//--------------------------------------------------------------------- /// <summary> /// Objects and Lists must be initialized. /// </summary> public AgentParameters(int sppCount, int ecoCount) { SppParameters = new ISppParameters[sppCount]; EcoParameters = new IEcoParameters[ecoCount]; EcoWeatherIndexNormal = new double[ecoCount]; disturbanceTypes = new List <IDisturbanceType>(); negSppList = new List <ISpecies>(); climateVarDefn = new List <IClimateVariableDefinition>(); derivedClimateVars = new List <IDerivedClimateVariable>(); weatherIndexVars = new List <string>(); climateDataTable = new DataTable(); for (int i = 0; i < sppCount; i++) { SppParameters[i] = new SppParameters(); } for (int i = 0; i < ecoCount; i++) { EcoParameters[i] = new EcoParameters(); } }
//--------------------------------------------------------------------- protected override IAgent Parse() { InputVar <string> landisData = new InputVar <string>("LandisData"); ReadVar(landisData); if (landisData.Value.Actual != LandisDataValue) { throw new InputValueException(landisData.Value.String, "The value is not \"{0}\"", LandisDataValue); } AgentParameters agentParameters = new AgentParameters(PlugIn.ModelCore.Species.Count, PlugIn.ModelCore.Ecoregions.Count); InputVar <string> agentName = new InputVar <string>("EDAAgentName"); ReadVar(agentName); agentParameters.AgentName = agentName.Value; InputVar <SHImode> shi = new InputVar <SHImode>("SHIMode"); ReadVar(shi); agentParameters.SHImode = shi.Value; InputVar <int> startYear = new InputVar <int>("StartYear"); if (CurrentName == "StartYear") { ReadVar(startYear); agentParameters.StartYear = startYear.Value; } else { agentParameters.StartYear = 0; } InputVar <int> endYear = new InputVar <int>("EndYear"); if (CurrentName == "EndYear") { ReadVar(endYear); agentParameters.EndYear = endYear.Value; } else { agentParameters.EndYear = PlugIn.ModelCore.EndTime; } // - Climate Input - //ADD HERE // Read Climate Variables ReadName("ClimateVariables"); Dictionary <string, int> lineNumbers = new Dictionary <string, int>(); lineNumbers.Clear(); InputVar <string> climateVarName = new InputVar <string>("Climate Variable Name"); InputVar <string> climateLibraryVarName = new InputVar <string>("Climate Library Variable Name"); InputVar <string> sourceName = new InputVar <string>("Source Name"); InputVar <string> transform = new InputVar <string>("Tranformation"); IClimateVariableDefinition climateVarDefn = null; while (!AtEndOfInput && (CurrentName != "DerivedClimateVariables")) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(climateVarName, currentLine); CheckForRepeatedName(climateVarName.Value, "var name", lineNumbers); climateVarDefn = new ClimateVariableDefinition(); climateVarDefn.Name = climateVarName.Value; ReadValue(sourceName, currentLine); climateVarDefn.SourceName = sourceName.Value; ReadValue(climateLibraryVarName, currentLine); climateVarDefn.ClimateLibVariable = climateLibraryVarName.Value; ReadValue(transform, currentLine); climateVarDefn.Transform = transform.Value; agentParameters.ClimateVars.Add(climateVarDefn); GetNextLine(); } // Read Derived Climate Variables ReadName("DerivedClimateVariables"); lineNumbers.Clear(); InputVar <string> derivedClimateVarName = new InputVar <string>("Derived Climate Variable Name"); InputVar <string> derSource = new InputVar <string>("Derived Climate Variable Source"); InputVar <string> derVariableName = new InputVar <string>("Derived Climate Variable source Variable Name"); InputVar <string> function = new InputVar <string>("Function"); InputVar <string> time = new InputVar <string>("Time"); InputVar <int> count = new InputVar <int>("Count"); IDerivedClimateVariable derivedClimateVars = null; Queue <string> formulaVars = new Queue <string>(); while (!AtEndOfInput && !(formulaVars.Contains(CurrentName))) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(derivedClimateVarName, currentLine); CheckForRepeatedName(derivedClimateVarName.Value, "var name", lineNumbers); derivedClimateVars = new DerivedClimateVariable(); derivedClimateVars.Name = derivedClimateVarName.Value; ReadValue(derSource, currentLine); derivedClimateVars.Source = derSource.Value; if (derivedClimateVars.Source == "Formula") { formulaVars.Enqueue(derivedClimateVars.Name); } ReadValue(derVariableName, currentLine); derivedClimateVars.ClimateVariable = derVariableName.Value; ReadValue(function, currentLine); derivedClimateVars.Function = function.Value; ReadValue(time, currentLine); derivedClimateVars.Time = time.Value; ReadValue(count, currentLine); derivedClimateVars.Count = count.Value; agentParameters.DerivedClimateVars.Add(derivedClimateVars); GetNextLine(); } foreach (string formulaName in formulaVars) { // Read Temp Index model ReadName(formulaName); formulaVars.Dequeue(); lineNumbers.Clear(); InputVar <string> tempIndexVarName = new InputVar <string>("Temp Index Variable Name"); InputVar <string> tempIndexParamValue = new InputVar <string>("Parameter Value"); List <string> tempIndexParameters = new List <string>(); List <string> tempIndexParamValues = new List <string>(); IFormula tempIndexModel = new Formula(); while (!AtEndOfInput && (CurrentName != "WeatherIndexVariables") && !(formulaVars.Contains(CurrentName))) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(tempIndexVarName, currentLine); CheckForRepeatedName(tempIndexVarName.Value, "var name", lineNumbers); tempIndexModel.Parameters.Add(tempIndexVarName.Value); //agentParameters.TempIndexModel.Parameters.Add(tempIndexVarName.Value); ReadValue(tempIndexParamValue, currentLine); tempIndexModel.Values.Add(tempIndexParamValue.Value); //agentParameters.TempIndexModel.Values.Add(tempIndexParamValue.Value); GetNextLine(); } agentParameters.VarFormula = tempIndexModel; if (formulaVars.Count == 0) { break; } } // Read Weather Index Variables ReadName("WeatherIndexVariables"); lineNumbers.Clear(); InputVar <string> weatherIndexVarName = new InputVar <string>("Weather Index Variable Name"); while (!AtEndOfInput && (CurrentName != "AnnualWeatherIndex")) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(weatherIndexVarName, currentLine); CheckForRepeatedName(weatherIndexVarName.Value, "var name", lineNumbers); agentParameters.WeatherIndexVars.Add(weatherIndexVarName.Value); GetNextLine(); } //Read Annual Weather Index ReadName("AnnualWeatherIndex"); WeatherIndex weatherIndex = new WeatherIndex(); StringReader annualWeatherLine = new StringReader(CurrentLine); InputVar <int> minMonth = new InputVar <int>("Min Month"); InputVar <int> maxMonth = new InputVar <int>("Max Month"); InputVar <string> annualWeatherFunction = new InputVar <string>("Function"); ReadValue(minMonth, annualWeatherLine); weatherIndex.MinMonth = minMonth.Value; TextReader.SkipWhitespace(annualWeatherLine); string currentWord = TextReader.ReadWord(annualWeatherLine); if (currentWord != "to") { StringBuilder message = new StringBuilder(); message.AppendFormat("Expected \"to\" after the minimum month ({0})", minMonth.Value.String); if (currentWord.Length > 0) { message.AppendFormat(", but found \"{0}\" instead", currentWord); } throw NewParseException(message.ToString()); } ReadValue(maxMonth, annualWeatherLine); weatherIndex.MaxMonth = maxMonth.Value; ReadValue(annualWeatherFunction, annualWeatherLine); weatherIndex.Function = annualWeatherFunction.Value; agentParameters.AnnualWeatherIndex = weatherIndex; GetNextLine(); // - Transmission Input - InputVar <double> tr = new InputVar <double>("TransmissionRate"); ReadVar(tr); agentParameters.TransmissionRate = tr.Value; InputVar <double> ar = new InputVar <double>("AcquisitionRate"); ReadVar(ar); agentParameters.AcquisitionRate = ar.Value; InputVar <string> epiMap = new InputVar <string>("InitialEpidemMap"); ReadVar(epiMap); agentParameters.InitEpiMap = epiMap.Value; InputVar <DispersalType> dt = new InputVar <DispersalType>("DispersalType"); ReadVar(dt); agentParameters.DispersalType = dt.Value; InputVar <DispersalTemplate> dk = new InputVar <DispersalTemplate>("DispersalKernel"); ReadVar(dk); agentParameters.DispersalKernel = dk.Value; InputVar <int> dmax = new InputVar <int>("DispersalMaxDist"); ReadVar(dmax); agentParameters.DispersalMaxDist = dmax.Value; InputVar <double> ac = new InputVar <double>("AlphaCoef"); ReadVar(ac); agentParameters.AlphaCoef = ac.Value; //--------- Read In Ecoregion Table --------------------------------------- PlugIn.ModelCore.UI.WriteLine("Begin parsing ECOREGION table."); InputVar <string> ecoName = new InputVar <string>("Ecoregion Name"); InputVar <double> ecoModifier = new InputVar <double>("Ecoregion Modifier"); lineNumbers.Clear(); const string DistParms = "DisturbanceModifiers"; const string SppParms = "EDASpeciesParameters"; while (!AtEndOfInput && CurrentName != DistParms && CurrentName != SppParms) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(ecoName, currentLine); IEcoregion ecoregion = EcoregionsDataset[ecoName.Value.Actual]; if (ecoregion == null) { throw new InputValueException(ecoName.Value.String, "{0} is not an ecoregion name.", ecoName.Value.String); } int lineNumber; if (lineNumbers.TryGetValue(ecoregion.Name, out lineNumber)) { throw new InputValueException(ecoName.Value.String, "The ecoregion {0} was previously used on line {1}", ecoName.Value.String, lineNumber); } else { lineNumbers[ecoregion.Name] = LineNumber; } IEcoParameters ecoParms = new EcoParameters(); agentParameters.EcoParameters[ecoregion.Index] = ecoParms; ReadValue(ecoModifier, currentLine); ecoParms.EcoModifier = ecoModifier.Value; CheckNoDataAfter("the " + ecoModifier.Name + " column", currentLine); GetNextLine(); } if (CurrentName == DistParms) { //--------- Read In Disturbance Modifier Table ------------------------------- PlugIn.ModelCore.UI.WriteLine("Begin parsing DISTURBANCE table."); ReadName(DistParms); InputVar <string> prescriptionName = new InputVar <string>("Disturbance Type"); InputVar <int> duration = new InputVar <int>("Duration"); InputVar <double> distModifier = new InputVar <double>("Disturbance Modifier"); lineNumbers = new Dictionary <string, int>(); Dictionary <int, int> DisturbanceTypeLineNumbers = new Dictionary <int, int>(); while (!AtEndOfInput && CurrentName != SppParms) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(distModifier, currentLine); IDisturbanceType currentDisturbanceType = new DisturbanceType(); agentParameters.DisturbanceTypes.Add(currentDisturbanceType); currentDisturbanceType.SHIModifier = distModifier.Value; ReadValue(duration, currentLine); currentDisturbanceType.ImpactDuration = duration.Value; List <string> prescriptionNames = new List <string>(); TextReader.SkipWhitespace(currentLine); while (currentLine.Peek() != -1) { ReadValue(prescriptionName, currentLine); prescriptionNames.Add(prescriptionName.Value); TextReader.SkipWhitespace(currentLine); } if (prescriptionNames.Count == 0) { throw NewParseException("At least one disturbance type is required."); } currentDisturbanceType.PrescriptionNames = prescriptionNames; CheckNoDataAfter("the " + distModifier.Name + " column", currentLine); GetNextLine(); } } //--------- Read In Species Table --------------------------------------- PlugIn.ModelCore.UI.WriteLine("Begin parsing SPECIES table."); ReadName(SppParms); //Species Name InputVar <string> sppName = new InputVar <string>("Species"); //SHI (Host Index) InputVar <int> lowHostAge = new InputVar <int>("Low Host Index Age"); InputVar <int> lowHostScore = new InputVar <int>("Low Host Index Score"); InputVar <int> mediumHostAge = new InputVar <int>("Medium Host Index Age"); InputVar <int> mediumHostScore = new InputVar <int>("Medium Host Index Score"); InputVar <int> highHostAge = new InputVar <int>("High Host Index Age"); InputVar <int> highHostScore = new InputVar <int>("High Host Index Score"); //SHV (Vulnerability) InputVar <int> lowVulnHostAge = new InputVar <int>("Low Vulnerability Host Age"); InputVar <double> lowVulnHostMortProb = new InputVar <double>("Low Vulnerability Host MortProb"); InputVar <int> mediumVulnHostAge = new InputVar <int>("Medium Vulnerability Host Age"); InputVar <double> mediumVulnHostMortProb = new InputVar <double>("Medium Vulnerability Host MortProb"); InputVar <int> highVulnHostAge = new InputVar <int>("High Vulnerability Host Age"); InputVar <double> highVulnHostMortProb = new InputVar <double>("High Vulnerability Host MortProb"); //CFS InputVar <bool> cfsConifer = new InputVar <bool>("CFS Conifer type: yes/no"); //MORTALITY SPECIES TO CONSIDER FOR PLOTTING InputVar <bool> mortSppFlag = new InputVar <bool>("Mortality plot: yes/no"); // species to ignore in SHI calculation const string NegSpp = "IgnoredSpecies"; while ((!AtEndOfInput) && (CurrentName != NegSpp)) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(sppName, currentLine); ISpecies species = SpeciesDataset[sppName.Value.Actual]; if (species == null) { throw new InputValueException(sppName.Value.String, "{0} is not a species name.", sppName.Value.String); } int lineNumber; if (lineNumbers.TryGetValue(species.Name, out lineNumber)) { throw new InputValueException(sppName.Value.String, "The species {0} was previously used on line {1}", sppName.Value.String, lineNumber); } else { lineNumbers[species.Name] = LineNumber; } ISppParameters sppParms = new SppParameters(); agentParameters.SppParameters[species.Index] = sppParms; //SHI ReadValue(lowHostAge, currentLine); sppParms.LowHostAge = lowHostAge.Value; ReadValue(lowHostScore, currentLine); sppParms.LowHostScore = lowHostScore.Value; ReadValue(mediumHostAge, currentLine); sppParms.MediumHostAge = mediumHostAge.Value; ReadValue(mediumHostScore, currentLine); sppParms.MediumHostScore = mediumHostScore.Value; ReadValue(highHostAge, currentLine); sppParms.HighHostAge = highHostAge.Value; ReadValue(highHostScore, currentLine); sppParms.HighHostScore = highHostScore.Value; //SHV ReadValue(lowVulnHostAge, currentLine); sppParms.LowVulnHostAge = lowVulnHostAge.Value; ReadValue(lowVulnHostMortProb, currentLine); sppParms.LowVulnHostMortProb = lowVulnHostMortProb.Value; ReadValue(mediumVulnHostAge, currentLine); sppParms.MediumVulnHostAge = mediumVulnHostAge.Value; ReadValue(mediumVulnHostMortProb, currentLine); sppParms.MediumVulnHostMortProb = mediumVulnHostMortProb.Value; ReadValue(highVulnHostAge, currentLine); sppParms.HighVulnHostAge = highVulnHostAge.Value; ReadValue(highVulnHostMortProb, currentLine); sppParms.HighVulnHostMortProb = highVulnHostMortProb.Value; //CFS ReadValue(cfsConifer, currentLine); sppParms.CFSConifer = cfsConifer.Value; //MORTALITY SPECIES FLAG ReadValue(mortSppFlag, currentLine); sppParms.MortSppFlag = mortSppFlag.Value; CheckNoDataAfter("the " + mortSppFlag.Name + " column", currentLine); GetNextLine(); } //--------- Read In Ignored Species List --------------------------------------- List <ISpecies> negSppList = new List <ISpecies>(); if (!AtEndOfInput) { ReadName(NegSpp); InputVar <string> negSppName = new InputVar <string>("Ignored Spp Name"); while (!AtEndOfInput) { StringReader currentLine = new StringReader(CurrentLine); ReadValue(negSppName, currentLine); ISpecies species = SpeciesDataset[negSppName.Value.Actual]; if (species == null) { throw new InputValueException(negSppName.Value.String, "{0} is not a species name.", negSppName.Value.String); } int lineNumber; if (lineNumbers.TryGetValue(species.Name, out lineNumber)) { PlugIn.ModelCore.UI.WriteLine("WARNING: The species {0} was previously used on line {1}. Being listed in the IgnoredSpecies list will override any settings in the Host table.", negSppName.Value.String, lineNumber); } else { lineNumbers[species.Name] = LineNumber; } negSppList.Add(species); GetNextLine(); } } agentParameters.NegSppList = negSppList; return(agentParameters); }