Field Detail

• BallList

  public ArrayList<Balloon> BallList

• ipb

  public ij.process.ImageProcessor ipb

• N

  public int N

• id

  public int id

• topo

  public boolean[][] topo

• IMB

  public int[][][] IMB

• contacts

  public int[][] contacts

• ref_topo

  public Matrix ref_topo

• area

  public int area

• XXi

  public int[] XXi

• YYi

  public int[] YYi

• max_n0

  public int max_n0

• max_length

  public int max_length

Constructor Detail

• BalloonPopulation

  public BalloonPopulation(ij.process.ImageProcessor ip,
                           int index,
                           int rgbchannel)

  BalloonPopulation constructor: need to specify the image processor it is associated with and the id of the population

Method Detail

• AddNewBalloon

  public void AddNewBalloon(int[] X,
                            int[] Y)

  Add a balloon with custom shape defined by arrays X and Y

• AddNewBalloon

  public void AddNewBalloon(int x,
                            int y)

  Add a circular balloon centrerd on x,y with id ID

• importSeeds

  public void importSeeds(String directory,
                          String file_name)

  Add a circular balloon centrerd on x,y with id ID

• remove

  public void remove(int i)

  remove balloon i

• clear

  public void clear()

  clear all balloons in population

• ConnectExistingBalloons

  public void ConnectExistingBalloons()

  initialise the contact data structure used when loading from file because connectivity is not saved currently (TODO)

• ConnectRefinedBalloons

  public void ConnectRefinedBalloons()

  initialise the contact data structure after refine

• sample

  public void sample(float HL)

  PLace randomly seeds on the image

• EnvelopBoundaries

  public void EnvelopBoundaries()

  Find envelop delimiting the boundaries of the population

• refineStructure

  public void refineStructure()

  Refine the structure of the balloons

• InitiateGrowingRegion

  public void InitiateGrowingRegion()

• MakeTopo

  public void MakeTopo()

  Initiate the matrix of cells in contact (the "contacts" 2D array) by null contacts, and set the potential connection (the "topo" 2D array) for checking during expansion of balloons by a modified delaunay algorithm

• Tick_inflate

  public void Tick_inflate(int PixLevel,
                           int t)

  perform a time step of the physical engine for all balloons in the population by calling the Inflate_inc method in balloon Checks for contacts

• Tick_inflate

  public void Tick_inflate(int PixLevel)

• Tick_contact

  public void Tick_contact(Balloon B)

  perform a contact check from the potential connection "topo" identified before running the expansion

• set_boundaries

  public void set_boundaries(int[][][] B)

  set the matrix of inside/outside pixels IMB and compute the area occupied by the colony

• modify_boundaries

  public void modify_boundaries(int[] XXi,
                                int[] YYi)

  Modify the boundaries given a new set of coordinates

• calc_area

  public void calc_area()

  compute the area occupied by the colony

• mass_Geometry

  public void mass_Geometry()

  Determines the geometric properties of each cell, by running the mass_geometry method for every cell in the population

• Draw_kinematics

  public ij.process.ColorProcessor Draw_kinematics()

  Use the image prossessor associated with the population of cell and use the Fill_balloon method to add a plot of the each balloon

• Draw_lineage

  public ij.process.ColorProcessor Draw_lineage(int seq)

  Use the image prossessor associated with the population of cell and use the Fill_balloon method to add a plot of the each balloon

• CenterList

  public int[][] CenterList()

  Produce an array with centers of balloons