public GOTerm(SimulationParameters.GOTermParam termParams)
{
name = termParams.termName;
description = termParams.description;
pValue = termParams.pValue;
weight = termParams.startingValue;
}
public FinalCell(Vector3 position, SimulationParameters.SimpleBehaviorParam behaviorConfig, int startingFood)
: base(position, startingFood)
{
cellBehaviors = new SimpleBehaviorAggregate(behaviorConfig);
this.generation = 1;
initializeFinalCell();
checkChildProbabilities(this);
}
public BlastCell(Vector3 position, SimulationParameters.SimpleBehaviorParam behaviorConfig, int startingFood)
: base(position, startingFood)
{
cellBehaviors = new SimpleBehaviorAggregate(behaviorConfig);
Console.WriteLine("creating first blast cell at: " + position);
initializeBlastCell();
checkChildProbabilities(this);
}
public Environment(SimulationParameters simulationParams)
{
instance = this;
firstCorner = simulationParams.environmentFirstCorner;
secondCorner = simulationParams.environmentSecondCorner;
BlastCellTotal = 0;
FinalCellTotal = 0;
MutatedCellTotal = 0;
tissues = new List<Tissue>();
foreach (SimulationParameters.TissueParameters tissueParam in simulationParams.tissueParams)
{
tissues.Add(new Tissue(tissueParam));
}
cells = new List<TissueCell>();
newCells = new List<TissueCell>();
dyingCells = new List<TissueCell>();
signals = new List<Signal>();
newSignals = new List<Signal>();
expiredSignals = new List<Signal>();
pressurePoints = new List<LocationContents>();
Console.WriteLine("setting up environment matrix");
environmentMatrix = new LocationContents[(int)secondCorner.X + 1, (int)secondCorner.Y + 1, (int)secondCorner.Z + 1];
createMatrix(firstCorner, secondCorner);
Console.WriteLine("setting up initial pressure around the [" + tissues.Count + "] tissue(s)");
foreach(Tissue t in tissues)
setupPressureAroundTissue(t, simulationParams.SectorPressureDistance, simulationParams.SectorPressureInitial, simulationParams.SectorPressureIncrement);
Console.WriteLine("setting up sectors");
sectorMap = new Sector[(int)secondCorner.X + 1, (int)secondCorner.Y + 1, (int)secondCorner.Z + 1];
List<Sector> sectors = sectorSetup(simulationParams.SectorHeight, simulationParams.SectorWidth, simulationParams.SectorDepth);
Console.WriteLine("there are [" + sectors.Count + "] total sectors");
Console.WriteLine("creating location->sector map");
CreateSectorMap(sectors);
Console.WriteLine("initializing circulatory system");
circulatorySystem = new CirculatorySystem(simulationParams.PipeParams, simulationParams.PipeCorners);
Console.WriteLine("setting up initial pressue around the pipes");
setupPressureAroundPipes(circulatorySystem, simulationParams.PipePressureDistance, simulationParams.PipePressureInitial, simulationParams.PipePressureIncrement);
Console.WriteLine("initializing cells");
Console.WriteLine("behavior: " + simulationParams.behaviorType);
BlastCell.InitializeDivideProbabilities(simulationParams.cellParameters.BlastCellDivideIntoBlastProbability, simulationParams.cellParameters.BlastCellDivideIntoFinalProbability);
initializeCells(simulationParams.startingCells, simulationParams.behaviorType);
}
public BlastCell(Vector3 position, SimulationParameters.GOTermBehaviorParams behaviorConfig, int startingFood)
: base(position, startingFood)
{
throw new NotImplementedException("haven't tested GO behavior");
//insantiate go behavior aggregate
//cellBehaviors = new GOBehaviorAggregate(behaviorConfig, this);
Console.WriteLine("creating first blast cell at: " + position);
initializeBlastCell();
checkChildProbabilities(this);
}
public CirculatorySystem(SimulationParameters.PipeParameters pipeParams, SimulationParameters.PipeLocations pipeCorners)
{
instance = this;
this.pipeShrinkRate = pipeParams.PipeShrink;
pipeCells = new List<EndothelialCell>();
hungryCells = new List<TissueCell>();
growingPipes = new List<GrowingPipe>();
maxNumGrowthsPerTurn = pipeParams.MaxGrowthPerTurn;
EndothelialCell root = new EndothelialCell(pipeCorners.location, pipeParams.PipeRootOrientation, pipeParams.PipeStartingWidth, null);
setupPipes(root, pipeCorners.children);
}
public Tissue(SimulationParameters.TissueParameters tissueParams)
{
firstCorner = tissueParams.firstCorner;
secondCorner = tissueParams.secondCorner;
}
public FinalCell(Vector3 position, SimulationParameters.GOTermBehaviorParams behaviorConfig, int startingFood)
: base(position, startingFood)
{
throw new NotImplementedException("havent tested GO behaviors");
}
private void initializeCells(List<SimulationParameters.CellStartConfig> startingCells, SimulationParameters.BehaviorTypes cellBehaviorType)
{
foreach (SimulationParameters.CellStartConfig cellConfig in startingCells)
{
if (!GoodPoint(cellConfig.location))
throw new Exception("invalid cell start location " + cellConfig.location + "... it isn't part of tissue [" + firstCorner + "," + secondCorner + "]");
if (cellBehaviorType == SimulationParameters.BehaviorTypes.SimpleBehaviors)
{
if (cellConfig.cellType == typeof(BlastCell))
AddNewCell(new BlastCell(cellConfig.location, cellConfig.simpleBehavior, cellConfig.startingFood));
else if (cellConfig.cellType == typeof(FinalCell))
AddNewCell(new FinalCell(cellConfig.location, cellConfig.simpleBehavior, cellConfig.startingFood));
else
throw new Exception("unsupported cell type [" + cellConfig.cellType + "]");
}
else if (cellBehaviorType == SimulationParameters.BehaviorTypes.GOBehaviors)
throw new NotImplementedException("haven't tested GO behaviors yet");
else
throw new Exception("unsupported cell behavior type");
}
}
public SimpleBehaviorAggregate(SimulationParameters.SimpleBehaviorParam startingValues)
{
if (startingValues.startingDivideRate == 0)
Console.WriteLine("possible invalid divide rate param");
divideBehavior = new SimpleDivide(startingValues.startingDivideRate);
SimpleDivide.MaxValue = 1.0;
SimpleDivide.MinValue = 0.0;
if (startingValues.startingDeathRate == 0)
Console.WriteLine("possible invalid death rate param");
deathBehavior = new SimpleDeathBehavior(startingValues.startingDeathRate);
SimpleDeathBehavior.MaxValue = 1.0;
SimpleDeathBehavior.MinValue = 0.0;
if (startingValues.startingPressureToleranceAtLocation == 0)
Console.WriteLine("possible invalid pressure tol @ location param");
pressureToleranceAtLocation = new SimplePressureToleranceAtLocation(startingValues.startingPressureToleranceAtLocation);
SimplePressureToleranceAtLocation.MaxValue = SimulationCore.Instance.SimulationParams.cellParameters.MaxPressureToleranceAtLocation;
SimplePressureToleranceAtLocation.MinValue = SimulationCore.Instance.SimulationParams.cellParameters.MinPressureToleranceAtLocation;
if (startingValues.startingPressureToleranceAtNeighbors == 0)
Console.WriteLine("possible invalid perssure tol @ neighbors param");
pressureToleranceAtNeighbors = new SimplePressureToleranceAtNeighbors(startingValues.startingPressureToleranceAtNeighbors);
SimplePressureToleranceAtNeighbors.MaxValue = SimulationCore.Instance.SimulationParams.cellParameters.MaxPressureToleranceAtNeighbors;
SimplePressureToleranceAtNeighbors.MinValue = SimulationCore.Instance.SimulationParams.cellParameters.MinPressureToleranceAtNeighbors;
if (startingValues.FoodConsumptionRate == 0)
Console.WriteLine("possible inavlid food consumption rate param");
foodConsumptionBehavior = new SimpleFoodConsumptionRate(startingValues.FoodConsumptionRate);
SimpleFoodConsumptionRate.MaxValue = SimulationCore.Instance.SimulationParams.cellParameters.MaxFoodConsumptionRate;
SimpleFoodConsumptionRate.MinValue = SimulationCore.Instance.SimulationParams.cellParameters.MinFoodConsumptionRate;
if (startingValues.FoodMaxStorage == 0)
Console.WriteLine("possible invalid food max storage rate param");
foodMaxStorage = new SimpleFoodMaxStorage(startingValues.FoodMaxStorage);
SimpleFoodMaxStorage.MaxValue = SimulationCore.Instance.SimulationParams.cellParameters.MaxFoodStorage;
SimpleFoodMaxStorage.MinValue = SimulationCore.Instance.SimulationParams.cellParameters.MinFoodStorage;
if (startingValues.FoodConcernLevel == 0)
Console.WriteLine("possible invalid food concern lvl param");
foodConcern = new SimpleFoodConcern(startingValues.FoodConcernLevel);
SimpleFoodConcern.MaxValue = SimulationCore.Instance.SimulationParams.cellParameters.MaxFoodConcernLevel;
SimpleFoodConcern.MinValue = SimulationCore.Instance.SimulationParams.cellParameters.MinFoodConcernLevel;
//if (startingValues.MoveProbability == 0)
// Console.WriteLine("possible invalid move probablity param");
moveAbility = new SimpleMove(startingValues.MoveProbability);
SimpleMove.MaxValue = 1.0;
SimpleMove.MinValue = 0.0;
pipeEnter = new SimplePipeEnter(startingValues.EnterPipeProbability);
SimplePipeEnter.MaxValue = 1.0;
SimplePipeEnter.MinValue = 0.0;
pipeLeave = new SimplePipeLeave(startingValues.LeavePipeProbability);
SimplePipeLeave.MaxValue = 1.0;
SimplePipeLeave.MinValue = 0.0;
pipeSurvival = new SimplePipeSurvival(startingValues.SurvivePipeProbability);
SimplePipeSurvival.MaxValue = 1.0;
SimplePipeSurvival.MinValue = 0.0;
callPipeProbability = new SimpleCallPipe(startingValues.CallPipeProbability);
SimpleCallPipe.MaxValue = 1.0;
SimpleCallPipe.MinValue = 0.0;
}
private VertexPositionColor[] getSingleTissueBorderVertices(SimulationParameters.TissueParameters tissueParams)
{
// cubes are drawn from center of 3d coordinate, they spill over 0.5 units into surrounding locations
// because of this, need to offset border vertices for clean look
Vector3 first = tissueParams.firstCorner - new Vector3(0.5f, 0.5f, 0.5f);
Vector3 second = tissueParams.secondCorner + new Vector3(0.5f, 0.5f, 0.5f);
VertexPositionColor a = new VertexPositionColor(first, tissueBorderColor);
VertexPositionColor b = new VertexPositionColor(new Vector3(first.X, first.Y, second.Z), tissueBorderColor);
VertexPositionColor c = new VertexPositionColor(new Vector3(second.X, first.Y, second.Z), tissueBorderColor);
VertexPositionColor d = new VertexPositionColor(new Vector3(second.X, first.Y, first.Z), tissueBorderColor);
VertexPositionColor e = new VertexPositionColor(new Vector3(first.X, second.Y, first.Z), tissueBorderColor);
VertexPositionColor f = new VertexPositionColor(new Vector3(first.X, second.Y, second.Z), tissueBorderColor);
VertexPositionColor g = new VertexPositionColor(second, tissueBorderColor);
VertexPositionColor h = new VertexPositionColor(new Vector3(second.X, second.Y, first.Z), tissueBorderColor);
VertexPositionColor[] tissueBorderVertices = {a,b, b,c, c,d, d,a, a,e, b,f, c,g, d,h, e,f, f,g, g,h, h,e};
return tissueBorderVertices;
}
public void StartSimulation(String configName)
{
Console.WriteLine("reading config file [" + configName + "]");
SimulationParameters simulationParams = readParamsFromFile(configName); //new SimulationParameters();
this.SimulationParams = simulationParams;
Console.WriteLine("instantiating environment");
environment = new Environment(simulationParams);
Console.WriteLine("setting up tissue borders");
tissueBorderVertices = getTissueBorderVertices(simulationParams.tissueParams);
Console.WriteLine("initializing camera");
Console.WriteLine("eye: " + simulationParams.CameraEye);
Console.WriteLine("look at: " + simulationParams.CameraLookAt);
initializeCamera(simulationParams.CameraEye, simulationParams.CameraLookAt);
runningSimulation = true;
allowMovement = false;
}
