public override void Run()
{
if (LAI != null)
{
System.Console.WriteLine("Updating output variable: LAI");
// Total LAI per site
ISiteVar <byte> values = cohorts.GetIsiteVar(o => o.CanopyLAImax);
string FileName = FileNames.ReplaceTemplateVars(LAI.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <byte, byte>(FileName, values, o => o);
// Values per species each time step
LAI.output_table_ecoregions.WriteUpdate(PlugIn.ModelCore.CurrentTime, values);
}
if (Biomass != null)
{
System.Console.WriteLine("Updating output variable: Biomass");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <int> > Biom = cohorts.GetIsiteVar(o => o.BiomassPerSpecies);
foreach (ISpecies spc in PlugIn.SelectedSpecies)
{
ISiteVar <int> Biom_spc = modelCore.Landscape.NewSiteVar <int>();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
Biom_spc[site] = Biom[site][spc];
}
new OutputMapSpecies(Biom_spc, spc, Biomass.MapNameTemplate);
}
OutputFilePerTStepPerSpecies.Write <int>(Biomass.MapNameTemplate, Biomass.units, PlugIn.ModelCore.CurrentTime, Biom);
ISiteVar <float> Biomass_site = cohorts.GetIsiteVar(x => x.BiomassSum);
Biomass.output_table_ecoregions.WriteUpdate <float>(PlugIn.ModelCore.CurrentTime, Biomass_site);
}
if (AbovegroundBiomass != null)
{
System.Console.WriteLine("Updating output variable: Aboveground Biomass");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <int> > AGBiom = cohorts.GetIsiteVar(o => o.AbovegroundBiomassPerSpecies);
foreach (ISpecies spc in PlugIn.SelectedSpecies)
{
ISiteVar <int> AGBiom_spc = modelCore.Landscape.NewSiteVar <int>();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
AGBiom_spc[site] = AGBiom[site][spc];
}
new OutputMapSpecies(AGBiom_spc, spc, AbovegroundBiomass.MapNameTemplate);
}
OutputFilePerTStepPerSpecies.Write <int>(AbovegroundBiomass.MapNameTemplate, AbovegroundBiomass.units, PlugIn.ModelCore.CurrentTime, AGBiom);
ISiteVar <float> AGBiomass_site = cohorts.GetIsiteVar(x => x.AbovegroundBiomassSum);
AbovegroundBiomass.output_table_ecoregions.WriteUpdate <float>(PlugIn.ModelCore.CurrentTime, AGBiomass_site);
}
if (WoodySenescence != null)
{
System.Console.WriteLine("Updating output variable: Woody Senescence");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <int> > Senes = cohorts.GetIsiteVar(o => o.WoodySenescencePerSpecies);
/*
* foreach (ISpecies spc in PlugIn.SelectedSpecies)
* {
* ISiteVar<int> Senes_spc = modelCore.Landscape.NewSiteVar<int>();
*
* foreach (ActiveSite site in PlugIn.modelCore.Landscape)
* {
* Senes_spc[site] = Senes[site][spc];
*
* }
*
* new OutputMapSpecies(Senes_spc, spc, WoodySenescence.MapNameTemplate);
* }
*/
OutputFilePerTStepPerSpecies.Write <int>(WoodySenescence.MapNameTemplate, WoodySenescence.units, PlugIn.ModelCore.CurrentTime, Senes);
ISiteVar <float> Senescence_site = cohorts.GetIsiteVar(x => x.WoodySenescenceSum);
WoodySenescence.output_table_ecoregions.WriteUpdate <float>(PlugIn.ModelCore.CurrentTime, Senescence_site);
}
if (FoliageSenescence != null)
{
System.Console.WriteLine("Updating output variable: Foliage Senescence");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <int> > Senes = cohorts.GetIsiteVar(o => o.FoliageSenescencePerSpecies);
/*foreach (ISpecies spc in PlugIn.SelectedSpecies)
* {
* ISiteVar<int> Senes_spc = modelCore.Landscape.NewSiteVar<int>();
*
* foreach (ActiveSite site in PlugIn.modelCore.Landscape)
* {
* Senes_spc[site] = Senes[site][spc];
* }
*
* new OutputMapSpecies(Senes_spc, spc, FoliageSenescence.MapNameTemplate);
* }
*/
OutputFilePerTStepPerSpecies.Write <int>(FoliageSenescence.MapNameTemplate, FoliageSenescence.units, PlugIn.ModelCore.CurrentTime, Senes);
ISiteVar <float> Senescence_site = cohorts.GetIsiteVar(x => x.FoliageSenescenceSum);
FoliageSenescence.output_table_ecoregions.WriteUpdate <float>(PlugIn.ModelCore.CurrentTime, Senescence_site);
}
if (AETAvg != null)
{
ISiteVar <float> AET_site = cohorts.GetIsiteVar(x => x.AETSum);
AETAvg.output_table_ecoregions.WriteUpdate <float>(PlugIn.ModelCore.CurrentTime, AET_site);
}
if (MonthlyFolResp != null)
{
ISiteVar <float[]> monthlyFolResp = cohorts.GetIsiteVar(site => site.FolResp);
WriteMonthlyOutput(monthlyFolResp, MonthlyFolResp.MapNameTemplate);
}
if (MonthlyGrossPsn != null)
{
ISiteVar <float[]> monthlyGrossPsn = cohorts.GetIsiteVar(site => site.GrossPsn);
WriteMonthlyOutput(monthlyGrossPsn, MonthlyGrossPsn.MapNameTemplate);
}
if (MonthlyNetPsn != null)
{
ISiteVar <float[]> monthlyNetPsn = cohorts.GetIsiteVar(site => site.NetPsn);
WriteMonthlyOutput(monthlyNetPsn, MonthlyNetPsn.MapNameTemplate);
}
if (MonthlyMaintResp != null)
{
ISiteVar <float[]> monthlyMaintResp = cohorts.GetIsiteVar(site => site.MaintResp);
WriteMonthlyOutput(monthlyMaintResp, MonthlyMaintResp.MapNameTemplate);
}
if (BelowGround != null)
{
System.Console.WriteLine("Updating output variable: BelowGround");
ISiteVar <uint> values = cohorts.GetIsiteVar(o => o.BelowGroundBiomass);
string FileName = FileNames.ReplaceTemplateVars(BelowGround.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <uint, uint>(FileName, values, o => o);
}
if (CohortsPerSpc != null)
{
System.Console.WriteLine("Updating output variable: CohortsPerSpc");
// Nr of Cohorts per site and per species
ISiteVar <Landis.Library.Parameters.Species.AuxParm <int> > cps = cohorts.GetIsiteVar(x => x.CohortCountPerSpecies);
new OutputHistogramCohort <int>(CohortsPerSpc.MapNameTemplate, "CohortsPerSpcPerSite", 10).WriteOutputHist(cps);
foreach (ISpecies spc in PlugIn.SelectedSpecies)
{
string FileName = FileNames.ReplaceTemplateVars(CohortsPerSpc.MapNameTemplate, spc.Name, PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <Landis.Library.Parameters.Species.AuxParm <int>, int>(FileName, cps, o => o[spc]);
}
OutputFilePerTStepPerSpecies.WriteSum <int>(CohortsPerSpc.MapNameTemplate, CohortsPerSpc.units, PlugIn.ModelCore.CurrentTime, cps);
}
if (EstablishmentProbability != null)
{
System.Console.WriteLine("Updating output variable: EstablishmentProbability");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <byte> > pest = (ISiteVar <Landis.Library.Parameters.Species.AuxParm <byte> >)cohorts.GetIsiteVar(o => o.EstablishmentProbability.Probability);
foreach (ISpecies spc in PlugIn.SelectedSpecies)
{
ISiteVar <int> _pest = modelCore.Landscape.NewSiteVar <int>();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
_pest[site] = pest[site][spc];
}
new OutputMapSpecies(_pest, spc, EstablishmentProbability.MapNameTemplate);
}
}
if (SpeciesEstablishment != null)
{
System.Console.WriteLine("Updating output variable: SpeciesEstablishment");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <bool> > SpeciesIsThere = cohorts.GetIsiteVar(o => o.SpeciesPresent);
if (SpeciesWasThere != null)
{
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
ISiteVar <int> comp = PlugIn.modelCore.Landscape.NewSiteVar <int>();
MapComparison m = new MapComparison();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
if (SpeciesWasThere[site] == null)
{
SpeciesWasThere[site] = new Library.Parameters.Species.AuxParm <bool>(PlugIn.modelCore.Species);
}
comp[site] = m[SpeciesWasThere[site][spc], SpeciesIsThere[site][spc]];
SpeciesWasThere[site][spc] = SpeciesIsThere[site][spc];
}
OutputMapSpecies output_map = new OutputMapSpecies(comp, spc, SpeciesEstablishment.MapNameTemplate);
// map label text
m.PrintLabels(SpeciesEstablishment.MapNameTemplate, spc);
}
}
else
{
SpeciesWasThere = modelCore.Landscape.NewSiteVar <Landis.Library.Parameters.Species.AuxParm <bool> >();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
SpeciesWasThere[site] = new Library.Parameters.Species.AuxParm <bool>(PlugIn.modelCore.Species);
}
}
ISiteVar <Landis.Library.Parameters.Species.AuxParm <bool> > Established_spc = cohorts.GetIsiteVar(x => x.SpeciesPresent);
Landis.Library.Parameters.Species.AuxParm <int> Est_Sum = new Landis.Library.Parameters.Species.AuxParm <int>(PlugIn.modelCore.Species);
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
if (Established_spc[site][spc] == true)
{
Est_Sum[spc]++;
}
}
}
OutputFilePerTStepPerSpecies.Write <int>(SpeciesEstablishment.MapNameTemplate, SpeciesEstablishment.units, PlugIn.ModelCore.CurrentTime, Est_Sum);
}
if (AnnualPsn != null)
{
System.Console.WriteLine("Updating output variable: AnnualPsn");
ISiteVar <int> annualNetPsn = cohorts.GetIsiteVar(site => (int)site.NetPsnSum);
string FileName = FileNames.ReplaceTemplateVars(AnnualPsn.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <int, int>(FileName, annualNetPsn, o => o);
}
if (Water != null)
{
System.Console.WriteLine("Updating output variable: Water");
ISiteVar <float> Water_site = cohorts.GetIsiteVar(x => x.WaterMax);
string FileName = FileNames.ReplaceTemplateVars(Water.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <float, float>(FileName, Water_site, o => o);
Water.output_table_ecoregions.WriteUpdate(PlugIn.ModelCore.CurrentTime, Water_site);
}
if (SubCanopyPAR != null)
{
System.Console.WriteLine("Updating output variable: SubCanopyPAR");
ISiteVar <float> SubCanopyRadiation = cohorts.GetIsiteVar(x => x.SubCanopyParMAX);
string FileName = FileNames.ReplaceTemplateVars(SubCanopyPAR.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <float, float>(FileName, SubCanopyRadiation, o => o);
}
if (NonWoodyDebris != null)
{
System.Console.WriteLine("Updating output variable: NonWoodyDebris");
ISiteVar <double> Litter = cohorts.GetIsiteVar(x => x.Litter);
string FileName = FileNames.ReplaceTemplateVars(NonWoodyDebris.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <double, double>(FileName, Litter, o => o);
}
if (WoodyDebris != null)
{
System.Console.WriteLine("Updating output variable: WoodyDebris");
ISiteVar <double> woody_debris = cohorts.GetIsiteVar(x => x.WoodyDebris);
string FileName = FileNames.ReplaceTemplateVars(WoodyDebris.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <double, double>(FileName, woody_debris, o => o);
}
if (AgeDistribution != null)
{
System.Console.WriteLine("Updating output variable: AgeDistribution");
ISiteVar <Landis.Library.Parameters.Species.AuxParm <List <ushort> > > values = cohorts.GetIsiteVar(o => o.CohortAges);
new OutputHistogramCohort <ushort>(AgeDistribution.MapNameTemplate, "NrOfCohortsAtAge", 10).WriteOutputHist(values);
System.Console.WriteLine("Updating output variable: MaxAges");
ISiteVar <int> maxage = cohorts.GetIsiteVar(x => x.AgeMax);
string FileName = FileNames.ReplaceTemplateVars(AgeDistribution.MapNameTemplate, "", PlugIn.ModelCore.CurrentTime);
new OutputMapSiteVar <int, int>(FileName, maxage, o => o);
}
if (overalloutputs != null)
{
System.Console.WriteLine("Updating output variable: overalloutputs");
OutputAggregatedTable.WriteNrOfCohortsBalance();
}
if (establishmentTable != null)
{
System.Console.WriteLine("Updating output variable: establishmentTable");
OutputEstablishmentTable.WriteEstablishmentTable();
}
if (mortalityTable != null)
{
System.Console.WriteLine("Updating output variable: MortalityTable");
OutputMortalityTable.WriteMortalityTable();
}
}
//---------------------------------------------------------------------
public override void Initialize()
{
Timestep = parameters.Timestep;
selectedspecies = parameters.SelectedSpecies;
tstep = parameters.Timestep;
cohorts = PlugIn.ModelCore.GetSiteVar <Landis.Extension.Succession.BiomassPnET.ISiteCohorts>("Succession.CohortsPnET");
woodyDebris = PlugIn.ModelCore.GetSiteVar <Landis.Library.Biomass.Pool>("Succession.WoodyDebris");
litter = PlugIn.ModelCore.GetSiteVar <Landis.Library.Biomass.Pool>("Succession.Litter");
if (parameters.CohortsPerSpecies != null)
{
CohortsPerSpc = new OutputVariable(parameters.CohortsPerSpecies, "#");
}
if (parameters.SpeciesBiom != null)
{
Biomass = new OutputVariable(parameters.SpeciesBiom, "g/m2");
Biomass.output_table_ecoregions = new OutputTableEcoregions(Biomass.MapNameTemplate);
}
if (parameters.SpeciesAbovegroundBiom != null)
{
AbovegroundBiomass = new OutputVariable(parameters.SpeciesAbovegroundBiom, "g/m2");
AbovegroundBiomass.output_table_ecoregions = new OutputTableEcoregions(AbovegroundBiomass.MapNameTemplate);
}
if (parameters.SpeciesWoodySenescence != null)
{
WoodySenescence = new OutputVariable(parameters.SpeciesWoodySenescence, "g/m2");
WoodySenescence.output_table_ecoregions = new OutputTableEcoregions(WoodySenescence.MapNameTemplate);
}
if (parameters.SpeciesFoliageSenescence != null)
{
FoliageSenescence = new OutputVariable(parameters.SpeciesFoliageSenescence, "g/m2");
FoliageSenescence.output_table_ecoregions = new OutputTableEcoregions(FoliageSenescence.MapNameTemplate);
}
if (parameters.AETAvg != null)
{
AETAvg = new OutputVariable(parameters.AETAvg, "");
AETAvg.output_table_ecoregions = new OutputTableEcoregions(AETAvg.MapNameTemplate);
}
if (parameters.BelowgroundBiomass != null)
{
BelowGround = new OutputVariable(parameters.BelowgroundBiomass, "g/m2");
}
if (parameters.LeafAreaIndex != null)
{
LAI = new OutputVariable(parameters.LeafAreaIndex, "m2");
LAI.output_table_ecoregions = new OutputTableEcoregions(LAI.MapNameTemplate);
}
if (parameters.MonthlyFolResp != null)
{
MonthlyFolResp = new OutputVariable(parameters.MonthlyFolResp, "gC/mo");
}
if (parameters.MonthlyGrossPsn != null)
{
MonthlyGrossPsn = new OutputVariable(parameters.MonthlyGrossPsn, "gC/mo");
}
if (parameters.MonthlyMaintResp != null)
{
MonthlyMaintResp = new OutputVariable(parameters.MonthlyMaintResp, "gC/mo");
}
if (parameters.MonthlyNetPsn != null)
{
MonthlyNetPsn = new OutputVariable(parameters.MonthlyNetPsn, "gC/mo");
}
if (parameters.EstablishmentProbability != null)
{
EstablishmentProbability = new OutputVariable(parameters.EstablishmentProbability, "");
}
if (parameters.SpeciesEst != null)
{
SpeciesEstablishment = new OutputVariable(parameters.SpeciesEst, "");
}
if (parameters.Water != null)
{
Water = new OutputVariable(parameters.Water, "mm");
Water.output_table_ecoregions = new OutputTableEcoregions(Water.MapNameTemplate);
}
if (parameters.SubCanopyPAR != null)
{
SubCanopyPAR = new OutputVariable(parameters.SubCanopyPAR, "W/m2 or mmol/m2");
}
if (parameters.Litter != null)
{
NonWoodyDebris = new OutputVariable(parameters.Litter, "g/m2");
}
if (parameters.WoodyDebris != null)
{
WoodyDebris = new OutputVariable(parameters.WoodyDebris, "g/m2");
}
if (parameters.AgeDistribution != null)
{
AgeDistribution = new OutputVariable(parameters.AgeDistribution, "yr");
}
if (parameters.AnnualPsn != null)
{
AnnualPsn = new OutputVariable(parameters.AnnualPsn, "g/m2");
}
if (parameters.CohortBalance != null)
{
overalloutputs = new OutputAggregatedTable(parameters.CohortBalance);
}
if (parameters.EstablishmentTable != null)
{
establishmentTable = new OutputEstablishmentTable(parameters.EstablishmentTable);
}
if (parameters.MortalityTable != null)
{
mortalityTable = new OutputMortalityTable(parameters.MortalityTable);
}
MetadataHandler.InitializeMetadata(Timestep, LAI, Biomass, AbovegroundBiomass, EstablishmentProbability,
SpeciesWasThere, AnnualPsn, BelowGround, CohortsPerSpc, Water, SubCanopyPAR, NonWoodyDebris,
WoodyDebris, AgeDistribution, MonthlyFolResp, MonthlyGrossPsn, MonthlyNetPsn, MonthlyMaintResp,
SpeciesEstablishment, LastBiom, overalloutputs, parameters.CohortBalance);
}