Examples with ILayoutInitialiser edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.layout.ILayoutInitialiser used on opensource projects

Example 1 with ILayoutInitialiser

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.layout.ILayoutInitialiser in project clusterMaker2 by RBVI.

the class ClusterPostProcessingTask method runClustering.

private void runClustering(ConnectedComponent cc) {
    ConnectedComponent ccCopy = cc.copy(true);
    // ccCopy.setClusteringScore(Double.MAX_VALUE);
    new GreedyClusterer(ccCopy);
    if (!TaskConfig.fixedParameter || cc.getNodeNumber() >= TaskConfig.fixedParameterMax)
        TaskConfig.fpStopped = true;
    if (TaskConfig.fixedParameter && cc.getNodeNumber() < TaskConfig.fixedParameterMax) {
        new FixedParameterClusterer(cc, ccCopy.getClusteringScore());
    }
    if (TaskConfig.greedy && TaskConfig.fpStopped) {
        cc.setClusteringScore(Double.MAX_VALUE);
        TaskConfig.fpStopped = false;
    } else if (TaskConfig.fpStopped) {
        // cc.initialiseClusterInfo(ccCopy.getNumberOfClusters());
        // cc.setClusters(ccCopy.getClusters());
        /* ====== LAYOUTING PHASE ====== */
        TaskConfig.fpStopped = false;
        /* iterate over layouters */
        ILayouter previousLayouter = null;
        for (int i = 0; i < this.layouterEnumTypes.length; i++) {
            IParameters param = this.allparameters[i];
            /* create correct layouter */
            ILayouter layouter = this.layouterEnumTypes[i].createLayouter();
            if (previousLayouter == null) {
                /* initialise cc positions if in clustering mode */
                if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE || TaskConfig.mode == TaskConfig.COMPARISON_MODE || TaskConfig.mode == TaskConfig.HIERARICHAL_MODE) {
                    ILayoutInitialiser li = this.layouterEnumTypes[i].createLayoutInitialiser();
                    li.initLayoutInitialiser(cc);
                    /* initialise and run layouter */
                    layouter.initLayouter(cc, li, param);
                    layouter.run();
                    previousLayouter = layouter;
                } else if (TaskConfig.mode == TaskConfig.GENERAL_TRAINING_MODE) {
                    // else positions already set for training mode
                    layouter.initLayouter(cc, param);
                    layouter.run();
                    previousLayouter = layouter;
                }
            } else {
                /*
					 * initialise and run layouter with previous calculated
					 * positions
					 */
                layouter.initLayouter(cc, previousLayouter, param);
                layouter.run();
            }
        }
        /* ====== GEOMETRIC CLUSTERING */
        IGeometricClusterer geoClust = TaskConfig.geometricClusteringEnum.createGeometricClusterer();
        geoClust.initGeometricClusterer(cc);
        geoClust.run();
    }
    /* ====== POST-PROCESSING ====== */
    if (TaskConfig.doPostProcessing && cc.getClusteringScore() != Double.MAX_VALUE) {
        IPostProcessing pp = PostProcessingFactory.EnumPostProcessingClass.PP_REARRANGE_AND_MERGE_BEST.createPostProcessor();
        pp.initPostProcessing(cc);
        /* run post processing */
        pp.run();
    }
    if (TaskConfig.doPostProcessing && ccCopy.getClusteringScore() != Double.MAX_VALUE) {
        IPostProcessing pp = PostProcessingFactory.EnumPostProcessingClass.PP_REARRANGE_AND_MERGE_BEST.createPostProcessor();
        pp.initPostProcessing(ccCopy);
        /* run post processing */
        pp.run();
    }
    // if(ccCopy.getClusteringScore()<cc.getClusteringScore()&&ccCopy.getClusteringScore()<=ccCopy2.getClusteringScore()){
    if (ccCopy.getClusteringScore() < cc.getClusteringScore()) {
        cc.initialiseClusterInfo(ccCopy.getNumberOfClusters());
        cc.setClusters(ccCopy.getClusters());
        cc.calculateClusterDistribution();
        cc.setClusteringScore(ccCopy.getClusteringScore());
    }
// else if(ccCopy2.getClusteringScore()<cc.getClusteringScore()&&ccCopy.getClusteringScore()>ccCopy2.getClusteringScore()){
// cc.initialiseClusterInfo(ccCopy2.getNumberOfClusters());
// cc.setClusters(ccCopy2.getClusters());
// cc.calculateClusterDistribution();
// cc.setClusteringScore(ccCopy2.getClusteringScore());
// }else{
// }
}

Example 2 with ILayoutInitialiser

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.layout.ILayoutInitialiser in project clusterMaker2 by RBVI.

the class FORCEnDLayouter method initLayouter.

/**
 * This Constructor is for the parameter training. Here the positions should
 * have already been initialised. If this is not so, then the positions are
 * initialised with the correct {@link ILayoutInitialiser} implementation.
 *
 * @param cc
 *            The connected Component.
 * @param parameters
 *            The parameters for FORCEnD.
 */
public void initLayouter(ConnectedComponent cc, IParameters parameters) {
    this.dim = TaskConfig.dimension;
    this.cc = cc;
    this.parameters = (FORCEnDParameters) parameters;
    if (cc.getCCPositions() == null) {
        log.warning("Positions have not been initialised, perhaps" + "wrong use of this constructor!");
        ILayoutInitialiser li;
        li = LayoutFactory.EnumLayouterClass.FORCEND.createLayoutInitialiser();
        li.initLayoutInitialiser(cc);
        li.run();
    }
}

Example 3 with ILayoutInitialiser

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.layout.ILayoutInitialiser in project clusterMaker2 by RBVI.

the class ParameterTraining_SE method run.

public IParameters run(ConnectedComponent cc) {
    boolean terminateTraining = false;
    /*
		 * initialise positions of the cc - the same initial positions are used
		 * for all training rounds
		 */
    ILayoutInitialiser li = layouterEnum.createLayoutInitialiser();
    li.initLayoutInitialiser(cc);
    li.run();
    /* run initial generation */
    IParameters[] initialGeneration = createInitialParameterGeneration();
    runOneGeneration(initialGeneration, cc, 0);
    terminateTraining = terminateTraining(initialGeneration);
    /* add the best 10 random configs to the bestConfigs collection Vector */
    for (int i = 0; i < 10; i++) {
        // TODO
        this.bestConfigs.add(initialGeneration[i]);
    }
    // System.out.println("terminate training? "+terminateTraining);
    /* run all following generations */
    IParameters[] generation;
    for (int i = 1; i <= this.noOfGenerations; i++) {
        if (terminateTraining) {
            break;
        }
        generation = createParameterGeneration();
        runOneGeneration(generation, cc, i);
        terminateTraining = terminateTraining(generation);
        for (int j = 0; j < this.generationSize / 2; j++) {
            this.bestConfigs.add(generation[j]);
        }
    }
    /* convert best configurations vector to array */
    IParameters[] bestConfigsArray = new IParameters[bestConfigs.size()];
    for (int i = 0; i < bestConfigs.size(); i++) {
        bestConfigsArray[i] = bestConfigs.get(i);
    }
    /*
		 * sort the IParameters array according to their score and return the
		 * best parameter set.
		 */
    Arrays.sort(bestConfigsArray, this.paramComparator);
    this.bestPreviousIParameters = bestConfigsArray[0];
    bestConfigsArray[0].setScore(0.0);
    return bestConfigsArray[0];
}

Example 4 with ILayoutInitialiser

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.layout.ILayoutInitialiser in project clusterMaker2 by RBVI.

the class ClusteringTask method runClustering.

private void runClustering(ConnectedComponent cc) {
    ConnectedComponent ccCopy = cc.copy(true);
    new GreedyClusterer(ccCopy);
    if (!TaskConfig.fixedParameter || cc.getNodeNumber() >= TaskConfig.fixedParameterMax)
        TaskConfig.fpStopped = true;
    if (TaskConfig.fixedParameter && cc.getNodeNumber() < TaskConfig.fixedParameterMax) {
        new FixedParameterClusterer(cc, ccCopy.getClusteringScore());
    }
    if (TaskConfig.greedy && TaskConfig.fpStopped) {
        cc.setClusteringScore(Double.MAX_VALUE);
        TaskConfig.fpStopped = false;
    } else if (TaskConfig.fpStopped) {
        // cc.initialiseClusterInfo(ccCopy.getNumberOfClusters());
        // cc.setClusters(ccCopy.getClusters());
        /* ====== LAYOUTING PHASE ====== */
        TaskConfig.fpStopped = false;
        /* iterate over layouters */
        ILayouter previousLayouter = null;
        for (int i = 0; i < this.layouterEnumTypes.length; i++) {
            IParameters param = parameters[i];
            /* create correct layouter */
            ILayouter layouter = this.layouterEnumTypes[i].createLayouter();
            if (previousLayouter == null) {
                /* initialise cc positions if in clustering mode */
                if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE || TaskConfig.mode == TaskConfig.COMPARISON_MODE || TaskConfig.mode == TaskConfig.HIERARICHAL_MODE) {
                    ILayoutInitialiser li = this.layouterEnumTypes[i].createLayoutInitialiser();
                    li.initLayoutInitialiser(cc);
                    /* initialise and run layouter */
                    layouter.initLayouter(cc, li, param);
                    layouter.run();
                    previousLayouter = layouter;
                } else if (TaskConfig.mode == TaskConfig.GENERAL_TRAINING_MODE) {
                    ILayoutInitialiser li = this.layouterEnumTypes[i].createLayoutInitialiser();
                    li.initLayoutInitialiser(cc);
                    /* initialise and run layouter */
                    layouter.initLayouter(cc, li, param);
                    layouter.run();
                    previousLayouter = layouter;
                // // else positions already set for training mode
                // layouter.initLayouter(cc, param);
                // layouter.run();
                // previousLayouter = layouter;
                } else {
                }
            } else {
                /*
					 * initialise and run layouter with previous calculated
					 * positions
					 */
                layouter.initLayouter(cc, previousLayouter, param);
                layouter.run();
            }
        }
        /* ====== GEOMETRIC CLUSTERING */
        IGeometricClusterer geoClust = TaskConfig.geometricClusteringEnum.createGeometricClusterer();
        geoClust.initGeometricClusterer(cc);
        geoClust.run();
    }
    /* ====== POST-PROCESSING ====== */
    if (TaskConfig.doPostProcessing && cc.getClusteringScore() != Double.MAX_VALUE) {
        PostProcessingFactory.EnumPostProcessingClass ppEnum = TaskConfig.postProcessingEnum;
        IPostProcessing pp = ppEnum.createPostProcessor();
        pp.initPostProcessing(cc);
        // additional parameters.
        if (ppEnum.equals(PostProcessingFactory.EnumPostProcessingClass.PP_DIVIDE_AND_RECLUSTER)) {
            ((PP_DivideAndRecluster) pp).setLayoutingInfo(this.parameters, this.layouterEnumTypes);
        } else if (ppEnum.equals(PostProcessingFactory.EnumPostProcessingClass.PP_DIVIDE_AND_RECLUSTER_RECURSIVELY)) {
            ((PP_DivideAndReclusterRecursively) pp).setLayoutingInfo(this.parameters, this.layouterEnumTypes);
        }
        /* run post processing */
        pp.run();
    // ppEnum = PostProcessingFactory.EnumPostProcessingClass.PP_REARRANGE_AND_MERGE_BEST;
    // pp = ppEnum.createPostProcessor();
    // pp.initPostProcessing(cc);
    // pp.run();
    }
    if (TaskConfig.doPostProcessing && ccCopy.getClusteringScore() != Double.MAX_VALUE) {
        PostProcessingFactory.EnumPostProcessingClass ppEnum = TaskConfig.postProcessingEnum;
        IPostProcessing pp = ppEnum.createPostProcessor();
        pp.initPostProcessing(ccCopy);
        // additional parameters.
        if (ppEnum.equals(PostProcessingFactory.EnumPostProcessingClass.PP_DIVIDE_AND_RECLUSTER)) {
            ((PP_DivideAndRecluster) pp).setLayoutingInfo(this.parameters, this.layouterEnumTypes);
        } else if (ppEnum.equals(PostProcessingFactory.EnumPostProcessingClass.PP_DIVIDE_AND_RECLUSTER_RECURSIVELY)) {
            ((PP_DivideAndReclusterRecursively) pp).setLayoutingInfo(this.parameters, this.layouterEnumTypes);
        }
        /* run post processing */
        pp.run();
    // ppEnum = PostProcessingFactory.EnumPostProcessingClass.PP_REARRANGE_AND_MERGE_BEST;
    // pp = ppEnum.createPostProcessor();
    // pp.initPostProcessing(cc);
    // pp.run();
    }
    // if(ccCopy.getClusteringScore()<cc.getClusteringScore()&&ccCopy.getClusteringScore()<=ccCopy2.getClusteringScore()){
    if (ccCopy.getClusteringScore() < cc.getClusteringScore()) {
        cc.initialiseClusterInfo(ccCopy.getNumberOfClusters());
        cc.setClusters(ccCopy.getClusters());
        cc.calculateClusterDistribution();
        cc.setClusteringScore(ccCopy.getClusteringScore());
    } else // else if(ccCopy2.getClusteringScore()<cc.getClusteringScore()&&ccCopy.getClusteringScore()>ccCopy2.getClusteringScore()){
    // cc.initialiseClusterInfo(ccCopy2.getNumberOfClusters());
    // cc.setClusters(ccCopy2.getClusters());
    // cc.calculateClusterDistribution();
    // cc.setClusteringScore(ccCopy2.getClusteringScore());
    // }
    {
    }
}

Example 5 with ILayoutInitialiser

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.layout.ILayoutInitialiser in project clusterMaker2 by RBVI.

the class GeneralParameterTraining method runGeneralTraining.

/**
 * Starts the general parameter training using a simple evolutionary method
 * for the whole input directory (or just one file if
 * this was given). Saves the best found parameters of each layout algorithm to the
 * respective config classes. But does not create a config file.
 *
 * @return The best set of IParameters as an Array.
 * @throws InvalidInputFileException If the input file/directory is somehow
 * 					incorrect or cannot be read.
 * @throws InvalidTypeException If an method type does not exist or hasn't
 * 					been included properly.
 */
public IParameters[] runGeneralTraining() throws InvalidInputFileException, InvalidTypeException {
    /* initialise connected components and parameters */
    this.clusteringManager.initParametersAndCCs();
    ArrayList<File> connectedComponents = clusteringManager.getConnectedComponents();
    /*
		 * initialise positions of the cc with respect to the FIRST layouter - the same 
		 * initial positions are used for all training rounds
		 */
    for (File cc : connectedComponents) {
        ILayoutInitialiser li = TaskConfig.layouterEnumTypes[0].createLayoutInitialiser();
        li.initLayoutInitialiser(new CostMatrixReader(cc).getConnectedComponent());
        li.run();
    }
    boolean terminateTraining = false;
    /* run initial generation */
    IParameters[][] initialGeneration = createInitialParameterGeneration();
    runOneGeneration(initialGeneration, connectedComponents, 0);
    terminateTraining = terminateTraining(initialGeneration);
    /* add the best 10 random configs to the bestConfigs collection Vector */
    for (int i = 0; i < initialGeneration.length; i++) {
        this.bestConfigs.add(initialGeneration[i]);
    }
    /* run all following generations */
    IParameters[][] generation;
    for (int i = 1; i <= this.noOfGenerations; i++) {
        if (terminateTraining) {
            break;
        }
        generation = createParameterGeneration();
        runOneGeneration(generation, connectedComponents, i);
        terminateTraining = terminateTraining(generation);
        for (int j = 0; j < this.generationSize / 2; j++) {
            this.bestConfigs.add(initialGeneration[j]);
        }
    }
    /* convert best configurations vector to array */
    IParameters[][] bestConfigsArray = new IParameters[bestConfigs.size()][TaskConfig.layouterEnumTypes.length];
    for (int i = 0; i < bestConfigs.size(); i++) {
        bestConfigsArray[i] = bestConfigs.get(i);
    }
    /*
		 * sort the IParameters array according to their score and return the
		 * best parameter set.
		 */
    Arrays.sort(bestConfigsArray, this.paramComparator);
    this.bestPreviousIParameters = bestConfigsArray[0];
    for (int i = 0; i < bestConfigsArray[0].length; i++) {
        bestConfigsArray[0][i].saveParametersToConfig();
    }
    for (int i = 0; i < 30; i++) {
        FORCEnDParameters ip = (FORCEnDParameters) bestConfigsArray[i][0];
        ip.printParamters();
    }
    return bestConfigsArray[0];
}