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

Example 6 with InvalidInputFileException

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.InvalidInputFileException 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;
}

Example 7 with InvalidInputFileException

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

the class ClusteringManagerTask method run.

public void run() {
    try {
        TaskConfig.monitor.setStatusMessage("-----------------------------------");
        TaskConfig.monitor.setStatusMessage("Running ... " + TaskConfig.NAME + " v" + TaskConfig.VERSION);
        Date date = new Date(System.currentTimeMillis());
        TaskConfig.monitor.setStatusMessage(date.toString());
        TaskConfig.monitor.setStatusMessage("-----------------------------------");
        if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE) {
            long time = System.currentTimeMillis();
            this.clusterManager = new ClusteringManager(TaskConfig.cmPath);
            try {
                this.clusterManager.initParametersAndCCs();
                this.clusterManager.runClustering();
                // System.out.println(this.clusterManager.getConnectedComponents().size());
                time = System.currentTimeMillis() - time;
                TaskConfig.monitor.setStatusMessage("Time taken for complete clustering process: " + TaskUtility.convertTime(time));
            } catch (InvalidInputFileException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
                // e.printStackTrace();
                System.exit(-1);
            } catch (InvalidTypeException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
                // e.printStackTrace();
                System.exit(-1);
            }
        } else /* start general training */
        if (TaskConfig.mode == TaskConfig.GENERAL_TRAINING_MODE) {
            try {
                long time = System.currentTimeMillis();
                ClusteringManager clustermanage = new ClusteringManager(TaskConfig.cmPath);
                GeneralParameterTraining generalParameterTraining = new GeneralParameterTraining(clustermanage);
                IParameters[] layoutParams = generalParameterTraining.runGeneralTraining();
                /* save newly found parameters to config file */
                TaskConfig.saveConfigurationsToConfigFile(TaskConfig.outConfigPath);
                /* print out information about training */
                TaskConfig.monitor.setStatusMessage(TaskConfig.NL + "###### Best Parameter Configurations Found ######");
                for (int i = 0; i < layoutParams.length; i++) {
                    TaskConfig.monitor.setStatusMessage(layoutParams[i].toString());
                    InfoFile.appendLnProjectResults(layoutParams[i].toString());
                }
                time = System.currentTimeMillis() - time;
                TaskConfig.monitor.setStatusMessage("Time taken for complete general training: " + TaskUtility.convertTime(time));
            } catch (InvalidInputFileException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
            // e.printStackTrace();
            } catch (InvalidTypeException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
            // e.printStackTrace();
            }
        } else if (TaskConfig.mode == TaskConfig.COMPARISON_MODE || TaskConfig.mode == TaskConfig.HIERARICHAL_MODE) {
            Thread t = new IteratorThread();
            t.start();
        } else /* no such mode */
        {
            TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "ERROR: This mode does not exist: " + TaskConfig.mode);
        }
        /* create info file */
        if (TaskConfig.info) {
            InfoFile info = new InfoFile();
            info.instantiateFile(TaskConfig.infoPath);
            info.createAndCloseInfoFile();
            /* clear information from StringBuffers in InfoFile */
            InfoFile.clearData();
        }
    // /* ====== CLEAN UP AT END ====== */
    } catch (Exception e) {
        TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "ERROR occured in run with the following message: " + e.getMessage());
    // e.printStackTrace();
    }
    /* release permit in semaphore if necessary */
    if (semaphore != null) {
        semaphore.release();
    }
/* reset the run button back to "RUN" and reset action command */
}

Example 8 with InvalidInputFileException

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.InvalidInputFileException 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];
}

Example 9 with InvalidInputFileException

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

the class Console method parseArgsAndInitProgram.

/**
 * This method parses the input parameters from the console and starts the
 * program with the correct parameters and in the correct mode. At this
 * stage all input parameters are in this form: key value. Both key and
 * value contain no spaces and if the value does, then it is bounded by
 * apostrophes.
 *
 * @throws InvalidInputFileException
 * @throws ArgsParseException
 * @throws IOException
 */
private void parseArgsAndInitProgram() throws InvalidInputFileException, ArgsParseException, IOException {
    boolean inputAndOutputGiven = findAndReadConfigIfGivenAndSetMode();
    initGivenParameters();
    if (TaskConfig.gui) {
    /* start gui with previous set parameters */
    } else if (inputAndOutputGiven && !TaskConfig.gui) {
        ClusteringManagerTask manageTask = new ClusteringManagerTask();
        // run without initialising new thread.
        manageTask.run();
    } else {
        /* either input or output is missing */
        throw new ArgsParseException("Either input file/directory (-i) or output file (-o) is missing!");
    }
}

Example 10 with InvalidInputFileException

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

the class Console method findAndReadConfigIfGivenAndSetMode.

/**
 * Looks through the input variables to see if a config file is defined. If
 * so all parameters are read from this config file. If some do not exist, a
 * warning is given, but the program continues. It may be the case that
 * these parameters are unwanted or belong to an unused implementation. It
 * also looks if a mode was given and sets this, otherwise the default is
 * used.
 *
 * It also checks whether input AND output files/directories are given,
 * which is compulsory when starting with the console and not with the gui.
 *
 * @return boolean value if an input and an output file (both) are given.
 * @throws InvalidInputFileException
 *             If the given config class does not end in .conf.
 */
private boolean findAndReadConfigIfGivenAndSetMode() throws InvalidInputFileException, ArgsParseException {
    boolean input = false;
    boolean output = false;
    String configPath = TaskConfig.DEFAULTCONFIG;
    for (int i = 0; i < args.length; i++) {
        /* check whether an input file is given */
        if (args[i].trim().equals("-i")) {
            input = true;
            ++i;
        }
        if (args[i].trim().equals("-o")) {
            output = true;
            ++i;
        }
        /* check for mode parameter */
        if (args[i].trim().equals("-mode")) {
            String value = args[i + 1].trim();
            try {
                int md = Integer.parseInt(value);
                if (md == TaskConfig.GENERAL_TRAINING_MODE) {
                    TaskConfig.mode = TaskConfig.GENERAL_TRAINING_MODE;
                } else if (md == TaskConfig.CLUSTERING_MODE) {
                    TaskConfig.mode = TaskConfig.CLUSTERING_MODE;
                } else if (md == TaskConfig.COMPARISON_MODE) {
                    TaskConfig.mode = TaskConfig.COMPARISON_MODE;
                } else if (md == TaskConfig.HIERARICHAL_MODE) {
                    TaskConfig.mode = TaskConfig.HIERARICHAL_MODE;
                } else {
                    throw new ArgsParseException("The given mode is incorrect - it does not exist! " + md);
                }
            } catch (Exception e) {
                throw new ArgsParseException("The given mode is not an interger value: " + value);
            }
            ++i;
        }
        /* check for config parameter */
        if (args[i].trim().equals("-config")) {
            String value = args[i + 1].trim();
            if (value.endsWith(".conf")) {
                TaskConfig.useConfigFile = true;
                TaskConfig.inputConfigPath = value;
                configPath = value;
            } else {
                throw new InvalidInputFileException("An invalid config file was entered. The file must end with '.conf'. Please try again! Given file=" + value);
            }
            ++i;
        }
        /* check for if -cf parameter is set */
        if (args[i].trim().equals("-cf")) {
            TaskConfig.useConfigFile = Boolean.parseBoolean(args[i + 1].trim());
            ++i;
        }
    }
    if (TaskConfig.useConfigFile) {
        try {
            FileInputStream s = new FileInputStream(configPath);
            PropertyResourceBundle configrb = new PropertyResourceBundle(s);
            // log.debug("Using config file " + configPath);
            TaskConfig.initFromConfigFile(configrb);
            FORCEnDLayoutConfig.initFromConfigFile(configrb);
            GeometricClusteringConfig.initSLCFromConfigFile(configrb);
            GeometricClusteringConfig.initKmeansFromConfigFile(configrb);
        } catch (MissingResourceException ex) {
            TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "WARNING: Resources are missing in the given config file: " + TaskConfig.DEFAULTCONFIG + ", key=" + ex.getKey() + ". Either you have defined these parameters in the input, or the default values are used from the " + TaskConfig.DEFAULTCONFIG + ". Or these parameters do not interest you, because they belong to an unused implemtation.");
        } catch (IOException ex) {
            TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "ERROR: Unable to read the given config file: " + configPath);
            System.exit(-1);
        } catch (InvalidTypeException ex) {
            TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "ERROR: You have perhaps given an incorrect class name of an " + "implemtation. Please note that this is case sensitive.");
            System.exit(-1);
        }
    }
    if (input && output)
        return true;
    else
        return false;
}