/*
* 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.visual;
import javax.media.j3d.Appearance;
import javax.media.j3d.BranchGroup;
import javax.media.j3d.ColoringAttributes;
import javax.media.j3d.LineArray;
import javax.media.j3d.PolygonAttributes;
import javax.media.j3d.QuadArray;
import javax.media.j3d.Shape3D;
import javax.media.j3d.TransformGroup;
import javax.media.j3d.TransparencyAttributes;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3f;
import org.apache.log4j.Logger;
import org.neugen.datastructures.Region;
/**
*
* @author sergeiwolf
*
*
* Die Test-Region mißt 600 x 600 x 900 Miktometer.
* 900 Mikrometer hoch, ref: The hippocampus book S134, 135
*
* stratum oriens ca.: 200 um
* stratum pyramidale ca.: 100 um
* stratum radiatum ca. : 500 um
* stratum lacunosum/moleculare ca.: 100 um.
*/
public final class RegionCA1 extends Shape3D {
//private final static float scale = 0.001f;
private final float lengthX;
private final float widthY;
private final float heightZ;
private final float stratumOriens;
private final float stratumPyramidale;
private final float stratumRadiatum;
private final float stratumLacunosum;
private float scale;
private static final Logger logger = Logger.getLogger(RegionCA1.class.getName());
public RegionCA1(float scale) {
super();
this.scale = scale;
Region.Param.CA1Param regPar = Region.Param.getInstance().getCa1Param();
lengthX = regPar.getLength() * scale;
widthY = regPar.getWidth() * scale;
stratumOriens = regPar.getStratumOriens() * scale;
stratumPyramidale = regPar.getStratumPyramidale() * scale;
stratumRadiatum = regPar.getStratumRadiatum() * scale;
stratumLacunosum = regPar.getStratumLacunosum() * scale;
heightZ = regPar.getHeight() * scale;
Appearance ap = new Appearance();
ColoringAttributes ca = new ColoringAttributes();
ca.setColor(Utils3D.grey);
ap.setColoringAttributes(ca);
TransparencyAttributes myTA = new TransparencyAttributes();
myTA.setTransparency(0.7f);
myTA.setTransparencyMode(TransparencyAttributes.FASTEST);
ap.setTransparencyAttributes(myTA);
//render the Box as a wire frame
PolygonAttributes polyAttrbutes = new PolygonAttributes();
polyAttrbutes.setPolygonMode(PolygonAttributes.POLYGON_LINE);
polyAttrbutes.setCullFace(PolygonAttributes.CULL_NONE);
ap.setPolygonAttributes(polyAttrbutes);
setAppearance(ap);
}
public void addBox(TransformGroup scene) {
QuadArray box = new QuadArray(20, QuadArray.COORDINATES);
Point3d verts[] = new Point3d[20];
//float scaleText = 0.025f;
float scaleText = 3.0f * scale;
//float leftPos = -3.0f * scale;
float textPosX = (lengthX + 250.0f * scale);
logger.info("textPosX " + textPosX);
//unten
// stratum oriens 0.002 mm
Vector3f textPos = new Vector3f(textPosX, widthY / 2.0f, stratumOriens / 2.0f);
Utils3D.addText3D(scene, "stratum oriens", textPos, scaleText, Utils3D.grey);
verts[0] = new Point3d(0, 0, 0);
verts[1] = new Point3d(lengthX, 0, 0);
verts[2] = new Point3d(lengthX, widthY, 0);
verts[3] = new Point3d(0, widthY, 0);
// stratum pyramidale 0.001 mm
textPos = new Vector3f(textPosX, widthY / 2.0f, stratumOriens + stratumPyramidale / 2.0f);
Utils3D.addText3D(scene, "stratum pyramidale", textPos, scaleText, Utils3D.grey);
verts[4] = new Point3d(0, 0, stratumOriens);
verts[5] = new Point3d(lengthX, 0, stratumOriens);
verts[6] = new Point3d(lengthX, widthY, stratumOriens);
verts[7] = new Point3d(0, widthY, stratumOriens);
float stratumPyramidaleEnd = stratumOriens + stratumPyramidale;
// stratum radiatum 0.005 mm
textPos = new Vector3f(textPosX, widthY / 2.0f, stratumPyramidaleEnd + stratumRadiatum / 2.0f);
Utils3D.addText3D(scene, "stratum radiatum", textPos, scaleText, Utils3D.grey);
verts[8] = new Point3d(0, 0, stratumPyramidaleEnd);
verts[9] = new Point3d(lengthX, 0, stratumPyramidaleEnd);
verts[10] = new Point3d(lengthX, widthY, stratumPyramidaleEnd);
verts[11] = new Point3d(0, widthY, stratumPyramidaleEnd);
float stratumRadiatumEnd = stratumPyramidaleEnd + stratumRadiatum;
// stratum lacunosum/moleculare 0.001 mm hoch
textPos = new Vector3f(textPosX, widthY / 2.0f, stratumRadiatumEnd + stratumLacunosum / 1.5f);
Utils3D.addText3D(scene, "stratum lacunosum-moleculare", textPos, scaleText, Utils3D.grey);
verts[12] = new Point3d(0, 0, stratumRadiatumEnd);
verts[13] = new Point3d(lengthX, 0, stratumRadiatumEnd);
verts[14] = new Point3d(lengthX, widthY, stratumRadiatumEnd);
verts[15] = new Point3d(0, widthY, stratumRadiatumEnd);
// oben
verts[16] = new Point3d(0, 0, heightZ);
verts[17] = new Point3d(lengthX, 0, heightZ);
verts[18] = new Point3d(lengthX, widthY, heightZ);
verts[19] = new Point3d(0, widthY, heightZ);
box.setCoordinates(0, verts);
setGeometry(box);
}
public void addLines() {
LineArray ver_Line = new LineArray(8, LineArray.COORDINATES);
Point3d verts2[] = new Point3d[8];
//bottom two lines
verts2[0] = new Point3d(0, 0, 0);
verts2[1] = new Point3d(0, 0, heightZ);
verts2[2] = new Point3d(lengthX, 0, 0);
verts2[3] = new Point3d(lengthX, 0, heightZ);
//top two lines
verts2[4] = new Point3d(0, widthY, 0);
verts2[5] = new Point3d(0, widthY, heightZ);
verts2[6] = new Point3d(lengthX, widthY, 0);
verts2[7] = new Point3d(lengthX, widthY, heightZ);
ver_Line.setCoordinates(0, verts2);
setGeometry(ver_Line);
}
}