public static void Save(Madingley.Common.FunctionalGroupDefinitions c, string filename)
{
var definitionHeaders = c.Definitions.Select(k => String.Format("DEFINITION_{0}", k));
var propertyHeaders = c.Properties.Select(k => String.Format("PROPERTY_{0}", k));
var cohortRows =
c.Data.Select(data =>
{
var definitionsElements =
c.Definitions.Select(definition =>
data.Definitions.ContainsKey(definition) ? data.Definitions[definition] : "");
var propertyElements =
c.Properties.Select(property =>
data.Properties.ContainsKey(property) ? data.Properties[property].ToString("G17") : "");
var allElements = definitionsElements.Concat(propertyElements);
return(System.String.Join(",", allElements));
});
var allHeaders = definitionHeaders.Concat(propertyHeaders);
var header = System.String.Join(",", allHeaders);
using (var writer = new StreamWriter(filename))
{
writer.WriteLine(header);
cohortRows.ToList().ForEach(line => writer.WriteLine(line));
}
}
public static FunctionalGroupDefinitions ConvertFunctionalGroupDefinitions(Madingley.Common.FunctionalGroupDefinitions data)
{
// Initialise the lists
var length = data.Data.Count();
var IndexLookupFromTrait = new SortedDictionary <string, SortedDictionary <string, int[]> >();
var FunctionalGroupProperties = new SortedList <string, double[]>();
var TraitLookupFromIndex = new SortedDictionary <string, string[]>();
var AllFunctionalGroupsIndex = new int[length];
// Loop over columns in the functional group definitions file
foreach (var traitName in data.Definitions)
{
var traitValues =
data.Data.Select(d => d.Definitions.First(kv => kv.Key == traitName).Value).ToArray();
// Declare a sorted dictionary to hold the index values for each unique trait value
SortedDictionary <string, int[]> TraitIndexValuesList = new SortedDictionary <string, int[]>();
// Create a string array with the values of this trait
for (int nn = 0; nn < length; nn++)
{
// Add the functional group index to the list of all indices
AllFunctionalGroupsIndex[nn] = nn;
}
// Add the trait values to the trait-value lookup list
TraitLookupFromIndex.Add(traitName, traitValues);
// Get the unique values for this trait
var DistinctValues = traitValues.Distinct().ToArray();
//Loop over the unique values for this trait and list all the functional group indices with the value
foreach (string DistinctTraitValue in DistinctValues.ToArray())
{
List <int> FunctionalGroupIndex = new List <int>();
//Loop over the string array associated with this trait and add the index values of matching string to a list
for (int kk = 0; kk < traitValues.Length; kk++)
{
if (traitValues[kk].Equals(DistinctTraitValue))
{
FunctionalGroupIndex.Add(kk);
}
}
//Add the unique trait value and the functional group indices to the temporary list
TraitIndexValuesList.Add(DistinctTraitValue, FunctionalGroupIndex.ToArray());
}
// Add the unique trait values and corresponding functional group indices to the functional group index lookup
IndexLookupFromTrait.Add(traitName, TraitIndexValuesList);
}
// For functional group properties
foreach (var traitName in data.Properties)
{
var traitValues =
data.Data.Select(d => d.Properties.First(kv => kv.Key == traitName).Value).ToArray();
// Get the values for this property
double[] TempDouble = new double[length];
for (int nn = 0; nn < length; nn++)
{
TempDouble[nn] = Convert.ToDouble(traitValues.GetValue(nn));
}
// Add the values to the list of functional group properties
FunctionalGroupProperties.Add(traitName, TempDouble);
}
return(new FunctionalGroupDefinitions(
IndexLookupFromTrait,
FunctionalGroupProperties,
TraitLookupFromIndex,
AllFunctionalGroupsIndex));
}
public static Madingley.Common.Configuration Deserialize(TextReader sr)
{
Func <Newtonsoft.Json.JsonTextReader, Madingley.Common.FunctionalGroupDefinition> JsonReadFunctionalGroupDefinition = (reader) =>
{
var ret = new Madingley.Common.FunctionalGroupDefinition();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Definitions": ret.Definitions = Common.Reader.ReadKeyValuePairs(reader, Common.Reader.ReadString); break;
case "Properties": ret.Properties = Common.Reader.ReadKeyValuePairs(reader, Common.Reader.ReadDouble); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return(ret);
};
Func <Newtonsoft.Json.JsonTextReader, Madingley.Common.FunctionalGroupDefinitions> JsonReadFunctionalGroupDefinitions = (reader) =>
{
var ret = new Madingley.Common.FunctionalGroupDefinitions();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Data": ret.Data = Common.Reader.ReadArray(reader, JsonReadFunctionalGroupDefinition); break;
case "Definitions": ret.Definitions = Common.Reader.ReadArray(reader, Common.Reader.ReadString); break;
case "Properties": ret.Properties = Common.Reader.ReadArray(reader, Common.Reader.ReadString); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return(ret);
};
Func <Newtonsoft.Json.JsonTextReader, Madingley.Common.ScenarioParameter> JsonReadScenarioParameter = (reader) =>
{
var ret = new Madingley.Common.ScenarioParameter();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "ParamString": ret.ParamString = Common.Reader.ReadString(reader); break;
case "ParamDouble1": ret.ParamDouble1 = Common.Reader.ReadDouble(reader); break;
case "ParamDouble2": ret.ParamDouble2 = Common.Reader.ReadDouble(reader); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return(ret);
};
Func <Newtonsoft.Json.JsonTextReader, IDictionary <string, Madingley.Common.ScenarioParameter> > JsonReadKVPScenarioParameter = (reader) =>
{
var ret = new Dictionary <string, Madingley.Common.ScenarioParameter>();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var key = Convert.ToString(reader.Value);
reader.Read();
var value = JsonReadScenarioParameter(reader);
ret.Add(key, value);
}
return(ret);
};
Func <Newtonsoft.Json.JsonTextReader, Madingley.Common.ScenarioParameters> JsonReadScenarioParameters = (reader) =>
{
var ret = new Madingley.Common.ScenarioParameters();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Label": ret.Label = Common.Reader.ReadString(reader); break;
case "SimulationNumber": ret.SimulationNumber = Common.Reader.ReadInt(reader); break;
case "Parameters": ret.Parameters = JsonReadKVPScenarioParameter(reader); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return(ret);
};
Func <Newtonsoft.Json.JsonTextReader, Madingley.Common.EcologicalParameters> JsonReadEcologicalParameters = (reader) =>
{
var ret = new Madingley.Common.EcologicalParameters();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Parameters": ret.Parameters = Common.Reader.ReadKeyValuePairs(reader, Common.Reader.ReadDouble); break;
case "TimeUnits": ret.TimeUnits = Common.Reader.ReadArray(reader, Common.Reader.ReadString); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return(ret);
};
var configuration = new Madingley.Common.Configuration();
using (var reader = new Newtonsoft.Json.JsonTextReader(sr))
{
reader.Read();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "GlobalModelTimeStepUnit": configuration.GlobalModelTimeStepUnit = Common.Reader.ReadString(reader); break;
case "NumTimeSteps": configuration.NumTimeSteps = Common.Reader.ReadInt(reader); break;
case "BurninTimeSteps": configuration.BurninTimeSteps = Common.Reader.ReadInt(reader); break;
case "ImpactTimeSteps": configuration.ImpactTimeSteps = Common.Reader.ReadInt(reader); break;
case "RecoveryTimeSteps": configuration.RecoveryTimeSteps = Common.Reader.ReadInt(reader); break;
case "RunCellsInParallel": configuration.RunCellsInParallel = Common.Reader.ReadBoolean(reader); break;
case "RunSimulationsInParallel": configuration.RunSimulationsInParallel = Common.Reader.ReadBoolean(reader); break;
case "RunRealm": configuration.RunRealm = Common.Reader.ReadString(reader); break;
case "DrawRandomly": configuration.DrawRandomly = Common.Reader.ReadBoolean(reader); break;
case "ExtinctionThreshold": configuration.ExtinctionThreshold = Common.Reader.ReadDouble(reader); break;
case "MaxNumberOfCohorts": configuration.MaxNumberOfCohorts = Common.Reader.ReadInt(reader); break;
case "DispersalOnly": configuration.DispersalOnly = Common.Reader.ReadBoolean(reader); break;
case "DispersalOnlyType": configuration.DispersalOnlyType = Common.Reader.ReadString(reader); break;
case "PlanktonDispersalThreshold": configuration.PlanktonDispersalThreshold = Common.Reader.ReadDouble(reader); break;
case "CohortFunctionalGroupDefinitions": configuration.CohortFunctionalGroupDefinitions = JsonReadFunctionalGroupDefinitions(reader); break;
case "StockFunctionalGroupDefinitions": configuration.StockFunctionalGroupDefinitions = JsonReadFunctionalGroupDefinitions(reader); break;
case "ImpactCellIndices": configuration.ImpactCellIndices = Common.Reader.ReadArray(reader, Common.Reader.ReadInt); break;
case "ImpactAll": configuration.ImpactAll = Common.Reader.ReadBoolean(reader); break;
case "ScenarioParameters": configuration.ScenarioParameters = Common.Reader.ReadArray(reader, JsonReadScenarioParameters).ToList(); break;
case "ScenarioIndex": configuration.ScenarioIndex = Common.Reader.ReadInt(reader); break;
case "Simulation": configuration.Simulation = Common.Reader.ReadInt(reader); break;
case "EcologicalParameters": configuration.EcologicalParameters = JsonReadEcologicalParameters(reader); break;
case "FileNames": configuration.FileNames = Common.Reader.ReadArray(reader, Common.Reader.ReadString).ToList(); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
}
return(configuration);
}
public static Madingley.Common.Configuration Deserialize(TextReader sr)
{
Func<Newtonsoft.Json.JsonTextReader, Madingley.Common.FunctionalGroupDefinition> JsonReadFunctionalGroupDefinition = (reader) =>
{
var ret = new Madingley.Common.FunctionalGroupDefinition();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Definitions": ret.Definitions = Common.Reader.ReadKeyValuePairs(reader, Common.Reader.ReadString); break;
case "Properties": ret.Properties = Common.Reader.ReadKeyValuePairs(reader, Common.Reader.ReadDouble); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return ret;
};
Func<Newtonsoft.Json.JsonTextReader, Madingley.Common.FunctionalGroupDefinitions> JsonReadFunctionalGroupDefinitions = (reader) =>
{
var ret = new Madingley.Common.FunctionalGroupDefinitions();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Data": ret.Data = Common.Reader.ReadArray(reader, JsonReadFunctionalGroupDefinition); break;
case "Definitions": ret.Definitions = Common.Reader.ReadArray(reader, Common.Reader.ReadString); break;
case "Properties": ret.Properties = Common.Reader.ReadArray(reader, Common.Reader.ReadString); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return ret;
};
Func<Newtonsoft.Json.JsonTextReader, Madingley.Common.ScenarioParameter> JsonReadScenarioParameter = (reader) =>
{
var ret = new Madingley.Common.ScenarioParameter();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "ParamString": ret.ParamString = Common.Reader.ReadString(reader); break;
case "ParamDouble1": ret.ParamDouble1 = Common.Reader.ReadDouble(reader); break;
case "ParamDouble2": ret.ParamDouble2 = Common.Reader.ReadDouble(reader); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return ret;
};
Func<Newtonsoft.Json.JsonTextReader, IDictionary<string, Madingley.Common.ScenarioParameter>> JsonReadKVPScenarioParameter = (reader) =>
{
var ret = new Dictionary<string, Madingley.Common.ScenarioParameter>();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var key = Convert.ToString(reader.Value);
reader.Read();
var value = JsonReadScenarioParameter(reader);
ret.Add(key, value);
}
return ret;
};
Func<Newtonsoft.Json.JsonTextReader, Madingley.Common.ScenarioParameters> JsonReadScenarioParameters = (reader) =>
{
var ret = new Madingley.Common.ScenarioParameters();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Label": ret.Label = Common.Reader.ReadString(reader); break;
case "SimulationNumber": ret.SimulationNumber = Common.Reader.ReadInt(reader); break;
case "Parameters": ret.Parameters = JsonReadKVPScenarioParameter(reader); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return ret;
};
Func<Newtonsoft.Json.JsonTextReader, Madingley.Common.EcologicalParameters> JsonReadEcologicalParameters = (reader) =>
{
var ret = new Madingley.Common.EcologicalParameters();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "Parameters": ret.Parameters = Common.Reader.ReadKeyValuePairs(reader, Common.Reader.ReadDouble); break;
case "TimeUnits": ret.TimeUnits = Common.Reader.ReadArray(reader, Common.Reader.ReadString); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
return ret;
};
var configuration = new Madingley.Common.Configuration();
using (var reader = new Newtonsoft.Json.JsonTextReader(sr))
{
reader.Read();
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.StartObject);
while (reader.Read() &&
reader.TokenType != Newtonsoft.Json.JsonToken.EndObject)
{
Debug.Assert(reader.TokenType == Newtonsoft.Json.JsonToken.PropertyName);
Debug.Assert(reader.ValueType == typeof(string));
var property = Convert.ToString(reader.Value);
reader.Read();
switch (property)
{
case "GlobalModelTimeStepUnit": configuration.GlobalModelTimeStepUnit = Common.Reader.ReadString(reader); break;
case "NumTimeSteps": configuration.NumTimeSteps = Common.Reader.ReadInt(reader); break;
case "BurninTimeSteps": configuration.BurninTimeSteps = Common.Reader.ReadInt(reader); break;
case "ImpactTimeSteps": configuration.ImpactTimeSteps = Common.Reader.ReadInt(reader); break;
case "RecoveryTimeSteps": configuration.RecoveryTimeSteps = Common.Reader.ReadInt(reader); break;
case "RunCellsInParallel": configuration.RunCellsInParallel = Common.Reader.ReadBoolean(reader); break;
case "RunSimulationsInParallel": configuration.RunSimulationsInParallel = Common.Reader.ReadBoolean(reader); break;
case "RunRealm": configuration.RunRealm = Common.Reader.ReadString(reader); break;
case "DrawRandomly": configuration.DrawRandomly = Common.Reader.ReadBoolean(reader); break;
case "ExtinctionThreshold": configuration.ExtinctionThreshold = Common.Reader.ReadDouble(reader); break;
case "MaxNumberOfCohorts": configuration.MaxNumberOfCohorts = Common.Reader.ReadInt(reader); break;
case "DispersalOnly": configuration.DispersalOnly = Common.Reader.ReadBoolean(reader); break;
case "DispersalOnlyType": configuration.DispersalOnlyType = Common.Reader.ReadString(reader); break;
case "PlanktonDispersalThreshold": configuration.PlanktonDispersalThreshold = Common.Reader.ReadDouble(reader); break;
case "CohortFunctionalGroupDefinitions": configuration.CohortFunctionalGroupDefinitions = JsonReadFunctionalGroupDefinitions(reader); break;
case "StockFunctionalGroupDefinitions": configuration.StockFunctionalGroupDefinitions = JsonReadFunctionalGroupDefinitions(reader); break;
case "ImpactCellIndices": configuration.ImpactCellIndices = Common.Reader.ReadArray(reader, Common.Reader.ReadInt); break;
case "ImpactAll": configuration.ImpactAll = Common.Reader.ReadBoolean(reader); break;
case "ScenarioParameters": configuration.ScenarioParameters = Common.Reader.ReadArray(reader, JsonReadScenarioParameters).ToList(); break;
case "ScenarioIndex": configuration.ScenarioIndex = Common.Reader.ReadInt(reader); break;
case "Simulation": configuration.Simulation = Common.Reader.ReadInt(reader); break;
case "EcologicalParameters": configuration.EcologicalParameters = JsonReadEcologicalParameters(reader); break;
case "FileNames": configuration.FileNames = Common.Reader.ReadArray(reader, Common.Reader.ReadString).ToList(); break;
default: throw new Exception(string.Format("Unexpected property: {0}", property));
}
}
}
return configuration;
}
