/**
* \brief Add the total concentration of an agent on received grid
*
* <p>Add the total concentration of an agent on received grid
*
* @param aSpG Spatial grid used to sum total mass
*/
public void fitMassOnGrid(SpatialGrid aSpG) {
if (isDead) return;
double value = _totalMass / aSpG.getVoxelVolume();
if (Double.isNaN(value) | Double.isInfinite(value)) value = 0;
aSpG.addValueAt(value, _location);
}
/**
* \brief Add the reacting concentration of an agent to the received grid
*
* <p>Add the reacting concentration of an agent to the received grid
*
* @param aSpG Spatial grid used to sum catalysing mass
* @param catalystIndex Index of the compartment of the cell supporting the reaction
*/
public void fitMassOnGrid(SpatialGrid aSpG, int catalystIndex) {
if (isDead) return;
double value = particleMass[catalystIndex] / aSpG.getVoxelVolume();
if (Double.isNaN(value) | Double.isInfinite(value)) value = 0;
aSpG.addValueAt(value, _location);
}
/**
* \brief Add the reaction/growth rate of an agent on received grid, for a specified reaction
*
* <p>Add the total reaction/growth rate of an agent on received grid, for a specified reaction
*
* @param aRateGrid Spatial grid used to store total reaction rate
* @param reactionIndex Index of this declared reaction in the simulation dictionary
*/
public void fitReacRateOnGrid(SpatialGrid aRateGrid, int reactionIndex) {
if (isDead) return;
// growthRate is in [fgX.hr-1] so convert to concentration:
// [fgX.um-3.hr-1 = gX.L-1.hr-1]
double value = growthRate[reactionIndex] / aRateGrid.getVoxelVolume();
if (Double.isNaN(value) | Double.isInfinite(value)) value = 0;
aRateGrid.addValueAt(value, _location);
}
@Override
public Double getWeightFromLink(Link link, Coord cellCentroid) {
Cell cellOfLink = links2Cells.get(link);
if (cellOfLink == null) {
return 0.0;
} else {
Cell receivingCell = grid.getCellForCoordinate(cellCentroid);
return calcDistanceFactorFromCells(cellOfLink, receivingCell);
}
}
private Map<Link, Cell> mapLinksToGridCells(Collection<Link> links, SpatialGrid grid) {
links2Cells = new HashMap<Link, Cell>();
for (Link link : links) {
Cell cCell = grid.getCellForCoordinate(link.getCoord());
if (cCell != null) links2Cells.put(link, cCell);
}
System.out.println("Mapped " + links2Cells.size() + " links to grid");
System.out.println((links.size() - links2Cells.size()) + " links were not mapped.");
return links2Cells;
}
/**
* \brief Add the total volume rate of an agent on received grid
*
* <p>Add the total volume rate of an agent on received grid
*
* @param aSpG Spatial grid used to sum volume
*/
public void fitVolRateOnGrid(SpatialGrid aSpG) {
double value;
value = _netVolumeRate / aSpG.getVoxelVolume();
if (Double.isNaN(value) | Double.isInfinite(value)) value = 0;
aSpG.addValueAt(value, _location);
}
@Override
public Double getWeightFromCoord(Coord emittingCoord, Coord receivingCoord) {
Cell emittingCell = grid.getCellForCoordinate(emittingCoord);
Cell receivingCell = grid.getCellForCoordinate(receivingCoord);
return calcDistanceFactorFromCells(emittingCell, receivingCell);
}
