/*
* 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.datastructures;
import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
import org.apache.log4j.Logger;
import org.neugen.gui.DensityDialog;
/**
* Class for an Iterator for VoxelVolume.
*
* @author Jens P Eberhard
* @author Simone Eberhard
*/
public class VoxelVolumeIterator {
/** Use to log messages */
private final static Logger logger = Logger.getLogger(VoxelVolumeIterator.class.getName());
/** The VoxelVolume for the Iterator */
private VoxelVolume vv;
/** The counter */
private int counter;
/** Voxel length */
private Point3i voxelSize;
/** number of Voxels in voxelArray */
int numberOfVoxelsInArray;
private Point3i voxelNumber;
/** Constructor */
public VoxelVolumeIterator(VoxelVolume vVolume) {
vv = vVolume;
counter = 0;
voxelSize = new Point3i(); // size of voxels (x, y, z)
voxelSize = vv.getVoxelSize();
voxelNumber = vv.getVoxelNumber();
numberOfVoxelsInArray = voxelNumber.x * voxelNumber.y * voxelNumber.z;
}
/**
* value of the next element
*
* @return the value of the next element
*/
public float next() {
if ((vv.getDensityPart().equals(DensityDialog.DensityPart.DENDRITIC)
|| vv.getDensityPart().equals(DensityDialog.DensityPart.AXONAL))
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.LENGTH)) {
return vv.getVoxelArray().get(counter++).getLengthContent();
} else if ((vv.getDensityPart().equals(DensityDialog.DensityPart.DENDRITIC)
|| vv.getDensityPart().equals(DensityDialog.DensityPart.AXONAL))
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.VOLUME)) {
return vv.getVoxelArray().get(counter++).getVolumeContent();
} else if (vv.getDensityPart().equals(DensityDialog.DensityPart.SYNAPTIC)
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.NUMBER)) {
return vv.getVoxelArray().get(counter++).getNumberContent();
} else if (vv.getDensityPart().equals(DensityDialog.DensityPart.IMAGE)
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.NUMBER)) {
return vv.getVoxelArray().get(counter++).getNumberContent();
} else {
return 0.0f;
}
}
/** test for end of struture */
public boolean hasNext() {
if (counter < vv.getVoxelArray().size()) {
return true;
}
return false;
}
/**
* get the value at specified coordinates in VoxelVolume
*
* @return the value at specified coordinates in VoxelVolume
*/
public float get(int x, int y, int z) {
Point3f coords = new Point3f();
coords.x = (float) x * voxelSize.x;
coords.y = (float) y * voxelSize.y;
coords.z = (float) z * voxelSize.z;
int index = vv.getVoxelIndex(coords);
if (index < vv.getVoxelArray().size()) {
if ((vv.getDensityPart().equals(DensityDialog.DensityPart.DENDRITIC)
|| vv.getDensityPart().equals(DensityDialog.DensityPart.AXONAL))
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.LENGTH)) {
return vv.getVoxelArray().get(index).getLengthContent();
} else if ((vv.getDensityPart().equals(DensityDialog.DensityPart.DENDRITIC)
|| vv.getDensityPart().equals(DensityDialog.DensityPart.AXONAL))
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.VOLUME)) {
return vv.getVoxelArray().get(index).getVolumeContent();
} else if (vv.getDensityPart().equals(DensityDialog.DensityPart.SYNAPTIC)
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.NUMBER)) {
return vv.getVoxelArray().get(index).getNumberContent();
} else if (vv.getDensityPart().equals(DensityDialog.DensityPart.IMAGE)
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.NUMBER)) {
return vv.getVoxelArray().get(index).getNumberContent();
} else {
return 0.0f;
}
} else {
logger.info("ERROR: index too big");
return 0.0f;
}
}
/**
* get the value at specified index in voxelArray
*
* @return the value at specified index in voxelArray
*/
public float get(int index) {
if (index < vv.getVoxelArray().size()) {
if ((vv.getDensityPart().equals(DensityDialog.DensityPart.DENDRITIC)
|| vv.getDensityPart().equals(DensityDialog.DensityPart.AXONAL))
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.LENGTH)) {
return vv.getVoxelArray().get(index).getLengthContent();
} else if ((vv.getDensityPart().equals(DensityDialog.DensityPart.DENDRITIC)
|| vv.getDensityPart().equals(DensityDialog.DensityPart.AXONAL))
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.VOLUME)) {
return vv.getVoxelArray().get(index).getVolumeContent();
} else if (vv.getDensityPart().equals(DensityDialog.DensityPart.SYNAPTIC)
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.NUMBER)) {
return vv.getVoxelArray().get(index).getNumberContent();
} else if (vv.getDensityPart().equals(DensityDialog.DensityPart.IMAGE)
&& vv.getDensityMethod().equals(DensityDialog.DensityMethod.NUMBER)) {
return vv.getVoxelArray().get(index).getNumberContent();
} else {
return 0.0f;
}
} else {
logger.info("ERROR : index too big");
return 0.0f;
}
}
public Point3i getVoxelNumber() {
return voxelNumber;
}
/**
* get number of Voxels in voxelArray
*
* @return the number of Voxels in voxelArray
*/
public int getNumberOfVoxelsInArray() {
return numberOfVoxelsInArray;
}
}