public float RunSiriusModel(string calibrationRoundID, string dataDirectory, string workDirectory, string projectDirectory, string genericAlgorithmsDirectory,
ArrayList observationArray, ArrayList stdArray, int[] kParameterSiteIndex, int amplificationFactor, double CV, ArrayList observationDateArray, ArrayList observationSeperator)
{
#region Input variables
//Assign the random values generated above to each of the parameters.
int observationNumber = observationArray.Count;
//Get the number of observations.
string outputFileName = "ModelOutput";
string outputFileExtention = ".txt";
string wholeOutputFileName = workDirectory + genericAlgorithmsDirectory + outputFileName + outputFileExtention;//Assign the path of the text file to save the model outputs concerned.
File.WriteAllText(wholeOutputFileName, "");
//Create a txt file to save model outputs concerned and clean up the output contents of last model run before a new run.
#endregion
#region Run the model
AutomaticModelRun.ModelRun(
TheArray,
calibrationRoundID,
dataDirectory,
workDirectory,
projectDirectory,
wholeOutputFileName,
kParameterSiteIndex,
observationDateArray,
observationSeperator
);
//Call the AutomaticModelRun statis class to run the model.
#endregion
#region Read model outputs
List <double> modelOutputs = new List <double>();
StreamReader SR = File.OpenText(wholeOutputFileName);
string fileLineContent = null;
modelOutputs.Clear();
while ((fileLineContent = SR.ReadLine()) != null)
{
modelOutputs.Add(Convert.ToDouble(fileLineContent));
}
SR.Close();
//Read the model outputs saved during the model run and save them in a list.
#endregion
#region Fitness calculation
// fitness for the closest predictions to observations.
predictionArray.Clear();
for (int i = 0; i < observationNumber; i++)
{
predictionArray.Add(modelOutputs[i]);
}
//Prediction of anthesis dates and FLN of the hight nitrogen treatment at Clermont-Ferrand in 2007 and 2008 in order.
//Declare an array to save the predictions concerned, e.g. anthesis date, final leaf number, LAI, etc.
float[] fitnessValues = new float[observationNumber];
float CurrentFitness = 1;
for (int i = 0; i < observationNumber; i++)
{
double observationValue = Convert.ToDouble(observationArray[i]);
double stdValue = Convert.ToDouble(stdArray[i]);
double predictionValue = Convert.ToDouble(predictionArray[i]);
//Console.WriteLine(amplificationFactor);
if (observationValue != -999 & predictionValue != -999)
{
//fitnessValues[i] = (float)(Math.Exp(-Math.Abs((float)Math.Pow((observationValue - predictionValue), 2) / (2 * (float)Math.Pow((stdValue* amplificationFactor), 2)))));
fitnessValues[i] = (float)(Math.Exp(-Math.Abs((float)Math.Pow((observationValue - predictionValue), 2) / (2 * (float)Math.Pow((observationValue * CV), 2))))) * amplificationFactor;
//The CV was modified to a variable for different sub-models since the fitness values are hard to calculate for many observation points.
}
else
{
fitnessValues[i] = 1;
}
//Console.WriteLine("***");
//Console.WriteLine(fitnessValues[i]);
CurrentFitness = CurrentFitness * fitnessValues[i];
}
Console.WriteLine("The fitness value is {0}", Math.Round(CurrentFitness, 15));
return(CurrentFitness);
#endregion
}
static void Main(string[] args)
{
Console.WriteLine("Global sensitivity analysis is starting, please wait...");//The procedure of GSA is starting.
#region Working directory of the model.
//int numberOfRandomLines = 860;
//int numberOfParameters = 85; //For 85 parameters.
int numberOfRandomLines = 770;
int numberOfParameters = 76;//For 76 parameters.
string projectDirectory = @"C:\Postdoc Research\INRA\SiriusQuality1.5\Data\v1.5-Project\";
string projectFileName = @"v1.5-SensitivityAnalysis.sqpro";//The name of the run file of sensitivity analysis.
string projectPath = projectDirectory + projectFileName;
//Console.WriteLine(projectPath);
string GSADirectory = @"C:\Postdoc Research\INRA\SiriusQuality1.5\Data\INRA-BBSRC 16cv project\Sensitivity Analysis\";//GSA=global sensitivity analysis
string inputDirectory = @"Morris\";
//string RandomInputFileName = @"All Parameter-Morris-860.txt";
string RandomInputFileName = @"76 Parameter-Morris.txt"; //It was changed to 76 parameters now.
string RandomInputFilePath = GSADirectory + inputDirectory + RandomInputFileName;
//Console.WriteLine(RandomInputFileName);
string outputDirectory = @"Morris\";
string outputFileName = "ModelOutput_Morris_";
string[] treatmentNames = new string[] { "AV-HighN", "AV-LowN", "CF-HighN", "CF-LowN", "RR-HighN", "RR-LowN" };
string outputFileExtention = ".txt";
string[] wholeOutputFileNames = new string[treatmentNames.Length];
for (int i = 0; i < wholeOutputFileNames.Length; i++)
{
string wholeOutputFileName = GSADirectory + outputDirectory + outputFileName + treatmentNames[i] + outputFileExtention; //Assign the path of the text file to save the temporary model outputs concerned.
File.WriteAllText(wholeOutputFileName, ""); //Clear the temp ouput file that contains model outputs concerned.
wholeOutputFileNames[i] = wholeOutputFileName;
//Console.WriteLine(wholeOutputFileNames[i]);
}
#endregion
ReadTextFile readTextFile = new ReadTextFile();
string[,] randoms = readTextFile.ReadText(RandomInputFilePath, numberOfRandomLines, numberOfParameters); //Read the input file of random parameter sets.
int usedRandomLines = randoms.GetLength(0); //The integer to show how many model runs will be conducted in current simulation.
//int usedRandomLines = 200;
for (int i = 0; i < usedRandomLines; i++)
{
#region 1. Load random parameter set.
List <double> inputParameterValues = new List <double>();
for (int j = 0; j < randoms.GetLength(1); j++)
{
double temParameterValue = Convert.ToDouble(randoms[i, j]);
inputParameterValues.Add(temParameterValue);
}
#endregion
#region 2. Run the model.
AutomaticModelRun.ModelRun(inputParameterValues, GSADirectory, projectPath, wholeOutputFileNames);
inputParameterValues.Clear();//Run the project.
#endregion
Console.WriteLine("Parameter set {0} is finished, please wait...", i + 1);
}
Console.WriteLine("Global Sensitivity Analysis is finished!");
//Console.ReadLine();
}
