Merge pull request #209 from kreft/April_fixes

Fix for agent spawners not completing spine function initialization

src/agent/AgentHelperMethods.java

@@ -0,0 +1,56 @@
+package agent;
+
+import dataIO.Log;
+import expression.Expression;
+import idynomics.Global;
+import idynomics.Idynomics;
+import referenceLibrary.AspectRef;
+import surface.link.LinearSpring;
+import surface.link.Spring;
+import surface.link.TorsionSpring;
+import utility.Helper;
+
+public class AgentHelperMethods {
+    public static void springInitialization(Agent a)
+    {
+        Body b = (Body) a.get(AspectRef.agentBody);
+        for( Spring s : b.getSpringsToEvaluate())
+        {
+            if( s != null )
+            {
+                if( !s.ready())
+                {
+                    s.setStiffness( Helper.setIfNone( a.getDouble(AspectRef.spineStiffness),
+                            1e6));
+                    //TODO warn user if not set
+                    if( s instanceof LinearSpring)
+                    {
+                        Expression spineFun;
+                        if ( !Helper.isNullOrEmpty( a.getValue(
+                                AspectRef.agentSpineFunction )))
+                            spineFun = new Expression((String)
+                                    a.getValue(AspectRef.agentSpineFunction ));
+                        else
+                            spineFun = Global.fallback_spinefunction;
+                        s.setSpringFunction( spineFun );
+                    }
+                    else if( s instanceof TorsionSpring)
+                    {
+                        Expression torsFun = null;
+                        if ( !Helper.isNullOrEmpty(
+                                a.getValue(AspectRef.torsionFunction)))
+                            torsFun = (Expression)
+                                    a.getValue(AspectRef.torsionFunction);
+                        else
+                        {
+                            /* TODO set default maybe? */
+                            Idynomics.simulator.interupt(
+                                    "missing torsion spring function in relax");
+                        }
+                        s.setSpringFunction( torsFun );
+                    }
+                }
+            }
+        }
+    }
+}

src/agent/Body.java

@@ -230,6 +230,7 @@ public Body(Morphology morphology, double[] positionA, double[] positionB,
 			default: 
 				break;
 		}
+		this.constructBody();
 	}
 
 	/**

src/compartment/agentStaging/DistributedSpawner.java

@@ -2,6 +2,7 @@
 
 import java.util.LinkedList;
 
+import agent.AgentHelperMethods;
 import org.w3c.dom.Element;
 
 import agent.Agent;
@@ -120,6 +121,7 @@ private void spawnAgent(double[] location)
 		newAgent.set(AspectRef.agentBody, 
 				new Body( this.getMorphology(), location, 0.0, 0.0 ) );
 		newAgent.setCompartment( this.getCompartment() );
+		AgentHelperMethods.springInitialization(newAgent);
 		newAgent.registerBirth();
 	}
 }

src/compartment/agentStaging/RandomSpawner.java

@@ -1,5 +1,6 @@
 package compartment.agentStaging;
 
+import agent.AgentHelperMethods;
 import org.w3c.dom.Element;
 
 import agent.Agent;
@@ -32,6 +33,7 @@ public void spawn()
 			newRandom.set(AspectRef.agentBody, 
 					new Body( this.getMorphology(), this.getSpawnDomain() ));
 			newRandom.setCompartment( this.getCompartment() );
+			AgentHelperMethods.springInitialization(newRandom);
 			newRandom.registerBirth();
 		}
 	}

src/idynomics/Global.java

@@ -4,6 +4,7 @@
 import java.text.SimpleDateFormat;
 import java.util.Date;
 
+import expression.Expression;
 import org.w3c.dom.Element;
 
 import dataIO.Log;
@@ -382,4 +383,11 @@ public void updateSettings()
 	 * Number of digits (including leading zeros) in file numbering
 	 */
 	public static int file_number_of_digits = 5;
+
+	/**
+	 * fall back spine function for if nothing is set TODO it may be a better option to just
+	 * warn and instruct the user, function might not be the best as a default
+	 */
+	public static Expression fallback_spinefunction =
+			new Expression( "stiffness * ( dh + SIGN(dh) * dh * dh * 100.0 )" );
 }

src/processManager/library/AgentRelaxation.java

@@ -177,13 +177,13 @@ private enum Method
 	 * limit duration of biofilm compression 
 	 */
 	private double compresionDuration = 0.0;
-	
+
 	/**
 	 * TODO check whether implementation is finished
 	 * Default spine function, fall back for if none is defined by the agent.
 	 */
-	private Expression _spineFunction = 
-			new Expression( "stiffness * ( dh + SIGN(dh) * dh * dh * 100.0 )" );
+	//private Expression _spineFunction =
+	//		new Expression( "stiffness * ( dh + SIGN(dh) * dh * dh * 100.0 )" );
 
 	private Boolean _decompression;
 
@@ -274,13 +274,6 @@ public void init(Element xmlElem, EnvironmentContainer environment,
 		this.compresionDuration = Helper.setIfNone( 
 				this.getDouble(COMPRESSION_DURATION), 0.0 );
 
-		/* Set default spine function for rod type agents, this function is
-		 * used if it is not overwritten by the agent, obtain
-		 * ComponentExpression from process manager otherwise fall back default
-		 * is used. */
-		if ( ! Helper.isNullOrEmpty( this.getValue(SPINE_FUNCTION) ) )
-			this._spineFunction = new Expression((String) this.getValue(SPINE_FUNCTION));
-
 		/* Include decompression */
 		this._decompression = Helper.setIfNone( this.getBoolean(DECOMPRESSION), 
 				false);
@@ -609,7 +602,7 @@ private void springEvaluation(Agent a, Body b)
 							spineFun = new Expression((String) 
 									a.getValue(AspectRef.agentSpineFunction ));
 						else
-							spineFun = this._spineFunction;
+							spineFun = Global.fallback_spinefunction;
 						s.setSpringFunction( spineFun );
 					}
 					else if( s instanceof TorsionSpring )