//---------------------------------------------------------------------
protected override IInputParameters Parse()
{
InputVar <string> landisData = new InputVar <string>("LandisData");
ReadVar(landisData);
if (landisData.Value.Actual != PlugIn.ExtensionName)
{
throw new InputValueException(landisData.Value.String, "The value is not \"{0}\"", PlugIn.ExtensionName);
}
InputParameters parameters = new InputParameters();
InputVar <int> timestep = new InputVar <int>(Names.Timestep);
ReadVar(timestep);
parameters.Timestep = timestep.Value;
InputVar <int> StartYear = new InputVar <int>(Names.StartYear);
ReadVar(StartYear);
parameters.StartYear = StartYear.Value;
InputVar <SeedingAlgorithms> seedAlg = new InputVar <SeedingAlgorithms>(Names.SeedingAlgorithm);
ReadVar(seedAlg);
parameters.SeedAlgorithm = seedAlg.Value;
//---------------------------------------------------------------------------------
InputVar <string> initCommunities = new InputVar <string>("InitialCommunities");
ReadVar(initCommunities);
parameters.InitialCommunities = initCommunities.Value;
InputVar <string> communitiesMap = new InputVar <string>("InitialCommunitiesMap");
ReadVar(communitiesMap);
parameters.InitialCommunitiesMap = communitiesMap.Value;
InputVar <string> climateFileName = new InputVar <string>(Names.climateFileName);
ReadVar(climateFileName);
parameters.climateFileName = climateFileName.Value;
InputVar <int> Latitude = new InputVar <int>(Names.Latitude);
ReadVar(Latitude);
parameters.Latitude = Util.CheckBiomassParm(Latitude.Value, -90, 90);
InputVar <string> CanopyLayerBiomassCategories = new InputVar <string>(Names.CanopyLayerBiomassCategories);
ReadVar(CanopyLayerBiomassCategories);
CanopyLayerCategories.InitializeCanopyLayers(Names.CanopyLayerBiomassCategories, CanopyLayerBiomassCategories.Value);
//InputVar<int> CanopyLayerAgeSpan = new InputVar<int>(Names.CanopyLayerAgeSpan);
//ReadVar(CanopyLayerAgeSpan);
//parameters.CanopyLayerAgeSpan = int.Parse(Util.CheckBiomassParm(CanopyLayerAgeSpan.Value, 0, int.MaxValue).ToString());
if (ReadOptionalName(Names.PNEToutputsites) == true)
{
while (!AtEndOfInput && CurrentName != Names.SpeciesParameterFile)
{
StringReader currentLine = new StringReader(CurrentLine);
InputVar <int> row = new InputVar <int>("Output row");
InputVar <int> col = new InputVar <int>("Output column");
ReadValue(row, currentLine);
ReadValue(col, currentLine);
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
if (site.Location.Row == row.Value && site.Location.Column == col.Value)
{
parameters.HasSiteOutput[site] = true;
}
}
GetNextLine();
}
}
//-------------------------
// SpeciesParameters table
InputVar <string> SpeciesParameterFile = new InputVar <string>(Names.SpeciesParameterFile);
ReadVar(SpeciesParameterFile);
parameters = ReadSpeciesParameters(SpeciesParameterFile.Value, parameters);
InputVar <string> EstRadSensitivity = new InputVar <string>(Names.EstRadSensitivity);
if (ReadOptionalVar(EstRadSensitivity))
{
InitEstablishmentTable(EstRadSensitivity.Value, Names.EstRadSensitivity, parameters.EstRadSensitivity);
}
else
{
InitEstablishmentTable(Names.EstRadSensitivity, parameters.EstRadSensitivity);
}
InputVar <string> EstMoistureSensitivity = new InputVar <string>(Names.EstMoistureSensitivity);
if (ReadOptionalVar(EstMoistureSensitivity))
{
InitEstablishmentTable(EstMoistureSensitivity.Value, Names.EstMoistureSensitivity, parameters.EstMoistureSensitivity);
}
else
{
InitEstablishmentTable(Names.EstMoistureSensitivity, parameters.EstMoistureSensitivity);
}
ReadName(Names.EcoregionParameters);
InputVar <string> ecoregionName = new InputVar <string>("Ecoregion Name");
InputVar <int> aet = new InputVar <int>("Actual Evapotranspiration");
InputVar <float> whc = new InputVar <float>("Water holding capacity");
InputVar <float> evaporationfraction = new InputVar <float>("EvaporationFraction");
InputVar <float> leakagefraction = new InputVar <float>("LeakageFraction");
Dictionary <string, int> lineNumbers = new Dictionary <string, int>();
string lastColumn = "the " + aet.Name + " column";
while (!AtEndOfInput && CurrentName != Names.AgeOnlyDisturbanceParms)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(ecoregionName, currentLine);
IEcoregion ecoregion = GetEcoregion(ecoregionName.Value,
lineNumbers);
ReadValue(aet, currentLine);
parameters.AET[ecoregion] = Util.CheckBiomassParm(aet.Value, 0, int.MaxValue);
ReadValue(whc, currentLine);
parameters.WHC[ecoregion] = Util.CheckBiomassParm(whc.Value, 0, int.MaxValue);
ReadValue(evaporationfraction, currentLine);
parameters.EvaporationFraction[ecoregion] = Util.CheckBiomassParm(evaporationfraction.Value, 0, 1);
ReadValue(leakagefraction, currentLine);
parameters.LeakageFraction[ecoregion] = Util.CheckBiomassParm(leakagefraction.Value, 0, 1);
CheckNoDataAfter(lastColumn, currentLine);
GetNextLine();
}
string lastParameter = null;
if (!AtEndOfInput && CurrentName == Names.AgeOnlyDisturbanceParms)
{
InputVar <string> ageOnlyDisturbanceParms = new InputVar <string>(Names.AgeOnlyDisturbanceParms);
ReadVar(ageOnlyDisturbanceParms);
parameters.AgeOnlyDisturbanceParms = ageOnlyDisturbanceParms.Value;
lastParameter = "the " + Names.AgeOnlyDisturbanceParms + " parameter";
}
if (lastParameter != null)
{
CheckNoDataAfter(lastParameter);
}
return(parameters);
}
static public void DefineBiomassLayers(ActiveSite site)
{
if (PlugIn.Cohorts[site] == null)
{
return;
}
CalculateBiomassSums(site);
canopy.Clear();
int maxage = 0;
List <ISpecies> species = new List <ISpecies>();
List <int> cohort_index = new List <int>();
List <float> biomass = new List <float>();
List <int> old_canopylayers = new List <int>();
foreach (ISpeciesCohorts speciesCohorts in PlugIn.Cohorts[site])
{
int index = 0;
foreach (ICohort cohort in speciesCohorts)
{
if (cohort.Age > maxage)
{
maxage = cohort.Age;
}
int a = 0;
for (a = 0; a < biomass.Count; a++)
{
if (biomass[a] > cohort.Biomass)
{
biomass.Insert(a, cohort.Biomass);
species.Insert(a, cohort.Species);
cohort_index.Insert(a, index);
old_canopylayers.Insert(a, cohort.CanopyLayer);
break;
}
}
if (a == biomass.Count)
{
species.Add(cohort.Species);
biomass.Add(cohort.Biomass);
cohort_index.Add(index);
old_canopylayers.Add(cohort.CanopyLayer);
}
index++;
}
}
if (TotalBiomass[site] <= 0)
{
return;
}
float[] fractions = CanopyLayerCategories.GetCumBiomFractions(maxage);
float includedbiomfrac = 0;
for (int b = 0; b < biomass.Count(); b++)
{
includedbiomfrac += biomass[b] / TotalBiomass[site];
for (int f = 0; f < fractions.Count(); f++)
{
if (includedbiomfrac <= fractions[f])
{
int CanopyLayer = Math.Max(old_canopylayers[b], f);
while (canopy.Count < CanopyLayer + 1)
{
canopy.Add(new CanopyLayerBiomass());
}
canopy[CanopyLayer].Add(new CohortBiomass(site, PlugIn.Cohorts[site][species[b]].Get(cohort_index[b]), cohort_index[b]));
break;
}
}
}
}