/// <summary>
/// Constructor for process tracker: Initialises the trackers for individual processes
/// </summary>
/// <param name="numTimesteps">The number of time steps in the model</param>
/// <param name="lats">The latitudes of active grid cells in the model</param>
/// <param name="lons">The longitudes of active grid cells in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="Filenames">The filenames of the output files to write the tracking results to</param>
/// <param name="trackProcesses">Whether to track processes</param>
/// <param name="cohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="missingValue">The missing value to use in process tracking output files</param>
/// <param name="outputFileSuffix">The suffix to be applied to output files from process tracking</param>
/// <param name="outputPath">The path to the folder to be used for process tracking outputs</param>
/// <param name="trackerMassBins">The mass bins to use for categorising output data in the process trackers</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="latCellSize">The size of grid cells latitudinally</param>
/// <param name="lonCellSize">The size of grid cells longitudinally</param>
public GlobalProcessTracker(uint numTimesteps,
float[] lats, float[] lons,
List<uint[]> cellIndices,
SortedList<string, string> Filenames,
Boolean trackProcesses,
FunctionalGroupDefinitions cohortDefinitions,
FunctionalGroupDefinitions stockDefinitions,
double missingValue,
string outputFileSuffix,
string outputPath, MassBinsHandler trackerMassBins,
Boolean specificLocations,
MadingleyModelInitialisation initialisation,
float latCellSize,
float lonCellSize)
{
// Initialise trackers for ecological processes
_TrackProcesses = trackProcesses;
if (_TrackProcesses)
{
_TrackNPP = new GlobalNPPTracker(outputPath, lats.Length, lons.Length, lats, lons, latCellSize, lonCellSize,
(int)numTimesteps,stockDefinitions.GetNumberOfFunctionalGroups(),outputFileSuffix);
}
}
/// <summary>
/// Reads the initalization file to get information for the set of simulations to be run
/// </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>
public MadingleyModelInitialisation(string simulationInitialisationFilename, string definitionsFilename, string outputsFilename, string outputPath)
#endif
{
// Write to console
Console.WriteLine("Initializing model...\n");
// Initialize the mass bins to be used during the model run
_ModelMassBins = new MassBinsHandler();
// Read the intialisation files and copy them to the output directory
#if true
ReadAndCopyInitialisationFiles(simulationInitialisationFilename, definitionsFilename, outputsFilename, outputPath, inputPath);
#else
ReadAndCopyInitialisationFiles(simulationInitialisationFilename, definitionsFilename, outputsFilename, outputPath);
// Copy parameter values to an output file
//Don't do this now as the parameter values are read in from file and this file is copied to the output directory
//CopyParameterValues(outputPath);
#endif
}
/// <summary>
/// Set up the predation tracker
/// </summary>_
/// <param name="numTimeSteps">The total number of timesteps for this simulation</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="massFlowsFilename">Filename for outputs of the flows of mass between predators and prey</param>
/// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="missingValue">The missing value to be used in the output file</param>
/// <param name="outputFileSuffix">The suffix to be applied to the output file</param>
/// <param name="outputPath">The path to write the output file to</param>
/// <param name="trackerMassBins">The mass bin handler containing the mass bins to be used for predation tracking</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
public PredationTracker(uint numTimeSteps,
List <uint[]> cellIndices,
string massFlowsFilename,
FunctionalGroupDefinitions cohortDefinitions,
double missingValue,
string outputFileSuffix,
string outputPath, MassBinsHandler trackerMassBins, int cellIndex)
{
// Assign the missing value
_MissingValue = missingValue;
// Get the mass bins to use for the predation tracker and the number of mass bins that this correpsonds to
_MassBins = trackerMassBins.GetSpecifiedMassBins();
_NumMassBins = trackerMassBins.NumMassBins;
// Initialise the array to hold data on mass flows between mass bins
_MassFlows = new double[_NumMassBins, _NumMassBins];
// Define the model time steps to be used in the output file
float[] TimeSteps = new float[numTimeSteps];
for (int i = 1; i <= numTimeSteps; i++)
{
TimeSteps[i - 1] = i;
}
// Initialise the data converter
DataConverter = new ArraySDSConvert();
// Initialise the SDS object creator
SDSCreator = new CreateSDSObject();
// Create an SDS object to hold the predation tracker data
MassFlowsDataSet = SDSCreator.CreateSDS("netCDF", massFlowsFilename + outputFileSuffix + "_Cell" + cellIndex, outputPath);
// Define the dimensions to be used in the predation tracker output file
string[] dimensions = { "Predator mass bin", "Prey mass bin", "Time steps" };
// Add the mass flow variable to the predation tracker
DataConverter.AddVariable(MassFlowsDataSet, "Log mass (g)", 3, dimensions, _MissingValue, _MassBins, _MassBins, TimeSteps);
}
/// <summary>
/// Set up the predation tracker
/// </summary>_
/// <param name="numTimeSteps">The total number of timesteps for this simulation</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="massFlowsFilename">Filename for outputs of the flows of mass between predators and prey</param>
/// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="missingValue">The missing value to be used in the output file</param>
/// <param name="outputFileSuffix">The suffix to be applied to the output file</param>
/// <param name="outputPath">The path to write the output file to</param>
/// <param name="trackerMassBins">The mass bin handler containing the mass bins to be used for predation tracking</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
public PredationTracker(uint numTimeSteps,
List<uint[]> cellIndices,
string massFlowsFilename,
FunctionalGroupDefinitions cohortDefinitions,
double missingValue,
string outputFileSuffix,
string outputPath, MassBinsHandler trackerMassBins, int cellIndex)
{
// Assign the missing value
_MissingValue = missingValue;
// Get the mass bins to use for the predation tracker and the number of mass bins that this correpsonds to
_MassBins = trackerMassBins.GetSpecifiedMassBins();
_NumMassBins = trackerMassBins.NumMassBins;
// Initialise the array to hold data on mass flows between mass bins
_MassFlows = new double[_NumMassBins, _NumMassBins];
// Define the model time steps to be used in the output file
float[] TimeSteps = new float[numTimeSteps];
for (int i = 1; i <= numTimeSteps; i++)
{
TimeSteps[i - 1] = i;
}
// Initialise the data converter
DataConverter = new ArraySDSConvert();
// Initialise the SDS object creator
SDSCreator = new CreateSDSObject();
// Create an SDS object to hold the predation tracker data
MassFlowsDataSet = SDSCreator.CreateSDS("netCDF", massFlowsFilename + outputFileSuffix + "_Cell" + cellIndex, outputPath);
// Define the dimensions to be used in the predation tracker output file
string[] dimensions = { "Predator mass bin", "Prey mass bin", "Time steps" };
// Add the mass flow variable to the predation tracker
DataConverter.AddVariable(MassFlowsDataSet, "Log mass (g)", 3, dimensions, _MissingValue, _MassBins, _MassBins, TimeSteps);
}
/// <summary>
/// Constructor for process tracker: Initialises the trackers for individual processes
/// </summary>
/// <param name="numTimesteps">The number of time steps in the model</param>
/// <param name="lats">The latitudes of active grid cells in the model</param>
/// <param name="lons">The longitudes of active grid cells in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="Filenames">The filenames of the output files to write the tracking results to</param>
/// <param name="trackProcesses">Whether to track processes</param>
/// <param name="cohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="missingValue">The missing value to use in process tracking output files</param>
/// <param name="outputFileSuffix">The suffix to be applied to output files from process tracking</param>
/// <param name="outputPath">The path to the folder to be used for process tracking outputs</param>
/// <param name="trackerMassBins">The mass bins to use for categorising output data in the process trackers</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="latCellSize">The size of grid cells latitudinally</param>
/// <param name="lonCellSize">The size of grid cells longitudinally</param>
public GlobalProcessTracker(uint numTimesteps,
float[] lats, float[] lons,
List <uint[]> cellIndices,
SortedList <string, string> Filenames,
Boolean trackProcesses,
FunctionalGroupDefinitions cohortDefinitions,
FunctionalGroupDefinitions stockDefinitions,
double missingValue,
string outputFileSuffix,
string outputPath, MassBinsHandler trackerMassBins,
Boolean specificLocations,
MadingleyModelInitialisation initialisation,
float latCellSize,
float lonCellSize)
{
// Initialise trackers for ecological processes
_TrackProcesses = trackProcesses;
if (_TrackProcesses)
{
_TrackNPP = new GlobalNPPTracker(outputPath, lats.Length, lons.Length, lats, lons, latCellSize, lonCellSize, (int)numTimesteps, stockDefinitions.GetNumberOfFunctionalGroups());
}
}
/// <summary>
/// Constructor for process tracker: Initialises the trackers for individual processes
/// </summary>
/// <param name="numTimesteps">The number of time steps in the model</param>
/// <param name="lats">The latitudes of active grid cells in the model</param>
/// <param name="lons">The longitudes of active grid cells in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="Filenames">The filenames of the output files to write the tracking results to</param>
/// <param name="trackProcesses">Whether to track processes</param>
/// <param name="cohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="missingValue">The missing value to use in process tracking output files</param>
/// <param name="outputFileSuffix">The suffix to be applied to output files from process tracking</param>
/// <param name="outputPath">The path to the folder to be used for process tracking outputs</param>
/// <param name="trackerMassBins">The mass bins to use for categorising output data in the process trackers</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
/// <param name="latCellSize">The size of grid cells in the latitudinal direction</param>
/// <param name="lonCellSize">The size of grid cells in the longitudinal direction</param>
public ProcessTracker(uint numTimesteps,
float[] lats, float[] lons,
List <uint[]> cellIndices,
SortedList <string, string> Filenames,
Boolean trackProcesses,
FunctionalGroupDefinitions cohortDefinitions,
double missingValue,
string outputFileSuffix,
string outputPath, MassBinsHandler trackerMassBins,
Boolean specificLocations,
int cellIndex,
MadingleyModelInitialisation initialisation,
bool marineCell,
float latCellSize,
float lonCellSize)
{
// Initialise trackers for ecological processes
_TrackProcesses = trackProcesses;
if (_TrackProcesses)
{
_TrackReproduction = new ReproductionTracker(numTimesteps, (uint)lats.Length, (uint)lons.Length, cellIndices, Filenames["NewCohortsOutput"], Filenames["MaturityOutput"], outputFileSuffix, outputPath, cellIndex);
_TrackEating = new EatingTracker((uint)lats.Length, (uint)lons.Length, Filenames["TrophicFlowsOutput"], outputFileSuffix, outputPath, cellIndex, initialisation, marineCell);
_TrackGrowth = new GrowthTracker(numTimesteps, (uint)lats.Length, (uint)lons.Length, cellIndices, Filenames["GrowthOutput"], outputFileSuffix, outputPath, cellIndex);
_TrackMortality = new MortalityTracker(numTimesteps, (uint)lats.Length, (uint)lons.Length, cellIndices, Filenames["MortalityOutput"], outputFileSuffix, outputPath, cellIndex);
_TrackExtinction = new ExtinctionTracker(Filenames["ExtinctionOutput"], outputPath, outputFileSuffix, cellIndex);
_TrackMetabolism = new MetabolismTracker(Filenames["MetabolismOutput"], outputPath, outputFileSuffix, cellIndex);
// Initialise the predation and herbivory trackers only for runs with specific locations
if (specificLocations == true)
{
_TrackPredation = new PredationTracker(numTimesteps, cellIndices, Filenames["PredationFlowsOutput"], cohortDefinitions,
missingValue, outputFileSuffix, outputPath, trackerMassBins, cellIndex);
}
}
}
/// <summary>
/// Constructor for the cell output class
/// </summary>
/// <param name="outputDetail">The level of detail to include in the ouputs: 'low', 'medium' or 'high'</param>
/// <param name="modelInitialisation">Model initialisation object</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
public OutputCell(string outputDetail, MadingleyModelInitialisation modelInitialisation,
int cellIndex)
{
// Set the output path
_OutputPath = modelInitialisation.OutputPath;
// Set the initial maximum value for the y-axis of the live display
MaximumYValue = 1000000;
// Set the local copy of the mass bin handler from the model initialisation
_MassBinHandler = modelInitialisation.ModelMassBins;
// Get the number of mass bins to be used
MassBinNumber = _MassBinHandler.NumMassBins;
// Get the specified mass bins
MassBins = modelInitialisation.ModelMassBins.GetSpecifiedMassBins();
// Set the output detail level
if (outputDetail == "low")
ModelOutputDetail = OutputDetailLevel.Low;
else if (outputDetail == "medium")
ModelOutputDetail = OutputDetailLevel.Medium;
else if (outputDetail == "high")
ModelOutputDetail = OutputDetailLevel.High;
else
Debug.Fail("Specified output detail level is not valid, must be 'low', 'medium' or 'high'");
// Get whether to track marine specifics
TrackMarineSpecifics = modelInitialisation.TrackMarineSpecifics;
// Get whether to track marine specifics
OutputMetrics = modelInitialisation.OutputMetrics;
//Initialise the EcosystemMetrics class
Metrics = new EcosytemMetrics();
// Initialise the data converter
DataConverter = new ArraySDSConvert();
// Initialise the SDS object creator
SDSCreator = new CreateSDSObject();
// Initialise the grid viewer
GridViewer = new ViewGrid();
// Set the local variable designating whether to display live outputs
if (modelInitialisation.LiveOutputs)
LiveOutputs = true;
}
/// <summary>
/// Constructor for process tracker: Initialises the trackers for individual processes
/// </summary>
/// <param name="numTimesteps">The number of time steps in the model</param>
/// <param name="lats">The latitudes of active grid cells in the model</param>
/// <param name="lons">The longitudes of active grid cells in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="Filenames">The filenames of the output files to write the tracking results to</param>
/// <param name="trackProcesses">Whether to track processes</param>
/// <param name="cohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="missingValue">The missing value to use in process tracking output files</param>
/// <param name="outputFileSuffix">The suffix to be applied to output files from process tracking</param>
/// <param name="outputPath">The path to the folder to be used for process tracking outputs</param>
/// <param name="trackerMassBins">The mass bins to use for categorising output data in the process trackers</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
/// <param name="latCellSize">The size of grid cells in the latitudinal direction</param>
/// <param name="lonCellSize">The size of grid cells in the longitudinal direction</param>
public ProcessTracker(uint numTimesteps,
float[] lats, float[] lons,
List<uint[]> cellIndices,
SortedList<string, string> Filenames,
Boolean trackProcesses,
FunctionalGroupDefinitions cohortDefinitions,
double missingValue,
string outputFileSuffix,
string outputPath, MassBinsHandler trackerMassBins,
Boolean specificLocations,
int cellIndex,
MadingleyModelInitialisation initialisation,
bool marineCell,
float latCellSize,
float lonCellSize)
{
// Initialise trackers for ecological processes
_TrackProcesses = trackProcesses;
if (_TrackProcesses)
{
_TrackReproduction = new ReproductionTracker(numTimesteps, (uint)lats.Length, (uint)lons.Length, cellIndices, Filenames["NewCohortsOutput"], Filenames["MaturityOutput"], outputFileSuffix, outputPath, cellIndex);
_TrackEating = new EatingTracker((uint)lats.Length, (uint)lons.Length, Filenames["TrophicFlowsOutput"], outputFileSuffix, outputPath, cellIndex, initialisation, marineCell);
_TrackGrowth = new GrowthTracker(numTimesteps, (uint)lats.Length, (uint)lons.Length, cellIndices, Filenames["GrowthOutput"], outputFileSuffix, outputPath, cellIndex);
_TrackMortality = new MortalityTracker(numTimesteps, (uint)lats.Length, (uint)lons.Length, cellIndices, Filenames["MortalityOutput"], outputFileSuffix, outputPath, cellIndex);
_TrackExtinction = new ExtinctionTracker(Filenames["ExtinctionOutput"], outputPath, outputFileSuffix, cellIndex);
_TrackMetabolism = new MetabolismTracker(Filenames["MetabolismOutput"], outputPath, outputFileSuffix, cellIndex);
// Initialise the predation and herbivory trackers only for runs with specific locations
if (specificLocations == true)
{
_TrackPredation = new PredationTracker(numTimesteps, cellIndices, Filenames["PredationFlowsOutput"], cohortDefinitions,
missingValue, outputFileSuffix, outputPath, trackerMassBins, cellIndex);
}
}
}
/// <summary>
/// Reads the initalization file to get information for the set of simulations to be run
/// </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>
public MadingleyModelInitialisation(string simulationInitialisationFilename, string definitionsFilename, string outputsFilename, string outputPath)
{
// Write to console
Console.WriteLine("Initializing model...\n");
// Initialize the mass bins to be used during the model run
_ModelMassBins = new MassBinsHandler();
// Initialize the lists for storing information about model states
_ModelStatePath = new List<string>();
_ModelStateFilename = new List<string>();
// Read the intialisation files and copy them to the output directory
ReadAndCopyInitialisationFiles(simulationInitialisationFilename, definitionsFilename, outputsFilename, outputPath);
// Copy parameter values to an output file
//Don't do this now as the parameter values are read in from file and this file is copied to the output directory
//CopyParameterValues(outputPath);
}
/// <summary>
/// Reads the initalization file to get information for the set of simulations to be run
/// </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>
public MadingleyModelInitialisation(string simulationInitialisationFilename, string definitionsFilename, string outputsFilename, string outputPath)
#endif
{
// Write to console
Console.WriteLine("Initializing model...\n");
// Initialize the mass bins to be used during the model run
_ModelMassBins = new MassBinsHandler();
// Read the intialisation files and copy them to the output directory
#if true
ReadAndCopyInitialisationFiles(simulationInitialisationFilename, definitionsFilename, outputsFilename, outputPath, inputPath);
#else
ReadAndCopyInitialisationFiles(simulationInitialisationFilename, definitionsFilename, outputsFilename, outputPath);
// Copy parameter values to an output file
//Don't do this now as the parameter values are read in from file and this file is copied to the output directory
//CopyParameterValues(outputPath);
#endif
}