/*5/5/14, JTC, added persistent species data for players; system parameter masterSpeciesList,
replaces mSpecies.
Get previous timestep biomass for all species from web service*/
public HashMap<Integer, SpeciesZoneType> getPrediction(
String networkOrManipulationId,
int startTimestep,
int runTimestep,
Map<Integer, Integer> addSpeciesNodeList,
ZoneNodes zoneNodes)
throws SimulationException {
long milliseconds = System.currentTimeMillis();
Log.printf("\nPrediction at %d\n", startTimestep);
// Get previous timestep biomass for all species from web service
// JTC, use new HashMap containing all current settings from zoneNodes, masterSpeciesList
// HJR changing to make a deep copy here , I am getting a null while iterating
HashMap<Integer, SpeciesZoneType> masterSpeciesList =
new HashMap<Integer, SpeciesZoneType>(zoneNodes.getNodes());
HashMap<Integer, SpeciesZoneType> mNewSpecies = new HashMap<Integer, SpeciesZoneType>();
// JTC, mUpdateBiomass renamed from mUpdateSpecies
HashMap<Integer, SpeciesZoneType> mUpdateBiomass = new HashMap<Integer, SpeciesZoneType>();
// JTC, added new update type, mUpdateParams
HashMap<Integer, SpeciesZoneType> mUpdateParams = new HashMap<Integer, SpeciesZoneType>();
SpeciesZoneType szt;
String nodeConfig = null;
SimJob job = new SimJob();
// {70=2494, 5=2000, 42=240, 14=1752, 31=1415}
for (int node_id : addSpeciesNodeList.keySet()) {
int addedBiomass = addSpeciesNodeList.get(node_id);
if (!masterSpeciesList.containsKey(node_id)) {
szt = createSpeciesZoneType(node_id, addedBiomass);
mNewSpecies.put(node_id, szt);
// jtc - 04/19/15
masterSpeciesList.put(node_id, szt);
} else {
szt = masterSpeciesList.get(node_id);
szt.setCurrentBiomass(Math.max(0, szt.getCurrentBiomass() + addedBiomass));
szt.setBiomassUpdated(true);
}
}
// //JTC, separated this to capture biomass updates made to ZoneNodes that
// //are not received through addSpeciesNodeList (biomass and param updates)
// for (SpeciesZoneType species : masterSpeciesList.values()) {
// //param update also updates biomass, so insert into that list
// //preferentially; o/w use biomass update list
// if (species.paramUpdated) {
// mUpdateParams.put(species.getNodeIndex(), species);
// species.setParamUpdated(false);
// } else if (species.biomassUpdated) {
// mUpdateBiomass.put(species.getNodeIndex(), species);
// species.setBiomassUpdated(false);
// }
// }
// Insert new species using web services
if (!mNewSpecies.isEmpty()) {
zoneNodes.addNodes(mNewSpecies);
}
try {
nodeConfig =
addMultipleSpeciesType(
mNewSpecies, masterSpeciesList, startTimestep, false, networkOrManipulationId);
} catch (Exception ex) {
Log.println_e(ex.getMessage());
}
// // Update biomass changes to existing species using web services
// if (!mUpdateBiomass.isEmpty()) {
// List<NodeBiomass> lNodeBiomass = new ArrayList<NodeBiomass>();
// for (SpeciesZoneType s : mUpdateBiomass.values()) {
// Log.printf("Updating Biomass: [%d] %s %f\n", s.getNodeIndex(), s.getName(),
// s.getCurrentBiomass() / Constants.BIOMASS_SCALE);
// lNodeBiomass.add(new NodeBiomass(
// s.getCurrentBiomass() / Constants.BIOMASS_SCALE, s.getNodeIndex()));
// }
// try {
//// updateBiomass(networkOrManipulationId, lNodeBiomass, startTimestep);
// } catch (Exception ex) {
// Log.println_e(ex.getMessage());
// }
// }
// // JTC Update changes to existing species parameters using web services (also
// // resubmits biomass, but couldn't find a way to do params w/o biomass
// if (!mUpdateParams.isEmpty()) {
// try {
//// increaseMultipleSpeciesType(
//// mUpdateBiomass,
//// masterSpeciesList,
//// startTimestep,
//// false,
//// networkOrManipulationId
//// );
// } catch (Exception ex) {
// Log.println_e(ex.getMessage());
// }
// }
// run(startTimestep, runTimestep, networkOrManipulationId);
// get new predicted biomass
try {
// JTC - changed variable from "mSpecies = " to "mUpdateBiomass = "
// mUpdateBiomass = getBiomass(networkOrManipulationId, 0, startTimestep + runTimestep);
if (!masterSpeciesList.isEmpty() || !mNewSpecies.isEmpty()) {
mUpdateBiomass =
submitManipRequest("ATN", nodeConfig, startTimestep + runTimestep, false, null);
}
} catch (Exception ex) {
Log.println_e(ex.getMessage());
return null;
}
// getBiomassInfo(networkOrManipulationId);
// JTC - add loop to update persistent player species biomass information
SpeciesZoneType updS;
for (SpeciesZoneType priorS : masterSpeciesList.values()) {
System.out.println("priorS.nodeIndex " + priorS.nodeIndex);
updS = mUpdateBiomass.get(priorS.nodeIndex);
if (updS != null && updS.currentBiomass != 0) {
masterSpeciesList
.get(priorS.nodeIndex)
.setCurrentBiomass(Math.ceil(updS.getCurrentBiomass()));
}
// else {
// zoneNodes.removeNode(priorS.nodeIndex);
// }
}
Log.printf(
"Total Time (Get Prediction): %.2f seconds",
Math.round((System.currentTimeMillis() - milliseconds) / 10.0) / 100.0);
return (HashMap) zoneNodes.getNodes();
}
// loop through current job/results, assembling dataset
private HashMap<Integer, SpeciesZoneType> genSpeciesDataset(
SimJob job,
EcosystemTimesteps ecosysTimesteps,
Map<Integer, NodeRelationships> ecosysRelationships) {
// calc information relevant to entire ecosystem
int speciesCnt = ecosysTimesteps.getNodeList().size(); // Number of species
int timesteps = ecosysTimesteps.getTimesteps(); // Maximum number of timesteps to run simulation
int timestepsToSave = 0; // Number of timesteps of data to save to output file
int[] matchingTimesteps =
null; // Array of matching timesteps returned by findMatchingTimesteps()
// read in link parameters; this was explicitly configured to allow
// manipulation of link parameter values, but no manipulation is
// performed in this version
LinkParams lPs = new LinkParams(propertiesConfig);
// loop through node values and assemble summary data
int[] speciesID = new int[speciesCnt];
SimJobSZT[] sztArray = new SimJobSZT[speciesCnt];
int spNum = 0;
for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(nodeTimesteps.getNodeId());
sztArray[spNum] = sjSzt;
speciesID[spNum] = sjSzt.getNodeIndex();
spNum++;
}
// define objects to track species' contributions
double[][][] contribs = new double[timesteps][speciesCnt][speciesCnt];
double[][] calcBiomass = new double[timesteps][speciesCnt];
double[][] contribsT; // current timestep
// note: WebServices ATN Model uses B0 with default = 0.5. This presumes
// that biomasses are small, i.e. < 1.0. Division by biomassScale
// here is consistent with usage in WoB_Server.SimulationEngine to
// normalize biomasses.
// need to store bm as it varies over time through integration;
// start with initial bm for each species
double[] currBiomass = new double[speciesCnt];
for (int i = 0; i < speciesCnt; i++) {
NodeTimesteps nodeTimeSteps = ecosysTimesteps.getTimestepMap().get(speciesID[i]);
// manually set biomass vals for excluded initial timesteps; this
// includes the first value to be used as input
currBiomass[i] = nodeTimeSteps.getBiomass(initTimeIdx) / biomassScale;
calcBiomass[0][i] = currBiomass[i];
}
if (Constants.useCommonsMathIntegrator) {
// Use Apache Commons Math GraggBulirschStoerIntegrator
FirstOrderIntegrator integrator =
new GraggBulirschStoerIntegrator(
1.0e-8, // minimal step
100.0, // maximal step
ATNEquations.EXTINCT, // allowed absolute error
1.0e-10); // allowed relative error
// Set up the ATN equations based on the current food web and parameters
ATNEquations ode = new ATNEquations(sztArray, ecosysRelationships, lPs);
ATNEventHandler eventHandler = new ATNEventHandler(ode);
// FIXME: Choose best parameter values
integrator.addEventHandler(
new EventFilter(eventHandler, FilterType.TRIGGER_ONLY_DECREASING_EVENTS),
1, // maximal time interval between switching function checks (this interval prevents
// missing sign changes in case the integration steps becomes very large)
0.0001, // convergence threshold in the event time search
1000, // upper limit of the iteration count in the event time search
new BisectionSolver());
// Set up the StepHandler, which is triggered at each time step by the integrator,
// and copies the current biomass of each species into calcBiomass[timestep].
// See the "Continuous Output" section of
// https://commons.apache.org/proper/commons-math/userguide/ode.html
FixedStepHandler fixedStepHandler =
new FixedStepHandler() {
public void init(double t0, double[] y0, double t) {}
private int timestep = 0;
public void handleStep(double t, double[] y, double[] yDot, boolean isLast) {
// Ensure we don't go past the last time step due to rounding error
if (timestep < calcBiomass.length) {
System.arraycopy(y, 0, calcBiomass[timestep], 0, speciesCnt);
}
timestep++;
}
};
StepHandler stepHandler = new StepNormalizer(timeIntvl, fixedStepHandler);
integrator.addStepHandler(stepHandler);
// Run the integrator to compute the biomass time series
integrator.integrate(ode, 0.0, currBiomass, timeIntvl * timesteps, currBiomass);
if (eventHandler.integrationWasStopped()) {
timestepsToSave = (int) (eventHandler.getTimeStopped() / timeIntvl);
} else {
// Check for an oscillating steady state,
// and only save the data through the first period of the oscillation
matchingTimesteps = findMatchingTimesteps(calcBiomass, timesteps - 1);
System.err.println("\nmatchingTimesteps = " + Arrays.toString(matchingTimesteps));
// Save timesteps up through the second matching timestep,
// or all timesteps if there was no second matching timestep.
if (matchingTimesteps[1] != -1) {
timestepsToSave = matchingTimesteps[1] + 1;
} else {
timestepsToSave = timesteps;
}
}
} else {
// Use BulirschStoerIntegration
// create integration object
boolean isTest = false;
BulirschStoerIntegration bsi =
new BulirschStoerIntegration(
timeIntvl, speciesID, sztArray, ecosysRelationships, lPs, maxBSIErr, equationSet);
// calculate delta-biomass and biomass "contributions" from each related
// species
for (int t = initTimeIdx + 1; t < timesteps; t++) {
boolean success = bsi.performIntegration(time(initTime, t), currBiomass);
if (!success) {
System.out.printf("Integration failed to converge, t = %d\n", t);
System.out.print(bsi.extrapArrayToString(biomassScale));
break;
}
currBiomass = bsi.getYNew();
System.arraycopy(currBiomass, 0, calcBiomass[t], 0, speciesCnt);
contribsT = bsi.getContribs();
for (int i = 0; i < speciesCnt; i++) {
System.arraycopy(contribsT[i], 0, contribs[t - 1][i], 0, speciesCnt);
}
} // timestep loop
}
if (useHDF5) {
saveHDF5OutputFile(
calcBiomass, speciesID, matchingTimesteps, job.getNode_Config(), timestepsToSave);
return null;
}
double[][] webServicesData = new double[speciesCnt][timesteps];
if (Constants.useSimEngine) { // We need the webServicesData only for marginOfErrorCalculation
// extract timestep data from CSV
Functions.extractCSVDataRelns(job.getCsv(), ecosysTimesteps, ecosysRelationships);
spNum = 0;
for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
// copy nodetimestep data to local array for easier access
System.arraycopy(nodeTimesteps.getBiomassArray(), 0, webServicesData[spNum], 0, timesteps);
spNum++;
}
}
// output data
// A. print header
psATN.printf("timesteps");
for (int i = 0; i < timesteps; i++) {
psATN.printf(",%d", i);
}
psATN.println();
/* Convert to CSV String */
String biomassCSV = "";
biomassCSV = "Manipulation_id: " + job.getATNManipulationId() + "\n\n";
int maxTimestep = job.getTimesteps();
// Create Timestep Labels
for (int j = 1; j <= maxTimestep; j++) {
biomassCSV += "," + j;
}
HashMap<Integer, SpeciesZoneType> mSpecies = new HashMap<Integer, SpeciesZoneType>();
// loop through each species
for (int i = 0; i < speciesCnt; i++) {
if (Constants.useSimEngine) {
psATN.printf("i.%d.sim", speciesID[i]);
// B. print WebServices simulation data for species
for (int t = 0; t < timesteps; t++) {
psATN.printf(",%9.0f", webServicesData[i][t]);
}
psATN.println();
}
// B. print combined biomass contributions (i.e. locally calculated biomass)
// for current species.
psATN.printf("i.%d.calc", speciesID[i]);
for (int t = 0; t < timesteps; t++) {
psATN.printf(",%9.0f", calcBiomass[t][i] * biomassScale);
}
psATN.println();
// //C. print individual biomass contributions from other species
// for (int j = 0; j < speciesCnt; j++) {
// psATN.printf("i.%d.j.%d.", speciesID[i], speciesID[j]);
// for (int t = 0; t < timesteps; t++) {
// psATN.printf(",%9.0f", contribs[t][i][j] * biomassScale);
// }
// psATN.println();
// }
float extinction = 1.E-15f;
SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(speciesID[i]);
// add nodes to list in the order that they are received from infos
String name = sjSzt.getName().replaceAll(",", " ") + " [" + sjSzt.getNodeIndex() + "]";
String tempStr = name;
for (int t = 0; t < maxTimestep; t++) {
tempStr += ",";
double biomass = calcBiomass[t][i] * biomassScale;
if (biomass > 0) {
tempStr += biomass > extinction ? Math.ceil(biomass) : 0;
}
if (t == maxTimestep - 1) {
SpeciesZoneType szt = null;
if (!mSpecies.containsKey(sjSzt.getNodeIndex())) {
szt = new SpeciesZoneType(sjSzt.getName(), sjSzt.getNodeIndex(), 0, 0, biomass, null);
mSpecies.put(sjSzt.getNodeIndex(), szt);
} else { // update existing species current biomass
szt = mSpecies.get(sjSzt.getNodeIndex());
szt.setCurrentBiomass(biomass);
}
}
}
biomassCSV += "\n" + tempStr;
}
// Append node config to the ATN CSV
psATN.println();
psATN.println("\"node-config: " + job.getNode_Config() + "\"");
biomassCSV += "\n\n";
biomassCSV += job.getConsumeMap().toString() + "\n\n";
biomassCSV += job.getPathTable().toString();
job.setBiomassCsv(biomassCSV);
// System.out.println(biomassCSV);
return mSpecies;
}