//! Load the diffusion reactions from an array of files and a Medium list
/*!
* \param files Array of files which contain information about diffusion reaction.
* \param mediums The list of all the mediums.
*
* This function loads the diffusion reactions based on Fick model. It takes an Array of file paths
* and a list of Medium that should contain all the mediums of the simulation.
* This function creates the list of all the reactions between all Medium which exist and initialize their parameters to 0.
* Only the reactions explicitly defined in files are initialized to the values explicited in files.
* If a parameter of a fick reaction is not specified in files then this parameter will be equal to 0.
*/
public void loadFicksReactionsFromFiles(string[] files, LinkedList <Medium> mediums)
{
Logger.Log("Fick::loadFicksReactionsFromFiles("
+ Logger.EnumerableToString <string> (files)
+ ") starts"
, Logger.Level.INFO);
LinkedList <FickProperties> propsList = new LinkedList <FickProperties> ();
LinkedList <FickProperties> newPropList;
foreach (string file in files)
{
newPropList = loadObjectsFromFile <FickProperties> (file, "ficks");
if (newPropList != null)
{
LinkedListExtensions.AppendRange <FickProperties> (propsList, newPropList);
}
}
_reactions = FickReaction.getFickReactionsFromMediumList(mediums);
finalizeFickReactionFromProps(propsList, _reactions);
Logger.Log("Fick::loadFicksReactionsFromFiles("
+ Logger.EnumerableToString <string> (files)
+ ") starts"
, Logger.Level.INFO);
}
public FickReaction(FickReaction r) : base(r)
{
_surface = r._surface;
_P = r._P;
_medium1 = r._medium1;
_medium2 = r._medium2;
}
public FickReaction(FickReaction r) : base(r)
{
_surface = r._surface;
_P = r._P;
_medium1 = r._medium1;
_medium2 = r._medium2;
}
void OnTriggerEnter(Collider collider)
{
Logger.Log("PhenoFickContact::OnTriggerEnter collider=" + collider, Logger.Level.DEBUG);
PhysicalMedium PMext = collider.gameObject.GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter collider.PMext == null", Logger.Level.TRACE);
return;
}
int colliderMediumIdExt = PMext.MediumId;
Medium colliderMediumExt = ReactionEngine.getMediumFromId(colliderMediumIdExt, _reactionEngine.getMediumList());
if (colliderMediumExt == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter The collided medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
PhysicalMedium PM = GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter this.PMext == null", Logger.Level.TRACE);
return;
}
int mediumId = PM.MediumId;
Medium medium = ReactionEngine.getMediumFromId(mediumId, _reactionEngine.getMediumList());
if (medium == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter The medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
float surface = Math.Min(PM.Size, PMext.Size);
Fick fick = _reactionEngine.getFick();
FickReaction reaction = Fick.getFickReactionFromIds(colliderMediumIdExt, mediumId, fick.getFickReactions());
if (reaction == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter This FickReaction does not exist.", Logger.Level.WARN);
return;
}
reaction.setSurface(surface);
// set medium as medium of collider
Logger.Log("colliderMediumIdExt : " + colliderMediumIdExt, Logger.Level.INFO);
configureExternalDisplays(colliderMediumIdExt);
_collidedMediumIds.AddLast(colliderMediumIdExt);
/*
* Logger.Log("PhenoFickContact::OnTriggerEnter"
+" reaction.setSurface("+surface+")"
+" _collidedMediumIds.Count="+_collidedMediumIds.Count
+" _collidedMediumIds.Last.Value="+_collidedMediumIds.Last.Value
* ,Logger.Level.);
*/
}
/* !
* \brief Checks that two reactions have the same FickReaction field values.
* \param reaction The reaction that will be compared to 'this'.
*/
protected override bool PartialEquals(IReaction reaction)
{
FickReaction fick = reaction as FickReaction;
return((fick != null) &&
base.PartialEquals(reaction) &&
(_surface == fick._surface) &&
(_P == fick._P) &&
_medium1.Equals(fick._medium1) &&
_medium2.Equals(fick._medium2));
//TODO check Medium equality
}
public static IReaction buildFickReactionFromProps(FickProperties props, LinkedList <Medium> mediums)
{
FickReaction reaction = new FickReaction();
Medium med1 = ReactionEngine.getMediumFromId(props.MediumId1, mediums);
Medium med2 = ReactionEngine.getMediumFromId(props.MediumId2, mediums);
if (med1 == null || med2 == null)
{
Debug.Log("failed to build FickReaction from FickProperties beacause one or all the medium id don't exist");
return(null);
}
reaction.setSurface(props.surface);
reaction.setPermCoef(props.P);
reaction.setMedium1(med1);
reaction.setMedium2(med2);
reaction.setEnergyCost(props.energyCost);
return(reaction);
}
//! Return all the FickReactions possible from a Medium list.
/*!
* \param mediums The list of mediums.
*
* \details
* This function return all the possible combinaisons of FickReaction in Medium list.
*
* Example :
* - Medium1 + Medium2 + Medium3 = FickReaction(1, 2) + FickReaction(1, 3) + FickReaction(2, 3)
*/
public static LinkedList <FickReaction> getFickReactionsFromMediumList(LinkedList <Medium> mediums)
{
FickReaction newReaction;
LinkedListNode <Medium> node;
LinkedListNode <Medium> start = mediums.First;
LinkedList <FickReaction> fickReactions = new LinkedList <FickReaction>();
while (start != null)
{
node = start.Next;
while (node != null)
{
newReaction = new FickReaction();
newReaction.setMedium1(start.Value);
newReaction.setMedium2(node.Value);
fickReactions.AddLast(newReaction);
node = node.Next;
}
start = start.Next;
}
return(fickReactions);
}
//! Return all the FickReactions possible from a Medium list.
/*!
\param mediums The list of mediums.
\details
This function return all the possible combinaisons of FickReaction in Medium list.
Example :
- Medium1 + Medium2 + Medium3 = FickReaction(1, 2) + FickReaction(1, 3) + FickReaction(2, 3)
*/
public static LinkedList<FickReaction> getFickReactionsFromMediumList(LinkedList<Medium> mediums)
{
FickReaction newReaction;
LinkedListNode<Medium> node;
LinkedListNode<Medium> start = mediums.First;
LinkedList<FickReaction> fickReactions = new LinkedList<FickReaction>();
while (start != null)
{
node = start.Next;
while (node != null)
{
newReaction = new FickReaction();
newReaction.setMedium1(start.Value);
newReaction.setMedium2(node.Value);
fickReactions.AddLast(newReaction);
node = node.Next;
}
start = start.Next;
}
return fickReactions;
}
public static IReaction buildFickReactionFromProps(FickProprieties props, LinkedList<Medium> mediums)
{
FickReaction reaction = new FickReaction();
Medium med1 = ReactionEngine.getMediumFromId(props.MediumId1, mediums);
Medium med2 = ReactionEngine.getMediumFromId(props.MediumId2, mediums);
if (med1 == null || med2 == null)
{
Debug.Log("failed to build FickReaction from FickProprieties beacause one or all the medium id don't exist");
return null;
}
reaction.setSurface(props.surface);
reaction.setPermCoef(props.P);
reaction.setMedium1(med1);
reaction.setMedium2(med2);
reaction.setEnergyCost(props.energyCost);
return reaction;
}
public void OnTriggerExit(Collider collider)
{
Logger.Log("PhenoFickContact::OnTriggerExit collider=" + collider, Logger.Level.DEBUG);
PhysicalMedium PMext = collider.gameObject.GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit collider.PMext == null", Logger.Level.TRACE);
return;
}
int colliderMediumIdExt = PMext.MediumId;
Medium colliderMediumExt = ReactionEngine.getMediumFromId(colliderMediumIdExt, _reactionEngine.getMediumList());
if (colliderMediumExt == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit The collided medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
PhysicalMedium PM = GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit this.PMext == null", Logger.Level.TRACE);
return;
}
int mediumId = PM.MediumId;
Medium medium = ReactionEngine.getMediumFromId(mediumId, _reactionEngine.getMediumList());
if (medium == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit The medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
// un-set medium as medium of collider
_collidedMediumIds.Remove(colliderMediumIdExt);
//string nullLast = (null != _collidedMediumIds.Last)?_collidedMediumIds.Last.Value.ToString():"null";
/*
* Logger.Log("PhenoFickContact::OnTriggerExit"
+" _collidedMediumIds.Count="+_collidedMediumIds.Count
+" _collidedMediumIds.Last.Value="+nullLast
* ,Logger.Level.);
*/
//Logger.Log("PhenoFickContact::OnTriggerExit _collidedMediumIds.Last.Value="+nullLast, Logger.Level.);
if (null != _collidedMediumIds.Last)
{
// TODO consider the current medium as superposition of mediums the ids of which are _collidedMediumIds
configureExternalDisplays(_collidedMediumIds.Last.Value);
}
else
{
//not in any Fick contact anymore
configureExternalDisplays(_vectroPanelInitMediumId);
Fick fick = _reactionEngine.getFick();
FickReaction reaction = Fick.getFickReactionFromIds(colliderMediumIdExt, mediumId, fick.getFickReactions());
if (reaction == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit This FickReaction does not exist.", Logger.Level.WARN);
}
reaction.setSurface(0);
}
}