Examples with ClusterFile edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.io.ClusterFile used on opensource projects

Example 1 with ClusterFile

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.io.ClusterFile in project clusterMaker2 by RBVI.

the class ClusteringManager method runClusteringForOneConnectedComponent.

/**
 * Runs clustering for one {@link ConnectedComponent} and sets the total score to
 * the parameters if in the general training mode.
 * @param cc The connected component object.
 * @param clusterFile The clusters file (null if in general training mode)
 * @param semaphore The Semaphore to give to the clustering task to keep track of it.
 * @param time
 * @throws InvalidInputFileException
 */
public void runClusteringForOneConnectedComponent(ConnectedComponent cc, ClusterFile clusterFile, Semaphore semaphore, Semaphore maxThreadSemaphore, long time) throws InvalidInputFileException {
    /* check whether layouterParameters has been initialised */
    if (this.layouterParameters == null) {
        if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE || TaskConfig.mode == TaskConfig.GENERAL_TRAINING_MODE)
            log.warning("Incorrect use of the ClusteringManager, the layouter parameters list" + "hadn't been initialised. Called method to initialise this and the connected components from " + "the config");
        this.initParametersAndCCs();
    }
    // if(TaskConfig.mode == TaskConfig.CLUSTERING_MODE){
    if (TaskConfig.doLayoutParameterTraining && !TaskConfig.greedy) {
        for (int i = 0; i < this.layouterParameters.length; i++) {
            /* start parameter training for the cc */
            IParameterTraining paramTrain = TaskConfig.parameterTrainingEnum.createParameterTrainer();
            paramTrain.initialise(TaskConfig.layouterEnumTypes[i], TaskConfig.noOfParameterConfigurationsPerGeneration, TaskConfig.noOfGenerations);
            paramTrain.setMaxThreadSemaphoreAndThreadsList(maxThreadSemaphore, this.allThreads);
            IParameters bestparam = paramTrain.run(cc);
            log.fine("PARAMETER TRAINING RESULT\n: " + cc.getCcPath() + "\n" + bestparam.toString());
            this.layouterParameters[i] = bestparam;
        }
    }
    // }
    /* run clustering with the previously determined parameters */
    ClusteringTask clusterTask = new ClusteringTask(cc, this.layouterParameters, TaskConfig.layouterEnumTypes, clusterFile);
    clusterTask.setTime(time);
    // if(!TaskConfig.doLayoutParameterTraining&&TaskConfig.useThreads){
    // clusterTask.setSemaphore(semaphore);
    // Thread t = new Thread(clusterTask);
    // clusterTask.setMaxThreadSemaphore(maxThreadSemaphore, allThreads, t);
    // t.start();
    // }else{
    clusterTask.run();
// }
}

Example 2 with ClusterFile

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.io.ClusterFile in project clusterMaker2 by RBVI.

the class ClusteringManager method runClustering.

/**
 * Runs the clustering with the given configurations in the config class: {@link TaskConfig}.
 * Clusters each {@link ConnectedComponent} separately and waits until all are done.
 * Differes between the modes clustering and general training. Creates a Config file if
 * the training mode is used.
 * @throws InvalidInputFileException If the file/directory given produces an error.
 * @throws InvalidTypeException An incorrect method implementation was given, or some
 * other error occured with this.
 */
public void runClustering() throws InvalidInputFileException, InvalidTypeException {
    /* initialise ClusterFile if in clustering mode */
    ClusterFile clusterFile = null;
    if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE) {
        log.fine("Running clustering in clustering mode!");
        clusterFile = new ClusterFile();
        clusterFile.instantiateFile(TaskConfig.clustersPath);
        clusterFile.printPreProcessingClusters(TaskConfig.transitiveConnectedComponents);
        /* check whether connectedComponents has been initialised */
        if (this.connectedComponents == null) {
            if (TaskConfig.transitiveConnectedComponents == null) {
                log.warning("Incorrect use of the ClusteringManager, the connected components list" + "hadn't been initialised. Called method to initialise this and the parameters from " + "the config. Or only a TCC file was given and no connected components.");
                this.initParametersAndCCs();
            } else {
                log.info("No cost matrices were given, just a transitive connected components file, which" + "is converted to a clusters file. NO CLUSTERING IS PERFORMED!");
                InfoFile.appendToProjectDetails("No cost matrices were given, just a transitive connected components file, which" + "is converted to a clusters file. NO CLUSTERING IS PERFORMED!");
            }
        }
    }
    if (this.connectedComponents != null) {
        /* go through cc list and start training for each and control thread use */
        ArrayList<Semaphore> allSemaphores = new ArrayList<Semaphore>();
        Semaphore maxThreadSemaphore = new Semaphore(TaskConfig.maxNoThreads, true);
        for (int i = 0; i < this.connectedComponents.size(); i++) {
            Semaphore semaphore = new Semaphore(1);
            allSemaphores.add(semaphore);
            long time = System.currentTimeMillis();
            CostMatrixReader cmReader = new CostMatrixReader(this.connectedComponents.get(i));
            ConnectedComponent cc = cmReader.getConnectedComponent();
            runClusteringForOneConnectedComponent(cc, clusterFile, semaphore, maxThreadSemaphore, time);
        }
        /* wait for all clustering tasks to finish */
        for (Semaphore s : allSemaphores) {
            try {
                s.acquire();
            } catch (InterruptedException e) {
                log.severe(e.getMessage());
                e.printStackTrace();
            }
        }
    }
    if (clusterFile != null)
        clusterFile.closeFile();
    /* END OF CLUSTERING */
    log.info("Clustering scores sum: " + totalScoreSum);
    if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE) {
        InfoFile.appendLnProjectResults("Total sum of clustering scores for given input: " + TaskUtility.round(totalScoreSum, 2));
    }
    /* set score to IParameters objects for general training mode */
    if (TaskConfig.mode == TaskConfig.GENERAL_TRAINING_MODE) {
        log.fine("Setting parameters score for training mode!");
        for (IParameters parameter : this.layouterParameters) {
            parameter.setScore(totalScoreSum);
        }
    }
    totalScoreSum = 0;
}