public synchronized VolumeGrid getVolumeGrid() {
if (this.volumeGrid == null) {
final Morphology morph = this.getMorphology();
final TreePoint[] tpa = morph.getTreePoints();
final Discretization disc = this.getDiscretization();
double d = disc.getDefaultMaxElementSide();
double deltaX = disc.spineDeltaX != null ? disc.spineDeltaX : d;
// <--WK 6 22 2007
// (1) iterate through all endpoints and their associated radii.
// (2) divide each radius by successively increasing odd numbers until
// the divided value becomes less than the defaultMaxElementSide.
// (3) select the smallest among the divided radii values as d.
double[] diameters = new double[tpa.length];
double[] candidate_grid_sizes = new double[tpa.length];
for (int i = 0; i < tpa.length; i++) {
double diameter = tpa[i].getRadius() * 2;
diameters[i] = diameter;
double denominator = 1;
while (diameter / denominator > d) denominator += 2; // divide by successive odd numbers
candidate_grid_sizes[i] = diameter / denominator;
}
d = Math.min(d, ArrayUtil.min(candidate_grid_sizes));
log.info(
"Subvolume grid size is: {} (from radii {}, candidates {}, default {})",
d,
diameters,
candidate_grid_sizes,
disc.getDefaultMaxElementSide());
if (disc.curvedElements()) {
TreeCurvedElementDiscretizer tced = new TreeCurvedElementDiscretizer(tpa);
volumeGrid =
tced.buildGrid(
d, disc.getResolutionHM(), disc.getSurfaceLayers(), disc.getMaxAspectRatio());
} else
volumeGrid =
TreeBoxDiscretizer.buildGrid(
tpa,
d,
disc.getResolutionHM(),
disc.getSurfaceLayers(),
this.getGeometry(),
this.depth2D);
SpineLocator.locate(this.spineSeed, morph.getSpineDistribution(), deltaX, volumeGrid);
volumeGrid.fix();
log.info("{} subvolumes", volumeGrid.size());
}
return this.volumeGrid;
}
public double stepSize() {
return Math.min(
Math.min(this.getFixedStepDt(), this.getOutputInterval()),
this.getEndTime() - this.getStartTime());
}