public void SetCellNeighbourhood(int cellId)
{
MGCell cell = cells[cellId];
cell.neighbours.Clear();
if (MGModel.hexagonalNeighbourhoodForCells)
{
cell.neighbours = Helper.GetHexagonalNeighbourhood3D(cellId, maxPopulationSize, populationSize);
//Console.WriteLine("Hexagonal");
}
else if (MGModel.mooreNeighbourhoodForCells)
{
//cell.neighbours = Helper.GetMooreNeighbourhood3D(cellId, maxPopulationSize, populationSize);
cell.neighbours = Helper.GetMooreNeighbourhood3D(cellId, dim, populationSize);
//Console.WriteLine(maxPopulationSize + ", " + populationSize);
}
else
{
//Console.WriteLine("Population Size: " + populationSize);
//Console.WriteLine("Cell ID: " + cellId);
for (int i = 0; i < populationSize; i++)
{
double distance = Vector.Distance(cell.GetPosition(), cells[i].GetPosition());
if (i != cellId && distance < MGModel.maximumNeighbourDistance && cell.neighbours.Count < 26)
{
cell.neighbours.Add(i);
//Console.WriteLine(cellId + ":" + cell.GetPosition() + ", " + i + ":" + cells[i].GetPosition() + ", " + distance + ", " + MGModel.maximumNeighbourDistance);
}
}
}
}
public CellPopulation(int popMaxSize, List <Tissue> tissueList)
{
Simulator.interCellEdges = new StringBuilder();
Simulator.interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
populationSize = 0;
maxPopulationSize = popMaxSize;
cells = new MGCell[popMaxSize];
sigma = new int[popMaxSize];
double d = Math.Round(Math.Pow(maxPopulationSize, 1f / 3f));
dim = new Vector(d, d, d);
halfDim = dim / 2;
tissues = tissueList;
int start = 0;
for (int i = 0; i < tissueList.Count; i++)
{
tissues[i].indices = new int[tissues[i].maxPopulationSize];
start += i == 0 ? 0 : tissueList[i - 1].populationSize;
for (int j = 0; j < tissueList[i].populationSize; j++)
{
int index = start + j;
cells[index] = new MGCell(index, tissueList[i].cells[j]);
cells[index].tissueName = tissueList[i].name;
tissues[i].indices[j] = index;
tissues[i].cells[j] = cells[index];
sigma[index] = index;
}
populationSize += tissueList[i].populationSize;
}
}
public void CreatePopulation(int popSize, int popMaxSize)
{
//interCellEdges = new StringBuilder();
//interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
Simulator.interCellEdges = new StringBuilder();
Simulator.interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
populationSize = popSize;
maxPopulationSize = popMaxSize;
cells = new MGCell[popMaxSize];
sigma = new int[maxPopulationSize];
dim = new Vector(Math.Pow(maxPopulationSize, 1f / 3f), Math.Pow(maxPopulationSize, 1f / 3f), Math.Pow(maxPopulationSize, 1f / 3f));
halfDim = dim / 2;
contacts = new int[maxPopulationSize];
contactsIndices = new int[maxPopulationSize];
for (int i = 0; i < populationSize; i++)
{
cells[i] = new MGCell(i);
//Console.WriteLine("Created cell " + i + ", " + cells[i].cellId);
}
tissues = new List <Tissue>();
}
public void AddCell(MGCell cell)
{
if (populationSize < maxPopulationSize)
{
cells[populationSize] = cell;
populationSize++;
}
}
public void AddCell(int tissueId, MGCell cell)
{
if (populationSize < maxPopulationSize)
{
tissues[tissueId].AddCell(cell);
cells[populationSize] = cell;
populationSize++;
}
}
public CellPopulation(int popSize, int popMaxSize, List <Tissue> tissueList, short cellType, bool randomCycleTime)
{
//interCellEdges = new StringBuilder();
//interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
Simulator.interCellEdges = new StringBuilder();
Simulator.interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
populationSize = popSize;
maxPopulationSize = popMaxSize;
//Console.WriteLine(popMaxSize);
cells = new MGCell[popMaxSize];
sigma = new int[popMaxSize];
double d = Math.Round(Math.Pow(maxPopulationSize, 1f / 3f));
dim = new Vector(d, d, d);
halfDim = dim / 2;
contacts = new int[maxPopulationSize];
contactsIndices = new int[maxPopulationSize];
tissues = tissueList;
int start = 0;
Random rand = new Random(0);
for (int i = 0; i < tissueList.Count; i++)
{
tissues[i].indices = new int[tissues[i].maxPopulationSize];
start += i == 0 ? 0 : tissueList[i - 1].populationSize;
for (int j = 0; j < tissueList[i].populationSize; j++)
{
int index = start + j;
cells[index] = new MGCell(index, tissueList[i].mesh);
cells[index].tissueId = i;
cells[index].tissueName = tissueList[i].name;
tissues[i].indices[j] = index;
tissues[i].cells[j] = cells[index];
sigma[index] = index;
cells[index].cycleTime = 0;// rand.Next(MGModel.cellCyclePeriod);
contactsIndices[index] = index;
contacts[index] = 0;
}
}
}
public CellPopulation(int popSize, int popMaxSize, List <Tissue> tissueList, short cellType)
{
Simulator.interCellEdges = new StringBuilder();
Simulator.interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
populationSize = popSize;
maxPopulationSize = popMaxSize;
cells = new MGCell[popMaxSize];
sigma = new int[popMaxSize];
double d = Math.Round(Math.Pow(maxPopulationSize, 1f / 3f));
dim = new Vector(d, d, d);
halfDim = dim / 2;
contacts = new int[maxPopulationSize];
contactsIndices = new int[maxPopulationSize];
tissues = tissueList;
int start = 0;
for (int i = 0; i < tissueList.Count; i++)
{
tissues[i].indices = new int[tissues[i].maxPopulationSize];
start += i == 0 ? 0 : tissueList[i - 1].populationSize;
for (int j = 0; j < tissueList[i].populationSize; j++)
{
int index = start + j;
switch (cellType)
{
case 1: cells[index] = new RedBloodCell(index, tissueList[i].mesh); break;
case 2: cells[index] = new EpithelialCell(index, tissueList[i].mesh); break;
default: cells[index] = new MGCell(index, tissueList[i].mesh); break;
}
//cells[index] = new MGCell(index, tissueList[i].mesh);
cells[index].tissueName = tissueList[i].name;
tissues[i].indices[j] = index;
tissues[i].cells[j] = cells[index];
sigma[index] = index;
contactsIndices[index] = index;
contacts[index] = 0;
}
}
}
public void AddTissue(Tissue tissue)
{
int i = tissues.Count;
tissue.indices = new int[tissue.maxPopulationSize];
int start = populationSize;
for (int j = 0; j < tissue.populationSize; j++)
{
int index = start + j;
cells[index] = new MGCell(index, tissue.mesh);
tissue.indices[j] = index;
tissue.cells[j] = cells[index];
sigma[index] = index;
}
tissues.Add(tissue);
populationSize += tissue.populationSize;
}
public void CreatePopulation(int popSize, int popMaxSize)
{
//interCellEdges = new StringBuilder();
//interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
Simulator.interCellEdges = new StringBuilder();
Simulator.interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
populationSize = popSize;
maxPopulationSize = popMaxSize;
cells = new MGCell[popMaxSize];
sigma = new int[maxPopulationSize];
dim = new Vector(Math.Pow(maxPopulationSize, 1f / 3f), Math.Pow(maxPopulationSize, 1f / 3f), Math.Pow(maxPopulationSize, 1f / 3f));
halfDim = dim / 2;
for (int i = 0; i < populationSize; i++)
{
cells[i] = new MGCell(i);
}
}
public CellPopulation(int popSize, Vector dim)
{
Simulator.interCellEdges = new StringBuilder();
Simulator.interCellEdges.AppendLine("frame,cell1,p1,cell2,p2");
populationSize = popSize;
maxPopulationSize = (int)(dim.x * dim.y * dim.z);
cells = new MGCell[maxPopulationSize];
sigma = new int[maxPopulationSize];
this.dim = dim;
halfDim = dim / 2;
contacts = new int[maxPopulationSize];
contactsIndices = new int[maxPopulationSize];
for (int i = 0; i < populationSize; i++)
{
cells[i] = new MGCell(i);
contactsIndices[i] = i;
contacts[i] = 0;
}
}
void CreateCellPopulation(string folder)
{
CellProvider provider = new CellProvider();
provider.ReadParameters(folder);
provider.ReadResults();
provider.ReadParticleNeighbourhoods();
provider.PlayResults(0);
populationSize = provider.popSize;
maxPopulationSize = provider.maxPopSize;
cells = new MGCell[provider.maxPopSize];
sigma = new int[provider.maxPopSize];
contacts = new int[maxPopulationSize];
contactsIndices = new int[maxPopulationSize];
int start = 0;
tissues = new List <Tissue>(provider.nbOfCellTypes);
Random rand = new Random(0);
for (int i = 0; i < provider.nbOfCellTypesPerFrame[provider.nbOfFrames - 1]; i++)
{
//Console.WriteLine(provider.nbOfCellsPerTypePerFrame[provider.nbOfFrames - 1][i]);
tissues.Add(new Tissue(provider.nbOfCellsPerTypePerFrame[provider.nbOfFrames - 1][i], provider.maxPopSize));
tissues[i].indices = new int[tissues[i].maxPopulationSize];
start += i == 0 ? 0 : tissues[i - 1].populationSize;
for (int j = 0; j < tissues[i].populationSize; j++)
{
int index = start + j;
//Console.WriteLine(index);
cells[index] = new MGCell(index, i, provider.meshPerCell[index]);
//Console.WriteLine(index + ", " + provider.meshPerCell[index].vertexCount());
cells[index].tissueId = i;
tissues[i].indices[j] = index;
tissues[i].cells[j] = cells[index];
sigma[index] = index;
cells[index].cycleTime = rand.Next(MGModel.cellCyclePeriod);
tissues[i].reference += cells[index].ComputeCentreFromMesh();
//Console.WriteLine(cells[index].cycleTime);
contactsIndices[index] = index;
contacts[index] = 0;
}
tissues[i].mesh = provider.meshPerCell[start];
tissues[i].reference /= tissues[i].populationSize;
}
for (int i = 0; i < provider.externalEdges.Count; i++)
{
Edge edge = new Edge(cells[(int)provider.externalEdges[i].x].vertices[(int)provider.externalEdges[i].y],
cells[(int)provider.externalEdges[i].z].vertices[(int)provider.externalEdges[i].w]);
cells[(int)provider.externalEdges[i].x].externalEdges.add(edge);
cells[(int)provider.externalEdges[i].z].externalEdges.add(new Edge(edge.ends[1], edge.ends[0]));
cells[(int)provider.externalEdges[i].x].vertices[(int)provider.externalEdges[i].y].externalNeighbours.Add(new int[] {
(int)provider.externalEdges[i].z,
(int)provider.externalEdges[i].w
});
cells[(int)provider.externalEdges[i].z].vertices[(int)provider.externalEdges[i].w].externalNeighbours.Add(new int[] {
(int)provider.externalEdges[i].x,
(int)provider.externalEdges[i].y
});
if ((int)provider.externalEdges[i].x == 0 && (int)provider.externalEdges[i].y == 26)
{
//Console.WriteLine(provider.externalEdges[i].z + ", " + provider.externalEdges[i].w);
}
}
for (int i = 0; i < populationSize; i++)
{
contacts[i] = cells[i].externalEdges.getCount();
}
}
void CreateCellPopulation(string folder)
{
CellProvider provider = new CellProvider();
provider.ReadParameters(folder);
provider.ReadResults();
provider.PlayResults(0);
populationSize = provider.popSize;
maxPopulationSize = provider.maxPopSize;
cells = new MGCell[provider.maxPopSize];
sigma = new int[provider.maxPopSize];
int start = 0;
tissues = new List <Tissue>(provider.nbOfCellTypes);
/*
* for (int i = 0; i < provider.nbOfCellTypes; i++)
* {
* tissues.Add(new Tissue(provider.nbOfCellsPerType[i], provider.maxPopSize));
* tissues[i].indices = new int[tissues[i].maxPopulationSize];
*
* start += i == 0 ? 0 : tissues[i - 1].populationSize;
* for (int j = 0; j < tissues[i].populationSize; j++)
* {
* int index = start + j;
*
* //Console.WriteLine(index);
* cells[index] = new MGCell(index, provider.meshPerCell[index]);
* //Console.WriteLine(index + ", " + provider.meshPerCell[index].vertexCount());
* cells[index].tissueId = i;
*
* tissues[i].indices[j] = index;
* tissues[i].cells[j] = cells[index];
* sigma[index] = index;
* cells[index].cycleTime = new Random().Next(MGModel.cellCyclePeriod);
* tissues[i].reference += cells[index].ComputeCentreFromMesh();
* }
* tissues[i].mesh = provider.meshPerCell[start];
* tissues[i].reference /= tissues[i].populationSize;
* }
*/
for (int i = 0; i < provider.nbOfCellTypesPerFrame[provider.nbOfFrames - 1]; i++)
{
//Console.WriteLine(provider.nbOfCellsPerTypePerFrame[provider.nbOfFrames - 1][i]);
tissues.Add(new Tissue(provider.nbOfCellsPerTypePerFrame[provider.nbOfFrames - 1][i], provider.maxPopSize));
tissues[i].indices = new int[tissues[i].maxPopulationSize];
start += i == 0 ? 0 : tissues[i - 1].populationSize;
for (int j = 0; j < tissues[i].populationSize; j++)
{
int index = start + j;
//Console.WriteLine(index);
cells[index] = new MGCell(index, provider.meshPerCell[index]);
//Console.WriteLine(index + ", " + provider.meshPerCell[index].vertexCount());
cells[index].tissueId = i;
tissues[i].indices[j] = index;
tissues[i].cells[j] = cells[index];
sigma[index] = index;
cells[index].cycleTime = new Random().Next(MGModel.cellCyclePeriod);
tissues[i].reference += cells[index].ComputeCentreFromMesh();
}
tissues[i].mesh = provider.meshPerCell[start];
tissues[i].reference /= tissues[i].populationSize;
}
//Console.WriteLine(tissues.Capacity);
/*
* int cellTypeStartStates = 0;
* for (int i = 0; i < provider.nbOfCellTypes; i++)
* {
* if (i > 0) cellTypeStartStates += provider.nbOfCellsPerType[i - 1];
* for (int j = 0; j < provider.nbOfCellsPerType[i]; j++)
* {
* cells[cellTypeStartStates + j] = new MGCell(cellTypeStartStates + j, provider.meshPerCell[cellTypeStartStates + j]);
* }
* }
* //*/
}
