.add(nodes, exemplar);
                // System.out.println("New cluster ["+iCluster+"]");
                clusterCount++;
            }
            updateClusters(iCluster, clusterMap);
        }
    }
    return clusterMap;
}

Example 8 with Clusters

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.Clusters in project clusterMaker2 by RBVI.

the class AbstractFuzzyNetworkClusterer method createFuzzyTable.

/**
 * Method creates a table to store the information about Fuzzy Clusters and adds it to the network
 *
 * @param clusters List of FuzzyNodeCLusters, which have to be put in the table
 */
protected void createFuzzyTable(List<FuzzyNodeCluster> clusters) {
    CyTable networkTable = network.getTable(CyNetwork.class, CyNetwork.LOCAL_ATTRS);
    CyTable FuzzyClusterTable = null;
    if (!CyTableUtil.getColumnNames(networkTable).contains(clusterAttributeName + "_Table.SUID")) {
        network.getDefaultNetworkTable().createColumn(clusterAttributeName + "_Table.SUID", Long.class, false);
        FuzzyClusterTable = tableFactory.createTable(clusterAttributeName + "_Table", "Fuzzy_Node.SUID", Long.class, true, true);
    } else {
        long FuzzyClusterTableSUID = network.getRow(network).get(clusterAttributeName + "_Table.SUID", Long.class);
        FuzzyClusterTable = tableManager.getTable(FuzzyClusterTableSUID);
    }
    for (FuzzyNodeCluster cluster : clusters) {
        if (FuzzyClusterTable.getColumn("Cluster_" + cluster.getClusterNumber()) == null) {
            FuzzyClusterTable.createColumn("Cluster_" + cluster.getClusterNumber(), Double.class, false);
        }
    }
    CyRow TableRow;
    for (CyNode node : network.getNodeList()) {
        TableRow = FuzzyClusterTable.getRow(node.getSUID());
        for (FuzzyNodeCluster cluster : clusters) {
            TableRow.set("Cluster_" + cluster.getClusterNumber(), cluster.getMembership(node));
        }
    }
    network.getRow(network).set(clusterAttributeName + "_Table.SUID", FuzzyClusterTable.getSUID());
    tableManager.addTable(FuzzyClusterTable);
}

Example 9 with Clusters

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.Clusters in project clusterMaker2 by RBVI.

the class AbstractNetworkClusterer method createFuzzyGroups.

protected List<List<CyNode>> createFuzzyGroups(CyNetwork network, List<FuzzyNodeCluster> clusters, String group_attr) {
    // List of node lists
    List<List<CyNode>> clusterList = new ArrayList<List<CyNode>>();
    // keep track of the groups we create
    List<Long> groupList = new ArrayList<Long>();
    for (FuzzyNodeCluster cluster : clusters) {
        int clusterNumber = cluster.getClusterNumber();
        String groupName = clusterAttributeName + "_" + clusterNumber;
        List<CyNode> nodeList = new ArrayList<CyNode>();
        for (CyNode node : cluster) {
            nodeList.add(node);
            // network.getRow(node).set(clusterAttributeName, clusterNumber);
            if (FuzzyNodeCluster.hasScore()) {
                ModelUtils.createAndSetLocal(network, node, clusterAttributeName + "_" + clusterNumber + "_Membership", cluster.getMembership(node), Double.class, null);
            // network.getRow(node).set(clusterAttributeName+"_Score", cluster.getClusterScore());
            }
        }
        if (createGroups) {
            CyGroup group = clusterManager.createGroup(network, clusterAttributeName + "_" + clusterNumber, nodeList, null, true);
            if (group != null)
                groupList.add(group.getGroupNode().getSUID());
        }
        clusterList.add(nodeList);
    }
    // Adding a column per node by the clusterAttributeName, which will store a list of all the clusters to which the node belongs
    List<CyNode> nodeList = network.getNodeList();
    for (int i = 0; i < nodeList.size(); i++) {
        CyNode node = nodeList.get(i);
        List<Integer> listOfClusters = new ArrayList<Integer>();
        for (FuzzyNodeCluster cluster : clusters) {
            if (cluster.getMembership(node) != null) {
                listOfClusters.add(cluster.getClusterNumber());
            }
        }
        ModelUtils.createAndSetLocal(network, node, clusterAttributeName, listOfClusters, List.class, Integer.class);
    }
    ModelUtils.createAndSetLocal(network, network, group_attr, groupList, List.class, Long.class);
    ModelUtils.createAndSetLocal(network, network, ClusterManager.CLUSTER_TYPE_ATTRIBUTE, getShortName(), String.class, null);
    ModelUtils.createAndSetLocal(network, network, ClusterManager.CLUSTER_ATTRIBUTE, clusterAttributeName, String.class, null);
    if (params != null)
        ModelUtils.createAndSetLocal(network, network, ClusterManager.CLUSTER_PARAMS_ATTRIBUTE, params, List.class, String.class);
    return clusterList;
}

Example 10 with Clusters

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.Clusters in project clusterMaker2 by RBVI.

the class APCluster method run.

public void run(TaskMonitor monitor) {
    monitor.setTitle("Performing AP cluster");
    this.monitor = monitor;
    if (network == null)
        network = clusterManager.getNetwork();
    // Make sure to update the context
    context.setNetwork(network);
    NodeCluster.init();
    CyMatrix matrix = context.edgeAttributeHandler.getMatrix();
    if (matrix == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
        return;
    }
    // Update our tunable results
    clusterAttributeName = context.getClusterAttribute();
    createGroups = context.advancedAttributes.createGroups;
    if (canceled)
        return;
    // Cluster the nodes
    runAP = new RunAP(matrix, context.lambda, context.preference, context.rNumber, monitor, debug);
    if (canceled)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
    List<NodeCluster> clusters = runAP.run(network, monitor);
    // Canceled?
    if (clusters == null)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, GROUP_ATTRIBUTE);
    monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
    params = new ArrayList<String>();
    context.edgeAttributeHandler.setParams(params);
    setParams(params);
    List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
    results = new AbstractClusterResults(network, clusters);
    monitor.showMessage(TaskMonitor.Level.INFO, "Done.  AP results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !context.edgeAttributeHandler.selectedOnly));
    }
}