private Segment addRelativeDendrite(Segment parent, Point3f relPosition) {
Point3f newPosition = (new Point3f(parent.getEndPointPosition()));
newPosition.add(relPosition);
float newRadius = parent.getRadius() * .6f;
String newName = "Dend_" + getOnlyDendriticSegments().size();
Segment tempDend =
addDendriticSegment(newRadius, newName, newPosition, parent, 1, newName + "_Sec", true);
return tempDend;
}
private Segment addRelativeAxon(Segment parent, Point3f relPosition, float radius) {
Point3f newPosition = (new Point3f(parent.getEndPointPosition()));
newPosition.add(relPosition);
String newName = "Axon_" + getOnlyAxonalSegments().size();
Segment tempAxon = addAxonalSegment(radius, newName, newPosition, parent, 1, newName + "_Sec");
return tempAxon;
}
public boolean isCellWithinRegion(Point3f point, Cell cell, boolean completelyInside) {
logger.logComment("Checking point: " + point + " in: " + toString());
float minXLoc, minYLoc, minZLoc;
float maxXLoc, maxYLoc, maxZLoc;
Segment firstSeg = cell.getFirstSomaSegment();
if (completelyInside) logger.logComment("Cell needs to be completely inside");
else
logger.logComment(
"Only cell centre (" + firstSeg.getStartPointPosition() + ") needs to be inside");
int factor = 0;
if (completelyInside) factor = 1;
minXLoc = parameterList[0].value + factor * firstSeg.getSection().getStartRadius();
minYLoc = parameterList[1].value + factor * firstSeg.getSection().getStartRadius();
minZLoc = parameterList[2].value + factor * firstSeg.getSection().getStartRadius();
maxXLoc =
parameterList[0].value
+ parameterList[3].value
- factor * firstSeg.getSection().getStartRadius();
maxYLoc =
parameterList[1].value
+ parameterList[4].value
- factor * firstSeg.getSection().getStartRadius();
maxZLoc =
parameterList[2].value
+ parameterList[5].value
- factor * firstSeg.getSection().getStartRadius();
Point3f actualStartOfSoma =
new Point3f(
point.x + firstSeg.getSection().getStartPointPositionX(),
point.y + firstSeg.getSection().getStartPointPositionY(),
point.z + firstSeg.getSection().getStartPointPositionZ());
logger.logComment(
"actualStartOfSoma: "
+ actualStartOfSoma
+ ", radius: "
+ firstSeg.getSection().getStartRadius());
if (actualStartOfSoma.x < minXLoc
|| actualStartOfSoma.x > maxXLoc
|| actualStartOfSoma.y < minYLoc
|| actualStartOfSoma.y > maxYLoc
|| actualStartOfSoma.z < minZLoc
|| actualStartOfSoma.z > maxZLoc) return false;
if (completelyInside) {
Vector somaSegments = cell.getOnlySomaSegments();
for (int i = 0; i < somaSegments.size(); i++) {
Segment nextSeg = (Segment) somaSegments.elementAt(i);
Point3f actualEndPoint =
new Point3f(
point.x + nextSeg.getEndPointPositionX(),
point.y + nextSeg.getEndPointPositionY(),
point.z + nextSeg.getEndPointPositionZ());
logger.logComment("actualEndPoint: " + actualEndPoint + ", radius: " + nextSeg.getRadius());
if (actualEndPoint.x < parameterList[0].value + nextSeg.getRadius()
|| actualEndPoint.x
> parameterList[0].value + parameterList[3].value - nextSeg.getRadius()
|| actualEndPoint.y < parameterList[1].value + nextSeg.getRadius()
|| actualEndPoint.y
> parameterList[1].value + parameterList[4].value - nextSeg.getRadius()
|| actualEndPoint.z < parameterList[2].value + nextSeg.getRadius()
|| actualEndPoint.z
> parameterList[2].value + parameterList[5].value - nextSeg.getRadius())
return false;
}
}
return true;
}
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);
}
}