/// <summary> Called on the day of emergence to get the initials leaf cohorts to appear </summary>
private void DoLeafInitilisation()
{
CohortToInitialise = leaf.CohortsAtInitialisation;
for (int i = 1; i <= leaf.TipsAtEmergence; i++)
{
InitParams = new CohortInitParams();
PotLeafTipsAppeared += 1;
CohortToInitialise += 1;
InitParams.Rank = CohortToInitialise;
AddLeafCohort?.Invoke(this, InitParams);
DoLeafTipAppearance();
leavesInitialised = true;
firstPass = true;
}
}
/// <summary>
/// Called on the day of emergence to get the initials leaf cohorts to appear
/// </summary>
public void DoEmergence()
{
CohortToInitialise = Leaf.CohortsAtInitialisation;
for (int i = 1; i <= Leaf.TipsAtEmergence; i++)
{
InitParams = new CohortInitParams();
PotLeafTipsAppeared += 1;
CohortToInitialise += 1;
InitParams.Rank = CohortToInitialise;
if (AddLeafCohort != null)
{
AddLeafCohort.Invoke(this, InitParams);
}
DoLeafTipAppearance();
}
}
/// <summary>
/// Removes nodes from main-stem in defoliation event
/// </summary>
/// <param name="NodesToRemove"></param>
public void doNodeRemoval(int NodesToRemove)
{
//Remove nodes from Structure properties
LeafTipsAppeared = Math.Max(LeafTipsAppeared - NodesToRemove, 0);
PotLeafTipsAppeared = Math.Max(PotLeafTipsAppeared - NodesToRemove, 0);
//Remove corresponding cohorts from leaf
int NodesStillToRemove = Math.Min(NodesToRemove + Leaf.ApicalCohortNo, Leaf.InitialisedCohortNo);
while (NodesStillToRemove > 0)
{
TipToAppear -= 1;
CohortToInitialise -= 1;
Leaf.RemoveHighestLeaf();
NodesStillToRemove -= 1;
}
TipToAppear = Math.Max(TipToAppear + Leaf.CohortsAtInitialisation, 1);
CohortToInitialise = Math.Max(CohortToInitialise, 1);
//Reinitiate apical cohorts ready for regrowth
if (Leaf.InitialisedCohortNo > 0) //Sone cohorts remain after defoliation
{
for (int i = 1; i <= Leaf.CohortsAtInitialisation; i++)
{
InitParams = new CohortInitParams();
CohortToInitialise += 1;
InitParams.Rank = CohortToInitialise;
if (AddLeafCohort != null)
{
AddLeafCohort.Invoke(this, InitParams);
}
}
}
else //If all nodes have been removed initalise again
{
Leaf.Reset();
InitialiseLeafCohorts.Invoke(this, args);
Initialised = true;
DoEmergence();
}
}
/// <summary> Removes nodes from main-stem in defoliation event </summary>
public void DoNodeRemoval(int NodesToRemove)
{
//Remove nodes from Structure properties
LeafTipsAppeared = Math.Max(LeafTipsAppeared - NodesToRemove, 0);
PotLeafTipsAppeared = Math.Max(PotLeafTipsAppeared - NodesToRemove, 0);
//Remove corresponding cohorts from leaf
int NodesStillToRemove = Math.Min(NodesToRemove + leaf.ApicalCohortNo, leaf.InitialisedCohortNo);
while (NodesStillToRemove > 0)
{
TipToAppear -= 1;
CohortToInitialise -= 1;
leaf.RemoveHighestLeaf();
NodesStillToRemove -= 1;
}
//TipToAppear = Math.Max(TipToAppear + leaf.CohortsAtInitialisation, 1);
CohortToInitialise = Math.Max(CohortToInitialise, 1);
if (CohortToInitialise == LeafTipsAppeared) // If leaf appearance had reached final leaf number need to add another cohort back to get things moving again.
{
CohortToInitialise += 1;
}
InitParams = new CohortInitParams()
{
};
InitParams.Rank = CohortToInitialise;
if (AddLeafCohort != null)
{
AddLeafCohort.Invoke(this, InitParams);
}
//Reinitiate apical cohorts ready for regrowth
if (leaf.InitialisedCohortNo == 0) //If all nodes have been removed initalise again
{
leaf.Reset();
InitialiseLeafCohorts.Invoke(this, new EventArgs());
DoLeafInitilisation();
}
}
private void OnDoPotentialPlantGrowth(object sender, EventArgs e)
{
if (cohortsInitialised)
{
DeltaHaunStage = 0;
if (phyllochron.Value() > 0)
{
DeltaHaunStage = thermalTime.Value() / phyllochron.Value();
}
if (leavesInitialised)
{
bool AllCohortsInitialised = (leaf.InitialisedCohortNo >= finalLeafNumber.Value());
AllLeavesAppeared = (leaf.AppearedCohortNo == leaf.InitialisedCohortNo);
bool LastLeafAppearing = ((Math.Truncate(LeafTipsAppeared) + 1) == leaf.InitialisedCohortNo);
if ((AllCohortsInitialised) && (LastLeafAppearing))
{
// fixme - this guard is really a bandaid over some problems in the leaf cohort code
// which seems to assume that growth duration is never 0. Can't set NextLeafProp to
// 0, because then GrowthDuration will be 0. However it can be close to 0 if final leaf #
// happens to have a very small fractional part (e.g. 14.00001).
// If your crop is never progressing to flag leaf, this might be why (try reducing epsilon).
NextLeafProportion = Math.Max(1e-10, 1 - (leaf.InitialisedCohortNo - finalLeafNumber.Value()));
}
else
{
NextLeafProportion = 1.0;
}
//Increment MainStemNode Number based on phyllochorn and theremal time
if (firstPass == true)
{
firstPass = false;
DeltaTipNumber = 0; //Don't increment node number on day of emergence
}
else
{
DeltaTipNumber = DeltaHaunStage; //DeltaTipNumber is only positive after emergence whereas deltaHaunstage is positive from germination
}
PotLeafTipsAppeared += DeltaTipNumber;
LeafTipsAppeared = Math.Min(PotLeafTipsAppeared, finalLeafNumber.Value());
TimeForAnotherLeaf = PotLeafTipsAppeared >= (leaf.AppearedCohortNo + 1);
int LeavesToAppear = (int)(LeafTipsAppeared - (leaf.AppearedCohortNo - (1 - NextLeafProportion)));
//Each time main-stem node number increases by one or more initiate the additional cohorts until final leaf number is reached
if (TimeForAnotherLeaf && (AllCohortsInitialised == false))
{
int i = 1;
for (i = 1; i <= LeavesToAppear; i++)
{
CohortToInitialise += 1;
InitParams = new CohortInitParams()
{
};
InitParams.Rank = CohortToInitialise;
if (AddLeafCohort != null)
{
AddLeafCohort.Invoke(this, InitParams);
}
}
}
//Each time main-stem node number increases by one appear another cohort until all cohorts have appeared
if (TimeForAnotherLeaf && (AllLeavesAppeared == false))
{
int i = 1;
for (i = 1; i <= LeavesToAppear; i++)
{
TotalStemPopn += branchingRate.Value() * MainStemPopn;
BranchNumber += branchingRate.Value();
TotalLeavesPerShoot += BranchNumber + 1;
DoLeafTipAppearance();
}
}
//Reduce population if there has been plant mortality
if (DeltaPlantPopulation > 0)
{
TotalStemPopn -= DeltaPlantPopulation * TotalStemPopn / plant.Population;
}
//Reduce stem number incase of mortality
double PropnMortality = 0;
PropnMortality = branchMortality.Value();
{
double DeltaPopn = Math.Min(PropnMortality * (TotalStemPopn - MainStemPopn), TotalStemPopn - plant.Population);
TotalStemPopn -= DeltaPopn;
ProportionBranchMortality = PropnMortality;
}
}
}
}
private void OnDoPotentialPlantGrowth(object sender, EventArgs e)
{
if (Plant.IsGerminated)
{
DeltaHaunStage = 0;
if (Phyllochron.Value() > 0)
{
DeltaHaunStage = ThermalTime.Value() / Phyllochron.Value();
}
if (Germinated == false) // We have no leaves set up and nodes have just started appearing - Need to initialise Leaf cohorts
{
Germinated = true;
//On the day of germination set up the first cohorts
if (InitialiseLeafCohorts != null)
{
InitialiseLeafCohorts.Invoke(this, args);
}
Initialised = true;
}
if (Plant.IsEmerged)
{
if (Emerged == false)
{
NextLeafProportion = 1.0;
DoEmergence();
}
bool AllCohortsInitialised = (Leaf.InitialisedCohortNo >= FinalLeafNumber.Value());
bool AllLeavesAppeared = (Leaf.AppearedCohortNo == Leaf.InitialisedCohortNo);
bool LastLeafAppearing = ((Math.Truncate(LeafTipsAppeared) + 1) == Leaf.InitialisedCohortNo);
if ((AllCohortsInitialised) && (LastLeafAppearing))
{
NextLeafProportion = 1 - (Leaf.InitialisedCohortNo - FinalLeafNumber.Value());
}
else
{
NextLeafProportion = 1.0;
}
//Increment MainStemNode Number based on phyllochorn and theremal time
if (Emerged == false)
{
Emerged = true;
DeltaTipNumber = 0; //Don't increment node number on day of emergence
}
else
{
DeltaTipNumber = DeltaHaunStage; //DeltaTipNumber is only positive after emergence whereas deltaHaunstage is positive from germination
}
PotLeafTipsAppeared += DeltaTipNumber;
//if (PotLeafTipsAppeared > MainStemFinalNodeNumber.Value)
// FinalLeafDeltaTipNumberonDayOfAppearance = PotLeafTipsAppeared - MainStemFinalNodeNumber.Value;
LeafTipsAppeared = Math.Min(PotLeafTipsAppeared, FinalLeafNumber.Value());
bool TimeForAnotherLeaf = PotLeafTipsAppeared >= (Leaf.AppearedCohortNo + 1);
int LeavesToAppear = (int)(LeafTipsAppeared - (Leaf.AppearedCohortNo - (1 - NextLeafProportion)));
//Each time main-stem node number increases by one or more initiate the additional cohorts until final leaf number is reached
if (TimeForAnotherLeaf && (AllCohortsInitialised == false))
{
int i = 1;
for (i = 1; i <= LeavesToAppear; i++)
{
CohortToInitialise += 1;
InitParams = new CohortInitParams()
{
};
InitParams.Rank = CohortToInitialise;
if (AddLeafCohort != null)
{
AddLeafCohort.Invoke(this, InitParams);
}
}
}
//Each time main-stem node number increases by one appear another cohort until all cohorts have appeared
if (TimeForAnotherLeaf && (AllLeavesAppeared == false))
{
int i = 1;
for (i = 1; i <= LeavesToAppear; i++)
{
TotalStemPopn += BranchingRate.Value() * MainStemPopn;
BranchNumber += BranchingRate.Value();
DoLeafTipAppearance();
}
// Apex calculation
ApexNum += (BranchingRate.Value() - BranchMortality.Value()) * PrimaryBudNo;
if (Phenology.Stage > 4 & !SenescenceByAge)
{
double senescenceNum = Leaf.ApexNumByAge(StemSenescenceAge.Value());
ApexNum -= senescenceNum;
SenescenceByAge = true;
TotalStemPopn -= senescenceNum * Plant.Population;
}
}
//Reduce population if there has been plant mortality
if (DeltaPlantPopulation > 0)
{
TotalStemPopn -= DeltaPlantPopulation * TotalStemPopn / Plant.Population;
}
//Reduce stem number incase of mortality
double PropnMortality = 0;
PropnMortality = BranchMortality.Value();
{
double DeltaPopn = Math.Min(PropnMortality * (TotalStemPopn - MainStemPopn), TotalStemPopn - Plant.Population);
TotalStemPopn -= DeltaPopn;
ProportionBranchMortality = PropnMortality;
}
}
}
}
private void OnDoPotentialPlantGrowth(object sender, EventArgs e)
{
if (cohortsInitialised)
{
DeltaHaunStage = 0;
if (phyllochron.Value() > 0)
{
DeltaHaunStage = thermalTime.Value() / phyllochron.Value();
}
if (leavesInitialised)
{
bool AllCohortsInitialised = (leaf.InitialisedCohortNo >= finalLeafNumber.Value());
AllLeavesAppeared = (leaf.AppearedCohortNo == leaf.InitialisedCohortNo);
bool LastLeafAppearing = ((Math.Truncate(LeafTipsAppeared) + 1) == leaf.InitialisedCohortNo);
if ((AllCohortsInitialised) && (LastLeafAppearing))
{
NextLeafProportion = 1 - (leaf.InitialisedCohortNo - finalLeafNumber.Value());
}
else
{
NextLeafProportion = 1.0;
}
//Increment MainStemNode Number based on phyllochorn and theremal time
if (firstPass == true)
{
firstPass = false;
DeltaTipNumber = 0; //Don't increment node number on day of emergence
}
else
{
DeltaTipNumber = DeltaHaunStage; //DeltaTipNumber is only positive after emergence whereas deltaHaunstage is positive from germination
}
PotLeafTipsAppeared += DeltaTipNumber;
LeafTipsAppeared = Math.Min(PotLeafTipsAppeared, finalLeafNumber.Value());
TimeForAnotherLeaf = PotLeafTipsAppeared >= (leaf.AppearedCohortNo + 1);
int LeavesToAppear = (int)(LeafTipsAppeared - (leaf.AppearedCohortNo - (1 - NextLeafProportion)));
//Each time main-stem node number increases by one or more initiate the additional cohorts until final leaf number is reached
if (TimeForAnotherLeaf && (AllCohortsInitialised == false))
{
int i = 1;
for (i = 1; i <= LeavesToAppear; i++)
{
CohortToInitialise += 1;
InitParams = new CohortInitParams()
{
};
InitParams.Rank = CohortToInitialise;
if (AddLeafCohort != null)
{
AddLeafCohort.Invoke(this, InitParams);
}
}
}
//Each time main-stem node number increases by one appear another cohort until all cohorts have appeared
if (TimeForAnotherLeaf && (AllLeavesAppeared == false))
{
int i = 1;
for (i = 1; i <= LeavesToAppear; i++)
{
TotalStemPopn += branchingRate.Value() * MainStemPopn;
BranchNumber += branchingRate.Value();
DoLeafTipAppearance();
}
}
//Reduce population if there has been plant mortality
if (DeltaPlantPopulation > 0)
{
TotalStemPopn -= DeltaPlantPopulation * TotalStemPopn / plant.Population;
}
//Reduce stem number incase of mortality
double PropnMortality = 0;
PropnMortality = branchMortality.Value();
{
double DeltaPopn = Math.Min(PropnMortality * (TotalStemPopn - MainStemPopn), TotalStemPopn - plant.Population);
TotalStemPopn -= DeltaPopn;
ProportionBranchMortality = PropnMortality;
}
}
}
}