public void Cylinder34Squamous2Columnar2(float scaleH)
{
//int gridSize = 2;
//int ySize = 3;
//innerRadius = new Vector(.5f, .5f, .5f);
//innerRadius0 = new Vector(r, 1f, r);
Mesh m = new Cylinder34(new Vector(.5f, .5f, .5f));
targetVertices = m.GetVertexPositions();
innerRadius.y *= scaleH;
Vector nucleus = new Vector(0, -.5f, 0);
for (int i = 0; i < vertices.getCount(); i++)
{
//Vector vec = new Vector();
//vec.x = 2 * innerRadius.x * vec.x / gridSize - innerRadius.x;
targetVertices[i].y = targetVertices[i].y * scaleH;
//vec.z = 2 * innerRadius.z * vec.z / gridSize - innerRadius.z;
}
for (int i = 0; i < nbOfParticles; i++)
{
nucleusEdges[i].l0 = (targetVertices[i] - nucleus).norm();
}
for (int j = 0; j < edgeCount(); j++)
{
edges[j].l0 = Vector.Distance(targetVertices[edges[j].ends[0].pos], targetVertices[edges[j].ends[1].pos]);
}
}
public override void SetupSimulation()
{
nbOfSimulationSteps = 2000;
logFrequency = 10;
//logVTK = true;
popSize = 8;
popMaxSize = 64;
Cylinder34 mesh = new Cylinder34(new Vector(.5f, 1f, .5f), false);
Tissue t1 = new Tissue(8, popMaxSize, mesh);
List <Tissue> tissueList = new List <Tissue>()
{
t1
};
nbCellTypes = tissueList.Count;
cellPopulation = new CellPopulation(popSize, popMaxSize, tissueList, 2);
Helper.SetNCubedInN(popMaxSize);
cellPopulation.PositionCells(false);
}
public void CloseEPI2()
{
Cylinder34 cy = new Cylinder34(new Vector(.5f, 1f, .5f), false);
int[] lookUp = cy.LookUp();
int[] ring = new int[] { 58, 59, 60, 61, 62, 65, 66, 67, 68, 69, 72, 73, 74, 75, 76, 79, 80, 81, 82, 83, 86, 87, 88, 89, 90 };
/*
* List<int> TE = new List<int>(){ 50, 51, 52, 53, 54,
* 55, 56, 57, 58, 59,
* 60, 61, 62, 63, 64,
* 65, 66, 67, 68, 69,
* 70, 71, 72, 73, 74};
* //*/
//*
List <int> TE = new List <int>();
for (int i = 0; i < 49; i++)
{
TE.Add(50 + i);
}
//*/
int[] pFoyer = { 6, 7, 8, 11, 12, 13, 16, 17, 18 };
int[] pZmin = { 0, 1, 2, 3, 4 };
int[] pXmax = { 4, 9, 14, 19, 24 };
int[] pZmax = { 24, 23, 22, 21, 20 };
int[] pXmin = { 20, 15, 10, 5, 0 };
//int[] cSup = { 25, 27, 29, 31, 32 };
int[] cSup = { 24, 25, 26, 27, 28, 29, 30, 31, 32 };
int[] cZmin = cy.CZmin().ToArray();
int[] cZmax = cy.CZmax().ToArray();
int[] cXmin = cy.CXmin().ToArray();
int[] cXmax = cy.CXmax().ToArray();
int edgeCount = 0;
List <Edge> newEdges = new List <Edge>();
for (int i = 0; i < pZmin.Length; i++)
{
for (int j = 0; j < cZmin.Length; j++)
{
//Console.WriteLine(pZmin[i] + ", " + cZmin[j]);
Edge edge = new Edge(cells[pZmin[i]].vertices[cZmin[j]], cells[pZmin[i] + 25].vertices[lookUp[cZmin[j]]]);
newEdges.Add(edge);
edgeCount++;
}
}
for (int i = 0; i < pZmax.Length; i++)
{
for (int j = 0; j < cZmax.Length; j++)
{
Edge edge = new Edge(cells[pZmax[i]].vertices[cZmax[j]], cells[pZmax[i] + 25].vertices[lookUp[cZmax[j]]]);
//Edge edge = new Edge(cells[pZmax[i]].vertices[cZmax[j]], cells[pZmax[i] + 25].vertices[cZmax[j]]);
newEdges.Add(edge);
edgeCount++;
}
}
for (int i = 0; i < pXmin.Length; i++)
{
for (int j = 0; j < cXmin.Length; j++)
{
Edge edge = new Edge(cells[pXmin[i]].vertices[cXmin[j]], cells[pXmin[i] + 25].vertices[lookUp[cXmin[j]]]);
//Edge edge = new Edge(cells[pZmin[i]].vertices[cXmin[j]], cells[pZmin[i] + 25].vertices[cXmin[j]]);
newEdges.Add(edge);
edgeCount++;
}
}
for (int i = 0; i < pXmax.Length; i++)
{
for (int j = 0; j < cXmax.Length; j++)
{
Edge edge = new Edge(cells[pXmax[i]].vertices[cXmax[j]], cells[pXmax[i] + 25].vertices[lookUp[cXmax[j]]]);
newEdges.Add(edge);
edgeCount++;
}
}
for (int i = 0; i < pFoyer.Length; i++)
{
for (int j = 0; j < cSup.Length; j++)
{
Edge edge = new Edge(cells[pFoyer[i]].vertices[cSup[j]], cells[pFoyer[i] + 25].vertices[lookUp[cSup[j]]]);
for (int n = 0; n < edge.ends[1].externalNeighbours.Count; n++)
{
int l = edge.ends[1].externalNeighbours[n][0];
int k = edge.ends[1].externalNeighbours[n][1];
Edge e1 = new Edge(edge.ends[0], cells[l].vertices[k]);
newEdges.Add(e1);
}
newEdges.Add(edge);
edgeCount++;
}
}
//newEdges = newEdges.Distinct().ToList<Edge>();
newEdges = Helper.Distinct(newEdges);
int count = 0;
//*
for (int i = 0; i < newEdges.Count; i++)
{
count++;
Vector midPoint = (newEdges[i].ends[0].v + newEdges[i].ends[1].v) * .5;
newEdges[i].ends[0].v = new Vector(midPoint);
newEdges[i].ends[1].v = new Vector(midPoint);
Vertex v0 = newEdges[i].ends[0];
Vertex v1 = newEdges[i].ends[1];
/*
* if(v0.cellId == 22 && v0.pos == 4 && v1.cellId == 47 && v1.pos == 2)
* {
* for (int j = 0; j < v1.externalNeighbours.Count; j++)
* {
* int l = v1.externalNeighbours[j][0];
* int k = v1.externalNeighbours[j][1];
*
* //Console.WriteLine(l + ", " + k);
* }
* }
*/
//*
for (int j = 0; j < v0.externalNeighbours.Count; j++)
{
int l = v0.externalNeighbours[j][0];
int k = v0.externalNeighbours[j][1];
if (l != v1.cellId)
{
Edge newEdge = new Edge(v1, cells[l].vertices[k]);
cells[v1.cellId].externalEdges.add(newEdge);
cells[l].externalEdges.add(new Edge(cells[l].vertices[k], v1));
//v1.externalNeighbours.Add(new int[] { l, k });
}
}
for (int j = 0; j < v1.externalNeighbours.Count; j++)
{
int l = v1.externalNeighbours[j][0];
int k = v1.externalNeighbours[j][1];
//cells[l].vertices[k].v = new Vector(v1.v);
if (l != v0.cellId)
{
if (TE.Contains(l))// && !TE.Contains(l))
{
Edge newEdge = new Edge(v1, cells[l].vertices[k]);
cells[v1.cellId].externalEdges.remove(newEdge);
cells[l].externalEdges.remove(new Edge(cells[l].vertices[k], v1));
}
else
{
Edge newEdge = new Edge(v0, cells[l].vertices[k]);
cells[v0.cellId].externalEdges.add(newEdge);
cells[l].externalEdges.add(new Edge(cells[l].vertices[k], v0));
//v0.externalNeighbours.Add(new int[] { l, k });
}
}
}
//*/
v0.externalNeighbours.Add(new int[] { v1.cellId, v1.pos });
v1.externalNeighbours.Add(new int[] { v0.cellId, v0.pos });
cells[newEdges[i].ends[0].cellId].externalEdges.add(newEdges[i]);
cells[newEdges[i].ends[1].cellId].externalEdges.add(new Edge(newEdges[i].ends[1], newEdges[i].ends[0]));
}
//*/
int[] corners = new int[] { 0, 4, 24, 20 };
for (int i = 0; i < corners.Length; i++)
{
Cylinder34 cl = new Cylinder34(new Vector(.5f, 1f, .5f), false);
cl.ApicalConstrictionWithPositionChange(.4f, Vector.up);
Cylinder34 clDown = new Cylinder34(new Vector(.5f, 1f, .5f), false);
clDown.ApicalConstrictionWithPositionChange(.4f, Vector.down);
Vector normal = new Vector();
Vector normal25 = new Vector();
if (i == 0)
{
normal = new Vector(cl.vertices[0].v.x, 0, cl.vertices[0].v.z);
//normal25 = new Vector(cl.vertices[4].v.x, 0, cl.vertices[4].v.z);
normal25 = new Vector(cl.vertices[6].v.x, 0, cl.vertices[6].v.z);
}
if (i == 1)
{
normal = new Vector(cl.vertices[2].v.x, 0, cl.vertices[2].v.z);
//normal25 = new Vector(cl.vertices[6].v.x, 0, cl.vertices[6].v.z);
normal25 = new Vector(cl.vertices[4].v.x, 0, cl.vertices[4].v.z);
}
if (i == 2)
{
normal = new Vector(cl.vertices[4].v.x, 0, cl.vertices[4].v.z);
//normal25 = new Vector(cl.vertices[0].v.x, 0, cl.vertices[0].v.z);
normal25 = new Vector(cl.vertices[2].v.x, 0, cl.vertices[2].v.z);
}
if (i == 3)
{
normal = new Vector(cl.vertices[6].v.x, 0, cl.vertices[6].v.z);
//normal25 = new Vector(cl.vertices[2].v.x, 0, cl.vertices[2].v.z);
normal25 = new Vector(cl.vertices[0].v.x, 0, cl.vertices[0].v.z);
}
cells[corners[i]].SetElengths(cl.Slice(normal, true));
cells[corners[i] + 25].SetElengths(clDown.Slice(normal25, false));
//for(int )
//cells[corners[i]].SetElengths(cl.Slice(normal, true));
//cells[corners[i] + 25].SetElengths(clDown.Slice(normal25, true));
//cells[corners[i] + 25].SetEdgeELengths();
}
}
