public StudentEditViewModel(string connectionString, int id)
{
_connectionString = connectionString;
allExercises = GetAllExercises().Select(exercise => new SelectListItem()
{
Text = exercise.exerciseName,
Value = exercise.Id.ToString(),
Selected = student.exerciseList.Find(assignedExercise => assignedExercise.Id == exercise.Id) != null
})
.ToList();
Cohorts = GetAllCohorts()
.Select(cohort => new SelectListItem()
{
Text = cohort.cohortName,
Value = cohort.Id.ToString()
})
.ToList();
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose a cohort",
Value = "0"
});
allExercises.Insert(0, new SelectListItem
{
Text = "Assign an exercise",
Value = "0"
});
}
public StudentEditViewModel(string connectionString)
{
_connectionString = connectionString;
//student = StudentRepository.GetOneStudent(studentId);
// Get the exercises that are currently assigned to this student
// The student model already has a list for this!
Student.StudentExs = GetAssignedExercisesByStudent(studentId);
allExercises = ExerciseRepository.GetAllExercises()
.Select(singleExercise => new SelectListItem()
{
Text = singleExercise.Name,
Value = singleExercise.id.ToString(),
Selected = Student.StudentExs.Find(assignedExercise => assignedExercise.id == singleExercise.id) != null
})
.ToList();
//Query the database to get all cohorts
Cohorts = GetAllCohorts()
.Select(cohort => new SelectListItem()
{
Text = cohort.CohortName,
Value = cohort.CohortId.ToString()
})
.ToList();
// Add an option with instructions for how to use the dropdown
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose a cohort",
Value = "0"
});
}
private void AddChildren(ExtractionConfiguration extractionConfiguration, DescendancyList descendancy)
{
HashSet <object> children = new HashSet <object>();
var parameters = AllGlobalExtractionFilterParameters.Where(p => p.ExtractionConfiguration_ID == extractionConfiguration.ID)
.ToArray();
if (parameters.Any())
{
var parameterNode = new ParametersNode(extractionConfiguration, parameters);
children.Add(parameterNode);
}
//if it has a cohort
if (extractionConfiguration.Cohort_ID != null)
{
var cohort = Cohorts.Single(c => c.ID == extractionConfiguration.Cohort_ID);
children.Add(new LinkedCohortNode(extractionConfiguration, cohort));
}
//if it has extractable datasets add those
foreach (SelectedDataSets ds in GetDatasets(extractionConfiguration))
{
children.Add(ds);
AddChildren(ds, descendancy.Add(ds));
}
AddToDictionaries(children, descendancy);
}
public void CalcCohorts(List <ChemExIcon> exIcons, Cohorts cohorts)
{
foreach (var exIcon in exIcons)
{
foreach (var pop in exIcon.Pops)
{
cohorts[pop.Key] += pop.Value;
}
}
}
private void AddChildren(ExternalCohortTable externalCohortTable, DescendancyList descendancy)
{
var cohorts = Cohorts.Where(c => c.ExternalCohortTable_ID == externalCohortTable.ID).ToArray();
foreach (ExtractableCohort cohort in cohorts)
{
cohort.InjectKnown(externalCohortTable);
}
AddToDictionaries(new HashSet <object>(cohorts), descendancy);
}
public InstructorEditViewModel(string config)
{
_connectionString = config;
/*
* Query the database to get all cohorts
*/
using (SqlConnection conn = Connection)
{
conn.Open();
using (SqlCommand cmd = conn.CreateCommand())
{
cmd.CommandText = "SELECT Id, CohortName FROM Cohort";
SqlDataReader reader = cmd.ExecuteReader();
List <Cohort> cohorts = new List <Cohort>();
while (reader.Read())
{
cohorts.Add(new Cohort
{
Id = reader.GetInt32(reader.GetOrdinal("Id")),
CohortName = reader.GetString(reader.GetOrdinal("CohortName")),
});
}
Cohorts = cohorts.Select(c => new SelectListItem
{
Text = c.CohortName,
Value = c.Id.ToString()
})
.ToList();
Cohorts
.Insert(0, new SelectListItem
{
Text = "Choose cohort...",
Value = "0"
});
reader.Close();
}
}
/*
* Use the LINQ .Select() method to convert
* the list of Cohort into a list of SelectListItem
* objects
*/
}
private void Blacklist(ExternalCohortTable source, Exception ex)
{
BlackListedSources.Add(source);
_errorsCheckNotifier.OnCheckPerformed(new CheckEventArgs("Could not reach cohort '" + source + "' (it may be slow responding or inaccessible due to user permissions)", CheckResult.Fail, ex));
//tell them not to bother looking for the cohort data because its inaccessible
foreach (ExtractableCohort cohort in Cohorts.Where(c => c.ExternalCohortTable_ID == source.ID).ToArray())
{
cohort.InjectKnown((ExternalCohortDefinitionData)null);
}
}
/// <summary>
/// Cleanup the list of cohorts by removing any that have no population.
/// </summary>
public void RemoveEmptyCohorts()
{
int i = Cohorts.Count - 1;
while (i >= 0)
{
if (Cohorts[i].Count < 0.001)
{
Cohorts.RemoveAt(i);
}
i--;
}
}
/// <summary>
/// Construct a new cohort, add it to the list and return a reference to it.
/// </summary>
/// <returns>A new initialised cohort object</returns>
public Cohort NewCohort()
{
if (Cohorts == null)
{
Cohorts = new List <Cohort>();
}
Cohort a = new Cohort(this);
a.Count = 0;
a.ChronoAge = 0;
a.PhysiologicalAge = 0;
Cohorts.Add(a);
return(a);
}
public StudentCreateViewModel(string connectionString)
{
_connectionString = connectionString;
Cohorts = GetAllCohorts().Select(li => new SelectListItem
{
Text = li.Name,
Value = li.Id.ToString()
}).ToList();
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose cohort...",
Value = "0"
});
}
public GetApprovedProvidersQueryHandlerFixture AddNotApprovedCohortAndProviderForAccount()
{
Provider.Add(
new Provider(GetNextProviderId(), "Foo", DateTime.UtcNow, DateTime.UtcNow)
);
Cohorts.Add(new Cohort
{
EmployerAccountId = AccountId,
Id = GetNextCohortId(),
EditStatus = Types.EditStatus.EmployerOnly,
TransferSenderId = null,
ProviderId = 1
});
return(this);
}
public GetApprovedProvidersQueryHandlerFixture AddApprovedCohortAndProviderForAccount()
{
var provider = new Provider(GetNextProviderId(), "Foo", DateTime.UtcNow, DateTime.UtcNow);
Provider.Add(provider);
Cohorts.Add(new Cohort
{
EmployerAccountId = AccountId,
Id = GetNextCohortId(),
EditStatus = 0,
TransferSenderId = null,
ProviderId = provider.UkPrn
});
return(this);
}
public void RemoveNulls(Cohorts cohorts)
{
List <string> keysToBeRemoved = new List <string>();
foreach (var cohortKey in cohorts.Keys)
{
if (cohorts[cohortKey] == 0)
{
keysToBeRemoved.Add(cohortKey);
}
}
foreach (var keyToBeRemoved in keysToBeRemoved)
{
cohorts.Remove(keyToBeRemoved);
}
}
public GetApprovedProvidersQueryHandlerFixture AddCohortAndProvider_WithTransfserSenderNotApproved()
{
var provider = new Provider(GetNextProviderId(), "Foo", DateTime.UtcNow, DateTime.UtcNow);
Provider.Add(provider);
Cohorts.Add(new Cohort
{
EmployerAccountId = AccountId,
Id = GetNextCohortId(),
EditStatus = 0,
TransferSenderId = 1,
ProviderId = provider.UkPrn,
TransferApprovalStatus = Types.TransferApprovalStatus.Pending
});
return(this);
}
public InstructorCreateViewModel(string connectionString)
{
_connectionString = connectionString;
Cohorts = GetAllCohorts()
.Select(cohort => new SelectListItem()
{
Text = cohort.cohortName,
Value = cohort.Id.ToString()
})
.ToList();
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose a cohort",
Value = "0"
});
}
public InstructorCreateViewModel(string connectionString)
{
_connectionString = connectionString;
Cohorts = GetAllCohorts()
.Select(cohort => new SelectListItem()
{
Text = cohort.Name,
Value = cohort.Id.ToString()
})
.ToList();
// Add an option with instructiosn for how to use the dropdown
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose a cohort",
Value = "0"
});
}
public InstructorCreateViewModel(IConfiguration config)
{
using (IDbConnection conn = new SqlConnection(config.GetConnectionString("DefaultConnection")))
{
Cohorts = conn.Query <Cohort>(@"
SELECT Id, Name FROM Cohort;
")
.AsEnumerable()
.Select(li => new SelectListItem
{
Text = li.Name,
Value = li.Id.ToString()
}).ToList();
;
}
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose cohort...",
Value = "0"
});
}
// This is an example of method overloading! We have one constructor with no parameter and another constructor that's expecting a connection string. We can call either one!
public CreateStudentViewModel(string connectionString)
{
_connectionString = connectionString;
// When we create a new instance of this view model, we'll call the internal methods to get all the cohorts from the database
// Then we'll map over them and convert the list of cohorts to a list of select list items
Cohorts = GetAllCohorts()
.Select(cohort => new SelectListItem()
{
Text = cohort.name,
Value = cohort.id.ToString()
})
.ToList();
// Add an option with instructiosn for how to use the dropdown
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose a cohort",
Value = "0"
});
}
public StudentEditViewModel(Student student, List <Cohort> cohortList, List <Instructor> instructorList, List <Exercise> exerciseList)
{
Student = student;
//add exercises that are already assigned to the student to the AssignExercise list
student.Exercises.ForEach(exercise => AssignedExercises.Add(exercise.Id));
//use cohort data to create a list of select items
Cohorts = cohortList
.Select(cohort => new SelectListItem
{
Text = cohort.Name,
Value = cohort.Id.ToString()
})
.ToList();
Cohorts.Insert(0, new SelectListItem
{
Text = "Choose cohort...",
Value = "0"
});
//if there are no instructors for that student's cohort, then exercises shouldn't be able to be assigned to that student
if (instructorList.Count > 0)
{
Instructors = instructorList
.Select(i => new SelectListItem
{
Text = i.FullName,
Value = i.Id.ToString()
})
.ToList();
Exercises = exerciseList
.Select(e => new SelectListItem
{
Text = e.Name,
Value = e.Id.ToString()
})
.ToList();
}
}
//---------------------------------------------------------------------
public static void WriteLogFile(int CurrentTime)
{
double[] avgLiveB = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgAG_NPP = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgDefoliation = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgLitterB = new double[PlugIn.ModelCore.Ecoregions.Count];
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
avgLiveB[ecoregion.Index] = 0.0;
avgAG_NPP[ecoregion.Index] = 0.0;
avgDefoliation[ecoregion.Index] = 0.0;
avgLitterB[ecoregion.Index] = 0.0;
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
int youngBiomass; //ignored
avgLiveB[ecoregion.Index] += Cohorts.ComputeBiomass(SiteVars.Cohorts[site], out youngBiomass);
avgAG_NPP[ecoregion.Index] += SiteVars.AGNPP[site];
avgDefoliation[ecoregion.Index] += SiteVars.Defoliation[site];
avgLitterB[ecoregion.Index] += SiteVars.Litter[site].Mass;
}
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
if (EcoregionData.ActiveSiteCount[ecoregion] > 0)
{
PlugIn.summaryLog.Clear();
SummaryLog sl = new SummaryLog();
sl.Time = CurrentTime;
sl.EcoName = ecoregion.Name;
sl.ActiveCount = EcoregionData.ActiveSiteCount[ecoregion];
sl.AvgAG_NPP = (avgAG_NPP[ecoregion.Index] / (double)EcoregionData.ActiveSiteCount[ecoregion]);
sl.AvgDefoliation = (avgDefoliation[ecoregion.Index] / (double)EcoregionData.ActiveSiteCount[ecoregion]);
sl.AvgLitterB = (avgLitterB[ecoregion.Index] / (double)EcoregionData.ActiveSiteCount[ecoregion]);
sl.AvgLiveB = (avgLiveB[ecoregion.Index] / (double)EcoregionData.ActiveSiteCount[ecoregion]);
PlugIn.summaryLog.AddObject(sl);
PlugIn.summaryLog.WriteToFile();
}
}
string path = MapNames.ReplaceTemplateVars(@"biomass-succession\biomass-anpp-{timestep}.img", PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <IntPixel> outputRaster = PlugIn.ModelCore.CreateRaster <IntPixel>(path, PlugIn.ModelCore.Landscape.Dimensions))
{
IntPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (int)SiteVars.AGNPP[site];
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
}
public void GrowCohorts(DateTime date,
DateTime ToTime,
bool issuccessionTimestep)
{
if (Cohorts == null)
{
return;
}
while (date.CompareTo(ToTime) < 0)
{
PlugIn.SetYear(date.Year);
if (date.Month == (int)Months.January || canopy == null)
{
canopylaimax = 0;
if (cohorts == null)
{
return;
}
}
if (date.Month == (int)Months.June)
{
Defoliate(site);
}
hydrology.UpdateSiteHydrology(date);
canopy.Grow(date, site, hydrology, forestfloor, cohorts, siteoutput);
canopylaimax = canopy.CanopyLAImax;
foreach (Cohort cohort in canopy.DeadCohorts)
{
DeadCohortAges[cohort.Species].Add(cohort.Age);
deadcohorts[cohort.Species]++;
Cohorts[cohort.Species].RemoveCohort(cohort, site, null);
canopy.ResetDeadCohorts();
}
if (issuccessionTimestep)
{
Establishment.ComputeEstablishment(date, this);
if (HasSiteOutput)
{
estoutput.UpdateEstData(date, this);
}
}
if (HasSiteOutput)
{
siteoutput.UpdateSiteData(date, this);
siteoutput.WriteSiteData();
}
if (date.Month == (int)Months.December)
{
Cohorts.IncrementCohortsAge();
forestfloor.Decompose();
forestfloor.Decompose();
}
date = date.AddMonths(1);
}
if (CohortBiomass.HasDeadCohorts)
{
CohortBiomass.HasDeadCohorts = false;
}
}
public void Init(Cohorts cohorts)
{
DataTable tpsTable;
List <DataTable> tpsTables = new List <DataTable>();
foreach (var chType in chTypes)
{
stringBuilder.Clear();
stringBuilder.Append(agent).Append('_').Append(chType).Append("_TPS");
tpsTable = dataService.GetTable(stringBuilder.ToString());
if (tpsTable != null)
{
tpsTables.Add(tpsTable);
}
else
{
throw new Exception($"Cannot find the TPS table in the database for the {agent} - {chType} pair.");
}
foreach (DataRow row in tpsTable.Rows)
{
stringBuilder.Clear();
stringBuilder
.Append(agent).Append('_').Append(chType).Append('_').Append(row.Field <string>("InjuryProfileLabel"));
cohorts.Add(stringBuilder.ToString(), 0);
}
}
if (chTypes.Count > 1)
{
foreach (DataRow row0 in tpsTables[0].Rows)
{
foreach (DataRow row1 in tpsTables[1].Rows)
{
stringBuilder.Clear();
stringBuilder
.Append(agent).Append('_').Append(chTypes[0]).Append('_').Append(row0.Field <string>("InjuryProfileLabel"))
.Append(":")
.Append(agent).Append('_').Append(chTypes[1]).Append('_').Append(row1.Field <string>("InjuryProfileLabel"));
cohorts.Add(stringBuilder.ToString(), 0);
}
}
}
if (chTypes.Count == 3)
{
foreach (DataRow row0 in tpsTables[0].Rows)
{
foreach (DataRow row1 in tpsTables[1].Rows)
{
foreach (DataRow row2 in tpsTables[2].Rows)
{
stringBuilder.Clear();
stringBuilder
.Append(agent).Append('_').Append(chTypes[0]).Append('_').Append(row0.Field <string>("InjuryProfileLabel"))
.Append(":")
.Append(agent).Append('_').Append(chTypes[1]).Append('_').Append(row1.Field <string>("InjuryProfileLabel"))
.Append(":")
.Append(agent).Append('_').Append(chTypes[2]).Append('_').Append(row2.Field <string>("InjuryProfileLabel"));
cohorts.Add(stringBuilder.ToString(), 0);
}
}
}
}
}
private long GetNextCohortId() => Cohorts.Count == 0 ? 1 : Cohorts.Max(x => x.Id) + 1;
/// <summary>Loop through each cohort in this LifeCyclePhase to calculate development, mortality, graduation and reproduciton</summary>
public void Process()
{
if (Cohorts?.Count > 13000) //Check cohort number are not becomming silly
{
throw new Exception(FullPath + " has over 1500 cohorts which is to many really. This is why your simulation is slow and the data store is about to chuck it in. Check your " + this.Parent.Name.ToString() + " model to ensure development and mortality are sufficient.");
}
ZeorDeltas(); //Zero reporting properties for daily summing
if (Cohorts != null)
{
// Calculate daily deltas
foreach (Cohort c in Cohorts)
{
CurrentCohort = c;
c.ChronologicalAge += 1;
//Do development for each cohort
c.PhysiologicalAge = Math.Min(1.0, c.PhysiologicalAge + development.Value());
//Do mortality for each cohort
c.Mortalities = mortality.Value();
Mortalities += c.Mortalities;
c.Population = Math.Max(0.0, c.Population - c.Mortalities);
//Do reproduction for each cohort
c.Progeny = reproduction.Value();
Progeny += c.Progeny;
//Do migration for each cohort
c.Emigrants = migration.Value();
Emigrants += c.Emigrants;
c.Population = Math.Max(0.0, c.Population - c.Emigrants);
}
//Add Migrants into destination phase
if (Emigrants > 0)
{
double SumMigrantAge = 0;
double SumMigrantPAge = 0;
foreach (Cohort c in Cohorts)
{
if (c.Emigrants > 0)
{
SumMigrantAge += c.Emigrants * c.ChronologicalAge;
SumMigrantPAge += c.Emigrants * c.PhysiologicalAge;
}
}
double MeanMigrantAge = SumMigrantAge / Emigrants;
double MeanMigrantPAge = SumMigrantPAge / Emigrants;
if (MigrantDestinations.Count == 0)
{
throw new Exception(FullPath + " is predicting values for migration but has no MigrationDestinationPhase specified");
}
double MtotalProportion = 0;
foreach (MigrantDestinationPhase mdest in MigrantDestinations)
{
double destEmigrants = Emigrants * mdest.ProportionOfMigrants;
if ((MigrantDestinations.Count == 0) && (destEmigrants > 0))
{
throw new Exception(FullPath + " is predicting values for migration but has not MigrantDestinationPhase specified");
}
if (destEmigrants > 0)
{
IModel zone = Parent.FindAncestor <Zone>();
LifeCycle mDestinationCycle = zone.FindInScope <LifeCycle>(mdest.NameOfLifeCycleForMigrants);
if (mDestinationCycle == null)
{
throw new Exception(FullPath + " could not find a destination LifeCycle for migrants called " + mdest.NameOfLifeCycleForMigrants);
}
LifeCyclePhase mDestinationPhase = mDestinationCycle.FindChild <LifeCyclePhase>(mdest.NameOfPhaseForMigrants);
if (mDestinationPhase == null)
{
throw new Exception(FullPath + " could not find a destination LifeCyclePhase for migrants called " + mdest.NameOfPhaseForMigrants);
}
SourceInfo ImigrantInfo = new SourceInfo();
ImigrantInfo.LifeCycle = Parent.Name;
ImigrantInfo.LifeCyclePhase = this.Name;
ImigrantInfo.Type = SourceInfo.TypeOptions.Reproduction;
ImigrantInfo.Population = Emigrants;
ImigrantInfo.ChronologicalAge = MeanMigrantAge;
ImigrantInfo.PhysiologicalAge = MeanMigrantPAge;
mDestinationPhase?.NewCohort(ImigrantInfo);
MtotalProportion += mdest.ProportionOfMigrants;
}
}
if ((MtotalProportion > 1.001) && (Emigrants > 0))
{
throw new Exception("The sum of ProportionOfMigrants values in " + FullPath + " ProgenyDestinationPhases is greater than 1.0");
}
}
// Add progeny into destination phases
if (Progeny > 0)
{
if ((ProgenyDestinations.Count == 0) && (Progeny > 0))
{
throw new Exception(FullPath + " is predicting values for reproduction but has no ProgenyDestinationPhase specified");
}
double PtotalProportion = 0;
foreach (ProgenyDestinationPhase pdest in ProgenyDestinations)
{
double arrivals = Progeny * pdest.ProportionOfProgeny;
if (arrivals > 0)
{
IModel zone = Parent.FindAncestor <Zone>();
LifeCycle pDestinationCylce = zone.FindInScope <LifeCycle>(pdest.NameOfLifeCycleForProgeny);
if (pDestinationCylce == null)
{
throw new Exception(FullPath + " could not find a destination LifeCycle for progeny called " + pdest.NameOfLifeCycleForProgeny);
}
LifeCyclePhase pDestinationPhase = pDestinationCylce.FindChild <LifeCyclePhase>(pdest.NameOfPhaseForProgeny);
if (pDestinationPhase == null)
{
throw new Exception(FullPath + " could not find a destination LifeCyclePhase for progeny called " + pdest.NameOfPhaseForProgeny);
}
SourceInfo ArivalsInfo = new SourceInfo();
ArivalsInfo.LifeCycle = Parent.Name;
ArivalsInfo.LifeCyclePhase = this.Name;
ArivalsInfo.Type = SourceInfo.TypeOptions.Reproduction;
ArivalsInfo.Population = arrivals;
ArivalsInfo.ChronologicalAge = 0;
ArivalsInfo.PhysiologicalAge = 0;
pDestinationPhase?.NewCohort(ArivalsInfo);
PtotalProportion += pdest.ProportionOfProgeny;
}
}
if (((PtotalProportion < 0.999) || (PtotalProportion > 1.001)) && (Progeny > 0))
{
throw new Exception("The sum of ProportionOfProgeny values in " + FullPath + " ProgenyDestinationPhases does not equal 1.0");
}
}
// Move garduates to destination phase
foreach (Cohort c in Cohorts.ToArray())
{
if (c.PhysiologicalAge >= 1.0) //Members ready to graduate or die
{
if (LifeCyclePhaseForGraduates != null)
{
Graduates += c.Population; //Members graduate
}
else
{
Mortalities += c.Population; //Members die
}
Cohorts.Remove(c); //Remove mature cohort
}
if (c.Population < 0.001) //Remove cohort if all members dead
{
Cohorts.Remove(c);
}
}
if (Graduates > 0) //Promote graduates to cohort in next LifeCyclePhase
{
SourceInfo GraduateInfo = new SourceInfo();
GraduateInfo.LifeCycle = Parent.Name;
GraduateInfo.LifeCyclePhase = this.Name;
GraduateInfo.Type = SourceInfo.TypeOptions.Graduation;
GraduateInfo.Population = Graduates;
GraduateInfo.ChronologicalAge = 0;
GraduateInfo.PhysiologicalAge = 0;
LifeCyclePhaseForGraduates?.NewCohort(GraduateInfo);
}
}
}
/// <summary>
/// Empty the cohort list
/// </summary>
public void Clear()
{
Cohorts.Clear();
}
/// <summary>
/// Remove a specified cohort item
/// </summary>
/// <param name="aCohort">The cohort object to be removed</param>
public void Remove(Cohort aCohort)
{
Cohorts.Remove(aCohort);
}
/// <summary>
/// Remove the cohort at the end of the list
/// </summary>
public void RemoveLastCohort()
{
Cohorts.RemoveAt(Cohorts.Count - 1);
}
/// <summary>Loop through each cohort in this LifeCyclePhase to calculate development, mortality, graduation and reproduciton</summary>
public void Process()
{
if (Cohorts?.Count > 500) //Check cohort number are not becomming silly
{
throw new Exception(Apsim.FullPath(this) + " has over 500 cohorts which is to many really. This is why your simulation is slow and the data store is about to chuck it in. Check your " + this.Parent.Name.ToString() + " model to ensure development and mortality are sufficient.");
}
ZeorDeltas(); //Zero reporting properties for daily summing
foreach (ProgenyDestinationPhase pdest in ProgenyDestinations)
{
pdest.ProgenyToDestination = 0;
}
if (Cohorts != null)
{
// Calculate daily deltas
foreach (Cohort c in Cohorts)
{
CurrentCohort = c;
c.ChronologicalAge += 1;
//Do development for each cohort
c.PhysiologicalAge = Math.Min(1.0, c.PhysiologicalAge + development.Value());
//Do mortality for each cohort
c.Mortalities = mortality.Value();
Mortalities += c.Mortalities;
c.Population = Math.Max(0.0, c.Population - c.Mortalities);
//Do reproduction for each cohort
Progeny += reproduction.Value();
foreach (ProgenyDestinationPhase dest in ProgenyDestinations)
{
dest.ProgenyToDestination += reproduction.Value() * dest.ProportionOfProgeny;
}
//Do migration for each cohort
Migrants += migration.Value();
if (Migrants > 0)
{
if (MigrantDestinations.Count == 0)
{
throw new Exception(Apsim.FullPath(this) + " is predicting values for migration but has no MigrationDestinationPhase specified");
}
double MtotalProportion = 0;
foreach (MigrantDestinationPhase mdest in MigrantDestinations)
{
double cohortMigrants = migration.Value() * mdest.ProportionOfMigrants;
if ((MigrantDestinations.Count == 0) && (cohortMigrants > 0))
{
throw new Exception(Apsim.FullPath(this) + " is predicting values for migration but has not MigrantDestinationPhase specified");
}
if (cohortMigrants > 0)
{
IModel zone = Apsim.Parent(this.Parent, typeof(Zone));
LifeCycle mDestinationCycle = Apsim.Find(zone, mdest.NameOfLifeCycleForMigrants) as LifeCycle;
if (mDestinationCycle == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCycle for migrants called " + mdest.NameOfLifeCycleForMigrants);
}
LifeCyclePhase mDestinationPhase = Apsim.Child(mDestinationCycle, mdest.NameOfPhaseForMigrants) as LifeCyclePhase;
if (mDestinationPhase == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCyclePhase for migrants called " + mdest.NameOfPhaseForMigrants);
}
mDestinationPhase.NewCohort(cohortMigrants, c.ChronologicalAge, c.PhysiologicalAge);
MtotalProportion += mdest.ProportionOfMigrants;
}
}
if ((MtotalProportion > 1.001) && (Migrants > 0))
{
throw new Exception("The sum of ProportionOfMigrants values in " + Apsim.FullPath(this) + " ProgenyDestinationPhases is greater than 1.0");
}
}
}
// Add progeny into destination phase
if ((ProgenyDestinations.Count == 0) && (Progeny > 0))
{
throw new Exception(Apsim.FullPath(this) + " is predicting values for reproduction but has no ProgenyDestinationPhase specified");
}
double PtotalProportion = 0;
foreach (ProgenyDestinationPhase pdest in ProgenyDestinations)
{
if (pdest.ProgenyToDestination > 0)
{
IModel zone = Apsim.Parent(this.Parent, typeof(Zone));
LifeCycle pDestinationCylce = Apsim.Find(zone, pdest.NameOfLifeCycleForProgeny) as LifeCycle;
if (pDestinationCylce == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCycle for progeny called " + pdest.NameOfLifeCycleForProgeny);
}
LifeCyclePhase pDestinationPhase = Apsim.Child(pDestinationCylce, pdest.NameOfPhaseForProgeny) as LifeCyclePhase;
if (pDestinationPhase == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCyclePhase for progeny called " + pdest.NameOfPhaseForProgeny);
}
pDestinationPhase.NewCohort(pdest.ProgenyToDestination, 0, 0);
PtotalProportion += pdest.ProportionOfProgeny;
}
}
if (((PtotalProportion < 0.999) || (PtotalProportion > 1.001)) && (Progeny > 0))
{
throw new Exception("The sum of ProportionOfProgeny values in " + Apsim.FullPath(this) + " ProgenyDestinationPhases does not equal 1.0");
}
// Move garduates to destination phase
foreach (Cohort c in Cohorts.ToArray())
{
if (c.PhysiologicalAge >= 1.0) //Members ready to graduate or die
{
if (LifeCyclePhaseForGraduates != null)
{
Graduates += c.Population; //Members graduate
}
else
{
Mortalities += c.Population; //Members die
}
Cohorts.Remove(c); //Remove mature cohort
}
if (c.Population < 0.001) //Remove cohort if all members dead
{
Cohorts.Remove(c);
}
}
if (Graduates > 0) //Promote graduates to cohort in next LifeCyclePhase
{
LifeCyclePhaseForGraduates?.NewCohort(Graduates, 0.0, 0.0);
}
}
}
