Exemple #1
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  /**
   * \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;
  }
Exemple #2
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 /**
  * \brief For self-attach scenarios, corrects 2D coordinates that have crossed the left of right
  * boundary (x0z and xNz)
  *
  * <p>For self-attach scenarios, corrects 2D coordinates that have crossed the left of right
  * boundary (x0z and xNz). 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 correctCrossedLeftRightBoundaries(AllBC boundaryCrossed) {
   // Cell has passed through the boundary on the left or right hand side
   // 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.y = swimmingAgentPosition.y % domain.length_Y;
   } else {
     // Can simply take the correct value of the new Y coordinate and
     // reflect it the correct side of the boundary.
     swimmingAgentPosition.y = -swimmingAgentPosition.y % domain.length_Y;
     // Now we need to change the angle to note the change of direction.
     angleOfMovingAgentXY = 2 * Math.PI - angleOfMovingAgentXY;
   }
 }
Exemple #3
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 /**
  * \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);
 }
Exemple #4
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  /**
   * \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;
    }
  }
Exemple #5
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  /**
   * \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);
  }
Exemple #6
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  /**
   * \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);
  }
Exemple #7
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  /**
   * \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");
  }