public static SphericalRegion getEnclosingSphere(RectangularBox box) {
Point3f centre =
new Point3f(
(box.getHighestXValue() + box.getLowestXValue()) / 2,
(box.getHighestYValue() + box.getLowestYValue()) / 2,
(box.getHighestZValue() + box.getLowestZValue()) / 2);
float radius =
centre.distance(
new Point3f(box.getLowestXValue(), box.getLowestYValue(), box.getLowestZValue()));
SphericalRegion newSphere = new SphericalRegion(centre.x, centre.y, centre.z, radius);
return newSphere;
}
protected Point3f generateNextPosition() throws CellPackingException {
Point3f proposedPoint = null;
logger.logComment(
"---- Generating next position. positionsAlreadyTaken.size() = "
+ getNumPosAlreadyTaken());
float minXLoc, minYLoc, minZLoc, maxXLoc, maxYLoc, maxZLoc;
if (mustBeCompletelyInsideRegion()) {
// limit the extent for possible location of soma centre to box which
// will preclude soma wall impacting region boundary.
minXLoc = myRegion.getLowestXValue() - CellTopologyHelper.getMinXExtent(myCell, true, false);
minYLoc = myRegion.getLowestYValue() - CellTopologyHelper.getMinYExtent(myCell, true, false);
minZLoc = myRegion.getLowestZValue() - CellTopologyHelper.getMinZExtent(myCell, true, false);
maxXLoc = myRegion.getHighestXValue() - CellTopologyHelper.getMaxXExtent(myCell, true, false);
maxYLoc = myRegion.getHighestYValue() - CellTopologyHelper.getMaxYExtent(myCell, true, false);
maxZLoc = myRegion.getHighestZValue() - CellTopologyHelper.getMaxZExtent(myCell, true, false);
} else {
// in this case the soma centre can be anywhere inside the region..
minXLoc = myRegion.getLowestXValue();
minYLoc = myRegion.getLowestYValue();
minZLoc = myRegion.getLowestZValue();
maxXLoc = myRegion.getHighestXValue();
maxYLoc = myRegion.getHighestYValue();
maxZLoc = myRegion.getHighestZValue();
}
Point3f startPoint = new Point3f(minXLoc, minYLoc, minZLoc);
logger.logComment("minXLoc: " + minXLoc + ", maxXLoc: " + maxXLoc);
if (maxXLoc - minXLoc < 0 || maxYLoc - minYLoc < 0 || maxZLoc - minZLoc < 0) {
throw new CellPackingException("Diameter of cell is smaller than region");
}
if (getNumPosAlreadyTaken() >= getNumberCells()) {
throw new CellPackingException("All cells successfully placed");
}
if (getNumberCells() == 0) {
throw new CellPackingException("Cell number set to zero!!");
} else if (getNumberCells() == 1) {
if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_X) {
proposedPoint = new Point3f((minXLoc + maxXLoc) / 2, minYLoc, minZLoc);
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Y) {
proposedPoint = new Point3f(minXLoc, (minYLoc + maxYLoc) / 2, minZLoc);
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Z) {
proposedPoint = new Point3f(minXLoc, minYLoc, (minZLoc + maxZLoc) / 2);
}
} else {
// Point3f lastPositionedPoint = getLastPosTaken();
if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_X) {
float distanceApart = (maxXLoc - minXLoc) / (getNumberCells() - 1);
proposedPoint = new Point3f(startPoint);
proposedPoint.add(new Point3f(distanceApart * numProposedPoints, 0, 0));
logger.logComment(
"Placing one of "
+ getNumberCells()
+ " cells in x dim..."
+ distanceApart
+ " apart, new: "
+ proposedPoint
+ ", already proposed: "
+ numProposedPoints);
if (proposedPoint.x > maxXLoc) throw new CellPackingException("Reached end of x dimension");
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Y) {
logger.logComment("Placing cell in y dim...");
float distanceApart = (maxYLoc - minYLoc) / (getNumberCells() - 1);
proposedPoint = new Point3f(startPoint);
proposedPoint.add(new Point3f(0, distanceApart * numProposedPoints, 0));
if (proposedPoint.y > maxYLoc) throw new CellPackingException("Reached end of y dimension");
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Z) {
logger.logComment("Placing cell in z dim...");
float distanceApart = (maxZLoc - minZLoc) / (getNumberCells() - 1);
proposedPoint = new Point3f(startPoint);
proposedPoint.add(new Point3f(0, 0, distanceApart * numProposedPoints));
if (proposedPoint.z > maxZLoc) throw new CellPackingException("Reached end of z dimension");
}
if (proposedPoint == null) throw new CellPackingException("Cannot successfully place cell.");
}
// lastProposedPoint = new Point3d(proposedPoint);
numProposedPoints++;
return new Point3f(proposedPoint);
}