/*
* 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
*
*/
/*
* File: VisualizationDensityTask.java
* Created on 27.07.2009, 12:00:22
*
*/
package org.neugen.gui;
import com.sun.j3d.loaders.IncorrectFormatException;
import com.sun.j3d.loaders.ParsingErrorException;
import com.sun.j3d.loaders.Scene;
import com.sun.j3d.loaders.objectfile.ObjectFile;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import ij.process.StackConverter;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Locale;
import java.util.StringTokenizer;
import javax.media.j3d.BranchGroup;
import javax.media.j3d.Node;
import javax.swing.ImageIcon;
import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
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.VolumeOfVoxels;
import org.neugen.datastructures.VoxelVolume;
import org.neugen.datastructures.VoxelVolumeIterator;
import org.neugen.utils.NGImageIO;
import org.neugen.utils.Utils;
/**
* @author Sergei Wolf
*/
public final class DensityVisualizationTask extends org.jdesktop.application.Task<Void, Void> {
/** use to log messages */
private static Logger logger = Logger.getLogger(DensityVisualizationTask.class.getName());
private DensityVisualizationConfiguration ngVisConfig;
private static DensityVisualizationTask instance;
private File dir, selectedFile;
private float scale = 0.001f;
private float scaleZ = 0.001f;
private Scene s;
public float getScaleZ() {
return scaleZ;
}
public float getScale() {
return scale;
}
public enum Density {
NET, IMAGE;
}
private Density dens;
public DensityVisualizationTask(Application application, Density dens, File f) {
super(application);
this.dens = dens;
this.dir = f.getParentFile();
this.selectedFile = f;
}
public DensityVisualizationTask(Application application, Density dens) {
super(application);
this.dens = dens;
}
public static DensityVisualizationTask getInstance() {
return instance;
}
public static void setInstance(Task instance) {
DensityVisualizationTask.instance = (DensityVisualizationTask) instance;
}
public void setMyProgress(int value, int min, int max) {
setProgress(value, min, max);
}
public void setMyProgress(float percentage) {
if (Float.isInfinite(percentage)) {
logger.info("percentage infinite: " + percentage);
percentage = 1.0f;
}
setProgress(percentage);
}
public DensityVisualizationConfiguration getNgVisConfig() {
return ngVisConfig;
}
@Override
protected Void doInBackground() throws Exception {
switch (dens) {
case NET: {
DensityDialog densDialog = new DensityDialog(NeuGenView.getInstance().getFrame(), true);
densDialog.setVisible(true);
densDialog.setLocationRelativeTo(null);
if (densDialog.getReturnStatus() == DensityDialog.RET_OK) {
Point3f volumeEnd = new Point3f(Region.getInstance().getUpRightCorner());
if (VisualizationTask.getInstance() != null) {
if (VisualizationTask.getInstance().getNGVisualization() != null) {
scale = VisualizationTask.getInstance().getNGVisualization().getScale();
}
}
volumeEnd.scale(scale);
logger.info(volumeEnd.toString());
NeuGenView ngView = NeuGenView.getInstance();
Net net = ngView.getNet();
VoxelVolume vv = new VoxelVolume(net, densDialog.getVoxelLenght(), densDialog.getDensityPart(), densDialog.getDensityMethod());
VoxelVolumeIterator voxelVolumeIterator = new VoxelVolumeIterator(vv);
Point3i voxelNumber = voxelVolumeIterator.getVoxelNumber();
VolumeOfVoxels volumeOfVoxels = new VolumeOfVoxels(voxelNumber, volumeEnd);
int thisindex = 0;
float value = 0.0f;
int voxelArraySize = vv.getVoxelArray().size();
while (voxelVolumeIterator.hasNext()) {
value = voxelVolumeIterator.next();
volumeOfVoxels.setVoxelValue(thisindex, value); // same index
thisindex++;
setMyProgress(thisindex, 0, voxelArraySize);
}
ngVisConfig = new DensityVisualizationConfiguration(volumeOfVoxels);
DensityVisualizationConfiguration.setInstance(ngVisConfig);
ngVisConfig.setVisible(true);
ngVisConfig.setLocationRelativeTo(null);
} else {
NeuGenView.getInstance().enableButtons();
}
break;
}
case IMAGE: {
VoxelDialog vDialog = new VoxelDialog(NeuGenView.getInstance().getFrame(), true);
vDialog.setVisible(true);
vDialog.setLocationRelativeTo(null);
if (vDialog.getReturnStatus() == VoxelDialog.RET_OK) {
//NGImageIO imageIO = new NGImageIO();
//List<ImageProducer> fileList = imageIO.getFileList(dir);
logger.info("image density task, dir path: " + dir.getAbsolutePath());
NeuGenView ngView = NeuGenView.getInstance();
boolean imageSequence = ngView.isImageSequence();
ArrayList<int[][]> dataList = new ArrayList<int[][]>();
//int numFiles = fileList.size();
//logger.info("anzahl bilder: " + numFiles);
int count = 0;
int width = 0;
int height= 0;
int stackSize = 0;
BranchGroup bg = null;
//ArrayList<ImageIcon> fileList = new ArrayList<ImageIcon>();
if (dir != null) {
File[] listFiles = dir.listFiles();
boolean stackLoaded = false;
for (File file : listFiles) {
if (NGImageIO.isImage(file.getName())) {
if(!imageSequence && !selectedFile.getName().equals(file.getName())) {
continue;
}
ngView.outPrintln("image stack name: " + file.getName());
if (stackLoaded && !imageSequence) {
logger.info("stack schon geladen!");
continue;
}
try {
/*
Image img = Jimi.getImage(file.getAbsolutePath());
ImageIcon imgIcon = new ImageIcon(img);
fileList.add(imgIcon);
*
*/
logger.info("file name: " + file.getName());
ImagePlus imp = ij.IJ.openImage(file.getAbsolutePath());
stackSize = imp.getStackSize();
if (stackSize > 1) {
StackConverter sc = new StackConverter(imp);
sc.convertToGray8();
} else {
count++;
ImageConverter im = new ImageConverter(imp);
im.convertToGray8();
}
ImageStack stack = imp.getStack();
if (stack.getSize() > 1) {
stackLoaded = true;
}
for (int i = 1; i <= stack.getSize(); i++) {
ImageProcessor ip = stack.getProcessor(i);
byte[] pixels = (byte[]) ip.getPixels();
width = ip.getWidth();
height = ip.getHeight();
//Array zu Matrix konvertieren
int[][] bildMatrix = new int[width][height];
int x = 0; //Anfangswert fuer x
int y = 0; //Anfangswert fuer y
//fuer alle Elemente des Feldes
for (int j = 0; j < width * height; j++) {
//wenn alle Elemente der Reihe durchlaufen
if (x == width) {
x = 0; //mit dem ersten Element
y++; //der naechsten Reihe beginnen
}//if
bildMatrix[x][y] = pixels[j];
x++; //naechstes Element
}//for
dataList.add(bildMatrix);
}
} catch (Exception ex) {
logger.error(ex, ex);
}
} else if (NGImageIO.isGeom(file.getName())) {
bg = getGeom(file);
}
}
}
/*
for (ImageIcon image : fileList) {
//Image image = ngView.getFrame().createImage(imageProd);
//image.flush();
//System.out.println(image.getIconHeight());
//System.out.println(image.getIconWidth());
try {
PixelGrabber grabber = new PixelGrabber(image.getImage(), 0, 0, -1, -1, false);
if (grabber.grabPixels()) {
int width = grabber.getWidth();
int height = grabber.getHeight();
int[][] data = imageIO.getData(image.getImage(), width, height);
dataList.add(data);
//setMyProgress(count, 0, numFiles);
} else {
logger.info("geht nichts..");
}
} catch (InterruptedException ex) {
logger.error(ex, ex);
}
count++;
}
*
*/
ngView.outPrintln("image stack size: " + dataList.size());
logger.info("image density task, anzahl bilder: " + dataList.size());
Point3i voxelLength = vDialog.getVoxelLenght();
logger.info("voxelLenght: " + voxelLength.toString());
int intensity = vDialog.getThreshold();
int weight = vDialog.getWeight();
float scannedImgHeight = vDialog.getImgHeight();
float scannedImgWidth = vDialog.getImgWidth();
float scannedDepth = vDialog.getDepth();
logger.info("scanned height: " + scannedImgHeight);
logger.info("scanned width: " + scannedImgWidth);
logger.info("scanned depth: " + scannedDepth);
//this.scale = 0.0065f;
//this.scale = 0.01f;
//this.scale = 0.0077f;
this.scale = scannedImgHeight / height; //um pro pixel
this.scale /= 10.0f;
//float scaleZ = 0.0498f / 5.0f;
float optDepth = 0.1f;
float faktor = scannedDepth / optDepth;
scaleZ = 0.0f;
if(stackSize > 0) {
float stackDepth = stackSize * scannedDepth;
logger.info("tiefe: " + stackDepth);
scaleZ = scannedDepth;
scaleZ /= 10.0f;
} else {
scaleZ = scannedDepth / faktor;
scaleZ /= 10.0f;
}
logger.info("scale: " + scale);
logger.info("scaleZ: " + scaleZ);
logger.info("stack size: " + stackSize);
VoxelVolume vv = new VoxelVolume(dataList, voxelLength, intensity, weight);
Point3f volumeEnd = new Point3f(Region.getInstance().getUpRightCorner());
logger.info("volumeEnd: " + volumeEnd.toString());
volumeEnd.x *= scale;
volumeEnd.z *= scale;
volumeEnd.y *= scaleZ;
VoxelVolumeIterator voxelVolumeIterator = new VoxelVolumeIterator(vv);
Point3i voxelNumber = voxelVolumeIterator.getVoxelNumber();
VolumeOfVoxels volumeOfVoxels = new VolumeOfVoxels(voxelNumber, volumeEnd);
int thisindex = 0;
float value = 0.0f;
int voxelArraySize = vv.getVoxelArray().size();
while (voxelVolumeIterator.hasNext()) {
value = voxelVolumeIterator.next();
volumeOfVoxels.setVoxelValue(thisindex, value); // same index
thisindex++;
setMyProgress(thisindex, 0, voxelArraySize);
}
if (bg != null) {
ngVisConfig = new DensityVisualizationConfiguration(volumeOfVoxels, bg);
} else {
ngVisConfig = new DensityVisualizationConfiguration(volumeOfVoxels);
}
DensityVisualizationConfiguration.setInstance(ngVisConfig);
ngVisConfig.setVisible(true);
ngVisConfig.setLocationRelativeTo(null);
} else {
NeuGenView.getInstance().enableButtons();
}
break;
}
}
return null;
}
private BranchGroup getGeom(File file) throws FileNotFoundException, IOException {
Reader in = new FileReader(file);
BufferedReader lineReader = new BufferedReader(in);
String nextLine = null;
nextLine = lineReader.readLine().trim();
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);
}
/*
TransformGroup objScale = new TransformGroup();
Transform3D t3d = new Transform3D();
t3d.setScale(1.0);
objScale.setTransform(t3d);
s.getSceneGroup().addChild(objScale);
*
*/
Node bg = s.getSceneGroup();//.cloneTree();
return (BranchGroup) bg;
}
@Override
protected void succeeded(Void result) {
System.gc();
NeuGenView ngView = NeuGenView.getInstance();
ngView.outPrintln(Utils.getMemoryStatus());
ngView.enableVisualizeDensity();
ngView.enableVisualize();
switch(dens) {
case IMAGE: {
ngView.enableWriteNeuGenBG();
}
}
}
}