/**
* \brief Computes the shortest distance between this agent and another, stored as
* ContinuousVectors. This may be around the cyclic boundary
*
* <p>Computes the distance between this agent and another, stored as ContinuousVectors. This may
* be around the cyclic boundary
*
* @param me ContinuousVector stating first agent location
* @param him ContinuousVector stating other agent location
* @return the shortest movement vector to go from a to b, take into account the cyclic boundary
* @see addOverlapMovement
* @see addPullMovement works in 2 and 3D
*/
public double computeDifferenceVector(ContinuousVector me, ContinuousVector him) {
double gridLength;
_diff.x = me.x - him.x;
// check periodicity in X
gridLength = _species.domain.length_X;
if (Math.abs(_diff.x) > .5 * gridLength) _diff.x -= Math.signum(_diff.x) * gridLength;
_diff.y = me.y - him.y;
// check periodicity in Y
gridLength = _species.domain.length_Y;
if (Math.abs(_diff.y) > .5 * gridLength) _diff.y -= Math.signum(_diff.y) * gridLength;
if (_agentGrid.is3D) {
_diff.z = me.z - him.z;
// check periodicity in Z
gridLength = _species.domain.length_Z;
if (Math.abs(_diff.z) > .5 * gridLength) _diff.z -= Math.signum(_diff.z) * gridLength;
} else {
_diff.z = 0;
}
double d = Math.sqrt(_diff.x * _diff.x + _diff.y * _diff.y + _diff.z * _diff.z);
if (d == 0) {
d = 1e-2 * _radius;
_diff.alea(_agentGrid.is3D);
}
return d;
}
/**
* \brief With the agent move calculated, apply this movement, taking care to respect boundary
* conditions
*
* <p>With the agent move calculated, apply this movement, taking care to respect boundary
* conditions
*/
public double move() {
if (!_movement.isValid()) {
LogFile.writeLog("Incorrect movement coordinates");
_movement.reset();
}
if (!_agentGrid.is3D && _movement.z != 0) {
_movement.z = 0;
_movement.reset();
LogFile.writeLog("Try to move in z direction !");
}
// No movement planned, finish here
if (_movement.isZero()) return 0;
// Test the boundaries
checkBoundaries();
// Now apply the movement
_location.set(_newLoc);
_agentGrid.registerMove(this);
double delta = _movement.norm();
_movement.reset();
return delta / _totalRadius;
}
/**
* \brief Select random coordinates for the new agent within a restricted birth area
*
* <p>Select random coordinates for the new agent within a restricted birth area. This restricted
* area is set within the protocol file, and defined as a ContinuousVector by the method
* defineSquareArea
*
* @param cc ContinuousVector that will hold the coordinates of this agent
* @param area Area within which these coordinates should be restricted
*/
public void shuffleCoordinates(ContinuousVector cc, ContinuousVector[] area) {
do {
cc.x = ExtraMath.getUniRandDbl(area[0].x, area[1].x);
cc.y = ExtraMath.getUniRandDbl(area[0].y, area[1].y);
cc.z = ExtraMath.getUniRandDbl(area[0].z, area[1].z);
} while (domain.testCrossedBoundary(cc) != null);
}
/**
* \brief For self-attach scenarios, corrects 3D coordinates that have crossed the front or back
* boundary (x0y and xNy)
*
* <p>For self-attach scenarios, corrects 3D coordinates that have crossed the front or back
* boundary (x0y and xNy). The coordinate is either placed on the opposite side for cyclic
* boundaries, or bounces off the boundary at the required angle
*
* @param boundaryCrossed The boundary that has been detected to have been crossed
* @param distanceMoving The distance that the cell is moving in this step of its repositioning
*/
public void correctCrossedFrontBackBoundaries(AllBC boundaryCrossed) {
// Cell has passed through the boundary on the front or back of the grid
// If is cyclic, the point is deemed to reappear at the opposite side
if (boundaryCrossed instanceof BoundaryCyclic) {
// This will be inside the grid at the amount that the move would
// have taken the point outside of the grid.
swimmingAgentPosition.z = swimmingAgentPosition.z % domain.length_Z;
} else {
// Can simply take the correct value of the new Z coordinate and
// reflect it the correct side of the boundary.
swimmingAgentPosition.z = -swimmingAgentPosition.z % domain.length_Z;
// Now we need to change the angle to note the change of direction
angleOfMovingAgentXZ = 2 * Math.PI - angleOfMovingAgentXZ;
}
}
/**
* \brief Set the location of this agent to the supplied continuous vector
*
* <p>Set the location of this agent to the supplied continuous vector
*
* @param cc Location which this agent should be assigned to
*/
public void setLocation(ContinuousVector cc) {
// sonia:chemostat
// set the location of the newborns to zero
if (Simulator.isChemostat) {
cc.set(0, 0, 0);
_location.x = cc.x;
_location.y = cc.y;
_location.z = cc.z;
} else {
_location.x = cc.x;
_location.y = cc.y;
_location.z = cc.z;
}
}
/**
* \brief Set the movement vector that states where to put a newly-created particle
*
* <p>Set the movement vector that states where to put a newly-created particle
*
* @param distance Distance between the this agent and the new agent
*/
public void setDivisionDirection(double distance) {
double phi, theta;
phi = 2 * Math.PI * ExtraMath.getUniRandDbl();
theta = 2 * Math.PI * ExtraMath.getUniRandDbl();
_divisionDirection.x = distance * Math.sin(phi) * Math.cos(theta);
_divisionDirection.y = distance * Math.sin(phi) * Math.sin(theta);
_divisionDirection.z = (_agentGrid.is3D ? distance * Math.cos(phi) : 0);
}
/**
* \brief Determine if a swimming agent has left the boundary layer and returned to the bulk
*
* <p>For self attachment, an agent starts at the top of the boundary layer and swims in a random
* direction until it attaches somewhere. If however it returns to the bulk, we assume this cell
* does not return. This method checks the move to determine if the cell is moving in a trajectory
* that has returned it to the bulk
*
* @return Boolean stating whether the cell has returned to the bulk
*/
public boolean isNewCoordAboveBoundaryLayer() {
// Get the top of the bulk - note we may need to correct here. The
// method that calls this calculates new positions. However this is run
// before it is determined whether any boundaries have been crossed (as
// it would be silly to check all boundaries when there is a high
// chance, especially at the start, that the cell may return into the
// bulk. Thus, a high Y or Z value may be sent in here, which when
// referenced to the boundary layer array, will cause an error. So if
// the Y or Z values are higher than the size of the grid, we will use
// the size of the grid as the array reference
if (swimmingAgentPosition.y > domain.length_Y) swimmingAgentPosition.y = domain.length_Y - 1;
if (swimmingAgentPosition.z > domain.length_Z) swimmingAgentPosition.z = domain.length_Z - 1;
// System.out.println("Checking if "+swimmingAgentPosition.toString()+" above boundary layer");
// Now calculate the top of the boundary layer at the y, z coordinate.
int j = (int) (swimmingAgentPosition.y / domain._resolution);
int k = (int) (swimmingAgentPosition.z / domain._resolution);
double boundaryAtThisPoint = domain._topOfBoundaryLayer[j + 1][k + 1];
boundaryAtThisPoint *= domain._resolution;
// System.out.println("..."+(swimmingAgentPosition.x > boundaryAtThisPoint));
// Check if we are above it
return (swimmingAgentPosition.x > boundaryAtThisPoint);
}
/**
* \brief For self-attachment scenarios, initialises agents on the boundary layer rather than
* substrarum, and models their swim to the surface or biofilm
*
* <p>For self-attachment scenarios, the agents are initialised at the top of the boundary layer
* rather than on the substratum. These agents then perform a 'run and tumble' motion until they
* either attach to the substratum or forming biofilm. This method captures this behaviour for
* cells that are created for a time step. Once this swimming action has been performed, the agent
* is created at its final position. Note that input of agents onto the boundary layer is decided
* by a parameter set in the protocol file, cellAttachmentFrequency, measured in hours. The number
* of cells is adjusted to suit the global time step that is being used. Also note that this
* injection of cells can be for a set period (specified in the protocol file as parameter
* cellInjectionPeriod), or can be stopped and started (modelling a 'settling' period) using
* parameters cellInjectionOffPeriod and cellInjectionStopHour. This is explained in detail in the
* tutorial for version 1.2 of iDynoMiCS.
*
* @param spRoot The Species markup from the protocol file for one particular species being
* initialised
* @param numberAttachedInjectedAgents The number of agents of this type that need to be created
* in this global timestep
*/
public void createBoundaryLayerPop(XMLParser spRoot, int numberAttachedInjectedAgents) {
LogFile.writeLog(
"\t\tAttempting to create "
+ numberAttachedInjectedAgents
+ " agents of "
+ speciesName
+ " in the boundary layer");
// Create all the required agents
// Note that this continues UNTIL THE DESIRED NUMBER OF CELLS HAVE ATTACHED SOMEWHERE
// Just out of interest, I've decided to keep a count of how many cells are required for this to
// happen
int totalNumberOfInjectedAgents = 0;
int agentsReturnedToBulk = 0;
int requiredNumAttachedAgents = numberAttachedInjectedAgents;
// Temporary DiscreteVector to make finding the boundary layer tidier.
DiscreteVector dV = new DiscreteVector();
while (numberAttachedInjectedAgents > 0) {
totalNumberOfInjectedAgents++;
if (_progenitor instanceof LocatedAgent) {
swimmingAgentPosition.reset();
// Now to choose coordinates for this particular agent
while (true) {
// This cell needs to take a random location in the Z and Y
// directions. The X will come from the position of the
// boundary layer on those axes. Generate these randomly.
swimmingAgentPosition.y = ExtraMath.getUniRandDbl() * domain.length_Y;
if (domain.is3D) {
swimmingAgentPosition.z = ExtraMath.getUniRandDbl() * domain.length_Z;
}
// Now to work out the X coordinate. This is based on where
// the top of the boundary layer is when this agent is
// created. The top of the boundary layer is calculated in
// Domain at each step. Now the resolution differs (this is
// in nI x nJ x nK rather than microns - so this will need
// to be converted accordingly. Method to calculate this:
// - get the value from the top of the boundary layer
// - reduce by 1 (such that the micron value will be the
// top of the layer)
// - multiply by resolution of this domain.
dV.set(swimmingAgentPosition, domain._resolution);
if (!domain.is3D) dV.k = 1;
swimmingAgentPosition.x = domain._topOfBoundaryLayer[dV.j][dV.k] - 1.0;
swimmingAgentPosition.x *= domain._resolution;
// Check this is ok.
// System.out.println("Trying starting position "+dV.toString()+" =>
// "+this.swimmingAgentPosition.toString());
if (domain.testCrossedBoundary(swimmingAgentPosition) == null) break;
}
// Now we can do the run and tumble motion of these cells
int cellRunResult = performRunAndTumble(spRoot);
// If increment the relevant counters, as these may be useful
switch (cellRunResult) {
case 1: // Successfully Attached
numberAttachedInjectedAgents--;
// Create the agent at these coordinates
((LocatedAgent) _progenitor).createNewAgent(this.swimmingAgentPosition);
// System.out.println("Cell "+swimmingAgentPosition.toString()+" attached");
break;
case 2:
// System.out.println("Cell at "+swimmingAgentPosition.toString()+" returned to bulk");
agentsReturnedToBulk++;
break;
}
} else {
// If this isn't a located species, just create a new agent.
_progenitor.createNewAgent();
}
}
// Write the stats to the log file incase of interest
LogFile.writeLog(
requiredNumAttachedAgents
+ " agents of species "
+ speciesName
+ " for self-attachment successfully created");
LogFile.writeLog(
totalNumberOfInjectedAgents + " agents of species " + speciesName + " attempted to attach");
LogFile.writeLog(
agentsReturnedToBulk + " agents of species " + speciesName + " returned to the bulk");
}