public void removeClot(int node_id)
{
VascularNode nd = this.vascular_system.Find(x => x.id == node_id);
Thread thr = this.node2thread[nd];
thr.removeClot(nd);
}
public BoundaryCondition(VascularNode _core_node, double start_time)
{
core_node = _core_node;
//Only 1 neughbour is possible for terminal node
neighbour_node = _core_node.neighbours[0];
current_time = start_time;
previous_time = current_time - TIMEGAP;
v_sign = new int[2];
DefineSign();
}
public override void removeClot(VascularNode nd)
{
int clt_id = clotes.FindIndex(x => x.c_nd == nd);
if (clt_id != -1)
{
Clot clt = clotes[clt_id];
clt.tgr_degree = 0.0;
clotes[clt_id] = clt;
}
}
public override bool setFFRClot(VascularNode nd, float FFR_degree)
{
int nd_id = 0;
for (int i = 0; i < nodes.GetLength(0); i++)
{
if (nodes[i] == nd)
{
nd_id = i; break;
}
}
if (clotes.FindIndex(x => x.c_nd == nd) == -1)
{
FFRClot clt = new FFRClot(current_time, GlobalDefs.FRICTION_C);
clt.nd = new List <VascularNode>();
int L = 2;
if (nd_id - L - 1 >= 0)
{
clt.proximal_nd = nodes[nd_id - L - 1];
}
else
{
return(false);
}
if (nd_id + L + 1 < nodes.GetLength(0))
{
clt.distal_nd = nodes[nd_id + L + 1];
}
else
{
return(false);
}
for (int i = -L; i < L + 1; i++)
{
if (nd_id + i >= 0 && nd_id + i < nodes.GetLength(0))
{
clt.nd.Add(nodes[nd_id + i]);
}
}
clt.thread_id = nd_id;
clt.init();
ffr_clotes.Add(clt);
return(true);
}
return(false);
}
public bool setCloth(int node_id, float degree)
{
VascularNode nd = this.vascular_system.Find(x => x.id == node_id);
try {
Thread thr = this.node2thread[nd];
foreach (var child in nd.neighbours)
{
var th = this.node2thread[child];
}
return(thr.setClot(nd, degree));
// return (thr.setFFRClot(nd, degree));
} catch (Exception) {
return(false);
}
}
public bool update_clot(double curr_time, double heart_period)
{
double dt = curr_time - last_time;
last_time = curr_time;
p_pressure_acc += proximal_nd.pressure * dt;
d_pressure_acc += distal_nd.pressure * dt;
av_flux_acc += proximal_nd.velocity * proximal_nd.lumen_sq * dt;
if (curr_time % heart_period <= dt)
{
proximal_pressure = p_pressure_acc / heart_period;
p_pressure_acc = 0;
distal_pressure = d_pressure_acc / heart_period;
d_pressure_acc = 0;
av_flux = Math.Abs(av_flux_acc);
av_flux_acc = 0;
if (proximal_pressure < distal_pressure)
{
VascularNode tmp = proximal_nd;
double tmp_p = proximal_pressure;
proximal_nd = distal_nd;
distal_nd = tmp;
proximal_pressure = distal_pressure;
distal_pressure = tmp_p;
}
curr_ffr = distal_pressure / proximal_pressure;
effective_visc = effective_visc * (1 + 4 * (curr_ffr - tg_ffr));
//(1 - tg_ffr) / length / alpha / Math.PI * proximal_pressure / av_flux;
return(true);
}
return(false);
}
public Knot(VascularNode _core_node, double start_time)
{
core_node = _core_node;
nodes = (VascularNode[])core_node.neighbours.ToArray().Clone();
int L = nodes.GetLength(0);
velocity = new double[L];
pressure = new double[L];
lumen_sq = new double[L];
for (int i = 0; i < core_node.neighbours.Count; i++)
{
lumen_sq[i] = core_node.neighbours[i].lumen_sq_0;
}
DefineSigns();
current_time = start_time;
previous_time = current_time - 1e-3;
}
public override bool setClot(VascularNode nd, float degree)
{
int nd_id = 0;
for (int i = 0; i < nodes.GetLength(0); i++)
{
if (nodes[i] == nd)
{
nd_id = i; break;
}
}
if (clotes.FindIndex(x => x.c_nd == nd) == -1)
{
Clot clt = new Clot();
clt.c_nd = nd;
clt.normal_lumen = new List <double>();
clt.nd = new List <VascularNode>();
int L = 2;
for (int i = -L; i < L + 1; i++)
{
if (nd_id + i >= 0 && nd_id + i < nodes.GetLength(0))
{
clt.nd.Add(nodes[nd_id + i]);
clt.normal_lumen.Add(lumen_sq_0[nd_id + i]);
}
}
clt.tgr_degree = degree;
clt.curr_degree = 0;
clt.thread_id = nd_id;
clotes.Add(clt);
return(true);
}
return(false);
}
public virtual void removeClot(VascularNode nd)
{
}
public virtual bool setFFRClot(VascularNode nd, float FFR_degree)
{
return(false);
}
public void defineNodeDirVectors(int[] initial_set, out getFloatValueDelegate getProximaDst, out setFloatValueDelegate setProximaDst)
{
float curr_value = 0;
List <VascularNode> curr_front;
curr_front = new List <VascularNode>();
List <VascularNode> tmp_curr_front = new List <VascularNode>();
foreach (var id in initial_set)
{
curr_front.Add(vascular_system[0]);
}
getFloatValueDelegate get_del;
setFloatValueDelegate set_del;
VascularNode.newFloatValueLayer(out get_del, out set_del);
foreach (var n in curr_front)
{
set_del(n, curr_value);
}
while (true)
{
foreach (var n in curr_front)
{
foreach (var ng in n.neighbours)
{
if (get_del(ng) > curr_value)
{
set_del(ng, curr_value);
tmp_curr_front.Add(ng);
}
}
}
if (curr_front.Count == 0)
{
break;
}
curr_front = new List <VascularNode>(tmp_curr_front);
tmp_curr_front.Clear();
curr_value += 1.0f;
}
foreach (var n in vascular_system)
{
if (n.neighbours.Count < 3)
{
//Console.WriteLine(n.id);
//if (n.id == 1717)
//{
// Console.WriteLine("1");
//}
//Console.WriteLine(get_del(n.neighbours.First()));
//Console.WriteLine(get_del(n));
if (n.neighbours.Last().position < n.neighbours.First().position)
{
n.neighbours.Reverse();
}
n.defDirVector();
}
}
getProximaDst = get_del;
setProximaDst = set_del;
}
static public bool LoadTopologyFromString(string text, out VascularNet r_vnet)
{
ILoadVascularNet vnet = new VascularNet();
System.Threading.Thread.CurrentThread.CurrentCulture = System.Globalization.CultureInfo.CreateSpecificCulture("en-US");
string[] readText = text.Split(new[] { '\r', '\n' });
Regex regex = new Regex(@"^name:\s*(\w+)$", RegexOptions.IgnoreCase);
int i = 0;
while (!regex.IsMatch(readText[i]))
{
i++;
if (i >= readText.Length)
{
throw new TopReadingException("No correct name of vascular system in found\n");
}
}
Match name_match = regex.Match(readText[i]);
vnet.name = name_match.Groups[1].Value;
Regex regex_1 = new Regex(@"^Coordinates:\s*$", RegexOptions.IgnoreCase);
Regex regex_2 = new Regex(@"^Bonds:\s*$", RegexOptions.IgnoreCase);
List <List <int> > bonds_index = new List <List <int> >();
int node_count = 0;
int bond_string_count = 0;
while (true)
{
i++;
if (regex_1.IsMatch(readText[i]))
{
while (true)
{
i++;
if (i >= readText.Length)
{
break;
}
//regex = new Regex(@"^\s*(\d+)\s+X:(-*\d+.\d+)\s+Y:(-*\d+.\d+)\s+Z:(-*\d+.\d+)\s+R:(-*\d+.\d+)\s+C:(\d+.\d+)$", RegexOptions.IgnoreCase);
regex = new Regex(@"^\s*(\d+)\s+L:(-*\d+.\d+)\s+R:(-*\d+.\d+)\s+E:(-*\d+.\d+)\s+T:(-*\d+)$", RegexOptions.IgnoreCase);
Match node_match = regex.Match(readText[i]);
if (node_match.Groups.Count < 4)
{
//regex = new Regex(@"^\s*(\d+)\s+X:(-*\d+.\d+)\s+Y:(-*\d+.\d+)\s+Z:(-*\d+.\d+)\s+R:(-*\d+.\d+)$", RegexOptions.IgnoreCase);
regex = new Regex(@"^\s*(\d+)\s+L:(-*\d+.\d+)\s+R:(-*\d+.\d+)$", RegexOptions.IgnoreCase);
node_match = regex.Match(readText[i]);
if (node_match.Groups.Count < 4)
{
break;
}
}
int id = int.Parse(node_match.Groups[1].Value);
//convert to meter from millimeter
Vector1 position = new Vector1(double.Parse(node_match.Groups[2].Value) * 1e-3);
double rad = double.Parse(node_match.Groups[3].Value);
double elasticity = double.Parse(node_match.Groups[4].Value) * 1e6;
int nodetype = int.Parse(node_match.Groups[5].Value);
vnet.vascular_system.Add(new VascularNode(id, position, rad * 1e-3, elasticity, nodetype));
node_count++;
}
}
else
if (regex_2.IsMatch(readText[i]))
{
while (true)
{
i++;
if (i >= readText.Length)
{
break;
}
regex = new Regex(@"(\d+)\s*", RegexOptions.IgnoreCase);
MatchCollection node_match = regex.Matches(readText[i]);
if (node_match.Count < 2)
{
break;
}
int id = int.Parse(node_match[0].Value);
bonds_index.Add(new List <int>());
bonds_index[bonds_index.Count - 1].Add(id);
for (int n = 1; n < node_match.Count; n++)
{
bonds_index[bonds_index.Count - 1].Add(int.Parse(node_match[n].Value));
}
bond_string_count++;
}
}
if (i >= readText.Length - 1)
{
foreach (var str in bonds_index)
{
VascularNode nd = vnet.vascular_system.Find(x => x.id == str[0]);
for (int s = 1; s < str.Count; s++)
{
nd.addNeighbours(new VascularNode[] { vnet.vascular_system.Find(x => x.id == str[s]) });
}
}
break;
}
}
r_vnet = (VascularNet)vnet;
return(false);
}
public void defineNet(getFloatValueDelegate getProximalDistance, setFloatValueDelegate setProximalDistance, List <ClotNode> ClotNodes)
{
int count_id = vascular_system.Count;
foreach (var n in vascular_system)
{
n.defDirVector();
}
// this we should get from import
List <VascularNode> knot_nodes = getSubsystem(x => x.nodetype == 1);
List <VascularNode> term_nodes = getSubsystem(x => x.nodetype == 2);
for (int i = 0; i < ClotNodes.Count; i++)
{
ClotNodes[i].Node = vascular_system.Find(x => x.id == ClotNodes[i].Node_id);
}
foreach (var node in ClotNodes)
{
node.Node.nodetype = 3;
}
foreach (var node in vascular_system)
{
if (node.nodetype == 3)
{
foreach (var nnode in node.neighbours)
{
if (nnode.nodetype <= 1)
{
node.nodetype = 4;
term_nodes.Add(node);
}
}
}
}
// remove connections between clot boundary and the clot (terminal definition)
foreach (var node in vascular_system)
{
if (node.nodetype >= 3)
{
List <VascularNode> dellist = new List <VascularNode>();
foreach (var nnode in node.neighbours)
{
if (nnode.nodetype == 4)
{
//term_nodes.Add(node);
dellist.Add(nnode);
}
}
foreach (var nnode in dellist)
{
node.excludeNeighbour(nnode);
nnode.excludeNeighbour(node);
}
}
}
//List<int> list = new List<int>();
//foreach (var node in ClotNodes)
//{
// list.Add(node.Clot_id);
//}
//list = list.Distinct().ToList();
////List<ClotNode> clotboundary = new List<ClotNode>();
//foreach (int clotid in list)
//{
// List<ClotNode> listnodes = new List<ClotNode>();
// foreach (var node in ClotNodes)
// {
// if (node.Clot_id == clotid)
// listnodes.Add(node);
// }
// List<VascularNode> Node1 = getSubsystem(x => x.id == listnodes[0].Node_id);
// List<VascularNode> Node2 = getSubsystem(x => x.id == listnodes[listnodes.Count - 1].Node_id);
// //clotboundary.Add(listnodes[0]);
// //clotboundary.Add(listnodes[listnodes.Count - 1]);
//}
knots = new List <Knot>();
bounds = new List <BoundaryCondition>();
foreach (var tn in term_nodes)
{
bounds.Add(new BoundaryCondition(tn, 0)); // Just abstract BC, which do nothing
}
foreach (var kn in knot_nodes)
{
knots.Add(new Knot(kn, 0)); // Just abstract knot, which do nothing and don't pass the solution through itself
}
//foreach (var kn in knot_nodes)
//{
// List<VascularNode> b_nodes = new List<VascularNode>();
// List<VascularNode> n_nodes = new List<VascularNode>(kn.neighbours);
// // change this part to switch roles for temp nodes
// foreach (var n in n_nodes)
// {
// Vector1 pos = kn.position - (kn.position - n.position) * 0.001;
// double r = Math.Sqrt(n.lumen_sq_0 / Math.PI);
// VascularNode b_n = new VascularNode(count_id, pos, r);
// b_n.neighbours.Add(kn);
// b_n.neighbours.Add(n);
// setProximalDistance(b_n, (getProximalDistance(kn) + getProximalDistance(n)) / 2);
// kn.neighbours.Remove(n);// do we need to remove neighbours?
// n.neighbours.Remove(kn);
// kn.addNeighbour(b_n);
// n.addNeighbour(b_n);
// b_nodes.Add(b_n);
// count_id++;
// }
// knots.Add(new Knot(kn, 0)); // Just abstract knot, which do nothing and don't pass the solution through itself
//}
List <string> writeText = new List <string>();
threads = new List <Thread> ();
node2thread = new Dictionary <VascularNode, Thread>();
getBoolValueDelegate isProcessed;
setBoolValueDelegate setProcessed;
VascularNode.newBoolValueLayer(out isProcessed, out setProcessed);
VascularNode curr_node;
//VascularNode next_node;
foreach (var kn in knots)
{
setProcessed(kn.core_node, true);
}
// Define threads starting from bounds
foreach (var bc in bounds)
{
curr_node = bc.core_node;
List <VascularNode> protothread = new List <VascularNode>();
while (true)
{
protothread.Add(curr_node);
setProcessed(curr_node, true);
try
{
curr_node = curr_node.neighbours.First(x => (!isProcessed(x)));
}
catch
{
break;
}
}
if (protothread.Count > 1)
{
//if(getProximalDistance(protothread.First()) > getProximalDistance(protothread.Last()))
if (protothread[1].position > protothread.Last().position)
{
protothread.Reverse();
}
threads.Add(new Thread(protothread));
foreach (var n in protothread)
{
node2thread.Add(n, threads.Last());
}
}
}
// Define threads starting from knots
foreach (var kn in knots)
{
foreach (var start in kn.nodes)
{
curr_node = start;
List <VascularNode> protothread = new List <VascularNode>();
while (true)
{
protothread.Add(curr_node);
setProcessed(curr_node, true);
try
{
curr_node = curr_node.neighbours.First(x => (!isProcessed(x)));
}
catch
{
break;
}
}
if (protothread.Count > 1)
{
//if(getProximalDistance(protothread.First()) > getProximalDistance(protothread.Last()))
if (protothread[1].position > protothread.Last().position)
{
protothread.Reverse();
}
threads.Add(new Thread(protothread));
foreach (var n in protothread)
{
node2thread.Add(n, threads.Last());
}
}
}
}
VascularNode.terminateBoolValueLayer(ref isProcessed);
}
public bool excludeNeighbour(VascularNode neighbour)
{
return(neighbours.Remove(neighbour));
}
public void addNeighbour(VascularNode neighbour)
{
neighbours.Remove(neighbour);
neighbours.Add(neighbour);
}
static public int NumOfNeigbours(VascularNode node)
{
return(node.neighbours.Count);
}
public void setOutletBC(int start_point_id, List <BodyPartInlet> parts, float Q_total, float C_total, float R_total)
{
Dictionary <int, List <VascularNode> > outlet_groups = new Dictionary <int, List <VascularNode> >();
List <VascularNode> reference_points = new List <VascularNode>();
foreach (var p in parts)
{
reference_points.AddRange(p.inlet);
}
List <VascularNode> front_0 = new List <VascularNode>();
List <VascularNode> front_1 = new List <VascularNode>();
getFloatValueDelegate get_dist;
setFloatValueDelegate set_dist;
getFloatValueDelegate get_group;
setFloatValueDelegate set_group;
VascularNode.newFloatValueLayer(out get_dist, out set_dist);
VascularNode.newFloatValueLayer(out get_group, out set_group);
VascularNode start_point = v_net.vascular_system.Find(x => x.id == start_point_id);
front_0.Add(start_point);
set_dist(start_point, 0);
/* Q_total = 0;
* for (int i = 0; i < parts.Count; i++)
* Q_total += (float)parts[i].inlet_flux.Sum();*/
while (true)
{
foreach (var n in front_0)
{
if (reference_points.Contains(n) && (!outlet_groups.ContainsKey(n.id)))
{
outlet_groups.Add(n.id, new List <VascularNode>());
set_group(n, n.id);
}
foreach (var nn in n.neighbours)
{
if (get_dist(nn) > get_dist(n))
{
set_dist(nn, get_dist(n) + 1);
if (!front_1.Contains(nn))
{
front_1.Add(nn);
set_group(nn, get_group(n));
if (outlet_groups.ContainsKey((int)get_group(n)))
{
outlet_groups[(int)get_group(n)].Add(nn);
}
}
}
}
}
front_1 = front_1.Distinct().ToList();
front_0 = new List <VascularNode>(front_1);
front_1.Clear();
if (front_0.Count == 0)
{
break;
}
}
foreach (var part in parts)
{
foreach (var root in part.inlet)
{
if (outlet_groups.ContainsKey(root.id))
{
foreach (var n in outlet_groups[root.id])
{
if (n.neighbours.Count == 1)
{
part.outlet.Add(v_net.bounds.Find(x => x.core_node == n));
}
}
}
}
}
for (int i = 0; i < parts.Count; i++)
{
double outlet_cube_summ = 0;
double inlet_cube_summ = 0;
foreach (var on in parts[i].outlet)
{
outlet_cube_summ += Math.Pow(on.core_node.radius, 3);
}
foreach (var inp_n in parts[i].inlet)
{
inlet_cube_summ += Math.Pow(inp_n.radius, 3);
}
Console.WriteLine(parts[i].name + " inlet/outlet: " + inlet_cube_summ / outlet_cube_summ);
}
for (int i = 0; i < parts.Count; i++)
{
double a_cube_outlet = 0;
double tot_inlet_flux = 0;
for (int j = 0; j < parts[i].outlet.Count; j++)
{
a_cube_outlet += Math.Pow(parts[i].outlet[j].core_node.radius, 3);
}
for (int j = 0; j < parts[i].inlet_flux.Count; j++)
{
tot_inlet_flux += parts[i].inlet_flux[j];
}
double R_part = (Q_total / tot_inlet_flux) * R_total;
foreach (PressureOutletRCR bc in parts[i].outlet)
{
double Rt = a_cube_outlet / Math.Pow(bc.core_node.radius, 3) * R_part;
// inv_tot_R += 1.0 / Rt;
double R2 = Rt - bc.R1;
if (R2 < 0)
{
R2 = 0.1;
bc.R1 = Rt - R2;
}
bc.R2 = R2;
bc.C = C_total * R_total / Rt;
}
}
}
