Examples with ClusterManager edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager used on opensource projects

Example 6 with ClusterManager

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager in project clusterMaker2 by RBVI.

the class CyActivator method start.

public void start(BundleContext bc) {
    // See if we have a graphics console or not
    boolean haveGUI = true;
    CySwingApplication swingAppRef = getService(bc, CySwingApplication.class);
    if (swingAppRef == null) {
        // if haveGUI is false, we don't want to provide any hooks to the treeview
        haveGUI = false;
    }
    CyApplicationManager appRef = getService(bc, CyApplicationManager.class);
    CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    CyGroupManager groupManager = getService(bc, CyGroupManager.class);
    CyGroupFactory groupFactory = getService(bc, CyGroupFactory.class);
    CyTableFactory tableFactory = getService(bc, CyTableFactory.class);
    CyTableManager tableManager = getService(bc, CyTableManager.class);
    // Create our context object.  This will probably keep track of all of the
    // registered clustering algorithms, settings, etc.
    ClusterManagerImpl clusterManager = new ClusterManagerImpl(appRef, serviceRegistrar, groupFactory, groupManager, tableFactory, tableManager);
    registerServiceListener(bc, clusterManager, "addClusterAlgorithm", "removeClusterAlgorithm", ClusterTaskFactory.class);
    registerServiceListener(bc, clusterManager, "addClusterVisualizer", "removeClusterVisualizer", ClusterVizFactory.class);
    registerServiceListener(bc, clusterManager, "addRankingAlgorithm", "removeRankingAlgorithm", RankFactory.class);
    // Register each of our algorithms
    // Attribute clusterers
    registerService(bc, new AttributeClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new AutoSOMETaskFactory(clusterManager, true), ClusterTaskFactory.class, new Properties());
    registerService(bc, new FeatureVectorTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new HierarchicalTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new KMeansTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new KMedoidTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new HopachPAMTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new PAMTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    // FIXME: FFT is seriously broken!
    registerService(bc, new FFTTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new DBSCANTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    /*
		 * Hold off on these until we get improve the performance sufficiently
		 * to allow them to be useful
		 */
    // registerService(bc, new BicFinderTaskFactory(clusterManager),
    // ClusterTaskFactory.class, new Properties());
    // registerService(bc, new BiMineTaskFactory(clusterManager),
    // ClusterTaskFactory.class, new Properties());
    registerService(bc, new ChengChurchTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    // Network clusterers
    registerService(bc, new NetworkClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new APClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new AutoSOMETaskFactory(clusterManager, false), ClusterTaskFactory.class, new Properties());
    registerService(bc, new FuzzifierTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new GLayClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new ConnectedComponentsTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new FCMClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new MCLClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new MCODEClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new SCPSClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new TransClustClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    // Cluster ranking
    registerService(bc, new MAATaskFactory(clusterManager), RankFactory.class, new Properties());
    registerService(bc, new MAMTaskFactory(clusterManager), RankFactory.class, new Properties());
    registerService(bc, new PRWPTaskFactory(clusterManager), RankFactory.class, new Properties());
    registerService(bc, new PRTaskFactory(clusterManager), RankFactory.class, new Properties());
    registerService(bc, new HITSTaskFactory(clusterManager), RankFactory.class, new Properties());
    // Filters
    registerService(bc, new FilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new BestNeighborFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new CuttingEdgeFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new DensityFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new HairCutFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    // registerService(bc, new UITaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    // Visualizations
    registerService(bc, new NewNetworkViewFactory(clusterManager, false), ClusterVizFactory.class, new Properties());
    registerService(bc, new NewNetworkViewFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
    registerService(bc, new HeatMapViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
    registerService(bc, new KnnViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
    registerService(bc, new BiclusterViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
    registerService(bc, new TreeViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
    registerService(bc, new CreateResultsPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
    registerService(bc, new CreateRankingPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
    registerService(bc, new DestroyResultsPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
    registerService(bc, new DestroyRankingPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
    // Dimensionality Reduction
    // registerService(bc, new PCAMenuTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new PCATaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new PCoATaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    registerService(bc, new tSNETaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
    {
        // Link Network Selections
        LinkSelectionTaskFactory linkTaskFactory = new LinkSelectionTaskFactory(clusterManager);
        Properties linkSelectionProps = new Properties();
        linkSelectionProps.setProperty(INSERT_SEPARATOR_BEFORE, "true");
        linkSelectionProps.setProperty(PREFERRED_MENU, "Apps.clusterMaker Visualizations");
        linkSelectionProps.setProperty(TITLE, "Link selection across networks");
        linkSelectionProps.setProperty(COMMAND, "linkSelection");
        linkSelectionProps.setProperty(COMMAND_NAMESPACE, "clusterviz");
        linkSelectionProps.setProperty(ENABLE_FOR, "networkAndView");
        linkSelectionProps.setProperty(IN_MENU_BAR, "true");
        linkSelectionProps.setProperty(MENU_GRAVITY, "100.0");
        registerService(bc, linkTaskFactory, NetworkTaskFactory.class, linkSelectionProps);
    }
    {
        // UnLink Network Selections
        UnlinkSelectionTaskFactory unlinkTaskFactory = new UnlinkSelectionTaskFactory(clusterManager);
        Properties unlinkSelectionProps = new Properties();
        unlinkSelectionProps.setProperty(PREFERRED_MENU, "Apps.clusterMaker Visualizations");
        unlinkSelectionProps.setProperty(TITLE, "Unlink selection across networks");
        unlinkSelectionProps.setProperty(COMMAND, "unlinkSelection");
        unlinkSelectionProps.setProperty(COMMAND_NAMESPACE, "clusterviz");
        unlinkSelectionProps.setProperty(ENABLE_FOR, "networkAndView");
        unlinkSelectionProps.setProperty(IN_MENU_BAR, "true");
        unlinkSelectionProps.setProperty(MENU_GRAVITY, "100.0");
        registerService(bc, unlinkTaskFactory, NetworkTaskFactory.class, unlinkSelectionProps);
    }
    // Commands
    // These task factories provide useful commands that only make sense in the context of REST or
    // the command interface
    {
        TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "hascluster");
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "cluster");
        props.setProperty(COMMAND, CommandTaskFactory.HASCLUSTER);
        props.setProperty(COMMAND_DESCRIPTION, "Test to see if this network has a cluster of the requested type");
        registerService(bc, commandTaskFactory, TaskFactory.class, props);
    }
    {
        TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "getnetworkcluster");
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "cluster");
        props.setProperty(COMMAND, CommandTaskFactory.GETNETWORKCLUSTER);
        props.setProperty(COMMAND_DESCRIPTION, "Get a cluster network cluster result");
        registerService(bc, commandTaskFactory, TaskFactory.class, props);
    }
    {
        TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "getcluster");
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "cluster");
        props.setProperty(COMMAND, CommandTaskFactory.GETCLUSTER);
        props.setProperty(COMMAND_DESCRIPTION, "Get an attribute cluster result");
        registerService(bc, commandTaskFactory, TaskFactory.class, props);
    }
}

Example 7 with ClusterManager

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager in project clusterMaker2 by RBVI.

the class AutoSOMECluster method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    String networkID = ModelUtils.getNetworkName(network);
    // Update settings from our context
    settings = context.getSettings();
    // got back to parent to cluster again
    if (networkID.contains("--AutoSOME")) {
        String[] tokens = networkID.split("--AutoSOME");
        networkID = tokens[0];
        network = ModelUtils.getNetworkWithName(clusterManager, networkID);
    }
    List<String> dataAttributes = context.attributeList.getNodeAttributeList();
    // Cluster the nodes
    runAutoSOME = new RunAutoSOME(clusterManager, dataAttributes, network, settings, monitor);
    runAutoSOME.setIgnoreMissing(context.ignoreMissing);
    runAutoSOME.setSelectedOnly(context.selectedOnly);
    runAutoSOME.setDebug(debug);
    monitor.setStatusMessage("Running AutoSOME" + ((settings.distMatrix) ? " Fuzzy Clustering" : ""));
    nodeCluster = runAutoSOME.run(monitor);
    if (nodeCluster == null) {
        monitor.setStatusMessage("Clustering failed!");
        return;
    }
    if (nodeCluster.size() > 0)
        finishedClustering = true;
    monitor.setStatusMessage("Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, getShortName());
    monitor.setStatusMessage("Creating groups");
    if (settings.distMatrix)
        runAutoSOME.getEdges(context.maxEdges);
    attrList = runAutoSOME.attrList;
    attrOrderList = runAutoSOME.attrOrderList;
    nodeOrderList = runAutoSOME.nodeOrderList;
    ModelUtils.createAndSetLocal(network, network, ClusterManager.CLUSTER_NODE_ATTRIBUTE, attrList, List.class, String.class);
    ModelUtils.createAndSetLocal(network, network, ClusterManager.ARRAY_ORDER_ATTRIBUTE, attrOrderList, List.class, String.class);
    ModelUtils.createAndSetLocal(network, network, ClusterManager.NODE_ORDER_ATTRIBUTE, nodeOrderList, List.class, String.class);
    ModelUtils.createAndSetLocal(network, network, ClusterManager.CLUSTER_TYPE_ATTRIBUTE, getShortName(), String.class, null);
    List<List<CyNode>> nodeClusters;
    if (!settings.distMatrix) {
        nodeClusters = createGroups(network, nodeCluster, GROUP_ATTRIBUTE);
        results = new AbstractClusterResults(network, nodeCluster);
        monitor.setStatusMessage("Done.  AutoSOME results:\n" + results);
    } else {
        nodeClusters = new ArrayList<List<CyNode>>();
        /*
			for (NodeCluster cluster: clusters) {
				List<CyNode>nodeList = new ArrayList();

				for (CyNode node: cluster) {
					nodeList.add(node);
				}
				nodeClusters.add(nodeList);
			}
	   */
        monitor.setStatusMessage("Done.  AutoSOME results:\n" + nodeCluster.size() + " clusters found.");
    }
    if (context.showViz) {
        if (heatmap)
            insertTasksAfterCurrentTask(new KnnView(clusterManager));
        else
            insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, false, !context.selectedOnly));
    }
}

Example 8 with ClusterManager

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager in project clusterMaker2 by RBVI.

the class KMedoidCluster method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (context.selectedOnly && CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true).size() < 3) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least three nodes to cluster");
        return;
    }
    createGroups = context.createGroups;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        // To make debugging easier, sort the attribute list
        Collections.sort(nodeAttributeList);
    }
    // Get our attributes we're going to use for the cluster
    String[] attributeArray;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        attributeArray = new String[nodeAttributeList.size()];
        int i = 0;
        for (String attr : nodeAttributeList) {
            attributeArray[i++] = "node." + attr;
        }
    } else {
        attributeArray = new String[1];
        attributeArray[0] = "edge." + edgeAttribute;
    }
    monitor.setStatusMessage("Initializing");
    // System.out.println("Initializing");
    resetAttributes(network, SHORTNAME);
    // Create a new clusterer
    RunKMedoidCluster algorithm = new RunKMedoidCluster(network, attributeArray, distanceMetric, monitor, context, this);
    // System.out.println("Algorithm defined");
    String resultsString = "K-Medoid results:";
    // Cluster the attributes, if requested
    if (context.clusterAttributes && attributeArray.length > 1) {
        monitor.setStatusMessage("Clustering attributes");
        // System.out.println("Clustering attributes");
        Integer[] rowOrder = algorithm.cluster(clusterManager, context.kcluster.kNumber, context.iterations, true, SHORTNAME, context.kcluster, false);
        attributeList = algorithm.getAttributeList();
        updateAttributes(network, SHORTNAME, rowOrder, attributeArray, attributeList, algorithm.getMatrix());
        attributeSilhouette = algorithm.getSilhouettes();
        attributeOrder = getOrder(rowOrder, algorithm.getMatrix());
    }
    // Cluster the nodes
    monitor.setStatusMessage("Clustering nodes");
    // System.out.println("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(clusterManager, context.kcluster.kNumber, context.iterations, false, SHORTNAME, context.kcluster, createGroups);
    nodeList = algorithm.getAttributeList();
    updateAttributes(network, SHORTNAME, rowOrder, attributeArray, algorithm.getAttributeList(), algorithm.getMatrix());
    nodeSilhouette = algorithm.getSilhouettes();
    nodeOrder = getOrder(rowOrder, algorithm.getMatrix());
    // System.out.println(resultsString);
    if (context.showUI) {
        insertTasksAfterCurrentTask(new KnnView(clusterManager));
    }
}

Example 9 with ClusterManager

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager in project clusterMaker2 by RBVI.

the class HierarchicalCluster method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (context.selectedOnly && nodeAttributeList != null && nodeAttributeList.size() > 1 && CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true).size() < 3) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least three nodes to cluster");
        return;
    }
    // Get our attributes we're going to use for the cluster
    String[] attributeArray;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        Collections.sort(nodeAttributeList);
        attributeArray = new String[nodeAttributeList.size()];
        int i = 0;
        for (String attr : nodeAttributeList) {
            attributeArray[i++] = "node." + attr;
        }
    } else {
        attributeArray = new String[1];
        attributeArray[0] = "edge." + edgeAttribute;
    }
    monitor.showMessage(TaskMonitor.Level.INFO, "Initializing");
    // System.out.println("Initializing");
    resetAttributes(network, SHORTNAME);
    // Create a new clusterer
    DistanceMetric metric = context.metric.getSelectedValue();
    RunHierarchical algorithm = new RunHierarchical(network, attributeArray, metric, clusterMethod, monitor, context);
    // Cluster the attributes, if requested
    if (context.clusterAttributes && (attributeArray.length > 1 || context.isAssymetric())) {
        monitor.setStatusMessage("Clustering attributes");
        // System.out.println("Clustering attributes");
        Integer[] rowOrder = algorithm.cluster(true);
        attributeTree = algorithm.getAttributeList();
        CyMatrix matrix = algorithm.getMatrix();
        updateAttributes(network, SHORTNAME, rowOrder, attributeArray, attributeTree, matrix);
        attributeOrder = new ArrayList<String>();
        for (int i = 0; i < rowOrder.length; i++) {
            attributeOrder.add(matrix.getRowLabel(rowOrder[i]));
        }
    }
    monitor.setStatusMessage("Clustering nodes");
    // Cluster the nodes
    // System.out.println("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(false);
    nodeTree = algorithm.getAttributeList();
    CyMatrix matrix = algorithm.getMatrix();
    updateAttributes(network, SHORTNAME, rowOrder, attributeArray, nodeTree, matrix);
    nodeOrder = new ArrayList<CyNode>();
    for (int i = 0; i < rowOrder.length; i++) {
        nodeOrder.add(matrix.getRowNode(rowOrder[i]));
    }
    // TODO: Deal with params!
    List<String> params = context.getParams(algorithm.getMatrix());
    updateParams(network, params);
    if (context.showUI) {
        insertTasksAfterCurrentTask(new TreeView(clusterManager));
    }
    monitor.setStatusMessage("Done");
}

Example 10 with ClusterManager

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager in project clusterMaker2 by RBVI.

the class FFT method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (context.selectedOnly && CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true).size() < 3) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least three nodes to cluster");
        return;
    }
    createGroups = context.createGroups;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        // To make debugging easier, sort the attribute list
        Collections.sort(nodeAttributeList);
    }
    // Get our attributes we're going to use for the cluster
    String[] attributeArray;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        attributeArray = new String[nodeAttributeList.size()];
        int i = 0;
        for (String attr : nodeAttributeList) {
            attributeArray[i++] = "node." + attr;
        }
    } else {
        attributeArray = new String[1];
        attributeArray[0] = "edge." + edgeAttribute;
    }
    monitor.setStatusMessage("Initializing");
    resetAttributes(network, SHORTNAME);
    // Create a new clusterer
    RunFFT algorithm = new RunFFT(network, attributeArray, distanceMetric, monitor, context, this);
    // System.out.println("Algorithm defined");
    String resultsString = "FFT results:";
    // Cluster the attributes, if requested
    if (context.clusterAttributes && attributeArray.length > 1) {
        monitor.setStatusMessage("Clustering attributes");
        Integer[] rowOrder = algorithm.cluster(clusterManager, context.kcluster.kNumber, 1, true, "fft", context.kcluster, false);
        updateAttributes(network, SHORTNAME, rowOrder, attributeArray, algorithm.getAttributeList(), algorithm.getMatrix());
    }
    // Cluster the nodes
    monitor.setStatusMessage("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(clusterManager, context.kcluster.kNumber, 1, false, "fft", context.kcluster, createGroups);
    updateAttributes(network, SHORTNAME, rowOrder, attributeArray, algorithm.getAttributeList(), algorithm.getMatrix());
    // System.out.println(resultsString);
    if (context.showUI) {
        insertTasksAfterCurrentTask(new KnnView(clusterManager));
    }
}