/*
* 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 com.sun.j3d.loaders.IncorrectFormatException;
import com.sun.j3d.loaders.ParsingErrorException;
import com.sun.j3d.loaders.Scene;
import com.sun.j3d.loaders.SceneBase;
import com.sun.j3d.loaders.objectfile.ObjectFile;
import com.sun.j3d.utils.scenegraph.io.SceneGraphFileReader;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.neugen.gui.*;
import java.io.File;
import java.io.FileReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.StringTokenizer;
import javax.media.j3d.BranchGroup;
import org.apache.log4j.Logger;
import org.jdesktop.application.Task;
import org.jdesktop.application.Application;
import org.neugen.utils.Utils;
/**
*
* @author Sergei
*/
public final class OBJReader extends Task<Scene, Void> {
private final File file;
private static final Logger logger = Logger.getLogger(OBJReader.class.getName());
private Scene s;
private ReaderType rt;
public enum ReaderType {
TXT, OBJ, BG;
}
public OBJReader(Application app, File f, ReaderType rt) {
super(app);
this.file = f;
this.rt = rt;
}
public void setMyProgress(int value, int min, int max) {
setProgress(value, min, max);
}
public Scene getScene() {
return s;
}
@Override
protected Scene doInBackground() throws FileNotFoundException, IOException {
setMessage("simple obj");
Reader in = new FileReader(file);
BufferedReader lineReader = new BufferedReader(in);
String nextLine = null;
nextLine = lineReader.readLine().trim();
switch (rt) {
case TXT: {
String[] dataArray = nextLine.split(" ");
int verticesVal = Integer.parseInt(dataArray[0]);
int facesVal = Integer.parseInt(dataArray[1]);
logger.info("first line: " + nextLine);
logger.info("vertices: " + verticesVal);
logger.info("faces:" + facesVal);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < verticesVal; i++) {
nextLine = lineReader.readLine().trim();
StringTokenizer st = new StringTokenizer(nextLine);
st.nextToken();
sb.append('v').append(' ');
sb.append(st.nextToken()).append(' ');
sb.append(st.nextToken()).append(' ');
sb.append(st.nextToken()).append('\n');
}
for (int i = 0; i < facesVal; i++) {
nextLine = lineReader.readLine().trim();
StringTokenizer st = new StringTokenizer(nextLine);
st.nextToken();
int v1 = Integer.parseInt(st.nextToken()) + 1;
int v2 = Integer.parseInt(st.nextToken()) + 1;
int v3 = Integer.parseInt(st.nextToken()) + 1;
sb.append('f').append(' ');
sb.append(v1).append(' ');
sb.append(v2).append(' ');
sb.append(v3).append('\n');
}
Reader sr = new StringReader(sb.toString());
int flags = ObjectFile.RESIZE | ObjectFile.STRIPIFY | ObjectFile.TRIANGULATE;
ObjectFile f = new ObjectFile(flags, (float) (60.0 * Math.PI / 180.0));
try {
s = f.load(sr);
} catch (FileNotFoundException e) {
logger.error(e);
System.exit(1);
} catch (ParsingErrorException e) {
logger.error(e);
System.exit(1);
} catch (IncorrectFormatException e) {
logger.error(e);
System.exit(1);
}
break;
}
case OBJ: {
StringBuilder sb = new StringBuilder();
while ((nextLine = lineReader.readLine()) != null) {
nextLine = nextLine.trim();
if (nextLine.length() > 0) {
if (nextLine.startsWith("o")) {
continue;
}
sb.append(nextLine).append('\n');
}
}
Reader sr = new StringReader(sb.toString());
int flags = ObjectFile.RESIZE | ObjectFile.STRIPIFY | ObjectFile.TRIANGULATE;
ObjectFile f = new ObjectFile(flags, (float) (60.0 * Math.PI / 180.0));
try {
s = f.load(sr);
} catch (FileNotFoundException e) {
logger.error(e);
System.exit(1);
} catch (ParsingErrorException e) {
logger.error(e);
System.exit(1);
} catch (IncorrectFormatException e) {
logger.error(e);
System.exit(1);
}
break;
}
case BG: {
SceneGraphFileReader reader = new SceneGraphFileReader(file);
int size = reader.getBranchGraphCount();
SceneBase sb = new SceneBase();
for (int i = 0; i < size; i++) {
BranchGroup bg = reader.readBranchGraph(i)[0];
sb.setSceneGroup(bg);
}
s = (Scene) sb;
reader.close();
}
}
in.close();
lineReader.close();
return s; // return your result
}
@Override
protected void succeeded(Scene result) {
NeuGenView ngView = NeuGenView.getInstance();
ngView.setScene(s);
ngView.enableButtons();
System.gc();
ngView.outPrintln(Utils.getMemoryStatus());
if (ngView.visualizeData() == null) {
logger.info("is null!");
}
ngView.visualizeData().run();
}
}