public Region getTranslatedRegion(Vector3f trans) {
RectangularBox newBox =
new RectangularBox(
this.getLowestXValue() + trans.x,
this.getLowestYValue() + trans.y,
this.getLowestZValue() + trans.z,
Math.abs(this.parameterList[3].value),
Math.abs(this.parameterList[4].value),
Math.abs(this.parameterList[5].value));
return newBox;
}
public float getHighestZValue() {
// just in case the length is negative...
return Math.max(parameterList[2].value, parameterList[2].value + parameterList[5].value);
};
public float getLowestYValue() {
// just in case the length is negative...
return Math.min(parameterList[1].value, parameterList[1].value + parameterList[4].value);
};
private void createSections() {
float axonRadius = .5f;
Point3f posnEndPoint = new Point3f(0, -15, 0);
Segment rootAxon =
addAxonalSegment(axonRadius, "root", posnEndPoint, somaSection, 1, "axonRootSec");
Vector<Segment> layer = new Vector<Segment>();
layer.add(addRelativeAxon(rootAxon, new Point3f(-30, -20, -30), axonRadius));
layer.add(addRelativeAxon(rootAxon, new Point3f(-30, -20, 30), axonRadius));
layer.add(addRelativeAxon(rootAxon, new Point3f(30, -20, 30), axonRadius));
layer.add(addRelativeAxon(rootAxon, new Point3f(30, -20, -30), axonRadius));
for (int i = 0; i < layer.size(); i++) {
Segment axon = (Segment) layer.elementAt(i);
Segment a1 = addRelativeAxon(axon, new Point3f(-6, -4, -6), axonRadius);
Segment a2 = addRelativeAxon(axon, new Point3f(6, -4, -6), axonRadius);
Segment a3 = addRelativeAxon(axon, new Point3f(-6, -4, 6), axonRadius);
Segment a4 = addRelativeAxon(axon, new Point3f(6, -4, 6), axonRadius);
a1.getSection().addToGroup(axonSynGroup);
a2.getSection().addToGroup(axonSynGroup);
a3.getSection().addToGroup(axonSynGroup);
a4.getSection().addToGroup(axonSynGroup);
}
float dendriteDiam = 2;
int numDendrites = 6;
for (int i = 0; i < numDendrites; i++) {
double theta = ((2 * Math.PI) / numDendrites) * i;
float xFact = (float) Math.sin(theta);
float zFact = (float) Math.cos(theta);
posnEndPoint = new Point3f(60 * xFact, 60, 60 * zFact);
Segment radialDend =
addDendriticSegment(
dendriteDiam,
"radialDend_" + i,
posnEndPoint,
somaSection,
0,
"radialDend_" + i + "_Sec",
false);
Point3f posnNew = new Point3f(30 * xFact, 40, 30 * zFact);
Segment radialDend2 = addRelativeDendrite(radialDend, posnNew);
radialDend2.getSection().addToGroup(dendSynGroup);
Point3f posnNew2 = new Point3f(0, 30, 0);
Segment radialDend3 = addRelativeDendrite(radialDend2, posnNew2);
radialDend3.getSection().addToGroup(dendSynGroup);
Point3f posnNew3 = new Point3f(-10 * xFact, 30, -10 * zFact);
Segment radialDend4 = addRelativeDendrite(radialDend, posnNew3);
radialDend4.getSection().addToGroup(dendSynGroup);
Point3f posnNew4 = new Point3f(0, 25, 0);
Segment radialDend5 = addRelativeDendrite(radialDend4, posnNew4);
radialDend5.getSection().addToGroup(dendSynGroup);
}
}