//! 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); } }