NeuGenReaderTask.java

/* 
 * Copyright (c) 2005–2012 Goethe Center for Scientific Computing - Simulation and Modelling (G-CSC Frankfurt)
 * Copyright (c) 2012-2015 Goethe Center for Scientific Computing - Computational Neuroscience (G-CSC Frankfurt)
 * 
 * This file is part of NeuGen.
 *
 * NeuGen is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License version 3
 * as published by the Free Software Foundation.
 * 
 * see: http://opensource.org/licenses/LGPL-3.0
 *      file://path/to/NeuGen/LICENSE
 *
 * NeuGen is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * This version of NeuGen includes copyright notice and attribution requirements.
 * According to the LGPL this information must be displayed even if you modify
 * the source code of NeuGen. The copyright statement/attribution may not be removed.
 *
 * Attribution Requirements:
 *
 * If you create derived work you must do the following regarding copyright
 * notice and author attribution.
 *
 * Add an additional notice, stating that you modified NeuGen. In addition
 * you must cite the publications listed below. A suitable notice might read
 * "NeuGen source code modified by YourName 2012".
 * 
 * Note, that these requirements are in full accordance with the LGPL v3
 * (see 7. Additional Terms, b).
 *
 * Publications:
 *
 * S. Wolf, S. Grein, G. Queisser. NeuGen 2.0 -
 * Employing NeuGen 2.0 to automatically generate realistic
 * morphologies of hippocapal neurons and neural networks in 3D.
 * Neuroinformatics, 2013, 11(2), pp. 137-148, doi: 10.1007/s12021-012-9170-1
 *
 *
 * J. P. Eberhard, A. Wanner, G. Wittum. NeuGen -
 * A tool for the generation of realistic morphology 
 * of cortical neurons and neural networks in 3D.
 * Neurocomputing, 70(1-3), pp. 327-343, doi: 10.1016/j.neucom.2006.01.028
 *
 */
package org.neugen.parsers;

import org.neugen.utils.Utils;
import java.io.BufferedInputStream;
import org.neugen.gui.*;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import org.apache.log4j.Logger;
import org.jdesktop.application.Application;
import org.jdesktop.application.Task;
import org.neugen.datastructures.Net;
import org.neugen.datastructures.Region;
import org.neugen.datastructures.neuron.Neuron;

/**
 * @author Sergei Wolf
 */
public final class NeuGenReaderTask extends Task<Void, Void> {

    private final static Logger logger = Logger.getLogger(NeuroMLReaderTask.class.getName());

    public NeuGenView ngView;

    public NeuGenReaderTask(Application app) {
        super(app);
        ngView = NeuGenView.getInstance();
    }

    public void setMyProgress(int value, int min, int max) {
        setProgress(value, min, max);
    }

    @Override
    protected Void doInBackground() throws IOException {
        try {
            ngView.outPrintln("Reading NeuGen Project data..");
            String netSer = ngView.getProjectDirPath() + System.getProperty("file.separator") + "net.ser";
            ObjectInputStream netIn = new ObjectInputStream(new BufferedInputStream(new FileInputStream(netSer)));
            try {
                Net net = (Net) netIn.readObject();
                if(net != null) {
                    Region.setInstance(net.getRegion());
                    for (Neuron neuron : net.getNeuronList()) {
                        neuron.infoNeuron();
                    }
                    //net.setTotalNumberOfSegments();
                    ngView.setNet(net);
                    String synMes = "\n";
                    synMes += " number of synapses: " + net.getNumSynapse() + "\n";
                    long nbilSyn = net.getNumSynapse() - net.getNumNonFunSynapses();
                    synMes += " number of bilateral synapses: " + nbilSyn + "\n";
                    synMes += " nonfunctional synapses: " + net.getNumNonFunSynapses() + "\n";
                    ngView.outPrintln(synMes);
                }
            } catch (ClassNotFoundException ex) {
                logger.error(ex, ex);
            }
            netIn.close();
        } catch (IOException ex) {
            logger.error(ex, ex);
        }
        return null;
    }

    @Override
    protected void succeeded(Void result) {
        ngView.setNetExist(true);
        ngView.enableButtons();
        System.gc();
        ngView.outPrintln(Utils.getMemoryStatus());
    }
}