//---------------------------------------------------------------------
protected SpeciesParameters[] ReadSpeciesParameters()
{
speciesLineNumbers.Clear(); // for re-use during unit testing
SpeciesParameters[] allSpeciesParameters = new SpeciesParameters[speciesDataset.Count];
InputVar <string> speciesName = new InputVar <string>("Species");
InputVar <int> minSeeds = new InputVar <int>("Minimum Seeds Produced");
InputVar <int> maxSeeds = new InputVar <int>("Maximum Seeds Produced");
InputVar <double> leafArea = new InputVar <double>("Seedling Leaf Area");
InputVar <double> dispersalMean1 = new InputVar <double>("Dispersal Mean1");
InputVar <double> dispersalMean2 = new InputVar <double>("Dispersal Mean2");
InputVar <double> dispersalWeight1 = new InputVar <double>("Dispersal Weight1");
string lastColumn = "the " + dispersalWeight1.Name + " column";
while (!AtEndOfInput && CurrentName != Names.EmergenceProbabilities)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(speciesName, currentLine);
ISpecies species = ValidateSpeciesName(speciesName);
SpeciesParameters parameters = new SpeciesParameters();
ReadValue(minSeeds, currentLine);
parameters.MinSeedsProduced = minSeeds.Value;
ReadValue(maxSeeds, currentLine);
parameters.MaxSeedsProduced = maxSeeds.Value;
ReadValue(leafArea, currentLine);
parameters.LeafArea = leafArea.Value;
ReadValue(dispersalMean1, currentLine);
parameters.DispersalMean1 = dispersalMean1.Value;
ReadValue(dispersalMean2, currentLine);
parameters.DispersalMean2 = dispersalMean2.Value;
ReadValue(dispersalWeight1, currentLine);
parameters.DispersalWeight1 = dispersalWeight1.Value;
CheckNoDataAfter(lastColumn, currentLine);
allSpeciesParameters[species.Index] = parameters;
GetNextLine();
}
if (speciesLineNumbers.Count == 0)
{
throw NewParseException("Expected a line starting with a species name");
}
return(allSpeciesParameters);
}
//---------------------------------------------------------------------
protected void ReadProbabilities(string tableName,
string probabilityName,
string nameAfterTable,
SpeciesParameters[] allSpeciesParameters,
GetProbabilities getProbabilities)
{
ReadName(tableName);
speciesLineNumbers.Clear();
InputVar <string> speciesName = new InputVar <string>("Species");
InputVar <double> probability = new InputVar <double>(probabilityName);
IEcoregion lastEcoregion = Model.Core.Ecoregions[Model.Core.Ecoregions.Count - 1];
string lastColumn = "the " + lastEcoregion.Name + " ecoregion column";
while (!AtEndOfInput && CurrentName != nameAfterTable)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(speciesName, currentLine);
ISpecies species = ValidateSpeciesName(speciesName);
SpeciesParameters parameters = allSpeciesParameters[species.Index];
double[] probabilities = getProbabilities(parameters);
foreach (IEcoregion ecoregion in Model.Core.Ecoregions)
{
ReadValue(probability, currentLine);
if (probability.Value < 0.0 || probability.Value > 1.0)
{
throw new InputValueException(probability.Value.String,
"Probability for ecoregion " + ecoregion.Name + " is not between 0.0 and 1.0");
}
probabilities[ecoregion.Index] = probability.Value;
}
CheckNoDataAfter(lastColumn, currentLine);
GetNextLine();
}
}
//---------------------------------------------------------------------
/// <summary>
/// Initializes the demographic seeding algorithm
/// </summary>
/// <param name="successionTimestep">
/// The length of the succession extension's timestep (units: years).
/// </param>
public Algorithm(int successionTimestep)
{
int numTimeSteps; // the number of succession time steps to loop over
int maxCohortAge; // maximum age allowed for any species, in years
numTimeSteps = (Model.Core.EndTime - Model.Core.StartTime) / successionTimestep;
maxCohortAge = 0;
foreach (ISpecies species in Model.Core.Species)
{
if (species.Longevity > maxCohortAge)
{
maxCohortAge = species.Longevity;
}
}
// The library's code comments say max_age_steps represents
// "maximum age allowed for any species, in years", but it's
// used in the code as though it represents the maximum age of
// any species' cohort IN NUMBER OF SUCCESSION TIMESTEPS. So if
// the oldest species' Longevity is 2,000 years, and the succession
// timestep is 10 years, then max_age_steps is 200 timesteps.
int max_age_steps = maxCohortAge / successionTimestep;
seedingData = new Seed_Dispersal.Map(
Model.Core.Landscape.Columns,
Model.Core.Landscape.Rows,
Model.Core.Species.Count,
numTimeSteps,
successionTimestep,
Model.Core.Ecoregions.Count,
max_age_steps);
seedingData.pixel_size = Model.Core.CellLength;
// Initialize some species parameters from the core.
foreach (ISpecies species in Model.Core.Species)
{
seedingData.all_species[species.Index].shade_tolerance = species.ShadeTolerance;
seedingData.all_species[species.Index].reproductive_age = species.Maturity;
}
// Load user-specified parameters
string path = "demographic-seeding.txt"; // hard-wired for now, so no changes required to succession extensions
Model.Core.UI.WriteLine("Reading demographic seeding parameters from {0} ...", path);
ParameterParser parser = new ParameterParser(Model.Core.Species);
Parameters parameters = Landis.Data.Load <Parameters>(path, parser);
seedingData.dispersal_model = parameters.Kernel;
seedingData.seed_model = parameters.SeedProductionModel;
seedingData.mc_draws = parameters.MonteCarloDraws;
seedingData.max_leaf_area = parameters.MaxLeafArea;
seedingData.cohort_threshold = parameters.CohortThreshold;
seedRainMaps = parameters.SeedRainMaps;
seedlingEmergenceMaps = parameters.SeedlingEmergenceMaps;
dispersalProbabilitiesFilename = parameters.DispersalProbabilitiesLog;
if (dispersalProbabilitiesFilename != null)
{
// Truncate DispersalProbabilitiesLog file and write header
using (System.IO.StreamWriter file = new System.IO.StreamWriter(dispersalProbabilitiesFilename, false))
{
file.WriteLine("Timestep, Species, Distance, Probability");
}
}
foreach (ISpecies species in Model.Core.Species)
{
SpeciesParameters speciesParameters = parameters.SpeciesParameters[species.Index];
seedingData.all_species[species.Index].min_seed = speciesParameters.MinSeedsProduced;
seedingData.all_species[species.Index].max_seed = speciesParameters.MaxSeedsProduced;
seedingData.all_species[species.Index].leaf_area = speciesParameters.LeafArea;
CopyArray(speciesParameters.DispersalParameters,
seedingData.all_species[species.Index].dispersal_parameters);
CopyArray(speciesParameters.EmergenceProbabilities,
seedingData.emergence_probability[species.Index]);
CopyArray(speciesParameters.SurvivalProbabilities,
seedingData.survival_probability[species.Index]);
}
seedingData.Initialize();
WriteProbabilities();
}
