/// <summary>
/// Reads in all initialisation files and copies them to the output directory for future reference
/// </summary>
/// <param name="initialisationFile">The name of the initialization file with information on the simulations to be run</param>
/// <param name="outputPath">The path to folder in which outputs will be stored</param>
/// <todo>Need to adjust this file to deal with incorrect inputs, extra columns etc by throwing an error</todo>
/// <todo>Also need to strip leading spaces</todo>
public void ReadAndCopyInitialisationFiles(string simulationInitialisationFilename, string definitionsFilename, string outputsFilename, string outputPath)
{
// Construct file names
string SimulationFileString = "msds:csv?file=input/Model setup/" + simulationInitialisationFilename + "&openMode=readOnly";
string DefinitionsFileString = "msds:csv?file=input/Model setup/" + definitionsFilename + "&openMode=readOnly";
string OutputsFileString = "msds:csv?file=input/Model setup/" + outputsFilename + "&openMode=readOnly";
// Copy the initialisation files to the output directory
System.IO.File.Copy("input/Model setup/" + simulationInitialisationFilename, outputPath + simulationInitialisationFilename, true);
System.IO.File.Copy("input/Model setup/" + definitionsFilename, outputPath + definitionsFilename, true);
System.IO.File.Copy("input/Model setup/" + outputsFilename, outputPath + outputsFilename, true);
// Read in the definitions data
InternalData = DataSet.Open(DefinitionsFileString);
// Get the names of parameters in the initialization file
VarParameters = InternalData.Variables[1].GetData();
// Get the values for the parameters
VarValues = InternalData.Variables[0].GetData();
#endif
// Loop over the parameters
for (int row = 0; row < VarParameters.Length; row++)
{
// Switch based on the name of the parameter, and write the value to the appropriate field
switch (VarParameters.GetValue(row).ToString().ToLower())
{
case "mass bin filename":
// Set up the mass bins as specified in the initialization file
#if true
_ModelMassBins.SetUpMassBins(VarValues.GetValue(row).ToString(), outputPath, inputPath);
#else
_ModelMassBins.SetUpMassBins(VarValues.GetValue(row).ToString(), outputPath);
#endif
break;
}
}
InternalData.Dispose();
// Read in the outputs data
InternalData = DataSet.Open(OutputsFileString);
// Get the names of parameters in the initialization file
VarParameters = InternalData.Variables[1].GetData();
// Get the values for the parameters
VarValues = InternalData.Variables[0].GetData();
// Loop over the parameters
for (int row = 0; row < VarParameters.Length; row++)
{
// Switch based on the name of the parameter, and write the value to the appropriate field
switch (VarParameters.GetValue(row).ToString().ToLower())
{
case "track processes":
switch (VarValues.GetValue(row).ToString().ToLower())
{
case "yes":
_TrackProcesses = true;
break;
case "no":
_TrackProcesses = false;
break;
}
break;
case "track cross cell processes":
switch (VarValues.GetValue(row).ToString().ToLower())
{
case "yes":
_TrackCrossCellProcesses = true;
break;
case "no":
_TrackCrossCellProcesses = false;
break;
}
break;
case "track global processes":
switch (VarValues.GetValue(row).ToString().ToLower())
{
case "yes":
_TrackGlobalProcesses = true;
break;
case "no":
_TrackGlobalProcesses = false;
break;
}
break;
case "new cohorts filename":
_ProcessTrackingOutputs.Add("NewCohortsOutput", VarValues.GetValue(row).ToString());
break;
case "maturity filename":
_ProcessTrackingOutputs.Add("MaturityOutput", VarValues.GetValue(row).ToString());
break;
case "biomasses eaten filename":
_ProcessTrackingOutputs.Add("BiomassesEatenOutput", VarValues.GetValue(row).ToString());
break;
case "trophic flows filename":
_ProcessTrackingOutputs.Add("TrophicFlowsOutput", VarValues.GetValue(row).ToString());
break;
case "growth filename":
_ProcessTrackingOutputs.Add("GrowthOutput", VarValues.GetValue(row).ToString());
break;
case "metabolism filename":
_ProcessTrackingOutputs.Add("MetabolismOutput", VarValues.GetValue(row).ToString());
break;
case "npp output filename":
_ProcessTrackingOutputs.Add("NPPOutput", VarValues.GetValue(row).ToString());
break;
case "predation flows filename":
_ProcessTrackingOutputs.Add("PredationFlowsOutput", VarValues.GetValue(row).ToString());
break;
case "herbivory flows filename":
_ProcessTrackingOutputs.Add("HerbivoryFlowsOutput", VarValues.GetValue(row).ToString());
break;
case "mortality filename":
_ProcessTrackingOutputs.Add("MortalityOutput", VarValues.GetValue(row).ToString());
break;
case "extinction filename":
_ProcessTrackingOutputs.Add("ExtinctionOutput", VarValues.GetValue(row).ToString());
break;
case "output detail":
_InitialisationFileStrings.Add("OutputDetail", VarValues.GetValue(row).ToString());
break;
case "live outputs":
if (VarValues.GetValue(row).ToString() == "yes")
{
_LiveOutputs = true;
}
else
{
_LiveOutputs = false;
}
break;
case "track marine specifics":
if (VarValues.GetValue(row).ToString() == "yes")
{
_TrackMarineSpecifics = true;
}
else
{
_TrackMarineSpecifics = false;
}
break;
case "output metrics":
if (VarValues.GetValue(row).ToString() == "yes")
{
_OutputMetrics = true;
}
else
{
_OutputMetrics = false;
}
break;
case "output model state timesteps":
if (VarValues.GetValue(row).ToString() != "no")
{
string[] OutputStateTimesSteps = VarValues.GetValue(row).ToString().Split(new char[] { ';' });
foreach (string t in OutputStateTimesSteps)
{
if (t.Split(new char[] { '-' }).Length > 1)
{
string[] range = t.Split(new char[] { '-' });
for (uint i = Convert.ToUInt32(range[0]); i <= Convert.ToUInt32(range[1]); i++)
{
_OutputStateTimestep.Add(i);
}
}
else
{
_OutputStateTimestep.Add(Convert.ToUInt32(Convert.ToInt32(t)));
}
}
}
break;
}
}
InternalData.Dispose();
}
/* Method: Dispose
*
* Disposes of the training data.
*/
public void Dispose()
{
InternalData.Dispose();
}