/// <summary>
/// Start this program.
/// </summary>
static void Main()
{
var executePath = Environment.CurrentDirectory; // The executable path.
var exit = false; // while you want to redo this.
while (!exit)
{
var startDate = DateTime.Now; // Reccord running time.
const bool DoMulti = false; // Run all multi run.
const bool DoMultiRef = false; // Generate multi run reference.
const bool DoRefactorRef = false; // Generate the refactor test reference.
const bool DoRefactorTest = false; // Do the refactor test.
const bool DoCalibAreaIndex = false; // Do the area index calibration.
const bool DoPhenoRun = true; // Do the pheno run.
#region For each project
// Enter a for each project loop if needed.
if (DoMulti || DoMultiRef || DoRefactorRef || DoCalibAreaIndex || DoPhenoRun) // it is not a good idea to do all at one time
{
foreach (var projectPath in ProjectPaths) // Iterate throught all projects.
{
try
{
if (ToNotLoad.Contains(projectPath))
{
continue; // Skip this project if it is marked as ToNotLoad.
}
var absoluteProjectPath = FileHelper.GetAbsolute(executePath, projectPath);
Console.Write("Loading: " + absoluteProjectPath);
ProjectFile.Load(absoluteProjectPath); // Loading the project.
Console.WriteLine(".");
Console.WriteLine();
#region Simple multi runs
if (DoMulti)
{
ProjectHelper.ForEachMultiRun("Mutli run", true, true, "", DataDirectory, ToNotRun, null, true);
}
if (DoMultiRef)
{
ProjectHelper.ForEachMultiRun("Multi run ref", true, true, "-ref", DataMultiRefDirectory, ToNotRun, null, true);
}
if (DoRefactorRef)
{
ProjectHelper.ForEachMultiRun("Refactor run ref", true, true, "", DataRefactorRefDirectory, ToNotRun, null, true);
}
#endregion
#region Calib area index
if (DoCalibAreaIndex)
{
const double minArea = 15;
const double maxArea = 45;
ProjectHelper.ForEachMultiRun("Calib area index", false, false, "", DataDirectory, (rimm, i, s) =>
{
var multiRunItem = rimm.MultiRuns[i]; // Get mutli run item defintion.
var runName = multiRunItem.DailyOutputFileName.Replace(".sqsro", "");
if (!LeafAreaIndexAtAnthesis.ContainsKey(runName))
{
return(true); // No observation, return.
}
var obs = LeafAreaIndexAtAnthesis[runName];
var variety = ProjectFile.This.FileContainer.VarietyFile[multiRunItem.VarietyItemSelected];
var initialValue = variety.AreaPLL; // Save inital AreaPLL value.
var bestAreaIndex = double.PositiveInfinity;
var bestParameter = double.NaN;
try
{
for (var area = minArea; area <= maxArea; ++area) // Run current multi run item for all area.
{
rimm.StepRun(s, i);
var runObject = RunCore.RunInstance;
var universes = runObject.SavedUniverses;
var lastUniverse = universes[universes.Count - 1];
var anthesisDate = lastUniverse.Calendar_[GrowthStage.ZC_65_Anthesis];
if (anthesisDate == null)
{
continue;
}
var anthesisUniverse = runObject.GetUniverse(anthesisDate.Value);
var laiAnthesis = anthesisUniverse.Crop_.Phytomers_.LaminaeAI;
if (Math.Abs(obs - laiAnthesis) > Math.Abs(obs - bestAreaIndex))
{
continue;
}
bestAreaIndex = laiAnthesis; // A better value has been found.
bestParameter = area;
}
if (!double.IsPositiveInfinity(bestAreaIndex)) // Print best value.
{
Console.Write(variety.Name + " Area PLL : " + bestParameter + " Error: " + Math.Abs(obs - bestAreaIndex).ToString("0.000"));
}
else // No value found (all run in Error).
{
Console.Write("No min found");
}
Console.WriteLine(" ]");
Console.Write("{0,20}", "");
}
finally
{
variety.AreaPLL = initialValue; // Restore intial AreaPLL value.
}
return(false); // Run has not been skipped.
}, ToNotRun, VarietyToRun, true);
}
#endregion
#region Pheno run
if (DoPhenoRun)
{
const int numberOfPerturbation = 1000; // Number of perturbation for each multi run item.
// The pheno run f2akes a sensitivity run of 5 parameters.
var paramNames = new[] { "Phyllochron", "PhyllFLLAnth", "SLDL", "VAI", "VBEE" }; // Parameters names which are perturbed.
var paramMinValues = new[] { 70.0, 1.0, 0.20, 0.0002, 0.0040 }; // Minimum of the parameters.
var paramMaxValues = new[] { 140.0, 4.0, 1.0, 0.0030, 0.0150 }; // Maximum of the parameters.
var paramSteps = new[] { 1.0, 0.05, 0.01, 0.00002, 0.0001 }; // Step between each values in the space.
var paramValues = new[] { double.NaN, double.NaN, double.NaN, double.NaN, double.NaN }; // Parameters values which are perturbed.
var paramStepCounts = new[] { 1 + (int)((paramMaxValues[0] - paramMinValues[0]) / paramSteps[0]), // Step count for each parameters.
1 + (int)((paramMaxValues[1] - paramMinValues[1]) / paramSteps[1]), // This is the space length of each parameter.
1 + (int)((paramMaxValues[2] - paramMinValues[2]) / paramSteps[2]),
1 + (int)((paramMaxValues[3] - paramMinValues[3]) / paramSteps[3]),
1 + (int)((paramMaxValues[4] - paramMinValues[4]) / paramSteps[4]) };
const int indexPhyllochron = 0; // Index of the Phyllochron parameter in the array above.
const int indexPhyllFLLAnth = 1; // Index of the PhyllFLLAnth parameter in the array above.
const int indexSLDL = 2; // Index of the SLDL parameter in the array above.
const int indexVAI = 3; // Index of the VAI parameter in the array above.
const int indexVBEE = 4; // Index of the VBEE parameter in the array above.
const int numberOfParameter = 5; // Number of parameter to pertube.
var initialOutputVersion = ProjectFile.This.FileContainer.OutputVersion; // Save initial output version.
try
{
ProjectFile.This.FileContainer.OutputVersion = OutputVersion.V15; // Ensure Output version 1.5, as it is the only one supporting sensitivity output.
ProjectHelper.ForEachMultiRun("Pheno run", false, false, "", DataDirectory, (rimm, i, s) =>
{
var multiRunItem = rimm.MultiRuns[i]; // Get mutli run item defintion.
var runFileName = multiRunItem.DailyOutputFileName.Replace(".sqsro", ".sqsrs"); // Get summary output file name.
var runName = runFileName.Replace(".sqsro", "");
if (PhenoRunSelection.FirstOrDefault(runName.Contains) == null)
{
return(true); // Multi run item is not selected for the pheno run, return.
}
runFileName = runFileName.Replace("01-ALC", ""); // Remove vareity name.
var variety = ProjectFile.This.FileContainer.VarietyFile[multiRunItem.VarietyItemSelected];
// Save initial values.
var initialPhyllochron = variety.Phyllochron;
var initialPhyllFllAnth = variety.PhyllFLLAnth;
var initialSLDL = variety.SLDL;
var initialVAI = variety.VAI;
var initialVBEE = variety.VBEE;
try
{
// Create a new output file.
var page = OutputFile.ExtractSensitivityRunHeader(paramNames); // Generate header of the sensitivity file.
// var page = new PageData(); // Use this line to create the page if you don't want the header.
Random = new Random(RandomSeed); // Uncomment this line to always generate the same pertubations for each varieties on each site.
for (var permut = 0; permut < numberOfPerturbation; ++permut) // Perturbe and run loop.
{
for (var param = 0; param < numberOfParameter; ++param) // Generate a new vector.
{
// Random.Next(paramStepCounts[param]) == random number in [0, paramStepCounts[param] - 1].
paramValues[param] = paramMinValues[param] + paramSteps[param] * Random.Next(paramStepCounts[param]);
}
// Assign variety parameters.
variety.Phyllochron = paramValues[indexPhyllochron];
variety.PhyllFLLAnth = paramValues[indexPhyllFLLAnth];
variety.SLDL = paramValues[indexSLDL];
variety.VAI = paramValues[indexVAI];
variety.VBEE = paramValues[indexVBEE];
rimm.StepRun(s, i); // Run the model with the vector generated above.
page.Add(OutputFile.ExtractSensitivityRunLine(RunCore.RunInstance, paramValues)); // Save the summary of the run above.
}
Serialization.SerializeText(page, rimm.AbsoluteOutputDirectory + "\\" + runFileName); // Save the summary file.
}
finally
{
// Restore initial values.
variety.Phyllochron = initialPhyllochron;
variety.PhyllFLLAnth = initialPhyllFllAnth;
variety.SLDL = initialSLDL;
variety.VAI = initialVAI;
variety.VBEE = initialVBEE;
}
return(false); // Run has not been skipped.
}, ToNotRun, VarietyToRun, true);
}
finally
{
ProjectFile.This.FileContainer.OutputVersion = initialOutputVersion; // Restore initial output version.
}
}
#endregion
}
catch (Exception e)
{
Console.WriteLine("Error: " + e.Message);
}
ProjectFile.New();
}
}
#endregion
#region Refactor test
if (DoRefactorTest)
{
Console.WriteLine("Refactor test");
var stack = new Stack <DirectoryInfo>();
stack.Push(new DirectoryInfo(DataRefactorRefDirectory));
do
{
var onTop = stack.Pop();
var error = 0;
Console.Write("{0,50}", onTop.FullName.Replace(DataRefactorRefDirectory, ""));
Console.Write(" [");
foreach (var fileRef in onTop.GetFiles())
{
if (!ExtensionToTest.Contains(fileRef.Extension))
{
continue;
}
try
{
var fileNew = new FileInfo(DataDirectory + fileRef.FullName.Replace(DataRefactorRefDirectory, ""));
using (var streamRef = fileRef.OpenRead())
{
using (var streamNew = fileNew.OpenRead())
{
var differences = 0L;
var count = 0L;
var readRef = 0;
var readNew = 0;
do
{
}while ((readRef = streamRef.ReadByte()) != -1 && readRef != '\n');
do
{
}while ((readNew = streamNew.ReadByte()) != -1 && readNew != '\n');
while ((readRef = streamRef.ReadByte()) != -1 &&
(readNew = streamNew.ReadByte()) != -1)
{
++count;
if (readRef != readNew)
{
++differences;
}
}
if (count == 0)
{
Console.Write(" ");
}
else if (differences > 0)
{
Console.Write("*");
}
else
{
Console.Write(".");
}
}
}
}
catch (Exception)
{
++error;
Console.Write("!");
}
}
Console.WriteLine("]");
foreach (var subDirectory in onTop.GetDirectories())
{
stack.Push(subDirectory);
}
}while (stack.Count != 0);
}
#endregion
var stopDate = DateTime.Now; // Reccord running time.
Console.WriteLine();
Console.WriteLine("done (" + (stopDate - startDate).TotalSeconds.ToString("0.00") + " s), redo ?");
exit = Console.ReadKey().Key != ConsoleKey.Y; // We redo if user press Y.
/*
* Create output file example.
*
* var p = new PageData(); // Create a new output file.
* p.NewLine().Add("Parameter1").Add("Parameter2").Add("Value1").Add("Value2"); // Print a header for this file.
* // Here 2 parameters and 2 values.
* foreach (var run in allRun) // The run loop, replace by what run you want to do, like for the PhenoRun.
* {
* run.Run(); // Make your run.
* p.NewLine().Add(run.Parameter1).Add(run.Parameter2).Add(run.Value1).Add(run.Value2); // Write one output line, with
* // 2 parameter values, 2 output values.
* }
* Serialization.SerializeText(p, "MyFilePath.out"); // Save the output file.
* p.Clear(); // Clean memory.
* p = null;*/
}
}
private static void RunProjectFile(string varietyToOverride = null, string parameterName = null, double parameterValue = 0)
{
ProjectHelper.ForEachMultiRun("Running " + ProjectFilePath, true, OutputSingleRun, null, null, null, null, ShowProgress, varietyToOverride, parameterName, parameterValue);
}
